3DEM-Methods - User contributions [en]

2015Hanson Continuum

2017-07-20T06:16:30Z

CoSS: Created page with "== Citation == Hanson, B.; Richardson, R.; Oliver, R.; Read, D. J.; Harlen, O. & Harris, S. Modelling biomacromolecular assemblies with continuum mechanics. Biochemical Socie..."

== Citation ==

Hanson, B.; Richardson, R.; Oliver, R.; Read, D. J.; Harlen, O. & Harris, S. Modelling biomacromolecular assemblies with continuum mechanics. Biochemical Society transactions, 2015, 43, 186-192

== Abstract ==

We have developed a continuum mechanical description of proteins using a finite element algorithm which has been generalized to include thermal fluctuations and which is therefore known as fluctuating finite element analysis (FFEA). Whereas conventional molecular dynamics (MD) simulations provide a trajectory in which each individual atomic position fluctuates, a FFEA trajectory shows how the overall shape of the protein changes due to thermal agitation. We describe the theoretical background to FFEA, its relationship to more established biomolecular modelling methods and provide examples of its application to the mesoscale biomolecular dynamics of the molecular motor dynein.

== Keywords ==

== Links ==

http://www.biochemsoctrans.org/content/43/2/186

== Related software ==

== Related methods ==

== Comments ==

Main Page

2017-07-20T06:14:18Z

CoSS: /* Fitting and docking */

== Presentation ==

This web page is intended to be an extensive repository of three-dimensional electron microscopy (3DEM) methods. The advantages of having such a repository are

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== Citation ==

== Abstract ==

== Keywords ==

== Links ==

== Related software ==

== Related methods ==

== Comments ==

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== Electron microscopy images ==

=== Online courses ===

CALTECH: http://cryo-em-course.caltech.edu/

MRC: ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/EM-course/

CNB-CSIC: http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/MadridJan2014EM

Workshop on Computational methods for CryoEM: https://www.youtube.com/watch?v=XdKO1iaPP8o

Workshop on Management of large CryoEM facilities: https://www.youtube.com/watch?v=as4seOPszL0

Icknield Course on Model Building and Refinement for High Resolution EM Maps: http://www.ccpem.ac.uk/training/icknield_2017/icknield_2017.php

=== Image formation ===

{|

| Paper
| [[1971Erickson_CTF]]
| CTF model
|-

| Paper
| [[1971Glaeser_Damage]]
| Radiation damage
|-

| Chapter
| [[1971Hanszen_CTF]]
| Image formation model
|-

| Paper
| [[1971Thon_Model]]
| CTF model
|-

| Paper
| [[1975Unwin_Imaging]]
| Radiation dose
|-

| Paper
| [[1977Wade_Model]]
| CTF model
|-

| Paper
| [[1978Wade_Model]]
| CTF model
|-

| Paper
| [[1979Hayward_Radiation]]
| Radiation damage
|-

| Paper
| [[1984Cohen_Validity]]
| Validity of the CTF model at high frequencies
|-

| Paper
| [[1988Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[1992Wade_Model]]
| CTF model
|-

| Paper
| [[1993Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2004Egerton_Damage]]
| Radiation damage
|-

| Paper
| [[2004Sorzano_Normalization]]
| Background noise is Gaussian
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2009Baxter_NoiseCharacterization]]
| Characterization of the different noise sources in cryo-EM
|-

| Paper
| [[2010Baker_Damage]]
| Radiation damage dependence on resolution
|-

| Paper
| [[2010Bammes_Damage]]
| Radiation damage dependence on temperature
|-

| Paper
| [[2010Gomez_Multislice]]
| Simulation of the multi slice model
|-

| Paper
| [[2010Zewail_FourDimensional]]
| Review on the use of ultrafast EM
|-

| Paper
| [[2011Bammes_CCD]]
| Performance of CCD cameras
|-

| Paper
| [[2011Glaeser_Coma]]
| Image formation model including coma
|-

| Paper
| [[2011Milazzo_DirectDetectors]]
| Evaluation of Direct Detectors
|-

| Paper
| [[2011Rullgard_ImageSimulation]]
| Accurate simulation of EM images
|-

| Paper
| [[2011Zhang LimitingFactors]]
| Limiting factor for atomic resolution in EM
|-

| Paper
| [[2012Bammes_DirectDetection]]
| Performance of Direct detectors
|-

| Paper
| [[2012Campbell_MotionCorrection]]
| Beam induced motion correction and direct detectors
|-

| Paper
| [[2012Shang_HydrationLayer]]
| Simulation of PDB volumes explicitly considering the hydration layer
|-

| Paper
| [[2013Egerton_RadiationDamage]]
| Review of TEM radiation damage and experimental ways of reducing it
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu H_Noisemodels]]
| Noise models and cryo-EM drift correction with a direct-electron camera
|-

| Paper
| [[2013Li X K2 noisemodels]]
| Influence of electron dose rate on electron counting images recorded with the K2 camera
|-

| Paper
| [[2013Vulovic_CTFApproximations]]
| When to use the different approximations performed so that a projection with linear CTF is valid
|-

| Thesis
| [[2013Vulovic_ImageFormation]]
| Ph.D. Thesis on the image formation in cryo-EM
|-

| Paper
| [[2014Danev_PhasePlate]]
| Volta potential phase plate
|-

| Paper
| [[2015Chiu_K2]]
| Characterization of K2
|-

| Paper
| [[2015Hawkes_AberrationCorrection]]
| Historical account of the development of lens corrections
|-

| Paper
| [[2015Koeck_Quadratic]]
| Limitations of the linear approximation and use of the quadratic terms
|-

| Paper
| [[2015Kuijper_FEI]]
| Description of the FEI Falcons
|-

| Paper
| [[2015Lobato_MULTEM]]
| Simulation of multislice diffraction
|-

| Paper
| [[2015McMullan_AmorphousIce]]
| Beam induced movement is caused by Brownian motion
|-

| Paper
| [[2016Koeck_ADF]]
| Simulations of Annular Dark Field TEM
|-

| Paper
| [[2017Mishyna_DNARadiation]]
| Review of radiation damage on DNA
|-

|}

=== Collection geometry ===

{|

| Chapter
| [[1980Hoppe_Wedge]]
| Missing wedge
|-

| Paper
| [[1987Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1995Penczek_Dual]]
| Dual axis tomography
|-

| Paper
| [[1997Mastronarde_Dual]]
| Dual axis tomography
|-

| Paper
| [[2003Ludtke_FocusPairs]]
| Focus pairs for single particles
|-

| Paper
| [[2005Lanzavecchia_Conical]]
| Conical tomography
|-

| Paper
| [[2005Zampighi_Conical]]
| Conical tomography
|-

| Paper
| [[2006Leschziner_OT]]
| Orthogonal Tilt
|-

| Paper
| [[2006Messaoudi_Multiple]]
| Multiple axis tomography
|-

| Paper
| [[2012Kudryashev_FocusPairs]]
| Focus pairs tomography
|-

| Paper
| [[2014Hovden_TiltFocus]]
| Combining tilt series with focus series
|-

| Paper
| [[2015Sorzano_RandomConicalTilt]]
| General formulation of Random Conical Tilt
|-

| Paper
| [[2017Hagen_DoseTomography]]
| Dose optimization for subtomogram averaging
|-

|}

=== Sample preparation ===

{|

| Paper
| [[1982Dubochet_Sample]]
| Vitreous ice
|-

| Paper
| [[1986Lepault_Sample]]
| Fast freezing
|-

| Paper
| [[1995Dubochet_Sample]]
| High-pressure freezing
|-

| Paper
| [[1995VanMarle_Sample]]
| Sample damages in resin
|-

| Paper
| [[1998Adrian_Sample]]
| Cryo negative staining
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2002Hsieh_Sample]]
| Cryofixation
|-

| Paper
| [[2004AlAmoudi_Sample]]
| CEMOVIS
|-

| Paper
| [[2008Studer_Sample]]
| Review on high pressure freezing
|-

| Paper
| [[2009Pierson_Sample]]
| Review on sample preparation for electron tomography
|-

| Paper
| [[2010Zhang_NegativeStaining]]
| Negative staining for small protein imaging
|-

| Paper
| [[2012Zhang_PositiveStaining]]
| Positive staining
|-

| Paper
| [[2014Rames_NegativeStaining]]
| Optimized negative staining
|-

| Paper
| [[2014Russo_GoldGrids]]
| Gold grids for single particles
|-

| Paper
| [[2015Cabra_Sample]]
| Review on sample preparation for single particles with videos
|-

| Paper
| [[2016Passmore_Review]]
| Tutorial chapter on sample preparation
|-

| Paper
| [[2016Razinkov_Vitrification]]
| New vitrification method
|-

| Paper
| [[2016Takizawa_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2016Thompson_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2017Arnold_BlottingFree]]
| Blotting-free preparation
|-

| Paper
| [[2017Feng_SprayingPlunging]]
| Spraying plunging
|-

| Paper
| [[2017He_FIB]]
| Cryo FIB lamella for TEM
|-

| Paper
| [[2017Peitsch_Sample]]
| iMEM: Isolation of Plasma Membrane for Cryoelectron Microscopy
|-

| Paper
| [[2017Scapin_Storage]]
| Cryo storage of samples
|-

| Paper
| [[2017Schaffer_FocusedIonBeam]]
| Focused Ion Beam sample preparation for membrane proteins
|-

| Paper
| [[2017Scherr_HydrogelNanomembranes]]
| Sample preparation for membrane proteins
|-

|}

=== Automated data collection ===

{|

| Paper
| [[1992Dierksen_Automatic]]
| Automated data collection
|-

| Paper
| [[1992Koster_Automatic]]
| Automated data collection
|-

| Paper
| [[1996Fung_Automatic]]
| Automated data collection for tomography
|-

| Paper
| [[2001Zhang_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2003Ziese_Automatic]]
| Automated autofocusing
|-

| Paper
| [[2004Potter_Automatic]]
| Automated sample loading
|-

| Paper
| [[2004Zheng_Automatic]]
| Automated data collection
|-

| Paper
| [[2005Lei_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2005Suloway_Automatic]]
| Automated data collection: Leginon
|-

| Paper
| [[2007Yoshioka_RCT]]
| Automated Random Conical Tilt
|-

| Paper
| [[2011Korinek_TOM2]]
| Automated acquisition with TOM2
|-

| Paper
| [[2015Li_UCSFImage]]
| Automated acquisition with UCSFImage
|-

| Paper
| [[2016Gil_Fuzzy]]
| Real time decisions during acquisition with neuro-fuzzy method
|-

| Paper
| [[2016Liu_TiltControl]]
| Accurate control of the tilt angle for electron tomography
|-

| Paper
| [[2016Vargas_FoilHole]]
| Determination of image quality at low magnification
|-

| Paper
| [[2017Biyani_Focus]]
| Automatic processing of micrographs
|-

|}

== Single particles ==

=== Automatic particle picking ===

{|

| Paper
| [[1982VanHeel_Detection]]
| Detection of particles in micrographs
|-

| Paper
| [[2001Nicholson_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2001Zhu_Filaments]]
| Automatic identification of filaments in micrographs
|-

| Paper
| [[2004Sigworth_Detection]]
| Classical detection theory and the cryo-EM particle selection problem
|-

| Paper
| [[2004Volkmann_ParticlePicking]]
| An approach to automated particle picking from electron micrographs based on reduced representation templates
|-

| Paper
| [[2004Wong_ParticlePicking]]
| Model-based particle picking for cryo-electron microscopy
|-

| Paper
| [[2004Zhu_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2007Chen_Signature]]
| Automatic particle picking program: Signature
|-

| Paper
| [[2007Woolford_SwarmPS]]
| Automatic particle picking with several criteria, implemented in EMAN Boxer
|-

| Paper
| [[2009Sorzano_MachineLearning]]
| Automatic particle picking based on machine learning of rotational invariants
|-

| Paper
| [[2011Arbelaez_Comparison]]
| Evaluation of the performance of software for automated particle-boxing
|-

| Paper
| [[2013Abrishami_MachineLearning]]
| A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs
|-

| Paper
| [[2013Hauer_2013]]
| Automatic tilt pair detection in Random Conical Tilt
|-

| Paper
| [[2013Shatsky_ParticlePicking]]
| Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Langlois_ParticlePicking]]
| Automatic particle picking
|-

| Paper
| [[2016Vilas_AutomaticTilt]]
| Automatic identification of image pairs in untilted-tilted micrograph pairs
|-

|}

=== 2D Preprocessing ===

{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast enhancement through DPR
|-

| Paper
| [[2004Sorzano_Normalization]]
| Normalization procedures and their statistical properties.
|-

| Paper
| [[2006Sorzano_Denoising]]
| Strong denoising in wavelet space
|-

| Conference
| [[2009Sorzano_Downsampling]]
| Differences between the different downsampling schemes
|-

| Paper
| [[2012Brilot_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Campbell_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Zhao_Denoising]]
| Denoising using an invariant Fourier-Bessel eigenspace
|-

| Paper
| [[2013Norousi_Screening]]
| Screening particles to identify outliers
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu_Movies]]
| Drift correction for movies considering dark field
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Scheres_Movies]]
| Beam induced motion correction
|-

| Paper
| [[2015Abrishami_Movies]]
| Alignment of direct detection device micrographs
|-

| Paper
| [[2015Grant_Anisotropic]]
| Automatic estimation and correction of anisotropic magnification
|-

| Paper
| [[2015Grant_OptimalExposure]]
| Filter movies according to the radiation damage
|-

| Paper
| [[2015Rubinstein_Alignment]]
| Frame alignment at the level of particle
|-

| Paper
| [[2015Spear_DoseCompensation]]
| Effect of dose compensation on resolution
|-

| Paper
| [[2015Zhao_AnisotropicMagnification]]
| Correction of anisotropic magnification
|-

| Conference
| [[2016Bajic_Denoising]]
| Denoising and deconvolution of micrographs
|-

| Paper
| [[2016Jensen_RemovalVesicles]]
| Removal of vesicles in membrane proteins
|-

| Paper
| [[2016Bhamre_Denoising]]
| Denoising by 2D covariance estimation
|-

| Paper
| [[2017McLeod_Zorro]]
| Movie alignment by Zorro
|-

| Paper
| [[2017Zheng_MotionCorr2]]
| Movie alignment by MotionCorr2
|-

|}

=== 2D Alignment ===

{|

| Paper
| [[1981Frank_Averaging]]
| 2D averaging and phase residual
|-

| Paper
| [[1982Saxton_Averaging]]
| 2D averaging using correlation
|-

| Paper
| [[1998Sigworth_ML2D]]
| Maximum likelihood alignment in 2D
|-

| Paper
| [[2003Cong_FRM2D]]
| Fast Rotational Matching in 2D
|-

| Paper
| [[2005Cong_FRM2D]]
| Fast Rotational Matching in 2D introduced in a 3D Alignment algorithm
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

|}

=== 2D Classification and clustering ===

{|

| Paper
| [[1981VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[1984VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2011Singer_DiffusionMaps]]
| Classification in 2D based on graph analysis of the projections
|-

| Paper
| [[2012Yang_ISAC]]
| Iterative Stable Alignment and clustering
|-

| Paper
| [[2014Sorzano_Outlier]]
| Outlier detection in 2D classifications.
|-

| Paper
| [[2014Zhao_Aspire]]
| Fast classification based on rotational invariants and vector diffusion maps
|-

| Paper
| [[2015Huang_Robust]]
| Robust w-estimators of 2D classes
|-

| Paper
| [[2016Reboul_Stochastic]]
| Stochastic Hill Climbing for calculating 2D classes
|-

| Conference
| [[2017Bhamre_Mahalanobis]]
| 2D classification using Mahalanobis distance
|-

|}

=== 3D Alignment ===

{|

| Paper
| [[1980Kam_AutoCorrelation]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[1986Goncharov_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1987VanHeel_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1988Provencher_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Vogel_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1990Gelfand_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Goncharov_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Harauz_Quaternions]]
| Use of quaternions to represent rotations
|-

| Paper
| [[1994Penczek_Real]]
| Angular assignment using projection matching in real space
|-

| Paper
| [[1994Radermacher_Radon]]
| Angular assignment in Radon space
|-

| Paper
| [[1996Penczek_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[2003Rosenthal_DPR]]
| Angular assignment using DPR
|-

| Paper
| [[2004Sorzano_Wavelet]]
| Angular assignment in the wavelet space.
|-

| Paper
| [[2005Jonic_Splines]]
| Angular assignment in Fourier space using spline interpolation.
|-

| Paper
| [[2005Yang_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[2006Ogura_SimulatedAnnealing]]
| Angular asignment by simulated annealing
|-

| Paper
| [[2007Grigorieff_Continuous]]
| Continuous angular assignment in Fourier space
|-

| Paper
| [[2010Jaitly_Bayesian]]
| Angular assignment by a Bayesian method and annealing
|-

| Paper
| [[2010Sanz_Random]]
| Random model method
|-

| Paper
| [[2010Singer_Voting]]
| Detecting consistent common lines by voting (reference free)
|-

| Paper
| [[2011Singer_SDP]]
| Angular assignment by semidefinite programming and eigenvectors (reference free)
|-

| Paper
| [[2012Giannakis_Scattering]]
| Construction of an initial volume, reference free, by graph analysis of the projections
|-

| Paper
| [[2012Shkolnisky_Sync]]
| Angular assignment by synchronization of rotations (reference free)
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Wang_LUD]]
| Angular assignment by least unsquared deviations (reference free)
|-

| Paper
| [[2014Vargas_RANSAC]]
| Initial model using RANSAC (reference free)
|-

| Paper
| [[2015Joubert_Pseudoatoms]]
| Initial model based on pseudo-atoms
|-

| Paper
| [[2015Singer_Kam]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[2015Sorzano_Significant]]
| Statistical approach to the initial volume estimation (reconstruct significant)
|-

| Conference
| [[2016Michels_Heterogeneous]]
| Initial volume in the presence of heterogeneity
|-

| Paper
| [[2016Cossio_BayesianGPU]]
| GPU implementation of the Bayesian 3D reconstruction approach
|-

|}

=== 3D Reconstruction ===
{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1986Harauz_FBP]]
| Exact filters for Filtered Back Projection
|-

| Chapter
| [[1992Radermacher_WBP]]
| Exact filters for Weighted Back Projection
|-

| Paper
| [[1997Zhu_RecCTF]]
| 3D Reconstruction (SIRT like) and simultaneous CTF correction
|-

| Paper
| [[1998Boisset_Uneven]]
| Artifacts in SIRT and WBP under uneven angular distributions
|-

| Paper
| [[1998Marabini_ART]]
| Algebraic Reconstruction Technique with blobs (Xmipp)
|-

| Paper
| [[2001Sorzano_Uneven]]
| Free parameter selection under uneven angular distributions
|-

| Paper
| [[2005Sorzano_Parameters]]
| Free parameter selection for optimizing multiple tasks
|-

| Paper
| [[2008Sorzano_Constraints]]
| Mass, surface, positivity and symmetry constraints for real-space algorithms
|-

| Paper
| [[2009Bilbao_ParallelART]]
| Efficient parallelization of ART
|-

| Paper
| [[2011Li_GradientFlow]]
| Regularized 3D Reconstruction by Gradient Flow
|-

| Paper
| [[2011Vonesch_Wavelets]]
| Fast wavelet-based 3D reconstruction
|-

| Paper
| [[2012Gopinath_ShapeRegularization]]
| Regularized 3D Reconstruction by Shape information
|-

| Paper
| [[2012Kucukelbir_adaptiveBasis]]
| 3D reconstruction in an adaptive basis promoting sparsity
|-

| Paper
| [[2012Sindelar_NoiseReduction]]
| Optimal noise reduction in 3D reconstructions
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Lyumkis_Optimod]]
| Construction of initial volumes with Optimod
|-

| Paper
| [[2013Wang FIRM]]
| Fast 3D reconstruction in Fourier domain
|-

| Paper
| [[2014Kunz_SART_OS]]
| Simultaneous ART with OS
|-

| Paper
| [[2015Abrishami_Fourier]]
| 3D Reconstruction in Fourier space
|-

| Paper
| [[2015Dvornek_SubspaceEM]]
| Fast Maximum a posteriori
|-

| Paper
| [[2015Moriya_Bayesian]]
| Bayesian approach to suppress limited angular artifacts
|-

| Paper
| [[2015Xu_GeometricFlow]]
| Multi-scale geometric flow
|-

| Arxiv
| [[2016Ye_Cohomology]]
| Cohomology properties of 3D reconstruction
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

| Paper
| [[2017Punjani_CryoSPARCTheory]]
| Theory related to CryoSPARC
|-

|}

=== 3D Heterogeneity ===

{|

| Paper
| [[2004White_Size]]
| Heterogeneity classification of differently sized images
|-

| Paper
| [[2006Penczek_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Scheres_ML3D]]
| Maximum Likelihood alignment and classification in 3D
|-

| Paper
| [[2009Spahn_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2010Elmlund_AbInitio]]
| Solving the initial volume problem with multiple conformations
|-

| Paper
| [[2010Shatsky_MultiVariate]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2012Scheres_Bayesian]]
| A Bayesian view on cryo-EM structure determination
|-

| Paper
| [[2012Zheng_Covariance]]
| Estimation of the volume covariance
|-

| Paper
| [[2013Wang_MLVariance]]
| Maximum Likelihood estimate of the map variance
|-

| Paper
| [[2013Lyumkis D_FREALIGN]]
| Likelihood-based classification of cryo-EM images using FREALIGN.
|-

| Paper
| [[2014Jin_NMA]]
| Continuous heterogeneity through Normal Mode Analysis
|-

| Paper
| [[2014Dashti_Brownian]]
| Continuous heterogeneity through Brownian trajectories
|-

| Paper
| [[2014Chen_Migration]]
| Particle migration analysis in 3D classification
|-

| Paper
| [[2015Anden_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Bai_Focused]]
| Focused classification
|-

| Paper
| [[2015Katsevich_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Klaholz_MRA]]
| Multivariate Statistical Analysis of Jackknife and Bootstrapping on random subsets
|-

| Paper
| [[2015Liao_Covariance]]
| Estimation of the 3D covariance from 2D projections
|-

| Paper
| [[2015Tagare_Direct]]
| Direct reconstruction of PCA components
|-

| Paper
| [[2016Gong_Mechanical]]
| Mechanical model for macromolecules
|-

| Paper
| [[2016Rawson_Movement]]
| Movement and flexibility
|-

| Paper
| [[2016Sorzano_StructMap]]
| Sorting a discrete set of conformational states
|-

| Paper
| [[2016Sorzano_Strain]]
| Calculate local stretches, strains and rotations from two conformational states
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

|}

=== Validation ===

{|

| Paper
| [[2008Stagg_TestBed]]
| Effect of voltage, dosis, number of particles and Euler jumps on resolution
|-

| Paper
| [[2011Henderson]]
| Tilt Validation
|-

| Paper
| [[2011Read]]
| Validation of PDBs
|-

| Paper
| [[2012Henderson]]
| EM Map Validation
|-

| Paper
| [[2013Cossio_Bayesian]]
| EM Map Validation in a probabilistic setting
|-

| Paper
| [[2013Chen_NoiseSubstitution]]
| Noise substitution at high resolution for measuring overfitting
|-

| Paper
| [[2014Russo_StatisticalSignificance]]
| EM Map Validation through the statistical significance of the tilt-pair angular assignment
|-

| Paper
| [[2014Stagg_Reslog]]
| EM Map Validation through the resolution evolution with the number of particles
|-

| Paper
| [[2014Wasilewski_Tilt]]
| Web implementation of the tilt pair validation
|-

| Paper
| [[2015Heymann_Alignability]]
| EM Map Validation through the resolution of reconstructions from particles and noise
|-

| Paper
| [[2015Oliveira_FreqLimited]]
| Comparison of gold standard and frequency limited optimization
|-

| Paper
| [[2015Wriggers_Secondary]]
| Validation by secondary structure
|-

| Paper
| [[2016Kim_SAXS]]
| Comparison of SAXS data and EM projections
|-

| Paper
| [[2016Rosenthal_Review]]
| Review of validation methods
|-

| Paper
| [[2016Vargas_Alignability]]
| Validation by studying the tendency of an angular assignment to cluster in the projection space
|-

| Paper
| [[2017Monroe_PDBRefinement]]
| Validation by comparison to a refined PDB
|-

|}

=== Resolution ===

{|

| Paper
| [[1986Harauz_FBP]]
| Fourier Shell Correlation
|-

| Paper
| [[1987Unser_SSNR]]
| 2D Spectral Signal to Noise Ratio
|-

| Paper
| [[2002Penczek_SSNR]]
| 3D Spectral Signal to Noise Ratio for Fourier based algorithms
|-

| Paper
| [[2003Rosenthal_DPR]]
| Review of the FSC and establishment of a new threshold
|-

| Paper
| [[2005Unser_SSNR]]
| 3D Spectral Signal to Noise Ratio for any kind of algorithms
|-

| Paper
| [[2005VanHeel_FSC]]
| Establishment of a new threshold for FSC
|-

| Paper
| [[2007Sousa_AbInitio]]
| Resolution measurement on neighbour Fourier voxels
|-

| Paper
| [[2014Kucukelbir_Local]]
| Quantifying the local resolution of cryo-EM density maps
|-

| Paper
| [[2016Pintilie_Probabilistic]]
| Probabilistic models and resolution
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Statistical properties of resolution measures defined in Fourier space
|-

|}

=== Sharpening of high resolution information ===
{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast restoration and map sharpening
|-

| Paper
| [[2008Fernandez_Bfactor]]
| Bfactor determination and restoration
|-

| Paper
| [[2013Fiddy_SaxtonAlgorithm]]
| Phase retrieval or extension
|-

| Paper
| [[2014Kishchenko_SphericalDeconvolution]]
| Spherical deconvolution
|-

| Paper
| [[2015Spiegel_VISDEM]]
| Visualization improvement by the use of pseudoatomic profiles
|-

| Paper
| [[2016Jonic_Pseudoatoms]]
| Approximation with pseudoatoms
|-

| Paper
| [[2016Jonic_Denoising]]
| Denoising and high-frequency boosting by pseudoatom approximation
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[1982Schiske_Correction]]
| CTF correction for tilted objects
|-

| Paper
| [[1988Toyoshima_Model]]
| CTF estimation
|-

| Paper
| [[1995Frank_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1996Skoglund_MaxEnt]]
| CTF correction with Maximum Entropy
|-

| Paper
| [[1996Zhou_Model]]
| CTF model and user interface for manual fitting
|-

| Paper
| [[1997Fernandez_AR]]
| PSD estimation using periodogram averaging and AR models
|-

| Paper
| [[1997Penczek_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1997Stark_Deconvolution]]
| CTF correction using deconvolution
|-

| Paper
| [[1997Zhu_RecCTF]]
| CTF correction and reconstruction
|-

| Paper
| [[2000DeRosier_EwaldCorrection]]
| CTF correction considering the Ewald sphere
|-

| Paper
| [[2000Jensen_TiltedCorrection]]
| CTF correction considering tilt in backprojection
|-

| Paper
| [[2001Saad_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Huang_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Mindell_CTFTILT]]
| CTF estimation for tilted micrographs
|-

| Paper
| [[2003Sander_MSA]]
| CTF estimation through MSA classification of PSDs
|-

| Paper
| [[2003Velazquez_ARMA]]
| PSD and CTF estimation using ARMA models
|-

| Paper
| [[2004Sorzano_IDR]]
| CTF restoration and reconstruction with Iterative Data Refinement
|-

| Conference
| [[2004Wan_CTF]]
| Spatially variant CTF
|-

| Paper
| [[2004Zubelli_Chahine]]
| CTF restoration and reconstruction with Chahine's multiplicative method
|-

| Conference
| [[2005Dubowy_SpaceVariant]]
| CTF correction when this is space variant
|-

| Paper
| [[2005Mallick_ACE]]
| CTF estimation
|-

| Paper
| [[2006Wolf_Ewald]]
| CTF correction considering Ewald sphere
|-

| Paper
| [[2007Jonic_EnhancedPSD]]
| PSD enhancement for better identification of Thon rings; Vitreous ice diffracts in Thon rings
|-

| Paper
| [[2007Philippsen_Model]]
| CTF Model for tilted specimens
|-

| Paper
| [[2007Sorzano_CTF]]
| CTF estimation using enhanced PSDs
|-

| Paper
| [[2009Sorzano_Sensitivity]]
| Error sensitivity of the CTF models, non-uniqueness of the CTF parameters
|-

| Paper
| [[2010Jiang2010_CTFCorrection]]
| Amplitude correction method
|-

| Paper
| [[2010Kasantsev_CTFCorrection]]
| Mathematical foundations of Kornberg and Jensen method
|-

| Paper
| [[2010Leong_CTFCorrection]]
| Correction for spatially variant CTF
|-

| Paper
| [[2011Glaeser_Coma]]
| The effect of coma at high-resolution
|-

| Paper
| [[2011Mariani_Tilted]]
| CTF simulation and correction of tilted specimens
|-

| Paper
| [[2011Sindelar_Wiener]]
| CTF correction using a modified version of Wiener filter
|-

| Paper
| [[2011Voortman_Tilted]]
| CTF correction for tilted specimen
|-

| Paper
| [[2012Voortman_VaryingCTF]]
| Correcting a spatially varying CTF
|-

| Paper
| [[2013Vargas_FastDef]]
| Fast defocus
|-

| Paper
| [[2015Rohou_CTFFind4]]
| CTF Find 4
|-

| Paper
| [[2015Sheth_CTFquality]]
| Visualization and quality assessment of CTF
|-

| Paper
| [[2016Zhang_GCTF]]
| gCTF
|-

|}

=== Segmentation ===

{|

| Paper
| [[2006Baker_segmentation]]
| Segmentation of molecular subunits
|-

|}

=== Fitting and docking ===

{|

| Paper
| [[1999Volkmann_Fitting]]
| Fitting in real space
|-

| Paper
| [[2001Baker_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2001Jones_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2003Kovacs_FRM3D]]
| Fast Rotational Alignment of two EM maps
|-

| Paper
| [[2004Tama_NMA1]]
| Flexible fitting with Normal Modes (I)
|-

| Paper
| [[2004Tama_NMA2]]
| Flexible fitting with Normal Modes (II)
|-

| Paper
| [[2005Velazquez_Superfamilies]]
| Recognition of the superfamily folding in medium-high resolution volumes
|-

| Paper
| [[2007DeVries_Haddock]]
| Docking with Haddock 2.0
|-

| Paper
| [[2007Kleywegt_QualityControl]]
| Quality control and validation of fitting
|-

| Paper
| [[2012Biswas_Secondary]]
| Secondary structure determination in EM volumes
|-

| Paper
| [[2012Velazquez_Constraints]]
| Multicomponent fitting by using constraints from other information sources
|-

| Paper
| [[2013Chapman MS_Atomicmodeling]]
| Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters
|-

| Paper
| [[2013Esquivel_Modelling]]
| Review on modelling (secondary structure, fitting, ...)
|-

| Paper
| [[2013Lopez_Imodfit]]
| Fitting based on vibrational analysis
|-

| Paper
| [[2013Nogales_3DEMLoupe]]
| Normal Mode Analysis of reconstructed volumes
|-

| Paper
| [[2014AlNasr_Secondary]]
| Identification of secondary structure elements in EM volumes
|-

| Paper
| [[2014Politis_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Rey_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Villa_Review]]
| Review of atomic fitting into EM volumes
|-

| Paper
| [[2015Barad_EMRinger]]
| Validation of hybrid models
|-

| Paper
| [[2015Bettadapura_PF2Fit]]
| Fast rigid fitting of PDBs into EM maps
|-

| Paper
| [[2015Carrillo_CapsidMaps]]
| Analysis of virus capsids using Google Maps
|-

| Paper
| [[2015Hanson_Continuum]]
| Modelling assemblies with continuum mechanics
|-

| Paper
| [[2015Schroeder_Hybrid]]
| Review on model building
|-

| Paper
| [[2015Tamo_Dynamics]]
| Dynamics in integrative modeling
|-

| Paper
| [[2015Sorzano_AtomsToVoxels]]
| Accurate conversion of an atomic model into a voxel density volume
|-

| Paper
| [[2016Joseph_Evolution]]
| Evolutionary constraints for the fitting of atomic models into density maps
|-

| Paper
| [[2016Segura_3Diana]]
| Validation of hybrid models
|-

| Paper
| [[2016Singharoy_MDFF]]
| Construction of hybrid models driven by EM density and molecular dynamics
|-

| Paper
| [[2016Wang_Rosetta]]
| Construction of hybrid models driven by EM density using Rosetta
|-

| Paper
| [[2017Joseph_Metrics]]
| Metrics analysis for the comparison of structures
|-

| Paper
| [[2017Hryc_WeightedAtoms]]
| Construction of hybrid models by locally weighting the different atoms
|-

| Paper
| [[2017Matsumoto_Distribution]]
| Estimating the distribution of conformations of atomic models
|-

| Paper
| [[2017Miyashita_EnsembleFitting]]
| Ensemble fitting using Molecular Dynamics
|-

| Paper
| [[2017Turk_ModelBuilding]]
| Tutorial on model building and protein visualization
|-

|}

=== Books and reviews ===

{|

| Book
| [[1980Herman_Tomography]]
| General book on tomography
|-

| Book
| [[1988Kak_Tomography]]
| General book on tomography
|-

| Paper
| [[2000Tao_Review]]
| Review of single particles
|-

| Paper
| [[2000VanHeel_Review]]
| Review of single particles
|-

| Paper
| [[2002Frank_Review]]
| Review of single particles
|-

| Paper
| [[2002Schmid_Review]]
| Review of single particles
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2004Subramaniam_Review]]
| Review of single particles
|-

| Paper
| [[2005Steven_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_book]]
| Book covering all aspects of electron microscopy of single particles
|-

| Paper
| [[2006Sorzano_Review]]
| Review of optimization problems in electron microscopy
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems in Electron Tomography
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2008Mueller_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2008Taylor_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2010DeRosier_Review]]
| Personal account of how 3DEM developed in the early days
|-

| Chapter
| [[2012Sorzano_Review]]
| Review of single particle analysis using Xmipp
|-

| Chapter
| [[2012Devaux_Protocol]]
| Protocols for performing single particle analysis
|-

| Paper
| [[2014Bai_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Carazo_Review]]
| Review of the reconstruction process
|-

| Paper
| [[2015Cheng_Review]]
| A primer to Single Particle Cryo-EM
|-

| Paper
| [[2015Cheng_Reviewb]]
| Single Particle Cryo-EM at crystallographic resolution
|-

| Paper
| [[2015Elmlund_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Henderson_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Nogales_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Schroeder_Review]]
| Review of advances in the electron microscope
|-

| Paper
| [[2015Wu_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Carroni_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Egelman_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Eisenstein_CryoEM]]
| News feature on the Method of the Year
|-

| Paper
| [[2016FernandezLeiro_Review]]
| Review of EM
|-

| Paper
| [[2016Glaeser_HowGood]]
| How good can cryo-EM become?
|-

| Paper
| [[2016Jonic_PseudoAtoms]]
| Review of the applications of the use of pseudoatoms in EM
|-

| Chapter
| [[2016Mio_Review]]
| Overview of the process to obtain EM reconstructions
|-

| Paper
| [[2016Jonic_Review]]
| A review of computational ways to handle heterogeneity
|-

| Paper
| [[2016Nogales_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Subramaniam_Review]]
| Why cryo-EM is now suitable for crystallographic journals
|-

| Paper
| [[2016Vinothkumar_Review]]
| Historical review and current limitations
|-

| Paper
| [[2017Frank_Review]]
| Historical review of EM
|-

| Paper
| [[2017Jonic_Review]]
| Review of computational methods to analyze conformational variability
|-

| Paper
| [[2017Rawson_Limitations]]
| Limitations of EM for drug design
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Review of statistical properties of resolution measures defined in Fourier space
|-
|}

=== Software ===

{|

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[1999Lutdke_Eman]]
| Eman
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Baldwin_AngularTransformations]]
| The Transform Class in SPARX and EMAN2
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Grigorieff_Frealign]]
| Frealign
|-

| Paper
| [[2008Scheres_XmippProtocols]]
| Xmipp Protocols
|-

| Paper
| [[2008Shaikh_SpiderProtocols]]
| Spider Protocols
|-

| Paper
| [[2012Wriggers_SitusConventions]]
| Conventions and workflows in Situs
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2015Cianfrocco_Cloud]]
| Software execution in the cloud
|-

| Paper
| [[2015Cheng_MRC2014]]
| Extensions to MRC file format
|-

| Paper
| [[2013DeLaRosa_Scipion]]
| Scipion
|-

| Paper
| [[2016Scheres_Relion]]
| Tutorial on the use of Relion
|-

| Paper
| [[2016Grigorieff_Frealign]]
| Tutorial on the use of Frealign
|-

| Paper
| [[2017Moriya_Sphire]]
| Tutorial on the use of Sphire
|-

|}

== Electron tomography ==

=== Image preprocessing ===

{|

| Paper
| [[2015Yan_thickness]]
| Determination of thickness, tilt and electron mean free path
|-

|}

=== Image alignment ===

{|

| Paper
| [[1982Guckenberger_commonOrigin]]
| Determination of a common origin in the micrographs of titl series in three-dimensional electron microscopy
|-

| Paper
| [[1992Lawrence_leastSquares]]
| Least squares solution of the alignment problem
|-

| Paper
| [[1995Penczek_dual]]
| Dual tilt alignment
|-

| Paper
| [[1996Owen_alignmentQuality]]
| Automatic alignment without fiducial markers and evaluation of alignment quality
|-

| Paper
| [[1998Grimm_normalization]]
| Discussion of several gray level normalization methods for electron tomography
|-

| Paper
| [[2001Brandt_Automatic1]]
| Automatic alignment without fiducial markers
|-

| Paper
| [[2001Brandt_Automatic2]]
| Automatic alignment with fiducial markers
|-

| Paper
| [[2006Winkler_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2006Castano_alignment]]
| Alignment with non-perpendicularity
|-

| Paper
| [[2007Castano_alignment]]
| Fiducial-less alignment of cryo-sections
|-

| Paper
| [[2009Sorzano_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2010Cantele_dualAlignment]]
| Alignment of dual series
|-

| Paper
| [[2014Tomonaga_Automatic]]
| Automatic alignment of tilt series using the projection themselves
|-

| Paper
| [[2014Han_Automatic]]
| Automatic alignment of tilt series using SIFT features
|-

| Paper
| [[2015Han_Automatic]]
| Automatic alignment of tilt series using fiducials
|-

| Paper
| [[2017Mastronarde_Automatic]]
| Automatic alignment and reconstruction of tilt series in IMOD
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[2003Winkler_CTF]]
| Focus gradient correction in electron tomography
|-

| Paper
| [[2006Fernandez_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Zanetti_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Xiong_CTF]]
| CTF determination and correction for low dose tomographic tilt series
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2017Kunz_3DCTF]]
| 3D CTF Correction
|-

|}

=== 3D reconstruction ===

{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1992Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[1997Marabini_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2002Fernandez_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2007Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[2008Fernandez_CARP]]
| Component Averaged Row Projections (CARP)
|-

| Paper
| [[2012Herman General Superiorization]]
| Superiorization: an optimization heuristic for medical physics
|-

| Paper
| [[2012Zhang_IPET_FETR]]
| IPET and FETR, a reconstruction algorithm for single molecule tomography
|-

| Paper
| [[2013Goris_SIRT_TV_DART]]
| Combination of SIRT, Total Variation and Discrete ART to reconstruct and segment at the same time
|-

| Paper
| [[2013Briegel A_Challenge]]
| The challenge of determining handedness in electron tomography and the use of DNA origami gold nanoparticle helices as molecular standards
|-

| Paper
| [[2013Messaoudi_EnergyFiltered]]
| 3D Reconstruction of Energy-Filtered TEM
|-

| Paper
| [[2016Deng_ICON]]
| 3D Reconstruction with missing information restoration
|-

| Paper
| [[2016Guay_Compressed]]
| 3D Reconstruction using compressed sensing
|-

|}

=== Noise reduction ===
{|

| Paper
| [[2001Frangakis_NAD]]
| Noise reduction with Nonlinear Anisotropic Diffusion
|-

| Paper
| [[2003Fernandez_AND]]
| Anisotropic nonlinear diffusion for electron tomography
|-

| Paper
| [[2003Jiang_Bilateral]]
| Bilateral denoising filter in electron microscopy
|-

| Paper
| [[2005Fernandez_AND]]
| Anisotropic nonlinear denoising in electron tomography
|-

| Paper
| [[2007Heide_median]]
| Iterative median filtering in electron tomography
|-

| Paper
| [[2007Fernandez_autAND]]
| Anisotropic nonlinear diffusion with automated parameter tuning
|-

| Paper
| [[2009Fernandez_Beltrami]]
| Nonlinear filtering based on Beltrami flow
|-

| Paper
| [[2010Bilbao_MeanShift]]
| Mean Shift Filtering
|-

| Paper
| [[2014Kovacik_wedgeArtefacts]]
| Removal of wedge artefacts
|-

| Paper
| [[2014Maiorca_beadArtefacts]]
| Removal of gold bead artefacts
|-

|}

=== Segmentation ===

{|

| Paper
| [[2002Frangakis_Eigenanalysis]]
| Segmentation using eigenvector analysis.
|-

| Paper
| [[2002Volkmann_Watershed]]
| Segmentation using watershed transform.
|-

| Paper
| [[2003Bajaj_BoundarySegmentation]]
| Segmentation based on fast marching.
|-

| Paper
| [[2005Cyrklaff_Thresholding]]
| Segmentation using optimal thresholding.
|-

| Paper
| [[2007Lebbink_TemplateMatching]]
| Segmentation using template matching.
|-

| Paper
| [[2007Sandberg_OrientationFields]]
| Segmentation using orientation fields.
|-

| Paper
| [[2007Sandberg_SegmentationReview]]
| Review on segmentation in electron tomography.
|-

| Paper
| [[2008Garduno_FuzzySegmentation]]
| Segmentation using fuzzy set theory principles.
|-

| Paper
| [[2009Lebbink_TemplateMatching2]]
| Segmentation using template matching.
|-

| Paper
| [[2012RubbiyaAli_EdgeDetection]]
| Parameter-Free Segmentation of Macromolecular Structures.
|-

| Conference
| [[2015Xu_TemplateMatching]]
| Detection of macromolecular complexes with a reduced representation of the templates.
|-

|}

=== Resolution ===
{|

| Paper
| [[2005Cardone_Resolution]]
| Resolution criterion for electron tomography
|-

| Chapter
| [[2007Penczek_Resolution]]
| Review of resolution criteria for electron tomography
|-

| Paper
| [[2015Diebolder_ConicalFSC]]
| Conical Fourier Shell Correlation
|-

|}

=== Subtomogram analysis ===

{|

| Paper
| [[2000Bohm_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2002Frangakis_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2006Nickell_Review]]
| Review of macromolecule finding by template matching (Visual Proteomics)
|-

| Paper
| [[2007Best_Review]]
| Review of Localization of Protein Complexes by Pattern Recognition
|-

| Paper
| [[2007Forster_Review]]
| Review of structure determination by subtomogram averaging
|-

| Paper
| [[2008Forster_Classification]]
| Classification of subtomograms using constrained correlation
|-

| Paper
| [[2008Bartesaghi_Classification]]
| Classification and averaging of subtomograms
|-

| Paper
| [[2008Schmid_Averaging]]
| Alignment and averaging of subtomograms
|-

| Paper
| [[2010Amat_Averaging]]
| Alignment and averaging of subtomograms exploiting thresholding in Fourier space
|-

| Paper
| [[2013Chen_Averaging]]
| Fast alignment of subtomograms using spherical harmonics
|-

| Paper
| [[2013Kuybeda_Averaging]]
| Alignment and averaging of subtomograms using the nuclear norm of the cluster
|-

| Paper
| [[2013Shatsky_Averaging]]
| Alignment and averaging of subtomograms with constrained cross-correlation
|-

| Paper
| [[2014Chen_Autofocus]]
| Subtomogram averaging and classification with special attention to differences
|-

| Paper
| [[2014Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2014Voortman_LimitingFactors]]
| Limiting factors of subtomogram averaging
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2015Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2016Bharat_Relion]]
| Subtomogram averaging with Relion
|-

| Paper
| [[2016Song_MatrixNorm]]
| Matrix norm minimization for tomographic reconstruction and alignment
|-

| Paper
| [[2017Castano_ParticlePicking]]
| Particle picking in tomograms for subtomogram averaging
|-

| Paper
| [[2017Frazier_Tomominer]]
| TomoMiner a software platform for large-scale subtomogram analysis
|-

|}

=== Single particle tomography ===

{|

| Paper
| [[2012Bartesaghi_Constrained]]
| 3D reconstruction by imposing geometrical constraints
|-

| Paper
| [[2015Galaz_SingleParticleTomography]]
| Set of tools for Single Particle Tomography in EMAN2
|-

| Paper
| [[2016Galaz_SingleParticleTomography]]
| Alignment algorithms and CTF correction
|-

|}

=== Books and reviews ===

{|

| Paper
| [[2000Baumeister_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Koster_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Sali_Review]]
| Review of electron tomography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2005Lucic_Review]]
| Review of electron tomography
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_TomoBook]]
| Electron Tomography
|-

| Book
| [[2007McIntosh_Book]]
| Cellular Electron Microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2012Kudryashev_Review]]
| Review of subtomogram averaging
|-

| Paper
| [[2016Beck_Review]]
| Review of molecular sociology
|-

| Paper
| [[2017Galaz_Review]]
| Review of single particle tomography
|-

|}

=== Software ===

{|

| Paper
| [[1996Kremer_IMOD]]
| IMOD
|-

| Paper
| [[1996Chen_Priism/IVE]]
| Priism/IVE
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2005Nickell_TOM]]
| TOM Toolbox
|-

| Paper
| [[2007Messaoudi_TomoJ]]
| TomoJ
|-

| Paper
| [[2008Heymann_BsoftTomo]]
| Bsoft
|-

| Paper
| [[2015Ding_CaltechTomography]]
| Caltech tomography database
|-

| Paper
| [[2015Noble_AppionProtomo]]
| Batch fiducial-less tilt-series alignment in Appion using Protomo
|-

| Paper
| [[2015vanAarle_Astra]]
| ASTRA Toolbox
|-

| Paper
| [[2017Wan_Simulator]]
| Electron Tomography Simulator
|-

|}

== 2D Crystals ==

=== 2D Preprocessing ===

{|

| Paper
| [[1986Henderson_Processing]]
| General 2D processing
|-

| Paper
| [[2000He_PhaseAlignment]]
| Phase consistency and Alignment
|-

| Paper
| [[2006Gil_Unbending]]
| Crystal unbending
|-

|}

=== Classification ===
{|

| Paper
| [[1988Frank_Classification]]
| MSA and classification in electron crystallography
|-

| Paper
| [[1996Fernandez_SOM]]
| Classification based on self organizing maps
|-

| Paper
| [[1998Sherman_MSA]]
| Classification based on MSA
|-

|}
=== 3D Reconstruction ===

{|

| Paper
| [[1985Wang_Solvent]]
| Solvent flattening
|-

| Paper
| [[1990Henderson_Processing]]
| General 3D processing
|-

| Paper
| [[2004Marabini_ART]]
| Algebraic Reconstruction Technique with blobs for crystals (Xmipp)
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1998Walz_Review]]
| Review of 2D crystallography
|-

| Paper
| [[1999Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Ellis_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of single particles, electron tomography and crystallography
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Gipson_2dx]]
| 2dx
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Philippsen_IPLT]]
| IPLT
|-

|}

== 3D Crystals - MicroED ==

=== Sample Preparation ===
{|
| Paper
| [[2016Shi_Preparation]]
| Sample Preparation
|}
=== Data Collection ===
{|
| Paper
| [[2014Nannenga_CR]]
| Continuous rotation

|}
=== Data Processing ===
{|

| Paper
| [[2011Wisedchaisri_PhaseExtension]]
| Fragment-based phase extension
|-

| Paper
| [[2015Hattne_Processing]]
| Data Processing
|-

| Paper
| [[2016Hattne_Correction]]
| Image correction
|}

=== Software ===
{|

| Paper
| [[2014Iadanza_Processing]]
| Data Processing of still diffraction data
|}

=== Books and Reviews ===
{|
| Paper
| [[2014Nannenga_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Liu_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Rodriguez_Review ]]
| Review of MicroED
|-

|}

== Helical particles ==

=== Filament corrections ===

{|

| Paper
| [[1986Egelman_Curved]]
| Algorithm for correcting curved filaments
|-

| Paper
| [[1988Bluemke_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2006Wang_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2016Yang_Flexible]]
| Algorithm for correcting filaments with flexible subunits
|-

|}

=== Reconstruction ===

{|

| Paper
| [[1952Cochran_Fourier]]
| Fourier Bessel transform of filamentous structures
|-

| Paper
| [[1958Klug_Fourier]]
| Fourier Bessel decomposition of the projection images
|-

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2005Wang_Iterative]]
| Iterative Fourier-Bessel algorithm
|-

| Paper
| [[2007Egelman_Iterative]]
| Iterative real-space algorithm
|-

| Paper
| [[2013Desfosses_Spring]]
| Helical processing with Spring
|-

| Paper
| [[2015Zhang_seam]]
| Workflow for the detection of the lattice seam
|-

| Paper
| [[2016Rohou_Frealix]]
| Helical processing with Frealix
|-

|}

=== Validation ===

{|

| Paper
| [[2014Egelman_ambiguity]]
| How to detect incorrect models
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Carragher_Phoelix]]
| Phoelix
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Owen_Brandeis]]
| Brandeis
|-

|}

== Icosahedral particles ==

=== Reconstruction ===

{|

| Paper
| [[1970Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1971Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1996Fuller_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1997Thuman_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

|}

=== Classification ===

{|

| Paper
| [[2005Scheres_Virus]]
| Classification of virus capsids in real space
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1999Baker_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[1999Conway_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2000Thuman_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Lee_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Navaza_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2006Grunewald_Review]]
| Review of reconstruction of icosahedral viruses
|-

|}

=== Software ===

{|

| Paper
| [[1996Baker_EMPFT]]
| EMPFT
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2013Morin_Sliz SBGrid]]
| SBGrid presentation for eLife
|-

|}

== Databases ==

{|

| Paper
| [[2003Boutselakis_EMSD]]
| EMSD database
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2011Kim_CDDB]]
| Conformational Dynamics Data Bank
|-

| Paper
| [[2011Lawson_EMDB]]
| Electron Microscopy Data Bank
|-

| Paper
| [[2013Ison_EDAM]]
| EDAM, an ontology of bioinformatics operations
|-

| Paper
| [[2016Iudin_EMPIAR]]
| EMPIAR raw data database
|-

| Paper
| [[2016Patwhardan_EMDB]]
| EMDB, PDB, ...
|-

| Paper
| [[2017Patwhardan_Trends]]
| Trends at EMDB
|-

| Paper
| [[2017Shao_PDBQuality]]
| Quality metrics in PDB
|-

| Blog
| http://www.mybiosoftware.com
| Huge list of bioinformatics programs (many of them structural bioinformatics)
|-

|}

== Relationship to other structural information sources ==

{|

| Paper
| [[2000Engel_AFM]]
| Review of Atomic Force Microscopy
|-

| Paper
| [[2001Dimmeler_AFM]]
| Constraints from Atomic Force Microscopy
|-

| Paper
| [[2003Mobus_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_Review]]
| Review on correlative microscopy
|-

| Paper
| [[2005Boudier_EFTETJ]]
| Software for Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2005Vestergaard_SAXS]]
| Example of comparison of 3DEM and Small-angle X-ray scattering
|-

| Paper
| [[2007Hamada_SAXS]]
| Constraints from Small-angle X-ray scattering
|-

| Paper
| [[2013Xu_FRET]]
| EM+FRET
|-

|}

== X-ray tomography ==

{|

| Paper
| [[2012Oton_ImageFormation]]
| Image formation model in X-ray cell microscopy
|-

|}

== Mathematical tools necessary ==

== People developing methods ==
Please, add yourself to this list (due to privacy reasons, please, do not add anyone else to the list without his/her explicit consent). Sort by first name alphabetical order.

[http://biocomp.cnb.csic.es/~coss Carlos Oscar S. Sorzano]: CSIC, Madrid, Spain 

[http://www.curie.fr/recherche/themes/detail_equipe.cfm/lang/_fr/id_equipe/241.htm Cédric Messaoudi]: Institute Curie, Paris, France 

[http://scholar.google.es/citations?user=_jNYGScAAAAJ&hl=en Javier Vargas]:[mailto:jvargas@cnb.csic.es mail]: CSIC, Madrid, Spain 

[http://scholar.google.es/citations?hl=es&user=g2ZJPIYAAAAJ Joaquín Otón]: CSIC, Madrid, Spain 

[mailto:jrbcast@gmail.com José Román Bilbao-Castro]: UAL, Almería, Spain; CSIC, Madrid, Spain 

[José Miguel de la Rosa Trevín]: Biocomputing Unit CNB-CSIC, Madrid, Spain 

[http://cryoem.janelia.org Tamir Gonen]: [mailto:gonent@janelia.hhmi.org mail]: Howard Hughes Medical Institute, Ashburn, VA, USA 

[mailto:vabrishami@cnb.csic.es Vahid Abrishami]: CSIC, Madrid, Spain 

== 3DEM sites ==
* [http://3dem.ucsd.edu/ 3DEM web site]

* [http://en.wikibooks.org/wiki/Software_Tools_For_Molecular_Microscopy Software tools for molecular microscopy]

* [http://www.emdatabank.org/ The Electron Microscopy Data Bank (EMDB)]

* [http://ccdb.ucsd.edu The Cell Centered Database (CCDB)]

* [http://conventions.cnb.csic.es The geometrical software conventions web page ]

== Editing useful links ==

* [http://www.mediawiki.org/wiki/Help:Formatting Text formatting in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Links Adding links in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Images Adding images in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Tables Making tables in Mediawiki]

2017He FIB

2017-07-20T06:03:12Z

CoSS: Created page with "== Citation == He, J.; Hsieh, C.; Wu, Y.; Schmelzer, T.; Wang, P.; Lin, Y.; Marko, M. & Sui, H. Cryo-FIB specimen preparation for use in a cartridge-type cryo-TEM. Journal of..."

== Citation ==

He, J.; Hsieh, C.; Wu, Y.; Schmelzer, T.; Wang, P.; Lin, Y.; Marko, M. & Sui, H. Cryo-FIB specimen preparation for use in a cartridge-type cryo-TEM. Journal of structural biology, 2017

== Abstract ==

Cryo-electron tomography (cryo-ET) is a well-established technique for studying 3D structural details of
subcellular macromolecular complexes and organelles in their nearly native context in the cell. A primary
limitation of the application of cryo-ET is the accessible specimen thickness, which is less than the diameters
of almost all eukaryotic cells. It has been shown that focused ion beam (FIB) milling can be used to
prepare thin, distortion-free lamellae of frozen biological material for high-resolution cryo-ET.
Commercial cryosystems are available for cryo-FIB specimen preparation, however re-engineering and
additional fixtures are often essential for reliable results with a particular cryo-FIB and cryotransmission
electron microscope (cryo-TEM). Here, we describe our optimized protocol and modified
instrumentation for cryo-FIB milling to produce thin lamellae and subsequent damage-free cryotransfer
of the lamellae into our cartridge-type cryo-TEM.

== Keywords ==

== Links ==

http://www.sciencedirect.com/science/article/pii/S1047847717300916

== Related software ==

== Related methods ==

== Comments ==

Main Page

2017-07-20T06:02:21Z

CoSS: /* Sample preparation */

== Presentation ==

This web page is intended to be an extensive repository of three-dimensional electron microscopy (3DEM) methods. The advantages of having such a repository are

* You know which are the relevant articles in a particular topic, therefore, paper introductions, reviews, etc. are easier to write and you make sure you will cite all the related articles.
* You will be sure that your paper has more chances of being cited.
* You can add whatever information you find relevant to your method, external links, links to other papers, etc.
* You can link your method to a web page providing the corresponding software, so you know people can use your algorithms.
* You can use the Wiki search capabilities to locate relevant articles even if they are not at the topic you are looking at.
* As a community we will "reconstruct" our history.
* You can select the "watch" option above to receive notifications in case of further changes in the Main Page.

Developing image processing methods for 3DEM is not "[[well-paid]]" in terms of citations and impact factor. However, it is crucial for the advance of the field. Gathering methodological papers in a portal will help to increase the recognition of the field.

Please:

* Add your articles at the right place (you can add a single article in several topics if it is relevant to all of them). The easiest way to add an article is by editing the corresponding topic in the main page, adding your entry, then save the main page. Click on the red link that appears on your new entry, copy and paste the Wiki following code, add the information of your article

== Citation ==

== Abstract ==

== Keywords ==

== Links ==

== Related software ==

== Related methods ==

== Comments ==

* Maintain the information of each article as complete as possible.
* Sort articles by years and authors.
* Be respectful to other people's work.

== How to subscribe to this page ==

You may subscribe to this page so that you will be notified every time someone adds a new method. To do so, you have to register in the page, and edit your preferences ("my preferences"). Be sure that you have activated the option "E-mail me when a page on my watchlist is changed". Finally, click on the "Watch" tab at the top of this page.

You may subscribe to changes on this page on the mailing list 3demmethods@cnb.csic.es. To send a new method to this mail list just send a mail to 3demmethods@cnb.csic.es

To subscribe to this list, visit the web page

https://listas.csic.es/cnb/wws/subscribe/3demmethods

Alternatively, you may write a mail to sympa6@cnb.csic.es with the subject

<code>subscribe 3demmethods YourName YourFamilyName</code>

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To unsubscribe visit the page

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or write sympa6@cnb.csic.es with the subject

<code>unsubscribe 3demmethods</code>

and an empty mail body.

== Electron microscopy images ==

=== Online courses ===

CALTECH: http://cryo-em-course.caltech.edu/

MRC: ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/EM-course/

CNB-CSIC: http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/MadridJan2014EM

Workshop on Computational methods for CryoEM: https://www.youtube.com/watch?v=XdKO1iaPP8o

Workshop on Management of large CryoEM facilities: https://www.youtube.com/watch?v=as4seOPszL0

Icknield Course on Model Building and Refinement for High Resolution EM Maps: http://www.ccpem.ac.uk/training/icknield_2017/icknield_2017.php

=== Image formation ===

{|

| Paper
| [[1971Erickson_CTF]]
| CTF model
|-

| Paper
| [[1971Glaeser_Damage]]
| Radiation damage
|-

| Chapter
| [[1971Hanszen_CTF]]
| Image formation model
|-

| Paper
| [[1971Thon_Model]]
| CTF model
|-

| Paper
| [[1975Unwin_Imaging]]
| Radiation dose
|-

| Paper
| [[1977Wade_Model]]
| CTF model
|-

| Paper
| [[1978Wade_Model]]
| CTF model
|-

| Paper
| [[1979Hayward_Radiation]]
| Radiation damage
|-

| Paper
| [[1984Cohen_Validity]]
| Validity of the CTF model at high frequencies
|-

| Paper
| [[1988Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[1992Wade_Model]]
| CTF model
|-

| Paper
| [[1993Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2004Egerton_Damage]]
| Radiation damage
|-

| Paper
| [[2004Sorzano_Normalization]]
| Background noise is Gaussian
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2009Baxter_NoiseCharacterization]]
| Characterization of the different noise sources in cryo-EM
|-

| Paper
| [[2010Baker_Damage]]
| Radiation damage dependence on resolution
|-

| Paper
| [[2010Bammes_Damage]]
| Radiation damage dependence on temperature
|-

| Paper
| [[2010Gomez_Multislice]]
| Simulation of the multi slice model
|-

| Paper
| [[2010Zewail_FourDimensional]]
| Review on the use of ultrafast EM
|-

| Paper
| [[2011Bammes_CCD]]
| Performance of CCD cameras
|-

| Paper
| [[2011Glaeser_Coma]]
| Image formation model including coma
|-

| Paper
| [[2011Milazzo_DirectDetectors]]
| Evaluation of Direct Detectors
|-

| Paper
| [[2011Rullgard_ImageSimulation]]
| Accurate simulation of EM images
|-

| Paper
| [[2011Zhang LimitingFactors]]
| Limiting factor for atomic resolution in EM
|-

| Paper
| [[2012Bammes_DirectDetection]]
| Performance of Direct detectors
|-

| Paper
| [[2012Campbell_MotionCorrection]]
| Beam induced motion correction and direct detectors
|-

| Paper
| [[2012Shang_HydrationLayer]]
| Simulation of PDB volumes explicitly considering the hydration layer
|-

| Paper
| [[2013Egerton_RadiationDamage]]
| Review of TEM radiation damage and experimental ways of reducing it
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu H_Noisemodels]]
| Noise models and cryo-EM drift correction with a direct-electron camera
|-

| Paper
| [[2013Li X K2 noisemodels]]
| Influence of electron dose rate on electron counting images recorded with the K2 camera
|-

| Paper
| [[2013Vulovic_CTFApproximations]]
| When to use the different approximations performed so that a projection with linear CTF is valid
|-

| Thesis
| [[2013Vulovic_ImageFormation]]
| Ph.D. Thesis on the image formation in cryo-EM
|-

| Paper
| [[2014Danev_PhasePlate]]
| Volta potential phase plate
|-

| Paper
| [[2015Chiu_K2]]
| Characterization of K2
|-

| Paper
| [[2015Hawkes_AberrationCorrection]]
| Historical account of the development of lens corrections
|-

| Paper
| [[2015Koeck_Quadratic]]
| Limitations of the linear approximation and use of the quadratic terms
|-

| Paper
| [[2015Kuijper_FEI]]
| Description of the FEI Falcons
|-

| Paper
| [[2015Lobato_MULTEM]]
| Simulation of multislice diffraction
|-

| Paper
| [[2015McMullan_AmorphousIce]]
| Beam induced movement is caused by Brownian motion
|-

| Paper
| [[2016Koeck_ADF]]
| Simulations of Annular Dark Field TEM
|-

| Paper
| [[2017Mishyna_DNARadiation]]
| Review of radiation damage on DNA
|-

|}

=== Collection geometry ===

{|

| Chapter
| [[1980Hoppe_Wedge]]
| Missing wedge
|-

| Paper
| [[1987Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1995Penczek_Dual]]
| Dual axis tomography
|-

| Paper
| [[1997Mastronarde_Dual]]
| Dual axis tomography
|-

| Paper
| [[2003Ludtke_FocusPairs]]
| Focus pairs for single particles
|-

| Paper
| [[2005Lanzavecchia_Conical]]
| Conical tomography
|-

| Paper
| [[2005Zampighi_Conical]]
| Conical tomography
|-

| Paper
| [[2006Leschziner_OT]]
| Orthogonal Tilt
|-

| Paper
| [[2006Messaoudi_Multiple]]
| Multiple axis tomography
|-

| Paper
| [[2012Kudryashev_FocusPairs]]
| Focus pairs tomography
|-

| Paper
| [[2014Hovden_TiltFocus]]
| Combining tilt series with focus series
|-

| Paper
| [[2015Sorzano_RandomConicalTilt]]
| General formulation of Random Conical Tilt
|-

| Paper
| [[2017Hagen_DoseTomography]]
| Dose optimization for subtomogram averaging
|-

|}

=== Sample preparation ===

{|

| Paper
| [[1982Dubochet_Sample]]
| Vitreous ice
|-

| Paper
| [[1986Lepault_Sample]]
| Fast freezing
|-

| Paper
| [[1995Dubochet_Sample]]
| High-pressure freezing
|-

| Paper
| [[1995VanMarle_Sample]]
| Sample damages in resin
|-

| Paper
| [[1998Adrian_Sample]]
| Cryo negative staining
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2002Hsieh_Sample]]
| Cryofixation
|-

| Paper
| [[2004AlAmoudi_Sample]]
| CEMOVIS
|-

| Paper
| [[2008Studer_Sample]]
| Review on high pressure freezing
|-

| Paper
| [[2009Pierson_Sample]]
| Review on sample preparation for electron tomography
|-

| Paper
| [[2010Zhang_NegativeStaining]]
| Negative staining for small protein imaging
|-

| Paper
| [[2012Zhang_PositiveStaining]]
| Positive staining
|-

| Paper
| [[2014Rames_NegativeStaining]]
| Optimized negative staining
|-

| Paper
| [[2014Russo_GoldGrids]]
| Gold grids for single particles
|-

| Paper
| [[2015Cabra_Sample]]
| Review on sample preparation for single particles with videos
|-

| Paper
| [[2016Passmore_Review]]
| Tutorial chapter on sample preparation
|-

| Paper
| [[2016Razinkov_Vitrification]]
| New vitrification method
|-

| Paper
| [[2016Takizawa_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2016Thompson_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2017Arnold_BlottingFree]]
| Blotting-free preparation
|-

| Paper
| [[2017Feng_SprayingPlunging]]
| Spraying plunging
|-

| Paper
| [[2017He_FIB]]
| Cryo FIB lamella for TEM
|-

| Paper
| [[2017Peitsch_Sample]]
| iMEM: Isolation of Plasma Membrane for Cryoelectron Microscopy
|-

| Paper
| [[2017Scapin_Storage]]
| Cryo storage of samples
|-

| Paper
| [[2017Schaffer_FocusedIonBeam]]
| Focused Ion Beam sample preparation for membrane proteins
|-

| Paper
| [[2017Scherr_HydrogelNanomembranes]]
| Sample preparation for membrane proteins
|-

|}

=== Automated data collection ===

{|

| Paper
| [[1992Dierksen_Automatic]]
| Automated data collection
|-

| Paper
| [[1992Koster_Automatic]]
| Automated data collection
|-

| Paper
| [[1996Fung_Automatic]]
| Automated data collection for tomography
|-

| Paper
| [[2001Zhang_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2003Ziese_Automatic]]
| Automated autofocusing
|-

| Paper
| [[2004Potter_Automatic]]
| Automated sample loading
|-

| Paper
| [[2004Zheng_Automatic]]
| Automated data collection
|-

| Paper
| [[2005Lei_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2005Suloway_Automatic]]
| Automated data collection: Leginon
|-

| Paper
| [[2007Yoshioka_RCT]]
| Automated Random Conical Tilt
|-

| Paper
| [[2011Korinek_TOM2]]
| Automated acquisition with TOM2
|-

| Paper
| [[2015Li_UCSFImage]]
| Automated acquisition with UCSFImage
|-

| Paper
| [[2016Gil_Fuzzy]]
| Real time decisions during acquisition with neuro-fuzzy method
|-

| Paper
| [[2016Liu_TiltControl]]
| Accurate control of the tilt angle for electron tomography
|-

| Paper
| [[2016Vargas_FoilHole]]
| Determination of image quality at low magnification
|-

| Paper
| [[2017Biyani_Focus]]
| Automatic processing of micrographs
|-

|}

== Single particles ==

=== Automatic particle picking ===

{|

| Paper
| [[1982VanHeel_Detection]]
| Detection of particles in micrographs
|-

| Paper
| [[2001Nicholson_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2001Zhu_Filaments]]
| Automatic identification of filaments in micrographs
|-

| Paper
| [[2004Sigworth_Detection]]
| Classical detection theory and the cryo-EM particle selection problem
|-

| Paper
| [[2004Volkmann_ParticlePicking]]
| An approach to automated particle picking from electron micrographs based on reduced representation templates
|-

| Paper
| [[2004Wong_ParticlePicking]]
| Model-based particle picking for cryo-electron microscopy
|-

| Paper
| [[2004Zhu_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2007Chen_Signature]]
| Automatic particle picking program: Signature
|-

| Paper
| [[2007Woolford_SwarmPS]]
| Automatic particle picking with several criteria, implemented in EMAN Boxer
|-

| Paper
| [[2009Sorzano_MachineLearning]]
| Automatic particle picking based on machine learning of rotational invariants
|-

| Paper
| [[2011Arbelaez_Comparison]]
| Evaluation of the performance of software for automated particle-boxing
|-

| Paper
| [[2013Abrishami_MachineLearning]]
| A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs
|-

| Paper
| [[2013Hauer_2013]]
| Automatic tilt pair detection in Random Conical Tilt
|-

| Paper
| [[2013Shatsky_ParticlePicking]]
| Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Langlois_ParticlePicking]]
| Automatic particle picking
|-

| Paper
| [[2016Vilas_AutomaticTilt]]
| Automatic identification of image pairs in untilted-tilted micrograph pairs
|-

|}

=== 2D Preprocessing ===

{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast enhancement through DPR
|-

| Paper
| [[2004Sorzano_Normalization]]
| Normalization procedures and their statistical properties.
|-

| Paper
| [[2006Sorzano_Denoising]]
| Strong denoising in wavelet space
|-

| Conference
| [[2009Sorzano_Downsampling]]
| Differences between the different downsampling schemes
|-

| Paper
| [[2012Brilot_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Campbell_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Zhao_Denoising]]
| Denoising using an invariant Fourier-Bessel eigenspace
|-

| Paper
| [[2013Norousi_Screening]]
| Screening particles to identify outliers
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu_Movies]]
| Drift correction for movies considering dark field
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Scheres_Movies]]
| Beam induced motion correction
|-

| Paper
| [[2015Abrishami_Movies]]
| Alignment of direct detection device micrographs
|-

| Paper
| [[2015Grant_Anisotropic]]
| Automatic estimation and correction of anisotropic magnification
|-

| Paper
| [[2015Grant_OptimalExposure]]
| Filter movies according to the radiation damage
|-

| Paper
| [[2015Rubinstein_Alignment]]
| Frame alignment at the level of particle
|-

| Paper
| [[2015Spear_DoseCompensation]]
| Effect of dose compensation on resolution
|-

| Paper
| [[2015Zhao_AnisotropicMagnification]]
| Correction of anisotropic magnification
|-

| Conference
| [[2016Bajic_Denoising]]
| Denoising and deconvolution of micrographs
|-

| Paper
| [[2016Jensen_RemovalVesicles]]
| Removal of vesicles in membrane proteins
|-

| Paper
| [[2016Bhamre_Denoising]]
| Denoising by 2D covariance estimation
|-

| Paper
| [[2017McLeod_Zorro]]
| Movie alignment by Zorro
|-

| Paper
| [[2017Zheng_MotionCorr2]]
| Movie alignment by MotionCorr2
|-

|}

=== 2D Alignment ===

{|

| Paper
| [[1981Frank_Averaging]]
| 2D averaging and phase residual
|-

| Paper
| [[1982Saxton_Averaging]]
| 2D averaging using correlation
|-

| Paper
| [[1998Sigworth_ML2D]]
| Maximum likelihood alignment in 2D
|-

| Paper
| [[2003Cong_FRM2D]]
| Fast Rotational Matching in 2D
|-

| Paper
| [[2005Cong_FRM2D]]
| Fast Rotational Matching in 2D introduced in a 3D Alignment algorithm
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

|}

=== 2D Classification and clustering ===

{|

| Paper
| [[1981VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[1984VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2011Singer_DiffusionMaps]]
| Classification in 2D based on graph analysis of the projections
|-

| Paper
| [[2012Yang_ISAC]]
| Iterative Stable Alignment and clustering
|-

| Paper
| [[2014Sorzano_Outlier]]
| Outlier detection in 2D classifications.
|-

| Paper
| [[2014Zhao_Aspire]]
| Fast classification based on rotational invariants and vector diffusion maps
|-

| Paper
| [[2015Huang_Robust]]
| Robust w-estimators of 2D classes
|-

| Paper
| [[2016Reboul_Stochastic]]
| Stochastic Hill Climbing for calculating 2D classes
|-

| Conference
| [[2017Bhamre_Mahalanobis]]
| 2D classification using Mahalanobis distance
|-

|}

=== 3D Alignment ===

{|

| Paper
| [[1980Kam_AutoCorrelation]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[1986Goncharov_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1987VanHeel_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1988Provencher_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Vogel_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1990Gelfand_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Goncharov_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Harauz_Quaternions]]
| Use of quaternions to represent rotations
|-

| Paper
| [[1994Penczek_Real]]
| Angular assignment using projection matching in real space
|-

| Paper
| [[1994Radermacher_Radon]]
| Angular assignment in Radon space
|-

| Paper
| [[1996Penczek_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[2003Rosenthal_DPR]]
| Angular assignment using DPR
|-

| Paper
| [[2004Sorzano_Wavelet]]
| Angular assignment in the wavelet space.
|-

| Paper
| [[2005Jonic_Splines]]
| Angular assignment in Fourier space using spline interpolation.
|-

| Paper
| [[2005Yang_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[2006Ogura_SimulatedAnnealing]]
| Angular asignment by simulated annealing
|-

| Paper
| [[2007Grigorieff_Continuous]]
| Continuous angular assignment in Fourier space
|-

| Paper
| [[2010Jaitly_Bayesian]]
| Angular assignment by a Bayesian method and annealing
|-

| Paper
| [[2010Sanz_Random]]
| Random model method
|-

| Paper
| [[2010Singer_Voting]]
| Detecting consistent common lines by voting (reference free)
|-

| Paper
| [[2011Singer_SDP]]
| Angular assignment by semidefinite programming and eigenvectors (reference free)
|-

| Paper
| [[2012Giannakis_Scattering]]
| Construction of an initial volume, reference free, by graph analysis of the projections
|-

| Paper
| [[2012Shkolnisky_Sync]]
| Angular assignment by synchronization of rotations (reference free)
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Wang_LUD]]
| Angular assignment by least unsquared deviations (reference free)
|-

| Paper
| [[2014Vargas_RANSAC]]
| Initial model using RANSAC (reference free)
|-

| Paper
| [[2015Joubert_Pseudoatoms]]
| Initial model based on pseudo-atoms
|-

| Paper
| [[2015Singer_Kam]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[2015Sorzano_Significant]]
| Statistical approach to the initial volume estimation (reconstruct significant)
|-

| Conference
| [[2016Michels_Heterogeneous]]
| Initial volume in the presence of heterogeneity
|-

| Paper
| [[2016Cossio_BayesianGPU]]
| GPU implementation of the Bayesian 3D reconstruction approach
|-

|}

=== 3D Reconstruction ===
{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1986Harauz_FBP]]
| Exact filters for Filtered Back Projection
|-

| Chapter
| [[1992Radermacher_WBP]]
| Exact filters for Weighted Back Projection
|-

| Paper
| [[1997Zhu_RecCTF]]
| 3D Reconstruction (SIRT like) and simultaneous CTF correction
|-

| Paper
| [[1998Boisset_Uneven]]
| Artifacts in SIRT and WBP under uneven angular distributions
|-

| Paper
| [[1998Marabini_ART]]
| Algebraic Reconstruction Technique with blobs (Xmipp)
|-

| Paper
| [[2001Sorzano_Uneven]]
| Free parameter selection under uneven angular distributions
|-

| Paper
| [[2005Sorzano_Parameters]]
| Free parameter selection for optimizing multiple tasks
|-

| Paper
| [[2008Sorzano_Constraints]]
| Mass, surface, positivity and symmetry constraints for real-space algorithms
|-

| Paper
| [[2009Bilbao_ParallelART]]
| Efficient parallelization of ART
|-

| Paper
| [[2011Li_GradientFlow]]
| Regularized 3D Reconstruction by Gradient Flow
|-

| Paper
| [[2011Vonesch_Wavelets]]
| Fast wavelet-based 3D reconstruction
|-

| Paper
| [[2012Gopinath_ShapeRegularization]]
| Regularized 3D Reconstruction by Shape information
|-

| Paper
| [[2012Kucukelbir_adaptiveBasis]]
| 3D reconstruction in an adaptive basis promoting sparsity
|-

| Paper
| [[2012Sindelar_NoiseReduction]]
| Optimal noise reduction in 3D reconstructions
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Lyumkis_Optimod]]
| Construction of initial volumes with Optimod
|-

| Paper
| [[2013Wang FIRM]]
| Fast 3D reconstruction in Fourier domain
|-

| Paper
| [[2014Kunz_SART_OS]]
| Simultaneous ART with OS
|-

| Paper
| [[2015Abrishami_Fourier]]
| 3D Reconstruction in Fourier space
|-

| Paper
| [[2015Dvornek_SubspaceEM]]
| Fast Maximum a posteriori
|-

| Paper
| [[2015Moriya_Bayesian]]
| Bayesian approach to suppress limited angular artifacts
|-

| Paper
| [[2015Xu_GeometricFlow]]
| Multi-scale geometric flow
|-

| Arxiv
| [[2016Ye_Cohomology]]
| Cohomology properties of 3D reconstruction
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

| Paper
| [[2017Punjani_CryoSPARCTheory]]
| Theory related to CryoSPARC
|-

|}

=== 3D Heterogeneity ===

{|

| Paper
| [[2004White_Size]]
| Heterogeneity classification of differently sized images
|-

| Paper
| [[2006Penczek_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Scheres_ML3D]]
| Maximum Likelihood alignment and classification in 3D
|-

| Paper
| [[2009Spahn_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2010Elmlund_AbInitio]]
| Solving the initial volume problem with multiple conformations
|-

| Paper
| [[2010Shatsky_MultiVariate]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2012Scheres_Bayesian]]
| A Bayesian view on cryo-EM structure determination
|-

| Paper
| [[2012Zheng_Covariance]]
| Estimation of the volume covariance
|-

| Paper
| [[2013Wang_MLVariance]]
| Maximum Likelihood estimate of the map variance
|-

| Paper
| [[2013Lyumkis D_FREALIGN]]
| Likelihood-based classification of cryo-EM images using FREALIGN.
|-

| Paper
| [[2014Jin_NMA]]
| Continuous heterogeneity through Normal Mode Analysis
|-

| Paper
| [[2014Dashti_Brownian]]
| Continuous heterogeneity through Brownian trajectories
|-

| Paper
| [[2014Chen_Migration]]
| Particle migration analysis in 3D classification
|-

| Paper
| [[2015Anden_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Bai_Focused]]
| Focused classification
|-

| Paper
| [[2015Katsevich_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Klaholz_MRA]]
| Multivariate Statistical Analysis of Jackknife and Bootstrapping on random subsets
|-

| Paper
| [[2015Liao_Covariance]]
| Estimation of the 3D covariance from 2D projections
|-

| Paper
| [[2015Tagare_Direct]]
| Direct reconstruction of PCA components
|-

| Paper
| [[2016Gong_Mechanical]]
| Mechanical model for macromolecules
|-

| Paper
| [[2016Rawson_Movement]]
| Movement and flexibility
|-

| Paper
| [[2016Sorzano_StructMap]]
| Sorting a discrete set of conformational states
|-

| Paper
| [[2016Sorzano_Strain]]
| Calculate local stretches, strains and rotations from two conformational states
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

|}

=== Validation ===

{|

| Paper
| [[2008Stagg_TestBed]]
| Effect of voltage, dosis, number of particles and Euler jumps on resolution
|-

| Paper
| [[2011Henderson]]
| Tilt Validation
|-

| Paper
| [[2011Read]]
| Validation of PDBs
|-

| Paper
| [[2012Henderson]]
| EM Map Validation
|-

| Paper
| [[2013Cossio_Bayesian]]
| EM Map Validation in a probabilistic setting
|-

| Paper
| [[2013Chen_NoiseSubstitution]]
| Noise substitution at high resolution for measuring overfitting
|-

| Paper
| [[2014Russo_StatisticalSignificance]]
| EM Map Validation through the statistical significance of the tilt-pair angular assignment
|-

| Paper
| [[2014Stagg_Reslog]]
| EM Map Validation through the resolution evolution with the number of particles
|-

| Paper
| [[2014Wasilewski_Tilt]]
| Web implementation of the tilt pair validation
|-

| Paper
| [[2015Heymann_Alignability]]
| EM Map Validation through the resolution of reconstructions from particles and noise
|-

| Paper
| [[2015Oliveira_FreqLimited]]
| Comparison of gold standard and frequency limited optimization
|-

| Paper
| [[2015Wriggers_Secondary]]
| Validation by secondary structure
|-

| Paper
| [[2016Kim_SAXS]]
| Comparison of SAXS data and EM projections
|-

| Paper
| [[2016Rosenthal_Review]]
| Review of validation methods
|-

| Paper
| [[2016Vargas_Alignability]]
| Validation by studying the tendency of an angular assignment to cluster in the projection space
|-

| Paper
| [[2017Monroe_PDBRefinement]]
| Validation by comparison to a refined PDB
|-

|}

=== Resolution ===

{|

| Paper
| [[1986Harauz_FBP]]
| Fourier Shell Correlation
|-

| Paper
| [[1987Unser_SSNR]]
| 2D Spectral Signal to Noise Ratio
|-

| Paper
| [[2002Penczek_SSNR]]
| 3D Spectral Signal to Noise Ratio for Fourier based algorithms
|-

| Paper
| [[2003Rosenthal_DPR]]
| Review of the FSC and establishment of a new threshold
|-

| Paper
| [[2005Unser_SSNR]]
| 3D Spectral Signal to Noise Ratio for any kind of algorithms
|-

| Paper
| [[2005VanHeel_FSC]]
| Establishment of a new threshold for FSC
|-

| Paper
| [[2007Sousa_AbInitio]]
| Resolution measurement on neighbour Fourier voxels
|-

| Paper
| [[2014Kucukelbir_Local]]
| Quantifying the local resolution of cryo-EM density maps
|-

| Paper
| [[2016Pintilie_Probabilistic]]
| Probabilistic models and resolution
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Statistical properties of resolution measures defined in Fourier space
|-

|}

=== Sharpening of high resolution information ===
{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast restoration and map sharpening
|-

| Paper
| [[2008Fernandez_Bfactor]]
| Bfactor determination and restoration
|-

| Paper
| [[2013Fiddy_SaxtonAlgorithm]]
| Phase retrieval or extension
|-

| Paper
| [[2014Kishchenko_SphericalDeconvolution]]
| Spherical deconvolution
|-

| Paper
| [[2015Spiegel_VISDEM]]
| Visualization improvement by the use of pseudoatomic profiles
|-

| Paper
| [[2016Jonic_Pseudoatoms]]
| Approximation with pseudoatoms
|-

| Paper
| [[2016Jonic_Denoising]]
| Denoising and high-frequency boosting by pseudoatom approximation
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[1982Schiske_Correction]]
| CTF correction for tilted objects
|-

| Paper
| [[1988Toyoshima_Model]]
| CTF estimation
|-

| Paper
| [[1995Frank_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1996Skoglund_MaxEnt]]
| CTF correction with Maximum Entropy
|-

| Paper
| [[1996Zhou_Model]]
| CTF model and user interface for manual fitting
|-

| Paper
| [[1997Fernandez_AR]]
| PSD estimation using periodogram averaging and AR models
|-

| Paper
| [[1997Penczek_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1997Stark_Deconvolution]]
| CTF correction using deconvolution
|-

| Paper
| [[1997Zhu_RecCTF]]
| CTF correction and reconstruction
|-

| Paper
| [[2000DeRosier_EwaldCorrection]]
| CTF correction considering the Ewald sphere
|-

| Paper
| [[2000Jensen_TiltedCorrection]]
| CTF correction considering tilt in backprojection
|-

| Paper
| [[2001Saad_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Huang_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Mindell_CTFTILT]]
| CTF estimation for tilted micrographs
|-

| Paper
| [[2003Sander_MSA]]
| CTF estimation through MSA classification of PSDs
|-

| Paper
| [[2003Velazquez_ARMA]]
| PSD and CTF estimation using ARMA models
|-

| Paper
| [[2004Sorzano_IDR]]
| CTF restoration and reconstruction with Iterative Data Refinement
|-

| Conference
| [[2004Wan_CTF]]
| Spatially variant CTF
|-

| Paper
| [[2004Zubelli_Chahine]]
| CTF restoration and reconstruction with Chahine's multiplicative method
|-

| Conference
| [[2005Dubowy_SpaceVariant]]
| CTF correction when this is space variant
|-

| Paper
| [[2005Mallick_ACE]]
| CTF estimation
|-

| Paper
| [[2006Wolf_Ewald]]
| CTF correction considering Ewald sphere
|-

| Paper
| [[2007Jonic_EnhancedPSD]]
| PSD enhancement for better identification of Thon rings; Vitreous ice diffracts in Thon rings
|-

| Paper
| [[2007Philippsen_Model]]
| CTF Model for tilted specimens
|-

| Paper
| [[2007Sorzano_CTF]]
| CTF estimation using enhanced PSDs
|-

| Paper
| [[2009Sorzano_Sensitivity]]
| Error sensitivity of the CTF models, non-uniqueness of the CTF parameters
|-

| Paper
| [[2010Jiang2010_CTFCorrection]]
| Amplitude correction method
|-

| Paper
| [[2010Kasantsev_CTFCorrection]]
| Mathematical foundations of Kornberg and Jensen method
|-

| Paper
| [[2010Leong_CTFCorrection]]
| Correction for spatially variant CTF
|-

| Paper
| [[2011Glaeser_Coma]]
| The effect of coma at high-resolution
|-

| Paper
| [[2011Mariani_Tilted]]
| CTF simulation and correction of tilted specimens
|-

| Paper
| [[2011Sindelar_Wiener]]
| CTF correction using a modified version of Wiener filter
|-

| Paper
| [[2011Voortman_Tilted]]
| CTF correction for tilted specimen
|-

| Paper
| [[2012Voortman_VaryingCTF]]
| Correcting a spatially varying CTF
|-

| Paper
| [[2013Vargas_FastDef]]
| Fast defocus
|-

| Paper
| [[2015Rohou_CTFFind4]]
| CTF Find 4
|-

| Paper
| [[2015Sheth_CTFquality]]
| Visualization and quality assessment of CTF
|-

| Paper
| [[2016Zhang_GCTF]]
| gCTF
|-

|}

=== Segmentation ===

{|

| Paper
| [[2006Baker_segmentation]]
| Segmentation of molecular subunits
|-

|}

=== Fitting and docking ===

{|

| Paper
| [[1999Volkmann_Fitting]]
| Fitting in real space
|-

| Paper
| [[2001Baker_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2001Jones_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2003Kovacs_FRM3D]]
| Fast Rotational Alignment of two EM maps
|-

| Paper
| [[2004Tama_NMA1]]
| Flexible fitting with Normal Modes (I)
|-

| Paper
| [[2004Tama_NMA2]]
| Flexible fitting with Normal Modes (II)
|-

| Paper
| [[2005Velazquez_Superfamilies]]
| Recognition of the superfamily folding in medium-high resolution volumes
|-

| Paper
| [[2007DeVries_Haddock]]
| Docking with Haddock 2.0
|-

| Paper
| [[2007Kleywegt_QualityControl]]
| Quality control and validation of fitting
|-

| Paper
| [[2012Biswas_Secondary]]
| Secondary structure determination in EM volumes
|-

| Paper
| [[2012Velazquez_Constraints]]
| Multicomponent fitting by using constraints from other information sources
|-

| Paper
| [[2013Chapman MS_Atomicmodeling]]
| Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters
|-

| Paper
| [[2013Esquivel_Modelling]]
| Review on modelling (secondary structure, fitting, ...)
|-

| Paper
| [[2013Lopez_Imodfit]]
| Fitting based on vibrational analysis
|-

| Paper
| [[2013Nogales_3DEMLoupe]]
| Normal Mode Analysis of reconstructed volumes
|-

| Paper
| [[2014AlNasr_Secondary]]
| Identification of secondary structure elements in EM volumes
|-

| Paper
| [[2014Politis_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Rey_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Villa_Review]]
| Review of atomic fitting into EM volumes
|-

| Paper
| [[2015Barad_EMRinger]]
| Validation of hybrid models
|-

| Paper
| [[2015Bettadapura_PF2Fit]]
| Fast rigid fitting of PDBs into EM maps
|-

| Paper
| [[2015Carrillo_CapsidMaps]]
| Analysis of virus capsids using Google Maps
|-

| Paper
| [[2015Schroeder_Hybrid]]
| Review on model building
|-

| Paper
| [[2015Tamo_Dynamics]]
| Dynamics in integrative modeling
|-

| Paper
| [[2015Sorzano_AtomsToVoxels]]
| Accurate conversion of an atomic model into a voxel density volume
|-

| Paper
| [[2016Joseph_Evolution]]
| Evolutionary constraints for the fitting of atomic models into density maps
|-

| Paper
| [[2016Segura_3Diana]]
| Validation of hybrid models
|-

| Paper
| [[2016Singharoy_MDFF]]
| Construction of hybrid models driven by EM density and molecular dynamics
|-

| Paper
| [[2016Wang_Rosetta]]
| Construction of hybrid models driven by EM density using Rosetta
|-

| Paper
| [[2017Joseph_Metrics]]
| Metrics analysis for the comparison of structures
|-

| Paper
| [[2017Hryc_WeightedAtoms]]
| Construction of hybrid models by locally weighting the different atoms
|-

| Paper
| [[2017Matsumoto_Distribution]]
| Estimating the distribution of conformations of atomic models
|-

| Paper
| [[2017Miyashita_EnsembleFitting]]
| Ensemble fitting using Molecular Dynamics
|-

| Paper
| [[2017Turk_ModelBuilding]]
| Tutorial on model building and protein visualization
|-

|}

=== Books and reviews ===

{|

| Book
| [[1980Herman_Tomography]]
| General book on tomography
|-

| Book
| [[1988Kak_Tomography]]
| General book on tomography
|-

| Paper
| [[2000Tao_Review]]
| Review of single particles
|-

| Paper
| [[2000VanHeel_Review]]
| Review of single particles
|-

| Paper
| [[2002Frank_Review]]
| Review of single particles
|-

| Paper
| [[2002Schmid_Review]]
| Review of single particles
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2004Subramaniam_Review]]
| Review of single particles
|-

| Paper
| [[2005Steven_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_book]]
| Book covering all aspects of electron microscopy of single particles
|-

| Paper
| [[2006Sorzano_Review]]
| Review of optimization problems in electron microscopy
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems in Electron Tomography
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2008Mueller_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2008Taylor_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2010DeRosier_Review]]
| Personal account of how 3DEM developed in the early days
|-

| Chapter
| [[2012Sorzano_Review]]
| Review of single particle analysis using Xmipp
|-

| Chapter
| [[2012Devaux_Protocol]]
| Protocols for performing single particle analysis
|-

| Paper
| [[2014Bai_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Carazo_Review]]
| Review of the reconstruction process
|-

| Paper
| [[2015Cheng_Review]]
| A primer to Single Particle Cryo-EM
|-

| Paper
| [[2015Cheng_Reviewb]]
| Single Particle Cryo-EM at crystallographic resolution
|-

| Paper
| [[2015Elmlund_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Henderson_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Nogales_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Schroeder_Review]]
| Review of advances in the electron microscope
|-

| Paper
| [[2015Wu_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Carroni_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Egelman_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Eisenstein_CryoEM]]
| News feature on the Method of the Year
|-

| Paper
| [[2016FernandezLeiro_Review]]
| Review of EM
|-

| Paper
| [[2016Glaeser_HowGood]]
| How good can cryo-EM become?
|-

| Paper
| [[2016Jonic_PseudoAtoms]]
| Review of the applications of the use of pseudoatoms in EM
|-

| Chapter
| [[2016Mio_Review]]
| Overview of the process to obtain EM reconstructions
|-

| Paper
| [[2016Jonic_Review]]
| A review of computational ways to handle heterogeneity
|-

| Paper
| [[2016Nogales_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Subramaniam_Review]]
| Why cryo-EM is now suitable for crystallographic journals
|-

| Paper
| [[2016Vinothkumar_Review]]
| Historical review and current limitations
|-

| Paper
| [[2017Frank_Review]]
| Historical review of EM
|-

| Paper
| [[2017Jonic_Review]]
| Review of computational methods to analyze conformational variability
|-

| Paper
| [[2017Rawson_Limitations]]
| Limitations of EM for drug design
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Review of statistical properties of resolution measures defined in Fourier space
|-
|}

=== Software ===

{|

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[1999Lutdke_Eman]]
| Eman
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Baldwin_AngularTransformations]]
| The Transform Class in SPARX and EMAN2
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Grigorieff_Frealign]]
| Frealign
|-

| Paper
| [[2008Scheres_XmippProtocols]]
| Xmipp Protocols
|-

| Paper
| [[2008Shaikh_SpiderProtocols]]
| Spider Protocols
|-

| Paper
| [[2012Wriggers_SitusConventions]]
| Conventions and workflows in Situs
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2015Cianfrocco_Cloud]]
| Software execution in the cloud
|-

| Paper
| [[2015Cheng_MRC2014]]
| Extensions to MRC file format
|-

| Paper
| [[2013DeLaRosa_Scipion]]
| Scipion
|-

| Paper
| [[2016Scheres_Relion]]
| Tutorial on the use of Relion
|-

| Paper
| [[2016Grigorieff_Frealign]]
| Tutorial on the use of Frealign
|-

| Paper
| [[2017Moriya_Sphire]]
| Tutorial on the use of Sphire
|-

|}

== Electron tomography ==

=== Image preprocessing ===

{|

| Paper
| [[2015Yan_thickness]]
| Determination of thickness, tilt and electron mean free path
|-

|}

=== Image alignment ===

{|

| Paper
| [[1982Guckenberger_commonOrigin]]
| Determination of a common origin in the micrographs of titl series in three-dimensional electron microscopy
|-

| Paper
| [[1992Lawrence_leastSquares]]
| Least squares solution of the alignment problem
|-

| Paper
| [[1995Penczek_dual]]
| Dual tilt alignment
|-

| Paper
| [[1996Owen_alignmentQuality]]
| Automatic alignment without fiducial markers and evaluation of alignment quality
|-

| Paper
| [[1998Grimm_normalization]]
| Discussion of several gray level normalization methods for electron tomography
|-

| Paper
| [[2001Brandt_Automatic1]]
| Automatic alignment without fiducial markers
|-

| Paper
| [[2001Brandt_Automatic2]]
| Automatic alignment with fiducial markers
|-

| Paper
| [[2006Winkler_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2006Castano_alignment]]
| Alignment with non-perpendicularity
|-

| Paper
| [[2007Castano_alignment]]
| Fiducial-less alignment of cryo-sections
|-

| Paper
| [[2009Sorzano_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2010Cantele_dualAlignment]]
| Alignment of dual series
|-

| Paper
| [[2014Tomonaga_Automatic]]
| Automatic alignment of tilt series using the projection themselves
|-

| Paper
| [[2014Han_Automatic]]
| Automatic alignment of tilt series using SIFT features
|-

| Paper
| [[2015Han_Automatic]]
| Automatic alignment of tilt series using fiducials
|-

| Paper
| [[2017Mastronarde_Automatic]]
| Automatic alignment and reconstruction of tilt series in IMOD
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[2003Winkler_CTF]]
| Focus gradient correction in electron tomography
|-

| Paper
| [[2006Fernandez_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Zanetti_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Xiong_CTF]]
| CTF determination and correction for low dose tomographic tilt series
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2017Kunz_3DCTF]]
| 3D CTF Correction
|-

|}

=== 3D reconstruction ===

{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1992Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[1997Marabini_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2002Fernandez_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2007Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[2008Fernandez_CARP]]
| Component Averaged Row Projections (CARP)
|-

| Paper
| [[2012Herman General Superiorization]]
| Superiorization: an optimization heuristic for medical physics
|-

| Paper
| [[2012Zhang_IPET_FETR]]
| IPET and FETR, a reconstruction algorithm for single molecule tomography
|-

| Paper
| [[2013Goris_SIRT_TV_DART]]
| Combination of SIRT, Total Variation and Discrete ART to reconstruct and segment at the same time
|-

| Paper
| [[2013Briegel A_Challenge]]
| The challenge of determining handedness in electron tomography and the use of DNA origami gold nanoparticle helices as molecular standards
|-

| Paper
| [[2013Messaoudi_EnergyFiltered]]
| 3D Reconstruction of Energy-Filtered TEM
|-

| Paper
| [[2016Deng_ICON]]
| 3D Reconstruction with missing information restoration
|-

| Paper
| [[2016Guay_Compressed]]
| 3D Reconstruction using compressed sensing
|-

|}

=== Noise reduction ===
{|

| Paper
| [[2001Frangakis_NAD]]
| Noise reduction with Nonlinear Anisotropic Diffusion
|-

| Paper
| [[2003Fernandez_AND]]
| Anisotropic nonlinear diffusion for electron tomography
|-

| Paper
| [[2003Jiang_Bilateral]]
| Bilateral denoising filter in electron microscopy
|-

| Paper
| [[2005Fernandez_AND]]
| Anisotropic nonlinear denoising in electron tomography
|-

| Paper
| [[2007Heide_median]]
| Iterative median filtering in electron tomography
|-

| Paper
| [[2007Fernandez_autAND]]
| Anisotropic nonlinear diffusion with automated parameter tuning
|-

| Paper
| [[2009Fernandez_Beltrami]]
| Nonlinear filtering based on Beltrami flow
|-

| Paper
| [[2010Bilbao_MeanShift]]
| Mean Shift Filtering
|-

| Paper
| [[2014Kovacik_wedgeArtefacts]]
| Removal of wedge artefacts
|-

| Paper
| [[2014Maiorca_beadArtefacts]]
| Removal of gold bead artefacts
|-

|}

=== Segmentation ===

{|

| Paper
| [[2002Frangakis_Eigenanalysis]]
| Segmentation using eigenvector analysis.
|-

| Paper
| [[2002Volkmann_Watershed]]
| Segmentation using watershed transform.
|-

| Paper
| [[2003Bajaj_BoundarySegmentation]]
| Segmentation based on fast marching.
|-

| Paper
| [[2005Cyrklaff_Thresholding]]
| Segmentation using optimal thresholding.
|-

| Paper
| [[2007Lebbink_TemplateMatching]]
| Segmentation using template matching.
|-

| Paper
| [[2007Sandberg_OrientationFields]]
| Segmentation using orientation fields.
|-

| Paper
| [[2007Sandberg_SegmentationReview]]
| Review on segmentation in electron tomography.
|-

| Paper
| [[2008Garduno_FuzzySegmentation]]
| Segmentation using fuzzy set theory principles.
|-

| Paper
| [[2009Lebbink_TemplateMatching2]]
| Segmentation using template matching.
|-

| Paper
| [[2012RubbiyaAli_EdgeDetection]]
| Parameter-Free Segmentation of Macromolecular Structures.
|-

| Conference
| [[2015Xu_TemplateMatching]]
| Detection of macromolecular complexes with a reduced representation of the templates.
|-

|}

=== Resolution ===
{|

| Paper
| [[2005Cardone_Resolution]]
| Resolution criterion for electron tomography
|-

| Chapter
| [[2007Penczek_Resolution]]
| Review of resolution criteria for electron tomography
|-

| Paper
| [[2015Diebolder_ConicalFSC]]
| Conical Fourier Shell Correlation
|-

|}

=== Subtomogram analysis ===

{|

| Paper
| [[2000Bohm_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2002Frangakis_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2006Nickell_Review]]
| Review of macromolecule finding by template matching (Visual Proteomics)
|-

| Paper
| [[2007Best_Review]]
| Review of Localization of Protein Complexes by Pattern Recognition
|-

| Paper
| [[2007Forster_Review]]
| Review of structure determination by subtomogram averaging
|-

| Paper
| [[2008Forster_Classification]]
| Classification of subtomograms using constrained correlation
|-

| Paper
| [[2008Bartesaghi_Classification]]
| Classification and averaging of subtomograms
|-

| Paper
| [[2008Schmid_Averaging]]
| Alignment and averaging of subtomograms
|-

| Paper
| [[2010Amat_Averaging]]
| Alignment and averaging of subtomograms exploiting thresholding in Fourier space
|-

| Paper
| [[2013Chen_Averaging]]
| Fast alignment of subtomograms using spherical harmonics
|-

| Paper
| [[2013Kuybeda_Averaging]]
| Alignment and averaging of subtomograms using the nuclear norm of the cluster
|-

| Paper
| [[2013Shatsky_Averaging]]
| Alignment and averaging of subtomograms with constrained cross-correlation
|-

| Paper
| [[2014Chen_Autofocus]]
| Subtomogram averaging and classification with special attention to differences
|-

| Paper
| [[2014Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2014Voortman_LimitingFactors]]
| Limiting factors of subtomogram averaging
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2015Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2016Bharat_Relion]]
| Subtomogram averaging with Relion
|-

| Paper
| [[2016Song_MatrixNorm]]
| Matrix norm minimization for tomographic reconstruction and alignment
|-

| Paper
| [[2017Castano_ParticlePicking]]
| Particle picking in tomograms for subtomogram averaging
|-

| Paper
| [[2017Frazier_Tomominer]]
| TomoMiner a software platform for large-scale subtomogram analysis
|-

|}

=== Single particle tomography ===

{|

| Paper
| [[2012Bartesaghi_Constrained]]
| 3D reconstruction by imposing geometrical constraints
|-

| Paper
| [[2015Galaz_SingleParticleTomography]]
| Set of tools for Single Particle Tomography in EMAN2
|-

| Paper
| [[2016Galaz_SingleParticleTomography]]
| Alignment algorithms and CTF correction
|-

|}

=== Books and reviews ===

{|

| Paper
| [[2000Baumeister_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Koster_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Sali_Review]]
| Review of electron tomography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2005Lucic_Review]]
| Review of electron tomography
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_TomoBook]]
| Electron Tomography
|-

| Book
| [[2007McIntosh_Book]]
| Cellular Electron Microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2012Kudryashev_Review]]
| Review of subtomogram averaging
|-

| Paper
| [[2016Beck_Review]]
| Review of molecular sociology
|-

| Paper
| [[2017Galaz_Review]]
| Review of single particle tomography
|-

|}

=== Software ===

{|

| Paper
| [[1996Kremer_IMOD]]
| IMOD
|-

| Paper
| [[1996Chen_Priism/IVE]]
| Priism/IVE
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2005Nickell_TOM]]
| TOM Toolbox
|-

| Paper
| [[2007Messaoudi_TomoJ]]
| TomoJ
|-

| Paper
| [[2008Heymann_BsoftTomo]]
| Bsoft
|-

| Paper
| [[2015Ding_CaltechTomography]]
| Caltech tomography database
|-

| Paper
| [[2015Noble_AppionProtomo]]
| Batch fiducial-less tilt-series alignment in Appion using Protomo
|-

| Paper
| [[2015vanAarle_Astra]]
| ASTRA Toolbox
|-

| Paper
| [[2017Wan_Simulator]]
| Electron Tomography Simulator
|-

|}

== 2D Crystals ==

=== 2D Preprocessing ===

{|

| Paper
| [[1986Henderson_Processing]]
| General 2D processing
|-

| Paper
| [[2000He_PhaseAlignment]]
| Phase consistency and Alignment
|-

| Paper
| [[2006Gil_Unbending]]
| Crystal unbending
|-

|}

=== Classification ===
{|

| Paper
| [[1988Frank_Classification]]
| MSA and classification in electron crystallography
|-

| Paper
| [[1996Fernandez_SOM]]
| Classification based on self organizing maps
|-

| Paper
| [[1998Sherman_MSA]]
| Classification based on MSA
|-

|}
=== 3D Reconstruction ===

{|

| Paper
| [[1985Wang_Solvent]]
| Solvent flattening
|-

| Paper
| [[1990Henderson_Processing]]
| General 3D processing
|-

| Paper
| [[2004Marabini_ART]]
| Algebraic Reconstruction Technique with blobs for crystals (Xmipp)
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1998Walz_Review]]
| Review of 2D crystallography
|-

| Paper
| [[1999Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Ellis_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of single particles, electron tomography and crystallography
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Gipson_2dx]]
| 2dx
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Philippsen_IPLT]]
| IPLT
|-

|}

== 3D Crystals - MicroED ==

=== Sample Preparation ===
{|
| Paper
| [[2016Shi_Preparation]]
| Sample Preparation
|}
=== Data Collection ===
{|
| Paper
| [[2014Nannenga_CR]]
| Continuous rotation

|}
=== Data Processing ===
{|

| Paper
| [[2011Wisedchaisri_PhaseExtension]]
| Fragment-based phase extension
|-

| Paper
| [[2015Hattne_Processing]]
| Data Processing
|-

| Paper
| [[2016Hattne_Correction]]
| Image correction
|}

=== Software ===
{|

| Paper
| [[2014Iadanza_Processing]]
| Data Processing of still diffraction data
|}

=== Books and Reviews ===
{|
| Paper
| [[2014Nannenga_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Liu_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Rodriguez_Review ]]
| Review of MicroED
|-

|}

== Helical particles ==

=== Filament corrections ===

{|

| Paper
| [[1986Egelman_Curved]]
| Algorithm for correcting curved filaments
|-

| Paper
| [[1988Bluemke_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2006Wang_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2016Yang_Flexible]]
| Algorithm for correcting filaments with flexible subunits
|-

|}

=== Reconstruction ===

{|

| Paper
| [[1952Cochran_Fourier]]
| Fourier Bessel transform of filamentous structures
|-

| Paper
| [[1958Klug_Fourier]]
| Fourier Bessel decomposition of the projection images
|-

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2005Wang_Iterative]]
| Iterative Fourier-Bessel algorithm
|-

| Paper
| [[2007Egelman_Iterative]]
| Iterative real-space algorithm
|-

| Paper
| [[2013Desfosses_Spring]]
| Helical processing with Spring
|-

| Paper
| [[2015Zhang_seam]]
| Workflow for the detection of the lattice seam
|-

| Paper
| [[2016Rohou_Frealix]]
| Helical processing with Frealix
|-

|}

=== Validation ===

{|

| Paper
| [[2014Egelman_ambiguity]]
| How to detect incorrect models
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Carragher_Phoelix]]
| Phoelix
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Owen_Brandeis]]
| Brandeis
|-

|}

== Icosahedral particles ==

=== Reconstruction ===

{|

| Paper
| [[1970Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1971Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1996Fuller_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1997Thuman_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

|}

=== Classification ===

{|

| Paper
| [[2005Scheres_Virus]]
| Classification of virus capsids in real space
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1999Baker_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[1999Conway_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2000Thuman_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Lee_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Navaza_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2006Grunewald_Review]]
| Review of reconstruction of icosahedral viruses
|-

|}

=== Software ===

{|

| Paper
| [[1996Baker_EMPFT]]
| EMPFT
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2013Morin_Sliz SBGrid]]
| SBGrid presentation for eLife
|-

|}

== Databases ==

{|

| Paper
| [[2003Boutselakis_EMSD]]
| EMSD database
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2011Kim_CDDB]]
| Conformational Dynamics Data Bank
|-

| Paper
| [[2011Lawson_EMDB]]
| Electron Microscopy Data Bank
|-

| Paper
| [[2013Ison_EDAM]]
| EDAM, an ontology of bioinformatics operations
|-

| Paper
| [[2016Iudin_EMPIAR]]
| EMPIAR raw data database
|-

| Paper
| [[2016Patwhardan_EMDB]]
| EMDB, PDB, ...
|-

| Paper
| [[2017Patwhardan_Trends]]
| Trends at EMDB
|-

| Paper
| [[2017Shao_PDBQuality]]
| Quality metrics in PDB
|-

| Blog
| http://www.mybiosoftware.com
| Huge list of bioinformatics programs (many of them structural bioinformatics)
|-

|}

== Relationship to other structural information sources ==

{|

| Paper
| [[2000Engel_AFM]]
| Review of Atomic Force Microscopy
|-

| Paper
| [[2001Dimmeler_AFM]]
| Constraints from Atomic Force Microscopy
|-

| Paper
| [[2003Mobus_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_Review]]
| Review on correlative microscopy
|-

| Paper
| [[2005Boudier_EFTETJ]]
| Software for Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2005Vestergaard_SAXS]]
| Example of comparison of 3DEM and Small-angle X-ray scattering
|-

| Paper
| [[2007Hamada_SAXS]]
| Constraints from Small-angle X-ray scattering
|-

| Paper
| [[2013Xu_FRET]]
| EM+FRET
|-

|}

== X-ray tomography ==

{|

| Paper
| [[2012Oton_ImageFormation]]
| Image formation model in X-ray cell microscopy
|-

|}

== Mathematical tools necessary ==

== People developing methods ==
Please, add yourself to this list (due to privacy reasons, please, do not add anyone else to the list without his/her explicit consent). Sort by first name alphabetical order.

[http://biocomp.cnb.csic.es/~coss Carlos Oscar S. Sorzano]: CSIC, Madrid, Spain 

[http://www.curie.fr/recherche/themes/detail_equipe.cfm/lang/_fr/id_equipe/241.htm Cédric Messaoudi]: Institute Curie, Paris, France 

[http://scholar.google.es/citations?user=_jNYGScAAAAJ&hl=en Javier Vargas]:[mailto:jvargas@cnb.csic.es mail]: CSIC, Madrid, Spain 

[http://scholar.google.es/citations?hl=es&user=g2ZJPIYAAAAJ Joaquín Otón]: CSIC, Madrid, Spain 

[mailto:jrbcast@gmail.com José Román Bilbao-Castro]: UAL, Almería, Spain; CSIC, Madrid, Spain 

[José Miguel de la Rosa Trevín]: Biocomputing Unit CNB-CSIC, Madrid, Spain 

[http://cryoem.janelia.org Tamir Gonen]: [mailto:gonent@janelia.hhmi.org mail]: Howard Hughes Medical Institute, Ashburn, VA, USA 

[mailto:vabrishami@cnb.csic.es Vahid Abrishami]: CSIC, Madrid, Spain 

== 3DEM sites ==
* [http://3dem.ucsd.edu/ 3DEM web site]

* [http://en.wikibooks.org/wiki/Software_Tools_For_Molecular_Microscopy Software tools for molecular microscopy]

* [http://www.emdatabank.org/ The Electron Microscopy Data Bank (EMDB)]

* [http://ccdb.ucsd.edu The Cell Centered Database (CCDB)]

* [http://conventions.cnb.csic.es The geometrical software conventions web page ]

== Editing useful links ==

* [http://www.mediawiki.org/wiki/Help:Formatting Text formatting in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Links Adding links in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Images Adding images in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Tables Making tables in Mediawiki]

Main Page

2017-07-20T06:01:34Z

CoSS: /* Sample preparation */

== Presentation ==

This web page is intended to be an extensive repository of three-dimensional electron microscopy (3DEM) methods. The advantages of having such a repository are

* You know which are the relevant articles in a particular topic, therefore, paper introductions, reviews, etc. are easier to write and you make sure you will cite all the related articles.
* You will be sure that your paper has more chances of being cited.
* You can add whatever information you find relevant to your method, external links, links to other papers, etc.
* You can link your method to a web page providing the corresponding software, so you know people can use your algorithms.
* You can use the Wiki search capabilities to locate relevant articles even if they are not at the topic you are looking at.
* As a community we will "reconstruct" our history.
* You can select the "watch" option above to receive notifications in case of further changes in the Main Page.

Developing image processing methods for 3DEM is not "[[well-paid]]" in terms of citations and impact factor. However, it is crucial for the advance of the field. Gathering methodological papers in a portal will help to increase the recognition of the field.

Please:

* Add your articles at the right place (you can add a single article in several topics if it is relevant to all of them). The easiest way to add an article is by editing the corresponding topic in the main page, adding your entry, then save the main page. Click on the red link that appears on your new entry, copy and paste the Wiki following code, add the information of your article

== Citation ==

== Abstract ==

== Keywords ==

== Links ==

== Related software ==

== Related methods ==

== Comments ==

* Maintain the information of each article as complete as possible.
* Sort articles by years and authors.
* Be respectful to other people's work.

== How to subscribe to this page ==

You may subscribe to this page so that you will be notified every time someone adds a new method. To do so, you have to register in the page, and edit your preferences ("my preferences"). Be sure that you have activated the option "E-mail me when a page on my watchlist is changed". Finally, click on the "Watch" tab at the top of this page.

You may subscribe to changes on this page on the mailing list 3demmethods@cnb.csic.es. To send a new method to this mail list just send a mail to 3demmethods@cnb.csic.es

To subscribe to this list, visit the web page

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Alternatively, you may write a mail to sympa6@cnb.csic.es with the subject

<code>subscribe 3demmethods YourName YourFamilyName</code>

and an empty mail body.

To unsubscribe visit the page

https://listas.csic.es/cnb/wws/sigrequest/3demmethods

or write sympa6@cnb.csic.es with the subject

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and an empty mail body.

== Electron microscopy images ==

=== Online courses ===

CALTECH: http://cryo-em-course.caltech.edu/

MRC: ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/EM-course/

CNB-CSIC: http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/MadridJan2014EM

Workshop on Computational methods for CryoEM: https://www.youtube.com/watch?v=XdKO1iaPP8o

Workshop on Management of large CryoEM facilities: https://www.youtube.com/watch?v=as4seOPszL0

Icknield Course on Model Building and Refinement for High Resolution EM Maps: http://www.ccpem.ac.uk/training/icknield_2017/icknield_2017.php

=== Image formation ===

{|

| Paper
| [[1971Erickson_CTF]]
| CTF model
|-

| Paper
| [[1971Glaeser_Damage]]
| Radiation damage
|-

| Chapter
| [[1971Hanszen_CTF]]
| Image formation model
|-

| Paper
| [[1971Thon_Model]]
| CTF model
|-

| Paper
| [[1975Unwin_Imaging]]
| Radiation dose
|-

| Paper
| [[1977Wade_Model]]
| CTF model
|-

| Paper
| [[1978Wade_Model]]
| CTF model
|-

| Paper
| [[1979Hayward_Radiation]]
| Radiation damage
|-

| Paper
| [[1984Cohen_Validity]]
| Validity of the CTF model at high frequencies
|-

| Paper
| [[1988Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[1992Wade_Model]]
| CTF model
|-

| Paper
| [[1993Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2004Egerton_Damage]]
| Radiation damage
|-

| Paper
| [[2004Sorzano_Normalization]]
| Background noise is Gaussian
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2009Baxter_NoiseCharacterization]]
| Characterization of the different noise sources in cryo-EM
|-

| Paper
| [[2010Baker_Damage]]
| Radiation damage dependence on resolution
|-

| Paper
| [[2010Bammes_Damage]]
| Radiation damage dependence on temperature
|-

| Paper
| [[2010Gomez_Multislice]]
| Simulation of the multi slice model
|-

| Paper
| [[2010Zewail_FourDimensional]]
| Review on the use of ultrafast EM
|-

| Paper
| [[2011Bammes_CCD]]
| Performance of CCD cameras
|-

| Paper
| [[2011Glaeser_Coma]]
| Image formation model including coma
|-

| Paper
| [[2011Milazzo_DirectDetectors]]
| Evaluation of Direct Detectors
|-

| Paper
| [[2011Rullgard_ImageSimulation]]
| Accurate simulation of EM images
|-

| Paper
| [[2011Zhang LimitingFactors]]
| Limiting factor for atomic resolution in EM
|-

| Paper
| [[2012Bammes_DirectDetection]]
| Performance of Direct detectors
|-

| Paper
| [[2012Campbell_MotionCorrection]]
| Beam induced motion correction and direct detectors
|-

| Paper
| [[2012Shang_HydrationLayer]]
| Simulation of PDB volumes explicitly considering the hydration layer
|-

| Paper
| [[2013Egerton_RadiationDamage]]
| Review of TEM radiation damage and experimental ways of reducing it
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu H_Noisemodels]]
| Noise models and cryo-EM drift correction with a direct-electron camera
|-

| Paper
| [[2013Li X K2 noisemodels]]
| Influence of electron dose rate on electron counting images recorded with the K2 camera
|-

| Paper
| [[2013Vulovic_CTFApproximations]]
| When to use the different approximations performed so that a projection with linear CTF is valid
|-

| Thesis
| [[2013Vulovic_ImageFormation]]
| Ph.D. Thesis on the image formation in cryo-EM
|-

| Paper
| [[2014Danev_PhasePlate]]
| Volta potential phase plate
|-

| Paper
| [[2015Chiu_K2]]
| Characterization of K2
|-

| Paper
| [[2015Hawkes_AberrationCorrection]]
| Historical account of the development of lens corrections
|-

| Paper
| [[2015Koeck_Quadratic]]
| Limitations of the linear approximation and use of the quadratic terms
|-

| Paper
| [[2015Kuijper_FEI]]
| Description of the FEI Falcons
|-

| Paper
| [[2015Lobato_MULTEM]]
| Simulation of multislice diffraction
|-

| Paper
| [[2015McMullan_AmorphousIce]]
| Beam induced movement is caused by Brownian motion
|-

| Paper
| [[2016Koeck_ADF]]
| Simulations of Annular Dark Field TEM
|-

| Paper
| [[2017Mishyna_DNARadiation]]
| Review of radiation damage on DNA
|-

|}

=== Collection geometry ===

{|

| Chapter
| [[1980Hoppe_Wedge]]
| Missing wedge
|-

| Paper
| [[1987Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1995Penczek_Dual]]
| Dual axis tomography
|-

| Paper
| [[1997Mastronarde_Dual]]
| Dual axis tomography
|-

| Paper
| [[2003Ludtke_FocusPairs]]
| Focus pairs for single particles
|-

| Paper
| [[2005Lanzavecchia_Conical]]
| Conical tomography
|-

| Paper
| [[2005Zampighi_Conical]]
| Conical tomography
|-

| Paper
| [[2006Leschziner_OT]]
| Orthogonal Tilt
|-

| Paper
| [[2006Messaoudi_Multiple]]
| Multiple axis tomography
|-

| Paper
| [[2012Kudryashev_FocusPairs]]
| Focus pairs tomography
|-

| Paper
| [[2014Hovden_TiltFocus]]
| Combining tilt series with focus series
|-

| Paper
| [[2015Sorzano_RandomConicalTilt]]
| General formulation of Random Conical Tilt
|-

| Paper
| [[2017Hagen_DoseTomography]]
| Dose optimization for subtomogram averaging
|-

|}

=== Sample preparation ===

{|

| Paper
| [[1982Dubochet_Sample]]
| Vitreous ice
|-

| Paper
| [[1986Lepault_Sample]]
| Fast freezing
|-

| Paper
| [[1995Dubochet_Sample]]
| High-pressure freezing
|-

| Paper
| [[1995VanMarle_Sample]]
| Sample damages in resin
|-

| Paper
| [[1998Adrian_Sample]]
| Cryo negative staining
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2002Hsieh_Sample]]
| Cryofixation
|-

| Paper
| [[2004AlAmoudi_Sample]]
| CEMOVIS
|-

| Paper
| [[2008Studer_Sample]]
| Review on high pressure freezing
|-

| Paper
| [[2009Pierson_Sample]]
| Review on sample preparation for electron tomography
|-

| Paper
| [[2010Zhang_NegativeStaining]]
| Negative staining for small protein imaging
|-

| Paper
| [[2012Zhang_PositiveStaining]]
| Positive staining
|-

| Paper
| [[2014Rames_NegativeStaining]]
| Optimized negative staining
|-

| Paper
| [[2014Russo_GoldGrids]]
| Gold grids for single particles
|-

| Paper
| [[2015Cabra_Sample]]
| Review on sample preparation for single particles with videos
|-

| Paper
| [[2016Passmore_Review]]
| Tutorial chapter on sample preparation
|-

| Paper
| [[2016Razinkov_Vitrification]]
| New vitrification method
|-

| Paper
| [[2016Takizawa_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2016Thompson_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2017Arnold_BlottingFree]]
| Blotting-free preparation
|-

| Paper
| [[2017Feng_SprayingPlunging]]
| Spraying plunging
|-

| Paper
| [[2017He_FIB]]
| Spraying plunging
|-

| Paper
| [[2017Peitsch_Sample]]
| iMEM: Isolation of Plasma Membrane for Cryoelectron Microscopy
|-

| Paper
| [[2017Scapin_Storage]]
| Cryo FIB lamella for TEM
|-

| Paper
| [[2017Schaffer_FocusedIonBeam]]
| Focused Ion Beam sample preparation for membrane proteins
|-

| Paper
| [[2017Scherr_HydrogelNanomembranes]]
| Sample preparation for membrane proteins
|-

|}

=== Automated data collection ===

{|

| Paper
| [[1992Dierksen_Automatic]]
| Automated data collection
|-

| Paper
| [[1992Koster_Automatic]]
| Automated data collection
|-

| Paper
| [[1996Fung_Automatic]]
| Automated data collection for tomography
|-

| Paper
| [[2001Zhang_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2003Ziese_Automatic]]
| Automated autofocusing
|-

| Paper
| [[2004Potter_Automatic]]
| Automated sample loading
|-

| Paper
| [[2004Zheng_Automatic]]
| Automated data collection
|-

| Paper
| [[2005Lei_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2005Suloway_Automatic]]
| Automated data collection: Leginon
|-

| Paper
| [[2007Yoshioka_RCT]]
| Automated Random Conical Tilt
|-

| Paper
| [[2011Korinek_TOM2]]
| Automated acquisition with TOM2
|-

| Paper
| [[2015Li_UCSFImage]]
| Automated acquisition with UCSFImage
|-

| Paper
| [[2016Gil_Fuzzy]]
| Real time decisions during acquisition with neuro-fuzzy method
|-

| Paper
| [[2016Liu_TiltControl]]
| Accurate control of the tilt angle for electron tomography
|-

| Paper
| [[2016Vargas_FoilHole]]
| Determination of image quality at low magnification
|-

| Paper
| [[2017Biyani_Focus]]
| Automatic processing of micrographs
|-

|}

== Single particles ==

=== Automatic particle picking ===

{|

| Paper
| [[1982VanHeel_Detection]]
| Detection of particles in micrographs
|-

| Paper
| [[2001Nicholson_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2001Zhu_Filaments]]
| Automatic identification of filaments in micrographs
|-

| Paper
| [[2004Sigworth_Detection]]
| Classical detection theory and the cryo-EM particle selection problem
|-

| Paper
| [[2004Volkmann_ParticlePicking]]
| An approach to automated particle picking from electron micrographs based on reduced representation templates
|-

| Paper
| [[2004Wong_ParticlePicking]]
| Model-based particle picking for cryo-electron microscopy
|-

| Paper
| [[2004Zhu_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2007Chen_Signature]]
| Automatic particle picking program: Signature
|-

| Paper
| [[2007Woolford_SwarmPS]]
| Automatic particle picking with several criteria, implemented in EMAN Boxer
|-

| Paper
| [[2009Sorzano_MachineLearning]]
| Automatic particle picking based on machine learning of rotational invariants
|-

| Paper
| [[2011Arbelaez_Comparison]]
| Evaluation of the performance of software for automated particle-boxing
|-

| Paper
| [[2013Abrishami_MachineLearning]]
| A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs
|-

| Paper
| [[2013Hauer_2013]]
| Automatic tilt pair detection in Random Conical Tilt
|-

| Paper
| [[2013Shatsky_ParticlePicking]]
| Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Langlois_ParticlePicking]]
| Automatic particle picking
|-

| Paper
| [[2016Vilas_AutomaticTilt]]
| Automatic identification of image pairs in untilted-tilted micrograph pairs
|-

|}

=== 2D Preprocessing ===

{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast enhancement through DPR
|-

| Paper
| [[2004Sorzano_Normalization]]
| Normalization procedures and their statistical properties.
|-

| Paper
| [[2006Sorzano_Denoising]]
| Strong denoising in wavelet space
|-

| Conference
| [[2009Sorzano_Downsampling]]
| Differences between the different downsampling schemes
|-

| Paper
| [[2012Brilot_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Campbell_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Zhao_Denoising]]
| Denoising using an invariant Fourier-Bessel eigenspace
|-

| Paper
| [[2013Norousi_Screening]]
| Screening particles to identify outliers
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu_Movies]]
| Drift correction for movies considering dark field
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Scheres_Movies]]
| Beam induced motion correction
|-

| Paper
| [[2015Abrishami_Movies]]
| Alignment of direct detection device micrographs
|-

| Paper
| [[2015Grant_Anisotropic]]
| Automatic estimation and correction of anisotropic magnification
|-

| Paper
| [[2015Grant_OptimalExposure]]
| Filter movies according to the radiation damage
|-

| Paper
| [[2015Rubinstein_Alignment]]
| Frame alignment at the level of particle
|-

| Paper
| [[2015Spear_DoseCompensation]]
| Effect of dose compensation on resolution
|-

| Paper
| [[2015Zhao_AnisotropicMagnification]]
| Correction of anisotropic magnification
|-

| Conference
| [[2016Bajic_Denoising]]
| Denoising and deconvolution of micrographs
|-

| Paper
| [[2016Jensen_RemovalVesicles]]
| Removal of vesicles in membrane proteins
|-

| Paper
| [[2016Bhamre_Denoising]]
| Denoising by 2D covariance estimation
|-

| Paper
| [[2017McLeod_Zorro]]
| Movie alignment by Zorro
|-

| Paper
| [[2017Zheng_MotionCorr2]]
| Movie alignment by MotionCorr2
|-

|}

=== 2D Alignment ===

{|

| Paper
| [[1981Frank_Averaging]]
| 2D averaging and phase residual
|-

| Paper
| [[1982Saxton_Averaging]]
| 2D averaging using correlation
|-

| Paper
| [[1998Sigworth_ML2D]]
| Maximum likelihood alignment in 2D
|-

| Paper
| [[2003Cong_FRM2D]]
| Fast Rotational Matching in 2D
|-

| Paper
| [[2005Cong_FRM2D]]
| Fast Rotational Matching in 2D introduced in a 3D Alignment algorithm
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

|}

=== 2D Classification and clustering ===

{|

| Paper
| [[1981VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[1984VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2011Singer_DiffusionMaps]]
| Classification in 2D based on graph analysis of the projections
|-

| Paper
| [[2012Yang_ISAC]]
| Iterative Stable Alignment and clustering
|-

| Paper
| [[2014Sorzano_Outlier]]
| Outlier detection in 2D classifications.
|-

| Paper
| [[2014Zhao_Aspire]]
| Fast classification based on rotational invariants and vector diffusion maps
|-

| Paper
| [[2015Huang_Robust]]
| Robust w-estimators of 2D classes
|-

| Paper
| [[2016Reboul_Stochastic]]
| Stochastic Hill Climbing for calculating 2D classes
|-

| Conference
| [[2017Bhamre_Mahalanobis]]
| 2D classification using Mahalanobis distance
|-

|}

=== 3D Alignment ===

{|

| Paper
| [[1980Kam_AutoCorrelation]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[1986Goncharov_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1987VanHeel_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1988Provencher_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Vogel_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1990Gelfand_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Goncharov_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Harauz_Quaternions]]
| Use of quaternions to represent rotations
|-

| Paper
| [[1994Penczek_Real]]
| Angular assignment using projection matching in real space
|-

| Paper
| [[1994Radermacher_Radon]]
| Angular assignment in Radon space
|-

| Paper
| [[1996Penczek_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[2003Rosenthal_DPR]]
| Angular assignment using DPR
|-

| Paper
| [[2004Sorzano_Wavelet]]
| Angular assignment in the wavelet space.
|-

| Paper
| [[2005Jonic_Splines]]
| Angular assignment in Fourier space using spline interpolation.
|-

| Paper
| [[2005Yang_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[2006Ogura_SimulatedAnnealing]]
| Angular asignment by simulated annealing
|-

| Paper
| [[2007Grigorieff_Continuous]]
| Continuous angular assignment in Fourier space
|-

| Paper
| [[2010Jaitly_Bayesian]]
| Angular assignment by a Bayesian method and annealing
|-

| Paper
| [[2010Sanz_Random]]
| Random model method
|-

| Paper
| [[2010Singer_Voting]]
| Detecting consistent common lines by voting (reference free)
|-

| Paper
| [[2011Singer_SDP]]
| Angular assignment by semidefinite programming and eigenvectors (reference free)
|-

| Paper
| [[2012Giannakis_Scattering]]
| Construction of an initial volume, reference free, by graph analysis of the projections
|-

| Paper
| [[2012Shkolnisky_Sync]]
| Angular assignment by synchronization of rotations (reference free)
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Wang_LUD]]
| Angular assignment by least unsquared deviations (reference free)
|-

| Paper
| [[2014Vargas_RANSAC]]
| Initial model using RANSAC (reference free)
|-

| Paper
| [[2015Joubert_Pseudoatoms]]
| Initial model based on pseudo-atoms
|-

| Paper
| [[2015Singer_Kam]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[2015Sorzano_Significant]]
| Statistical approach to the initial volume estimation (reconstruct significant)
|-

| Conference
| [[2016Michels_Heterogeneous]]
| Initial volume in the presence of heterogeneity
|-

| Paper
| [[2016Cossio_BayesianGPU]]
| GPU implementation of the Bayesian 3D reconstruction approach
|-

|}

=== 3D Reconstruction ===
{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1986Harauz_FBP]]
| Exact filters for Filtered Back Projection
|-

| Chapter
| [[1992Radermacher_WBP]]
| Exact filters for Weighted Back Projection
|-

| Paper
| [[1997Zhu_RecCTF]]
| 3D Reconstruction (SIRT like) and simultaneous CTF correction
|-

| Paper
| [[1998Boisset_Uneven]]
| Artifacts in SIRT and WBP under uneven angular distributions
|-

| Paper
| [[1998Marabini_ART]]
| Algebraic Reconstruction Technique with blobs (Xmipp)
|-

| Paper
| [[2001Sorzano_Uneven]]
| Free parameter selection under uneven angular distributions
|-

| Paper
| [[2005Sorzano_Parameters]]
| Free parameter selection for optimizing multiple tasks
|-

| Paper
| [[2008Sorzano_Constraints]]
| Mass, surface, positivity and symmetry constraints for real-space algorithms
|-

| Paper
| [[2009Bilbao_ParallelART]]
| Efficient parallelization of ART
|-

| Paper
| [[2011Li_GradientFlow]]
| Regularized 3D Reconstruction by Gradient Flow
|-

| Paper
| [[2011Vonesch_Wavelets]]
| Fast wavelet-based 3D reconstruction
|-

| Paper
| [[2012Gopinath_ShapeRegularization]]
| Regularized 3D Reconstruction by Shape information
|-

| Paper
| [[2012Kucukelbir_adaptiveBasis]]
| 3D reconstruction in an adaptive basis promoting sparsity
|-

| Paper
| [[2012Sindelar_NoiseReduction]]
| Optimal noise reduction in 3D reconstructions
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Lyumkis_Optimod]]
| Construction of initial volumes with Optimod
|-

| Paper
| [[2013Wang FIRM]]
| Fast 3D reconstruction in Fourier domain
|-

| Paper
| [[2014Kunz_SART_OS]]
| Simultaneous ART with OS
|-

| Paper
| [[2015Abrishami_Fourier]]
| 3D Reconstruction in Fourier space
|-

| Paper
| [[2015Dvornek_SubspaceEM]]
| Fast Maximum a posteriori
|-

| Paper
| [[2015Moriya_Bayesian]]
| Bayesian approach to suppress limited angular artifacts
|-

| Paper
| [[2015Xu_GeometricFlow]]
| Multi-scale geometric flow
|-

| Arxiv
| [[2016Ye_Cohomology]]
| Cohomology properties of 3D reconstruction
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

| Paper
| [[2017Punjani_CryoSPARCTheory]]
| Theory related to CryoSPARC
|-

|}

=== 3D Heterogeneity ===

{|

| Paper
| [[2004White_Size]]
| Heterogeneity classification of differently sized images
|-

| Paper
| [[2006Penczek_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Scheres_ML3D]]
| Maximum Likelihood alignment and classification in 3D
|-

| Paper
| [[2009Spahn_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2010Elmlund_AbInitio]]
| Solving the initial volume problem with multiple conformations
|-

| Paper
| [[2010Shatsky_MultiVariate]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2012Scheres_Bayesian]]
| A Bayesian view on cryo-EM structure determination
|-

| Paper
| [[2012Zheng_Covariance]]
| Estimation of the volume covariance
|-

| Paper
| [[2013Wang_MLVariance]]
| Maximum Likelihood estimate of the map variance
|-

| Paper
| [[2013Lyumkis D_FREALIGN]]
| Likelihood-based classification of cryo-EM images using FREALIGN.
|-

| Paper
| [[2014Jin_NMA]]
| Continuous heterogeneity through Normal Mode Analysis
|-

| Paper
| [[2014Dashti_Brownian]]
| Continuous heterogeneity through Brownian trajectories
|-

| Paper
| [[2014Chen_Migration]]
| Particle migration analysis in 3D classification
|-

| Paper
| [[2015Anden_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Bai_Focused]]
| Focused classification
|-

| Paper
| [[2015Katsevich_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Klaholz_MRA]]
| Multivariate Statistical Analysis of Jackknife and Bootstrapping on random subsets
|-

| Paper
| [[2015Liao_Covariance]]
| Estimation of the 3D covariance from 2D projections
|-

| Paper
| [[2015Tagare_Direct]]
| Direct reconstruction of PCA components
|-

| Paper
| [[2016Gong_Mechanical]]
| Mechanical model for macromolecules
|-

| Paper
| [[2016Rawson_Movement]]
| Movement and flexibility
|-

| Paper
| [[2016Sorzano_StructMap]]
| Sorting a discrete set of conformational states
|-

| Paper
| [[2016Sorzano_Strain]]
| Calculate local stretches, strains and rotations from two conformational states
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

|}

=== Validation ===

{|

| Paper
| [[2008Stagg_TestBed]]
| Effect of voltage, dosis, number of particles and Euler jumps on resolution
|-

| Paper
| [[2011Henderson]]
| Tilt Validation
|-

| Paper
| [[2011Read]]
| Validation of PDBs
|-

| Paper
| [[2012Henderson]]
| EM Map Validation
|-

| Paper
| [[2013Cossio_Bayesian]]
| EM Map Validation in a probabilistic setting
|-

| Paper
| [[2013Chen_NoiseSubstitution]]
| Noise substitution at high resolution for measuring overfitting
|-

| Paper
| [[2014Russo_StatisticalSignificance]]
| EM Map Validation through the statistical significance of the tilt-pair angular assignment
|-

| Paper
| [[2014Stagg_Reslog]]
| EM Map Validation through the resolution evolution with the number of particles
|-

| Paper
| [[2014Wasilewski_Tilt]]
| Web implementation of the tilt pair validation
|-

| Paper
| [[2015Heymann_Alignability]]
| EM Map Validation through the resolution of reconstructions from particles and noise
|-

| Paper
| [[2015Oliveira_FreqLimited]]
| Comparison of gold standard and frequency limited optimization
|-

| Paper
| [[2015Wriggers_Secondary]]
| Validation by secondary structure
|-

| Paper
| [[2016Kim_SAXS]]
| Comparison of SAXS data and EM projections
|-

| Paper
| [[2016Rosenthal_Review]]
| Review of validation methods
|-

| Paper
| [[2016Vargas_Alignability]]
| Validation by studying the tendency of an angular assignment to cluster in the projection space
|-

| Paper
| [[2017Monroe_PDBRefinement]]
| Validation by comparison to a refined PDB
|-

|}

=== Resolution ===

{|

| Paper
| [[1986Harauz_FBP]]
| Fourier Shell Correlation
|-

| Paper
| [[1987Unser_SSNR]]
| 2D Spectral Signal to Noise Ratio
|-

| Paper
| [[2002Penczek_SSNR]]
| 3D Spectral Signal to Noise Ratio for Fourier based algorithms
|-

| Paper
| [[2003Rosenthal_DPR]]
| Review of the FSC and establishment of a new threshold
|-

| Paper
| [[2005Unser_SSNR]]
| 3D Spectral Signal to Noise Ratio for any kind of algorithms
|-

| Paper
| [[2005VanHeel_FSC]]
| Establishment of a new threshold for FSC
|-

| Paper
| [[2007Sousa_AbInitio]]
| Resolution measurement on neighbour Fourier voxels
|-

| Paper
| [[2014Kucukelbir_Local]]
| Quantifying the local resolution of cryo-EM density maps
|-

| Paper
| [[2016Pintilie_Probabilistic]]
| Probabilistic models and resolution
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Statistical properties of resolution measures defined in Fourier space
|-

|}

=== Sharpening of high resolution information ===
{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast restoration and map sharpening
|-

| Paper
| [[2008Fernandez_Bfactor]]
| Bfactor determination and restoration
|-

| Paper
| [[2013Fiddy_SaxtonAlgorithm]]
| Phase retrieval or extension
|-

| Paper
| [[2014Kishchenko_SphericalDeconvolution]]
| Spherical deconvolution
|-

| Paper
| [[2015Spiegel_VISDEM]]
| Visualization improvement by the use of pseudoatomic profiles
|-

| Paper
| [[2016Jonic_Pseudoatoms]]
| Approximation with pseudoatoms
|-

| Paper
| [[2016Jonic_Denoising]]
| Denoising and high-frequency boosting by pseudoatom approximation
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[1982Schiske_Correction]]
| CTF correction for tilted objects
|-

| Paper
| [[1988Toyoshima_Model]]
| CTF estimation
|-

| Paper
| [[1995Frank_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1996Skoglund_MaxEnt]]
| CTF correction with Maximum Entropy
|-

| Paper
| [[1996Zhou_Model]]
| CTF model and user interface for manual fitting
|-

| Paper
| [[1997Fernandez_AR]]
| PSD estimation using periodogram averaging and AR models
|-

| Paper
| [[1997Penczek_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1997Stark_Deconvolution]]
| CTF correction using deconvolution
|-

| Paper
| [[1997Zhu_RecCTF]]
| CTF correction and reconstruction
|-

| Paper
| [[2000DeRosier_EwaldCorrection]]
| CTF correction considering the Ewald sphere
|-

| Paper
| [[2000Jensen_TiltedCorrection]]
| CTF correction considering tilt in backprojection
|-

| Paper
| [[2001Saad_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Huang_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Mindell_CTFTILT]]
| CTF estimation for tilted micrographs
|-

| Paper
| [[2003Sander_MSA]]
| CTF estimation through MSA classification of PSDs
|-

| Paper
| [[2003Velazquez_ARMA]]
| PSD and CTF estimation using ARMA models
|-

| Paper
| [[2004Sorzano_IDR]]
| CTF restoration and reconstruction with Iterative Data Refinement
|-

| Conference
| [[2004Wan_CTF]]
| Spatially variant CTF
|-

| Paper
| [[2004Zubelli_Chahine]]
| CTF restoration and reconstruction with Chahine's multiplicative method
|-

| Conference
| [[2005Dubowy_SpaceVariant]]
| CTF correction when this is space variant
|-

| Paper
| [[2005Mallick_ACE]]
| CTF estimation
|-

| Paper
| [[2006Wolf_Ewald]]
| CTF correction considering Ewald sphere
|-

| Paper
| [[2007Jonic_EnhancedPSD]]
| PSD enhancement for better identification of Thon rings; Vitreous ice diffracts in Thon rings
|-

| Paper
| [[2007Philippsen_Model]]
| CTF Model for tilted specimens
|-

| Paper
| [[2007Sorzano_CTF]]
| CTF estimation using enhanced PSDs
|-

| Paper
| [[2009Sorzano_Sensitivity]]
| Error sensitivity of the CTF models, non-uniqueness of the CTF parameters
|-

| Paper
| [[2010Jiang2010_CTFCorrection]]
| Amplitude correction method
|-

| Paper
| [[2010Kasantsev_CTFCorrection]]
| Mathematical foundations of Kornberg and Jensen method
|-

| Paper
| [[2010Leong_CTFCorrection]]
| Correction for spatially variant CTF
|-

| Paper
| [[2011Glaeser_Coma]]
| The effect of coma at high-resolution
|-

| Paper
| [[2011Mariani_Tilted]]
| CTF simulation and correction of tilted specimens
|-

| Paper
| [[2011Sindelar_Wiener]]
| CTF correction using a modified version of Wiener filter
|-

| Paper
| [[2011Voortman_Tilted]]
| CTF correction for tilted specimen
|-

| Paper
| [[2012Voortman_VaryingCTF]]
| Correcting a spatially varying CTF
|-

| Paper
| [[2013Vargas_FastDef]]
| Fast defocus
|-

| Paper
| [[2015Rohou_CTFFind4]]
| CTF Find 4
|-

| Paper
| [[2015Sheth_CTFquality]]
| Visualization and quality assessment of CTF
|-

| Paper
| [[2016Zhang_GCTF]]
| gCTF
|-

|}

=== Segmentation ===

{|

| Paper
| [[2006Baker_segmentation]]
| Segmentation of molecular subunits
|-

|}

=== Fitting and docking ===

{|

| Paper
| [[1999Volkmann_Fitting]]
| Fitting in real space
|-

| Paper
| [[2001Baker_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2001Jones_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2003Kovacs_FRM3D]]
| Fast Rotational Alignment of two EM maps
|-

| Paper
| [[2004Tama_NMA1]]
| Flexible fitting with Normal Modes (I)
|-

| Paper
| [[2004Tama_NMA2]]
| Flexible fitting with Normal Modes (II)
|-

| Paper
| [[2005Velazquez_Superfamilies]]
| Recognition of the superfamily folding in medium-high resolution volumes
|-

| Paper
| [[2007DeVries_Haddock]]
| Docking with Haddock 2.0
|-

| Paper
| [[2007Kleywegt_QualityControl]]
| Quality control and validation of fitting
|-

| Paper
| [[2012Biswas_Secondary]]
| Secondary structure determination in EM volumes
|-

| Paper
| [[2012Velazquez_Constraints]]
| Multicomponent fitting by using constraints from other information sources
|-

| Paper
| [[2013Chapman MS_Atomicmodeling]]
| Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters
|-

| Paper
| [[2013Esquivel_Modelling]]
| Review on modelling (secondary structure, fitting, ...)
|-

| Paper
| [[2013Lopez_Imodfit]]
| Fitting based on vibrational analysis
|-

| Paper
| [[2013Nogales_3DEMLoupe]]
| Normal Mode Analysis of reconstructed volumes
|-

| Paper
| [[2014AlNasr_Secondary]]
| Identification of secondary structure elements in EM volumes
|-

| Paper
| [[2014Politis_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Rey_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Villa_Review]]
| Review of atomic fitting into EM volumes
|-

| Paper
| [[2015Barad_EMRinger]]
| Validation of hybrid models
|-

| Paper
| [[2015Bettadapura_PF2Fit]]
| Fast rigid fitting of PDBs into EM maps
|-

| Paper
| [[2015Carrillo_CapsidMaps]]
| Analysis of virus capsids using Google Maps
|-

| Paper
| [[2015Schroeder_Hybrid]]
| Review on model building
|-

| Paper
| [[2015Tamo_Dynamics]]
| Dynamics in integrative modeling
|-

| Paper
| [[2015Sorzano_AtomsToVoxels]]
| Accurate conversion of an atomic model into a voxel density volume
|-

| Paper
| [[2016Joseph_Evolution]]
| Evolutionary constraints for the fitting of atomic models into density maps
|-

| Paper
| [[2016Segura_3Diana]]
| Validation of hybrid models
|-

| Paper
| [[2016Singharoy_MDFF]]
| Construction of hybrid models driven by EM density and molecular dynamics
|-

| Paper
| [[2016Wang_Rosetta]]
| Construction of hybrid models driven by EM density using Rosetta
|-

| Paper
| [[2017Joseph_Metrics]]
| Metrics analysis for the comparison of structures
|-

| Paper
| [[2017Hryc_WeightedAtoms]]
| Construction of hybrid models by locally weighting the different atoms
|-

| Paper
| [[2017Matsumoto_Distribution]]
| Estimating the distribution of conformations of atomic models
|-

| Paper
| [[2017Miyashita_EnsembleFitting]]
| Ensemble fitting using Molecular Dynamics
|-

| Paper
| [[2017Turk_ModelBuilding]]
| Tutorial on model building and protein visualization
|-

|}

=== Books and reviews ===

{|

| Book
| [[1980Herman_Tomography]]
| General book on tomography
|-

| Book
| [[1988Kak_Tomography]]
| General book on tomography
|-

| Paper
| [[2000Tao_Review]]
| Review of single particles
|-

| Paper
| [[2000VanHeel_Review]]
| Review of single particles
|-

| Paper
| [[2002Frank_Review]]
| Review of single particles
|-

| Paper
| [[2002Schmid_Review]]
| Review of single particles
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2004Subramaniam_Review]]
| Review of single particles
|-

| Paper
| [[2005Steven_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_book]]
| Book covering all aspects of electron microscopy of single particles
|-

| Paper
| [[2006Sorzano_Review]]
| Review of optimization problems in electron microscopy
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems in Electron Tomography
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2008Mueller_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2008Taylor_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2010DeRosier_Review]]
| Personal account of how 3DEM developed in the early days
|-

| Chapter
| [[2012Sorzano_Review]]
| Review of single particle analysis using Xmipp
|-

| Chapter
| [[2012Devaux_Protocol]]
| Protocols for performing single particle analysis
|-

| Paper
| [[2014Bai_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Carazo_Review]]
| Review of the reconstruction process
|-

| Paper
| [[2015Cheng_Review]]
| A primer to Single Particle Cryo-EM
|-

| Paper
| [[2015Cheng_Reviewb]]
| Single Particle Cryo-EM at crystallographic resolution
|-

| Paper
| [[2015Elmlund_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Henderson_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Nogales_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Schroeder_Review]]
| Review of advances in the electron microscope
|-

| Paper
| [[2015Wu_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Carroni_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Egelman_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Eisenstein_CryoEM]]
| News feature on the Method of the Year
|-

| Paper
| [[2016FernandezLeiro_Review]]
| Review of EM
|-

| Paper
| [[2016Glaeser_HowGood]]
| How good can cryo-EM become?
|-

| Paper
| [[2016Jonic_PseudoAtoms]]
| Review of the applications of the use of pseudoatoms in EM
|-

| Chapter
| [[2016Mio_Review]]
| Overview of the process to obtain EM reconstructions
|-

| Paper
| [[2016Jonic_Review]]
| A review of computational ways to handle heterogeneity
|-

| Paper
| [[2016Nogales_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Subramaniam_Review]]
| Why cryo-EM is now suitable for crystallographic journals
|-

| Paper
| [[2016Vinothkumar_Review]]
| Historical review and current limitations
|-

| Paper
| [[2017Frank_Review]]
| Historical review of EM
|-

| Paper
| [[2017Jonic_Review]]
| Review of computational methods to analyze conformational variability
|-

| Paper
| [[2017Rawson_Limitations]]
| Limitations of EM for drug design
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Review of statistical properties of resolution measures defined in Fourier space
|-
|}

=== Software ===

{|

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[1999Lutdke_Eman]]
| Eman
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Baldwin_AngularTransformations]]
| The Transform Class in SPARX and EMAN2
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Grigorieff_Frealign]]
| Frealign
|-

| Paper
| [[2008Scheres_XmippProtocols]]
| Xmipp Protocols
|-

| Paper
| [[2008Shaikh_SpiderProtocols]]
| Spider Protocols
|-

| Paper
| [[2012Wriggers_SitusConventions]]
| Conventions and workflows in Situs
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2015Cianfrocco_Cloud]]
| Software execution in the cloud
|-

| Paper
| [[2015Cheng_MRC2014]]
| Extensions to MRC file format
|-

| Paper
| [[2013DeLaRosa_Scipion]]
| Scipion
|-

| Paper
| [[2016Scheres_Relion]]
| Tutorial on the use of Relion
|-

| Paper
| [[2016Grigorieff_Frealign]]
| Tutorial on the use of Frealign
|-

| Paper
| [[2017Moriya_Sphire]]
| Tutorial on the use of Sphire
|-

|}

== Electron tomography ==

=== Image preprocessing ===

{|

| Paper
| [[2015Yan_thickness]]
| Determination of thickness, tilt and electron mean free path
|-

|}

=== Image alignment ===

{|

| Paper
| [[1982Guckenberger_commonOrigin]]
| Determination of a common origin in the micrographs of titl series in three-dimensional electron microscopy
|-

| Paper
| [[1992Lawrence_leastSquares]]
| Least squares solution of the alignment problem
|-

| Paper
| [[1995Penczek_dual]]
| Dual tilt alignment
|-

| Paper
| [[1996Owen_alignmentQuality]]
| Automatic alignment without fiducial markers and evaluation of alignment quality
|-

| Paper
| [[1998Grimm_normalization]]
| Discussion of several gray level normalization methods for electron tomography
|-

| Paper
| [[2001Brandt_Automatic1]]
| Automatic alignment without fiducial markers
|-

| Paper
| [[2001Brandt_Automatic2]]
| Automatic alignment with fiducial markers
|-

| Paper
| [[2006Winkler_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2006Castano_alignment]]
| Alignment with non-perpendicularity
|-

| Paper
| [[2007Castano_alignment]]
| Fiducial-less alignment of cryo-sections
|-

| Paper
| [[2009Sorzano_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2010Cantele_dualAlignment]]
| Alignment of dual series
|-

| Paper
| [[2014Tomonaga_Automatic]]
| Automatic alignment of tilt series using the projection themselves
|-

| Paper
| [[2014Han_Automatic]]
| Automatic alignment of tilt series using SIFT features
|-

| Paper
| [[2015Han_Automatic]]
| Automatic alignment of tilt series using fiducials
|-

| Paper
| [[2017Mastronarde_Automatic]]
| Automatic alignment and reconstruction of tilt series in IMOD
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[2003Winkler_CTF]]
| Focus gradient correction in electron tomography
|-

| Paper
| [[2006Fernandez_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Zanetti_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Xiong_CTF]]
| CTF determination and correction for low dose tomographic tilt series
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2017Kunz_3DCTF]]
| 3D CTF Correction
|-

|}

=== 3D reconstruction ===

{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1992Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[1997Marabini_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2002Fernandez_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2007Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[2008Fernandez_CARP]]
| Component Averaged Row Projections (CARP)
|-

| Paper
| [[2012Herman General Superiorization]]
| Superiorization: an optimization heuristic for medical physics
|-

| Paper
| [[2012Zhang_IPET_FETR]]
| IPET and FETR, a reconstruction algorithm for single molecule tomography
|-

| Paper
| [[2013Goris_SIRT_TV_DART]]
| Combination of SIRT, Total Variation and Discrete ART to reconstruct and segment at the same time
|-

| Paper
| [[2013Briegel A_Challenge]]
| The challenge of determining handedness in electron tomography and the use of DNA origami gold nanoparticle helices as molecular standards
|-

| Paper
| [[2013Messaoudi_EnergyFiltered]]
| 3D Reconstruction of Energy-Filtered TEM
|-

| Paper
| [[2016Deng_ICON]]
| 3D Reconstruction with missing information restoration
|-

| Paper
| [[2016Guay_Compressed]]
| 3D Reconstruction using compressed sensing
|-

|}

=== Noise reduction ===
{|

| Paper
| [[2001Frangakis_NAD]]
| Noise reduction with Nonlinear Anisotropic Diffusion
|-

| Paper
| [[2003Fernandez_AND]]
| Anisotropic nonlinear diffusion for electron tomography
|-

| Paper
| [[2003Jiang_Bilateral]]
| Bilateral denoising filter in electron microscopy
|-

| Paper
| [[2005Fernandez_AND]]
| Anisotropic nonlinear denoising in electron tomography
|-

| Paper
| [[2007Heide_median]]
| Iterative median filtering in electron tomography
|-

| Paper
| [[2007Fernandez_autAND]]
| Anisotropic nonlinear diffusion with automated parameter tuning
|-

| Paper
| [[2009Fernandez_Beltrami]]
| Nonlinear filtering based on Beltrami flow
|-

| Paper
| [[2010Bilbao_MeanShift]]
| Mean Shift Filtering
|-

| Paper
| [[2014Kovacik_wedgeArtefacts]]
| Removal of wedge artefacts
|-

| Paper
| [[2014Maiorca_beadArtefacts]]
| Removal of gold bead artefacts
|-

|}

=== Segmentation ===

{|

| Paper
| [[2002Frangakis_Eigenanalysis]]
| Segmentation using eigenvector analysis.
|-

| Paper
| [[2002Volkmann_Watershed]]
| Segmentation using watershed transform.
|-

| Paper
| [[2003Bajaj_BoundarySegmentation]]
| Segmentation based on fast marching.
|-

| Paper
| [[2005Cyrklaff_Thresholding]]
| Segmentation using optimal thresholding.
|-

| Paper
| [[2007Lebbink_TemplateMatching]]
| Segmentation using template matching.
|-

| Paper
| [[2007Sandberg_OrientationFields]]
| Segmentation using orientation fields.
|-

| Paper
| [[2007Sandberg_SegmentationReview]]
| Review on segmentation in electron tomography.
|-

| Paper
| [[2008Garduno_FuzzySegmentation]]
| Segmentation using fuzzy set theory principles.
|-

| Paper
| [[2009Lebbink_TemplateMatching2]]
| Segmentation using template matching.
|-

| Paper
| [[2012RubbiyaAli_EdgeDetection]]
| Parameter-Free Segmentation of Macromolecular Structures.
|-

| Conference
| [[2015Xu_TemplateMatching]]
| Detection of macromolecular complexes with a reduced representation of the templates.
|-

|}

=== Resolution ===
{|

| Paper
| [[2005Cardone_Resolution]]
| Resolution criterion for electron tomography
|-

| Chapter
| [[2007Penczek_Resolution]]
| Review of resolution criteria for electron tomography
|-

| Paper
| [[2015Diebolder_ConicalFSC]]
| Conical Fourier Shell Correlation
|-

|}

=== Subtomogram analysis ===

{|

| Paper
| [[2000Bohm_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2002Frangakis_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2006Nickell_Review]]
| Review of macromolecule finding by template matching (Visual Proteomics)
|-

| Paper
| [[2007Best_Review]]
| Review of Localization of Protein Complexes by Pattern Recognition
|-

| Paper
| [[2007Forster_Review]]
| Review of structure determination by subtomogram averaging
|-

| Paper
| [[2008Forster_Classification]]
| Classification of subtomograms using constrained correlation
|-

| Paper
| [[2008Bartesaghi_Classification]]
| Classification and averaging of subtomograms
|-

| Paper
| [[2008Schmid_Averaging]]
| Alignment and averaging of subtomograms
|-

| Paper
| [[2010Amat_Averaging]]
| Alignment and averaging of subtomograms exploiting thresholding in Fourier space
|-

| Paper
| [[2013Chen_Averaging]]
| Fast alignment of subtomograms using spherical harmonics
|-

| Paper
| [[2013Kuybeda_Averaging]]
| Alignment and averaging of subtomograms using the nuclear norm of the cluster
|-

| Paper
| [[2013Shatsky_Averaging]]
| Alignment and averaging of subtomograms with constrained cross-correlation
|-

| Paper
| [[2014Chen_Autofocus]]
| Subtomogram averaging and classification with special attention to differences
|-

| Paper
| [[2014Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2014Voortman_LimitingFactors]]
| Limiting factors of subtomogram averaging
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2015Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2016Bharat_Relion]]
| Subtomogram averaging with Relion
|-

| Paper
| [[2016Song_MatrixNorm]]
| Matrix norm minimization for tomographic reconstruction and alignment
|-

| Paper
| [[2017Castano_ParticlePicking]]
| Particle picking in tomograms for subtomogram averaging
|-

| Paper
| [[2017Frazier_Tomominer]]
| TomoMiner a software platform for large-scale subtomogram analysis
|-

|}

=== Single particle tomography ===

{|

| Paper
| [[2012Bartesaghi_Constrained]]
| 3D reconstruction by imposing geometrical constraints
|-

| Paper
| [[2015Galaz_SingleParticleTomography]]
| Set of tools for Single Particle Tomography in EMAN2
|-

| Paper
| [[2016Galaz_SingleParticleTomography]]
| Alignment algorithms and CTF correction
|-

|}

=== Books and reviews ===

{|

| Paper
| [[2000Baumeister_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Koster_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Sali_Review]]
| Review of electron tomography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2005Lucic_Review]]
| Review of electron tomography
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_TomoBook]]
| Electron Tomography
|-

| Book
| [[2007McIntosh_Book]]
| Cellular Electron Microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2012Kudryashev_Review]]
| Review of subtomogram averaging
|-

| Paper
| [[2016Beck_Review]]
| Review of molecular sociology
|-

| Paper
| [[2017Galaz_Review]]
| Review of single particle tomography
|-

|}

=== Software ===

{|

| Paper
| [[1996Kremer_IMOD]]
| IMOD
|-

| Paper
| [[1996Chen_Priism/IVE]]
| Priism/IVE
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2005Nickell_TOM]]
| TOM Toolbox
|-

| Paper
| [[2007Messaoudi_TomoJ]]
| TomoJ
|-

| Paper
| [[2008Heymann_BsoftTomo]]
| Bsoft
|-

| Paper
| [[2015Ding_CaltechTomography]]
| Caltech tomography database
|-

| Paper
| [[2015Noble_AppionProtomo]]
| Batch fiducial-less tilt-series alignment in Appion using Protomo
|-

| Paper
| [[2015vanAarle_Astra]]
| ASTRA Toolbox
|-

| Paper
| [[2017Wan_Simulator]]
| Electron Tomography Simulator
|-

|}

== 2D Crystals ==

=== 2D Preprocessing ===

{|

| Paper
| [[1986Henderson_Processing]]
| General 2D processing
|-

| Paper
| [[2000He_PhaseAlignment]]
| Phase consistency and Alignment
|-

| Paper
| [[2006Gil_Unbending]]
| Crystal unbending
|-

|}

=== Classification ===
{|

| Paper
| [[1988Frank_Classification]]
| MSA and classification in electron crystallography
|-

| Paper
| [[1996Fernandez_SOM]]
| Classification based on self organizing maps
|-

| Paper
| [[1998Sherman_MSA]]
| Classification based on MSA
|-

|}
=== 3D Reconstruction ===

{|

| Paper
| [[1985Wang_Solvent]]
| Solvent flattening
|-

| Paper
| [[1990Henderson_Processing]]
| General 3D processing
|-

| Paper
| [[2004Marabini_ART]]
| Algebraic Reconstruction Technique with blobs for crystals (Xmipp)
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1998Walz_Review]]
| Review of 2D crystallography
|-

| Paper
| [[1999Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Ellis_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of single particles, electron tomography and crystallography
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Gipson_2dx]]
| 2dx
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Philippsen_IPLT]]
| IPLT
|-

|}

== 3D Crystals - MicroED ==

=== Sample Preparation ===
{|
| Paper
| [[2016Shi_Preparation]]
| Sample Preparation
|}
=== Data Collection ===
{|
| Paper
| [[2014Nannenga_CR]]
| Continuous rotation

|}
=== Data Processing ===
{|

| Paper
| [[2011Wisedchaisri_PhaseExtension]]
| Fragment-based phase extension
|-

| Paper
| [[2015Hattne_Processing]]
| Data Processing
|-

| Paper
| [[2016Hattne_Correction]]
| Image correction
|}

=== Software ===
{|

| Paper
| [[2014Iadanza_Processing]]
| Data Processing of still diffraction data
|}

=== Books and Reviews ===
{|
| Paper
| [[2014Nannenga_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Liu_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Rodriguez_Review ]]
| Review of MicroED
|-

|}

== Helical particles ==

=== Filament corrections ===

{|

| Paper
| [[1986Egelman_Curved]]
| Algorithm for correcting curved filaments
|-

| Paper
| [[1988Bluemke_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2006Wang_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2016Yang_Flexible]]
| Algorithm for correcting filaments with flexible subunits
|-

|}

=== Reconstruction ===

{|

| Paper
| [[1952Cochran_Fourier]]
| Fourier Bessel transform of filamentous structures
|-

| Paper
| [[1958Klug_Fourier]]
| Fourier Bessel decomposition of the projection images
|-

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2005Wang_Iterative]]
| Iterative Fourier-Bessel algorithm
|-

| Paper
| [[2007Egelman_Iterative]]
| Iterative real-space algorithm
|-

| Paper
| [[2013Desfosses_Spring]]
| Helical processing with Spring
|-

| Paper
| [[2015Zhang_seam]]
| Workflow for the detection of the lattice seam
|-

| Paper
| [[2016Rohou_Frealix]]
| Helical processing with Frealix
|-

|}

=== Validation ===

{|

| Paper
| [[2014Egelman_ambiguity]]
| How to detect incorrect models
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Carragher_Phoelix]]
| Phoelix
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Owen_Brandeis]]
| Brandeis
|-

|}

== Icosahedral particles ==

=== Reconstruction ===

{|

| Paper
| [[1970Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1971Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1996Fuller_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1997Thuman_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

|}

=== Classification ===

{|

| Paper
| [[2005Scheres_Virus]]
| Classification of virus capsids in real space
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1999Baker_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[1999Conway_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2000Thuman_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Lee_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Navaza_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2006Grunewald_Review]]
| Review of reconstruction of icosahedral viruses
|-

|}

=== Software ===

{|

| Paper
| [[1996Baker_EMPFT]]
| EMPFT
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2013Morin_Sliz SBGrid]]
| SBGrid presentation for eLife
|-

|}

== Databases ==

{|

| Paper
| [[2003Boutselakis_EMSD]]
| EMSD database
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2011Kim_CDDB]]
| Conformational Dynamics Data Bank
|-

| Paper
| [[2011Lawson_EMDB]]
| Electron Microscopy Data Bank
|-

| Paper
| [[2013Ison_EDAM]]
| EDAM, an ontology of bioinformatics operations
|-

| Paper
| [[2016Iudin_EMPIAR]]
| EMPIAR raw data database
|-

| Paper
| [[2016Patwhardan_EMDB]]
| EMDB, PDB, ...
|-

| Paper
| [[2017Patwhardan_Trends]]
| Trends at EMDB
|-

| Paper
| [[2017Shao_PDBQuality]]
| Quality metrics in PDB
|-

| Blog
| http://www.mybiosoftware.com
| Huge list of bioinformatics programs (many of them structural bioinformatics)
|-

|}

== Relationship to other structural information sources ==

{|

| Paper
| [[2000Engel_AFM]]
| Review of Atomic Force Microscopy
|-

| Paper
| [[2001Dimmeler_AFM]]
| Constraints from Atomic Force Microscopy
|-

| Paper
| [[2003Mobus_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_Review]]
| Review on correlative microscopy
|-

| Paper
| [[2005Boudier_EFTETJ]]
| Software for Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2005Vestergaard_SAXS]]
| Example of comparison of 3DEM and Small-angle X-ray scattering
|-

| Paper
| [[2007Hamada_SAXS]]
| Constraints from Small-angle X-ray scattering
|-

| Paper
| [[2013Xu_FRET]]
| EM+FRET
|-

|}

== X-ray tomography ==

{|

| Paper
| [[2012Oton_ImageFormation]]
| Image formation model in X-ray cell microscopy
|-

|}

== Mathematical tools necessary ==

== People developing methods ==
Please, add yourself to this list (due to privacy reasons, please, do not add anyone else to the list without his/her explicit consent). Sort by first name alphabetical order.

[http://biocomp.cnb.csic.es/~coss Carlos Oscar S. Sorzano]: CSIC, Madrid, Spain 

[http://www.curie.fr/recherche/themes/detail_equipe.cfm/lang/_fr/id_equipe/241.htm Cédric Messaoudi]: Institute Curie, Paris, France 

[http://scholar.google.es/citations?user=_jNYGScAAAAJ&hl=en Javier Vargas]:[mailto:jvargas@cnb.csic.es mail]: CSIC, Madrid, Spain 

[http://scholar.google.es/citations?hl=es&user=g2ZJPIYAAAAJ Joaquín Otón]: CSIC, Madrid, Spain 

[mailto:jrbcast@gmail.com José Román Bilbao-Castro]: UAL, Almería, Spain; CSIC, Madrid, Spain 

[José Miguel de la Rosa Trevín]: Biocomputing Unit CNB-CSIC, Madrid, Spain 

[http://cryoem.janelia.org Tamir Gonen]: [mailto:gonent@janelia.hhmi.org mail]: Howard Hughes Medical Institute, Ashburn, VA, USA 

[mailto:vabrishami@cnb.csic.es Vahid Abrishami]: CSIC, Madrid, Spain 

== 3DEM sites ==
* [http://3dem.ucsd.edu/ 3DEM web site]

* [http://en.wikibooks.org/wiki/Software_Tools_For_Molecular_Microscopy Software tools for molecular microscopy]

* [http://www.emdatabank.org/ The Electron Microscopy Data Bank (EMDB)]

* [http://ccdb.ucsd.edu The Cell Centered Database (CCDB)]

* [http://conventions.cnb.csic.es The geometrical software conventions web page ]

== Editing useful links ==

* [http://www.mediawiki.org/wiki/Help:Formatting Text formatting in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Links Adding links in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Images Adding images in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Tables Making tables in Mediawiki]

2017Turk ModelBuilding

2017-07-04T06:14:15Z

CoSS: Created page with "== Citation == Turk, D. Boxes of Model Building and Visualization. Methods in molecular biology, 2017, 1607, 491-548 == Abstract == Macromolecular crystallography and elect..."

== Citation ==

Turk, D. Boxes of Model Building and Visualization. Methods in molecular biology, 2017, 1607, 491-548

== Abstract ==

Macromolecular crystallography and electron microscopy (single-particle and in situ tomography) are merging into a single approach used by the two coalescing scientific communities. The merger is a consequence of technical developments that enabled determination of atomic structures of macromolecules by electron microscopy. Technological progress in experimental methods of macromolecular structure determination, computer hardware, and software changed and continues to change the nature of model building and visualization of molecular structures. However, the increase in automation and availability of structure validation are reducing interactive manual model building to fiddling with details. On the other hand, interactive modeling tools increasingly rely on search and complex energy calculation procedures, which make manually driven changes in geometry increasingly powerful and at the same time less demanding. Thus, the need for accurate manual positioning of a model is decreasing. The user's push only needs to be sufficient to bring the model within the increasing convergence radius of the computing tools. It seems that we can now better than ever determine an average single structure. The tools work better, requirements for engagement of human brain are lowered, and the frontier of intellectual and scientific challenges has moved on. The quest for resolution of new challenges requires out-of-the-box thinking. A few issues such as model bias and correctness of structure, ongoing developments in parameters defining geometric restraints, limitations of the ideal average single structure, and limitations of Bragg spot data are discussed here, together with the challenges that lie ahead.

== Keywords ==

== Links ==

https://link.springer.com/protocol/10.1007/978-1-4939-7000-1_21

== Related software ==

== Related methods ==

== Comments ==

Main Page

2017-07-04T06:13:20Z

CoSS: /* Fitting and docking */

== Presentation ==

This web page is intended to be an extensive repository of three-dimensional electron microscopy (3DEM) methods. The advantages of having such a repository are

* You know which are the relevant articles in a particular topic, therefore, paper introductions, reviews, etc. are easier to write and you make sure you will cite all the related articles.
* You will be sure that your paper has more chances of being cited.
* You can add whatever information you find relevant to your method, external links, links to other papers, etc.
* You can link your method to a web page providing the corresponding software, so you know people can use your algorithms.
* You can use the Wiki search capabilities to locate relevant articles even if they are not at the topic you are looking at.
* As a community we will "reconstruct" our history.
* You can select the "watch" option above to receive notifications in case of further changes in the Main Page.

Developing image processing methods for 3DEM is not "[[well-paid]]" in terms of citations and impact factor. However, it is crucial for the advance of the field. Gathering methodological papers in a portal will help to increase the recognition of the field.

Please:

* Add your articles at the right place (you can add a single article in several topics if it is relevant to all of them). The easiest way to add an article is by editing the corresponding topic in the main page, adding your entry, then save the main page. Click on the red link that appears on your new entry, copy and paste the Wiki following code, add the information of your article

== Citation ==

== Abstract ==

== Keywords ==

== Links ==

== Related software ==

== Related methods ==

== Comments ==

* Maintain the information of each article as complete as possible.
* Sort articles by years and authors.
* Be respectful to other people's work.

== How to subscribe to this page ==

You may subscribe to this page so that you will be notified every time someone adds a new method. To do so, you have to register in the page, and edit your preferences ("my preferences"). Be sure that you have activated the option "E-mail me when a page on my watchlist is changed". Finally, click on the "Watch" tab at the top of this page.

You may subscribe to changes on this page on the mailing list 3demmethods@cnb.csic.es. To send a new method to this mail list just send a mail to 3demmethods@cnb.csic.es

To subscribe to this list, visit the web page

https://listas.csic.es/cnb/wws/subscribe/3demmethods

Alternatively, you may write a mail to sympa6@cnb.csic.es with the subject

<code>subscribe 3demmethods YourName YourFamilyName</code>

and an empty mail body.

To unsubscribe visit the page

https://listas.csic.es/cnb/wws/sigrequest/3demmethods

or write sympa6@cnb.csic.es with the subject

<code>unsubscribe 3demmethods</code>

and an empty mail body.

== Electron microscopy images ==

=== Online courses ===

CALTECH: http://cryo-em-course.caltech.edu/

MRC: ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/EM-course/

CNB-CSIC: http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/MadridJan2014EM

Workshop on Computational methods for CryoEM: https://www.youtube.com/watch?v=XdKO1iaPP8o

Workshop on Management of large CryoEM facilities: https://www.youtube.com/watch?v=as4seOPszL0

Icknield Course on Model Building and Refinement for High Resolution EM Maps: http://www.ccpem.ac.uk/training/icknield_2017/icknield_2017.php

=== Image formation ===

{|

| Paper
| [[1971Erickson_CTF]]
| CTF model
|-

| Paper
| [[1971Glaeser_Damage]]
| Radiation damage
|-

| Chapter
| [[1971Hanszen_CTF]]
| Image formation model
|-

| Paper
| [[1971Thon_Model]]
| CTF model
|-

| Paper
| [[1975Unwin_Imaging]]
| Radiation dose
|-

| Paper
| [[1977Wade_Model]]
| CTF model
|-

| Paper
| [[1978Wade_Model]]
| CTF model
|-

| Paper
| [[1979Hayward_Radiation]]
| Radiation damage
|-

| Paper
| [[1984Cohen_Validity]]
| Validity of the CTF model at high frequencies
|-

| Paper
| [[1988Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[1992Wade_Model]]
| CTF model
|-

| Paper
| [[1993Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2004Egerton_Damage]]
| Radiation damage
|-

| Paper
| [[2004Sorzano_Normalization]]
| Background noise is Gaussian
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2009Baxter_NoiseCharacterization]]
| Characterization of the different noise sources in cryo-EM
|-

| Paper
| [[2010Baker_Damage]]
| Radiation damage dependence on resolution
|-

| Paper
| [[2010Bammes_Damage]]
| Radiation damage dependence on temperature
|-

| Paper
| [[2010Gomez_Multislice]]
| Simulation of the multi slice model
|-

| Paper
| [[2010Zewail_FourDimensional]]
| Review on the use of ultrafast EM
|-

| Paper
| [[2011Bammes_CCD]]
| Performance of CCD cameras
|-

| Paper
| [[2011Glaeser_Coma]]
| Image formation model including coma
|-

| Paper
| [[2011Milazzo_DirectDetectors]]
| Evaluation of Direct Detectors
|-

| Paper
| [[2011Rullgard_ImageSimulation]]
| Accurate simulation of EM images
|-

| Paper
| [[2011Zhang LimitingFactors]]
| Limiting factor for atomic resolution in EM
|-

| Paper
| [[2012Bammes_DirectDetection]]
| Performance of Direct detectors
|-

| Paper
| [[2012Campbell_MotionCorrection]]
| Beam induced motion correction and direct detectors
|-

| Paper
| [[2012Shang_HydrationLayer]]
| Simulation of PDB volumes explicitly considering the hydration layer
|-

| Paper
| [[2013Egerton_RadiationDamage]]
| Review of TEM radiation damage and experimental ways of reducing it
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu H_Noisemodels]]
| Noise models and cryo-EM drift correction with a direct-electron camera
|-

| Paper
| [[2013Li X K2 noisemodels]]
| Influence of electron dose rate on electron counting images recorded with the K2 camera
|-

| Paper
| [[2013Vulovic_CTFApproximations]]
| When to use the different approximations performed so that a projection with linear CTF is valid
|-

| Thesis
| [[2013Vulovic_ImageFormation]]
| Ph.D. Thesis on the image formation in cryo-EM
|-

| Paper
| [[2014Danev_PhasePlate]]
| Volta potential phase plate
|-

| Paper
| [[2015Chiu_K2]]
| Characterization of K2
|-

| Paper
| [[2015Hawkes_AberrationCorrection]]
| Historical account of the development of lens corrections
|-

| Paper
| [[2015Koeck_Quadratic]]
| Limitations of the linear approximation and use of the quadratic terms
|-

| Paper
| [[2015Kuijper_FEI]]
| Description of the FEI Falcons
|-

| Paper
| [[2015Lobato_MULTEM]]
| Simulation of multislice diffraction
|-

| Paper
| [[2015McMullan_AmorphousIce]]
| Beam induced movement is caused by Brownian motion
|-

| Paper
| [[2016Koeck_ADF]]
| Simulations of Annular Dark Field TEM
|-

| Paper
| [[2017Mishyna_DNARadiation]]
| Review of radiation damage on DNA
|-

|}

=== Collection geometry ===

{|

| Chapter
| [[1980Hoppe_Wedge]]
| Missing wedge
|-

| Paper
| [[1987Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1995Penczek_Dual]]
| Dual axis tomography
|-

| Paper
| [[1997Mastronarde_Dual]]
| Dual axis tomography
|-

| Paper
| [[2003Ludtke_FocusPairs]]
| Focus pairs for single particles
|-

| Paper
| [[2005Lanzavecchia_Conical]]
| Conical tomography
|-

| Paper
| [[2005Zampighi_Conical]]
| Conical tomography
|-

| Paper
| [[2006Leschziner_OT]]
| Orthogonal Tilt
|-

| Paper
| [[2006Messaoudi_Multiple]]
| Multiple axis tomography
|-

| Paper
| [[2012Kudryashev_FocusPairs]]
| Focus pairs tomography
|-

| Paper
| [[2014Hovden_TiltFocus]]
| Combining tilt series with focus series
|-

| Paper
| [[2015Sorzano_RandomConicalTilt]]
| General formulation of Random Conical Tilt
|-

| Paper
| [[2017Hagen_DoseTomography]]
| Dose optimization for subtomogram averaging
|-

|}

=== Sample preparation ===

{|

| Paper
| [[1982Dubochet_Sample]]
| Vitreous ice
|-

| Paper
| [[1986Lepault_Sample]]
| Fast freezing
|-

| Paper
| [[1995Dubochet_Sample]]
| High-pressure freezing
|-

| Paper
| [[1995VanMarle_Sample]]
| Sample damages in resin
|-

| Paper
| [[1998Adrian_Sample]]
| Cryo negative staining
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2002Hsieh_Sample]]
| Cryofixation
|-

| Paper
| [[2004AlAmoudi_Sample]]
| CEMOVIS
|-

| Paper
| [[2008Studer_Sample]]
| Review on high pressure freezing
|-

| Paper
| [[2009Pierson_Sample]]
| Review on sample preparation for electron tomography
|-

| Paper
| [[2010Zhang_NegativeStaining]]
| Negative staining for small protein imaging
|-

| Paper
| [[2012Zhang_PositiveStaining]]
| Positive staining
|-

| Paper
| [[2014Rames_NegativeStaining]]
| Optimized negative staining
|-

| Paper
| [[2014Russo_GoldGrids]]
| Gold grids for single particles
|-

| Paper
| [[2015Cabra_Sample]]
| Review on sample preparation for single particles with videos
|-

| Paper
| [[2016Passmore_Review]]
| Tutorial chapter on sample preparation
|-

| Paper
| [[2016Razinkov_Vitrification]]
| New vitrification method
|-

| Paper
| [[2016Takizawa_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2016Thompson_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2017Arnold_BlottingFree]]
| Blotting-free preparation
|-

| Paper
| [[2017Feng_SprayingPlunging]]
| Spraying plunging
|-

| Paper
| [[2017Peitsch_Sample]]
| iMEM: Isolation of Plasma Membrane for Cryoelectron Microscopy
|-

| Paper
| [[2017Scapin_Storage]]
| Cryo storage of samples
|-

| Paper
| [[2017Schaffer_FocusedIonBeam]]
| Focused Ion Beam sample preparation for membrane proteins
|-

| Paper
| [[2017Scherr_HydrogelNanomembranes]]
| Sample preparation for membrane proteins
|-

|}

=== Automated data collection ===

{|

| Paper
| [[1992Dierksen_Automatic]]
| Automated data collection
|-

| Paper
| [[1992Koster_Automatic]]
| Automated data collection
|-

| Paper
| [[1996Fung_Automatic]]
| Automated data collection for tomography
|-

| Paper
| [[2001Zhang_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2003Ziese_Automatic]]
| Automated autofocusing
|-

| Paper
| [[2004Potter_Automatic]]
| Automated sample loading
|-

| Paper
| [[2004Zheng_Automatic]]
| Automated data collection
|-

| Paper
| [[2005Lei_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2005Suloway_Automatic]]
| Automated data collection: Leginon
|-

| Paper
| [[2007Yoshioka_RCT]]
| Automated Random Conical Tilt
|-

| Paper
| [[2011Korinek_TOM2]]
| Automated acquisition with TOM2
|-

| Paper
| [[2015Li_UCSFImage]]
| Automated acquisition with UCSFImage
|-

| Paper
| [[2016Gil_Fuzzy]]
| Real time decisions during acquisition with neuro-fuzzy method
|-

| Paper
| [[2016Liu_TiltControl]]
| Accurate control of the tilt angle for electron tomography
|-

| Paper
| [[2016Vargas_FoilHole]]
| Determination of image quality at low magnification
|-

| Paper
| [[2017Biyani_Focus]]
| Automatic processing of micrographs
|-

|}

== Single particles ==

=== Automatic particle picking ===

{|

| Paper
| [[1982VanHeel_Detection]]
| Detection of particles in micrographs
|-

| Paper
| [[2001Nicholson_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2001Zhu_Filaments]]
| Automatic identification of filaments in micrographs
|-

| Paper
| [[2004Sigworth_Detection]]
| Classical detection theory and the cryo-EM particle selection problem
|-

| Paper
| [[2004Volkmann_ParticlePicking]]
| An approach to automated particle picking from electron micrographs based on reduced representation templates
|-

| Paper
| [[2004Wong_ParticlePicking]]
| Model-based particle picking for cryo-electron microscopy
|-

| Paper
| [[2004Zhu_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2007Chen_Signature]]
| Automatic particle picking program: Signature
|-

| Paper
| [[2007Woolford_SwarmPS]]
| Automatic particle picking with several criteria, implemented in EMAN Boxer
|-

| Paper
| [[2009Sorzano_MachineLearning]]
| Automatic particle picking based on machine learning of rotational invariants
|-

| Paper
| [[2011Arbelaez_Comparison]]
| Evaluation of the performance of software for automated particle-boxing
|-

| Paper
| [[2013Abrishami_MachineLearning]]
| A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs
|-

| Paper
| [[2013Hauer_2013]]
| Automatic tilt pair detection in Random Conical Tilt
|-

| Paper
| [[2013Shatsky_ParticlePicking]]
| Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Langlois_ParticlePicking]]
| Automatic particle picking
|-

| Paper
| [[2016Vilas_AutomaticTilt]]
| Automatic identification of image pairs in untilted-tilted micrograph pairs
|-

|}

=== 2D Preprocessing ===

{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast enhancement through DPR
|-

| Paper
| [[2004Sorzano_Normalization]]
| Normalization procedures and their statistical properties.
|-

| Paper
| [[2006Sorzano_Denoising]]
| Strong denoising in wavelet space
|-

| Conference
| [[2009Sorzano_Downsampling]]
| Differences between the different downsampling schemes
|-

| Paper
| [[2012Brilot_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Campbell_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Zhao_Denoising]]
| Denoising using an invariant Fourier-Bessel eigenspace
|-

| Paper
| [[2013Norousi_Screening]]
| Screening particles to identify outliers
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu_Movies]]
| Drift correction for movies considering dark field
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Scheres_Movies]]
| Beam induced motion correction
|-

| Paper
| [[2015Abrishami_Movies]]
| Alignment of direct detection device micrographs
|-

| Paper
| [[2015Grant_Anisotropic]]
| Automatic estimation and correction of anisotropic magnification
|-

| Paper
| [[2015Grant_OptimalExposure]]
| Filter movies according to the radiation damage
|-

| Paper
| [[2015Rubinstein_Alignment]]
| Frame alignment at the level of particle
|-

| Paper
| [[2015Spear_DoseCompensation]]
| Effect of dose compensation on resolution
|-

| Paper
| [[2015Zhao_AnisotropicMagnification]]
| Correction of anisotropic magnification
|-

| Conference
| [[2016Bajic_Denoising]]
| Denoising and deconvolution of micrographs
|-

| Paper
| [[2016Jensen_RemovalVesicles]]
| Removal of vesicles in membrane proteins
|-

| Paper
| [[2016Bhamre_Denoising]]
| Denoising by 2D covariance estimation
|-

| Paper
| [[2017McLeod_Zorro]]
| Movie alignment by Zorro
|-

| Paper
| [[2017Zheng_MotionCorr2]]
| Movie alignment by MotionCorr2
|-

|}

=== 2D Alignment ===

{|

| Paper
| [[1981Frank_Averaging]]
| 2D averaging and phase residual
|-

| Paper
| [[1982Saxton_Averaging]]
| 2D averaging using correlation
|-

| Paper
| [[1998Sigworth_ML2D]]
| Maximum likelihood alignment in 2D
|-

| Paper
| [[2003Cong_FRM2D]]
| Fast Rotational Matching in 2D
|-

| Paper
| [[2005Cong_FRM2D]]
| Fast Rotational Matching in 2D introduced in a 3D Alignment algorithm
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

|}

=== 2D Classification and clustering ===

{|

| Paper
| [[1981VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[1984VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2011Singer_DiffusionMaps]]
| Classification in 2D based on graph analysis of the projections
|-

| Paper
| [[2012Yang_ISAC]]
| Iterative Stable Alignment and clustering
|-

| Paper
| [[2014Sorzano_Outlier]]
| Outlier detection in 2D classifications.
|-

| Paper
| [[2014Zhao_Aspire]]
| Fast classification based on rotational invariants and vector diffusion maps
|-

| Paper
| [[2015Huang_Robust]]
| Robust w-estimators of 2D classes
|-

| Paper
| [[2016Reboul_Stochastic]]
| Stochastic Hill Climbing for calculating 2D classes
|-

| Conference
| [[2017Bhamre_Mahalanobis]]
| 2D classification using Mahalanobis distance
|-

|}

=== 3D Alignment ===

{|

| Paper
| [[1980Kam_AutoCorrelation]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[1986Goncharov_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1987VanHeel_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1988Provencher_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Vogel_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1990Gelfand_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Goncharov_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Harauz_Quaternions]]
| Use of quaternions to represent rotations
|-

| Paper
| [[1994Penczek_Real]]
| Angular assignment using projection matching in real space
|-

| Paper
| [[1994Radermacher_Radon]]
| Angular assignment in Radon space
|-

| Paper
| [[1996Penczek_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[2003Rosenthal_DPR]]
| Angular assignment using DPR
|-

| Paper
| [[2004Sorzano_Wavelet]]
| Angular assignment in the wavelet space.
|-

| Paper
| [[2005Jonic_Splines]]
| Angular assignment in Fourier space using spline interpolation.
|-

| Paper
| [[2005Yang_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[2006Ogura_SimulatedAnnealing]]
| Angular asignment by simulated annealing
|-

| Paper
| [[2007Grigorieff_Continuous]]
| Continuous angular assignment in Fourier space
|-

| Paper
| [[2010Jaitly_Bayesian]]
| Angular assignment by a Bayesian method and annealing
|-

| Paper
| [[2010Sanz_Random]]
| Random model method
|-

| Paper
| [[2010Singer_Voting]]
| Detecting consistent common lines by voting (reference free)
|-

| Paper
| [[2011Singer_SDP]]
| Angular assignment by semidefinite programming and eigenvectors (reference free)
|-

| Paper
| [[2012Giannakis_Scattering]]
| Construction of an initial volume, reference free, by graph analysis of the projections
|-

| Paper
| [[2012Shkolnisky_Sync]]
| Angular assignment by synchronization of rotations (reference free)
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Wang_LUD]]
| Angular assignment by least unsquared deviations (reference free)
|-

| Paper
| [[2014Vargas_RANSAC]]
| Initial model using RANSAC (reference free)
|-

| Paper
| [[2015Joubert_Pseudoatoms]]
| Initial model based on pseudo-atoms
|-

| Paper
| [[2015Singer_Kam]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[2015Sorzano_Significant]]
| Statistical approach to the initial volume estimation (reconstruct significant)
|-

| Conference
| [[2016Michels_Heterogeneous]]
| Initial volume in the presence of heterogeneity
|-

| Paper
| [[2016Cossio_BayesianGPU]]
| GPU implementation of the Bayesian 3D reconstruction approach
|-

|}

=== 3D Reconstruction ===
{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1986Harauz_FBP]]
| Exact filters for Filtered Back Projection
|-

| Chapter
| [[1992Radermacher_WBP]]
| Exact filters for Weighted Back Projection
|-

| Paper
| [[1997Zhu_RecCTF]]
| 3D Reconstruction (SIRT like) and simultaneous CTF correction
|-

| Paper
| [[1998Boisset_Uneven]]
| Artifacts in SIRT and WBP under uneven angular distributions
|-

| Paper
| [[1998Marabini_ART]]
| Algebraic Reconstruction Technique with blobs (Xmipp)
|-

| Paper
| [[2001Sorzano_Uneven]]
| Free parameter selection under uneven angular distributions
|-

| Paper
| [[2005Sorzano_Parameters]]
| Free parameter selection for optimizing multiple tasks
|-

| Paper
| [[2008Sorzano_Constraints]]
| Mass, surface, positivity and symmetry constraints for real-space algorithms
|-

| Paper
| [[2009Bilbao_ParallelART]]
| Efficient parallelization of ART
|-

| Paper
| [[2011Li_GradientFlow]]
| Regularized 3D Reconstruction by Gradient Flow
|-

| Paper
| [[2011Vonesch_Wavelets]]
| Fast wavelet-based 3D reconstruction
|-

| Paper
| [[2012Gopinath_ShapeRegularization]]
| Regularized 3D Reconstruction by Shape information
|-

| Paper
| [[2012Kucukelbir_adaptiveBasis]]
| 3D reconstruction in an adaptive basis promoting sparsity
|-

| Paper
| [[2012Sindelar_NoiseReduction]]
| Optimal noise reduction in 3D reconstructions
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Lyumkis_Optimod]]
| Construction of initial volumes with Optimod
|-

| Paper
| [[2013Wang FIRM]]
| Fast 3D reconstruction in Fourier domain
|-

| Paper
| [[2014Kunz_SART_OS]]
| Simultaneous ART with OS
|-

| Paper
| [[2015Abrishami_Fourier]]
| 3D Reconstruction in Fourier space
|-

| Paper
| [[2015Dvornek_SubspaceEM]]
| Fast Maximum a posteriori
|-

| Paper
| [[2015Moriya_Bayesian]]
| Bayesian approach to suppress limited angular artifacts
|-

| Paper
| [[2015Xu_GeometricFlow]]
| Multi-scale geometric flow
|-

| Arxiv
| [[2016Ye_Cohomology]]
| Cohomology properties of 3D reconstruction
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

| Paper
| [[2017Punjani_CryoSPARCTheory]]
| Theory related to CryoSPARC
|-

|}

=== 3D Heterogeneity ===

{|

| Paper
| [[2004White_Size]]
| Heterogeneity classification of differently sized images
|-

| Paper
| [[2006Penczek_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Scheres_ML3D]]
| Maximum Likelihood alignment and classification in 3D
|-

| Paper
| [[2009Spahn_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2010Elmlund_AbInitio]]
| Solving the initial volume problem with multiple conformations
|-

| Paper
| [[2010Shatsky_MultiVariate]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2012Scheres_Bayesian]]
| A Bayesian view on cryo-EM structure determination
|-

| Paper
| [[2012Zheng_Covariance]]
| Estimation of the volume covariance
|-

| Paper
| [[2013Wang_MLVariance]]
| Maximum Likelihood estimate of the map variance
|-

| Paper
| [[2013Lyumkis D_FREALIGN]]
| Likelihood-based classification of cryo-EM images using FREALIGN.
|-

| Paper
| [[2014Jin_NMA]]
| Continuous heterogeneity through Normal Mode Analysis
|-

| Paper
| [[2014Dashti_Brownian]]
| Continuous heterogeneity through Brownian trajectories
|-

| Paper
| [[2014Chen_Migration]]
| Particle migration analysis in 3D classification
|-

| Paper
| [[2015Anden_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Bai_Focused]]
| Focused classification
|-

| Paper
| [[2015Katsevich_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Klaholz_MRA]]
| Multivariate Statistical Analysis of Jackknife and Bootstrapping on random subsets
|-

| Paper
| [[2015Liao_Covariance]]
| Estimation of the 3D covariance from 2D projections
|-

| Paper
| [[2015Tagare_Direct]]
| Direct reconstruction of PCA components
|-

| Paper
| [[2016Gong_Mechanical]]
| Mechanical model for macromolecules
|-

| Paper
| [[2016Rawson_Movement]]
| Movement and flexibility
|-

| Paper
| [[2016Sorzano_StructMap]]
| Sorting a discrete set of conformational states
|-

| Paper
| [[2016Sorzano_Strain]]
| Calculate local stretches, strains and rotations from two conformational states
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

|}

=== Validation ===

{|

| Paper
| [[2008Stagg_TestBed]]
| Effect of voltage, dosis, number of particles and Euler jumps on resolution
|-

| Paper
| [[2011Henderson]]
| Tilt Validation
|-

| Paper
| [[2011Read]]
| Validation of PDBs
|-

| Paper
| [[2012Henderson]]
| EM Map Validation
|-

| Paper
| [[2013Cossio_Bayesian]]
| EM Map Validation in a probabilistic setting
|-

| Paper
| [[2013Chen_NoiseSubstitution]]
| Noise substitution at high resolution for measuring overfitting
|-

| Paper
| [[2014Russo_StatisticalSignificance]]
| EM Map Validation through the statistical significance of the tilt-pair angular assignment
|-

| Paper
| [[2014Stagg_Reslog]]
| EM Map Validation through the resolution evolution with the number of particles
|-

| Paper
| [[2014Wasilewski_Tilt]]
| Web implementation of the tilt pair validation
|-

| Paper
| [[2015Heymann_Alignability]]
| EM Map Validation through the resolution of reconstructions from particles and noise
|-

| Paper
| [[2015Oliveira_FreqLimited]]
| Comparison of gold standard and frequency limited optimization
|-

| Paper
| [[2015Wriggers_Secondary]]
| Validation by secondary structure
|-

| Paper
| [[2016Kim_SAXS]]
| Comparison of SAXS data and EM projections
|-

| Paper
| [[2016Rosenthal_Review]]
| Review of validation methods
|-

| Paper
| [[2016Vargas_Alignability]]
| Validation by studying the tendency of an angular assignment to cluster in the projection space
|-

| Paper
| [[2017Monroe_PDBRefinement]]
| Validation by comparison to a refined PDB
|-

|}

=== Resolution ===

{|

| Paper
| [[1986Harauz_FBP]]
| Fourier Shell Correlation
|-

| Paper
| [[1987Unser_SSNR]]
| 2D Spectral Signal to Noise Ratio
|-

| Paper
| [[2002Penczek_SSNR]]
| 3D Spectral Signal to Noise Ratio for Fourier based algorithms
|-

| Paper
| [[2003Rosenthal_DPR]]
| Review of the FSC and establishment of a new threshold
|-

| Paper
| [[2005Unser_SSNR]]
| 3D Spectral Signal to Noise Ratio for any kind of algorithms
|-

| Paper
| [[2005VanHeel_FSC]]
| Establishment of a new threshold for FSC
|-

| Paper
| [[2007Sousa_AbInitio]]
| Resolution measurement on neighbour Fourier voxels
|-

| Paper
| [[2014Kucukelbir_Local]]
| Quantifying the local resolution of cryo-EM density maps
|-

| Paper
| [[2016Pintilie_Probabilistic]]
| Probabilistic models and resolution
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Statistical properties of resolution measures defined in Fourier space
|-

|}

=== Sharpening of high resolution information ===
{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast restoration and map sharpening
|-

| Paper
| [[2008Fernandez_Bfactor]]
| Bfactor determination and restoration
|-

| Paper
| [[2013Fiddy_SaxtonAlgorithm]]
| Phase retrieval or extension
|-

| Paper
| [[2014Kishchenko_SphericalDeconvolution]]
| Spherical deconvolution
|-

| Paper
| [[2015Spiegel_VISDEM]]
| Visualization improvement by the use of pseudoatomic profiles
|-

| Paper
| [[2016Jonic_Pseudoatoms]]
| Approximation with pseudoatoms
|-

| Paper
| [[2016Jonic_Denoising]]
| Denoising and high-frequency boosting by pseudoatom approximation
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[1982Schiske_Correction]]
| CTF correction for tilted objects
|-

| Paper
| [[1988Toyoshima_Model]]
| CTF estimation
|-

| Paper
| [[1995Frank_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1996Skoglund_MaxEnt]]
| CTF correction with Maximum Entropy
|-

| Paper
| [[1996Zhou_Model]]
| CTF model and user interface for manual fitting
|-

| Paper
| [[1997Fernandez_AR]]
| PSD estimation using periodogram averaging and AR models
|-

| Paper
| [[1997Penczek_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1997Stark_Deconvolution]]
| CTF correction using deconvolution
|-

| Paper
| [[1997Zhu_RecCTF]]
| CTF correction and reconstruction
|-

| Paper
| [[2000DeRosier_EwaldCorrection]]
| CTF correction considering the Ewald sphere
|-

| Paper
| [[2000Jensen_TiltedCorrection]]
| CTF correction considering tilt in backprojection
|-

| Paper
| [[2001Saad_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Huang_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Mindell_CTFTILT]]
| CTF estimation for tilted micrographs
|-

| Paper
| [[2003Sander_MSA]]
| CTF estimation through MSA classification of PSDs
|-

| Paper
| [[2003Velazquez_ARMA]]
| PSD and CTF estimation using ARMA models
|-

| Paper
| [[2004Sorzano_IDR]]
| CTF restoration and reconstruction with Iterative Data Refinement
|-

| Conference
| [[2004Wan_CTF]]
| Spatially variant CTF
|-

| Paper
| [[2004Zubelli_Chahine]]
| CTF restoration and reconstruction with Chahine's multiplicative method
|-

| Conference
| [[2005Dubowy_SpaceVariant]]
| CTF correction when this is space variant
|-

| Paper
| [[2005Mallick_ACE]]
| CTF estimation
|-

| Paper
| [[2006Wolf_Ewald]]
| CTF correction considering Ewald sphere
|-

| Paper
| [[2007Jonic_EnhancedPSD]]
| PSD enhancement for better identification of Thon rings; Vitreous ice diffracts in Thon rings
|-

| Paper
| [[2007Philippsen_Model]]
| CTF Model for tilted specimens
|-

| Paper
| [[2007Sorzano_CTF]]
| CTF estimation using enhanced PSDs
|-

| Paper
| [[2009Sorzano_Sensitivity]]
| Error sensitivity of the CTF models, non-uniqueness of the CTF parameters
|-

| Paper
| [[2010Jiang2010_CTFCorrection]]
| Amplitude correction method
|-

| Paper
| [[2010Kasantsev_CTFCorrection]]
| Mathematical foundations of Kornberg and Jensen method
|-

| Paper
| [[2010Leong_CTFCorrection]]
| Correction for spatially variant CTF
|-

| Paper
| [[2011Glaeser_Coma]]
| The effect of coma at high-resolution
|-

| Paper
| [[2011Mariani_Tilted]]
| CTF simulation and correction of tilted specimens
|-

| Paper
| [[2011Sindelar_Wiener]]
| CTF correction using a modified version of Wiener filter
|-

| Paper
| [[2011Voortman_Tilted]]
| CTF correction for tilted specimen
|-

| Paper
| [[2012Voortman_VaryingCTF]]
| Correcting a spatially varying CTF
|-

| Paper
| [[2013Vargas_FastDef]]
| Fast defocus
|-

| Paper
| [[2015Rohou_CTFFind4]]
| CTF Find 4
|-

| Paper
| [[2015Sheth_CTFquality]]
| Visualization and quality assessment of CTF
|-

| Paper
| [[2016Zhang_GCTF]]
| gCTF
|-

|}

=== Segmentation ===

{|

| Paper
| [[2006Baker_segmentation]]
| Segmentation of molecular subunits
|-

|}

=== Fitting and docking ===

{|

| Paper
| [[1999Volkmann_Fitting]]
| Fitting in real space
|-

| Paper
| [[2001Baker_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2001Jones_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2003Kovacs_FRM3D]]
| Fast Rotational Alignment of two EM maps
|-

| Paper
| [[2004Tama_NMA1]]
| Flexible fitting with Normal Modes (I)
|-

| Paper
| [[2004Tama_NMA2]]
| Flexible fitting with Normal Modes (II)
|-

| Paper
| [[2005Velazquez_Superfamilies]]
| Recognition of the superfamily folding in medium-high resolution volumes
|-

| Paper
| [[2007DeVries_Haddock]]
| Docking with Haddock 2.0
|-

| Paper
| [[2007Kleywegt_QualityControl]]
| Quality control and validation of fitting
|-

| Paper
| [[2012Biswas_Secondary]]
| Secondary structure determination in EM volumes
|-

| Paper
| [[2012Velazquez_Constraints]]
| Multicomponent fitting by using constraints from other information sources
|-

| Paper
| [[2013Chapman MS_Atomicmodeling]]
| Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters
|-

| Paper
| [[2013Esquivel_Modelling]]
| Review on modelling (secondary structure, fitting, ...)
|-

| Paper
| [[2013Lopez_Imodfit]]
| Fitting based on vibrational analysis
|-

| Paper
| [[2013Nogales_3DEMLoupe]]
| Normal Mode Analysis of reconstructed volumes
|-

| Paper
| [[2014AlNasr_Secondary]]
| Identification of secondary structure elements in EM volumes
|-

| Paper
| [[2014Politis_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Rey_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Villa_Review]]
| Review of atomic fitting into EM volumes
|-

| Paper
| [[2015Barad_EMRinger]]
| Validation of hybrid models
|-

| Paper
| [[2015Bettadapura_PF2Fit]]
| Fast rigid fitting of PDBs into EM maps
|-

| Paper
| [[2015Carrillo_CapsidMaps]]
| Analysis of virus capsids using Google Maps
|-

| Paper
| [[2015Schroeder_Hybrid]]
| Review on model building
|-

| Paper
| [[2015Tamo_Dynamics]]
| Dynamics in integrative modeling
|-

| Paper
| [[2015Sorzano_AtomsToVoxels]]
| Accurate conversion of an atomic model into a voxel density volume
|-

| Paper
| [[2016Joseph_Evolution]]
| Evolutionary constraints for the fitting of atomic models into density maps
|-

| Paper
| [[2016Segura_3Diana]]
| Validation of hybrid models
|-

| Paper
| [[2016Singharoy_MDFF]]
| Construction of hybrid models driven by EM density and molecular dynamics
|-

| Paper
| [[2016Wang_Rosetta]]
| Construction of hybrid models driven by EM density using Rosetta
|-

| Paper
| [[2017Joseph_Metrics]]
| Metrics analysis for the comparison of structures
|-

| Paper
| [[2017Hryc_WeightedAtoms]]
| Construction of hybrid models by locally weighting the different atoms
|-

| Paper
| [[2017Matsumoto_Distribution]]
| Estimating the distribution of conformations of atomic models
|-

| Paper
| [[2017Miyashita_EnsembleFitting]]
| Ensemble fitting using Molecular Dynamics
|-

| Paper
| [[2017Turk_ModelBuilding]]
| Tutorial on model building and protein visualization
|-

|}

=== Books and reviews ===

{|

| Book
| [[1980Herman_Tomography]]
| General book on tomography
|-

| Book
| [[1988Kak_Tomography]]
| General book on tomography
|-

| Paper
| [[2000Tao_Review]]
| Review of single particles
|-

| Paper
| [[2000VanHeel_Review]]
| Review of single particles
|-

| Paper
| [[2002Frank_Review]]
| Review of single particles
|-

| Paper
| [[2002Schmid_Review]]
| Review of single particles
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2004Subramaniam_Review]]
| Review of single particles
|-

| Paper
| [[2005Steven_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_book]]
| Book covering all aspects of electron microscopy of single particles
|-

| Paper
| [[2006Sorzano_Review]]
| Review of optimization problems in electron microscopy
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems in Electron Tomography
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2008Mueller_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2008Taylor_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2010DeRosier_Review]]
| Personal account of how 3DEM developed in the early days
|-

| Chapter
| [[2012Sorzano_Review]]
| Review of single particle analysis using Xmipp
|-

| Chapter
| [[2012Devaux_Protocol]]
| Protocols for performing single particle analysis
|-

| Paper
| [[2014Bai_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Carazo_Review]]
| Review of the reconstruction process
|-

| Paper
| [[2015Cheng_Review]]
| A primer to Single Particle Cryo-EM
|-

| Paper
| [[2015Cheng_Reviewb]]
| Single Particle Cryo-EM at crystallographic resolution
|-

| Paper
| [[2015Elmlund_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Henderson_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Nogales_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Schroeder_Review]]
| Review of advances in the electron microscope
|-

| Paper
| [[2015Wu_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Carroni_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Egelman_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Eisenstein_CryoEM]]
| News feature on the Method of the Year
|-

| Paper
| [[2016FernandezLeiro_Review]]
| Review of EM
|-

| Paper
| [[2016Glaeser_HowGood]]
| How good can cryo-EM become?
|-

| Paper
| [[2016Jonic_PseudoAtoms]]
| Review of the applications of the use of pseudoatoms in EM
|-

| Chapter
| [[2016Mio_Review]]
| Overview of the process to obtain EM reconstructions
|-

| Paper
| [[2016Jonic_Review]]
| A review of computational ways to handle heterogeneity
|-

| Paper
| [[2016Nogales_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Subramaniam_Review]]
| Why cryo-EM is now suitable for crystallographic journals
|-

| Paper
| [[2016Vinothkumar_Review]]
| Historical review and current limitations
|-

| Paper
| [[2017Frank_Review]]
| Historical review of EM
|-

| Paper
| [[2017Jonic_Review]]
| Review of computational methods to analyze conformational variability
|-

| Paper
| [[2017Rawson_Limitations]]
| Limitations of EM for drug design
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Review of statistical properties of resolution measures defined in Fourier space
|-
|}

=== Software ===

{|

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[1999Lutdke_Eman]]
| Eman
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Baldwin_AngularTransformations]]
| The Transform Class in SPARX and EMAN2
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Grigorieff_Frealign]]
| Frealign
|-

| Paper
| [[2008Scheres_XmippProtocols]]
| Xmipp Protocols
|-

| Paper
| [[2008Shaikh_SpiderProtocols]]
| Spider Protocols
|-

| Paper
| [[2012Wriggers_SitusConventions]]
| Conventions and workflows in Situs
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2015Cianfrocco_Cloud]]
| Software execution in the cloud
|-

| Paper
| [[2015Cheng_MRC2014]]
| Extensions to MRC file format
|-

| Paper
| [[2013DeLaRosa_Scipion]]
| Scipion
|-

| Paper
| [[2016Scheres_Relion]]
| Tutorial on the use of Relion
|-

| Paper
| [[2016Grigorieff_Frealign]]
| Tutorial on the use of Frealign
|-

| Paper
| [[2017Moriya_Sphire]]
| Tutorial on the use of Sphire
|-

|}

== Electron tomography ==

=== Image preprocessing ===

{|

| Paper
| [[2015Yan_thickness]]
| Determination of thickness, tilt and electron mean free path
|-

|}

=== Image alignment ===

{|

| Paper
| [[1982Guckenberger_commonOrigin]]
| Determination of a common origin in the micrographs of titl series in three-dimensional electron microscopy
|-

| Paper
| [[1992Lawrence_leastSquares]]
| Least squares solution of the alignment problem
|-

| Paper
| [[1995Penczek_dual]]
| Dual tilt alignment
|-

| Paper
| [[1996Owen_alignmentQuality]]
| Automatic alignment without fiducial markers and evaluation of alignment quality
|-

| Paper
| [[1998Grimm_normalization]]
| Discussion of several gray level normalization methods for electron tomography
|-

| Paper
| [[2001Brandt_Automatic1]]
| Automatic alignment without fiducial markers
|-

| Paper
| [[2001Brandt_Automatic2]]
| Automatic alignment with fiducial markers
|-

| Paper
| [[2006Winkler_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2006Castano_alignment]]
| Alignment with non-perpendicularity
|-

| Paper
| [[2007Castano_alignment]]
| Fiducial-less alignment of cryo-sections
|-

| Paper
| [[2009Sorzano_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2010Cantele_dualAlignment]]
| Alignment of dual series
|-

| Paper
| [[2014Tomonaga_Automatic]]
| Automatic alignment of tilt series using the projection themselves
|-

| Paper
| [[2014Han_Automatic]]
| Automatic alignment of tilt series using SIFT features
|-

| Paper
| [[2015Han_Automatic]]
| Automatic alignment of tilt series using fiducials
|-

| Paper
| [[2017Mastronarde_Automatic]]
| Automatic alignment and reconstruction of tilt series in IMOD
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[2003Winkler_CTF]]
| Focus gradient correction in electron tomography
|-

| Paper
| [[2006Fernandez_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Zanetti_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Xiong_CTF]]
| CTF determination and correction for low dose tomographic tilt series
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2017Kunz_3DCTF]]
| 3D CTF Correction
|-

|}

=== 3D reconstruction ===

{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1992Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[1997Marabini_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2002Fernandez_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2007Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[2008Fernandez_CARP]]
| Component Averaged Row Projections (CARP)
|-

| Paper
| [[2012Herman General Superiorization]]
| Superiorization: an optimization heuristic for medical physics
|-

| Paper
| [[2012Zhang_IPET_FETR]]
| IPET and FETR, a reconstruction algorithm for single molecule tomography
|-

| Paper
| [[2013Goris_SIRT_TV_DART]]
| Combination of SIRT, Total Variation and Discrete ART to reconstruct and segment at the same time
|-

| Paper
| [[2013Briegel A_Challenge]]
| The challenge of determining handedness in electron tomography and the use of DNA origami gold nanoparticle helices as molecular standards
|-

| Paper
| [[2013Messaoudi_EnergyFiltered]]
| 3D Reconstruction of Energy-Filtered TEM
|-

| Paper
| [[2016Deng_ICON]]
| 3D Reconstruction with missing information restoration
|-

| Paper
| [[2016Guay_Compressed]]
| 3D Reconstruction using compressed sensing
|-

|}

=== Noise reduction ===
{|

| Paper
| [[2001Frangakis_NAD]]
| Noise reduction with Nonlinear Anisotropic Diffusion
|-

| Paper
| [[2003Fernandez_AND]]
| Anisotropic nonlinear diffusion for electron tomography
|-

| Paper
| [[2003Jiang_Bilateral]]
| Bilateral denoising filter in electron microscopy
|-

| Paper
| [[2005Fernandez_AND]]
| Anisotropic nonlinear denoising in electron tomography
|-

| Paper
| [[2007Heide_median]]
| Iterative median filtering in electron tomography
|-

| Paper
| [[2007Fernandez_autAND]]
| Anisotropic nonlinear diffusion with automated parameter tuning
|-

| Paper
| [[2009Fernandez_Beltrami]]
| Nonlinear filtering based on Beltrami flow
|-

| Paper
| [[2010Bilbao_MeanShift]]
| Mean Shift Filtering
|-

| Paper
| [[2014Kovacik_wedgeArtefacts]]
| Removal of wedge artefacts
|-

| Paper
| [[2014Maiorca_beadArtefacts]]
| Removal of gold bead artefacts
|-

|}

=== Segmentation ===

{|

| Paper
| [[2002Frangakis_Eigenanalysis]]
| Segmentation using eigenvector analysis.
|-

| Paper
| [[2002Volkmann_Watershed]]
| Segmentation using watershed transform.
|-

| Paper
| [[2003Bajaj_BoundarySegmentation]]
| Segmentation based on fast marching.
|-

| Paper
| [[2005Cyrklaff_Thresholding]]
| Segmentation using optimal thresholding.
|-

| Paper
| [[2007Lebbink_TemplateMatching]]
| Segmentation using template matching.
|-

| Paper
| [[2007Sandberg_OrientationFields]]
| Segmentation using orientation fields.
|-

| Paper
| [[2007Sandberg_SegmentationReview]]
| Review on segmentation in electron tomography.
|-

| Paper
| [[2008Garduno_FuzzySegmentation]]
| Segmentation using fuzzy set theory principles.
|-

| Paper
| [[2009Lebbink_TemplateMatching2]]
| Segmentation using template matching.
|-

| Paper
| [[2012RubbiyaAli_EdgeDetection]]
| Parameter-Free Segmentation of Macromolecular Structures.
|-

| Conference
| [[2015Xu_TemplateMatching]]
| Detection of macromolecular complexes with a reduced representation of the templates.
|-

|}

=== Resolution ===
{|

| Paper
| [[2005Cardone_Resolution]]
| Resolution criterion for electron tomography
|-

| Chapter
| [[2007Penczek_Resolution]]
| Review of resolution criteria for electron tomography
|-

| Paper
| [[2015Diebolder_ConicalFSC]]
| Conical Fourier Shell Correlation
|-

|}

=== Subtomogram analysis ===

{|

| Paper
| [[2000Bohm_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2002Frangakis_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2006Nickell_Review]]
| Review of macromolecule finding by template matching (Visual Proteomics)
|-

| Paper
| [[2007Best_Review]]
| Review of Localization of Protein Complexes by Pattern Recognition
|-

| Paper
| [[2007Forster_Review]]
| Review of structure determination by subtomogram averaging
|-

| Paper
| [[2008Forster_Classification]]
| Classification of subtomograms using constrained correlation
|-

| Paper
| [[2008Bartesaghi_Classification]]
| Classification and averaging of subtomograms
|-

| Paper
| [[2008Schmid_Averaging]]
| Alignment and averaging of subtomograms
|-

| Paper
| [[2010Amat_Averaging]]
| Alignment and averaging of subtomograms exploiting thresholding in Fourier space
|-

| Paper
| [[2013Chen_Averaging]]
| Fast alignment of subtomograms using spherical harmonics
|-

| Paper
| [[2013Kuybeda_Averaging]]
| Alignment and averaging of subtomograms using the nuclear norm of the cluster
|-

| Paper
| [[2013Shatsky_Averaging]]
| Alignment and averaging of subtomograms with constrained cross-correlation
|-

| Paper
| [[2014Chen_Autofocus]]
| Subtomogram averaging and classification with special attention to differences
|-

| Paper
| [[2014Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2014Voortman_LimitingFactors]]
| Limiting factors of subtomogram averaging
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2015Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2016Bharat_Relion]]
| Subtomogram averaging with Relion
|-

| Paper
| [[2016Song_MatrixNorm]]
| Matrix norm minimization for tomographic reconstruction and alignment
|-

| Paper
| [[2017Castano_ParticlePicking]]
| Particle picking in tomograms for subtomogram averaging
|-

| Paper
| [[2017Frazier_Tomominer]]
| TomoMiner a software platform for large-scale subtomogram analysis
|-

|}

=== Single particle tomography ===

{|

| Paper
| [[2012Bartesaghi_Constrained]]
| 3D reconstruction by imposing geometrical constraints
|-

| Paper
| [[2015Galaz_SingleParticleTomography]]
| Set of tools for Single Particle Tomography in EMAN2
|-

| Paper
| [[2016Galaz_SingleParticleTomography]]
| Alignment algorithms and CTF correction
|-

|}

=== Books and reviews ===

{|

| Paper
| [[2000Baumeister_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Koster_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Sali_Review]]
| Review of electron tomography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2005Lucic_Review]]
| Review of electron tomography
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_TomoBook]]
| Electron Tomography
|-

| Book
| [[2007McIntosh_Book]]
| Cellular Electron Microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2012Kudryashev_Review]]
| Review of subtomogram averaging
|-

| Paper
| [[2016Beck_Review]]
| Review of molecular sociology
|-

| Paper
| [[2017Galaz_Review]]
| Review of single particle tomography
|-

|}

=== Software ===

{|

| Paper
| [[1996Kremer_IMOD]]
| IMOD
|-

| Paper
| [[1996Chen_Priism/IVE]]
| Priism/IVE
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2005Nickell_TOM]]
| TOM Toolbox
|-

| Paper
| [[2007Messaoudi_TomoJ]]
| TomoJ
|-

| Paper
| [[2008Heymann_BsoftTomo]]
| Bsoft
|-

| Paper
| [[2015Ding_CaltechTomography]]
| Caltech tomography database
|-

| Paper
| [[2015Noble_AppionProtomo]]
| Batch fiducial-less tilt-series alignment in Appion using Protomo
|-

| Paper
| [[2015vanAarle_Astra]]
| ASTRA Toolbox
|-

| Paper
| [[2017Wan_Simulator]]
| Electron Tomography Simulator
|-

|}

== 2D Crystals ==

=== 2D Preprocessing ===

{|

| Paper
| [[1986Henderson_Processing]]
| General 2D processing
|-

| Paper
| [[2000He_PhaseAlignment]]
| Phase consistency and Alignment
|-

| Paper
| [[2006Gil_Unbending]]
| Crystal unbending
|-

|}

=== Classification ===
{|

| Paper
| [[1988Frank_Classification]]
| MSA and classification in electron crystallography
|-

| Paper
| [[1996Fernandez_SOM]]
| Classification based on self organizing maps
|-

| Paper
| [[1998Sherman_MSA]]
| Classification based on MSA
|-

|}
=== 3D Reconstruction ===

{|

| Paper
| [[1985Wang_Solvent]]
| Solvent flattening
|-

| Paper
| [[1990Henderson_Processing]]
| General 3D processing
|-

| Paper
| [[2004Marabini_ART]]
| Algebraic Reconstruction Technique with blobs for crystals (Xmipp)
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1998Walz_Review]]
| Review of 2D crystallography
|-

| Paper
| [[1999Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Ellis_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of single particles, electron tomography and crystallography
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Gipson_2dx]]
| 2dx
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Philippsen_IPLT]]
| IPLT
|-

|}

== 3D Crystals - MicroED ==

=== Sample Preparation ===
{|
| Paper
| [[2016Shi_Preparation]]
| Sample Preparation
|}
=== Data Collection ===
{|
| Paper
| [[2014Nannenga_CR]]
| Continuous rotation

|}
=== Data Processing ===
{|

| Paper
| [[2011Wisedchaisri_PhaseExtension]]
| Fragment-based phase extension
|-

| Paper
| [[2015Hattne_Processing]]
| Data Processing
|-

| Paper
| [[2016Hattne_Correction]]
| Image correction
|}

=== Software ===
{|

| Paper
| [[2014Iadanza_Processing]]
| Data Processing of still diffraction data
|}

=== Books and Reviews ===
{|
| Paper
| [[2014Nannenga_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Liu_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Rodriguez_Review ]]
| Review of MicroED
|-

|}

== Helical particles ==

=== Filament corrections ===

{|

| Paper
| [[1986Egelman_Curved]]
| Algorithm for correcting curved filaments
|-

| Paper
| [[1988Bluemke_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2006Wang_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2016Yang_Flexible]]
| Algorithm for correcting filaments with flexible subunits
|-

|}

=== Reconstruction ===

{|

| Paper
| [[1952Cochran_Fourier]]
| Fourier Bessel transform of filamentous structures
|-

| Paper
| [[1958Klug_Fourier]]
| Fourier Bessel decomposition of the projection images
|-

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2005Wang_Iterative]]
| Iterative Fourier-Bessel algorithm
|-

| Paper
| [[2007Egelman_Iterative]]
| Iterative real-space algorithm
|-

| Paper
| [[2013Desfosses_Spring]]
| Helical processing with Spring
|-

| Paper
| [[2015Zhang_seam]]
| Workflow for the detection of the lattice seam
|-

| Paper
| [[2016Rohou_Frealix]]
| Helical processing with Frealix
|-

|}

=== Validation ===

{|

| Paper
| [[2014Egelman_ambiguity]]
| How to detect incorrect models
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Carragher_Phoelix]]
| Phoelix
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Owen_Brandeis]]
| Brandeis
|-

|}

== Icosahedral particles ==

=== Reconstruction ===

{|

| Paper
| [[1970Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1971Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1996Fuller_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1997Thuman_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

|}

=== Classification ===

{|

| Paper
| [[2005Scheres_Virus]]
| Classification of virus capsids in real space
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1999Baker_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[1999Conway_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2000Thuman_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Lee_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Navaza_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2006Grunewald_Review]]
| Review of reconstruction of icosahedral viruses
|-

|}

=== Software ===

{|

| Paper
| [[1996Baker_EMPFT]]
| EMPFT
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2013Morin_Sliz SBGrid]]
| SBGrid presentation for eLife
|-

|}

== Databases ==

{|

| Paper
| [[2003Boutselakis_EMSD]]
| EMSD database
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2011Kim_CDDB]]
| Conformational Dynamics Data Bank
|-

| Paper
| [[2011Lawson_EMDB]]
| Electron Microscopy Data Bank
|-

| Paper
| [[2013Ison_EDAM]]
| EDAM, an ontology of bioinformatics operations
|-

| Paper
| [[2016Iudin_EMPIAR]]
| EMPIAR raw data database
|-

| Paper
| [[2016Patwhardan_EMDB]]
| EMDB, PDB, ...
|-

| Paper
| [[2017Patwhardan_Trends]]
| Trends at EMDB
|-

| Paper
| [[2017Shao_PDBQuality]]
| Quality metrics in PDB
|-

| Blog
| http://www.mybiosoftware.com
| Huge list of bioinformatics programs (many of them structural bioinformatics)
|-

|}

== Relationship to other structural information sources ==

{|

| Paper
| [[2000Engel_AFM]]
| Review of Atomic Force Microscopy
|-

| Paper
| [[2001Dimmeler_AFM]]
| Constraints from Atomic Force Microscopy
|-

| Paper
| [[2003Mobus_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_Review]]
| Review on correlative microscopy
|-

| Paper
| [[2005Boudier_EFTETJ]]
| Software for Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2005Vestergaard_SAXS]]
| Example of comparison of 3DEM and Small-angle X-ray scattering
|-

| Paper
| [[2007Hamada_SAXS]]
| Constraints from Small-angle X-ray scattering
|-

| Paper
| [[2013Xu_FRET]]
| EM+FRET
|-

|}

== X-ray tomography ==

{|

| Paper
| [[2012Oton_ImageFormation]]
| Image formation model in X-ray cell microscopy
|-

|}

== Mathematical tools necessary ==

== People developing methods ==
Please, add yourself to this list (due to privacy reasons, please, do not add anyone else to the list without his/her explicit consent). Sort by first name alphabetical order.

[http://biocomp.cnb.csic.es/~coss Carlos Oscar S. Sorzano]: CSIC, Madrid, Spain 

[http://www.curie.fr/recherche/themes/detail_equipe.cfm/lang/_fr/id_equipe/241.htm Cédric Messaoudi]: Institute Curie, Paris, France 

[http://scholar.google.es/citations?user=_jNYGScAAAAJ&hl=en Javier Vargas]:[mailto:jvargas@cnb.csic.es mail]: CSIC, Madrid, Spain 

[http://scholar.google.es/citations?hl=es&user=g2ZJPIYAAAAJ Joaquín Otón]: CSIC, Madrid, Spain 

[mailto:jrbcast@gmail.com José Román Bilbao-Castro]: UAL, Almería, Spain; CSIC, Madrid, Spain 

[José Miguel de la Rosa Trevín]: Biocomputing Unit CNB-CSIC, Madrid, Spain 

[http://cryoem.janelia.org Tamir Gonen]: [mailto:gonent@janelia.hhmi.org mail]: Howard Hughes Medical Institute, Ashburn, VA, USA 

[mailto:vabrishami@cnb.csic.es Vahid Abrishami]: CSIC, Madrid, Spain 

== 3DEM sites ==
* [http://3dem.ucsd.edu/ 3DEM web site]

* [http://en.wikibooks.org/wiki/Software_Tools_For_Molecular_Microscopy Software tools for molecular microscopy]

* [http://www.emdatabank.org/ The Electron Microscopy Data Bank (EMDB)]

* [http://ccdb.ucsd.edu The Cell Centered Database (CCDB)]

* [http://conventions.cnb.csic.es The geometrical software conventions web page ]

== Editing useful links ==

* [http://www.mediawiki.org/wiki/Help:Formatting Text formatting in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Links Adding links in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Images Adding images in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Tables Making tables in Mediawiki]

2017Moriya Sphire

2017-07-04T06:10:42Z

CoSS: Created page with "== Citation == Moriya, T.; Saur, M.; Stabrin, M.; Merino, F.; Voicu, H.; Huang, Z.; Penczek, P. A.; Raunser, S. & Gatsogiannis, C. High-resolution Single Particle Analysis fr..."

== Citation ==

Moriya, T.; Saur, M.; Stabrin, M.; Merino, F.; Voicu, H.; Huang, Z.; Penczek, P. A.; Raunser, S. & Gatsogiannis, C. High-resolution Single Particle Analysis from Electron Cryo-microscopy Images Using SPHIRE. Journal of visualized experiments : JoVE, 2017

== Abstract ==

SPHIRE (SPARX for High-Resolution Electron Microscopy) is a novel open-source, user-friendly software suite for the semi-automated processing of single particle electron cryo-microscopy (cryo-EM) data. The protocol presented here describes in detail how to obtain a near-atomic resolution structure starting from cryo-EM micrograph movies by guiding users through all steps of the single particle structure determination pipeline. These steps are controlled from the new SPHIRE graphical user interface and require minimum user intervention. Using this protocol, a 3.5 Å structure of TcdA1, a Tc toxin complex from Photorhabdus luminescens, was derived from only 9500 single particles. This streamlined approach will help novice users without extensive processing experience and a priori structural information, to obtain noise-free and unbiased atomic models of their purified macromolecular complexes in their native state.

== Keywords ==

== Links ==

https://www.jove.com/video/55448/high-resolution-single-particle-analysis-from-electron-cryo

== Related software ==

== Related methods ==

== Comments ==

Main Page

2017-07-04T06:09:46Z

CoSS: /* Software */

== Presentation ==

This web page is intended to be an extensive repository of three-dimensional electron microscopy (3DEM) methods. The advantages of having such a repository are

* You know which are the relevant articles in a particular topic, therefore, paper introductions, reviews, etc. are easier to write and you make sure you will cite all the related articles.
* You will be sure that your paper has more chances of being cited.
* You can add whatever information you find relevant to your method, external links, links to other papers, etc.
* You can link your method to a web page providing the corresponding software, so you know people can use your algorithms.
* You can use the Wiki search capabilities to locate relevant articles even if they are not at the topic you are looking at.
* As a community we will "reconstruct" our history.
* You can select the "watch" option above to receive notifications in case of further changes in the Main Page.

Developing image processing methods for 3DEM is not "[[well-paid]]" in terms of citations and impact factor. However, it is crucial for the advance of the field. Gathering methodological papers in a portal will help to increase the recognition of the field.

Please:

* Add your articles at the right place (you can add a single article in several topics if it is relevant to all of them). The easiest way to add an article is by editing the corresponding topic in the main page, adding your entry, then save the main page. Click on the red link that appears on your new entry, copy and paste the Wiki following code, add the information of your article

== Citation ==

== Abstract ==

== Keywords ==

== Links ==

== Related software ==

== Related methods ==

== Comments ==

* Maintain the information of each article as complete as possible.
* Sort articles by years and authors.
* Be respectful to other people's work.

== How to subscribe to this page ==

You may subscribe to this page so that you will be notified every time someone adds a new method. To do so, you have to register in the page, and edit your preferences ("my preferences"). Be sure that you have activated the option "E-mail me when a page on my watchlist is changed". Finally, click on the "Watch" tab at the top of this page.

You may subscribe to changes on this page on the mailing list 3demmethods@cnb.csic.es. To send a new method to this mail list just send a mail to 3demmethods@cnb.csic.es

To subscribe to this list, visit the web page

https://listas.csic.es/cnb/wws/subscribe/3demmethods

Alternatively, you may write a mail to sympa6@cnb.csic.es with the subject

<code>subscribe 3demmethods YourName YourFamilyName</code>

and an empty mail body.

To unsubscribe visit the page

https://listas.csic.es/cnb/wws/sigrequest/3demmethods

or write sympa6@cnb.csic.es with the subject

<code>unsubscribe 3demmethods</code>

and an empty mail body.

== Electron microscopy images ==

=== Online courses ===

CALTECH: http://cryo-em-course.caltech.edu/

MRC: ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/EM-course/

CNB-CSIC: http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/MadridJan2014EM

Workshop on Computational methods for CryoEM: https://www.youtube.com/watch?v=XdKO1iaPP8o

Workshop on Management of large CryoEM facilities: https://www.youtube.com/watch?v=as4seOPszL0

Icknield Course on Model Building and Refinement for High Resolution EM Maps: http://www.ccpem.ac.uk/training/icknield_2017/icknield_2017.php

=== Image formation ===

{|

| Paper
| [[1971Erickson_CTF]]
| CTF model
|-

| Paper
| [[1971Glaeser_Damage]]
| Radiation damage
|-

| Chapter
| [[1971Hanszen_CTF]]
| Image formation model
|-

| Paper
| [[1971Thon_Model]]
| CTF model
|-

| Paper
| [[1975Unwin_Imaging]]
| Radiation dose
|-

| Paper
| [[1977Wade_Model]]
| CTF model
|-

| Paper
| [[1978Wade_Model]]
| CTF model
|-

| Paper
| [[1979Hayward_Radiation]]
| Radiation damage
|-

| Paper
| [[1984Cohen_Validity]]
| Validity of the CTF model at high frequencies
|-

| Paper
| [[1988Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[1992Wade_Model]]
| CTF model
|-

| Paper
| [[1993Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2004Egerton_Damage]]
| Radiation damage
|-

| Paper
| [[2004Sorzano_Normalization]]
| Background noise is Gaussian
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2009Baxter_NoiseCharacterization]]
| Characterization of the different noise sources in cryo-EM
|-

| Paper
| [[2010Baker_Damage]]
| Radiation damage dependence on resolution
|-

| Paper
| [[2010Bammes_Damage]]
| Radiation damage dependence on temperature
|-

| Paper
| [[2010Gomez_Multislice]]
| Simulation of the multi slice model
|-

| Paper
| [[2010Zewail_FourDimensional]]
| Review on the use of ultrafast EM
|-

| Paper
| [[2011Bammes_CCD]]
| Performance of CCD cameras
|-

| Paper
| [[2011Glaeser_Coma]]
| Image formation model including coma
|-

| Paper
| [[2011Milazzo_DirectDetectors]]
| Evaluation of Direct Detectors
|-

| Paper
| [[2011Rullgard_ImageSimulation]]
| Accurate simulation of EM images
|-

| Paper
| [[2011Zhang LimitingFactors]]
| Limiting factor for atomic resolution in EM
|-

| Paper
| [[2012Bammes_DirectDetection]]
| Performance of Direct detectors
|-

| Paper
| [[2012Campbell_MotionCorrection]]
| Beam induced motion correction and direct detectors
|-

| Paper
| [[2012Shang_HydrationLayer]]
| Simulation of PDB volumes explicitly considering the hydration layer
|-

| Paper
| [[2013Egerton_RadiationDamage]]
| Review of TEM radiation damage and experimental ways of reducing it
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu H_Noisemodels]]
| Noise models and cryo-EM drift correction with a direct-electron camera
|-

| Paper
| [[2013Li X K2 noisemodels]]
| Influence of electron dose rate on electron counting images recorded with the K2 camera
|-

| Paper
| [[2013Vulovic_CTFApproximations]]
| When to use the different approximations performed so that a projection with linear CTF is valid
|-

| Thesis
| [[2013Vulovic_ImageFormation]]
| Ph.D. Thesis on the image formation in cryo-EM
|-

| Paper
| [[2014Danev_PhasePlate]]
| Volta potential phase plate
|-

| Paper
| [[2015Chiu_K2]]
| Characterization of K2
|-

| Paper
| [[2015Hawkes_AberrationCorrection]]
| Historical account of the development of lens corrections
|-

| Paper
| [[2015Koeck_Quadratic]]
| Limitations of the linear approximation and use of the quadratic terms
|-

| Paper
| [[2015Kuijper_FEI]]
| Description of the FEI Falcons
|-

| Paper
| [[2015Lobato_MULTEM]]
| Simulation of multislice diffraction
|-

| Paper
| [[2015McMullan_AmorphousIce]]
| Beam induced movement is caused by Brownian motion
|-

| Paper
| [[2016Koeck_ADF]]
| Simulations of Annular Dark Field TEM
|-

| Paper
| [[2017Mishyna_DNARadiation]]
| Review of radiation damage on DNA
|-

|}

=== Collection geometry ===

{|

| Chapter
| [[1980Hoppe_Wedge]]
| Missing wedge
|-

| Paper
| [[1987Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1995Penczek_Dual]]
| Dual axis tomography
|-

| Paper
| [[1997Mastronarde_Dual]]
| Dual axis tomography
|-

| Paper
| [[2003Ludtke_FocusPairs]]
| Focus pairs for single particles
|-

| Paper
| [[2005Lanzavecchia_Conical]]
| Conical tomography
|-

| Paper
| [[2005Zampighi_Conical]]
| Conical tomography
|-

| Paper
| [[2006Leschziner_OT]]
| Orthogonal Tilt
|-

| Paper
| [[2006Messaoudi_Multiple]]
| Multiple axis tomography
|-

| Paper
| [[2012Kudryashev_FocusPairs]]
| Focus pairs tomography
|-

| Paper
| [[2014Hovden_TiltFocus]]
| Combining tilt series with focus series
|-

| Paper
| [[2015Sorzano_RandomConicalTilt]]
| General formulation of Random Conical Tilt
|-

| Paper
| [[2017Hagen_DoseTomography]]
| Dose optimization for subtomogram averaging
|-

|}

=== Sample preparation ===

{|

| Paper
| [[1982Dubochet_Sample]]
| Vitreous ice
|-

| Paper
| [[1986Lepault_Sample]]
| Fast freezing
|-

| Paper
| [[1995Dubochet_Sample]]
| High-pressure freezing
|-

| Paper
| [[1995VanMarle_Sample]]
| Sample damages in resin
|-

| Paper
| [[1998Adrian_Sample]]
| Cryo negative staining
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2002Hsieh_Sample]]
| Cryofixation
|-

| Paper
| [[2004AlAmoudi_Sample]]
| CEMOVIS
|-

| Paper
| [[2008Studer_Sample]]
| Review on high pressure freezing
|-

| Paper
| [[2009Pierson_Sample]]
| Review on sample preparation for electron tomography
|-

| Paper
| [[2010Zhang_NegativeStaining]]
| Negative staining for small protein imaging
|-

| Paper
| [[2012Zhang_PositiveStaining]]
| Positive staining
|-

| Paper
| [[2014Rames_NegativeStaining]]
| Optimized negative staining
|-

| Paper
| [[2014Russo_GoldGrids]]
| Gold grids for single particles
|-

| Paper
| [[2015Cabra_Sample]]
| Review on sample preparation for single particles with videos
|-

| Paper
| [[2016Passmore_Review]]
| Tutorial chapter on sample preparation
|-

| Paper
| [[2016Razinkov_Vitrification]]
| New vitrification method
|-

| Paper
| [[2016Takizawa_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2016Thompson_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2017Arnold_BlottingFree]]
| Blotting-free preparation
|-

| Paper
| [[2017Feng_SprayingPlunging]]
| Spraying plunging
|-

| Paper
| [[2017Peitsch_Sample]]
| iMEM: Isolation of Plasma Membrane for Cryoelectron Microscopy
|-

| Paper
| [[2017Scapin_Storage]]
| Cryo storage of samples
|-

| Paper
| [[2017Schaffer_FocusedIonBeam]]
| Focused Ion Beam sample preparation for membrane proteins
|-

| Paper
| [[2017Scherr_HydrogelNanomembranes]]
| Sample preparation for membrane proteins
|-

|}

=== Automated data collection ===

{|

| Paper
| [[1992Dierksen_Automatic]]
| Automated data collection
|-

| Paper
| [[1992Koster_Automatic]]
| Automated data collection
|-

| Paper
| [[1996Fung_Automatic]]
| Automated data collection for tomography
|-

| Paper
| [[2001Zhang_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2003Ziese_Automatic]]
| Automated autofocusing
|-

| Paper
| [[2004Potter_Automatic]]
| Automated sample loading
|-

| Paper
| [[2004Zheng_Automatic]]
| Automated data collection
|-

| Paper
| [[2005Lei_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2005Suloway_Automatic]]
| Automated data collection: Leginon
|-

| Paper
| [[2007Yoshioka_RCT]]
| Automated Random Conical Tilt
|-

| Paper
| [[2011Korinek_TOM2]]
| Automated acquisition with TOM2
|-

| Paper
| [[2015Li_UCSFImage]]
| Automated acquisition with UCSFImage
|-

| Paper
| [[2016Gil_Fuzzy]]
| Real time decisions during acquisition with neuro-fuzzy method
|-

| Paper
| [[2016Liu_TiltControl]]
| Accurate control of the tilt angle for electron tomography
|-

| Paper
| [[2016Vargas_FoilHole]]
| Determination of image quality at low magnification
|-

| Paper
| [[2017Biyani_Focus]]
| Automatic processing of micrographs
|-

|}

== Single particles ==

=== Automatic particle picking ===

{|

| Paper
| [[1982VanHeel_Detection]]
| Detection of particles in micrographs
|-

| Paper
| [[2001Nicholson_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2001Zhu_Filaments]]
| Automatic identification of filaments in micrographs
|-

| Paper
| [[2004Sigworth_Detection]]
| Classical detection theory and the cryo-EM particle selection problem
|-

| Paper
| [[2004Volkmann_ParticlePicking]]
| An approach to automated particle picking from electron micrographs based on reduced representation templates
|-

| Paper
| [[2004Wong_ParticlePicking]]
| Model-based particle picking for cryo-electron microscopy
|-

| Paper
| [[2004Zhu_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2007Chen_Signature]]
| Automatic particle picking program: Signature
|-

| Paper
| [[2007Woolford_SwarmPS]]
| Automatic particle picking with several criteria, implemented in EMAN Boxer
|-

| Paper
| [[2009Sorzano_MachineLearning]]
| Automatic particle picking based on machine learning of rotational invariants
|-

| Paper
| [[2011Arbelaez_Comparison]]
| Evaluation of the performance of software for automated particle-boxing
|-

| Paper
| [[2013Abrishami_MachineLearning]]
| A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs
|-

| Paper
| [[2013Hauer_2013]]
| Automatic tilt pair detection in Random Conical Tilt
|-

| Paper
| [[2013Shatsky_ParticlePicking]]
| Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Langlois_ParticlePicking]]
| Automatic particle picking
|-

| Paper
| [[2016Vilas_AutomaticTilt]]
| Automatic identification of image pairs in untilted-tilted micrograph pairs
|-

|}

=== 2D Preprocessing ===

{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast enhancement through DPR
|-

| Paper
| [[2004Sorzano_Normalization]]
| Normalization procedures and their statistical properties.
|-

| Paper
| [[2006Sorzano_Denoising]]
| Strong denoising in wavelet space
|-

| Conference
| [[2009Sorzano_Downsampling]]
| Differences between the different downsampling schemes
|-

| Paper
| [[2012Brilot_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Campbell_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Zhao_Denoising]]
| Denoising using an invariant Fourier-Bessel eigenspace
|-

| Paper
| [[2013Norousi_Screening]]
| Screening particles to identify outliers
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu_Movies]]
| Drift correction for movies considering dark field
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Scheres_Movies]]
| Beam induced motion correction
|-

| Paper
| [[2015Abrishami_Movies]]
| Alignment of direct detection device micrographs
|-

| Paper
| [[2015Grant_Anisotropic]]
| Automatic estimation and correction of anisotropic magnification
|-

| Paper
| [[2015Grant_OptimalExposure]]
| Filter movies according to the radiation damage
|-

| Paper
| [[2015Rubinstein_Alignment]]
| Frame alignment at the level of particle
|-

| Paper
| [[2015Spear_DoseCompensation]]
| Effect of dose compensation on resolution
|-

| Paper
| [[2015Zhao_AnisotropicMagnification]]
| Correction of anisotropic magnification
|-

| Conference
| [[2016Bajic_Denoising]]
| Denoising and deconvolution of micrographs
|-

| Paper
| [[2016Jensen_RemovalVesicles]]
| Removal of vesicles in membrane proteins
|-

| Paper
| [[2016Bhamre_Denoising]]
| Denoising by 2D covariance estimation
|-

| Paper
| [[2017McLeod_Zorro]]
| Movie alignment by Zorro
|-

| Paper
| [[2017Zheng_MotionCorr2]]
| Movie alignment by MotionCorr2
|-

|}

=== 2D Alignment ===

{|

| Paper
| [[1981Frank_Averaging]]
| 2D averaging and phase residual
|-

| Paper
| [[1982Saxton_Averaging]]
| 2D averaging using correlation
|-

| Paper
| [[1998Sigworth_ML2D]]
| Maximum likelihood alignment in 2D
|-

| Paper
| [[2003Cong_FRM2D]]
| Fast Rotational Matching in 2D
|-

| Paper
| [[2005Cong_FRM2D]]
| Fast Rotational Matching in 2D introduced in a 3D Alignment algorithm
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

|}

=== 2D Classification and clustering ===

{|

| Paper
| [[1981VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[1984VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2011Singer_DiffusionMaps]]
| Classification in 2D based on graph analysis of the projections
|-

| Paper
| [[2012Yang_ISAC]]
| Iterative Stable Alignment and clustering
|-

| Paper
| [[2014Sorzano_Outlier]]
| Outlier detection in 2D classifications.
|-

| Paper
| [[2014Zhao_Aspire]]
| Fast classification based on rotational invariants and vector diffusion maps
|-

| Paper
| [[2015Huang_Robust]]
| Robust w-estimators of 2D classes
|-

| Paper
| [[2016Reboul_Stochastic]]
| Stochastic Hill Climbing for calculating 2D classes
|-

| Conference
| [[2017Bhamre_Mahalanobis]]
| 2D classification using Mahalanobis distance
|-

|}

=== 3D Alignment ===

{|

| Paper
| [[1980Kam_AutoCorrelation]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[1986Goncharov_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1987VanHeel_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1988Provencher_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Vogel_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1990Gelfand_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Goncharov_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Harauz_Quaternions]]
| Use of quaternions to represent rotations
|-

| Paper
| [[1994Penczek_Real]]
| Angular assignment using projection matching in real space
|-

| Paper
| [[1994Radermacher_Radon]]
| Angular assignment in Radon space
|-

| Paper
| [[1996Penczek_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[2003Rosenthal_DPR]]
| Angular assignment using DPR
|-

| Paper
| [[2004Sorzano_Wavelet]]
| Angular assignment in the wavelet space.
|-

| Paper
| [[2005Jonic_Splines]]
| Angular assignment in Fourier space using spline interpolation.
|-

| Paper
| [[2005Yang_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[2006Ogura_SimulatedAnnealing]]
| Angular asignment by simulated annealing
|-

| Paper
| [[2007Grigorieff_Continuous]]
| Continuous angular assignment in Fourier space
|-

| Paper
| [[2010Jaitly_Bayesian]]
| Angular assignment by a Bayesian method and annealing
|-

| Paper
| [[2010Sanz_Random]]
| Random model method
|-

| Paper
| [[2010Singer_Voting]]
| Detecting consistent common lines by voting (reference free)
|-

| Paper
| [[2011Singer_SDP]]
| Angular assignment by semidefinite programming and eigenvectors (reference free)
|-

| Paper
| [[2012Giannakis_Scattering]]
| Construction of an initial volume, reference free, by graph analysis of the projections
|-

| Paper
| [[2012Shkolnisky_Sync]]
| Angular assignment by synchronization of rotations (reference free)
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Wang_LUD]]
| Angular assignment by least unsquared deviations (reference free)
|-

| Paper
| [[2014Vargas_RANSAC]]
| Initial model using RANSAC (reference free)
|-

| Paper
| [[2015Joubert_Pseudoatoms]]
| Initial model based on pseudo-atoms
|-

| Paper
| [[2015Singer_Kam]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[2015Sorzano_Significant]]
| Statistical approach to the initial volume estimation (reconstruct significant)
|-

| Conference
| [[2016Michels_Heterogeneous]]
| Initial volume in the presence of heterogeneity
|-

| Paper
| [[2016Cossio_BayesianGPU]]
| GPU implementation of the Bayesian 3D reconstruction approach
|-

|}

=== 3D Reconstruction ===
{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1986Harauz_FBP]]
| Exact filters for Filtered Back Projection
|-

| Chapter
| [[1992Radermacher_WBP]]
| Exact filters for Weighted Back Projection
|-

| Paper
| [[1997Zhu_RecCTF]]
| 3D Reconstruction (SIRT like) and simultaneous CTF correction
|-

| Paper
| [[1998Boisset_Uneven]]
| Artifacts in SIRT and WBP under uneven angular distributions
|-

| Paper
| [[1998Marabini_ART]]
| Algebraic Reconstruction Technique with blobs (Xmipp)
|-

| Paper
| [[2001Sorzano_Uneven]]
| Free parameter selection under uneven angular distributions
|-

| Paper
| [[2005Sorzano_Parameters]]
| Free parameter selection for optimizing multiple tasks
|-

| Paper
| [[2008Sorzano_Constraints]]
| Mass, surface, positivity and symmetry constraints for real-space algorithms
|-

| Paper
| [[2009Bilbao_ParallelART]]
| Efficient parallelization of ART
|-

| Paper
| [[2011Li_GradientFlow]]
| Regularized 3D Reconstruction by Gradient Flow
|-

| Paper
| [[2011Vonesch_Wavelets]]
| Fast wavelet-based 3D reconstruction
|-

| Paper
| [[2012Gopinath_ShapeRegularization]]
| Regularized 3D Reconstruction by Shape information
|-

| Paper
| [[2012Kucukelbir_adaptiveBasis]]
| 3D reconstruction in an adaptive basis promoting sparsity
|-

| Paper
| [[2012Sindelar_NoiseReduction]]
| Optimal noise reduction in 3D reconstructions
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Lyumkis_Optimod]]
| Construction of initial volumes with Optimod
|-

| Paper
| [[2013Wang FIRM]]
| Fast 3D reconstruction in Fourier domain
|-

| Paper
| [[2014Kunz_SART_OS]]
| Simultaneous ART with OS
|-

| Paper
| [[2015Abrishami_Fourier]]
| 3D Reconstruction in Fourier space
|-

| Paper
| [[2015Dvornek_SubspaceEM]]
| Fast Maximum a posteriori
|-

| Paper
| [[2015Moriya_Bayesian]]
| Bayesian approach to suppress limited angular artifacts
|-

| Paper
| [[2015Xu_GeometricFlow]]
| Multi-scale geometric flow
|-

| Arxiv
| [[2016Ye_Cohomology]]
| Cohomology properties of 3D reconstruction
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

| Paper
| [[2017Punjani_CryoSPARCTheory]]
| Theory related to CryoSPARC
|-

|}

=== 3D Heterogeneity ===

{|

| Paper
| [[2004White_Size]]
| Heterogeneity classification of differently sized images
|-

| Paper
| [[2006Penczek_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Scheres_ML3D]]
| Maximum Likelihood alignment and classification in 3D
|-

| Paper
| [[2009Spahn_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2010Elmlund_AbInitio]]
| Solving the initial volume problem with multiple conformations
|-

| Paper
| [[2010Shatsky_MultiVariate]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2012Scheres_Bayesian]]
| A Bayesian view on cryo-EM structure determination
|-

| Paper
| [[2012Zheng_Covariance]]
| Estimation of the volume covariance
|-

| Paper
| [[2013Wang_MLVariance]]
| Maximum Likelihood estimate of the map variance
|-

| Paper
| [[2013Lyumkis D_FREALIGN]]
| Likelihood-based classification of cryo-EM images using FREALIGN.
|-

| Paper
| [[2014Jin_NMA]]
| Continuous heterogeneity through Normal Mode Analysis
|-

| Paper
| [[2014Dashti_Brownian]]
| Continuous heterogeneity through Brownian trajectories
|-

| Paper
| [[2014Chen_Migration]]
| Particle migration analysis in 3D classification
|-

| Paper
| [[2015Anden_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Bai_Focused]]
| Focused classification
|-

| Paper
| [[2015Katsevich_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Klaholz_MRA]]
| Multivariate Statistical Analysis of Jackknife and Bootstrapping on random subsets
|-

| Paper
| [[2015Liao_Covariance]]
| Estimation of the 3D covariance from 2D projections
|-

| Paper
| [[2015Tagare_Direct]]
| Direct reconstruction of PCA components
|-

| Paper
| [[2016Gong_Mechanical]]
| Mechanical model for macromolecules
|-

| Paper
| [[2016Rawson_Movement]]
| Movement and flexibility
|-

| Paper
| [[2016Sorzano_StructMap]]
| Sorting a discrete set of conformational states
|-

| Paper
| [[2016Sorzano_Strain]]
| Calculate local stretches, strains and rotations from two conformational states
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

|}

=== Validation ===

{|

| Paper
| [[2008Stagg_TestBed]]
| Effect of voltage, dosis, number of particles and Euler jumps on resolution
|-

| Paper
| [[2011Henderson]]
| Tilt Validation
|-

| Paper
| [[2011Read]]
| Validation of PDBs
|-

| Paper
| [[2012Henderson]]
| EM Map Validation
|-

| Paper
| [[2013Cossio_Bayesian]]
| EM Map Validation in a probabilistic setting
|-

| Paper
| [[2013Chen_NoiseSubstitution]]
| Noise substitution at high resolution for measuring overfitting
|-

| Paper
| [[2014Russo_StatisticalSignificance]]
| EM Map Validation through the statistical significance of the tilt-pair angular assignment
|-

| Paper
| [[2014Stagg_Reslog]]
| EM Map Validation through the resolution evolution with the number of particles
|-

| Paper
| [[2014Wasilewski_Tilt]]
| Web implementation of the tilt pair validation
|-

| Paper
| [[2015Heymann_Alignability]]
| EM Map Validation through the resolution of reconstructions from particles and noise
|-

| Paper
| [[2015Oliveira_FreqLimited]]
| Comparison of gold standard and frequency limited optimization
|-

| Paper
| [[2015Wriggers_Secondary]]
| Validation by secondary structure
|-

| Paper
| [[2016Kim_SAXS]]
| Comparison of SAXS data and EM projections
|-

| Paper
| [[2016Rosenthal_Review]]
| Review of validation methods
|-

| Paper
| [[2016Vargas_Alignability]]
| Validation by studying the tendency of an angular assignment to cluster in the projection space
|-

| Paper
| [[2017Monroe_PDBRefinement]]
| Validation by comparison to a refined PDB
|-

|}

=== Resolution ===

{|

| Paper
| [[1986Harauz_FBP]]
| Fourier Shell Correlation
|-

| Paper
| [[1987Unser_SSNR]]
| 2D Spectral Signal to Noise Ratio
|-

| Paper
| [[2002Penczek_SSNR]]
| 3D Spectral Signal to Noise Ratio for Fourier based algorithms
|-

| Paper
| [[2003Rosenthal_DPR]]
| Review of the FSC and establishment of a new threshold
|-

| Paper
| [[2005Unser_SSNR]]
| 3D Spectral Signal to Noise Ratio for any kind of algorithms
|-

| Paper
| [[2005VanHeel_FSC]]
| Establishment of a new threshold for FSC
|-

| Paper
| [[2007Sousa_AbInitio]]
| Resolution measurement on neighbour Fourier voxels
|-

| Paper
| [[2014Kucukelbir_Local]]
| Quantifying the local resolution of cryo-EM density maps
|-

| Paper
| [[2016Pintilie_Probabilistic]]
| Probabilistic models and resolution
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Statistical properties of resolution measures defined in Fourier space
|-

|}

=== Sharpening of high resolution information ===
{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast restoration and map sharpening
|-

| Paper
| [[2008Fernandez_Bfactor]]
| Bfactor determination and restoration
|-

| Paper
| [[2013Fiddy_SaxtonAlgorithm]]
| Phase retrieval or extension
|-

| Paper
| [[2014Kishchenko_SphericalDeconvolution]]
| Spherical deconvolution
|-

| Paper
| [[2015Spiegel_VISDEM]]
| Visualization improvement by the use of pseudoatomic profiles
|-

| Paper
| [[2016Jonic_Pseudoatoms]]
| Approximation with pseudoatoms
|-

| Paper
| [[2016Jonic_Denoising]]
| Denoising and high-frequency boosting by pseudoatom approximation
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[1982Schiske_Correction]]
| CTF correction for tilted objects
|-

| Paper
| [[1988Toyoshima_Model]]
| CTF estimation
|-

| Paper
| [[1995Frank_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1996Skoglund_MaxEnt]]
| CTF correction with Maximum Entropy
|-

| Paper
| [[1996Zhou_Model]]
| CTF model and user interface for manual fitting
|-

| Paper
| [[1997Fernandez_AR]]
| PSD estimation using periodogram averaging and AR models
|-

| Paper
| [[1997Penczek_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1997Stark_Deconvolution]]
| CTF correction using deconvolution
|-

| Paper
| [[1997Zhu_RecCTF]]
| CTF correction and reconstruction
|-

| Paper
| [[2000DeRosier_EwaldCorrection]]
| CTF correction considering the Ewald sphere
|-

| Paper
| [[2000Jensen_TiltedCorrection]]
| CTF correction considering tilt in backprojection
|-

| Paper
| [[2001Saad_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Huang_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Mindell_CTFTILT]]
| CTF estimation for tilted micrographs
|-

| Paper
| [[2003Sander_MSA]]
| CTF estimation through MSA classification of PSDs
|-

| Paper
| [[2003Velazquez_ARMA]]
| PSD and CTF estimation using ARMA models
|-

| Paper
| [[2004Sorzano_IDR]]
| CTF restoration and reconstruction with Iterative Data Refinement
|-

| Conference
| [[2004Wan_CTF]]
| Spatially variant CTF
|-

| Paper
| [[2004Zubelli_Chahine]]
| CTF restoration and reconstruction with Chahine's multiplicative method
|-

| Conference
| [[2005Dubowy_SpaceVariant]]
| CTF correction when this is space variant
|-

| Paper
| [[2005Mallick_ACE]]
| CTF estimation
|-

| Paper
| [[2006Wolf_Ewald]]
| CTF correction considering Ewald sphere
|-

| Paper
| [[2007Jonic_EnhancedPSD]]
| PSD enhancement for better identification of Thon rings; Vitreous ice diffracts in Thon rings
|-

| Paper
| [[2007Philippsen_Model]]
| CTF Model for tilted specimens
|-

| Paper
| [[2007Sorzano_CTF]]
| CTF estimation using enhanced PSDs
|-

| Paper
| [[2009Sorzano_Sensitivity]]
| Error sensitivity of the CTF models, non-uniqueness of the CTF parameters
|-

| Paper
| [[2010Jiang2010_CTFCorrection]]
| Amplitude correction method
|-

| Paper
| [[2010Kasantsev_CTFCorrection]]
| Mathematical foundations of Kornberg and Jensen method
|-

| Paper
| [[2010Leong_CTFCorrection]]
| Correction for spatially variant CTF
|-

| Paper
| [[2011Glaeser_Coma]]
| The effect of coma at high-resolution
|-

| Paper
| [[2011Mariani_Tilted]]
| CTF simulation and correction of tilted specimens
|-

| Paper
| [[2011Sindelar_Wiener]]
| CTF correction using a modified version of Wiener filter
|-

| Paper
| [[2011Voortman_Tilted]]
| CTF correction for tilted specimen
|-

| Paper
| [[2012Voortman_VaryingCTF]]
| Correcting a spatially varying CTF
|-

| Paper
| [[2013Vargas_FastDef]]
| Fast defocus
|-

| Paper
| [[2015Rohou_CTFFind4]]
| CTF Find 4
|-

| Paper
| [[2015Sheth_CTFquality]]
| Visualization and quality assessment of CTF
|-

| Paper
| [[2016Zhang_GCTF]]
| gCTF
|-

|}

=== Segmentation ===

{|

| Paper
| [[2006Baker_segmentation]]
| Segmentation of molecular subunits
|-

|}

=== Fitting and docking ===

{|

| Paper
| [[1999Volkmann_Fitting]]
| Fitting in real space
|-

| Paper
| [[2001Baker_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2001Jones_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2003Kovacs_FRM3D]]
| Fast Rotational Alignment of two EM maps
|-

| Paper
| [[2004Tama_NMA1]]
| Flexible fitting with Normal Modes (I)
|-

| Paper
| [[2004Tama_NMA2]]
| Flexible fitting with Normal Modes (II)
|-

| Paper
| [[2005Velazquez_Superfamilies]]
| Recognition of the superfamily folding in medium-high resolution volumes
|-

| Paper
| [[2007DeVries_Haddock]]
| Docking with Haddock 2.0
|-

| Paper
| [[2007Kleywegt_QualityControl]]
| Quality control and validation of fitting
|-

| Paper
| [[2012Biswas_Secondary]]
| Secondary structure determination in EM volumes
|-

| Paper
| [[2012Velazquez_Constraints]]
| Multicomponent fitting by using constraints from other information sources
|-

| Paper
| [[2013Chapman MS_Atomicmodeling]]
| Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters
|-

| Paper
| [[2013Esquivel_Modelling]]
| Review on modelling (secondary structure, fitting, ...)
|-

| Paper
| [[2013Lopez_Imodfit]]
| Fitting based on vibrational analysis
|-

| Paper
| [[2013Nogales_3DEMLoupe]]
| Normal Mode Analysis of reconstructed volumes
|-

| Paper
| [[2014AlNasr_Secondary]]
| Identification of secondary structure elements in EM volumes
|-

| Paper
| [[2014Politis_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Rey_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Villa_Review]]
| Review of atomic fitting into EM volumes
|-

| Paper
| [[2015Barad_EMRinger]]
| Validation of hybrid models
|-

| Paper
| [[2015Bettadapura_PF2Fit]]
| Fast rigid fitting of PDBs into EM maps
|-

| Paper
| [[2015Carrillo_CapsidMaps]]
| Analysis of virus capsids using Google Maps
|-

| Paper
| [[2015Schroeder_Hybrid]]
| Review on model building
|-

| Paper
| [[2015Tamo_Dynamics]]
| Dynamics in integrative modeling
|-

| Paper
| [[2015Sorzano_AtomsToVoxels]]
| Accurate conversion of an atomic model into a voxel density volume
|-

| Paper
| [[2016Joseph_Evolution]]
| Evolutionary constraints for the fitting of atomic models into density maps
|-

| Paper
| [[2016Segura_3Diana]]
| Validation of hybrid models
|-

| Paper
| [[2016Singharoy_MDFF]]
| Construction of hybrid models driven by EM density and molecular dynamics
|-

| Paper
| [[2016Wang_Rosetta]]
| Construction of hybrid models driven by EM density using Rosetta
|-

| Paper
| [[2017Joseph_Metrics]]
| Metrics analysis for the comparison of structures
|-

| Paper
| [[2017Hryc_WeightedAtoms]]
| Construction of hybrid models by locally weighting the different atoms
|-

| Paper
| [[2017Matsumoto_Distribution]]
| Estimating the distribution of conformations of atomic models
|-

| Paper
| [[2017Miyashita_EnsembleFitting]]
| Ensemble fitting using Molecular Dynamics
|-

|}

=== Books and reviews ===

{|

| Book
| [[1980Herman_Tomography]]
| General book on tomography
|-

| Book
| [[1988Kak_Tomography]]
| General book on tomography
|-

| Paper
| [[2000Tao_Review]]
| Review of single particles
|-

| Paper
| [[2000VanHeel_Review]]
| Review of single particles
|-

| Paper
| [[2002Frank_Review]]
| Review of single particles
|-

| Paper
| [[2002Schmid_Review]]
| Review of single particles
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2004Subramaniam_Review]]
| Review of single particles
|-

| Paper
| [[2005Steven_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_book]]
| Book covering all aspects of electron microscopy of single particles
|-

| Paper
| [[2006Sorzano_Review]]
| Review of optimization problems in electron microscopy
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems in Electron Tomography
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2008Mueller_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2008Taylor_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2010DeRosier_Review]]
| Personal account of how 3DEM developed in the early days
|-

| Chapter
| [[2012Sorzano_Review]]
| Review of single particle analysis using Xmipp
|-

| Chapter
| [[2012Devaux_Protocol]]
| Protocols for performing single particle analysis
|-

| Paper
| [[2014Bai_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Carazo_Review]]
| Review of the reconstruction process
|-

| Paper
| [[2015Cheng_Review]]
| A primer to Single Particle Cryo-EM
|-

| Paper
| [[2015Cheng_Reviewb]]
| Single Particle Cryo-EM at crystallographic resolution
|-

| Paper
| [[2015Elmlund_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Henderson_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Nogales_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Schroeder_Review]]
| Review of advances in the electron microscope
|-

| Paper
| [[2015Wu_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Carroni_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Egelman_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Eisenstein_CryoEM]]
| News feature on the Method of the Year
|-

| Paper
| [[2016FernandezLeiro_Review]]
| Review of EM
|-

| Paper
| [[2016Glaeser_HowGood]]
| How good can cryo-EM become?
|-

| Paper
| [[2016Jonic_PseudoAtoms]]
| Review of the applications of the use of pseudoatoms in EM
|-

| Chapter
| [[2016Mio_Review]]
| Overview of the process to obtain EM reconstructions
|-

| Paper
| [[2016Jonic_Review]]
| A review of computational ways to handle heterogeneity
|-

| Paper
| [[2016Nogales_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Subramaniam_Review]]
| Why cryo-EM is now suitable for crystallographic journals
|-

| Paper
| [[2016Vinothkumar_Review]]
| Historical review and current limitations
|-

| Paper
| [[2017Frank_Review]]
| Historical review of EM
|-

| Paper
| [[2017Jonic_Review]]
| Review of computational methods to analyze conformational variability
|-

| Paper
| [[2017Rawson_Limitations]]
| Limitations of EM for drug design
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Review of statistical properties of resolution measures defined in Fourier space
|-
|}

=== Software ===

{|

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[1999Lutdke_Eman]]
| Eman
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Baldwin_AngularTransformations]]
| The Transform Class in SPARX and EMAN2
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Grigorieff_Frealign]]
| Frealign
|-

| Paper
| [[2008Scheres_XmippProtocols]]
| Xmipp Protocols
|-

| Paper
| [[2008Shaikh_SpiderProtocols]]
| Spider Protocols
|-

| Paper
| [[2012Wriggers_SitusConventions]]
| Conventions and workflows in Situs
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2015Cianfrocco_Cloud]]
| Software execution in the cloud
|-

| Paper
| [[2015Cheng_MRC2014]]
| Extensions to MRC file format
|-

| Paper
| [[2013DeLaRosa_Scipion]]
| Scipion
|-

| Paper
| [[2016Scheres_Relion]]
| Tutorial on the use of Relion
|-

| Paper
| [[2016Grigorieff_Frealign]]
| Tutorial on the use of Frealign
|-

| Paper
| [[2017Moriya_Sphire]]
| Tutorial on the use of Sphire
|-

|}

== Electron tomography ==

=== Image preprocessing ===

{|

| Paper
| [[2015Yan_thickness]]
| Determination of thickness, tilt and electron mean free path
|-

|}

=== Image alignment ===

{|

| Paper
| [[1982Guckenberger_commonOrigin]]
| Determination of a common origin in the micrographs of titl series in three-dimensional electron microscopy
|-

| Paper
| [[1992Lawrence_leastSquares]]
| Least squares solution of the alignment problem
|-

| Paper
| [[1995Penczek_dual]]
| Dual tilt alignment
|-

| Paper
| [[1996Owen_alignmentQuality]]
| Automatic alignment without fiducial markers and evaluation of alignment quality
|-

| Paper
| [[1998Grimm_normalization]]
| Discussion of several gray level normalization methods for electron tomography
|-

| Paper
| [[2001Brandt_Automatic1]]
| Automatic alignment without fiducial markers
|-

| Paper
| [[2001Brandt_Automatic2]]
| Automatic alignment with fiducial markers
|-

| Paper
| [[2006Winkler_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2006Castano_alignment]]
| Alignment with non-perpendicularity
|-

| Paper
| [[2007Castano_alignment]]
| Fiducial-less alignment of cryo-sections
|-

| Paper
| [[2009Sorzano_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2010Cantele_dualAlignment]]
| Alignment of dual series
|-

| Paper
| [[2014Tomonaga_Automatic]]
| Automatic alignment of tilt series using the projection themselves
|-

| Paper
| [[2014Han_Automatic]]
| Automatic alignment of tilt series using SIFT features
|-

| Paper
| [[2015Han_Automatic]]
| Automatic alignment of tilt series using fiducials
|-

| Paper
| [[2017Mastronarde_Automatic]]
| Automatic alignment and reconstruction of tilt series in IMOD
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[2003Winkler_CTF]]
| Focus gradient correction in electron tomography
|-

| Paper
| [[2006Fernandez_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Zanetti_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Xiong_CTF]]
| CTF determination and correction for low dose tomographic tilt series
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2017Kunz_3DCTF]]
| 3D CTF Correction
|-

|}

=== 3D reconstruction ===

{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1992Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[1997Marabini_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2002Fernandez_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2007Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[2008Fernandez_CARP]]
| Component Averaged Row Projections (CARP)
|-

| Paper
| [[2012Herman General Superiorization]]
| Superiorization: an optimization heuristic for medical physics
|-

| Paper
| [[2012Zhang_IPET_FETR]]
| IPET and FETR, a reconstruction algorithm for single molecule tomography
|-

| Paper
| [[2013Goris_SIRT_TV_DART]]
| Combination of SIRT, Total Variation and Discrete ART to reconstruct and segment at the same time
|-

| Paper
| [[2013Briegel A_Challenge]]
| The challenge of determining handedness in electron tomography and the use of DNA origami gold nanoparticle helices as molecular standards
|-

| Paper
| [[2013Messaoudi_EnergyFiltered]]
| 3D Reconstruction of Energy-Filtered TEM
|-

| Paper
| [[2016Deng_ICON]]
| 3D Reconstruction with missing information restoration
|-

| Paper
| [[2016Guay_Compressed]]
| 3D Reconstruction using compressed sensing
|-

|}

=== Noise reduction ===
{|

| Paper
| [[2001Frangakis_NAD]]
| Noise reduction with Nonlinear Anisotropic Diffusion
|-

| Paper
| [[2003Fernandez_AND]]
| Anisotropic nonlinear diffusion for electron tomography
|-

| Paper
| [[2003Jiang_Bilateral]]
| Bilateral denoising filter in electron microscopy
|-

| Paper
| [[2005Fernandez_AND]]
| Anisotropic nonlinear denoising in electron tomography
|-

| Paper
| [[2007Heide_median]]
| Iterative median filtering in electron tomography
|-

| Paper
| [[2007Fernandez_autAND]]
| Anisotropic nonlinear diffusion with automated parameter tuning
|-

| Paper
| [[2009Fernandez_Beltrami]]
| Nonlinear filtering based on Beltrami flow
|-

| Paper
| [[2010Bilbao_MeanShift]]
| Mean Shift Filtering
|-

| Paper
| [[2014Kovacik_wedgeArtefacts]]
| Removal of wedge artefacts
|-

| Paper
| [[2014Maiorca_beadArtefacts]]
| Removal of gold bead artefacts
|-

|}

=== Segmentation ===

{|

| Paper
| [[2002Frangakis_Eigenanalysis]]
| Segmentation using eigenvector analysis.
|-

| Paper
| [[2002Volkmann_Watershed]]
| Segmentation using watershed transform.
|-

| Paper
| [[2003Bajaj_BoundarySegmentation]]
| Segmentation based on fast marching.
|-

| Paper
| [[2005Cyrklaff_Thresholding]]
| Segmentation using optimal thresholding.
|-

| Paper
| [[2007Lebbink_TemplateMatching]]
| Segmentation using template matching.
|-

| Paper
| [[2007Sandberg_OrientationFields]]
| Segmentation using orientation fields.
|-

| Paper
| [[2007Sandberg_SegmentationReview]]
| Review on segmentation in electron tomography.
|-

| Paper
| [[2008Garduno_FuzzySegmentation]]
| Segmentation using fuzzy set theory principles.
|-

| Paper
| [[2009Lebbink_TemplateMatching2]]
| Segmentation using template matching.
|-

| Paper
| [[2012RubbiyaAli_EdgeDetection]]
| Parameter-Free Segmentation of Macromolecular Structures.
|-

| Conference
| [[2015Xu_TemplateMatching]]
| Detection of macromolecular complexes with a reduced representation of the templates.
|-

|}

=== Resolution ===
{|

| Paper
| [[2005Cardone_Resolution]]
| Resolution criterion for electron tomography
|-

| Chapter
| [[2007Penczek_Resolution]]
| Review of resolution criteria for electron tomography
|-

| Paper
| [[2015Diebolder_ConicalFSC]]
| Conical Fourier Shell Correlation
|-

|}

=== Subtomogram analysis ===

{|

| Paper
| [[2000Bohm_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2002Frangakis_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2006Nickell_Review]]
| Review of macromolecule finding by template matching (Visual Proteomics)
|-

| Paper
| [[2007Best_Review]]
| Review of Localization of Protein Complexes by Pattern Recognition
|-

| Paper
| [[2007Forster_Review]]
| Review of structure determination by subtomogram averaging
|-

| Paper
| [[2008Forster_Classification]]
| Classification of subtomograms using constrained correlation
|-

| Paper
| [[2008Bartesaghi_Classification]]
| Classification and averaging of subtomograms
|-

| Paper
| [[2008Schmid_Averaging]]
| Alignment and averaging of subtomograms
|-

| Paper
| [[2010Amat_Averaging]]
| Alignment and averaging of subtomograms exploiting thresholding in Fourier space
|-

| Paper
| [[2013Chen_Averaging]]
| Fast alignment of subtomograms using spherical harmonics
|-

| Paper
| [[2013Kuybeda_Averaging]]
| Alignment and averaging of subtomograms using the nuclear norm of the cluster
|-

| Paper
| [[2013Shatsky_Averaging]]
| Alignment and averaging of subtomograms with constrained cross-correlation
|-

| Paper
| [[2014Chen_Autofocus]]
| Subtomogram averaging and classification with special attention to differences
|-

| Paper
| [[2014Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2014Voortman_LimitingFactors]]
| Limiting factors of subtomogram averaging
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2015Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2016Bharat_Relion]]
| Subtomogram averaging with Relion
|-

| Paper
| [[2016Song_MatrixNorm]]
| Matrix norm minimization for tomographic reconstruction and alignment
|-

| Paper
| [[2017Castano_ParticlePicking]]
| Particle picking in tomograms for subtomogram averaging
|-

| Paper
| [[2017Frazier_Tomominer]]
| TomoMiner a software platform for large-scale subtomogram analysis
|-

|}

=== Single particle tomography ===

{|

| Paper
| [[2012Bartesaghi_Constrained]]
| 3D reconstruction by imposing geometrical constraints
|-

| Paper
| [[2015Galaz_SingleParticleTomography]]
| Set of tools for Single Particle Tomography in EMAN2
|-

| Paper
| [[2016Galaz_SingleParticleTomography]]
| Alignment algorithms and CTF correction
|-

|}

=== Books and reviews ===

{|

| Paper
| [[2000Baumeister_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Koster_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Sali_Review]]
| Review of electron tomography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2005Lucic_Review]]
| Review of electron tomography
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_TomoBook]]
| Electron Tomography
|-

| Book
| [[2007McIntosh_Book]]
| Cellular Electron Microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2012Kudryashev_Review]]
| Review of subtomogram averaging
|-

| Paper
| [[2016Beck_Review]]
| Review of molecular sociology
|-

| Paper
| [[2017Galaz_Review]]
| Review of single particle tomography
|-

|}

=== Software ===

{|

| Paper
| [[1996Kremer_IMOD]]
| IMOD
|-

| Paper
| [[1996Chen_Priism/IVE]]
| Priism/IVE
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2005Nickell_TOM]]
| TOM Toolbox
|-

| Paper
| [[2007Messaoudi_TomoJ]]
| TomoJ
|-

| Paper
| [[2008Heymann_BsoftTomo]]
| Bsoft
|-

| Paper
| [[2015Ding_CaltechTomography]]
| Caltech tomography database
|-

| Paper
| [[2015Noble_AppionProtomo]]
| Batch fiducial-less tilt-series alignment in Appion using Protomo
|-

| Paper
| [[2015vanAarle_Astra]]
| ASTRA Toolbox
|-

| Paper
| [[2017Wan_Simulator]]
| Electron Tomography Simulator
|-

|}

== 2D Crystals ==

=== 2D Preprocessing ===

{|

| Paper
| [[1986Henderson_Processing]]
| General 2D processing
|-

| Paper
| [[2000He_PhaseAlignment]]
| Phase consistency and Alignment
|-

| Paper
| [[2006Gil_Unbending]]
| Crystal unbending
|-

|}

=== Classification ===
{|

| Paper
| [[1988Frank_Classification]]
| MSA and classification in electron crystallography
|-

| Paper
| [[1996Fernandez_SOM]]
| Classification based on self organizing maps
|-

| Paper
| [[1998Sherman_MSA]]
| Classification based on MSA
|-

|}
=== 3D Reconstruction ===

{|

| Paper
| [[1985Wang_Solvent]]
| Solvent flattening
|-

| Paper
| [[1990Henderson_Processing]]
| General 3D processing
|-

| Paper
| [[2004Marabini_ART]]
| Algebraic Reconstruction Technique with blobs for crystals (Xmipp)
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1998Walz_Review]]
| Review of 2D crystallography
|-

| Paper
| [[1999Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Ellis_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of single particles, electron tomography and crystallography
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Gipson_2dx]]
| 2dx
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Philippsen_IPLT]]
| IPLT
|-

|}

== 3D Crystals - MicroED ==

=== Sample Preparation ===
{|
| Paper
| [[2016Shi_Preparation]]
| Sample Preparation
|}
=== Data Collection ===
{|
| Paper
| [[2014Nannenga_CR]]
| Continuous rotation

|}
=== Data Processing ===
{|

| Paper
| [[2011Wisedchaisri_PhaseExtension]]
| Fragment-based phase extension
|-

| Paper
| [[2015Hattne_Processing]]
| Data Processing
|-

| Paper
| [[2016Hattne_Correction]]
| Image correction
|}

=== Software ===
{|

| Paper
| [[2014Iadanza_Processing]]
| Data Processing of still diffraction data
|}

=== Books and Reviews ===
{|
| Paper
| [[2014Nannenga_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Liu_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Rodriguez_Review ]]
| Review of MicroED
|-

|}

== Helical particles ==

=== Filament corrections ===

{|

| Paper
| [[1986Egelman_Curved]]
| Algorithm for correcting curved filaments
|-

| Paper
| [[1988Bluemke_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2006Wang_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2016Yang_Flexible]]
| Algorithm for correcting filaments with flexible subunits
|-

|}

=== Reconstruction ===

{|

| Paper
| [[1952Cochran_Fourier]]
| Fourier Bessel transform of filamentous structures
|-

| Paper
| [[1958Klug_Fourier]]
| Fourier Bessel decomposition of the projection images
|-

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2005Wang_Iterative]]
| Iterative Fourier-Bessel algorithm
|-

| Paper
| [[2007Egelman_Iterative]]
| Iterative real-space algorithm
|-

| Paper
| [[2013Desfosses_Spring]]
| Helical processing with Spring
|-

| Paper
| [[2015Zhang_seam]]
| Workflow for the detection of the lattice seam
|-

| Paper
| [[2016Rohou_Frealix]]
| Helical processing with Frealix
|-

|}

=== Validation ===

{|

| Paper
| [[2014Egelman_ambiguity]]
| How to detect incorrect models
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Carragher_Phoelix]]
| Phoelix
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Owen_Brandeis]]
| Brandeis
|-

|}

== Icosahedral particles ==

=== Reconstruction ===

{|

| Paper
| [[1970Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1971Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1996Fuller_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1997Thuman_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

|}

=== Classification ===

{|

| Paper
| [[2005Scheres_Virus]]
| Classification of virus capsids in real space
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1999Baker_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[1999Conway_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2000Thuman_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Lee_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Navaza_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2006Grunewald_Review]]
| Review of reconstruction of icosahedral viruses
|-

|}

=== Software ===

{|

| Paper
| [[1996Baker_EMPFT]]
| EMPFT
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2013Morin_Sliz SBGrid]]
| SBGrid presentation for eLife
|-

|}

== Databases ==

{|

| Paper
| [[2003Boutselakis_EMSD]]
| EMSD database
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2011Kim_CDDB]]
| Conformational Dynamics Data Bank
|-

| Paper
| [[2011Lawson_EMDB]]
| Electron Microscopy Data Bank
|-

| Paper
| [[2013Ison_EDAM]]
| EDAM, an ontology of bioinformatics operations
|-

| Paper
| [[2016Iudin_EMPIAR]]
| EMPIAR raw data database
|-

| Paper
| [[2016Patwhardan_EMDB]]
| EMDB, PDB, ...
|-

| Paper
| [[2017Patwhardan_Trends]]
| Trends at EMDB
|-

| Paper
| [[2017Shao_PDBQuality]]
| Quality metrics in PDB
|-

| Blog
| http://www.mybiosoftware.com
| Huge list of bioinformatics programs (many of them structural bioinformatics)
|-

|}

== Relationship to other structural information sources ==

{|

| Paper
| [[2000Engel_AFM]]
| Review of Atomic Force Microscopy
|-

| Paper
| [[2001Dimmeler_AFM]]
| Constraints from Atomic Force Microscopy
|-

| Paper
| [[2003Mobus_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_Review]]
| Review on correlative microscopy
|-

| Paper
| [[2005Boudier_EFTETJ]]
| Software for Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2005Vestergaard_SAXS]]
| Example of comparison of 3DEM and Small-angle X-ray scattering
|-

| Paper
| [[2007Hamada_SAXS]]
| Constraints from Small-angle X-ray scattering
|-

| Paper
| [[2013Xu_FRET]]
| EM+FRET
|-

|}

== X-ray tomography ==

{|

| Paper
| [[2012Oton_ImageFormation]]
| Image formation model in X-ray cell microscopy
|-

|}

== Mathematical tools necessary ==

== People developing methods ==
Please, add yourself to this list (due to privacy reasons, please, do not add anyone else to the list without his/her explicit consent). Sort by first name alphabetical order.

[http://biocomp.cnb.csic.es/~coss Carlos Oscar S. Sorzano]: CSIC, Madrid, Spain 

[http://www.curie.fr/recherche/themes/detail_equipe.cfm/lang/_fr/id_equipe/241.htm Cédric Messaoudi]: Institute Curie, Paris, France 

[http://scholar.google.es/citations?user=_jNYGScAAAAJ&hl=en Javier Vargas]:[mailto:jvargas@cnb.csic.es mail]: CSIC, Madrid, Spain 

[http://scholar.google.es/citations?hl=es&user=g2ZJPIYAAAAJ Joaquín Otón]: CSIC, Madrid, Spain 

[mailto:jrbcast@gmail.com José Román Bilbao-Castro]: UAL, Almería, Spain; CSIC, Madrid, Spain 

[José Miguel de la Rosa Trevín]: Biocomputing Unit CNB-CSIC, Madrid, Spain 

[http://cryoem.janelia.org Tamir Gonen]: [mailto:gonent@janelia.hhmi.org mail]: Howard Hughes Medical Institute, Ashburn, VA, USA 

[mailto:vabrishami@cnb.csic.es Vahid Abrishami]: CSIC, Madrid, Spain 

== 3DEM sites ==
* [http://3dem.ucsd.edu/ 3DEM web site]

* [http://en.wikibooks.org/wiki/Software_Tools_For_Molecular_Microscopy Software tools for molecular microscopy]

* [http://www.emdatabank.org/ The Electron Microscopy Data Bank (EMDB)]

* [http://ccdb.ucsd.edu The Cell Centered Database (CCDB)]

* [http://conventions.cnb.csic.es The geometrical software conventions web page ]

== Editing useful links ==

* [http://www.mediawiki.org/wiki/Help:Formatting Text formatting in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Links Adding links in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Images Adding images in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Tables Making tables in Mediawiki]

2017Galaz Review

2017-07-04T06:07:33Z

CoSS: Created page with "== Citation == Galaz-Montoya, J. G. & Ludtke, S. J. The advent of structural biology in situ by single particle cryo-electron tomography Biophysics Reports, Springer, 2017, 1..."

== Citation ==

Galaz-Montoya, J. G. & Ludtke, S. J. The advent of structural biology in situ by single particle cryo-electron tomography Biophysics Reports, Springer, 2017, 1-19

== Abstract ==

Single particle tomography (SPT), also known as subtomogram averaging, is a powerful technique uniquely poised to address questions in structural biology that are not amenable to more traditional approaches like X-ray crystallography, nuclear magnetic resonance, and conventional cryoEM single particle analysis. Owing to its potential for in situ structural biology at subnanometer resolution, SPT has been gaining enormous momentum in the last five years and is becoming a prominent, widely used technique. This method can be applied to unambiguously determine the structures of macromolecular complexes that exhibit compositional and conformational heterogeneity, both in vitro and in situ. Here we review the development of SPT, highlighting its applications and identifying areas of ongoing development.

== Keywords ==

== Links ==

https://link.springer.com/article/10.1007/s41048-017-0040-0

== Related software ==

== Related methods ==

== Comments ==

Main Page

2017-07-04T06:06:50Z

CoSS: /* Books and reviews */

== Presentation ==

This web page is intended to be an extensive repository of three-dimensional electron microscopy (3DEM) methods. The advantages of having such a repository are

* You know which are the relevant articles in a particular topic, therefore, paper introductions, reviews, etc. are easier to write and you make sure you will cite all the related articles.
* You will be sure that your paper has more chances of being cited.
* You can add whatever information you find relevant to your method, external links, links to other papers, etc.
* You can link your method to a web page providing the corresponding software, so you know people can use your algorithms.
* You can use the Wiki search capabilities to locate relevant articles even if they are not at the topic you are looking at.
* As a community we will "reconstruct" our history.
* You can select the "watch" option above to receive notifications in case of further changes in the Main Page.

Developing image processing methods for 3DEM is not "[[well-paid]]" in terms of citations and impact factor. However, it is crucial for the advance of the field. Gathering methodological papers in a portal will help to increase the recognition of the field.

Please:

* Add your articles at the right place (you can add a single article in several topics if it is relevant to all of them). The easiest way to add an article is by editing the corresponding topic in the main page, adding your entry, then save the main page. Click on the red link that appears on your new entry, copy and paste the Wiki following code, add the information of your article

== Citation ==

== Abstract ==

== Keywords ==

== Links ==

== Related software ==

== Related methods ==

== Comments ==

* Maintain the information of each article as complete as possible.
* Sort articles by years and authors.
* Be respectful to other people's work.

== How to subscribe to this page ==

You may subscribe to this page so that you will be notified every time someone adds a new method. To do so, you have to register in the page, and edit your preferences ("my preferences"). Be sure that you have activated the option "E-mail me when a page on my watchlist is changed". Finally, click on the "Watch" tab at the top of this page.

You may subscribe to changes on this page on the mailing list 3demmethods@cnb.csic.es. To send a new method to this mail list just send a mail to 3demmethods@cnb.csic.es

To subscribe to this list, visit the web page

https://listas.csic.es/cnb/wws/subscribe/3demmethods

Alternatively, you may write a mail to sympa6@cnb.csic.es with the subject

<code>subscribe 3demmethods YourName YourFamilyName</code>

and an empty mail body.

To unsubscribe visit the page

https://listas.csic.es/cnb/wws/sigrequest/3demmethods

or write sympa6@cnb.csic.es with the subject

<code>unsubscribe 3demmethods</code>

and an empty mail body.

== Electron microscopy images ==

=== Online courses ===

CALTECH: http://cryo-em-course.caltech.edu/

MRC: ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/EM-course/

CNB-CSIC: http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/MadridJan2014EM

Workshop on Computational methods for CryoEM: https://www.youtube.com/watch?v=XdKO1iaPP8o

Workshop on Management of large CryoEM facilities: https://www.youtube.com/watch?v=as4seOPszL0

Icknield Course on Model Building and Refinement for High Resolution EM Maps: http://www.ccpem.ac.uk/training/icknield_2017/icknield_2017.php

=== Image formation ===

{|

| Paper
| [[1971Erickson_CTF]]
| CTF model
|-

| Paper
| [[1971Glaeser_Damage]]
| Radiation damage
|-

| Chapter
| [[1971Hanszen_CTF]]
| Image formation model
|-

| Paper
| [[1971Thon_Model]]
| CTF model
|-

| Paper
| [[1975Unwin_Imaging]]
| Radiation dose
|-

| Paper
| [[1977Wade_Model]]
| CTF model
|-

| Paper
| [[1978Wade_Model]]
| CTF model
|-

| Paper
| [[1979Hayward_Radiation]]
| Radiation damage
|-

| Paper
| [[1984Cohen_Validity]]
| Validity of the CTF model at high frequencies
|-

| Paper
| [[1988Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[1992Wade_Model]]
| CTF model
|-

| Paper
| [[1993Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2004Egerton_Damage]]
| Radiation damage
|-

| Paper
| [[2004Sorzano_Normalization]]
| Background noise is Gaussian
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2009Baxter_NoiseCharacterization]]
| Characterization of the different noise sources in cryo-EM
|-

| Paper
| [[2010Baker_Damage]]
| Radiation damage dependence on resolution
|-

| Paper
| [[2010Bammes_Damage]]
| Radiation damage dependence on temperature
|-

| Paper
| [[2010Gomez_Multislice]]
| Simulation of the multi slice model
|-

| Paper
| [[2010Zewail_FourDimensional]]
| Review on the use of ultrafast EM
|-

| Paper
| [[2011Bammes_CCD]]
| Performance of CCD cameras
|-

| Paper
| [[2011Glaeser_Coma]]
| Image formation model including coma
|-

| Paper
| [[2011Milazzo_DirectDetectors]]
| Evaluation of Direct Detectors
|-

| Paper
| [[2011Rullgard_ImageSimulation]]
| Accurate simulation of EM images
|-

| Paper
| [[2011Zhang LimitingFactors]]
| Limiting factor for atomic resolution in EM
|-

| Paper
| [[2012Bammes_DirectDetection]]
| Performance of Direct detectors
|-

| Paper
| [[2012Campbell_MotionCorrection]]
| Beam induced motion correction and direct detectors
|-

| Paper
| [[2012Shang_HydrationLayer]]
| Simulation of PDB volumes explicitly considering the hydration layer
|-

| Paper
| [[2013Egerton_RadiationDamage]]
| Review of TEM radiation damage and experimental ways of reducing it
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu H_Noisemodels]]
| Noise models and cryo-EM drift correction with a direct-electron camera
|-

| Paper
| [[2013Li X K2 noisemodels]]
| Influence of electron dose rate on electron counting images recorded with the K2 camera
|-

| Paper
| [[2013Vulovic_CTFApproximations]]
| When to use the different approximations performed so that a projection with linear CTF is valid
|-

| Thesis
| [[2013Vulovic_ImageFormation]]
| Ph.D. Thesis on the image formation in cryo-EM
|-

| Paper
| [[2014Danev_PhasePlate]]
| Volta potential phase plate
|-

| Paper
| [[2015Chiu_K2]]
| Characterization of K2
|-

| Paper
| [[2015Hawkes_AberrationCorrection]]
| Historical account of the development of lens corrections
|-

| Paper
| [[2015Koeck_Quadratic]]
| Limitations of the linear approximation and use of the quadratic terms
|-

| Paper
| [[2015Kuijper_FEI]]
| Description of the FEI Falcons
|-

| Paper
| [[2015Lobato_MULTEM]]
| Simulation of multislice diffraction
|-

| Paper
| [[2015McMullan_AmorphousIce]]
| Beam induced movement is caused by Brownian motion
|-

| Paper
| [[2016Koeck_ADF]]
| Simulations of Annular Dark Field TEM
|-

| Paper
| [[2017Mishyna_DNARadiation]]
| Review of radiation damage on DNA
|-

|}

=== Collection geometry ===

{|

| Chapter
| [[1980Hoppe_Wedge]]
| Missing wedge
|-

| Paper
| [[1987Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1995Penczek_Dual]]
| Dual axis tomography
|-

| Paper
| [[1997Mastronarde_Dual]]
| Dual axis tomography
|-

| Paper
| [[2003Ludtke_FocusPairs]]
| Focus pairs for single particles
|-

| Paper
| [[2005Lanzavecchia_Conical]]
| Conical tomography
|-

| Paper
| [[2005Zampighi_Conical]]
| Conical tomography
|-

| Paper
| [[2006Leschziner_OT]]
| Orthogonal Tilt
|-

| Paper
| [[2006Messaoudi_Multiple]]
| Multiple axis tomography
|-

| Paper
| [[2012Kudryashev_FocusPairs]]
| Focus pairs tomography
|-

| Paper
| [[2014Hovden_TiltFocus]]
| Combining tilt series with focus series
|-

| Paper
| [[2015Sorzano_RandomConicalTilt]]
| General formulation of Random Conical Tilt
|-

| Paper
| [[2017Hagen_DoseTomography]]
| Dose optimization for subtomogram averaging
|-

|}

=== Sample preparation ===

{|

| Paper
| [[1982Dubochet_Sample]]
| Vitreous ice
|-

| Paper
| [[1986Lepault_Sample]]
| Fast freezing
|-

| Paper
| [[1995Dubochet_Sample]]
| High-pressure freezing
|-

| Paper
| [[1995VanMarle_Sample]]
| Sample damages in resin
|-

| Paper
| [[1998Adrian_Sample]]
| Cryo negative staining
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2002Hsieh_Sample]]
| Cryofixation
|-

| Paper
| [[2004AlAmoudi_Sample]]
| CEMOVIS
|-

| Paper
| [[2008Studer_Sample]]
| Review on high pressure freezing
|-

| Paper
| [[2009Pierson_Sample]]
| Review on sample preparation for electron tomography
|-

| Paper
| [[2010Zhang_NegativeStaining]]
| Negative staining for small protein imaging
|-

| Paper
| [[2012Zhang_PositiveStaining]]
| Positive staining
|-

| Paper
| [[2014Rames_NegativeStaining]]
| Optimized negative staining
|-

| Paper
| [[2014Russo_GoldGrids]]
| Gold grids for single particles
|-

| Paper
| [[2015Cabra_Sample]]
| Review on sample preparation for single particles with videos
|-

| Paper
| [[2016Passmore_Review]]
| Tutorial chapter on sample preparation
|-

| Paper
| [[2016Razinkov_Vitrification]]
| New vitrification method
|-

| Paper
| [[2016Takizawa_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2016Thompson_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2017Arnold_BlottingFree]]
| Blotting-free preparation
|-

| Paper
| [[2017Feng_SprayingPlunging]]
| Spraying plunging
|-

| Paper
| [[2017Peitsch_Sample]]
| iMEM: Isolation of Plasma Membrane for Cryoelectron Microscopy
|-

| Paper
| [[2017Scapin_Storage]]
| Cryo storage of samples
|-

| Paper
| [[2017Schaffer_FocusedIonBeam]]
| Focused Ion Beam sample preparation for membrane proteins
|-

| Paper
| [[2017Scherr_HydrogelNanomembranes]]
| Sample preparation for membrane proteins
|-

|}

=== Automated data collection ===

{|

| Paper
| [[1992Dierksen_Automatic]]
| Automated data collection
|-

| Paper
| [[1992Koster_Automatic]]
| Automated data collection
|-

| Paper
| [[1996Fung_Automatic]]
| Automated data collection for tomography
|-

| Paper
| [[2001Zhang_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2003Ziese_Automatic]]
| Automated autofocusing
|-

| Paper
| [[2004Potter_Automatic]]
| Automated sample loading
|-

| Paper
| [[2004Zheng_Automatic]]
| Automated data collection
|-

| Paper
| [[2005Lei_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2005Suloway_Automatic]]
| Automated data collection: Leginon
|-

| Paper
| [[2007Yoshioka_RCT]]
| Automated Random Conical Tilt
|-

| Paper
| [[2011Korinek_TOM2]]
| Automated acquisition with TOM2
|-

| Paper
| [[2015Li_UCSFImage]]
| Automated acquisition with UCSFImage
|-

| Paper
| [[2016Gil_Fuzzy]]
| Real time decisions during acquisition with neuro-fuzzy method
|-

| Paper
| [[2016Liu_TiltControl]]
| Accurate control of the tilt angle for electron tomography
|-

| Paper
| [[2016Vargas_FoilHole]]
| Determination of image quality at low magnification
|-

| Paper
| [[2017Biyani_Focus]]
| Automatic processing of micrographs
|-

|}

== Single particles ==

=== Automatic particle picking ===

{|

| Paper
| [[1982VanHeel_Detection]]
| Detection of particles in micrographs
|-

| Paper
| [[2001Nicholson_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2001Zhu_Filaments]]
| Automatic identification of filaments in micrographs
|-

| Paper
| [[2004Sigworth_Detection]]
| Classical detection theory and the cryo-EM particle selection problem
|-

| Paper
| [[2004Volkmann_ParticlePicking]]
| An approach to automated particle picking from electron micrographs based on reduced representation templates
|-

| Paper
| [[2004Wong_ParticlePicking]]
| Model-based particle picking for cryo-electron microscopy
|-

| Paper
| [[2004Zhu_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2007Chen_Signature]]
| Automatic particle picking program: Signature
|-

| Paper
| [[2007Woolford_SwarmPS]]
| Automatic particle picking with several criteria, implemented in EMAN Boxer
|-

| Paper
| [[2009Sorzano_MachineLearning]]
| Automatic particle picking based on machine learning of rotational invariants
|-

| Paper
| [[2011Arbelaez_Comparison]]
| Evaluation of the performance of software for automated particle-boxing
|-

| Paper
| [[2013Abrishami_MachineLearning]]
| A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs
|-

| Paper
| [[2013Hauer_2013]]
| Automatic tilt pair detection in Random Conical Tilt
|-

| Paper
| [[2013Shatsky_ParticlePicking]]
| Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Langlois_ParticlePicking]]
| Automatic particle picking
|-

| Paper
| [[2016Vilas_AutomaticTilt]]
| Automatic identification of image pairs in untilted-tilted micrograph pairs
|-

|}

=== 2D Preprocessing ===

{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast enhancement through DPR
|-

| Paper
| [[2004Sorzano_Normalization]]
| Normalization procedures and their statistical properties.
|-

| Paper
| [[2006Sorzano_Denoising]]
| Strong denoising in wavelet space
|-

| Conference
| [[2009Sorzano_Downsampling]]
| Differences between the different downsampling schemes
|-

| Paper
| [[2012Brilot_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Campbell_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Zhao_Denoising]]
| Denoising using an invariant Fourier-Bessel eigenspace
|-

| Paper
| [[2013Norousi_Screening]]
| Screening particles to identify outliers
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu_Movies]]
| Drift correction for movies considering dark field
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Scheres_Movies]]
| Beam induced motion correction
|-

| Paper
| [[2015Abrishami_Movies]]
| Alignment of direct detection device micrographs
|-

| Paper
| [[2015Grant_Anisotropic]]
| Automatic estimation and correction of anisotropic magnification
|-

| Paper
| [[2015Grant_OptimalExposure]]
| Filter movies according to the radiation damage
|-

| Paper
| [[2015Rubinstein_Alignment]]
| Frame alignment at the level of particle
|-

| Paper
| [[2015Spear_DoseCompensation]]
| Effect of dose compensation on resolution
|-

| Paper
| [[2015Zhao_AnisotropicMagnification]]
| Correction of anisotropic magnification
|-

| Conference
| [[2016Bajic_Denoising]]
| Denoising and deconvolution of micrographs
|-

| Paper
| [[2016Jensen_RemovalVesicles]]
| Removal of vesicles in membrane proteins
|-

| Paper
| [[2016Bhamre_Denoising]]
| Denoising by 2D covariance estimation
|-

| Paper
| [[2017McLeod_Zorro]]
| Movie alignment by Zorro
|-

| Paper
| [[2017Zheng_MotionCorr2]]
| Movie alignment by MotionCorr2
|-

|}

=== 2D Alignment ===

{|

| Paper
| [[1981Frank_Averaging]]
| 2D averaging and phase residual
|-

| Paper
| [[1982Saxton_Averaging]]
| 2D averaging using correlation
|-

| Paper
| [[1998Sigworth_ML2D]]
| Maximum likelihood alignment in 2D
|-

| Paper
| [[2003Cong_FRM2D]]
| Fast Rotational Matching in 2D
|-

| Paper
| [[2005Cong_FRM2D]]
| Fast Rotational Matching in 2D introduced in a 3D Alignment algorithm
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

|}

=== 2D Classification and clustering ===

{|

| Paper
| [[1981VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[1984VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2011Singer_DiffusionMaps]]
| Classification in 2D based on graph analysis of the projections
|-

| Paper
| [[2012Yang_ISAC]]
| Iterative Stable Alignment and clustering
|-

| Paper
| [[2014Sorzano_Outlier]]
| Outlier detection in 2D classifications.
|-

| Paper
| [[2014Zhao_Aspire]]
| Fast classification based on rotational invariants and vector diffusion maps
|-

| Paper
| [[2015Huang_Robust]]
| Robust w-estimators of 2D classes
|-

| Paper
| [[2016Reboul_Stochastic]]
| Stochastic Hill Climbing for calculating 2D classes
|-

| Conference
| [[2017Bhamre_Mahalanobis]]
| 2D classification using Mahalanobis distance
|-

|}

=== 3D Alignment ===

{|

| Paper
| [[1980Kam_AutoCorrelation]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[1986Goncharov_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1987VanHeel_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1988Provencher_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Vogel_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1990Gelfand_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Goncharov_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Harauz_Quaternions]]
| Use of quaternions to represent rotations
|-

| Paper
| [[1994Penczek_Real]]
| Angular assignment using projection matching in real space
|-

| Paper
| [[1994Radermacher_Radon]]
| Angular assignment in Radon space
|-

| Paper
| [[1996Penczek_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[2003Rosenthal_DPR]]
| Angular assignment using DPR
|-

| Paper
| [[2004Sorzano_Wavelet]]
| Angular assignment in the wavelet space.
|-

| Paper
| [[2005Jonic_Splines]]
| Angular assignment in Fourier space using spline interpolation.
|-

| Paper
| [[2005Yang_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[2006Ogura_SimulatedAnnealing]]
| Angular asignment by simulated annealing
|-

| Paper
| [[2007Grigorieff_Continuous]]
| Continuous angular assignment in Fourier space
|-

| Paper
| [[2010Jaitly_Bayesian]]
| Angular assignment by a Bayesian method and annealing
|-

| Paper
| [[2010Sanz_Random]]
| Random model method
|-

| Paper
| [[2010Singer_Voting]]
| Detecting consistent common lines by voting (reference free)
|-

| Paper
| [[2011Singer_SDP]]
| Angular assignment by semidefinite programming and eigenvectors (reference free)
|-

| Paper
| [[2012Giannakis_Scattering]]
| Construction of an initial volume, reference free, by graph analysis of the projections
|-

| Paper
| [[2012Shkolnisky_Sync]]
| Angular assignment by synchronization of rotations (reference free)
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Wang_LUD]]
| Angular assignment by least unsquared deviations (reference free)
|-

| Paper
| [[2014Vargas_RANSAC]]
| Initial model using RANSAC (reference free)
|-

| Paper
| [[2015Joubert_Pseudoatoms]]
| Initial model based on pseudo-atoms
|-

| Paper
| [[2015Singer_Kam]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[2015Sorzano_Significant]]
| Statistical approach to the initial volume estimation (reconstruct significant)
|-

| Conference
| [[2016Michels_Heterogeneous]]
| Initial volume in the presence of heterogeneity
|-

| Paper
| [[2016Cossio_BayesianGPU]]
| GPU implementation of the Bayesian 3D reconstruction approach
|-

|}

=== 3D Reconstruction ===
{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1986Harauz_FBP]]
| Exact filters for Filtered Back Projection
|-

| Chapter
| [[1992Radermacher_WBP]]
| Exact filters for Weighted Back Projection
|-

| Paper
| [[1997Zhu_RecCTF]]
| 3D Reconstruction (SIRT like) and simultaneous CTF correction
|-

| Paper
| [[1998Boisset_Uneven]]
| Artifacts in SIRT and WBP under uneven angular distributions
|-

| Paper
| [[1998Marabini_ART]]
| Algebraic Reconstruction Technique with blobs (Xmipp)
|-

| Paper
| [[2001Sorzano_Uneven]]
| Free parameter selection under uneven angular distributions
|-

| Paper
| [[2005Sorzano_Parameters]]
| Free parameter selection for optimizing multiple tasks
|-

| Paper
| [[2008Sorzano_Constraints]]
| Mass, surface, positivity and symmetry constraints for real-space algorithms
|-

| Paper
| [[2009Bilbao_ParallelART]]
| Efficient parallelization of ART
|-

| Paper
| [[2011Li_GradientFlow]]
| Regularized 3D Reconstruction by Gradient Flow
|-

| Paper
| [[2011Vonesch_Wavelets]]
| Fast wavelet-based 3D reconstruction
|-

| Paper
| [[2012Gopinath_ShapeRegularization]]
| Regularized 3D Reconstruction by Shape information
|-

| Paper
| [[2012Kucukelbir_adaptiveBasis]]
| 3D reconstruction in an adaptive basis promoting sparsity
|-

| Paper
| [[2012Sindelar_NoiseReduction]]
| Optimal noise reduction in 3D reconstructions
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Lyumkis_Optimod]]
| Construction of initial volumes with Optimod
|-

| Paper
| [[2013Wang FIRM]]
| Fast 3D reconstruction in Fourier domain
|-

| Paper
| [[2014Kunz_SART_OS]]
| Simultaneous ART with OS
|-

| Paper
| [[2015Abrishami_Fourier]]
| 3D Reconstruction in Fourier space
|-

| Paper
| [[2015Dvornek_SubspaceEM]]
| Fast Maximum a posteriori
|-

| Paper
| [[2015Moriya_Bayesian]]
| Bayesian approach to suppress limited angular artifacts
|-

| Paper
| [[2015Xu_GeometricFlow]]
| Multi-scale geometric flow
|-

| Arxiv
| [[2016Ye_Cohomology]]
| Cohomology properties of 3D reconstruction
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

| Paper
| [[2017Punjani_CryoSPARCTheory]]
| Theory related to CryoSPARC
|-

|}

=== 3D Heterogeneity ===

{|

| Paper
| [[2004White_Size]]
| Heterogeneity classification of differently sized images
|-

| Paper
| [[2006Penczek_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Scheres_ML3D]]
| Maximum Likelihood alignment and classification in 3D
|-

| Paper
| [[2009Spahn_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2010Elmlund_AbInitio]]
| Solving the initial volume problem with multiple conformations
|-

| Paper
| [[2010Shatsky_MultiVariate]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2012Scheres_Bayesian]]
| A Bayesian view on cryo-EM structure determination
|-

| Paper
| [[2012Zheng_Covariance]]
| Estimation of the volume covariance
|-

| Paper
| [[2013Wang_MLVariance]]
| Maximum Likelihood estimate of the map variance
|-

| Paper
| [[2013Lyumkis D_FREALIGN]]
| Likelihood-based classification of cryo-EM images using FREALIGN.
|-

| Paper
| [[2014Jin_NMA]]
| Continuous heterogeneity through Normal Mode Analysis
|-

| Paper
| [[2014Dashti_Brownian]]
| Continuous heterogeneity through Brownian trajectories
|-

| Paper
| [[2014Chen_Migration]]
| Particle migration analysis in 3D classification
|-

| Paper
| [[2015Anden_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Bai_Focused]]
| Focused classification
|-

| Paper
| [[2015Katsevich_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Klaholz_MRA]]
| Multivariate Statistical Analysis of Jackknife and Bootstrapping on random subsets
|-

| Paper
| [[2015Liao_Covariance]]
| Estimation of the 3D covariance from 2D projections
|-

| Paper
| [[2015Tagare_Direct]]
| Direct reconstruction of PCA components
|-

| Paper
| [[2016Gong_Mechanical]]
| Mechanical model for macromolecules
|-

| Paper
| [[2016Rawson_Movement]]
| Movement and flexibility
|-

| Paper
| [[2016Sorzano_StructMap]]
| Sorting a discrete set of conformational states
|-

| Paper
| [[2016Sorzano_Strain]]
| Calculate local stretches, strains and rotations from two conformational states
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

|}

=== Validation ===

{|

| Paper
| [[2008Stagg_TestBed]]
| Effect of voltage, dosis, number of particles and Euler jumps on resolution
|-

| Paper
| [[2011Henderson]]
| Tilt Validation
|-

| Paper
| [[2011Read]]
| Validation of PDBs
|-

| Paper
| [[2012Henderson]]
| EM Map Validation
|-

| Paper
| [[2013Cossio_Bayesian]]
| EM Map Validation in a probabilistic setting
|-

| Paper
| [[2013Chen_NoiseSubstitution]]
| Noise substitution at high resolution for measuring overfitting
|-

| Paper
| [[2014Russo_StatisticalSignificance]]
| EM Map Validation through the statistical significance of the tilt-pair angular assignment
|-

| Paper
| [[2014Stagg_Reslog]]
| EM Map Validation through the resolution evolution with the number of particles
|-

| Paper
| [[2014Wasilewski_Tilt]]
| Web implementation of the tilt pair validation
|-

| Paper
| [[2015Heymann_Alignability]]
| EM Map Validation through the resolution of reconstructions from particles and noise
|-

| Paper
| [[2015Oliveira_FreqLimited]]
| Comparison of gold standard and frequency limited optimization
|-

| Paper
| [[2015Wriggers_Secondary]]
| Validation by secondary structure
|-

| Paper
| [[2016Kim_SAXS]]
| Comparison of SAXS data and EM projections
|-

| Paper
| [[2016Rosenthal_Review]]
| Review of validation methods
|-

| Paper
| [[2016Vargas_Alignability]]
| Validation by studying the tendency of an angular assignment to cluster in the projection space
|-

| Paper
| [[2017Monroe_PDBRefinement]]
| Validation by comparison to a refined PDB
|-

|}

=== Resolution ===

{|

| Paper
| [[1986Harauz_FBP]]
| Fourier Shell Correlation
|-

| Paper
| [[1987Unser_SSNR]]
| 2D Spectral Signal to Noise Ratio
|-

| Paper
| [[2002Penczek_SSNR]]
| 3D Spectral Signal to Noise Ratio for Fourier based algorithms
|-

| Paper
| [[2003Rosenthal_DPR]]
| Review of the FSC and establishment of a new threshold
|-

| Paper
| [[2005Unser_SSNR]]
| 3D Spectral Signal to Noise Ratio for any kind of algorithms
|-

| Paper
| [[2005VanHeel_FSC]]
| Establishment of a new threshold for FSC
|-

| Paper
| [[2007Sousa_AbInitio]]
| Resolution measurement on neighbour Fourier voxels
|-

| Paper
| [[2014Kucukelbir_Local]]
| Quantifying the local resolution of cryo-EM density maps
|-

| Paper
| [[2016Pintilie_Probabilistic]]
| Probabilistic models and resolution
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Statistical properties of resolution measures defined in Fourier space
|-

|}

=== Sharpening of high resolution information ===
{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast restoration and map sharpening
|-

| Paper
| [[2008Fernandez_Bfactor]]
| Bfactor determination and restoration
|-

| Paper
| [[2013Fiddy_SaxtonAlgorithm]]
| Phase retrieval or extension
|-

| Paper
| [[2014Kishchenko_SphericalDeconvolution]]
| Spherical deconvolution
|-

| Paper
| [[2015Spiegel_VISDEM]]
| Visualization improvement by the use of pseudoatomic profiles
|-

| Paper
| [[2016Jonic_Pseudoatoms]]
| Approximation with pseudoatoms
|-

| Paper
| [[2016Jonic_Denoising]]
| Denoising and high-frequency boosting by pseudoatom approximation
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[1982Schiske_Correction]]
| CTF correction for tilted objects
|-

| Paper
| [[1988Toyoshima_Model]]
| CTF estimation
|-

| Paper
| [[1995Frank_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1996Skoglund_MaxEnt]]
| CTF correction with Maximum Entropy
|-

| Paper
| [[1996Zhou_Model]]
| CTF model and user interface for manual fitting
|-

| Paper
| [[1997Fernandez_AR]]
| PSD estimation using periodogram averaging and AR models
|-

| Paper
| [[1997Penczek_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1997Stark_Deconvolution]]
| CTF correction using deconvolution
|-

| Paper
| [[1997Zhu_RecCTF]]
| CTF correction and reconstruction
|-

| Paper
| [[2000DeRosier_EwaldCorrection]]
| CTF correction considering the Ewald sphere
|-

| Paper
| [[2000Jensen_TiltedCorrection]]
| CTF correction considering tilt in backprojection
|-

| Paper
| [[2001Saad_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Huang_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Mindell_CTFTILT]]
| CTF estimation for tilted micrographs
|-

| Paper
| [[2003Sander_MSA]]
| CTF estimation through MSA classification of PSDs
|-

| Paper
| [[2003Velazquez_ARMA]]
| PSD and CTF estimation using ARMA models
|-

| Paper
| [[2004Sorzano_IDR]]
| CTF restoration and reconstruction with Iterative Data Refinement
|-

| Conference
| [[2004Wan_CTF]]
| Spatially variant CTF
|-

| Paper
| [[2004Zubelli_Chahine]]
| CTF restoration and reconstruction with Chahine's multiplicative method
|-

| Conference
| [[2005Dubowy_SpaceVariant]]
| CTF correction when this is space variant
|-

| Paper
| [[2005Mallick_ACE]]
| CTF estimation
|-

| Paper
| [[2006Wolf_Ewald]]
| CTF correction considering Ewald sphere
|-

| Paper
| [[2007Jonic_EnhancedPSD]]
| PSD enhancement for better identification of Thon rings; Vitreous ice diffracts in Thon rings
|-

| Paper
| [[2007Philippsen_Model]]
| CTF Model for tilted specimens
|-

| Paper
| [[2007Sorzano_CTF]]
| CTF estimation using enhanced PSDs
|-

| Paper
| [[2009Sorzano_Sensitivity]]
| Error sensitivity of the CTF models, non-uniqueness of the CTF parameters
|-

| Paper
| [[2010Jiang2010_CTFCorrection]]
| Amplitude correction method
|-

| Paper
| [[2010Kasantsev_CTFCorrection]]
| Mathematical foundations of Kornberg and Jensen method
|-

| Paper
| [[2010Leong_CTFCorrection]]
| Correction for spatially variant CTF
|-

| Paper
| [[2011Glaeser_Coma]]
| The effect of coma at high-resolution
|-

| Paper
| [[2011Mariani_Tilted]]
| CTF simulation and correction of tilted specimens
|-

| Paper
| [[2011Sindelar_Wiener]]
| CTF correction using a modified version of Wiener filter
|-

| Paper
| [[2011Voortman_Tilted]]
| CTF correction for tilted specimen
|-

| Paper
| [[2012Voortman_VaryingCTF]]
| Correcting a spatially varying CTF
|-

| Paper
| [[2013Vargas_FastDef]]
| Fast defocus
|-

| Paper
| [[2015Rohou_CTFFind4]]
| CTF Find 4
|-

| Paper
| [[2015Sheth_CTFquality]]
| Visualization and quality assessment of CTF
|-

| Paper
| [[2016Zhang_GCTF]]
| gCTF
|-

|}

=== Segmentation ===

{|

| Paper
| [[2006Baker_segmentation]]
| Segmentation of molecular subunits
|-

|}

=== Fitting and docking ===

{|

| Paper
| [[1999Volkmann_Fitting]]
| Fitting in real space
|-

| Paper
| [[2001Baker_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2001Jones_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2003Kovacs_FRM3D]]
| Fast Rotational Alignment of two EM maps
|-

| Paper
| [[2004Tama_NMA1]]
| Flexible fitting with Normal Modes (I)
|-

| Paper
| [[2004Tama_NMA2]]
| Flexible fitting with Normal Modes (II)
|-

| Paper
| [[2005Velazquez_Superfamilies]]
| Recognition of the superfamily folding in medium-high resolution volumes
|-

| Paper
| [[2007DeVries_Haddock]]
| Docking with Haddock 2.0
|-

| Paper
| [[2007Kleywegt_QualityControl]]
| Quality control and validation of fitting
|-

| Paper
| [[2012Biswas_Secondary]]
| Secondary structure determination in EM volumes
|-

| Paper
| [[2012Velazquez_Constraints]]
| Multicomponent fitting by using constraints from other information sources
|-

| Paper
| [[2013Chapman MS_Atomicmodeling]]
| Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters
|-

| Paper
| [[2013Esquivel_Modelling]]
| Review on modelling (secondary structure, fitting, ...)
|-

| Paper
| [[2013Lopez_Imodfit]]
| Fitting based on vibrational analysis
|-

| Paper
| [[2013Nogales_3DEMLoupe]]
| Normal Mode Analysis of reconstructed volumes
|-

| Paper
| [[2014AlNasr_Secondary]]
| Identification of secondary structure elements in EM volumes
|-

| Paper
| [[2014Politis_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Rey_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Villa_Review]]
| Review of atomic fitting into EM volumes
|-

| Paper
| [[2015Barad_EMRinger]]
| Validation of hybrid models
|-

| Paper
| [[2015Bettadapura_PF2Fit]]
| Fast rigid fitting of PDBs into EM maps
|-

| Paper
| [[2015Carrillo_CapsidMaps]]
| Analysis of virus capsids using Google Maps
|-

| Paper
| [[2015Schroeder_Hybrid]]
| Review on model building
|-

| Paper
| [[2015Tamo_Dynamics]]
| Dynamics in integrative modeling
|-

| Paper
| [[2015Sorzano_AtomsToVoxels]]
| Accurate conversion of an atomic model into a voxel density volume
|-

| Paper
| [[2016Joseph_Evolution]]
| Evolutionary constraints for the fitting of atomic models into density maps
|-

| Paper
| [[2016Segura_3Diana]]
| Validation of hybrid models
|-

| Paper
| [[2016Singharoy_MDFF]]
| Construction of hybrid models driven by EM density and molecular dynamics
|-

| Paper
| [[2016Wang_Rosetta]]
| Construction of hybrid models driven by EM density using Rosetta
|-

| Paper
| [[2017Joseph_Metrics]]
| Metrics analysis for the comparison of structures
|-

| Paper
| [[2017Hryc_WeightedAtoms]]
| Construction of hybrid models by locally weighting the different atoms
|-

| Paper
| [[2017Matsumoto_Distribution]]
| Estimating the distribution of conformations of atomic models
|-

| Paper
| [[2017Miyashita_EnsembleFitting]]
| Ensemble fitting using Molecular Dynamics
|-

|}

=== Books and reviews ===

{|

| Book
| [[1980Herman_Tomography]]
| General book on tomography
|-

| Book
| [[1988Kak_Tomography]]
| General book on tomography
|-

| Paper
| [[2000Tao_Review]]
| Review of single particles
|-

| Paper
| [[2000VanHeel_Review]]
| Review of single particles
|-

| Paper
| [[2002Frank_Review]]
| Review of single particles
|-

| Paper
| [[2002Schmid_Review]]
| Review of single particles
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2004Subramaniam_Review]]
| Review of single particles
|-

| Paper
| [[2005Steven_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_book]]
| Book covering all aspects of electron microscopy of single particles
|-

| Paper
| [[2006Sorzano_Review]]
| Review of optimization problems in electron microscopy
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems in Electron Tomography
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2008Mueller_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2008Taylor_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2010DeRosier_Review]]
| Personal account of how 3DEM developed in the early days
|-

| Chapter
| [[2012Sorzano_Review]]
| Review of single particle analysis using Xmipp
|-

| Chapter
| [[2012Devaux_Protocol]]
| Protocols for performing single particle analysis
|-

| Paper
| [[2014Bai_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Carazo_Review]]
| Review of the reconstruction process
|-

| Paper
| [[2015Cheng_Review]]
| A primer to Single Particle Cryo-EM
|-

| Paper
| [[2015Cheng_Reviewb]]
| Single Particle Cryo-EM at crystallographic resolution
|-

| Paper
| [[2015Elmlund_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Henderson_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Nogales_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Schroeder_Review]]
| Review of advances in the electron microscope
|-

| Paper
| [[2015Wu_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Carroni_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Egelman_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Eisenstein_CryoEM]]
| News feature on the Method of the Year
|-

| Paper
| [[2016FernandezLeiro_Review]]
| Review of EM
|-

| Paper
| [[2016Glaeser_HowGood]]
| How good can cryo-EM become?
|-

| Paper
| [[2016Jonic_PseudoAtoms]]
| Review of the applications of the use of pseudoatoms in EM
|-

| Chapter
| [[2016Mio_Review]]
| Overview of the process to obtain EM reconstructions
|-

| Paper
| [[2016Jonic_Review]]
| A review of computational ways to handle heterogeneity
|-

| Paper
| [[2016Nogales_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Subramaniam_Review]]
| Why cryo-EM is now suitable for crystallographic journals
|-

| Paper
| [[2016Vinothkumar_Review]]
| Historical review and current limitations
|-

| Paper
| [[2017Frank_Review]]
| Historical review of EM
|-

| Paper
| [[2017Jonic_Review]]
| Review of computational methods to analyze conformational variability
|-

| Paper
| [[2017Rawson_Limitations]]
| Limitations of EM for drug design
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Review of statistical properties of resolution measures defined in Fourier space
|-
|}

=== Software ===

{|

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[1999Lutdke_Eman]]
| Eman
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Baldwin_AngularTransformations]]
| The Transform Class in SPARX and EMAN2
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Grigorieff_Frealign]]
| Frealign
|-

| Paper
| [[2008Scheres_XmippProtocols]]
| Xmipp Protocols
|-

| Paper
| [[2008Shaikh_SpiderProtocols]]
| Spider Protocols
|-

| Paper
| [[2012Wriggers_SitusConventions]]
| Conventions and workflows in Situs
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2015Cianfrocco_Cloud]]
| Software execution in the cloud
|-

| Paper
| [[2015Cheng_MRC2014]]
| Extensions to MRC file format
|-

| Paper
| [[2013DeLaRosa_Scipion]]
| Scipion
|-

| Paper
| [[2016Scheres_Relion]]
| Tutorial on the use of Relion
|-

| Paper
| [[2016Grigorieff_Frealign]]
| Tutorial on the use of Frealign
|-

|}

== Electron tomography ==

=== Image preprocessing ===

{|

| Paper
| [[2015Yan_thickness]]
| Determination of thickness, tilt and electron mean free path
|-

|}

=== Image alignment ===

{|

| Paper
| [[1982Guckenberger_commonOrigin]]
| Determination of a common origin in the micrographs of titl series in three-dimensional electron microscopy
|-

| Paper
| [[1992Lawrence_leastSquares]]
| Least squares solution of the alignment problem
|-

| Paper
| [[1995Penczek_dual]]
| Dual tilt alignment
|-

| Paper
| [[1996Owen_alignmentQuality]]
| Automatic alignment without fiducial markers and evaluation of alignment quality
|-

| Paper
| [[1998Grimm_normalization]]
| Discussion of several gray level normalization methods for electron tomography
|-

| Paper
| [[2001Brandt_Automatic1]]
| Automatic alignment without fiducial markers
|-

| Paper
| [[2001Brandt_Automatic2]]
| Automatic alignment with fiducial markers
|-

| Paper
| [[2006Winkler_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2006Castano_alignment]]
| Alignment with non-perpendicularity
|-

| Paper
| [[2007Castano_alignment]]
| Fiducial-less alignment of cryo-sections
|-

| Paper
| [[2009Sorzano_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2010Cantele_dualAlignment]]
| Alignment of dual series
|-

| Paper
| [[2014Tomonaga_Automatic]]
| Automatic alignment of tilt series using the projection themselves
|-

| Paper
| [[2014Han_Automatic]]
| Automatic alignment of tilt series using SIFT features
|-

| Paper
| [[2015Han_Automatic]]
| Automatic alignment of tilt series using fiducials
|-

| Paper
| [[2017Mastronarde_Automatic]]
| Automatic alignment and reconstruction of tilt series in IMOD
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[2003Winkler_CTF]]
| Focus gradient correction in electron tomography
|-

| Paper
| [[2006Fernandez_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Zanetti_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Xiong_CTF]]
| CTF determination and correction for low dose tomographic tilt series
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2017Kunz_3DCTF]]
| 3D CTF Correction
|-

|}

=== 3D reconstruction ===

{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1992Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[1997Marabini_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2002Fernandez_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2007Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[2008Fernandez_CARP]]
| Component Averaged Row Projections (CARP)
|-

| Paper
| [[2012Herman General Superiorization]]
| Superiorization: an optimization heuristic for medical physics
|-

| Paper
| [[2012Zhang_IPET_FETR]]
| IPET and FETR, a reconstruction algorithm for single molecule tomography
|-

| Paper
| [[2013Goris_SIRT_TV_DART]]
| Combination of SIRT, Total Variation and Discrete ART to reconstruct and segment at the same time
|-

| Paper
| [[2013Briegel A_Challenge]]
| The challenge of determining handedness in electron tomography and the use of DNA origami gold nanoparticle helices as molecular standards
|-

| Paper
| [[2013Messaoudi_EnergyFiltered]]
| 3D Reconstruction of Energy-Filtered TEM
|-

| Paper
| [[2016Deng_ICON]]
| 3D Reconstruction with missing information restoration
|-

| Paper
| [[2016Guay_Compressed]]
| 3D Reconstruction using compressed sensing
|-

|}

=== Noise reduction ===
{|

| Paper
| [[2001Frangakis_NAD]]
| Noise reduction with Nonlinear Anisotropic Diffusion
|-

| Paper
| [[2003Fernandez_AND]]
| Anisotropic nonlinear diffusion for electron tomography
|-

| Paper
| [[2003Jiang_Bilateral]]
| Bilateral denoising filter in electron microscopy
|-

| Paper
| [[2005Fernandez_AND]]
| Anisotropic nonlinear denoising in electron tomography
|-

| Paper
| [[2007Heide_median]]
| Iterative median filtering in electron tomography
|-

| Paper
| [[2007Fernandez_autAND]]
| Anisotropic nonlinear diffusion with automated parameter tuning
|-

| Paper
| [[2009Fernandez_Beltrami]]
| Nonlinear filtering based on Beltrami flow
|-

| Paper
| [[2010Bilbao_MeanShift]]
| Mean Shift Filtering
|-

| Paper
| [[2014Kovacik_wedgeArtefacts]]
| Removal of wedge artefacts
|-

| Paper
| [[2014Maiorca_beadArtefacts]]
| Removal of gold bead artefacts
|-

|}

=== Segmentation ===

{|

| Paper
| [[2002Frangakis_Eigenanalysis]]
| Segmentation using eigenvector analysis.
|-

| Paper
| [[2002Volkmann_Watershed]]
| Segmentation using watershed transform.
|-

| Paper
| [[2003Bajaj_BoundarySegmentation]]
| Segmentation based on fast marching.
|-

| Paper
| [[2005Cyrklaff_Thresholding]]
| Segmentation using optimal thresholding.
|-

| Paper
| [[2007Lebbink_TemplateMatching]]
| Segmentation using template matching.
|-

| Paper
| [[2007Sandberg_OrientationFields]]
| Segmentation using orientation fields.
|-

| Paper
| [[2007Sandberg_SegmentationReview]]
| Review on segmentation in electron tomography.
|-

| Paper
| [[2008Garduno_FuzzySegmentation]]
| Segmentation using fuzzy set theory principles.
|-

| Paper
| [[2009Lebbink_TemplateMatching2]]
| Segmentation using template matching.
|-

| Paper
| [[2012RubbiyaAli_EdgeDetection]]
| Parameter-Free Segmentation of Macromolecular Structures.
|-

| Conference
| [[2015Xu_TemplateMatching]]
| Detection of macromolecular complexes with a reduced representation of the templates.
|-

|}

=== Resolution ===
{|

| Paper
| [[2005Cardone_Resolution]]
| Resolution criterion for electron tomography
|-

| Chapter
| [[2007Penczek_Resolution]]
| Review of resolution criteria for electron tomography
|-

| Paper
| [[2015Diebolder_ConicalFSC]]
| Conical Fourier Shell Correlation
|-

|}

=== Subtomogram analysis ===

{|

| Paper
| [[2000Bohm_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2002Frangakis_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2006Nickell_Review]]
| Review of macromolecule finding by template matching (Visual Proteomics)
|-

| Paper
| [[2007Best_Review]]
| Review of Localization of Protein Complexes by Pattern Recognition
|-

| Paper
| [[2007Forster_Review]]
| Review of structure determination by subtomogram averaging
|-

| Paper
| [[2008Forster_Classification]]
| Classification of subtomograms using constrained correlation
|-

| Paper
| [[2008Bartesaghi_Classification]]
| Classification and averaging of subtomograms
|-

| Paper
| [[2008Schmid_Averaging]]
| Alignment and averaging of subtomograms
|-

| Paper
| [[2010Amat_Averaging]]
| Alignment and averaging of subtomograms exploiting thresholding in Fourier space
|-

| Paper
| [[2013Chen_Averaging]]
| Fast alignment of subtomograms using spherical harmonics
|-

| Paper
| [[2013Kuybeda_Averaging]]
| Alignment and averaging of subtomograms using the nuclear norm of the cluster
|-

| Paper
| [[2013Shatsky_Averaging]]
| Alignment and averaging of subtomograms with constrained cross-correlation
|-

| Paper
| [[2014Chen_Autofocus]]
| Subtomogram averaging and classification with special attention to differences
|-

| Paper
| [[2014Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2014Voortman_LimitingFactors]]
| Limiting factors of subtomogram averaging
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2015Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2016Bharat_Relion]]
| Subtomogram averaging with Relion
|-

| Paper
| [[2016Song_MatrixNorm]]
| Matrix norm minimization for tomographic reconstruction and alignment
|-

| Paper
| [[2017Castano_ParticlePicking]]
| Particle picking in tomograms for subtomogram averaging
|-

| Paper
| [[2017Frazier_Tomominer]]
| TomoMiner a software platform for large-scale subtomogram analysis
|-

|}

=== Single particle tomography ===

{|

| Paper
| [[2012Bartesaghi_Constrained]]
| 3D reconstruction by imposing geometrical constraints
|-

| Paper
| [[2015Galaz_SingleParticleTomography]]
| Set of tools for Single Particle Tomography in EMAN2
|-

| Paper
| [[2016Galaz_SingleParticleTomography]]
| Alignment algorithms and CTF correction
|-

|}

=== Books and reviews ===

{|

| Paper
| [[2000Baumeister_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Koster_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Sali_Review]]
| Review of electron tomography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2005Lucic_Review]]
| Review of electron tomography
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_TomoBook]]
| Electron Tomography
|-

| Book
| [[2007McIntosh_Book]]
| Cellular Electron Microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2012Kudryashev_Review]]
| Review of subtomogram averaging
|-

| Paper
| [[2016Beck_Review]]
| Review of molecular sociology
|-

| Paper
| [[2017Galaz_Review]]
| Review of single particle tomography
|-

|}

=== Software ===

{|

| Paper
| [[1996Kremer_IMOD]]
| IMOD
|-

| Paper
| [[1996Chen_Priism/IVE]]
| Priism/IVE
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2005Nickell_TOM]]
| TOM Toolbox
|-

| Paper
| [[2007Messaoudi_TomoJ]]
| TomoJ
|-

| Paper
| [[2008Heymann_BsoftTomo]]
| Bsoft
|-

| Paper
| [[2015Ding_CaltechTomography]]
| Caltech tomography database
|-

| Paper
| [[2015Noble_AppionProtomo]]
| Batch fiducial-less tilt-series alignment in Appion using Protomo
|-

| Paper
| [[2015vanAarle_Astra]]
| ASTRA Toolbox
|-

| Paper
| [[2017Wan_Simulator]]
| Electron Tomography Simulator
|-

|}

== 2D Crystals ==

=== 2D Preprocessing ===

{|

| Paper
| [[1986Henderson_Processing]]
| General 2D processing
|-

| Paper
| [[2000He_PhaseAlignment]]
| Phase consistency and Alignment
|-

| Paper
| [[2006Gil_Unbending]]
| Crystal unbending
|-

|}

=== Classification ===
{|

| Paper
| [[1988Frank_Classification]]
| MSA and classification in electron crystallography
|-

| Paper
| [[1996Fernandez_SOM]]
| Classification based on self organizing maps
|-

| Paper
| [[1998Sherman_MSA]]
| Classification based on MSA
|-

|}
=== 3D Reconstruction ===

{|

| Paper
| [[1985Wang_Solvent]]
| Solvent flattening
|-

| Paper
| [[1990Henderson_Processing]]
| General 3D processing
|-

| Paper
| [[2004Marabini_ART]]
| Algebraic Reconstruction Technique with blobs for crystals (Xmipp)
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1998Walz_Review]]
| Review of 2D crystallography
|-

| Paper
| [[1999Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Ellis_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of single particles, electron tomography and crystallography
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Gipson_2dx]]
| 2dx
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Philippsen_IPLT]]
| IPLT
|-

|}

== 3D Crystals - MicroED ==

=== Sample Preparation ===
{|
| Paper
| [[2016Shi_Preparation]]
| Sample Preparation
|}
=== Data Collection ===
{|
| Paper
| [[2014Nannenga_CR]]
| Continuous rotation

|}
=== Data Processing ===
{|

| Paper
| [[2011Wisedchaisri_PhaseExtension]]
| Fragment-based phase extension
|-

| Paper
| [[2015Hattne_Processing]]
| Data Processing
|-

| Paper
| [[2016Hattne_Correction]]
| Image correction
|}

=== Software ===
{|

| Paper
| [[2014Iadanza_Processing]]
| Data Processing of still diffraction data
|}

=== Books and Reviews ===
{|
| Paper
| [[2014Nannenga_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Liu_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Rodriguez_Review ]]
| Review of MicroED
|-

|}

== Helical particles ==

=== Filament corrections ===

{|

| Paper
| [[1986Egelman_Curved]]
| Algorithm for correcting curved filaments
|-

| Paper
| [[1988Bluemke_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2006Wang_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2016Yang_Flexible]]
| Algorithm for correcting filaments with flexible subunits
|-

|}

=== Reconstruction ===

{|

| Paper
| [[1952Cochran_Fourier]]
| Fourier Bessel transform of filamentous structures
|-

| Paper
| [[1958Klug_Fourier]]
| Fourier Bessel decomposition of the projection images
|-

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2005Wang_Iterative]]
| Iterative Fourier-Bessel algorithm
|-

| Paper
| [[2007Egelman_Iterative]]
| Iterative real-space algorithm
|-

| Paper
| [[2013Desfosses_Spring]]
| Helical processing with Spring
|-

| Paper
| [[2015Zhang_seam]]
| Workflow for the detection of the lattice seam
|-

| Paper
| [[2016Rohou_Frealix]]
| Helical processing with Frealix
|-

|}

=== Validation ===

{|

| Paper
| [[2014Egelman_ambiguity]]
| How to detect incorrect models
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Carragher_Phoelix]]
| Phoelix
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Owen_Brandeis]]
| Brandeis
|-

|}

== Icosahedral particles ==

=== Reconstruction ===

{|

| Paper
| [[1970Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1971Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1996Fuller_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1997Thuman_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

|}

=== Classification ===

{|

| Paper
| [[2005Scheres_Virus]]
| Classification of virus capsids in real space
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1999Baker_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[1999Conway_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2000Thuman_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Lee_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Navaza_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2006Grunewald_Review]]
| Review of reconstruction of icosahedral viruses
|-

|}

=== Software ===

{|

| Paper
| [[1996Baker_EMPFT]]
| EMPFT
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2013Morin_Sliz SBGrid]]
| SBGrid presentation for eLife
|-

|}

== Databases ==

{|

| Paper
| [[2003Boutselakis_EMSD]]
| EMSD database
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2011Kim_CDDB]]
| Conformational Dynamics Data Bank
|-

| Paper
| [[2011Lawson_EMDB]]
| Electron Microscopy Data Bank
|-

| Paper
| [[2013Ison_EDAM]]
| EDAM, an ontology of bioinformatics operations
|-

| Paper
| [[2016Iudin_EMPIAR]]
| EMPIAR raw data database
|-

| Paper
| [[2016Patwhardan_EMDB]]
| EMDB, PDB, ...
|-

| Paper
| [[2017Patwhardan_Trends]]
| Trends at EMDB
|-

| Paper
| [[2017Shao_PDBQuality]]
| Quality metrics in PDB
|-

| Blog
| http://www.mybiosoftware.com
| Huge list of bioinformatics programs (many of them structural bioinformatics)
|-

|}

== Relationship to other structural information sources ==

{|

| Paper
| [[2000Engel_AFM]]
| Review of Atomic Force Microscopy
|-

| Paper
| [[2001Dimmeler_AFM]]
| Constraints from Atomic Force Microscopy
|-

| Paper
| [[2003Mobus_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_Review]]
| Review on correlative microscopy
|-

| Paper
| [[2005Boudier_EFTETJ]]
| Software for Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2005Vestergaard_SAXS]]
| Example of comparison of 3DEM and Small-angle X-ray scattering
|-

| Paper
| [[2007Hamada_SAXS]]
| Constraints from Small-angle X-ray scattering
|-

| Paper
| [[2013Xu_FRET]]
| EM+FRET
|-

|}

== X-ray tomography ==

{|

| Paper
| [[2012Oton_ImageFormation]]
| Image formation model in X-ray cell microscopy
|-

|}

== Mathematical tools necessary ==

== People developing methods ==
Please, add yourself to this list (due to privacy reasons, please, do not add anyone else to the list without his/her explicit consent). Sort by first name alphabetical order.

[http://biocomp.cnb.csic.es/~coss Carlos Oscar S. Sorzano]: CSIC, Madrid, Spain 

[http://www.curie.fr/recherche/themes/detail_equipe.cfm/lang/_fr/id_equipe/241.htm Cédric Messaoudi]: Institute Curie, Paris, France 

[http://scholar.google.es/citations?user=_jNYGScAAAAJ&hl=en Javier Vargas]:[mailto:jvargas@cnb.csic.es mail]: CSIC, Madrid, Spain 

[http://scholar.google.es/citations?hl=es&user=g2ZJPIYAAAAJ Joaquín Otón]: CSIC, Madrid, Spain 

[mailto:jrbcast@gmail.com José Román Bilbao-Castro]: UAL, Almería, Spain; CSIC, Madrid, Spain 

[José Miguel de la Rosa Trevín]: Biocomputing Unit CNB-CSIC, Madrid, Spain 

[http://cryoem.janelia.org Tamir Gonen]: [mailto:gonent@janelia.hhmi.org mail]: Howard Hughes Medical Institute, Ashburn, VA, USA 

[mailto:vabrishami@cnb.csic.es Vahid Abrishami]: CSIC, Madrid, Spain 

== 3DEM sites ==
* [http://3dem.ucsd.edu/ 3DEM web site]

* [http://en.wikibooks.org/wiki/Software_Tools_For_Molecular_Microscopy Software tools for molecular microscopy]

* [http://www.emdatabank.org/ The Electron Microscopy Data Bank (EMDB)]

* [http://ccdb.ucsd.edu The Cell Centered Database (CCDB)]

* [http://conventions.cnb.csic.es The geometrical software conventions web page ]

== Editing useful links ==

* [http://www.mediawiki.org/wiki/Help:Formatting Text formatting in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Links Adding links in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Images Adding images in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Tables Making tables in Mediawiki]

2017Scherr HydrogelNanomembranes

2017-07-04T06:02:03Z

CoSS: Created page with "== Citation == Scherr, J.; Parey, K.; Klusch, N.; Murphy, B. J.; Balser, S.; Neuhaus, A.; Zickermann, V.; Kühlbrandt, W.; Terfort, A. & Rhinow, D. Self-Perforated Hydrogel N..."

== Citation ==

Scherr, J.; Parey, K.; Klusch, N.; Murphy, B. J.; Balser, S.; Neuhaus, A.; Zickermann, V.; Kühlbrandt, W.; Terfort, A. & Rhinow, D. Self-Perforated Hydrogel Nanomembranes Facilitate Structural Analysis of Proteins by Electron Cryo-Microscopy. ACS nano, 2017, 11, 6467-6473

== Abstract ==

We developed a method to improve specimen preparation for electron cryo-microscopy of membrane proteins. The method features a perforated hydrogel nanomembrane that stabilizes the thin film of aqueous buffer spanning the holes of holey carbon films, while at the same time preventing the depletion of protein molecules from these holes. The membrane is obtained by cross-linking of thiolated polyglycerol dendrimer films on gold, which self-perforate upon transfer to holey carbon substrates, forming a sub-micron-sized hydrogel network. The perforated nanomembrane improves the distribution of the protein molecules in the ice considerably. This facilitates data acquisition as demonstrated with two eukaryotic membrane protein complexes.

== Keywords ==

== Links ==

https://www.ncbi.nlm.nih.gov/pubmed/28598595

== Related software ==

== Related methods ==

== Comments ==

Main Page

2017-07-04T06:00:20Z

CoSS: /* Sample preparation */

== Presentation ==

This web page is intended to be an extensive repository of three-dimensional electron microscopy (3DEM) methods. The advantages of having such a repository are

* You know which are the relevant articles in a particular topic, therefore, paper introductions, reviews, etc. are easier to write and you make sure you will cite all the related articles.
* You will be sure that your paper has more chances of being cited.
* You can add whatever information you find relevant to your method, external links, links to other papers, etc.
* You can link your method to a web page providing the corresponding software, so you know people can use your algorithms.
* You can use the Wiki search capabilities to locate relevant articles even if they are not at the topic you are looking at.
* As a community we will "reconstruct" our history.
* You can select the "watch" option above to receive notifications in case of further changes in the Main Page.

Developing image processing methods for 3DEM is not "[[well-paid]]" in terms of citations and impact factor. However, it is crucial for the advance of the field. Gathering methodological papers in a portal will help to increase the recognition of the field.

Please:

* Add your articles at the right place (you can add a single article in several topics if it is relevant to all of them). The easiest way to add an article is by editing the corresponding topic in the main page, adding your entry, then save the main page. Click on the red link that appears on your new entry, copy and paste the Wiki following code, add the information of your article

== Citation ==

== Abstract ==

== Keywords ==

== Links ==

== Related software ==

== Related methods ==

== Comments ==

* Maintain the information of each article as complete as possible.
* Sort articles by years and authors.
* Be respectful to other people's work.

== How to subscribe to this page ==

You may subscribe to this page so that you will be notified every time someone adds a new method. To do so, you have to register in the page, and edit your preferences ("my preferences"). Be sure that you have activated the option "E-mail me when a page on my watchlist is changed". Finally, click on the "Watch" tab at the top of this page.

You may subscribe to changes on this page on the mailing list 3demmethods@cnb.csic.es. To send a new method to this mail list just send a mail to 3demmethods@cnb.csic.es

To subscribe to this list, visit the web page

https://listas.csic.es/cnb/wws/subscribe/3demmethods

Alternatively, you may write a mail to sympa6@cnb.csic.es with the subject

<code>subscribe 3demmethods YourName YourFamilyName</code>

and an empty mail body.

To unsubscribe visit the page

https://listas.csic.es/cnb/wws/sigrequest/3demmethods

or write sympa6@cnb.csic.es with the subject

<code>unsubscribe 3demmethods</code>

and an empty mail body.

== Electron microscopy images ==

=== Online courses ===

CALTECH: http://cryo-em-course.caltech.edu/

MRC: ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/EM-course/

CNB-CSIC: http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/MadridJan2014EM

Workshop on Computational methods for CryoEM: https://www.youtube.com/watch?v=XdKO1iaPP8o

Workshop on Management of large CryoEM facilities: https://www.youtube.com/watch?v=as4seOPszL0

Icknield Course on Model Building and Refinement for High Resolution EM Maps: http://www.ccpem.ac.uk/training/icknield_2017/icknield_2017.php

=== Image formation ===

{|

| Paper
| [[1971Erickson_CTF]]
| CTF model
|-

| Paper
| [[1971Glaeser_Damage]]
| Radiation damage
|-

| Chapter
| [[1971Hanszen_CTF]]
| Image formation model
|-

| Paper
| [[1971Thon_Model]]
| CTF model
|-

| Paper
| [[1975Unwin_Imaging]]
| Radiation dose
|-

| Paper
| [[1977Wade_Model]]
| CTF model
|-

| Paper
| [[1978Wade_Model]]
| CTF model
|-

| Paper
| [[1979Hayward_Radiation]]
| Radiation damage
|-

| Paper
| [[1984Cohen_Validity]]
| Validity of the CTF model at high frequencies
|-

| Paper
| [[1988Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[1992Wade_Model]]
| CTF model
|-

| Paper
| [[1993Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2004Egerton_Damage]]
| Radiation damage
|-

| Paper
| [[2004Sorzano_Normalization]]
| Background noise is Gaussian
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2009Baxter_NoiseCharacterization]]
| Characterization of the different noise sources in cryo-EM
|-

| Paper
| [[2010Baker_Damage]]
| Radiation damage dependence on resolution
|-

| Paper
| [[2010Bammes_Damage]]
| Radiation damage dependence on temperature
|-

| Paper
| [[2010Gomez_Multislice]]
| Simulation of the multi slice model
|-

| Paper
| [[2010Zewail_FourDimensional]]
| Review on the use of ultrafast EM
|-

| Paper
| [[2011Bammes_CCD]]
| Performance of CCD cameras
|-

| Paper
| [[2011Glaeser_Coma]]
| Image formation model including coma
|-

| Paper
| [[2011Milazzo_DirectDetectors]]
| Evaluation of Direct Detectors
|-

| Paper
| [[2011Rullgard_ImageSimulation]]
| Accurate simulation of EM images
|-

| Paper
| [[2011Zhang LimitingFactors]]
| Limiting factor for atomic resolution in EM
|-

| Paper
| [[2012Bammes_DirectDetection]]
| Performance of Direct detectors
|-

| Paper
| [[2012Campbell_MotionCorrection]]
| Beam induced motion correction and direct detectors
|-

| Paper
| [[2012Shang_HydrationLayer]]
| Simulation of PDB volumes explicitly considering the hydration layer
|-

| Paper
| [[2013Egerton_RadiationDamage]]
| Review of TEM radiation damage and experimental ways of reducing it
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu H_Noisemodels]]
| Noise models and cryo-EM drift correction with a direct-electron camera
|-

| Paper
| [[2013Li X K2 noisemodels]]
| Influence of electron dose rate on electron counting images recorded with the K2 camera
|-

| Paper
| [[2013Vulovic_CTFApproximations]]
| When to use the different approximations performed so that a projection with linear CTF is valid
|-

| Thesis
| [[2013Vulovic_ImageFormation]]
| Ph.D. Thesis on the image formation in cryo-EM
|-

| Paper
| [[2014Danev_PhasePlate]]
| Volta potential phase plate
|-

| Paper
| [[2015Chiu_K2]]
| Characterization of K2
|-

| Paper
| [[2015Hawkes_AberrationCorrection]]
| Historical account of the development of lens corrections
|-

| Paper
| [[2015Koeck_Quadratic]]
| Limitations of the linear approximation and use of the quadratic terms
|-

| Paper
| [[2015Kuijper_FEI]]
| Description of the FEI Falcons
|-

| Paper
| [[2015Lobato_MULTEM]]
| Simulation of multislice diffraction
|-

| Paper
| [[2015McMullan_AmorphousIce]]
| Beam induced movement is caused by Brownian motion
|-

| Paper
| [[2016Koeck_ADF]]
| Simulations of Annular Dark Field TEM
|-

| Paper
| [[2017Mishyna_DNARadiation]]
| Review of radiation damage on DNA
|-

|}

=== Collection geometry ===

{|

| Chapter
| [[1980Hoppe_Wedge]]
| Missing wedge
|-

| Paper
| [[1987Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1995Penczek_Dual]]
| Dual axis tomography
|-

| Paper
| [[1997Mastronarde_Dual]]
| Dual axis tomography
|-

| Paper
| [[2003Ludtke_FocusPairs]]
| Focus pairs for single particles
|-

| Paper
| [[2005Lanzavecchia_Conical]]
| Conical tomography
|-

| Paper
| [[2005Zampighi_Conical]]
| Conical tomography
|-

| Paper
| [[2006Leschziner_OT]]
| Orthogonal Tilt
|-

| Paper
| [[2006Messaoudi_Multiple]]
| Multiple axis tomography
|-

| Paper
| [[2012Kudryashev_FocusPairs]]
| Focus pairs tomography
|-

| Paper
| [[2014Hovden_TiltFocus]]
| Combining tilt series with focus series
|-

| Paper
| [[2015Sorzano_RandomConicalTilt]]
| General formulation of Random Conical Tilt
|-

| Paper
| [[2017Hagen_DoseTomography]]
| Dose optimization for subtomogram averaging
|-

|}

=== Sample preparation ===

{|

| Paper
| [[1982Dubochet_Sample]]
| Vitreous ice
|-

| Paper
| [[1986Lepault_Sample]]
| Fast freezing
|-

| Paper
| [[1995Dubochet_Sample]]
| High-pressure freezing
|-

| Paper
| [[1995VanMarle_Sample]]
| Sample damages in resin
|-

| Paper
| [[1998Adrian_Sample]]
| Cryo negative staining
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2002Hsieh_Sample]]
| Cryofixation
|-

| Paper
| [[2004AlAmoudi_Sample]]
| CEMOVIS
|-

| Paper
| [[2008Studer_Sample]]
| Review on high pressure freezing
|-

| Paper
| [[2009Pierson_Sample]]
| Review on sample preparation for electron tomography
|-

| Paper
| [[2010Zhang_NegativeStaining]]
| Negative staining for small protein imaging
|-

| Paper
| [[2012Zhang_PositiveStaining]]
| Positive staining
|-

| Paper
| [[2014Rames_NegativeStaining]]
| Optimized negative staining
|-

| Paper
| [[2014Russo_GoldGrids]]
| Gold grids for single particles
|-

| Paper
| [[2015Cabra_Sample]]
| Review on sample preparation for single particles with videos
|-

| Paper
| [[2016Passmore_Review]]
| Tutorial chapter on sample preparation
|-

| Paper
| [[2016Razinkov_Vitrification]]
| New vitrification method
|-

| Paper
| [[2016Takizawa_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2016Thompson_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2017Arnold_BlottingFree]]
| Blotting-free preparation
|-

| Paper
| [[2017Feng_SprayingPlunging]]
| Spraying plunging
|-

| Paper
| [[2017Peitsch_Sample]]
| iMEM: Isolation of Plasma Membrane for Cryoelectron Microscopy
|-

| Paper
| [[2017Scapin_Storage]]
| Cryo storage of samples
|-

| Paper
| [[2017Schaffer_FocusedIonBeam]]
| Focused Ion Beam sample preparation for membrane proteins
|-

| Paper
| [[2017Scherr_HydrogelNanomembranes]]
| Sample preparation for membrane proteins
|-

|}

=== Automated data collection ===

{|

| Paper
| [[1992Dierksen_Automatic]]
| Automated data collection
|-

| Paper
| [[1992Koster_Automatic]]
| Automated data collection
|-

| Paper
| [[1996Fung_Automatic]]
| Automated data collection for tomography
|-

| Paper
| [[2001Zhang_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2003Ziese_Automatic]]
| Automated autofocusing
|-

| Paper
| [[2004Potter_Automatic]]
| Automated sample loading
|-

| Paper
| [[2004Zheng_Automatic]]
| Automated data collection
|-

| Paper
| [[2005Lei_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2005Suloway_Automatic]]
| Automated data collection: Leginon
|-

| Paper
| [[2007Yoshioka_RCT]]
| Automated Random Conical Tilt
|-

| Paper
| [[2011Korinek_TOM2]]
| Automated acquisition with TOM2
|-

| Paper
| [[2015Li_UCSFImage]]
| Automated acquisition with UCSFImage
|-

| Paper
| [[2016Gil_Fuzzy]]
| Real time decisions during acquisition with neuro-fuzzy method
|-

| Paper
| [[2016Liu_TiltControl]]
| Accurate control of the tilt angle for electron tomography
|-

| Paper
| [[2016Vargas_FoilHole]]
| Determination of image quality at low magnification
|-

| Paper
| [[2017Biyani_Focus]]
| Automatic processing of micrographs
|-

|}

== Single particles ==

=== Automatic particle picking ===

{|

| Paper
| [[1982VanHeel_Detection]]
| Detection of particles in micrographs
|-

| Paper
| [[2001Nicholson_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2001Zhu_Filaments]]
| Automatic identification of filaments in micrographs
|-

| Paper
| [[2004Sigworth_Detection]]
| Classical detection theory and the cryo-EM particle selection problem
|-

| Paper
| [[2004Volkmann_ParticlePicking]]
| An approach to automated particle picking from electron micrographs based on reduced representation templates
|-

| Paper
| [[2004Wong_ParticlePicking]]
| Model-based particle picking for cryo-electron microscopy
|-

| Paper
| [[2004Zhu_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2007Chen_Signature]]
| Automatic particle picking program: Signature
|-

| Paper
| [[2007Woolford_SwarmPS]]
| Automatic particle picking with several criteria, implemented in EMAN Boxer
|-

| Paper
| [[2009Sorzano_MachineLearning]]
| Automatic particle picking based on machine learning of rotational invariants
|-

| Paper
| [[2011Arbelaez_Comparison]]
| Evaluation of the performance of software for automated particle-boxing
|-

| Paper
| [[2013Abrishami_MachineLearning]]
| A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs
|-

| Paper
| [[2013Hauer_2013]]
| Automatic tilt pair detection in Random Conical Tilt
|-

| Paper
| [[2013Shatsky_ParticlePicking]]
| Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Langlois_ParticlePicking]]
| Automatic particle picking
|-

| Paper
| [[2016Vilas_AutomaticTilt]]
| Automatic identification of image pairs in untilted-tilted micrograph pairs
|-

|}

=== 2D Preprocessing ===

{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast enhancement through DPR
|-

| Paper
| [[2004Sorzano_Normalization]]
| Normalization procedures and their statistical properties.
|-

| Paper
| [[2006Sorzano_Denoising]]
| Strong denoising in wavelet space
|-

| Conference
| [[2009Sorzano_Downsampling]]
| Differences between the different downsampling schemes
|-

| Paper
| [[2012Brilot_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Campbell_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Zhao_Denoising]]
| Denoising using an invariant Fourier-Bessel eigenspace
|-

| Paper
| [[2013Norousi_Screening]]
| Screening particles to identify outliers
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu_Movies]]
| Drift correction for movies considering dark field
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Scheres_Movies]]
| Beam induced motion correction
|-

| Paper
| [[2015Abrishami_Movies]]
| Alignment of direct detection device micrographs
|-

| Paper
| [[2015Grant_Anisotropic]]
| Automatic estimation and correction of anisotropic magnification
|-

| Paper
| [[2015Grant_OptimalExposure]]
| Filter movies according to the radiation damage
|-

| Paper
| [[2015Rubinstein_Alignment]]
| Frame alignment at the level of particle
|-

| Paper
| [[2015Spear_DoseCompensation]]
| Effect of dose compensation on resolution
|-

| Paper
| [[2015Zhao_AnisotropicMagnification]]
| Correction of anisotropic magnification
|-

| Conference
| [[2016Bajic_Denoising]]
| Denoising and deconvolution of micrographs
|-

| Paper
| [[2016Jensen_RemovalVesicles]]
| Removal of vesicles in membrane proteins
|-

| Paper
| [[2016Bhamre_Denoising]]
| Denoising by 2D covariance estimation
|-

| Paper
| [[2017McLeod_Zorro]]
| Movie alignment by Zorro
|-

| Paper
| [[2017Zheng_MotionCorr2]]
| Movie alignment by MotionCorr2
|-

|}

=== 2D Alignment ===

{|

| Paper
| [[1981Frank_Averaging]]
| 2D averaging and phase residual
|-

| Paper
| [[1982Saxton_Averaging]]
| 2D averaging using correlation
|-

| Paper
| [[1998Sigworth_ML2D]]
| Maximum likelihood alignment in 2D
|-

| Paper
| [[2003Cong_FRM2D]]
| Fast Rotational Matching in 2D
|-

| Paper
| [[2005Cong_FRM2D]]
| Fast Rotational Matching in 2D introduced in a 3D Alignment algorithm
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

|}

=== 2D Classification and clustering ===

{|

| Paper
| [[1981VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[1984VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2011Singer_DiffusionMaps]]
| Classification in 2D based on graph analysis of the projections
|-

| Paper
| [[2012Yang_ISAC]]
| Iterative Stable Alignment and clustering
|-

| Paper
| [[2014Sorzano_Outlier]]
| Outlier detection in 2D classifications.
|-

| Paper
| [[2014Zhao_Aspire]]
| Fast classification based on rotational invariants and vector diffusion maps
|-

| Paper
| [[2015Huang_Robust]]
| Robust w-estimators of 2D classes
|-

| Paper
| [[2016Reboul_Stochastic]]
| Stochastic Hill Climbing for calculating 2D classes
|-

| Conference
| [[2017Bhamre_Mahalanobis]]
| 2D classification using Mahalanobis distance
|-

|}

=== 3D Alignment ===

{|

| Paper
| [[1980Kam_AutoCorrelation]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[1986Goncharov_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1987VanHeel_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1988Provencher_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Vogel_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1990Gelfand_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Goncharov_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Harauz_Quaternions]]
| Use of quaternions to represent rotations
|-

| Paper
| [[1994Penczek_Real]]
| Angular assignment using projection matching in real space
|-

| Paper
| [[1994Radermacher_Radon]]
| Angular assignment in Radon space
|-

| Paper
| [[1996Penczek_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[2003Rosenthal_DPR]]
| Angular assignment using DPR
|-

| Paper
| [[2004Sorzano_Wavelet]]
| Angular assignment in the wavelet space.
|-

| Paper
| [[2005Jonic_Splines]]
| Angular assignment in Fourier space using spline interpolation.
|-

| Paper
| [[2005Yang_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[2006Ogura_SimulatedAnnealing]]
| Angular asignment by simulated annealing
|-

| Paper
| [[2007Grigorieff_Continuous]]
| Continuous angular assignment in Fourier space
|-

| Paper
| [[2010Jaitly_Bayesian]]
| Angular assignment by a Bayesian method and annealing
|-

| Paper
| [[2010Sanz_Random]]
| Random model method
|-

| Paper
| [[2010Singer_Voting]]
| Detecting consistent common lines by voting (reference free)
|-

| Paper
| [[2011Singer_SDP]]
| Angular assignment by semidefinite programming and eigenvectors (reference free)
|-

| Paper
| [[2012Giannakis_Scattering]]
| Construction of an initial volume, reference free, by graph analysis of the projections
|-

| Paper
| [[2012Shkolnisky_Sync]]
| Angular assignment by synchronization of rotations (reference free)
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Wang_LUD]]
| Angular assignment by least unsquared deviations (reference free)
|-

| Paper
| [[2014Vargas_RANSAC]]
| Initial model using RANSAC (reference free)
|-

| Paper
| [[2015Joubert_Pseudoatoms]]
| Initial model based on pseudo-atoms
|-

| Paper
| [[2015Singer_Kam]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[2015Sorzano_Significant]]
| Statistical approach to the initial volume estimation (reconstruct significant)
|-

| Conference
| [[2016Michels_Heterogeneous]]
| Initial volume in the presence of heterogeneity
|-

| Paper
| [[2016Cossio_BayesianGPU]]
| GPU implementation of the Bayesian 3D reconstruction approach
|-

|}

=== 3D Reconstruction ===
{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1986Harauz_FBP]]
| Exact filters for Filtered Back Projection
|-

| Chapter
| [[1992Radermacher_WBP]]
| Exact filters for Weighted Back Projection
|-

| Paper
| [[1997Zhu_RecCTF]]
| 3D Reconstruction (SIRT like) and simultaneous CTF correction
|-

| Paper
| [[1998Boisset_Uneven]]
| Artifacts in SIRT and WBP under uneven angular distributions
|-

| Paper
| [[1998Marabini_ART]]
| Algebraic Reconstruction Technique with blobs (Xmipp)
|-

| Paper
| [[2001Sorzano_Uneven]]
| Free parameter selection under uneven angular distributions
|-

| Paper
| [[2005Sorzano_Parameters]]
| Free parameter selection for optimizing multiple tasks
|-

| Paper
| [[2008Sorzano_Constraints]]
| Mass, surface, positivity and symmetry constraints for real-space algorithms
|-

| Paper
| [[2009Bilbao_ParallelART]]
| Efficient parallelization of ART
|-

| Paper
| [[2011Li_GradientFlow]]
| Regularized 3D Reconstruction by Gradient Flow
|-

| Paper
| [[2011Vonesch_Wavelets]]
| Fast wavelet-based 3D reconstruction
|-

| Paper
| [[2012Gopinath_ShapeRegularization]]
| Regularized 3D Reconstruction by Shape information
|-

| Paper
| [[2012Kucukelbir_adaptiveBasis]]
| 3D reconstruction in an adaptive basis promoting sparsity
|-

| Paper
| [[2012Sindelar_NoiseReduction]]
| Optimal noise reduction in 3D reconstructions
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Lyumkis_Optimod]]
| Construction of initial volumes with Optimod
|-

| Paper
| [[2013Wang FIRM]]
| Fast 3D reconstruction in Fourier domain
|-

| Paper
| [[2014Kunz_SART_OS]]
| Simultaneous ART with OS
|-

| Paper
| [[2015Abrishami_Fourier]]
| 3D Reconstruction in Fourier space
|-

| Paper
| [[2015Dvornek_SubspaceEM]]
| Fast Maximum a posteriori
|-

| Paper
| [[2015Moriya_Bayesian]]
| Bayesian approach to suppress limited angular artifacts
|-

| Paper
| [[2015Xu_GeometricFlow]]
| Multi-scale geometric flow
|-

| Arxiv
| [[2016Ye_Cohomology]]
| Cohomology properties of 3D reconstruction
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

| Paper
| [[2017Punjani_CryoSPARCTheory]]
| Theory related to CryoSPARC
|-

|}

=== 3D Heterogeneity ===

{|

| Paper
| [[2004White_Size]]
| Heterogeneity classification of differently sized images
|-

| Paper
| [[2006Penczek_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Scheres_ML3D]]
| Maximum Likelihood alignment and classification in 3D
|-

| Paper
| [[2009Spahn_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2010Elmlund_AbInitio]]
| Solving the initial volume problem with multiple conformations
|-

| Paper
| [[2010Shatsky_MultiVariate]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2012Scheres_Bayesian]]
| A Bayesian view on cryo-EM structure determination
|-

| Paper
| [[2012Zheng_Covariance]]
| Estimation of the volume covariance
|-

| Paper
| [[2013Wang_MLVariance]]
| Maximum Likelihood estimate of the map variance
|-

| Paper
| [[2013Lyumkis D_FREALIGN]]
| Likelihood-based classification of cryo-EM images using FREALIGN.
|-

| Paper
| [[2014Jin_NMA]]
| Continuous heterogeneity through Normal Mode Analysis
|-

| Paper
| [[2014Dashti_Brownian]]
| Continuous heterogeneity through Brownian trajectories
|-

| Paper
| [[2014Chen_Migration]]
| Particle migration analysis in 3D classification
|-

| Paper
| [[2015Anden_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Bai_Focused]]
| Focused classification
|-

| Paper
| [[2015Katsevich_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Klaholz_MRA]]
| Multivariate Statistical Analysis of Jackknife and Bootstrapping on random subsets
|-

| Paper
| [[2015Liao_Covariance]]
| Estimation of the 3D covariance from 2D projections
|-

| Paper
| [[2015Tagare_Direct]]
| Direct reconstruction of PCA components
|-

| Paper
| [[2016Gong_Mechanical]]
| Mechanical model for macromolecules
|-

| Paper
| [[2016Rawson_Movement]]
| Movement and flexibility
|-

| Paper
| [[2016Sorzano_StructMap]]
| Sorting a discrete set of conformational states
|-

| Paper
| [[2016Sorzano_Strain]]
| Calculate local stretches, strains and rotations from two conformational states
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

|}

=== Validation ===

{|

| Paper
| [[2008Stagg_TestBed]]
| Effect of voltage, dosis, number of particles and Euler jumps on resolution
|-

| Paper
| [[2011Henderson]]
| Tilt Validation
|-

| Paper
| [[2011Read]]
| Validation of PDBs
|-

| Paper
| [[2012Henderson]]
| EM Map Validation
|-

| Paper
| [[2013Cossio_Bayesian]]
| EM Map Validation in a probabilistic setting
|-

| Paper
| [[2013Chen_NoiseSubstitution]]
| Noise substitution at high resolution for measuring overfitting
|-

| Paper
| [[2014Russo_StatisticalSignificance]]
| EM Map Validation through the statistical significance of the tilt-pair angular assignment
|-

| Paper
| [[2014Stagg_Reslog]]
| EM Map Validation through the resolution evolution with the number of particles
|-

| Paper
| [[2014Wasilewski_Tilt]]
| Web implementation of the tilt pair validation
|-

| Paper
| [[2015Heymann_Alignability]]
| EM Map Validation through the resolution of reconstructions from particles and noise
|-

| Paper
| [[2015Oliveira_FreqLimited]]
| Comparison of gold standard and frequency limited optimization
|-

| Paper
| [[2015Wriggers_Secondary]]
| Validation by secondary structure
|-

| Paper
| [[2016Kim_SAXS]]
| Comparison of SAXS data and EM projections
|-

| Paper
| [[2016Rosenthal_Review]]
| Review of validation methods
|-

| Paper
| [[2016Vargas_Alignability]]
| Validation by studying the tendency of an angular assignment to cluster in the projection space
|-

| Paper
| [[2017Monroe_PDBRefinement]]
| Validation by comparison to a refined PDB
|-

|}

=== Resolution ===

{|

| Paper
| [[1986Harauz_FBP]]
| Fourier Shell Correlation
|-

| Paper
| [[1987Unser_SSNR]]
| 2D Spectral Signal to Noise Ratio
|-

| Paper
| [[2002Penczek_SSNR]]
| 3D Spectral Signal to Noise Ratio for Fourier based algorithms
|-

| Paper
| [[2003Rosenthal_DPR]]
| Review of the FSC and establishment of a new threshold
|-

| Paper
| [[2005Unser_SSNR]]
| 3D Spectral Signal to Noise Ratio for any kind of algorithms
|-

| Paper
| [[2005VanHeel_FSC]]
| Establishment of a new threshold for FSC
|-

| Paper
| [[2007Sousa_AbInitio]]
| Resolution measurement on neighbour Fourier voxels
|-

| Paper
| [[2014Kucukelbir_Local]]
| Quantifying the local resolution of cryo-EM density maps
|-

| Paper
| [[2016Pintilie_Probabilistic]]
| Probabilistic models and resolution
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Statistical properties of resolution measures defined in Fourier space
|-

|}

=== Sharpening of high resolution information ===
{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast restoration and map sharpening
|-

| Paper
| [[2008Fernandez_Bfactor]]
| Bfactor determination and restoration
|-

| Paper
| [[2013Fiddy_SaxtonAlgorithm]]
| Phase retrieval or extension
|-

| Paper
| [[2014Kishchenko_SphericalDeconvolution]]
| Spherical deconvolution
|-

| Paper
| [[2015Spiegel_VISDEM]]
| Visualization improvement by the use of pseudoatomic profiles
|-

| Paper
| [[2016Jonic_Pseudoatoms]]
| Approximation with pseudoatoms
|-

| Paper
| [[2016Jonic_Denoising]]
| Denoising and high-frequency boosting by pseudoatom approximation
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[1982Schiske_Correction]]
| CTF correction for tilted objects
|-

| Paper
| [[1988Toyoshima_Model]]
| CTF estimation
|-

| Paper
| [[1995Frank_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1996Skoglund_MaxEnt]]
| CTF correction with Maximum Entropy
|-

| Paper
| [[1996Zhou_Model]]
| CTF model and user interface for manual fitting
|-

| Paper
| [[1997Fernandez_AR]]
| PSD estimation using periodogram averaging and AR models
|-

| Paper
| [[1997Penczek_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1997Stark_Deconvolution]]
| CTF correction using deconvolution
|-

| Paper
| [[1997Zhu_RecCTF]]
| CTF correction and reconstruction
|-

| Paper
| [[2000DeRosier_EwaldCorrection]]
| CTF correction considering the Ewald sphere
|-

| Paper
| [[2000Jensen_TiltedCorrection]]
| CTF correction considering tilt in backprojection
|-

| Paper
| [[2001Saad_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Huang_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Mindell_CTFTILT]]
| CTF estimation for tilted micrographs
|-

| Paper
| [[2003Sander_MSA]]
| CTF estimation through MSA classification of PSDs
|-

| Paper
| [[2003Velazquez_ARMA]]
| PSD and CTF estimation using ARMA models
|-

| Paper
| [[2004Sorzano_IDR]]
| CTF restoration and reconstruction with Iterative Data Refinement
|-

| Conference
| [[2004Wan_CTF]]
| Spatially variant CTF
|-

| Paper
| [[2004Zubelli_Chahine]]
| CTF restoration and reconstruction with Chahine's multiplicative method
|-

| Conference
| [[2005Dubowy_SpaceVariant]]
| CTF correction when this is space variant
|-

| Paper
| [[2005Mallick_ACE]]
| CTF estimation
|-

| Paper
| [[2006Wolf_Ewald]]
| CTF correction considering Ewald sphere
|-

| Paper
| [[2007Jonic_EnhancedPSD]]
| PSD enhancement for better identification of Thon rings; Vitreous ice diffracts in Thon rings
|-

| Paper
| [[2007Philippsen_Model]]
| CTF Model for tilted specimens
|-

| Paper
| [[2007Sorzano_CTF]]
| CTF estimation using enhanced PSDs
|-

| Paper
| [[2009Sorzano_Sensitivity]]
| Error sensitivity of the CTF models, non-uniqueness of the CTF parameters
|-

| Paper
| [[2010Jiang2010_CTFCorrection]]
| Amplitude correction method
|-

| Paper
| [[2010Kasantsev_CTFCorrection]]
| Mathematical foundations of Kornberg and Jensen method
|-

| Paper
| [[2010Leong_CTFCorrection]]
| Correction for spatially variant CTF
|-

| Paper
| [[2011Glaeser_Coma]]
| The effect of coma at high-resolution
|-

| Paper
| [[2011Mariani_Tilted]]
| CTF simulation and correction of tilted specimens
|-

| Paper
| [[2011Sindelar_Wiener]]
| CTF correction using a modified version of Wiener filter
|-

| Paper
| [[2011Voortman_Tilted]]
| CTF correction for tilted specimen
|-

| Paper
| [[2012Voortman_VaryingCTF]]
| Correcting a spatially varying CTF
|-

| Paper
| [[2013Vargas_FastDef]]
| Fast defocus
|-

| Paper
| [[2015Rohou_CTFFind4]]
| CTF Find 4
|-

| Paper
| [[2015Sheth_CTFquality]]
| Visualization and quality assessment of CTF
|-

| Paper
| [[2016Zhang_GCTF]]
| gCTF
|-

|}

=== Segmentation ===

{|

| Paper
| [[2006Baker_segmentation]]
| Segmentation of molecular subunits
|-

|}

=== Fitting and docking ===

{|

| Paper
| [[1999Volkmann_Fitting]]
| Fitting in real space
|-

| Paper
| [[2001Baker_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2001Jones_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2003Kovacs_FRM3D]]
| Fast Rotational Alignment of two EM maps
|-

| Paper
| [[2004Tama_NMA1]]
| Flexible fitting with Normal Modes (I)
|-

| Paper
| [[2004Tama_NMA2]]
| Flexible fitting with Normal Modes (II)
|-

| Paper
| [[2005Velazquez_Superfamilies]]
| Recognition of the superfamily folding in medium-high resolution volumes
|-

| Paper
| [[2007DeVries_Haddock]]
| Docking with Haddock 2.0
|-

| Paper
| [[2007Kleywegt_QualityControl]]
| Quality control and validation of fitting
|-

| Paper
| [[2012Biswas_Secondary]]
| Secondary structure determination in EM volumes
|-

| Paper
| [[2012Velazquez_Constraints]]
| Multicomponent fitting by using constraints from other information sources
|-

| Paper
| [[2013Chapman MS_Atomicmodeling]]
| Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters
|-

| Paper
| [[2013Esquivel_Modelling]]
| Review on modelling (secondary structure, fitting, ...)
|-

| Paper
| [[2013Lopez_Imodfit]]
| Fitting based on vibrational analysis
|-

| Paper
| [[2013Nogales_3DEMLoupe]]
| Normal Mode Analysis of reconstructed volumes
|-

| Paper
| [[2014AlNasr_Secondary]]
| Identification of secondary structure elements in EM volumes
|-

| Paper
| [[2014Politis_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Rey_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Villa_Review]]
| Review of atomic fitting into EM volumes
|-

| Paper
| [[2015Barad_EMRinger]]
| Validation of hybrid models
|-

| Paper
| [[2015Bettadapura_PF2Fit]]
| Fast rigid fitting of PDBs into EM maps
|-

| Paper
| [[2015Carrillo_CapsidMaps]]
| Analysis of virus capsids using Google Maps
|-

| Paper
| [[2015Schroeder_Hybrid]]
| Review on model building
|-

| Paper
| [[2015Tamo_Dynamics]]
| Dynamics in integrative modeling
|-

| Paper
| [[2015Sorzano_AtomsToVoxels]]
| Accurate conversion of an atomic model into a voxel density volume
|-

| Paper
| [[2016Joseph_Evolution]]
| Evolutionary constraints for the fitting of atomic models into density maps
|-

| Paper
| [[2016Segura_3Diana]]
| Validation of hybrid models
|-

| Paper
| [[2016Singharoy_MDFF]]
| Construction of hybrid models driven by EM density and molecular dynamics
|-

| Paper
| [[2016Wang_Rosetta]]
| Construction of hybrid models driven by EM density using Rosetta
|-

| Paper
| [[2017Joseph_Metrics]]
| Metrics analysis for the comparison of structures
|-

| Paper
| [[2017Hryc_WeightedAtoms]]
| Construction of hybrid models by locally weighting the different atoms
|-

| Paper
| [[2017Matsumoto_Distribution]]
| Estimating the distribution of conformations of atomic models
|-

| Paper
| [[2017Miyashita_EnsembleFitting]]
| Ensemble fitting using Molecular Dynamics
|-

|}

=== Books and reviews ===

{|

| Book
| [[1980Herman_Tomography]]
| General book on tomography
|-

| Book
| [[1988Kak_Tomography]]
| General book on tomography
|-

| Paper
| [[2000Tao_Review]]
| Review of single particles
|-

| Paper
| [[2000VanHeel_Review]]
| Review of single particles
|-

| Paper
| [[2002Frank_Review]]
| Review of single particles
|-

| Paper
| [[2002Schmid_Review]]
| Review of single particles
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2004Subramaniam_Review]]
| Review of single particles
|-

| Paper
| [[2005Steven_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_book]]
| Book covering all aspects of electron microscopy of single particles
|-

| Paper
| [[2006Sorzano_Review]]
| Review of optimization problems in electron microscopy
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems in Electron Tomography
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2008Mueller_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2008Taylor_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2010DeRosier_Review]]
| Personal account of how 3DEM developed in the early days
|-

| Chapter
| [[2012Sorzano_Review]]
| Review of single particle analysis using Xmipp
|-

| Chapter
| [[2012Devaux_Protocol]]
| Protocols for performing single particle analysis
|-

| Paper
| [[2014Bai_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Carazo_Review]]
| Review of the reconstruction process
|-

| Paper
| [[2015Cheng_Review]]
| A primer to Single Particle Cryo-EM
|-

| Paper
| [[2015Cheng_Reviewb]]
| Single Particle Cryo-EM at crystallographic resolution
|-

| Paper
| [[2015Elmlund_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Henderson_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Nogales_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Schroeder_Review]]
| Review of advances in the electron microscope
|-

| Paper
| [[2015Wu_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Carroni_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Egelman_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Eisenstein_CryoEM]]
| News feature on the Method of the Year
|-

| Paper
| [[2016FernandezLeiro_Review]]
| Review of EM
|-

| Paper
| [[2016Glaeser_HowGood]]
| How good can cryo-EM become?
|-

| Paper
| [[2016Jonic_PseudoAtoms]]
| Review of the applications of the use of pseudoatoms in EM
|-

| Chapter
| [[2016Mio_Review]]
| Overview of the process to obtain EM reconstructions
|-

| Paper
| [[2016Jonic_Review]]
| A review of computational ways to handle heterogeneity
|-

| Paper
| [[2016Nogales_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Subramaniam_Review]]
| Why cryo-EM is now suitable for crystallographic journals
|-

| Paper
| [[2016Vinothkumar_Review]]
| Historical review and current limitations
|-

| Paper
| [[2017Frank_Review]]
| Historical review of EM
|-

| Paper
| [[2017Jonic_Review]]
| Review of computational methods to analyze conformational variability
|-

| Paper
| [[2017Rawson_Limitations]]
| Limitations of EM for drug design
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Review of statistical properties of resolution measures defined in Fourier space
|-
|}

=== Software ===

{|

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[1999Lutdke_Eman]]
| Eman
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Baldwin_AngularTransformations]]
| The Transform Class in SPARX and EMAN2
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Grigorieff_Frealign]]
| Frealign
|-

| Paper
| [[2008Scheres_XmippProtocols]]
| Xmipp Protocols
|-

| Paper
| [[2008Shaikh_SpiderProtocols]]
| Spider Protocols
|-

| Paper
| [[2012Wriggers_SitusConventions]]
| Conventions and workflows in Situs
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2015Cianfrocco_Cloud]]
| Software execution in the cloud
|-

| Paper
| [[2015Cheng_MRC2014]]
| Extensions to MRC file format
|-

| Paper
| [[2013DeLaRosa_Scipion]]
| Scipion
|-

| Paper
| [[2016Scheres_Relion]]
| Tutorial on the use of Relion
|-

| Paper
| [[2016Grigorieff_Frealign]]
| Tutorial on the use of Frealign
|-

|}

== Electron tomography ==

=== Image preprocessing ===

{|

| Paper
| [[2015Yan_thickness]]
| Determination of thickness, tilt and electron mean free path
|-

|}

=== Image alignment ===

{|

| Paper
| [[1982Guckenberger_commonOrigin]]
| Determination of a common origin in the micrographs of titl series in three-dimensional electron microscopy
|-

| Paper
| [[1992Lawrence_leastSquares]]
| Least squares solution of the alignment problem
|-

| Paper
| [[1995Penczek_dual]]
| Dual tilt alignment
|-

| Paper
| [[1996Owen_alignmentQuality]]
| Automatic alignment without fiducial markers and evaluation of alignment quality
|-

| Paper
| [[1998Grimm_normalization]]
| Discussion of several gray level normalization methods for electron tomography
|-

| Paper
| [[2001Brandt_Automatic1]]
| Automatic alignment without fiducial markers
|-

| Paper
| [[2001Brandt_Automatic2]]
| Automatic alignment with fiducial markers
|-

| Paper
| [[2006Winkler_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2006Castano_alignment]]
| Alignment with non-perpendicularity
|-

| Paper
| [[2007Castano_alignment]]
| Fiducial-less alignment of cryo-sections
|-

| Paper
| [[2009Sorzano_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2010Cantele_dualAlignment]]
| Alignment of dual series
|-

| Paper
| [[2014Tomonaga_Automatic]]
| Automatic alignment of tilt series using the projection themselves
|-

| Paper
| [[2014Han_Automatic]]
| Automatic alignment of tilt series using SIFT features
|-

| Paper
| [[2015Han_Automatic]]
| Automatic alignment of tilt series using fiducials
|-

| Paper
| [[2017Mastronarde_Automatic]]
| Automatic alignment and reconstruction of tilt series in IMOD
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[2003Winkler_CTF]]
| Focus gradient correction in electron tomography
|-

| Paper
| [[2006Fernandez_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Zanetti_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Xiong_CTF]]
| CTF determination and correction for low dose tomographic tilt series
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2017Kunz_3DCTF]]
| 3D CTF Correction
|-

|}

=== 3D reconstruction ===

{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1992Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[1997Marabini_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2002Fernandez_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2007Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[2008Fernandez_CARP]]
| Component Averaged Row Projections (CARP)
|-

| Paper
| [[2012Herman General Superiorization]]
| Superiorization: an optimization heuristic for medical physics
|-

| Paper
| [[2012Zhang_IPET_FETR]]
| IPET and FETR, a reconstruction algorithm for single molecule tomography
|-

| Paper
| [[2013Goris_SIRT_TV_DART]]
| Combination of SIRT, Total Variation and Discrete ART to reconstruct and segment at the same time
|-

| Paper
| [[2013Briegel A_Challenge]]
| The challenge of determining handedness in electron tomography and the use of DNA origami gold nanoparticle helices as molecular standards
|-

| Paper
| [[2013Messaoudi_EnergyFiltered]]
| 3D Reconstruction of Energy-Filtered TEM
|-

| Paper
| [[2016Deng_ICON]]
| 3D Reconstruction with missing information restoration
|-

| Paper
| [[2016Guay_Compressed]]
| 3D Reconstruction using compressed sensing
|-

|}

=== Noise reduction ===
{|

| Paper
| [[2001Frangakis_NAD]]
| Noise reduction with Nonlinear Anisotropic Diffusion
|-

| Paper
| [[2003Fernandez_AND]]
| Anisotropic nonlinear diffusion for electron tomography
|-

| Paper
| [[2003Jiang_Bilateral]]
| Bilateral denoising filter in electron microscopy
|-

| Paper
| [[2005Fernandez_AND]]
| Anisotropic nonlinear denoising in electron tomography
|-

| Paper
| [[2007Heide_median]]
| Iterative median filtering in electron tomography
|-

| Paper
| [[2007Fernandez_autAND]]
| Anisotropic nonlinear diffusion with automated parameter tuning
|-

| Paper
| [[2009Fernandez_Beltrami]]
| Nonlinear filtering based on Beltrami flow
|-

| Paper
| [[2010Bilbao_MeanShift]]
| Mean Shift Filtering
|-

| Paper
| [[2014Kovacik_wedgeArtefacts]]
| Removal of wedge artefacts
|-

| Paper
| [[2014Maiorca_beadArtefacts]]
| Removal of gold bead artefacts
|-

|}

=== Segmentation ===

{|

| Paper
| [[2002Frangakis_Eigenanalysis]]
| Segmentation using eigenvector analysis.
|-

| Paper
| [[2002Volkmann_Watershed]]
| Segmentation using watershed transform.
|-

| Paper
| [[2003Bajaj_BoundarySegmentation]]
| Segmentation based on fast marching.
|-

| Paper
| [[2005Cyrklaff_Thresholding]]
| Segmentation using optimal thresholding.
|-

| Paper
| [[2007Lebbink_TemplateMatching]]
| Segmentation using template matching.
|-

| Paper
| [[2007Sandberg_OrientationFields]]
| Segmentation using orientation fields.
|-

| Paper
| [[2007Sandberg_SegmentationReview]]
| Review on segmentation in electron tomography.
|-

| Paper
| [[2008Garduno_FuzzySegmentation]]
| Segmentation using fuzzy set theory principles.
|-

| Paper
| [[2009Lebbink_TemplateMatching2]]
| Segmentation using template matching.
|-

| Paper
| [[2012RubbiyaAli_EdgeDetection]]
| Parameter-Free Segmentation of Macromolecular Structures.
|-

| Conference
| [[2015Xu_TemplateMatching]]
| Detection of macromolecular complexes with a reduced representation of the templates.
|-

|}

=== Resolution ===
{|

| Paper
| [[2005Cardone_Resolution]]
| Resolution criterion for electron tomography
|-

| Chapter
| [[2007Penczek_Resolution]]
| Review of resolution criteria for electron tomography
|-

| Paper
| [[2015Diebolder_ConicalFSC]]
| Conical Fourier Shell Correlation
|-

|}

=== Subtomogram analysis ===

{|

| Paper
| [[2000Bohm_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2002Frangakis_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2006Nickell_Review]]
| Review of macromolecule finding by template matching (Visual Proteomics)
|-

| Paper
| [[2007Best_Review]]
| Review of Localization of Protein Complexes by Pattern Recognition
|-

| Paper
| [[2007Forster_Review]]
| Review of structure determination by subtomogram averaging
|-

| Paper
| [[2008Forster_Classification]]
| Classification of subtomograms using constrained correlation
|-

| Paper
| [[2008Bartesaghi_Classification]]
| Classification and averaging of subtomograms
|-

| Paper
| [[2008Schmid_Averaging]]
| Alignment and averaging of subtomograms
|-

| Paper
| [[2010Amat_Averaging]]
| Alignment and averaging of subtomograms exploiting thresholding in Fourier space
|-

| Paper
| [[2013Chen_Averaging]]
| Fast alignment of subtomograms using spherical harmonics
|-

| Paper
| [[2013Kuybeda_Averaging]]
| Alignment and averaging of subtomograms using the nuclear norm of the cluster
|-

| Paper
| [[2013Shatsky_Averaging]]
| Alignment and averaging of subtomograms with constrained cross-correlation
|-

| Paper
| [[2014Chen_Autofocus]]
| Subtomogram averaging and classification with special attention to differences
|-

| Paper
| [[2014Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2014Voortman_LimitingFactors]]
| Limiting factors of subtomogram averaging
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2015Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2016Bharat_Relion]]
| Subtomogram averaging with Relion
|-

| Paper
| [[2016Song_MatrixNorm]]
| Matrix norm minimization for tomographic reconstruction and alignment
|-

| Paper
| [[2017Castano_ParticlePicking]]
| Particle picking in tomograms for subtomogram averaging
|-

| Paper
| [[2017Frazier_Tomominer]]
| TomoMiner a software platform for large-scale subtomogram analysis
|-

|}

=== Single particle tomography ===

{|

| Paper
| [[2012Bartesaghi_Constrained]]
| 3D reconstruction by imposing geometrical constraints
|-

| Paper
| [[2015Galaz_SingleParticleTomography]]
| Set of tools for Single Particle Tomography in EMAN2
|-

| Paper
| [[2016Galaz_SingleParticleTomography]]
| Alignment algorithms and CTF correction
|-

|}

=== Books and reviews ===

{|

| Paper
| [[2000Baumeister_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Koster_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Sali_Review]]
| Review of electron tomography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2005Lucic_Review]]
| Review of electron tomography
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_TomoBook]]
| Electron Tomography
|-

| Book
| [[2007McIntosh_Book]]
| Cellular Electron Microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2012Kudryashev_Review]]
| Review of subtomogram averaging
|-

| Paper
| [[2016Beck_Review]]
| Review of molecular sociology
|-

|}

=== Software ===

{|

| Paper
| [[1996Kremer_IMOD]]
| IMOD
|-

| Paper
| [[1996Chen_Priism/IVE]]
| Priism/IVE
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2005Nickell_TOM]]
| TOM Toolbox
|-

| Paper
| [[2007Messaoudi_TomoJ]]
| TomoJ
|-

| Paper
| [[2008Heymann_BsoftTomo]]
| Bsoft
|-

| Paper
| [[2015Ding_CaltechTomography]]
| Caltech tomography database
|-

| Paper
| [[2015Noble_AppionProtomo]]
| Batch fiducial-less tilt-series alignment in Appion using Protomo
|-

| Paper
| [[2015vanAarle_Astra]]
| ASTRA Toolbox
|-

| Paper
| [[2017Wan_Simulator]]
| Electron Tomography Simulator
|-

|}

== 2D Crystals ==

=== 2D Preprocessing ===

{|

| Paper
| [[1986Henderson_Processing]]
| General 2D processing
|-

| Paper
| [[2000He_PhaseAlignment]]
| Phase consistency and Alignment
|-

| Paper
| [[2006Gil_Unbending]]
| Crystal unbending
|-

|}

=== Classification ===
{|

| Paper
| [[1988Frank_Classification]]
| MSA and classification in electron crystallography
|-

| Paper
| [[1996Fernandez_SOM]]
| Classification based on self organizing maps
|-

| Paper
| [[1998Sherman_MSA]]
| Classification based on MSA
|-

|}
=== 3D Reconstruction ===

{|

| Paper
| [[1985Wang_Solvent]]
| Solvent flattening
|-

| Paper
| [[1990Henderson_Processing]]
| General 3D processing
|-

| Paper
| [[2004Marabini_ART]]
| Algebraic Reconstruction Technique with blobs for crystals (Xmipp)
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1998Walz_Review]]
| Review of 2D crystallography
|-

| Paper
| [[1999Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Ellis_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of single particles, electron tomography and crystallography
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Gipson_2dx]]
| 2dx
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Philippsen_IPLT]]
| IPLT
|-

|}

== 3D Crystals - MicroED ==

=== Sample Preparation ===
{|
| Paper
| [[2016Shi_Preparation]]
| Sample Preparation
|}
=== Data Collection ===
{|
| Paper
| [[2014Nannenga_CR]]
| Continuous rotation

|}
=== Data Processing ===
{|

| Paper
| [[2011Wisedchaisri_PhaseExtension]]
| Fragment-based phase extension
|-

| Paper
| [[2015Hattne_Processing]]
| Data Processing
|-

| Paper
| [[2016Hattne_Correction]]
| Image correction
|}

=== Software ===
{|

| Paper
| [[2014Iadanza_Processing]]
| Data Processing of still diffraction data
|}

=== Books and Reviews ===
{|
| Paper
| [[2014Nannenga_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Liu_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Rodriguez_Review ]]
| Review of MicroED
|-

|}

== Helical particles ==

=== Filament corrections ===

{|

| Paper
| [[1986Egelman_Curved]]
| Algorithm for correcting curved filaments
|-

| Paper
| [[1988Bluemke_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2006Wang_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2016Yang_Flexible]]
| Algorithm for correcting filaments with flexible subunits
|-

|}

=== Reconstruction ===

{|

| Paper
| [[1952Cochran_Fourier]]
| Fourier Bessel transform of filamentous structures
|-

| Paper
| [[1958Klug_Fourier]]
| Fourier Bessel decomposition of the projection images
|-

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2005Wang_Iterative]]
| Iterative Fourier-Bessel algorithm
|-

| Paper
| [[2007Egelman_Iterative]]
| Iterative real-space algorithm
|-

| Paper
| [[2013Desfosses_Spring]]
| Helical processing with Spring
|-

| Paper
| [[2015Zhang_seam]]
| Workflow for the detection of the lattice seam
|-

| Paper
| [[2016Rohou_Frealix]]
| Helical processing with Frealix
|-

|}

=== Validation ===

{|

| Paper
| [[2014Egelman_ambiguity]]
| How to detect incorrect models
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Carragher_Phoelix]]
| Phoelix
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Owen_Brandeis]]
| Brandeis
|-

|}

== Icosahedral particles ==

=== Reconstruction ===

{|

| Paper
| [[1970Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1971Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1996Fuller_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1997Thuman_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

|}

=== Classification ===

{|

| Paper
| [[2005Scheres_Virus]]
| Classification of virus capsids in real space
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1999Baker_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[1999Conway_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2000Thuman_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Lee_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Navaza_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2006Grunewald_Review]]
| Review of reconstruction of icosahedral viruses
|-

|}

=== Software ===

{|

| Paper
| [[1996Baker_EMPFT]]
| EMPFT
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2013Morin_Sliz SBGrid]]
| SBGrid presentation for eLife
|-

|}

== Databases ==

{|

| Paper
| [[2003Boutselakis_EMSD]]
| EMSD database
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2011Kim_CDDB]]
| Conformational Dynamics Data Bank
|-

| Paper
| [[2011Lawson_EMDB]]
| Electron Microscopy Data Bank
|-

| Paper
| [[2013Ison_EDAM]]
| EDAM, an ontology of bioinformatics operations
|-

| Paper
| [[2016Iudin_EMPIAR]]
| EMPIAR raw data database
|-

| Paper
| [[2016Patwhardan_EMDB]]
| EMDB, PDB, ...
|-

| Paper
| [[2017Patwhardan_Trends]]
| Trends at EMDB
|-

| Paper
| [[2017Shao_PDBQuality]]
| Quality metrics in PDB
|-

| Blog
| http://www.mybiosoftware.com
| Huge list of bioinformatics programs (many of them structural bioinformatics)
|-

|}

== Relationship to other structural information sources ==

{|

| Paper
| [[2000Engel_AFM]]
| Review of Atomic Force Microscopy
|-

| Paper
| [[2001Dimmeler_AFM]]
| Constraints from Atomic Force Microscopy
|-

| Paper
| [[2003Mobus_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_Review]]
| Review on correlative microscopy
|-

| Paper
| [[2005Boudier_EFTETJ]]
| Software for Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2005Vestergaard_SAXS]]
| Example of comparison of 3DEM and Small-angle X-ray scattering
|-

| Paper
| [[2007Hamada_SAXS]]
| Constraints from Small-angle X-ray scattering
|-

| Paper
| [[2013Xu_FRET]]
| EM+FRET
|-

|}

== X-ray tomography ==

{|

| Paper
| [[2012Oton_ImageFormation]]
| Image formation model in X-ray cell microscopy
|-

|}

== Mathematical tools necessary ==

== People developing methods ==
Please, add yourself to this list (due to privacy reasons, please, do not add anyone else to the list without his/her explicit consent). Sort by first name alphabetical order.

[http://biocomp.cnb.csic.es/~coss Carlos Oscar S. Sorzano]: CSIC, Madrid, Spain 

[http://www.curie.fr/recherche/themes/detail_equipe.cfm/lang/_fr/id_equipe/241.htm Cédric Messaoudi]: Institute Curie, Paris, France 

[http://scholar.google.es/citations?user=_jNYGScAAAAJ&hl=en Javier Vargas]:[mailto:jvargas@cnb.csic.es mail]: CSIC, Madrid, Spain 

[http://scholar.google.es/citations?hl=es&user=g2ZJPIYAAAAJ Joaquín Otón]: CSIC, Madrid, Spain 

[mailto:jrbcast@gmail.com José Román Bilbao-Castro]: UAL, Almería, Spain; CSIC, Madrid, Spain 

[José Miguel de la Rosa Trevín]: Biocomputing Unit CNB-CSIC, Madrid, Spain 

[http://cryoem.janelia.org Tamir Gonen]: [mailto:gonent@janelia.hhmi.org mail]: Howard Hughes Medical Institute, Ashburn, VA, USA 

[mailto:vabrishami@cnb.csic.es Vahid Abrishami]: CSIC, Madrid, Spain 

== 3DEM sites ==
* [http://3dem.ucsd.edu/ 3DEM web site]

* [http://en.wikibooks.org/wiki/Software_Tools_For_Molecular_Microscopy Software tools for molecular microscopy]

* [http://www.emdatabank.org/ The Electron Microscopy Data Bank (EMDB)]

* [http://ccdb.ucsd.edu The Cell Centered Database (CCDB)]

* [http://conventions.cnb.csic.es The geometrical software conventions web page ]

== Editing useful links ==

* [http://www.mediawiki.org/wiki/Help:Formatting Text formatting in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Links Adding links in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Images Adding images in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Tables Making tables in Mediawiki]

2017Joseph Metrics

2017-06-19T05:45:27Z

CoSS: Created page with "== Citation == Joseph, A. P.; Lagerstedt, I.; Patwardhan, A.; Topf, M. & Winn, M. Improved metrics for comparing structures of macromolecular assemblies determined by 3D elec..."

== Citation ==

Joseph, A. P.; Lagerstedt, I.; Patwardhan, A.; Topf, M. & Winn, M. Improved metrics for comparing structures of macromolecular assemblies determined by 3D electron-microscopy. Journal of structural biology, 2017, 199, 12-26

== Abstract ==

Recent developments in 3-dimensional electron microcopy (3D-EM) techniques and a concomitant drive to look at complex molecular structures, have led to a rapid increase in the amount of volume data available for biomolecules. This creates a demand for better methods to analyse the data, including improved scores for comparison, classification and integration of data at different resolutions. To this end, we developed and evaluated a set of scoring functions that compare 3D-EM volumes. To test our scores we used a benchmark set of volume alignments derived from the Electron Microscopy Data Bank. We find that the performance of different scores vary with the map-type, resolution and the extent of overlap between volumes. Importantly, adding the overlap information to the local scoring functions can significantly improve their precision and accuracy in a range of resolutions. A combined score involving the local mutual information and overlap (LMI_OV) performs best overall, irrespective of the map category, resolution or the extent of overlap, and we recommend this score for general use. The local mutual information score itself is found to be more discriminatory than cross-correlation coefficient for intermediate-to-low resolution maps or when the map size and density distribution differ significantly. For comparing map surfaces, we implemented two filters to detect the surface points, including one based on the 'extent of surface exposure'. We show that scores that compare surfaces are useful at low resolutions and for maps with evident surface features. All the scores discussed are implemented in TEMPy (http://tempy.ismb.lon.ac.uk/).

== Keywords ==

== Links ==

http://www.sciencedirect.com/science/article/pii/S1047847717300874

== Related software ==

== Related methods ==

== Comments ==

Main Page

2017-06-19T05:44:31Z

CoSS: /* Fitting and docking */

== Presentation ==

This web page is intended to be an extensive repository of three-dimensional electron microscopy (3DEM) methods. The advantages of having such a repository are

* You know which are the relevant articles in a particular topic, therefore, paper introductions, reviews, etc. are easier to write and you make sure you will cite all the related articles.
* You will be sure that your paper has more chances of being cited.
* You can add whatever information you find relevant to your method, external links, links to other papers, etc.
* You can link your method to a web page providing the corresponding software, so you know people can use your algorithms.
* You can use the Wiki search capabilities to locate relevant articles even if they are not at the topic you are looking at.
* As a community we will "reconstruct" our history.
* You can select the "watch" option above to receive notifications in case of further changes in the Main Page.

Developing image processing methods for 3DEM is not "[[well-paid]]" in terms of citations and impact factor. However, it is crucial for the advance of the field. Gathering methodological papers in a portal will help to increase the recognition of the field.

Please:

* Add your articles at the right place (you can add a single article in several topics if it is relevant to all of them). The easiest way to add an article is by editing the corresponding topic in the main page, adding your entry, then save the main page. Click on the red link that appears on your new entry, copy and paste the Wiki following code, add the information of your article

== Citation ==

== Abstract ==

== Keywords ==

== Links ==

== Related software ==

== Related methods ==

== Comments ==

* Maintain the information of each article as complete as possible.
* Sort articles by years and authors.
* Be respectful to other people's work.

== How to subscribe to this page ==

You may subscribe to this page so that you will be notified every time someone adds a new method. To do so, you have to register in the page, and edit your preferences ("my preferences"). Be sure that you have activated the option "E-mail me when a page on my watchlist is changed". Finally, click on the "Watch" tab at the top of this page.

You may subscribe to changes on this page on the mailing list 3demmethods@cnb.csic.es. To send a new method to this mail list just send a mail to 3demmethods@cnb.csic.es

To subscribe to this list, visit the web page

https://listas.csic.es/cnb/wws/subscribe/3demmethods

Alternatively, you may write a mail to sympa6@cnb.csic.es with the subject

<code>subscribe 3demmethods YourName YourFamilyName</code>

and an empty mail body.

To unsubscribe visit the page

https://listas.csic.es/cnb/wws/sigrequest/3demmethods

or write sympa6@cnb.csic.es with the subject

<code>unsubscribe 3demmethods</code>

and an empty mail body.

== Electron microscopy images ==

=== Online courses ===

CALTECH: http://cryo-em-course.caltech.edu/

MRC: ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/EM-course/

CNB-CSIC: http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/MadridJan2014EM

Workshop on Computational methods for CryoEM: https://www.youtube.com/watch?v=XdKO1iaPP8o

Workshop on Management of large CryoEM facilities: https://www.youtube.com/watch?v=as4seOPszL0

Icknield Course on Model Building and Refinement for High Resolution EM Maps: http://www.ccpem.ac.uk/training/icknield_2017/icknield_2017.php

=== Image formation ===

{|

| Paper
| [[1971Erickson_CTF]]
| CTF model
|-

| Paper
| [[1971Glaeser_Damage]]
| Radiation damage
|-

| Chapter
| [[1971Hanszen_CTF]]
| Image formation model
|-

| Paper
| [[1971Thon_Model]]
| CTF model
|-

| Paper
| [[1975Unwin_Imaging]]
| Radiation dose
|-

| Paper
| [[1977Wade_Model]]
| CTF model
|-

| Paper
| [[1978Wade_Model]]
| CTF model
|-

| Paper
| [[1979Hayward_Radiation]]
| Radiation damage
|-

| Paper
| [[1984Cohen_Validity]]
| Validity of the CTF model at high frequencies
|-

| Paper
| [[1988Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[1992Wade_Model]]
| CTF model
|-

| Paper
| [[1993Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2004Egerton_Damage]]
| Radiation damage
|-

| Paper
| [[2004Sorzano_Normalization]]
| Background noise is Gaussian
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2009Baxter_NoiseCharacterization]]
| Characterization of the different noise sources in cryo-EM
|-

| Paper
| [[2010Baker_Damage]]
| Radiation damage dependence on resolution
|-

| Paper
| [[2010Bammes_Damage]]
| Radiation damage dependence on temperature
|-

| Paper
| [[2010Gomez_Multislice]]
| Simulation of the multi slice model
|-

| Paper
| [[2010Zewail_FourDimensional]]
| Review on the use of ultrafast EM
|-

| Paper
| [[2011Bammes_CCD]]
| Performance of CCD cameras
|-

| Paper
| [[2011Glaeser_Coma]]
| Image formation model including coma
|-

| Paper
| [[2011Milazzo_DirectDetectors]]
| Evaluation of Direct Detectors
|-

| Paper
| [[2011Rullgard_ImageSimulation]]
| Accurate simulation of EM images
|-

| Paper
| [[2011Zhang LimitingFactors]]
| Limiting factor for atomic resolution in EM
|-

| Paper
| [[2012Bammes_DirectDetection]]
| Performance of Direct detectors
|-

| Paper
| [[2012Campbell_MotionCorrection]]
| Beam induced motion correction and direct detectors
|-

| Paper
| [[2012Shang_HydrationLayer]]
| Simulation of PDB volumes explicitly considering the hydration layer
|-

| Paper
| [[2013Egerton_RadiationDamage]]
| Review of TEM radiation damage and experimental ways of reducing it
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu H_Noisemodels]]
| Noise models and cryo-EM drift correction with a direct-electron camera
|-

| Paper
| [[2013Li X K2 noisemodels]]
| Influence of electron dose rate on electron counting images recorded with the K2 camera
|-

| Paper
| [[2013Vulovic_CTFApproximations]]
| When to use the different approximations performed so that a projection with linear CTF is valid
|-

| Thesis
| [[2013Vulovic_ImageFormation]]
| Ph.D. Thesis on the image formation in cryo-EM
|-

| Paper
| [[2014Danev_PhasePlate]]
| Volta potential phase plate
|-

| Paper
| [[2015Chiu_K2]]
| Characterization of K2
|-

| Paper
| [[2015Hawkes_AberrationCorrection]]
| Historical account of the development of lens corrections
|-

| Paper
| [[2015Koeck_Quadratic]]
| Limitations of the linear approximation and use of the quadratic terms
|-

| Paper
| [[2015Kuijper_FEI]]
| Description of the FEI Falcons
|-

| Paper
| [[2015Lobato_MULTEM]]
| Simulation of multislice diffraction
|-

| Paper
| [[2015McMullan_AmorphousIce]]
| Beam induced movement is caused by Brownian motion
|-

| Paper
| [[2016Koeck_ADF]]
| Simulations of Annular Dark Field TEM
|-

| Paper
| [[2017Mishyna_DNARadiation]]
| Review of radiation damage on DNA
|-

|}

=== Collection geometry ===

{|

| Chapter
| [[1980Hoppe_Wedge]]
| Missing wedge
|-

| Paper
| [[1987Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1995Penczek_Dual]]
| Dual axis tomography
|-

| Paper
| [[1997Mastronarde_Dual]]
| Dual axis tomography
|-

| Paper
| [[2003Ludtke_FocusPairs]]
| Focus pairs for single particles
|-

| Paper
| [[2005Lanzavecchia_Conical]]
| Conical tomography
|-

| Paper
| [[2005Zampighi_Conical]]
| Conical tomography
|-

| Paper
| [[2006Leschziner_OT]]
| Orthogonal Tilt
|-

| Paper
| [[2006Messaoudi_Multiple]]
| Multiple axis tomography
|-

| Paper
| [[2012Kudryashev_FocusPairs]]
| Focus pairs tomography
|-

| Paper
| [[2014Hovden_TiltFocus]]
| Combining tilt series with focus series
|-

| Paper
| [[2015Sorzano_RandomConicalTilt]]
| General formulation of Random Conical Tilt
|-

| Paper
| [[2017Hagen_DoseTomography]]
| Dose optimization for subtomogram averaging
|-

|}

=== Sample preparation ===

{|

| Paper
| [[1982Dubochet_Sample]]
| Vitreous ice
|-

| Paper
| [[1986Lepault_Sample]]
| Fast freezing
|-

| Paper
| [[1995Dubochet_Sample]]
| High-pressure freezing
|-

| Paper
| [[1995VanMarle_Sample]]
| Sample damages in resin
|-

| Paper
| [[1998Adrian_Sample]]
| Cryo negative staining
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2002Hsieh_Sample]]
| Cryofixation
|-

| Paper
| [[2004AlAmoudi_Sample]]
| CEMOVIS
|-

| Paper
| [[2008Studer_Sample]]
| Review on high pressure freezing
|-

| Paper
| [[2009Pierson_Sample]]
| Review on sample preparation for electron tomography
|-

| Paper
| [[2010Zhang_NegativeStaining]]
| Negative staining for small protein imaging
|-

| Paper
| [[2012Zhang_PositiveStaining]]
| Positive staining
|-

| Paper
| [[2014Rames_NegativeStaining]]
| Optimized negative staining
|-

| Paper
| [[2014Russo_GoldGrids]]
| Gold grids for single particles
|-

| Paper
| [[2015Cabra_Sample]]
| Review on sample preparation for single particles with videos
|-

| Paper
| [[2016Passmore_Review]]
| Tutorial chapter on sample preparation
|-

| Paper
| [[2016Razinkov_Vitrification]]
| New vitrification method
|-

| Paper
| [[2016Takizawa_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2016Thompson_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2017Arnold_BlottingFree]]
| Blotting-free preparation
|-

| Paper
| [[2017Feng_SprayingPlunging]]
| Spraying plunging
|-

| Paper
| [[2017Peitsch_Sample]]
| iMEM: Isolation of Plasma Membrane for Cryoelectron Microscopy
|-

| Paper
| [[2017Scapin_Storage]]
| Cryo storage of samples
|-

| Paper
| [[2017Schaffer_FocusedIonBeam]]
| Focused Ion Beam sample preparation for membrane proteins
|-

|}

=== Automated data collection ===

{|

| Paper
| [[1992Dierksen_Automatic]]
| Automated data collection
|-

| Paper
| [[1992Koster_Automatic]]
| Automated data collection
|-

| Paper
| [[1996Fung_Automatic]]
| Automated data collection for tomography
|-

| Paper
| [[2001Zhang_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2003Ziese_Automatic]]
| Automated autofocusing
|-

| Paper
| [[2004Potter_Automatic]]
| Automated sample loading
|-

| Paper
| [[2004Zheng_Automatic]]
| Automated data collection
|-

| Paper
| [[2005Lei_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2005Suloway_Automatic]]
| Automated data collection: Leginon
|-

| Paper
| [[2007Yoshioka_RCT]]
| Automated Random Conical Tilt
|-

| Paper
| [[2011Korinek_TOM2]]
| Automated acquisition with TOM2
|-

| Paper
| [[2015Li_UCSFImage]]
| Automated acquisition with UCSFImage
|-

| Paper
| [[2016Gil_Fuzzy]]
| Real time decisions during acquisition with neuro-fuzzy method
|-

| Paper
| [[2016Liu_TiltControl]]
| Accurate control of the tilt angle for electron tomography
|-

| Paper
| [[2016Vargas_FoilHole]]
| Determination of image quality at low magnification
|-

| Paper
| [[2017Biyani_Focus]]
| Automatic processing of micrographs
|-

|}

== Single particles ==

=== Automatic particle picking ===

{|

| Paper
| [[1982VanHeel_Detection]]
| Detection of particles in micrographs
|-

| Paper
| [[2001Nicholson_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2001Zhu_Filaments]]
| Automatic identification of filaments in micrographs
|-

| Paper
| [[2004Sigworth_Detection]]
| Classical detection theory and the cryo-EM particle selection problem
|-

| Paper
| [[2004Volkmann_ParticlePicking]]
| An approach to automated particle picking from electron micrographs based on reduced representation templates
|-

| Paper
| [[2004Wong_ParticlePicking]]
| Model-based particle picking for cryo-electron microscopy
|-

| Paper
| [[2004Zhu_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2007Chen_Signature]]
| Automatic particle picking program: Signature
|-

| Paper
| [[2007Woolford_SwarmPS]]
| Automatic particle picking with several criteria, implemented in EMAN Boxer
|-

| Paper
| [[2009Sorzano_MachineLearning]]
| Automatic particle picking based on machine learning of rotational invariants
|-

| Paper
| [[2011Arbelaez_Comparison]]
| Evaluation of the performance of software for automated particle-boxing
|-

| Paper
| [[2013Abrishami_MachineLearning]]
| A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs
|-

| Paper
| [[2013Hauer_2013]]
| Automatic tilt pair detection in Random Conical Tilt
|-

| Paper
| [[2013Shatsky_ParticlePicking]]
| Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Langlois_ParticlePicking]]
| Automatic particle picking
|-

| Paper
| [[2016Vilas_AutomaticTilt]]
| Automatic identification of image pairs in untilted-tilted micrograph pairs
|-

|}

=== 2D Preprocessing ===

{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast enhancement through DPR
|-

| Paper
| [[2004Sorzano_Normalization]]
| Normalization procedures and their statistical properties.
|-

| Paper
| [[2006Sorzano_Denoising]]
| Strong denoising in wavelet space
|-

| Conference
| [[2009Sorzano_Downsampling]]
| Differences between the different downsampling schemes
|-

| Paper
| [[2012Brilot_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Campbell_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Zhao_Denoising]]
| Denoising using an invariant Fourier-Bessel eigenspace
|-

| Paper
| [[2013Norousi_Screening]]
| Screening particles to identify outliers
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu_Movies]]
| Drift correction for movies considering dark field
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Scheres_Movies]]
| Beam induced motion correction
|-

| Paper
| [[2015Abrishami_Movies]]
| Alignment of direct detection device micrographs
|-

| Paper
| [[2015Grant_Anisotropic]]
| Automatic estimation and correction of anisotropic magnification
|-

| Paper
| [[2015Grant_OptimalExposure]]
| Filter movies according to the radiation damage
|-

| Paper
| [[2015Rubinstein_Alignment]]
| Frame alignment at the level of particle
|-

| Paper
| [[2015Spear_DoseCompensation]]
| Effect of dose compensation on resolution
|-

| Paper
| [[2015Zhao_AnisotropicMagnification]]
| Correction of anisotropic magnification
|-

| Conference
| [[2016Bajic_Denoising]]
| Denoising and deconvolution of micrographs
|-

| Paper
| [[2016Jensen_RemovalVesicles]]
| Removal of vesicles in membrane proteins
|-

| Paper
| [[2016Bhamre_Denoising]]
| Denoising by 2D covariance estimation
|-

| Paper
| [[2017McLeod_Zorro]]
| Movie alignment by Zorro
|-

| Paper
| [[2017Zheng_MotionCorr2]]
| Movie alignment by MotionCorr2
|-

|}

=== 2D Alignment ===

{|

| Paper
| [[1981Frank_Averaging]]
| 2D averaging and phase residual
|-

| Paper
| [[1982Saxton_Averaging]]
| 2D averaging using correlation
|-

| Paper
| [[1998Sigworth_ML2D]]
| Maximum likelihood alignment in 2D
|-

| Paper
| [[2003Cong_FRM2D]]
| Fast Rotational Matching in 2D
|-

| Paper
| [[2005Cong_FRM2D]]
| Fast Rotational Matching in 2D introduced in a 3D Alignment algorithm
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

|}

=== 2D Classification and clustering ===

{|

| Paper
| [[1981VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[1984VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2011Singer_DiffusionMaps]]
| Classification in 2D based on graph analysis of the projections
|-

| Paper
| [[2012Yang_ISAC]]
| Iterative Stable Alignment and clustering
|-

| Paper
| [[2014Sorzano_Outlier]]
| Outlier detection in 2D classifications.
|-

| Paper
| [[2014Zhao_Aspire]]
| Fast classification based on rotational invariants and vector diffusion maps
|-

| Paper
| [[2015Huang_Robust]]
| Robust w-estimators of 2D classes
|-

| Paper
| [[2016Reboul_Stochastic]]
| Stochastic Hill Climbing for calculating 2D classes
|-

| Conference
| [[2017Bhamre_Mahalanobis]]
| 2D classification using Mahalanobis distance
|-

|}

=== 3D Alignment ===

{|

| Paper
| [[1980Kam_AutoCorrelation]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[1986Goncharov_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1987VanHeel_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1988Provencher_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Vogel_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1990Gelfand_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Goncharov_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Harauz_Quaternions]]
| Use of quaternions to represent rotations
|-

| Paper
| [[1994Penczek_Real]]
| Angular assignment using projection matching in real space
|-

| Paper
| [[1994Radermacher_Radon]]
| Angular assignment in Radon space
|-

| Paper
| [[1996Penczek_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[2003Rosenthal_DPR]]
| Angular assignment using DPR
|-

| Paper
| [[2004Sorzano_Wavelet]]
| Angular assignment in the wavelet space.
|-

| Paper
| [[2005Jonic_Splines]]
| Angular assignment in Fourier space using spline interpolation.
|-

| Paper
| [[2005Yang_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[2006Ogura_SimulatedAnnealing]]
| Angular asignment by simulated annealing
|-

| Paper
| [[2007Grigorieff_Continuous]]
| Continuous angular assignment in Fourier space
|-

| Paper
| [[2010Jaitly_Bayesian]]
| Angular assignment by a Bayesian method and annealing
|-

| Paper
| [[2010Sanz_Random]]
| Random model method
|-

| Paper
| [[2010Singer_Voting]]
| Detecting consistent common lines by voting (reference free)
|-

| Paper
| [[2011Singer_SDP]]
| Angular assignment by semidefinite programming and eigenvectors (reference free)
|-

| Paper
| [[2012Giannakis_Scattering]]
| Construction of an initial volume, reference free, by graph analysis of the projections
|-

| Paper
| [[2012Shkolnisky_Sync]]
| Angular assignment by synchronization of rotations (reference free)
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Wang_LUD]]
| Angular assignment by least unsquared deviations (reference free)
|-

| Paper
| [[2014Vargas_RANSAC]]
| Initial model using RANSAC (reference free)
|-

| Paper
| [[2015Joubert_Pseudoatoms]]
| Initial model based on pseudo-atoms
|-

| Paper
| [[2015Singer_Kam]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[2015Sorzano_Significant]]
| Statistical approach to the initial volume estimation (reconstruct significant)
|-

| Conference
| [[2016Michels_Heterogeneous]]
| Initial volume in the presence of heterogeneity
|-

| Paper
| [[2016Cossio_BayesianGPU]]
| GPU implementation of the Bayesian 3D reconstruction approach
|-

|}

=== 3D Reconstruction ===
{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1986Harauz_FBP]]
| Exact filters for Filtered Back Projection
|-

| Chapter
| [[1992Radermacher_WBP]]
| Exact filters for Weighted Back Projection
|-

| Paper
| [[1997Zhu_RecCTF]]
| 3D Reconstruction (SIRT like) and simultaneous CTF correction
|-

| Paper
| [[1998Boisset_Uneven]]
| Artifacts in SIRT and WBP under uneven angular distributions
|-

| Paper
| [[1998Marabini_ART]]
| Algebraic Reconstruction Technique with blobs (Xmipp)
|-

| Paper
| [[2001Sorzano_Uneven]]
| Free parameter selection under uneven angular distributions
|-

| Paper
| [[2005Sorzano_Parameters]]
| Free parameter selection for optimizing multiple tasks
|-

| Paper
| [[2008Sorzano_Constraints]]
| Mass, surface, positivity and symmetry constraints for real-space algorithms
|-

| Paper
| [[2009Bilbao_ParallelART]]
| Efficient parallelization of ART
|-

| Paper
| [[2011Li_GradientFlow]]
| Regularized 3D Reconstruction by Gradient Flow
|-

| Paper
| [[2011Vonesch_Wavelets]]
| Fast wavelet-based 3D reconstruction
|-

| Paper
| [[2012Gopinath_ShapeRegularization]]
| Regularized 3D Reconstruction by Shape information
|-

| Paper
| [[2012Kucukelbir_adaptiveBasis]]
| 3D reconstruction in an adaptive basis promoting sparsity
|-

| Paper
| [[2012Sindelar_NoiseReduction]]
| Optimal noise reduction in 3D reconstructions
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Lyumkis_Optimod]]
| Construction of initial volumes with Optimod
|-

| Paper
| [[2013Wang FIRM]]
| Fast 3D reconstruction in Fourier domain
|-

| Paper
| [[2014Kunz_SART_OS]]
| Simultaneous ART with OS
|-

| Paper
| [[2015Abrishami_Fourier]]
| 3D Reconstruction in Fourier space
|-

| Paper
| [[2015Dvornek_SubspaceEM]]
| Fast Maximum a posteriori
|-

| Paper
| [[2015Moriya_Bayesian]]
| Bayesian approach to suppress limited angular artifacts
|-

| Paper
| [[2015Xu_GeometricFlow]]
| Multi-scale geometric flow
|-

| Arxiv
| [[2016Ye_Cohomology]]
| Cohomology properties of 3D reconstruction
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

| Paper
| [[2017Punjani_CryoSPARCTheory]]
| Theory related to CryoSPARC
|-

|}

=== 3D Heterogeneity ===

{|

| Paper
| [[2004White_Size]]
| Heterogeneity classification of differently sized images
|-

| Paper
| [[2006Penczek_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Scheres_ML3D]]
| Maximum Likelihood alignment and classification in 3D
|-

| Paper
| [[2009Spahn_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2010Elmlund_AbInitio]]
| Solving the initial volume problem with multiple conformations
|-

| Paper
| [[2010Shatsky_MultiVariate]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2012Scheres_Bayesian]]
| A Bayesian view on cryo-EM structure determination
|-

| Paper
| [[2012Zheng_Covariance]]
| Estimation of the volume covariance
|-

| Paper
| [[2013Wang_MLVariance]]
| Maximum Likelihood estimate of the map variance
|-

| Paper
| [[2013Lyumkis D_FREALIGN]]
| Likelihood-based classification of cryo-EM images using FREALIGN.
|-

| Paper
| [[2014Jin_NMA]]
| Continuous heterogeneity through Normal Mode Analysis
|-

| Paper
| [[2014Dashti_Brownian]]
| Continuous heterogeneity through Brownian trajectories
|-

| Paper
| [[2014Chen_Migration]]
| Particle migration analysis in 3D classification
|-

| Paper
| [[2015Anden_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Bai_Focused]]
| Focused classification
|-

| Paper
| [[2015Katsevich_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Klaholz_MRA]]
| Multivariate Statistical Analysis of Jackknife and Bootstrapping on random subsets
|-

| Paper
| [[2015Liao_Covariance]]
| Estimation of the 3D covariance from 2D projections
|-

| Paper
| [[2015Tagare_Direct]]
| Direct reconstruction of PCA components
|-

| Paper
| [[2016Gong_Mechanical]]
| Mechanical model for macromolecules
|-

| Paper
| [[2016Rawson_Movement]]
| Movement and flexibility
|-

| Paper
| [[2016Sorzano_StructMap]]
| Sorting a discrete set of conformational states
|-

| Paper
| [[2016Sorzano_Strain]]
| Calculate local stretches, strains and rotations from two conformational states
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

|}

=== Validation ===

{|

| Paper
| [[2008Stagg_TestBed]]
| Effect of voltage, dosis, number of particles and Euler jumps on resolution
|-

| Paper
| [[2011Henderson]]
| Tilt Validation
|-

| Paper
| [[2011Read]]
| Validation of PDBs
|-

| Paper
| [[2012Henderson]]
| EM Map Validation
|-

| Paper
| [[2013Cossio_Bayesian]]
| EM Map Validation in a probabilistic setting
|-

| Paper
| [[2013Chen_NoiseSubstitution]]
| Noise substitution at high resolution for measuring overfitting
|-

| Paper
| [[2014Russo_StatisticalSignificance]]
| EM Map Validation through the statistical significance of the tilt-pair angular assignment
|-

| Paper
| [[2014Stagg_Reslog]]
| EM Map Validation through the resolution evolution with the number of particles
|-

| Paper
| [[2014Wasilewski_Tilt]]
| Web implementation of the tilt pair validation
|-

| Paper
| [[2015Heymann_Alignability]]
| EM Map Validation through the resolution of reconstructions from particles and noise
|-

| Paper
| [[2015Oliveira_FreqLimited]]
| Comparison of gold standard and frequency limited optimization
|-

| Paper
| [[2015Wriggers_Secondary]]
| Validation by secondary structure
|-

| Paper
| [[2016Kim_SAXS]]
| Comparison of SAXS data and EM projections
|-

| Paper
| [[2016Rosenthal_Review]]
| Review of validation methods
|-

| Paper
| [[2016Vargas_Alignability]]
| Validation by studying the tendency of an angular assignment to cluster in the projection space
|-

| Paper
| [[2017Monroe_PDBRefinement]]
| Validation by comparison to a refined PDB
|-

|}

=== Resolution ===

{|

| Paper
| [[1986Harauz_FBP]]
| Fourier Shell Correlation
|-

| Paper
| [[1987Unser_SSNR]]
| 2D Spectral Signal to Noise Ratio
|-

| Paper
| [[2002Penczek_SSNR]]
| 3D Spectral Signal to Noise Ratio for Fourier based algorithms
|-

| Paper
| [[2003Rosenthal_DPR]]
| Review of the FSC and establishment of a new threshold
|-

| Paper
| [[2005Unser_SSNR]]
| 3D Spectral Signal to Noise Ratio for any kind of algorithms
|-

| Paper
| [[2005VanHeel_FSC]]
| Establishment of a new threshold for FSC
|-

| Paper
| [[2007Sousa_AbInitio]]
| Resolution measurement on neighbour Fourier voxels
|-

| Paper
| [[2014Kucukelbir_Local]]
| Quantifying the local resolution of cryo-EM density maps
|-

| Paper
| [[2016Pintilie_Probabilistic]]
| Probabilistic models and resolution
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Statistical properties of resolution measures defined in Fourier space
|-

|}

=== Sharpening of high resolution information ===
{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast restoration and map sharpening
|-

| Paper
| [[2008Fernandez_Bfactor]]
| Bfactor determination and restoration
|-

| Paper
| [[2013Fiddy_SaxtonAlgorithm]]
| Phase retrieval or extension
|-

| Paper
| [[2014Kishchenko_SphericalDeconvolution]]
| Spherical deconvolution
|-

| Paper
| [[2015Spiegel_VISDEM]]
| Visualization improvement by the use of pseudoatomic profiles
|-

| Paper
| [[2016Jonic_Pseudoatoms]]
| Approximation with pseudoatoms
|-

| Paper
| [[2016Jonic_Denoising]]
| Denoising and high-frequency boosting by pseudoatom approximation
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[1982Schiske_Correction]]
| CTF correction for tilted objects
|-

| Paper
| [[1988Toyoshima_Model]]
| CTF estimation
|-

| Paper
| [[1995Frank_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1996Skoglund_MaxEnt]]
| CTF correction with Maximum Entropy
|-

| Paper
| [[1996Zhou_Model]]
| CTF model and user interface for manual fitting
|-

| Paper
| [[1997Fernandez_AR]]
| PSD estimation using periodogram averaging and AR models
|-

| Paper
| [[1997Penczek_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1997Stark_Deconvolution]]
| CTF correction using deconvolution
|-

| Paper
| [[1997Zhu_RecCTF]]
| CTF correction and reconstruction
|-

| Paper
| [[2000DeRosier_EwaldCorrection]]
| CTF correction considering the Ewald sphere
|-

| Paper
| [[2000Jensen_TiltedCorrection]]
| CTF correction considering tilt in backprojection
|-

| Paper
| [[2001Saad_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Huang_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Mindell_CTFTILT]]
| CTF estimation for tilted micrographs
|-

| Paper
| [[2003Sander_MSA]]
| CTF estimation through MSA classification of PSDs
|-

| Paper
| [[2003Velazquez_ARMA]]
| PSD and CTF estimation using ARMA models
|-

| Paper
| [[2004Sorzano_IDR]]
| CTF restoration and reconstruction with Iterative Data Refinement
|-

| Conference
| [[2004Wan_CTF]]
| Spatially variant CTF
|-

| Paper
| [[2004Zubelli_Chahine]]
| CTF restoration and reconstruction with Chahine's multiplicative method
|-

| Conference
| [[2005Dubowy_SpaceVariant]]
| CTF correction when this is space variant
|-

| Paper
| [[2005Mallick_ACE]]
| CTF estimation
|-

| Paper
| [[2006Wolf_Ewald]]
| CTF correction considering Ewald sphere
|-

| Paper
| [[2007Jonic_EnhancedPSD]]
| PSD enhancement for better identification of Thon rings; Vitreous ice diffracts in Thon rings
|-

| Paper
| [[2007Philippsen_Model]]
| CTF Model for tilted specimens
|-

| Paper
| [[2007Sorzano_CTF]]
| CTF estimation using enhanced PSDs
|-

| Paper
| [[2009Sorzano_Sensitivity]]
| Error sensitivity of the CTF models, non-uniqueness of the CTF parameters
|-

| Paper
| [[2010Jiang2010_CTFCorrection]]
| Amplitude correction method
|-

| Paper
| [[2010Kasantsev_CTFCorrection]]
| Mathematical foundations of Kornberg and Jensen method
|-

| Paper
| [[2010Leong_CTFCorrection]]
| Correction for spatially variant CTF
|-

| Paper
| [[2011Glaeser_Coma]]
| The effect of coma at high-resolution
|-

| Paper
| [[2011Mariani_Tilted]]
| CTF simulation and correction of tilted specimens
|-

| Paper
| [[2011Sindelar_Wiener]]
| CTF correction using a modified version of Wiener filter
|-

| Paper
| [[2011Voortman_Tilted]]
| CTF correction for tilted specimen
|-

| Paper
| [[2012Voortman_VaryingCTF]]
| Correcting a spatially varying CTF
|-

| Paper
| [[2013Vargas_FastDef]]
| Fast defocus
|-

| Paper
| [[2015Rohou_CTFFind4]]
| CTF Find 4
|-

| Paper
| [[2015Sheth_CTFquality]]
| Visualization and quality assessment of CTF
|-

| Paper
| [[2016Zhang_GCTF]]
| gCTF
|-

|}

=== Segmentation ===

{|

| Paper
| [[2006Baker_segmentation]]
| Segmentation of molecular subunits
|-

|}

=== Fitting and docking ===

{|

| Paper
| [[1999Volkmann_Fitting]]
| Fitting in real space
|-

| Paper
| [[2001Baker_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2001Jones_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2003Kovacs_FRM3D]]
| Fast Rotational Alignment of two EM maps
|-

| Paper
| [[2004Tama_NMA1]]
| Flexible fitting with Normal Modes (I)
|-

| Paper
| [[2004Tama_NMA2]]
| Flexible fitting with Normal Modes (II)
|-

| Paper
| [[2005Velazquez_Superfamilies]]
| Recognition of the superfamily folding in medium-high resolution volumes
|-

| Paper
| [[2007DeVries_Haddock]]
| Docking with Haddock 2.0
|-

| Paper
| [[2007Kleywegt_QualityControl]]
| Quality control and validation of fitting
|-

| Paper
| [[2012Biswas_Secondary]]
| Secondary structure determination in EM volumes
|-

| Paper
| [[2012Velazquez_Constraints]]
| Multicomponent fitting by using constraints from other information sources
|-

| Paper
| [[2013Chapman MS_Atomicmodeling]]
| Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters
|-

| Paper
| [[2013Esquivel_Modelling]]
| Review on modelling (secondary structure, fitting, ...)
|-

| Paper
| [[2013Lopez_Imodfit]]
| Fitting based on vibrational analysis
|-

| Paper
| [[2013Nogales_3DEMLoupe]]
| Normal Mode Analysis of reconstructed volumes
|-

| Paper
| [[2014AlNasr_Secondary]]
| Identification of secondary structure elements in EM volumes
|-

| Paper
| [[2014Politis_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Rey_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Villa_Review]]
| Review of atomic fitting into EM volumes
|-

| Paper
| [[2015Barad_EMRinger]]
| Validation of hybrid models
|-

| Paper
| [[2015Bettadapura_PF2Fit]]
| Fast rigid fitting of PDBs into EM maps
|-

| Paper
| [[2015Carrillo_CapsidMaps]]
| Analysis of virus capsids using Google Maps
|-

| Paper
| [[2015Schroeder_Hybrid]]
| Review on model building
|-

| Paper
| [[2015Tamo_Dynamics]]
| Dynamics in integrative modeling
|-

| Paper
| [[2015Sorzano_AtomsToVoxels]]
| Accurate conversion of an atomic model into a voxel density volume
|-

| Paper
| [[2016Joseph_Evolution]]
| Evolutionary constraints for the fitting of atomic models into density maps
|-

| Paper
| [[2016Segura_3Diana]]
| Validation of hybrid models
|-

| Paper
| [[2016Singharoy_MDFF]]
| Construction of hybrid models driven by EM density and molecular dynamics
|-

| Paper
| [[2016Wang_Rosetta]]
| Construction of hybrid models driven by EM density using Rosetta
|-

| Paper
| [[2017Joseph_Metrics]]
| Metrics analysis for the comparison of structures
|-

| Paper
| [[2017Hryc_WeightedAtoms]]
| Construction of hybrid models by locally weighting the different atoms
|-

| Paper
| [[2017Matsumoto_Distribution]]
| Estimating the distribution of conformations of atomic models
|-

| Paper
| [[2017Miyashita_EnsembleFitting]]
| Ensemble fitting using Molecular Dynamics
|-

|}

=== Books and reviews ===

{|

| Book
| [[1980Herman_Tomography]]
| General book on tomography
|-

| Book
| [[1988Kak_Tomography]]
| General book on tomography
|-

| Paper
| [[2000Tao_Review]]
| Review of single particles
|-

| Paper
| [[2000VanHeel_Review]]
| Review of single particles
|-

| Paper
| [[2002Frank_Review]]
| Review of single particles
|-

| Paper
| [[2002Schmid_Review]]
| Review of single particles
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2004Subramaniam_Review]]
| Review of single particles
|-

| Paper
| [[2005Steven_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_book]]
| Book covering all aspects of electron microscopy of single particles
|-

| Paper
| [[2006Sorzano_Review]]
| Review of optimization problems in electron microscopy
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems in Electron Tomography
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2008Mueller_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2008Taylor_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2010DeRosier_Review]]
| Personal account of how 3DEM developed in the early days
|-

| Chapter
| [[2012Sorzano_Review]]
| Review of single particle analysis using Xmipp
|-

| Chapter
| [[2012Devaux_Protocol]]
| Protocols for performing single particle analysis
|-

| Paper
| [[2014Bai_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Carazo_Review]]
| Review of the reconstruction process
|-

| Paper
| [[2015Cheng_Review]]
| A primer to Single Particle Cryo-EM
|-

| Paper
| [[2015Cheng_Reviewb]]
| Single Particle Cryo-EM at crystallographic resolution
|-

| Paper
| [[2015Elmlund_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Henderson_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Nogales_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Schroeder_Review]]
| Review of advances in the electron microscope
|-

| Paper
| [[2015Wu_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Carroni_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Egelman_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Eisenstein_CryoEM]]
| News feature on the Method of the Year
|-

| Paper
| [[2016FernandezLeiro_Review]]
| Review of EM
|-

| Paper
| [[2016Glaeser_HowGood]]
| How good can cryo-EM become?
|-

| Paper
| [[2016Jonic_PseudoAtoms]]
| Review of the applications of the use of pseudoatoms in EM
|-

| Chapter
| [[2016Mio_Review]]
| Overview of the process to obtain EM reconstructions
|-

| Paper
| [[2016Jonic_Review]]
| A review of computational ways to handle heterogeneity
|-

| Paper
| [[2016Nogales_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Subramaniam_Review]]
| Why cryo-EM is now suitable for crystallographic journals
|-

| Paper
| [[2016Vinothkumar_Review]]
| Historical review and current limitations
|-

| Paper
| [[2017Frank_Review]]
| Historical review of EM
|-

| Paper
| [[2017Jonic_Review]]
| Review of computational methods to analyze conformational variability
|-

| Paper
| [[2017Rawson_Limitations]]
| Limitations of EM for drug design
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Review of statistical properties of resolution measures defined in Fourier space
|-
|}

=== Software ===

{|

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[1999Lutdke_Eman]]
| Eman
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Baldwin_AngularTransformations]]
| The Transform Class in SPARX and EMAN2
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Grigorieff_Frealign]]
| Frealign
|-

| Paper
| [[2008Scheres_XmippProtocols]]
| Xmipp Protocols
|-

| Paper
| [[2008Shaikh_SpiderProtocols]]
| Spider Protocols
|-

| Paper
| [[2012Wriggers_SitusConventions]]
| Conventions and workflows in Situs
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2015Cianfrocco_Cloud]]
| Software execution in the cloud
|-

| Paper
| [[2015Cheng_MRC2014]]
| Extensions to MRC file format
|-

| Paper
| [[2013DeLaRosa_Scipion]]
| Scipion
|-

| Paper
| [[2016Scheres_Relion]]
| Tutorial on the use of Relion
|-

| Paper
| [[2016Grigorieff_Frealign]]
| Tutorial on the use of Frealign
|-

|}

== Electron tomography ==

=== Image preprocessing ===

{|

| Paper
| [[2015Yan_thickness]]
| Determination of thickness, tilt and electron mean free path
|-

|}

=== Image alignment ===

{|

| Paper
| [[1982Guckenberger_commonOrigin]]
| Determination of a common origin in the micrographs of titl series in three-dimensional electron microscopy
|-

| Paper
| [[1992Lawrence_leastSquares]]
| Least squares solution of the alignment problem
|-

| Paper
| [[1995Penczek_dual]]
| Dual tilt alignment
|-

| Paper
| [[1996Owen_alignmentQuality]]
| Automatic alignment without fiducial markers and evaluation of alignment quality
|-

| Paper
| [[1998Grimm_normalization]]
| Discussion of several gray level normalization methods for electron tomography
|-

| Paper
| [[2001Brandt_Automatic1]]
| Automatic alignment without fiducial markers
|-

| Paper
| [[2001Brandt_Automatic2]]
| Automatic alignment with fiducial markers
|-

| Paper
| [[2006Winkler_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2006Castano_alignment]]
| Alignment with non-perpendicularity
|-

| Paper
| [[2007Castano_alignment]]
| Fiducial-less alignment of cryo-sections
|-

| Paper
| [[2009Sorzano_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2010Cantele_dualAlignment]]
| Alignment of dual series
|-

| Paper
| [[2014Tomonaga_Automatic]]
| Automatic alignment of tilt series using the projection themselves
|-

| Paper
| [[2014Han_Automatic]]
| Automatic alignment of tilt series using SIFT features
|-

| Paper
| [[2015Han_Automatic]]
| Automatic alignment of tilt series using fiducials
|-

| Paper
| [[2017Mastronarde_Automatic]]
| Automatic alignment and reconstruction of tilt series in IMOD
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[2003Winkler_CTF]]
| Focus gradient correction in electron tomography
|-

| Paper
| [[2006Fernandez_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Zanetti_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Xiong_CTF]]
| CTF determination and correction for low dose tomographic tilt series
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2017Kunz_3DCTF]]
| 3D CTF Correction
|-

|}

=== 3D reconstruction ===

{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1992Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[1997Marabini_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2002Fernandez_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2007Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[2008Fernandez_CARP]]
| Component Averaged Row Projections (CARP)
|-

| Paper
| [[2012Herman General Superiorization]]
| Superiorization: an optimization heuristic for medical physics
|-

| Paper
| [[2012Zhang_IPET_FETR]]
| IPET and FETR, a reconstruction algorithm for single molecule tomography
|-

| Paper
| [[2013Goris_SIRT_TV_DART]]
| Combination of SIRT, Total Variation and Discrete ART to reconstruct and segment at the same time
|-

| Paper
| [[2013Briegel A_Challenge]]
| The challenge of determining handedness in electron tomography and the use of DNA origami gold nanoparticle helices as molecular standards
|-

| Paper
| [[2013Messaoudi_EnergyFiltered]]
| 3D Reconstruction of Energy-Filtered TEM
|-

| Paper
| [[2016Deng_ICON]]
| 3D Reconstruction with missing information restoration
|-

| Paper
| [[2016Guay_Compressed]]
| 3D Reconstruction using compressed sensing
|-

|}

=== Noise reduction ===
{|

| Paper
| [[2001Frangakis_NAD]]
| Noise reduction with Nonlinear Anisotropic Diffusion
|-

| Paper
| [[2003Fernandez_AND]]
| Anisotropic nonlinear diffusion for electron tomography
|-

| Paper
| [[2003Jiang_Bilateral]]
| Bilateral denoising filter in electron microscopy
|-

| Paper
| [[2005Fernandez_AND]]
| Anisotropic nonlinear denoising in electron tomography
|-

| Paper
| [[2007Heide_median]]
| Iterative median filtering in electron tomography
|-

| Paper
| [[2007Fernandez_autAND]]
| Anisotropic nonlinear diffusion with automated parameter tuning
|-

| Paper
| [[2009Fernandez_Beltrami]]
| Nonlinear filtering based on Beltrami flow
|-

| Paper
| [[2010Bilbao_MeanShift]]
| Mean Shift Filtering
|-

| Paper
| [[2014Kovacik_wedgeArtefacts]]
| Removal of wedge artefacts
|-

| Paper
| [[2014Maiorca_beadArtefacts]]
| Removal of gold bead artefacts
|-

|}

=== Segmentation ===

{|

| Paper
| [[2002Frangakis_Eigenanalysis]]
| Segmentation using eigenvector analysis.
|-

| Paper
| [[2002Volkmann_Watershed]]
| Segmentation using watershed transform.
|-

| Paper
| [[2003Bajaj_BoundarySegmentation]]
| Segmentation based on fast marching.
|-

| Paper
| [[2005Cyrklaff_Thresholding]]
| Segmentation using optimal thresholding.
|-

| Paper
| [[2007Lebbink_TemplateMatching]]
| Segmentation using template matching.
|-

| Paper
| [[2007Sandberg_OrientationFields]]
| Segmentation using orientation fields.
|-

| Paper
| [[2007Sandberg_SegmentationReview]]
| Review on segmentation in electron tomography.
|-

| Paper
| [[2008Garduno_FuzzySegmentation]]
| Segmentation using fuzzy set theory principles.
|-

| Paper
| [[2009Lebbink_TemplateMatching2]]
| Segmentation using template matching.
|-

| Paper
| [[2012RubbiyaAli_EdgeDetection]]
| Parameter-Free Segmentation of Macromolecular Structures.
|-

| Conference
| [[2015Xu_TemplateMatching]]
| Detection of macromolecular complexes with a reduced representation of the templates.
|-

|}

=== Resolution ===
{|

| Paper
| [[2005Cardone_Resolution]]
| Resolution criterion for electron tomography
|-

| Chapter
| [[2007Penczek_Resolution]]
| Review of resolution criteria for electron tomography
|-

| Paper
| [[2015Diebolder_ConicalFSC]]
| Conical Fourier Shell Correlation
|-

|}

=== Subtomogram analysis ===

{|

| Paper
| [[2000Bohm_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2002Frangakis_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2006Nickell_Review]]
| Review of macromolecule finding by template matching (Visual Proteomics)
|-

| Paper
| [[2007Best_Review]]
| Review of Localization of Protein Complexes by Pattern Recognition
|-

| Paper
| [[2007Forster_Review]]
| Review of structure determination by subtomogram averaging
|-

| Paper
| [[2008Forster_Classification]]
| Classification of subtomograms using constrained correlation
|-

| Paper
| [[2008Bartesaghi_Classification]]
| Classification and averaging of subtomograms
|-

| Paper
| [[2008Schmid_Averaging]]
| Alignment and averaging of subtomograms
|-

| Paper
| [[2010Amat_Averaging]]
| Alignment and averaging of subtomograms exploiting thresholding in Fourier space
|-

| Paper
| [[2013Chen_Averaging]]
| Fast alignment of subtomograms using spherical harmonics
|-

| Paper
| [[2013Kuybeda_Averaging]]
| Alignment and averaging of subtomograms using the nuclear norm of the cluster
|-

| Paper
| [[2013Shatsky_Averaging]]
| Alignment and averaging of subtomograms with constrained cross-correlation
|-

| Paper
| [[2014Chen_Autofocus]]
| Subtomogram averaging and classification with special attention to differences
|-

| Paper
| [[2014Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2014Voortman_LimitingFactors]]
| Limiting factors of subtomogram averaging
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2015Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2016Bharat_Relion]]
| Subtomogram averaging with Relion
|-

| Paper
| [[2016Song_MatrixNorm]]
| Matrix norm minimization for tomographic reconstruction and alignment
|-

| Paper
| [[2017Castano_ParticlePicking]]
| Particle picking in tomograms for subtomogram averaging
|-

| Paper
| [[2017Frazier_Tomominer]]
| TomoMiner a software platform for large-scale subtomogram analysis
|-

|}

=== Single particle tomography ===

{|

| Paper
| [[2012Bartesaghi_Constrained]]
| 3D reconstruction by imposing geometrical constraints
|-

| Paper
| [[2015Galaz_SingleParticleTomography]]
| Set of tools for Single Particle Tomography in EMAN2
|-

| Paper
| [[2016Galaz_SingleParticleTomography]]
| Alignment algorithms and CTF correction
|-

|}

=== Books and reviews ===

{|

| Paper
| [[2000Baumeister_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Koster_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Sali_Review]]
| Review of electron tomography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2005Lucic_Review]]
| Review of electron tomography
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_TomoBook]]
| Electron Tomography
|-

| Book
| [[2007McIntosh_Book]]
| Cellular Electron Microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2012Kudryashev_Review]]
| Review of subtomogram averaging
|-

| Paper
| [[2016Beck_Review]]
| Review of molecular sociology
|-

|}

=== Software ===

{|

| Paper
| [[1996Kremer_IMOD]]
| IMOD
|-

| Paper
| [[1996Chen_Priism/IVE]]
| Priism/IVE
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2005Nickell_TOM]]
| TOM Toolbox
|-

| Paper
| [[2007Messaoudi_TomoJ]]
| TomoJ
|-

| Paper
| [[2008Heymann_BsoftTomo]]
| Bsoft
|-

| Paper
| [[2015Ding_CaltechTomography]]
| Caltech tomography database
|-

| Paper
| [[2015Noble_AppionProtomo]]
| Batch fiducial-less tilt-series alignment in Appion using Protomo
|-

| Paper
| [[2015vanAarle_Astra]]
| ASTRA Toolbox
|-

| Paper
| [[2017Wan_Simulator]]
| Electron Tomography Simulator
|-

|}

== 2D Crystals ==

=== 2D Preprocessing ===

{|

| Paper
| [[1986Henderson_Processing]]
| General 2D processing
|-

| Paper
| [[2000He_PhaseAlignment]]
| Phase consistency and Alignment
|-

| Paper
| [[2006Gil_Unbending]]
| Crystal unbending
|-

|}

=== Classification ===
{|

| Paper
| [[1988Frank_Classification]]
| MSA and classification in electron crystallography
|-

| Paper
| [[1996Fernandez_SOM]]
| Classification based on self organizing maps
|-

| Paper
| [[1998Sherman_MSA]]
| Classification based on MSA
|-

|}
=== 3D Reconstruction ===

{|

| Paper
| [[1985Wang_Solvent]]
| Solvent flattening
|-

| Paper
| [[1990Henderson_Processing]]
| General 3D processing
|-

| Paper
| [[2004Marabini_ART]]
| Algebraic Reconstruction Technique with blobs for crystals (Xmipp)
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1998Walz_Review]]
| Review of 2D crystallography
|-

| Paper
| [[1999Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Ellis_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of single particles, electron tomography and crystallography
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Gipson_2dx]]
| 2dx
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Philippsen_IPLT]]
| IPLT
|-

|}

== 3D Crystals - MicroED ==

=== Sample Preparation ===
{|
| Paper
| [[2016Shi_Preparation]]
| Sample Preparation
|}
=== Data Collection ===
{|
| Paper
| [[2014Nannenga_CR]]
| Continuous rotation

|}
=== Data Processing ===
{|

| Paper
| [[2011Wisedchaisri_PhaseExtension]]
| Fragment-based phase extension
|-

| Paper
| [[2015Hattne_Processing]]
| Data Processing
|-

| Paper
| [[2016Hattne_Correction]]
| Image correction
|}

=== Software ===
{|

| Paper
| [[2014Iadanza_Processing]]
| Data Processing of still diffraction data
|}

=== Books and Reviews ===
{|
| Paper
| [[2014Nannenga_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Liu_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Rodriguez_Review ]]
| Review of MicroED
|-

|}

== Helical particles ==

=== Filament corrections ===

{|

| Paper
| [[1986Egelman_Curved]]
| Algorithm for correcting curved filaments
|-

| Paper
| [[1988Bluemke_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2006Wang_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2016Yang_Flexible]]
| Algorithm for correcting filaments with flexible subunits
|-

|}

=== Reconstruction ===

{|

| Paper
| [[1952Cochran_Fourier]]
| Fourier Bessel transform of filamentous structures
|-

| Paper
| [[1958Klug_Fourier]]
| Fourier Bessel decomposition of the projection images
|-

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2005Wang_Iterative]]
| Iterative Fourier-Bessel algorithm
|-

| Paper
| [[2007Egelman_Iterative]]
| Iterative real-space algorithm
|-

| Paper
| [[2013Desfosses_Spring]]
| Helical processing with Spring
|-

| Paper
| [[2015Zhang_seam]]
| Workflow for the detection of the lattice seam
|-

| Paper
| [[2016Rohou_Frealix]]
| Helical processing with Frealix
|-

|}

=== Validation ===

{|

| Paper
| [[2014Egelman_ambiguity]]
| How to detect incorrect models
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Carragher_Phoelix]]
| Phoelix
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Owen_Brandeis]]
| Brandeis
|-

|}

== Icosahedral particles ==

=== Reconstruction ===

{|

| Paper
| [[1970Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1971Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1996Fuller_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1997Thuman_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

|}

=== Classification ===

{|

| Paper
| [[2005Scheres_Virus]]
| Classification of virus capsids in real space
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1999Baker_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[1999Conway_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2000Thuman_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Lee_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Navaza_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2006Grunewald_Review]]
| Review of reconstruction of icosahedral viruses
|-

|}

=== Software ===

{|

| Paper
| [[1996Baker_EMPFT]]
| EMPFT
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2013Morin_Sliz SBGrid]]
| SBGrid presentation for eLife
|-

|}

== Databases ==

{|

| Paper
| [[2003Boutselakis_EMSD]]
| EMSD database
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2011Kim_CDDB]]
| Conformational Dynamics Data Bank
|-

| Paper
| [[2011Lawson_EMDB]]
| Electron Microscopy Data Bank
|-

| Paper
| [[2013Ison_EDAM]]
| EDAM, an ontology of bioinformatics operations
|-

| Paper
| [[2016Iudin_EMPIAR]]
| EMPIAR raw data database
|-

| Paper
| [[2016Patwhardan_EMDB]]
| EMDB, PDB, ...
|-

| Paper
| [[2017Patwhardan_Trends]]
| Trends at EMDB
|-

| Paper
| [[2017Shao_PDBQuality]]
| Quality metrics in PDB
|-

| Blog
| http://www.mybiosoftware.com
| Huge list of bioinformatics programs (many of them structural bioinformatics)
|-

|}

== Relationship to other structural information sources ==

{|

| Paper
| [[2000Engel_AFM]]
| Review of Atomic Force Microscopy
|-

| Paper
| [[2001Dimmeler_AFM]]
| Constraints from Atomic Force Microscopy
|-

| Paper
| [[2003Mobus_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_Review]]
| Review on correlative microscopy
|-

| Paper
| [[2005Boudier_EFTETJ]]
| Software for Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2005Vestergaard_SAXS]]
| Example of comparison of 3DEM and Small-angle X-ray scattering
|-

| Paper
| [[2007Hamada_SAXS]]
| Constraints from Small-angle X-ray scattering
|-

| Paper
| [[2013Xu_FRET]]
| EM+FRET
|-

|}

== X-ray tomography ==

{|

| Paper
| [[2012Oton_ImageFormation]]
| Image formation model in X-ray cell microscopy
|-

|}

== Mathematical tools necessary ==

== People developing methods ==
Please, add yourself to this list (due to privacy reasons, please, do not add anyone else to the list without his/her explicit consent). Sort by first name alphabetical order.

[http://biocomp.cnb.csic.es/~coss Carlos Oscar S. Sorzano]: CSIC, Madrid, Spain 

[http://www.curie.fr/recherche/themes/detail_equipe.cfm/lang/_fr/id_equipe/241.htm Cédric Messaoudi]: Institute Curie, Paris, France 

[http://scholar.google.es/citations?user=_jNYGScAAAAJ&hl=en Javier Vargas]:[mailto:jvargas@cnb.csic.es mail]: CSIC, Madrid, Spain 

[http://scholar.google.es/citations?hl=es&user=g2ZJPIYAAAAJ Joaquín Otón]: CSIC, Madrid, Spain 

[mailto:jrbcast@gmail.com José Román Bilbao-Castro]: UAL, Almería, Spain; CSIC, Madrid, Spain 

[José Miguel de la Rosa Trevín]: Biocomputing Unit CNB-CSIC, Madrid, Spain 

[http://cryoem.janelia.org Tamir Gonen]: [mailto:gonent@janelia.hhmi.org mail]: Howard Hughes Medical Institute, Ashburn, VA, USA 

[mailto:vabrishami@cnb.csic.es Vahid Abrishami]: CSIC, Madrid, Spain 

== 3DEM sites ==
* [http://3dem.ucsd.edu/ 3DEM web site]

* [http://en.wikibooks.org/wiki/Software_Tools_For_Molecular_Microscopy Software tools for molecular microscopy]

* [http://www.emdatabank.org/ The Electron Microscopy Data Bank (EMDB)]

* [http://ccdb.ucsd.edu The Cell Centered Database (CCDB)]

* [http://conventions.cnb.csic.es The geometrical software conventions web page ]

== Editing useful links ==

* [http://www.mediawiki.org/wiki/Help:Formatting Text formatting in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Links Adding links in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Images Adding images in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Tables Making tables in Mediawiki]

2017Frazier Tomominer

2017-06-19T05:38:22Z

CoSS: Created page with "== Citation == Frazier, Z.; Xu, M. & Alber, F. TomoMiner and TomoMinerCloud: A Software Platform for Large-Scale Subtomogram Structural Analysis. Structure, 2017, 25, 951-961..."

== Citation ==

Frazier, Z.; Xu, M. & Alber, F. TomoMiner and TomoMinerCloud: A Software Platform for Large-Scale Subtomogram Structural Analysis. Structure, 2017, 25, 951-961.e2

== Abstract ==

Cryo-electron tomography (cryo-ET) captures the 3D electron density distribution of macromolecular complexes in close to native state. With the rapid advance of cryo-ET acquisition technologies, it is possible to generate large numbers (>100,000) of subtomograms, each containing a macromolecular complex. Often, these subtomograms represent a heterogeneous sample due to variations in the structure and composition of a complex in situ form or because particles are a mixture of different complexes. In this case subtomograms must be classified. However, classification of large numbers of subtomograms is a time-intensive task and often a limiting bottleneck. This paper introduces an open source software platform, TomoMiner, for large-scale subtomogram classification, template matching, subtomogram averaging, and alignment. Its scalable and robust parallel processing allows efficient classification of tens to hundreds of thousands of subtomograms. In addition, TomoMiner provides a pre-configured TomoMinerCloud computing service permitting users without sufficient computing resources instant access to TomoMiners high-performance features.

== Keywords ==

== Links ==

https://www.ncbi.nlm.nih.gov/pubmed/28552576

== Related software ==

== Related methods ==

== Comments ==

Main Page

2017-06-19T05:37:33Z

CoSS: /* Subtomogram analysis */

== Presentation ==

This web page is intended to be an extensive repository of three-dimensional electron microscopy (3DEM) methods. The advantages of having such a repository are

* You know which are the relevant articles in a particular topic, therefore, paper introductions, reviews, etc. are easier to write and you make sure you will cite all the related articles.
* You will be sure that your paper has more chances of being cited.
* You can add whatever information you find relevant to your method, external links, links to other papers, etc.
* You can link your method to a web page providing the corresponding software, so you know people can use your algorithms.
* You can use the Wiki search capabilities to locate relevant articles even if they are not at the topic you are looking at.
* As a community we will "reconstruct" our history.
* You can select the "watch" option above to receive notifications in case of further changes in the Main Page.

Developing image processing methods for 3DEM is not "[[well-paid]]" in terms of citations and impact factor. However, it is crucial for the advance of the field. Gathering methodological papers in a portal will help to increase the recognition of the field.

Please:

* Add your articles at the right place (you can add a single article in several topics if it is relevant to all of them). The easiest way to add an article is by editing the corresponding topic in the main page, adding your entry, then save the main page. Click on the red link that appears on your new entry, copy and paste the Wiki following code, add the information of your article

== Citation ==

== Abstract ==

== Keywords ==

== Links ==

== Related software ==

== Related methods ==

== Comments ==

* Maintain the information of each article as complete as possible.
* Sort articles by years and authors.
* Be respectful to other people's work.

== How to subscribe to this page ==

You may subscribe to this page so that you will be notified every time someone adds a new method. To do so, you have to register in the page, and edit your preferences ("my preferences"). Be sure that you have activated the option "E-mail me when a page on my watchlist is changed". Finally, click on the "Watch" tab at the top of this page.

You may subscribe to changes on this page on the mailing list 3demmethods@cnb.csic.es. To send a new method to this mail list just send a mail to 3demmethods@cnb.csic.es

To subscribe to this list, visit the web page

https://listas.csic.es/cnb/wws/subscribe/3demmethods

Alternatively, you may write a mail to sympa6@cnb.csic.es with the subject

<code>subscribe 3demmethods YourName YourFamilyName</code>

and an empty mail body.

To unsubscribe visit the page

https://listas.csic.es/cnb/wws/sigrequest/3demmethods

or write sympa6@cnb.csic.es with the subject

<code>unsubscribe 3demmethods</code>

and an empty mail body.

== Electron microscopy images ==

=== Online courses ===

CALTECH: http://cryo-em-course.caltech.edu/

MRC: ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/EM-course/

CNB-CSIC: http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/MadridJan2014EM

Workshop on Computational methods for CryoEM: https://www.youtube.com/watch?v=XdKO1iaPP8o

Workshop on Management of large CryoEM facilities: https://www.youtube.com/watch?v=as4seOPszL0

Icknield Course on Model Building and Refinement for High Resolution EM Maps: http://www.ccpem.ac.uk/training/icknield_2017/icknield_2017.php

=== Image formation ===

{|

| Paper
| [[1971Erickson_CTF]]
| CTF model
|-

| Paper
| [[1971Glaeser_Damage]]
| Radiation damage
|-

| Chapter
| [[1971Hanszen_CTF]]
| Image formation model
|-

| Paper
| [[1971Thon_Model]]
| CTF model
|-

| Paper
| [[1975Unwin_Imaging]]
| Radiation dose
|-

| Paper
| [[1977Wade_Model]]
| CTF model
|-

| Paper
| [[1978Wade_Model]]
| CTF model
|-

| Paper
| [[1979Hayward_Radiation]]
| Radiation damage
|-

| Paper
| [[1984Cohen_Validity]]
| Validity of the CTF model at high frequencies
|-

| Paper
| [[1988Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[1992Wade_Model]]
| CTF model
|-

| Paper
| [[1993Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2004Egerton_Damage]]
| Radiation damage
|-

| Paper
| [[2004Sorzano_Normalization]]
| Background noise is Gaussian
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2009Baxter_NoiseCharacterization]]
| Characterization of the different noise sources in cryo-EM
|-

| Paper
| [[2010Baker_Damage]]
| Radiation damage dependence on resolution
|-

| Paper
| [[2010Bammes_Damage]]
| Radiation damage dependence on temperature
|-

| Paper
| [[2010Gomez_Multislice]]
| Simulation of the multi slice model
|-

| Paper
| [[2010Zewail_FourDimensional]]
| Review on the use of ultrafast EM
|-

| Paper
| [[2011Bammes_CCD]]
| Performance of CCD cameras
|-

| Paper
| [[2011Glaeser_Coma]]
| Image formation model including coma
|-

| Paper
| [[2011Milazzo_DirectDetectors]]
| Evaluation of Direct Detectors
|-

| Paper
| [[2011Rullgard_ImageSimulation]]
| Accurate simulation of EM images
|-

| Paper
| [[2011Zhang LimitingFactors]]
| Limiting factor for atomic resolution in EM
|-

| Paper
| [[2012Bammes_DirectDetection]]
| Performance of Direct detectors
|-

| Paper
| [[2012Campbell_MotionCorrection]]
| Beam induced motion correction and direct detectors
|-

| Paper
| [[2012Shang_HydrationLayer]]
| Simulation of PDB volumes explicitly considering the hydration layer
|-

| Paper
| [[2013Egerton_RadiationDamage]]
| Review of TEM radiation damage and experimental ways of reducing it
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu H_Noisemodels]]
| Noise models and cryo-EM drift correction with a direct-electron camera
|-

| Paper
| [[2013Li X K2 noisemodels]]
| Influence of electron dose rate on electron counting images recorded with the K2 camera
|-

| Paper
| [[2013Vulovic_CTFApproximations]]
| When to use the different approximations performed so that a projection with linear CTF is valid
|-

| Thesis
| [[2013Vulovic_ImageFormation]]
| Ph.D. Thesis on the image formation in cryo-EM
|-

| Paper
| [[2014Danev_PhasePlate]]
| Volta potential phase plate
|-

| Paper
| [[2015Chiu_K2]]
| Characterization of K2
|-

| Paper
| [[2015Hawkes_AberrationCorrection]]
| Historical account of the development of lens corrections
|-

| Paper
| [[2015Koeck_Quadratic]]
| Limitations of the linear approximation and use of the quadratic terms
|-

| Paper
| [[2015Kuijper_FEI]]
| Description of the FEI Falcons
|-

| Paper
| [[2015Lobato_MULTEM]]
| Simulation of multislice diffraction
|-

| Paper
| [[2015McMullan_AmorphousIce]]
| Beam induced movement is caused by Brownian motion
|-

| Paper
| [[2016Koeck_ADF]]
| Simulations of Annular Dark Field TEM
|-

| Paper
| [[2017Mishyna_DNARadiation]]
| Review of radiation damage on DNA
|-

|}

=== Collection geometry ===

{|

| Chapter
| [[1980Hoppe_Wedge]]
| Missing wedge
|-

| Paper
| [[1987Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1995Penczek_Dual]]
| Dual axis tomography
|-

| Paper
| [[1997Mastronarde_Dual]]
| Dual axis tomography
|-

| Paper
| [[2003Ludtke_FocusPairs]]
| Focus pairs for single particles
|-

| Paper
| [[2005Lanzavecchia_Conical]]
| Conical tomography
|-

| Paper
| [[2005Zampighi_Conical]]
| Conical tomography
|-

| Paper
| [[2006Leschziner_OT]]
| Orthogonal Tilt
|-

| Paper
| [[2006Messaoudi_Multiple]]
| Multiple axis tomography
|-

| Paper
| [[2012Kudryashev_FocusPairs]]
| Focus pairs tomography
|-

| Paper
| [[2014Hovden_TiltFocus]]
| Combining tilt series with focus series
|-

| Paper
| [[2015Sorzano_RandomConicalTilt]]
| General formulation of Random Conical Tilt
|-

| Paper
| [[2017Hagen_DoseTomography]]
| Dose optimization for subtomogram averaging
|-

|}

=== Sample preparation ===

{|

| Paper
| [[1982Dubochet_Sample]]
| Vitreous ice
|-

| Paper
| [[1986Lepault_Sample]]
| Fast freezing
|-

| Paper
| [[1995Dubochet_Sample]]
| High-pressure freezing
|-

| Paper
| [[1995VanMarle_Sample]]
| Sample damages in resin
|-

| Paper
| [[1998Adrian_Sample]]
| Cryo negative staining
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2002Hsieh_Sample]]
| Cryofixation
|-

| Paper
| [[2004AlAmoudi_Sample]]
| CEMOVIS
|-

| Paper
| [[2008Studer_Sample]]
| Review on high pressure freezing
|-

| Paper
| [[2009Pierson_Sample]]
| Review on sample preparation for electron tomography
|-

| Paper
| [[2010Zhang_NegativeStaining]]
| Negative staining for small protein imaging
|-

| Paper
| [[2012Zhang_PositiveStaining]]
| Positive staining
|-

| Paper
| [[2014Rames_NegativeStaining]]
| Optimized negative staining
|-

| Paper
| [[2014Russo_GoldGrids]]
| Gold grids for single particles
|-

| Paper
| [[2015Cabra_Sample]]
| Review on sample preparation for single particles with videos
|-

| Paper
| [[2016Passmore_Review]]
| Tutorial chapter on sample preparation
|-

| Paper
| [[2016Razinkov_Vitrification]]
| New vitrification method
|-

| Paper
| [[2016Takizawa_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2016Thompson_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2017Arnold_BlottingFree]]
| Blotting-free preparation
|-

| Paper
| [[2017Feng_SprayingPlunging]]
| Spraying plunging
|-

| Paper
| [[2017Peitsch_Sample]]
| iMEM: Isolation of Plasma Membrane for Cryoelectron Microscopy
|-

| Paper
| [[2017Scapin_Storage]]
| Cryo storage of samples
|-

| Paper
| [[2017Schaffer_FocusedIonBeam]]
| Focused Ion Beam sample preparation for membrane proteins
|-

|}

=== Automated data collection ===

{|

| Paper
| [[1992Dierksen_Automatic]]
| Automated data collection
|-

| Paper
| [[1992Koster_Automatic]]
| Automated data collection
|-

| Paper
| [[1996Fung_Automatic]]
| Automated data collection for tomography
|-

| Paper
| [[2001Zhang_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2003Ziese_Automatic]]
| Automated autofocusing
|-

| Paper
| [[2004Potter_Automatic]]
| Automated sample loading
|-

| Paper
| [[2004Zheng_Automatic]]
| Automated data collection
|-

| Paper
| [[2005Lei_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2005Suloway_Automatic]]
| Automated data collection: Leginon
|-

| Paper
| [[2007Yoshioka_RCT]]
| Automated Random Conical Tilt
|-

| Paper
| [[2011Korinek_TOM2]]
| Automated acquisition with TOM2
|-

| Paper
| [[2015Li_UCSFImage]]
| Automated acquisition with UCSFImage
|-

| Paper
| [[2016Gil_Fuzzy]]
| Real time decisions during acquisition with neuro-fuzzy method
|-

| Paper
| [[2016Liu_TiltControl]]
| Accurate control of the tilt angle for electron tomography
|-

| Paper
| [[2016Vargas_FoilHole]]
| Determination of image quality at low magnification
|-

| Paper
| [[2017Biyani_Focus]]
| Automatic processing of micrographs
|-

|}

== Single particles ==

=== Automatic particle picking ===

{|

| Paper
| [[1982VanHeel_Detection]]
| Detection of particles in micrographs
|-

| Paper
| [[2001Nicholson_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2001Zhu_Filaments]]
| Automatic identification of filaments in micrographs
|-

| Paper
| [[2004Sigworth_Detection]]
| Classical detection theory and the cryo-EM particle selection problem
|-

| Paper
| [[2004Volkmann_ParticlePicking]]
| An approach to automated particle picking from electron micrographs based on reduced representation templates
|-

| Paper
| [[2004Wong_ParticlePicking]]
| Model-based particle picking for cryo-electron microscopy
|-

| Paper
| [[2004Zhu_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2007Chen_Signature]]
| Automatic particle picking program: Signature
|-

| Paper
| [[2007Woolford_SwarmPS]]
| Automatic particle picking with several criteria, implemented in EMAN Boxer
|-

| Paper
| [[2009Sorzano_MachineLearning]]
| Automatic particle picking based on machine learning of rotational invariants
|-

| Paper
| [[2011Arbelaez_Comparison]]
| Evaluation of the performance of software for automated particle-boxing
|-

| Paper
| [[2013Abrishami_MachineLearning]]
| A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs
|-

| Paper
| [[2013Hauer_2013]]
| Automatic tilt pair detection in Random Conical Tilt
|-

| Paper
| [[2013Shatsky_ParticlePicking]]
| Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Langlois_ParticlePicking]]
| Automatic particle picking
|-

| Paper
| [[2016Vilas_AutomaticTilt]]
| Automatic identification of image pairs in untilted-tilted micrograph pairs
|-

|}

=== 2D Preprocessing ===

{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast enhancement through DPR
|-

| Paper
| [[2004Sorzano_Normalization]]
| Normalization procedures and their statistical properties.
|-

| Paper
| [[2006Sorzano_Denoising]]
| Strong denoising in wavelet space
|-

| Conference
| [[2009Sorzano_Downsampling]]
| Differences between the different downsampling schemes
|-

| Paper
| [[2012Brilot_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Campbell_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Zhao_Denoising]]
| Denoising using an invariant Fourier-Bessel eigenspace
|-

| Paper
| [[2013Norousi_Screening]]
| Screening particles to identify outliers
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu_Movies]]
| Drift correction for movies considering dark field
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Scheres_Movies]]
| Beam induced motion correction
|-

| Paper
| [[2015Abrishami_Movies]]
| Alignment of direct detection device micrographs
|-

| Paper
| [[2015Grant_Anisotropic]]
| Automatic estimation and correction of anisotropic magnification
|-

| Paper
| [[2015Grant_OptimalExposure]]
| Filter movies according to the radiation damage
|-

| Paper
| [[2015Rubinstein_Alignment]]
| Frame alignment at the level of particle
|-

| Paper
| [[2015Spear_DoseCompensation]]
| Effect of dose compensation on resolution
|-

| Paper
| [[2015Zhao_AnisotropicMagnification]]
| Correction of anisotropic magnification
|-

| Conference
| [[2016Bajic_Denoising]]
| Denoising and deconvolution of micrographs
|-

| Paper
| [[2016Jensen_RemovalVesicles]]
| Removal of vesicles in membrane proteins
|-

| Paper
| [[2016Bhamre_Denoising]]
| Denoising by 2D covariance estimation
|-

| Paper
| [[2017McLeod_Zorro]]
| Movie alignment by Zorro
|-

| Paper
| [[2017Zheng_MotionCorr2]]
| Movie alignment by MotionCorr2
|-

|}

=== 2D Alignment ===

{|

| Paper
| [[1981Frank_Averaging]]
| 2D averaging and phase residual
|-

| Paper
| [[1982Saxton_Averaging]]
| 2D averaging using correlation
|-

| Paper
| [[1998Sigworth_ML2D]]
| Maximum likelihood alignment in 2D
|-

| Paper
| [[2003Cong_FRM2D]]
| Fast Rotational Matching in 2D
|-

| Paper
| [[2005Cong_FRM2D]]
| Fast Rotational Matching in 2D introduced in a 3D Alignment algorithm
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

|}

=== 2D Classification and clustering ===

{|

| Paper
| [[1981VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[1984VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2011Singer_DiffusionMaps]]
| Classification in 2D based on graph analysis of the projections
|-

| Paper
| [[2012Yang_ISAC]]
| Iterative Stable Alignment and clustering
|-

| Paper
| [[2014Sorzano_Outlier]]
| Outlier detection in 2D classifications.
|-

| Paper
| [[2014Zhao_Aspire]]
| Fast classification based on rotational invariants and vector diffusion maps
|-

| Paper
| [[2015Huang_Robust]]
| Robust w-estimators of 2D classes
|-

| Paper
| [[2016Reboul_Stochastic]]
| Stochastic Hill Climbing for calculating 2D classes
|-

| Conference
| [[2017Bhamre_Mahalanobis]]
| 2D classification using Mahalanobis distance
|-

|}

=== 3D Alignment ===

{|

| Paper
| [[1980Kam_AutoCorrelation]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[1986Goncharov_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1987VanHeel_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1988Provencher_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Vogel_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1990Gelfand_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Goncharov_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Harauz_Quaternions]]
| Use of quaternions to represent rotations
|-

| Paper
| [[1994Penczek_Real]]
| Angular assignment using projection matching in real space
|-

| Paper
| [[1994Radermacher_Radon]]
| Angular assignment in Radon space
|-

| Paper
| [[1996Penczek_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[2003Rosenthal_DPR]]
| Angular assignment using DPR
|-

| Paper
| [[2004Sorzano_Wavelet]]
| Angular assignment in the wavelet space.
|-

| Paper
| [[2005Jonic_Splines]]
| Angular assignment in Fourier space using spline interpolation.
|-

| Paper
| [[2005Yang_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[2006Ogura_SimulatedAnnealing]]
| Angular asignment by simulated annealing
|-

| Paper
| [[2007Grigorieff_Continuous]]
| Continuous angular assignment in Fourier space
|-

| Paper
| [[2010Jaitly_Bayesian]]
| Angular assignment by a Bayesian method and annealing
|-

| Paper
| [[2010Sanz_Random]]
| Random model method
|-

| Paper
| [[2010Singer_Voting]]
| Detecting consistent common lines by voting (reference free)
|-

| Paper
| [[2011Singer_SDP]]
| Angular assignment by semidefinite programming and eigenvectors (reference free)
|-

| Paper
| [[2012Giannakis_Scattering]]
| Construction of an initial volume, reference free, by graph analysis of the projections
|-

| Paper
| [[2012Shkolnisky_Sync]]
| Angular assignment by synchronization of rotations (reference free)
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Wang_LUD]]
| Angular assignment by least unsquared deviations (reference free)
|-

| Paper
| [[2014Vargas_RANSAC]]
| Initial model using RANSAC (reference free)
|-

| Paper
| [[2015Joubert_Pseudoatoms]]
| Initial model based on pseudo-atoms
|-

| Paper
| [[2015Singer_Kam]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[2015Sorzano_Significant]]
| Statistical approach to the initial volume estimation (reconstruct significant)
|-

| Conference
| [[2016Michels_Heterogeneous]]
| Initial volume in the presence of heterogeneity
|-

| Paper
| [[2016Cossio_BayesianGPU]]
| GPU implementation of the Bayesian 3D reconstruction approach
|-

|}

=== 3D Reconstruction ===
{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1986Harauz_FBP]]
| Exact filters for Filtered Back Projection
|-

| Chapter
| [[1992Radermacher_WBP]]
| Exact filters for Weighted Back Projection
|-

| Paper
| [[1997Zhu_RecCTF]]
| 3D Reconstruction (SIRT like) and simultaneous CTF correction
|-

| Paper
| [[1998Boisset_Uneven]]
| Artifacts in SIRT and WBP under uneven angular distributions
|-

| Paper
| [[1998Marabini_ART]]
| Algebraic Reconstruction Technique with blobs (Xmipp)
|-

| Paper
| [[2001Sorzano_Uneven]]
| Free parameter selection under uneven angular distributions
|-

| Paper
| [[2005Sorzano_Parameters]]
| Free parameter selection for optimizing multiple tasks
|-

| Paper
| [[2008Sorzano_Constraints]]
| Mass, surface, positivity and symmetry constraints for real-space algorithms
|-

| Paper
| [[2009Bilbao_ParallelART]]
| Efficient parallelization of ART
|-

| Paper
| [[2011Li_GradientFlow]]
| Regularized 3D Reconstruction by Gradient Flow
|-

| Paper
| [[2011Vonesch_Wavelets]]
| Fast wavelet-based 3D reconstruction
|-

| Paper
| [[2012Gopinath_ShapeRegularization]]
| Regularized 3D Reconstruction by Shape information
|-

| Paper
| [[2012Kucukelbir_adaptiveBasis]]
| 3D reconstruction in an adaptive basis promoting sparsity
|-

| Paper
| [[2012Sindelar_NoiseReduction]]
| Optimal noise reduction in 3D reconstructions
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Lyumkis_Optimod]]
| Construction of initial volumes with Optimod
|-

| Paper
| [[2013Wang FIRM]]
| Fast 3D reconstruction in Fourier domain
|-

| Paper
| [[2014Kunz_SART_OS]]
| Simultaneous ART with OS
|-

| Paper
| [[2015Abrishami_Fourier]]
| 3D Reconstruction in Fourier space
|-

| Paper
| [[2015Dvornek_SubspaceEM]]
| Fast Maximum a posteriori
|-

| Paper
| [[2015Moriya_Bayesian]]
| Bayesian approach to suppress limited angular artifacts
|-

| Paper
| [[2015Xu_GeometricFlow]]
| Multi-scale geometric flow
|-

| Arxiv
| [[2016Ye_Cohomology]]
| Cohomology properties of 3D reconstruction
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

| Paper
| [[2017Punjani_CryoSPARCTheory]]
| Theory related to CryoSPARC
|-

|}

=== 3D Heterogeneity ===

{|

| Paper
| [[2004White_Size]]
| Heterogeneity classification of differently sized images
|-

| Paper
| [[2006Penczek_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Scheres_ML3D]]
| Maximum Likelihood alignment and classification in 3D
|-

| Paper
| [[2009Spahn_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2010Elmlund_AbInitio]]
| Solving the initial volume problem with multiple conformations
|-

| Paper
| [[2010Shatsky_MultiVariate]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2012Scheres_Bayesian]]
| A Bayesian view on cryo-EM structure determination
|-

| Paper
| [[2012Zheng_Covariance]]
| Estimation of the volume covariance
|-

| Paper
| [[2013Wang_MLVariance]]
| Maximum Likelihood estimate of the map variance
|-

| Paper
| [[2013Lyumkis D_FREALIGN]]
| Likelihood-based classification of cryo-EM images using FREALIGN.
|-

| Paper
| [[2014Jin_NMA]]
| Continuous heterogeneity through Normal Mode Analysis
|-

| Paper
| [[2014Dashti_Brownian]]
| Continuous heterogeneity through Brownian trajectories
|-

| Paper
| [[2014Chen_Migration]]
| Particle migration analysis in 3D classification
|-

| Paper
| [[2015Anden_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Bai_Focused]]
| Focused classification
|-

| Paper
| [[2015Katsevich_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Klaholz_MRA]]
| Multivariate Statistical Analysis of Jackknife and Bootstrapping on random subsets
|-

| Paper
| [[2015Liao_Covariance]]
| Estimation of the 3D covariance from 2D projections
|-

| Paper
| [[2015Tagare_Direct]]
| Direct reconstruction of PCA components
|-

| Paper
| [[2016Gong_Mechanical]]
| Mechanical model for macromolecules
|-

| Paper
| [[2016Rawson_Movement]]
| Movement and flexibility
|-

| Paper
| [[2016Sorzano_StructMap]]
| Sorting a discrete set of conformational states
|-

| Paper
| [[2016Sorzano_Strain]]
| Calculate local stretches, strains and rotations from two conformational states
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

|}

=== Validation ===

{|

| Paper
| [[2008Stagg_TestBed]]
| Effect of voltage, dosis, number of particles and Euler jumps on resolution
|-

| Paper
| [[2011Henderson]]
| Tilt Validation
|-

| Paper
| [[2011Read]]
| Validation of PDBs
|-

| Paper
| [[2012Henderson]]
| EM Map Validation
|-

| Paper
| [[2013Cossio_Bayesian]]
| EM Map Validation in a probabilistic setting
|-

| Paper
| [[2013Chen_NoiseSubstitution]]
| Noise substitution at high resolution for measuring overfitting
|-

| Paper
| [[2014Russo_StatisticalSignificance]]
| EM Map Validation through the statistical significance of the tilt-pair angular assignment
|-

| Paper
| [[2014Stagg_Reslog]]
| EM Map Validation through the resolution evolution with the number of particles
|-

| Paper
| [[2014Wasilewski_Tilt]]
| Web implementation of the tilt pair validation
|-

| Paper
| [[2015Heymann_Alignability]]
| EM Map Validation through the resolution of reconstructions from particles and noise
|-

| Paper
| [[2015Oliveira_FreqLimited]]
| Comparison of gold standard and frequency limited optimization
|-

| Paper
| [[2015Wriggers_Secondary]]
| Validation by secondary structure
|-

| Paper
| [[2016Kim_SAXS]]
| Comparison of SAXS data and EM projections
|-

| Paper
| [[2016Rosenthal_Review]]
| Review of validation methods
|-

| Paper
| [[2016Vargas_Alignability]]
| Validation by studying the tendency of an angular assignment to cluster in the projection space
|-

| Paper
| [[2017Monroe_PDBRefinement]]
| Validation by comparison to a refined PDB
|-

|}

=== Resolution ===

{|

| Paper
| [[1986Harauz_FBP]]
| Fourier Shell Correlation
|-

| Paper
| [[1987Unser_SSNR]]
| 2D Spectral Signal to Noise Ratio
|-

| Paper
| [[2002Penczek_SSNR]]
| 3D Spectral Signal to Noise Ratio for Fourier based algorithms
|-

| Paper
| [[2003Rosenthal_DPR]]
| Review of the FSC and establishment of a new threshold
|-

| Paper
| [[2005Unser_SSNR]]
| 3D Spectral Signal to Noise Ratio for any kind of algorithms
|-

| Paper
| [[2005VanHeel_FSC]]
| Establishment of a new threshold for FSC
|-

| Paper
| [[2007Sousa_AbInitio]]
| Resolution measurement on neighbour Fourier voxels
|-

| Paper
| [[2014Kucukelbir_Local]]
| Quantifying the local resolution of cryo-EM density maps
|-

| Paper
| [[2016Pintilie_Probabilistic]]
| Probabilistic models and resolution
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Statistical properties of resolution measures defined in Fourier space
|-

|}

=== Sharpening of high resolution information ===
{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast restoration and map sharpening
|-

| Paper
| [[2008Fernandez_Bfactor]]
| Bfactor determination and restoration
|-

| Paper
| [[2013Fiddy_SaxtonAlgorithm]]
| Phase retrieval or extension
|-

| Paper
| [[2014Kishchenko_SphericalDeconvolution]]
| Spherical deconvolution
|-

| Paper
| [[2015Spiegel_VISDEM]]
| Visualization improvement by the use of pseudoatomic profiles
|-

| Paper
| [[2016Jonic_Pseudoatoms]]
| Approximation with pseudoatoms
|-

| Paper
| [[2016Jonic_Denoising]]
| Denoising and high-frequency boosting by pseudoatom approximation
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[1982Schiske_Correction]]
| CTF correction for tilted objects
|-

| Paper
| [[1988Toyoshima_Model]]
| CTF estimation
|-

| Paper
| [[1995Frank_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1996Skoglund_MaxEnt]]
| CTF correction with Maximum Entropy
|-

| Paper
| [[1996Zhou_Model]]
| CTF model and user interface for manual fitting
|-

| Paper
| [[1997Fernandez_AR]]
| PSD estimation using periodogram averaging and AR models
|-

| Paper
| [[1997Penczek_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1997Stark_Deconvolution]]
| CTF correction using deconvolution
|-

| Paper
| [[1997Zhu_RecCTF]]
| CTF correction and reconstruction
|-

| Paper
| [[2000DeRosier_EwaldCorrection]]
| CTF correction considering the Ewald sphere
|-

| Paper
| [[2000Jensen_TiltedCorrection]]
| CTF correction considering tilt in backprojection
|-

| Paper
| [[2001Saad_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Huang_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Mindell_CTFTILT]]
| CTF estimation for tilted micrographs
|-

| Paper
| [[2003Sander_MSA]]
| CTF estimation through MSA classification of PSDs
|-

| Paper
| [[2003Velazquez_ARMA]]
| PSD and CTF estimation using ARMA models
|-

| Paper
| [[2004Sorzano_IDR]]
| CTF restoration and reconstruction with Iterative Data Refinement
|-

| Conference
| [[2004Wan_CTF]]
| Spatially variant CTF
|-

| Paper
| [[2004Zubelli_Chahine]]
| CTF restoration and reconstruction with Chahine's multiplicative method
|-

| Conference
| [[2005Dubowy_SpaceVariant]]
| CTF correction when this is space variant
|-

| Paper
| [[2005Mallick_ACE]]
| CTF estimation
|-

| Paper
| [[2006Wolf_Ewald]]
| CTF correction considering Ewald sphere
|-

| Paper
| [[2007Jonic_EnhancedPSD]]
| PSD enhancement for better identification of Thon rings; Vitreous ice diffracts in Thon rings
|-

| Paper
| [[2007Philippsen_Model]]
| CTF Model for tilted specimens
|-

| Paper
| [[2007Sorzano_CTF]]
| CTF estimation using enhanced PSDs
|-

| Paper
| [[2009Sorzano_Sensitivity]]
| Error sensitivity of the CTF models, non-uniqueness of the CTF parameters
|-

| Paper
| [[2010Jiang2010_CTFCorrection]]
| Amplitude correction method
|-

| Paper
| [[2010Kasantsev_CTFCorrection]]
| Mathematical foundations of Kornberg and Jensen method
|-

| Paper
| [[2010Leong_CTFCorrection]]
| Correction for spatially variant CTF
|-

| Paper
| [[2011Glaeser_Coma]]
| The effect of coma at high-resolution
|-

| Paper
| [[2011Mariani_Tilted]]
| CTF simulation and correction of tilted specimens
|-

| Paper
| [[2011Sindelar_Wiener]]
| CTF correction using a modified version of Wiener filter
|-

| Paper
| [[2011Voortman_Tilted]]
| CTF correction for tilted specimen
|-

| Paper
| [[2012Voortman_VaryingCTF]]
| Correcting a spatially varying CTF
|-

| Paper
| [[2013Vargas_FastDef]]
| Fast defocus
|-

| Paper
| [[2015Rohou_CTFFind4]]
| CTF Find 4
|-

| Paper
| [[2015Sheth_CTFquality]]
| Visualization and quality assessment of CTF
|-

| Paper
| [[2016Zhang_GCTF]]
| gCTF
|-

|}

=== Segmentation ===

{|

| Paper
| [[2006Baker_segmentation]]
| Segmentation of molecular subunits
|-

|}

=== Fitting and docking ===

{|

| Paper
| [[1999Volkmann_Fitting]]
| Fitting in real space
|-

| Paper
| [[2001Baker_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2001Jones_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2003Kovacs_FRM3D]]
| Fast Rotational Alignment of two EM maps
|-

| Paper
| [[2004Tama_NMA1]]
| Flexible fitting with Normal Modes (I)
|-

| Paper
| [[2004Tama_NMA2]]
| Flexible fitting with Normal Modes (II)
|-

| Paper
| [[2005Velazquez_Superfamilies]]
| Recognition of the superfamily folding in medium-high resolution volumes
|-

| Paper
| [[2007DeVries_Haddock]]
| Docking with Haddock 2.0
|-

| Paper
| [[2007Kleywegt_QualityControl]]
| Quality control and validation of fitting
|-

| Paper
| [[2012Biswas_Secondary]]
| Secondary structure determination in EM volumes
|-

| Paper
| [[2012Velazquez_Constraints]]
| Multicomponent fitting by using constraints from other information sources
|-

| Paper
| [[2013Chapman MS_Atomicmodeling]]
| Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters
|-

| Paper
| [[2013Esquivel_Modelling]]
| Review on modelling (secondary structure, fitting, ...)
|-

| Paper
| [[2013Lopez_Imodfit]]
| Fitting based on vibrational analysis
|-

| Paper
| [[2013Nogales_3DEMLoupe]]
| Normal Mode Analysis of reconstructed volumes
|-

| Paper
| [[2014AlNasr_Secondary]]
| Identification of secondary structure elements in EM volumes
|-

| Paper
| [[2014Politis_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Rey_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Villa_Review]]
| Review of atomic fitting into EM volumes
|-

| Paper
| [[2015Barad_EMRinger]]
| Validation of hybrid models
|-

| Paper
| [[2015Bettadapura_PF2Fit]]
| Fast rigid fitting of PDBs into EM maps
|-

| Paper
| [[2015Carrillo_CapsidMaps]]
| Analysis of virus capsids using Google Maps
|-

| Paper
| [[2015Schroeder_Hybrid]]
| Review on model building
|-

| Paper
| [[2015Tamo_Dynamics]]
| Dynamics in integrative modeling
|-

| Paper
| [[2015Sorzano_AtomsToVoxels]]
| Accurate conversion of an atomic model into a voxel density volume
|-

| Paper
| [[2016Joseph_Evolution]]
| Evolutionary constraints for the fitting of atomic models into density maps
|-

| Paper
| [[2016Segura_3Diana]]
| Validation of hybrid models
|-

| Paper
| [[2016Singharoy_MDFF]]
| Construction of hybrid models driven by EM density and molecular dynamics
|-

| Paper
| [[2016Wang_Rosetta]]
| Construction of hybrid models driven by EM density using Rosetta
|-

| Paper
| [[2017Hryc_WeightedAtoms]]
| Construction of hybrid models by locally weighting the different atoms
|-

| Paper
| [[2017Matsumoto_Distribution]]
| Estimating the distribution of conformations of atomic models
|-

| Paper
| [[2017Miyashita_EnsembleFitting]]
| Ensemble fitting using Molecular Dynamics
|-

|}

=== Books and reviews ===

{|

| Book
| [[1980Herman_Tomography]]
| General book on tomography
|-

| Book
| [[1988Kak_Tomography]]
| General book on tomography
|-

| Paper
| [[2000Tao_Review]]
| Review of single particles
|-

| Paper
| [[2000VanHeel_Review]]
| Review of single particles
|-

| Paper
| [[2002Frank_Review]]
| Review of single particles
|-

| Paper
| [[2002Schmid_Review]]
| Review of single particles
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2004Subramaniam_Review]]
| Review of single particles
|-

| Paper
| [[2005Steven_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_book]]
| Book covering all aspects of electron microscopy of single particles
|-

| Paper
| [[2006Sorzano_Review]]
| Review of optimization problems in electron microscopy
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems in Electron Tomography
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2008Mueller_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2008Taylor_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2010DeRosier_Review]]
| Personal account of how 3DEM developed in the early days
|-

| Chapter
| [[2012Sorzano_Review]]
| Review of single particle analysis using Xmipp
|-

| Chapter
| [[2012Devaux_Protocol]]
| Protocols for performing single particle analysis
|-

| Paper
| [[2014Bai_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Carazo_Review]]
| Review of the reconstruction process
|-

| Paper
| [[2015Cheng_Review]]
| A primer to Single Particle Cryo-EM
|-

| Paper
| [[2015Cheng_Reviewb]]
| Single Particle Cryo-EM at crystallographic resolution
|-

| Paper
| [[2015Elmlund_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Henderson_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Nogales_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Schroeder_Review]]
| Review of advances in the electron microscope
|-

| Paper
| [[2015Wu_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Carroni_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Egelman_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Eisenstein_CryoEM]]
| News feature on the Method of the Year
|-

| Paper
| [[2016FernandezLeiro_Review]]
| Review of EM
|-

| Paper
| [[2016Glaeser_HowGood]]
| How good can cryo-EM become?
|-

| Paper
| [[2016Jonic_PseudoAtoms]]
| Review of the applications of the use of pseudoatoms in EM
|-

| Chapter
| [[2016Mio_Review]]
| Overview of the process to obtain EM reconstructions
|-

| Paper
| [[2016Jonic_Review]]
| A review of computational ways to handle heterogeneity
|-

| Paper
| [[2016Nogales_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Subramaniam_Review]]
| Why cryo-EM is now suitable for crystallographic journals
|-

| Paper
| [[2016Vinothkumar_Review]]
| Historical review and current limitations
|-

| Paper
| [[2017Frank_Review]]
| Historical review of EM
|-

| Paper
| [[2017Jonic_Review]]
| Review of computational methods to analyze conformational variability
|-

| Paper
| [[2017Rawson_Limitations]]
| Limitations of EM for drug design
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Review of statistical properties of resolution measures defined in Fourier space
|-
|}

=== Software ===

{|

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[1999Lutdke_Eman]]
| Eman
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Baldwin_AngularTransformations]]
| The Transform Class in SPARX and EMAN2
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Grigorieff_Frealign]]
| Frealign
|-

| Paper
| [[2008Scheres_XmippProtocols]]
| Xmipp Protocols
|-

| Paper
| [[2008Shaikh_SpiderProtocols]]
| Spider Protocols
|-

| Paper
| [[2012Wriggers_SitusConventions]]
| Conventions and workflows in Situs
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2015Cianfrocco_Cloud]]
| Software execution in the cloud
|-

| Paper
| [[2015Cheng_MRC2014]]
| Extensions to MRC file format
|-

| Paper
| [[2013DeLaRosa_Scipion]]
| Scipion
|-

| Paper
| [[2016Scheres_Relion]]
| Tutorial on the use of Relion
|-

| Paper
| [[2016Grigorieff_Frealign]]
| Tutorial on the use of Frealign
|-

|}

== Electron tomography ==

=== Image preprocessing ===

{|

| Paper
| [[2015Yan_thickness]]
| Determination of thickness, tilt and electron mean free path
|-

|}

=== Image alignment ===

{|

| Paper
| [[1982Guckenberger_commonOrigin]]
| Determination of a common origin in the micrographs of titl series in three-dimensional electron microscopy
|-

| Paper
| [[1992Lawrence_leastSquares]]
| Least squares solution of the alignment problem
|-

| Paper
| [[1995Penczek_dual]]
| Dual tilt alignment
|-

| Paper
| [[1996Owen_alignmentQuality]]
| Automatic alignment without fiducial markers and evaluation of alignment quality
|-

| Paper
| [[1998Grimm_normalization]]
| Discussion of several gray level normalization methods for electron tomography
|-

| Paper
| [[2001Brandt_Automatic1]]
| Automatic alignment without fiducial markers
|-

| Paper
| [[2001Brandt_Automatic2]]
| Automatic alignment with fiducial markers
|-

| Paper
| [[2006Winkler_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2006Castano_alignment]]
| Alignment with non-perpendicularity
|-

| Paper
| [[2007Castano_alignment]]
| Fiducial-less alignment of cryo-sections
|-

| Paper
| [[2009Sorzano_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2010Cantele_dualAlignment]]
| Alignment of dual series
|-

| Paper
| [[2014Tomonaga_Automatic]]
| Automatic alignment of tilt series using the projection themselves
|-

| Paper
| [[2014Han_Automatic]]
| Automatic alignment of tilt series using SIFT features
|-

| Paper
| [[2015Han_Automatic]]
| Automatic alignment of tilt series using fiducials
|-

| Paper
| [[2017Mastronarde_Automatic]]
| Automatic alignment and reconstruction of tilt series in IMOD
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[2003Winkler_CTF]]
| Focus gradient correction in electron tomography
|-

| Paper
| [[2006Fernandez_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Zanetti_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Xiong_CTF]]
| CTF determination and correction for low dose tomographic tilt series
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2017Kunz_3DCTF]]
| 3D CTF Correction
|-

|}

=== 3D reconstruction ===

{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1992Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[1997Marabini_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2002Fernandez_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2007Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[2008Fernandez_CARP]]
| Component Averaged Row Projections (CARP)
|-

| Paper
| [[2012Herman General Superiorization]]
| Superiorization: an optimization heuristic for medical physics
|-

| Paper
| [[2012Zhang_IPET_FETR]]
| IPET and FETR, a reconstruction algorithm for single molecule tomography
|-

| Paper
| [[2013Goris_SIRT_TV_DART]]
| Combination of SIRT, Total Variation and Discrete ART to reconstruct and segment at the same time
|-

| Paper
| [[2013Briegel A_Challenge]]
| The challenge of determining handedness in electron tomography and the use of DNA origami gold nanoparticle helices as molecular standards
|-

| Paper
| [[2013Messaoudi_EnergyFiltered]]
| 3D Reconstruction of Energy-Filtered TEM
|-

| Paper
| [[2016Deng_ICON]]
| 3D Reconstruction with missing information restoration
|-

| Paper
| [[2016Guay_Compressed]]
| 3D Reconstruction using compressed sensing
|-

|}

=== Noise reduction ===
{|

| Paper
| [[2001Frangakis_NAD]]
| Noise reduction with Nonlinear Anisotropic Diffusion
|-

| Paper
| [[2003Fernandez_AND]]
| Anisotropic nonlinear diffusion for electron tomography
|-

| Paper
| [[2003Jiang_Bilateral]]
| Bilateral denoising filter in electron microscopy
|-

| Paper
| [[2005Fernandez_AND]]
| Anisotropic nonlinear denoising in electron tomography
|-

| Paper
| [[2007Heide_median]]
| Iterative median filtering in electron tomography
|-

| Paper
| [[2007Fernandez_autAND]]
| Anisotropic nonlinear diffusion with automated parameter tuning
|-

| Paper
| [[2009Fernandez_Beltrami]]
| Nonlinear filtering based on Beltrami flow
|-

| Paper
| [[2010Bilbao_MeanShift]]
| Mean Shift Filtering
|-

| Paper
| [[2014Kovacik_wedgeArtefacts]]
| Removal of wedge artefacts
|-

| Paper
| [[2014Maiorca_beadArtefacts]]
| Removal of gold bead artefacts
|-

|}

=== Segmentation ===

{|

| Paper
| [[2002Frangakis_Eigenanalysis]]
| Segmentation using eigenvector analysis.
|-

| Paper
| [[2002Volkmann_Watershed]]
| Segmentation using watershed transform.
|-

| Paper
| [[2003Bajaj_BoundarySegmentation]]
| Segmentation based on fast marching.
|-

| Paper
| [[2005Cyrklaff_Thresholding]]
| Segmentation using optimal thresholding.
|-

| Paper
| [[2007Lebbink_TemplateMatching]]
| Segmentation using template matching.
|-

| Paper
| [[2007Sandberg_OrientationFields]]
| Segmentation using orientation fields.
|-

| Paper
| [[2007Sandberg_SegmentationReview]]
| Review on segmentation in electron tomography.
|-

| Paper
| [[2008Garduno_FuzzySegmentation]]
| Segmentation using fuzzy set theory principles.
|-

| Paper
| [[2009Lebbink_TemplateMatching2]]
| Segmentation using template matching.
|-

| Paper
| [[2012RubbiyaAli_EdgeDetection]]
| Parameter-Free Segmentation of Macromolecular Structures.
|-

| Conference
| [[2015Xu_TemplateMatching]]
| Detection of macromolecular complexes with a reduced representation of the templates.
|-

|}

=== Resolution ===
{|

| Paper
| [[2005Cardone_Resolution]]
| Resolution criterion for electron tomography
|-

| Chapter
| [[2007Penczek_Resolution]]
| Review of resolution criteria for electron tomography
|-

| Paper
| [[2015Diebolder_ConicalFSC]]
| Conical Fourier Shell Correlation
|-

|}

=== Subtomogram analysis ===

{|

| Paper
| [[2000Bohm_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2002Frangakis_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2006Nickell_Review]]
| Review of macromolecule finding by template matching (Visual Proteomics)
|-

| Paper
| [[2007Best_Review]]
| Review of Localization of Protein Complexes by Pattern Recognition
|-

| Paper
| [[2007Forster_Review]]
| Review of structure determination by subtomogram averaging
|-

| Paper
| [[2008Forster_Classification]]
| Classification of subtomograms using constrained correlation
|-

| Paper
| [[2008Bartesaghi_Classification]]
| Classification and averaging of subtomograms
|-

| Paper
| [[2008Schmid_Averaging]]
| Alignment and averaging of subtomograms
|-

| Paper
| [[2010Amat_Averaging]]
| Alignment and averaging of subtomograms exploiting thresholding in Fourier space
|-

| Paper
| [[2013Chen_Averaging]]
| Fast alignment of subtomograms using spherical harmonics
|-

| Paper
| [[2013Kuybeda_Averaging]]
| Alignment and averaging of subtomograms using the nuclear norm of the cluster
|-

| Paper
| [[2013Shatsky_Averaging]]
| Alignment and averaging of subtomograms with constrained cross-correlation
|-

| Paper
| [[2014Chen_Autofocus]]
| Subtomogram averaging and classification with special attention to differences
|-

| Paper
| [[2014Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2014Voortman_LimitingFactors]]
| Limiting factors of subtomogram averaging
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2015Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2016Bharat_Relion]]
| Subtomogram averaging with Relion
|-

| Paper
| [[2016Song_MatrixNorm]]
| Matrix norm minimization for tomographic reconstruction and alignment
|-

| Paper
| [[2017Castano_ParticlePicking]]
| Particle picking in tomograms for subtomogram averaging
|-

| Paper
| [[2017Frazier_Tomominer]]
| TomoMiner a software platform for large-scale subtomogram analysis
|-

|}

=== Single particle tomography ===

{|

| Paper
| [[2012Bartesaghi_Constrained]]
| 3D reconstruction by imposing geometrical constraints
|-

| Paper
| [[2015Galaz_SingleParticleTomography]]
| Set of tools for Single Particle Tomography in EMAN2
|-

| Paper
| [[2016Galaz_SingleParticleTomography]]
| Alignment algorithms and CTF correction
|-

|}

=== Books and reviews ===

{|

| Paper
| [[2000Baumeister_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Koster_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Sali_Review]]
| Review of electron tomography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2005Lucic_Review]]
| Review of electron tomography
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_TomoBook]]
| Electron Tomography
|-

| Book
| [[2007McIntosh_Book]]
| Cellular Electron Microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2012Kudryashev_Review]]
| Review of subtomogram averaging
|-

| Paper
| [[2016Beck_Review]]
| Review of molecular sociology
|-

|}

=== Software ===

{|

| Paper
| [[1996Kremer_IMOD]]
| IMOD
|-

| Paper
| [[1996Chen_Priism/IVE]]
| Priism/IVE
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2005Nickell_TOM]]
| TOM Toolbox
|-

| Paper
| [[2007Messaoudi_TomoJ]]
| TomoJ
|-

| Paper
| [[2008Heymann_BsoftTomo]]
| Bsoft
|-

| Paper
| [[2015Ding_CaltechTomography]]
| Caltech tomography database
|-

| Paper
| [[2015Noble_AppionProtomo]]
| Batch fiducial-less tilt-series alignment in Appion using Protomo
|-

| Paper
| [[2015vanAarle_Astra]]
| ASTRA Toolbox
|-

| Paper
| [[2017Wan_Simulator]]
| Electron Tomography Simulator
|-

|}

== 2D Crystals ==

=== 2D Preprocessing ===

{|

| Paper
| [[1986Henderson_Processing]]
| General 2D processing
|-

| Paper
| [[2000He_PhaseAlignment]]
| Phase consistency and Alignment
|-

| Paper
| [[2006Gil_Unbending]]
| Crystal unbending
|-

|}

=== Classification ===
{|

| Paper
| [[1988Frank_Classification]]
| MSA and classification in electron crystallography
|-

| Paper
| [[1996Fernandez_SOM]]
| Classification based on self organizing maps
|-

| Paper
| [[1998Sherman_MSA]]
| Classification based on MSA
|-

|}
=== 3D Reconstruction ===

{|

| Paper
| [[1985Wang_Solvent]]
| Solvent flattening
|-

| Paper
| [[1990Henderson_Processing]]
| General 3D processing
|-

| Paper
| [[2004Marabini_ART]]
| Algebraic Reconstruction Technique with blobs for crystals (Xmipp)
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1998Walz_Review]]
| Review of 2D crystallography
|-

| Paper
| [[1999Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Ellis_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of single particles, electron tomography and crystallography
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Gipson_2dx]]
| 2dx
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Philippsen_IPLT]]
| IPLT
|-

|}

== 3D Crystals - MicroED ==

=== Sample Preparation ===
{|
| Paper
| [[2016Shi_Preparation]]
| Sample Preparation
|}
=== Data Collection ===
{|
| Paper
| [[2014Nannenga_CR]]
| Continuous rotation

|}
=== Data Processing ===
{|

| Paper
| [[2011Wisedchaisri_PhaseExtension]]
| Fragment-based phase extension
|-

| Paper
| [[2015Hattne_Processing]]
| Data Processing
|-

| Paper
| [[2016Hattne_Correction]]
| Image correction
|}

=== Software ===
{|

| Paper
| [[2014Iadanza_Processing]]
| Data Processing of still diffraction data
|}

=== Books and Reviews ===
{|
| Paper
| [[2014Nannenga_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Liu_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Rodriguez_Review ]]
| Review of MicroED
|-

|}

== Helical particles ==

=== Filament corrections ===

{|

| Paper
| [[1986Egelman_Curved]]
| Algorithm for correcting curved filaments
|-

| Paper
| [[1988Bluemke_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2006Wang_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2016Yang_Flexible]]
| Algorithm for correcting filaments with flexible subunits
|-

|}

=== Reconstruction ===

{|

| Paper
| [[1952Cochran_Fourier]]
| Fourier Bessel transform of filamentous structures
|-

| Paper
| [[1958Klug_Fourier]]
| Fourier Bessel decomposition of the projection images
|-

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2005Wang_Iterative]]
| Iterative Fourier-Bessel algorithm
|-

| Paper
| [[2007Egelman_Iterative]]
| Iterative real-space algorithm
|-

| Paper
| [[2013Desfosses_Spring]]
| Helical processing with Spring
|-

| Paper
| [[2015Zhang_seam]]
| Workflow for the detection of the lattice seam
|-

| Paper
| [[2016Rohou_Frealix]]
| Helical processing with Frealix
|-

|}

=== Validation ===

{|

| Paper
| [[2014Egelman_ambiguity]]
| How to detect incorrect models
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Carragher_Phoelix]]
| Phoelix
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Owen_Brandeis]]
| Brandeis
|-

|}

== Icosahedral particles ==

=== Reconstruction ===

{|

| Paper
| [[1970Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1971Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1996Fuller_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1997Thuman_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

|}

=== Classification ===

{|

| Paper
| [[2005Scheres_Virus]]
| Classification of virus capsids in real space
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1999Baker_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[1999Conway_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2000Thuman_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Lee_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Navaza_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2006Grunewald_Review]]
| Review of reconstruction of icosahedral viruses
|-

|}

=== Software ===

{|

| Paper
| [[1996Baker_EMPFT]]
| EMPFT
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2013Morin_Sliz SBGrid]]
| SBGrid presentation for eLife
|-

|}

== Databases ==

{|

| Paper
| [[2003Boutselakis_EMSD]]
| EMSD database
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2011Kim_CDDB]]
| Conformational Dynamics Data Bank
|-

| Paper
| [[2011Lawson_EMDB]]
| Electron Microscopy Data Bank
|-

| Paper
| [[2013Ison_EDAM]]
| EDAM, an ontology of bioinformatics operations
|-

| Paper
| [[2016Iudin_EMPIAR]]
| EMPIAR raw data database
|-

| Paper
| [[2016Patwhardan_EMDB]]
| EMDB, PDB, ...
|-

| Paper
| [[2017Patwhardan_Trends]]
| Trends at EMDB
|-

| Paper
| [[2017Shao_PDBQuality]]
| Quality metrics in PDB
|-

| Blog
| http://www.mybiosoftware.com
| Huge list of bioinformatics programs (many of them structural bioinformatics)
|-

|}

== Relationship to other structural information sources ==

{|

| Paper
| [[2000Engel_AFM]]
| Review of Atomic Force Microscopy
|-

| Paper
| [[2001Dimmeler_AFM]]
| Constraints from Atomic Force Microscopy
|-

| Paper
| [[2003Mobus_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_Review]]
| Review on correlative microscopy
|-

| Paper
| [[2005Boudier_EFTETJ]]
| Software for Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2005Vestergaard_SAXS]]
| Example of comparison of 3DEM and Small-angle X-ray scattering
|-

| Paper
| [[2007Hamada_SAXS]]
| Constraints from Small-angle X-ray scattering
|-

| Paper
| [[2013Xu_FRET]]
| EM+FRET
|-

|}

== X-ray tomography ==

{|

| Paper
| [[2012Oton_ImageFormation]]
| Image formation model in X-ray cell microscopy
|-

|}

== Mathematical tools necessary ==

== People developing methods ==
Please, add yourself to this list (due to privacy reasons, please, do not add anyone else to the list without his/her explicit consent). Sort by first name alphabetical order.

[http://biocomp.cnb.csic.es/~coss Carlos Oscar S. Sorzano]: CSIC, Madrid, Spain 

[http://www.curie.fr/recherche/themes/detail_equipe.cfm/lang/_fr/id_equipe/241.htm Cédric Messaoudi]: Institute Curie, Paris, France 

[http://scholar.google.es/citations?user=_jNYGScAAAAJ&hl=en Javier Vargas]:[mailto:jvargas@cnb.csic.es mail]: CSIC, Madrid, Spain 

[http://scholar.google.es/citations?hl=es&user=g2ZJPIYAAAAJ Joaquín Otón]: CSIC, Madrid, Spain 

[mailto:jrbcast@gmail.com José Román Bilbao-Castro]: UAL, Almería, Spain; CSIC, Madrid, Spain 

[José Miguel de la Rosa Trevín]: Biocomputing Unit CNB-CSIC, Madrid, Spain 

[http://cryoem.janelia.org Tamir Gonen]: [mailto:gonent@janelia.hhmi.org mail]: Howard Hughes Medical Institute, Ashburn, VA, USA 

[mailto:vabrishami@cnb.csic.es Vahid Abrishami]: CSIC, Madrid, Spain 

== 3DEM sites ==
* [http://3dem.ucsd.edu/ 3DEM web site]

* [http://en.wikibooks.org/wiki/Software_Tools_For_Molecular_Microscopy Software tools for molecular microscopy]

* [http://www.emdatabank.org/ The Electron Microscopy Data Bank (EMDB)]

* [http://ccdb.ucsd.edu The Cell Centered Database (CCDB)]

* [http://conventions.cnb.csic.es The geometrical software conventions web page ]

== Editing useful links ==

* [http://www.mediawiki.org/wiki/Help:Formatting Text formatting in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Links Adding links in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Images Adding images in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Tables Making tables in Mediawiki]

2017Punjani CryoSPARCTheory

2017-06-19T05:34:55Z

CoSS: Created page with "== Citation == Punjani, A.; Brubaker, M. A. & Fleet, D. J. Building Proteins in a Day: Efficient 3D Molecular Structure Estimation with Electron Cryomicroscopy. IEEE transact..."

== Citation ==

Punjani, A.; Brubaker, M. A. & Fleet, D. J. Building Proteins in a Day: Efficient 3D Molecular Structure Estimation with Electron Cryomicroscopy. IEEE transactions on pattern analysis and machine intelligence, 2017, 39, 706-718

== Abstract ==

Discovering the 3D atomic-resolution structure of molecules such as proteins and viruses is one of the foremost research problems in biology and medicine. Electron Cryomicroscopy (cryo-EM) is a promising vision-based technique for structure estimation which attempts to reconstruct 3D atomic structures from a large set of 2D transmission electron microscope images. This paper presents a new Bayesian framework for cryo-EM structure estimation that builds on modern stochastic optimization techniques to allow one to scale to very large datasets. We also introduce a novel Monte-Carlo technique that reduces the cost of evaluating the objective function during optimization by over five orders of magnitude. The net result is an approach capable of estimating 3D molecular structure from large-scale datasets in about a day on a single CPU workstation.

== Keywords ==

== Links ==

https://www.ncbi.nlm.nih.gov/pubmed/27849524

== Related software ==

== Related methods ==

== Comments ==

Main Page

2017-06-19T05:33:48Z

CoSS: /* 3D Reconstruction */

== Presentation ==

This web page is intended to be an extensive repository of three-dimensional electron microscopy (3DEM) methods. The advantages of having such a repository are

* You know which are the relevant articles in a particular topic, therefore, paper introductions, reviews, etc. are easier to write and you make sure you will cite all the related articles.
* You will be sure that your paper has more chances of being cited.
* You can add whatever information you find relevant to your method, external links, links to other papers, etc.
* You can link your method to a web page providing the corresponding software, so you know people can use your algorithms.
* You can use the Wiki search capabilities to locate relevant articles even if they are not at the topic you are looking at.
* As a community we will "reconstruct" our history.
* You can select the "watch" option above to receive notifications in case of further changes in the Main Page.

Developing image processing methods for 3DEM is not "[[well-paid]]" in terms of citations and impact factor. However, it is crucial for the advance of the field. Gathering methodological papers in a portal will help to increase the recognition of the field.

Please:

* Add your articles at the right place (you can add a single article in several topics if it is relevant to all of them). The easiest way to add an article is by editing the corresponding topic in the main page, adding your entry, then save the main page. Click on the red link that appears on your new entry, copy and paste the Wiki following code, add the information of your article

== Citation ==

== Abstract ==

== Keywords ==

== Links ==

== Related software ==

== Related methods ==

== Comments ==

* Maintain the information of each article as complete as possible.
* Sort articles by years and authors.
* Be respectful to other people's work.

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== Electron microscopy images ==

=== Online courses ===

CALTECH: http://cryo-em-course.caltech.edu/

MRC: ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/EM-course/

CNB-CSIC: http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/MadridJan2014EM

Workshop on Computational methods for CryoEM: https://www.youtube.com/watch?v=XdKO1iaPP8o

Workshop on Management of large CryoEM facilities: https://www.youtube.com/watch?v=as4seOPszL0

Icknield Course on Model Building and Refinement for High Resolution EM Maps: http://www.ccpem.ac.uk/training/icknield_2017/icknield_2017.php

=== Image formation ===

{|

| Paper
| [[1971Erickson_CTF]]
| CTF model
|-

| Paper
| [[1971Glaeser_Damage]]
| Radiation damage
|-

| Chapter
| [[1971Hanszen_CTF]]
| Image formation model
|-

| Paper
| [[1971Thon_Model]]
| CTF model
|-

| Paper
| [[1975Unwin_Imaging]]
| Radiation dose
|-

| Paper
| [[1977Wade_Model]]
| CTF model
|-

| Paper
| [[1978Wade_Model]]
| CTF model
|-

| Paper
| [[1979Hayward_Radiation]]
| Radiation damage
|-

| Paper
| [[1984Cohen_Validity]]
| Validity of the CTF model at high frequencies
|-

| Paper
| [[1988Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[1992Wade_Model]]
| CTF model
|-

| Paper
| [[1993Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2004Egerton_Damage]]
| Radiation damage
|-

| Paper
| [[2004Sorzano_Normalization]]
| Background noise is Gaussian
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2009Baxter_NoiseCharacterization]]
| Characterization of the different noise sources in cryo-EM
|-

| Paper
| [[2010Baker_Damage]]
| Radiation damage dependence on resolution
|-

| Paper
| [[2010Bammes_Damage]]
| Radiation damage dependence on temperature
|-

| Paper
| [[2010Gomez_Multislice]]
| Simulation of the multi slice model
|-

| Paper
| [[2010Zewail_FourDimensional]]
| Review on the use of ultrafast EM
|-

| Paper
| [[2011Bammes_CCD]]
| Performance of CCD cameras
|-

| Paper
| [[2011Glaeser_Coma]]
| Image formation model including coma
|-

| Paper
| [[2011Milazzo_DirectDetectors]]
| Evaluation of Direct Detectors
|-

| Paper
| [[2011Rullgard_ImageSimulation]]
| Accurate simulation of EM images
|-

| Paper
| [[2011Zhang LimitingFactors]]
| Limiting factor for atomic resolution in EM
|-

| Paper
| [[2012Bammes_DirectDetection]]
| Performance of Direct detectors
|-

| Paper
| [[2012Campbell_MotionCorrection]]
| Beam induced motion correction and direct detectors
|-

| Paper
| [[2012Shang_HydrationLayer]]
| Simulation of PDB volumes explicitly considering the hydration layer
|-

| Paper
| [[2013Egerton_RadiationDamage]]
| Review of TEM radiation damage and experimental ways of reducing it
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu H_Noisemodels]]
| Noise models and cryo-EM drift correction with a direct-electron camera
|-

| Paper
| [[2013Li X K2 noisemodels]]
| Influence of electron dose rate on electron counting images recorded with the K2 camera
|-

| Paper
| [[2013Vulovic_CTFApproximations]]
| When to use the different approximations performed so that a projection with linear CTF is valid
|-

| Thesis
| [[2013Vulovic_ImageFormation]]
| Ph.D. Thesis on the image formation in cryo-EM
|-

| Paper
| [[2014Danev_PhasePlate]]
| Volta potential phase plate
|-

| Paper
| [[2015Chiu_K2]]
| Characterization of K2
|-

| Paper
| [[2015Hawkes_AberrationCorrection]]
| Historical account of the development of lens corrections
|-

| Paper
| [[2015Koeck_Quadratic]]
| Limitations of the linear approximation and use of the quadratic terms
|-

| Paper
| [[2015Kuijper_FEI]]
| Description of the FEI Falcons
|-

| Paper
| [[2015Lobato_MULTEM]]
| Simulation of multislice diffraction
|-

| Paper
| [[2015McMullan_AmorphousIce]]
| Beam induced movement is caused by Brownian motion
|-

| Paper
| [[2016Koeck_ADF]]
| Simulations of Annular Dark Field TEM
|-

| Paper
| [[2017Mishyna_DNARadiation]]
| Review of radiation damage on DNA
|-

|}

=== Collection geometry ===

{|

| Chapter
| [[1980Hoppe_Wedge]]
| Missing wedge
|-

| Paper
| [[1987Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1995Penczek_Dual]]
| Dual axis tomography
|-

| Paper
| [[1997Mastronarde_Dual]]
| Dual axis tomography
|-

| Paper
| [[2003Ludtke_FocusPairs]]
| Focus pairs for single particles
|-

| Paper
| [[2005Lanzavecchia_Conical]]
| Conical tomography
|-

| Paper
| [[2005Zampighi_Conical]]
| Conical tomography
|-

| Paper
| [[2006Leschziner_OT]]
| Orthogonal Tilt
|-

| Paper
| [[2006Messaoudi_Multiple]]
| Multiple axis tomography
|-

| Paper
| [[2012Kudryashev_FocusPairs]]
| Focus pairs tomography
|-

| Paper
| [[2014Hovden_TiltFocus]]
| Combining tilt series with focus series
|-

| Paper
| [[2015Sorzano_RandomConicalTilt]]
| General formulation of Random Conical Tilt
|-

| Paper
| [[2017Hagen_DoseTomography]]
| Dose optimization for subtomogram averaging
|-

|}

=== Sample preparation ===

{|

| Paper
| [[1982Dubochet_Sample]]
| Vitreous ice
|-

| Paper
| [[1986Lepault_Sample]]
| Fast freezing
|-

| Paper
| [[1995Dubochet_Sample]]
| High-pressure freezing
|-

| Paper
| [[1995VanMarle_Sample]]
| Sample damages in resin
|-

| Paper
| [[1998Adrian_Sample]]
| Cryo negative staining
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2002Hsieh_Sample]]
| Cryofixation
|-

| Paper
| [[2004AlAmoudi_Sample]]
| CEMOVIS
|-

| Paper
| [[2008Studer_Sample]]
| Review on high pressure freezing
|-

| Paper
| [[2009Pierson_Sample]]
| Review on sample preparation for electron tomography
|-

| Paper
| [[2010Zhang_NegativeStaining]]
| Negative staining for small protein imaging
|-

| Paper
| [[2012Zhang_PositiveStaining]]
| Positive staining
|-

| Paper
| [[2014Rames_NegativeStaining]]
| Optimized negative staining
|-

| Paper
| [[2014Russo_GoldGrids]]
| Gold grids for single particles
|-

| Paper
| [[2015Cabra_Sample]]
| Review on sample preparation for single particles with videos
|-

| Paper
| [[2016Passmore_Review]]
| Tutorial chapter on sample preparation
|-

| Paper
| [[2016Razinkov_Vitrification]]
| New vitrification method
|-

| Paper
| [[2016Takizawa_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2016Thompson_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2017Arnold_BlottingFree]]
| Blotting-free preparation
|-

| Paper
| [[2017Feng_SprayingPlunging]]
| Spraying plunging
|-

| Paper
| [[2017Peitsch_Sample]]
| iMEM: Isolation of Plasma Membrane for Cryoelectron Microscopy
|-

| Paper
| [[2017Scapin_Storage]]
| Cryo storage of samples
|-

| Paper
| [[2017Schaffer_FocusedIonBeam]]
| Focused Ion Beam sample preparation for membrane proteins
|-

|}

=== Automated data collection ===

{|

| Paper
| [[1992Dierksen_Automatic]]
| Automated data collection
|-

| Paper
| [[1992Koster_Automatic]]
| Automated data collection
|-

| Paper
| [[1996Fung_Automatic]]
| Automated data collection for tomography
|-

| Paper
| [[2001Zhang_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2003Ziese_Automatic]]
| Automated autofocusing
|-

| Paper
| [[2004Potter_Automatic]]
| Automated sample loading
|-

| Paper
| [[2004Zheng_Automatic]]
| Automated data collection
|-

| Paper
| [[2005Lei_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2005Suloway_Automatic]]
| Automated data collection: Leginon
|-

| Paper
| [[2007Yoshioka_RCT]]
| Automated Random Conical Tilt
|-

| Paper
| [[2011Korinek_TOM2]]
| Automated acquisition with TOM2
|-

| Paper
| [[2015Li_UCSFImage]]
| Automated acquisition with UCSFImage
|-

| Paper
| [[2016Gil_Fuzzy]]
| Real time decisions during acquisition with neuro-fuzzy method
|-

| Paper
| [[2016Liu_TiltControl]]
| Accurate control of the tilt angle for electron tomography
|-

| Paper
| [[2016Vargas_FoilHole]]
| Determination of image quality at low magnification
|-

| Paper
| [[2017Biyani_Focus]]
| Automatic processing of micrographs
|-

|}

== Single particles ==

=== Automatic particle picking ===

{|

| Paper
| [[1982VanHeel_Detection]]
| Detection of particles in micrographs
|-

| Paper
| [[2001Nicholson_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2001Zhu_Filaments]]
| Automatic identification of filaments in micrographs
|-

| Paper
| [[2004Sigworth_Detection]]
| Classical detection theory and the cryo-EM particle selection problem
|-

| Paper
| [[2004Volkmann_ParticlePicking]]
| An approach to automated particle picking from electron micrographs based on reduced representation templates
|-

| Paper
| [[2004Wong_ParticlePicking]]
| Model-based particle picking for cryo-electron microscopy
|-

| Paper
| [[2004Zhu_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2007Chen_Signature]]
| Automatic particle picking program: Signature
|-

| Paper
| [[2007Woolford_SwarmPS]]
| Automatic particle picking with several criteria, implemented in EMAN Boxer
|-

| Paper
| [[2009Sorzano_MachineLearning]]
| Automatic particle picking based on machine learning of rotational invariants
|-

| Paper
| [[2011Arbelaez_Comparison]]
| Evaluation of the performance of software for automated particle-boxing
|-

| Paper
| [[2013Abrishami_MachineLearning]]
| A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs
|-

| Paper
| [[2013Hauer_2013]]
| Automatic tilt pair detection in Random Conical Tilt
|-

| Paper
| [[2013Shatsky_ParticlePicking]]
| Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Langlois_ParticlePicking]]
| Automatic particle picking
|-

| Paper
| [[2016Vilas_AutomaticTilt]]
| Automatic identification of image pairs in untilted-tilted micrograph pairs
|-

|}

=== 2D Preprocessing ===

{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast enhancement through DPR
|-

| Paper
| [[2004Sorzano_Normalization]]
| Normalization procedures and their statistical properties.
|-

| Paper
| [[2006Sorzano_Denoising]]
| Strong denoising in wavelet space
|-

| Conference
| [[2009Sorzano_Downsampling]]
| Differences between the different downsampling schemes
|-

| Paper
| [[2012Brilot_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Campbell_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Zhao_Denoising]]
| Denoising using an invariant Fourier-Bessel eigenspace
|-

| Paper
| [[2013Norousi_Screening]]
| Screening particles to identify outliers
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu_Movies]]
| Drift correction for movies considering dark field
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Scheres_Movies]]
| Beam induced motion correction
|-

| Paper
| [[2015Abrishami_Movies]]
| Alignment of direct detection device micrographs
|-

| Paper
| [[2015Grant_Anisotropic]]
| Automatic estimation and correction of anisotropic magnification
|-

| Paper
| [[2015Grant_OptimalExposure]]
| Filter movies according to the radiation damage
|-

| Paper
| [[2015Rubinstein_Alignment]]
| Frame alignment at the level of particle
|-

| Paper
| [[2015Spear_DoseCompensation]]
| Effect of dose compensation on resolution
|-

| Paper
| [[2015Zhao_AnisotropicMagnification]]
| Correction of anisotropic magnification
|-

| Conference
| [[2016Bajic_Denoising]]
| Denoising and deconvolution of micrographs
|-

| Paper
| [[2016Jensen_RemovalVesicles]]
| Removal of vesicles in membrane proteins
|-

| Paper
| [[2016Bhamre_Denoising]]
| Denoising by 2D covariance estimation
|-

| Paper
| [[2017McLeod_Zorro]]
| Movie alignment by Zorro
|-

| Paper
| [[2017Zheng_MotionCorr2]]
| Movie alignment by MotionCorr2
|-

|}

=== 2D Alignment ===

{|

| Paper
| [[1981Frank_Averaging]]
| 2D averaging and phase residual
|-

| Paper
| [[1982Saxton_Averaging]]
| 2D averaging using correlation
|-

| Paper
| [[1998Sigworth_ML2D]]
| Maximum likelihood alignment in 2D
|-

| Paper
| [[2003Cong_FRM2D]]
| Fast Rotational Matching in 2D
|-

| Paper
| [[2005Cong_FRM2D]]
| Fast Rotational Matching in 2D introduced in a 3D Alignment algorithm
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

|}

=== 2D Classification and clustering ===

{|

| Paper
| [[1981VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[1984VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2011Singer_DiffusionMaps]]
| Classification in 2D based on graph analysis of the projections
|-

| Paper
| [[2012Yang_ISAC]]
| Iterative Stable Alignment and clustering
|-

| Paper
| [[2014Sorzano_Outlier]]
| Outlier detection in 2D classifications.
|-

| Paper
| [[2014Zhao_Aspire]]
| Fast classification based on rotational invariants and vector diffusion maps
|-

| Paper
| [[2015Huang_Robust]]
| Robust w-estimators of 2D classes
|-

| Paper
| [[2016Reboul_Stochastic]]
| Stochastic Hill Climbing for calculating 2D classes
|-

| Conference
| [[2017Bhamre_Mahalanobis]]
| 2D classification using Mahalanobis distance
|-

|}

=== 3D Alignment ===

{|

| Paper
| [[1980Kam_AutoCorrelation]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[1986Goncharov_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1987VanHeel_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1988Provencher_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Vogel_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1990Gelfand_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Goncharov_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Harauz_Quaternions]]
| Use of quaternions to represent rotations
|-

| Paper
| [[1994Penczek_Real]]
| Angular assignment using projection matching in real space
|-

| Paper
| [[1994Radermacher_Radon]]
| Angular assignment in Radon space
|-

| Paper
| [[1996Penczek_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[2003Rosenthal_DPR]]
| Angular assignment using DPR
|-

| Paper
| [[2004Sorzano_Wavelet]]
| Angular assignment in the wavelet space.
|-

| Paper
| [[2005Jonic_Splines]]
| Angular assignment in Fourier space using spline interpolation.
|-

| Paper
| [[2005Yang_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[2006Ogura_SimulatedAnnealing]]
| Angular asignment by simulated annealing
|-

| Paper
| [[2007Grigorieff_Continuous]]
| Continuous angular assignment in Fourier space
|-

| Paper
| [[2010Jaitly_Bayesian]]
| Angular assignment by a Bayesian method and annealing
|-

| Paper
| [[2010Sanz_Random]]
| Random model method
|-

| Paper
| [[2010Singer_Voting]]
| Detecting consistent common lines by voting (reference free)
|-

| Paper
| [[2011Singer_SDP]]
| Angular assignment by semidefinite programming and eigenvectors (reference free)
|-

| Paper
| [[2012Giannakis_Scattering]]
| Construction of an initial volume, reference free, by graph analysis of the projections
|-

| Paper
| [[2012Shkolnisky_Sync]]
| Angular assignment by synchronization of rotations (reference free)
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Wang_LUD]]
| Angular assignment by least unsquared deviations (reference free)
|-

| Paper
| [[2014Vargas_RANSAC]]
| Initial model using RANSAC (reference free)
|-

| Paper
| [[2015Joubert_Pseudoatoms]]
| Initial model based on pseudo-atoms
|-

| Paper
| [[2015Singer_Kam]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[2015Sorzano_Significant]]
| Statistical approach to the initial volume estimation (reconstruct significant)
|-

| Conference
| [[2016Michels_Heterogeneous]]
| Initial volume in the presence of heterogeneity
|-

| Paper
| [[2016Cossio_BayesianGPU]]
| GPU implementation of the Bayesian 3D reconstruction approach
|-

|}

=== 3D Reconstruction ===
{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1986Harauz_FBP]]
| Exact filters for Filtered Back Projection
|-

| Chapter
| [[1992Radermacher_WBP]]
| Exact filters for Weighted Back Projection
|-

| Paper
| [[1997Zhu_RecCTF]]
| 3D Reconstruction (SIRT like) and simultaneous CTF correction
|-

| Paper
| [[1998Boisset_Uneven]]
| Artifacts in SIRT and WBP under uneven angular distributions
|-

| Paper
| [[1998Marabini_ART]]
| Algebraic Reconstruction Technique with blobs (Xmipp)
|-

| Paper
| [[2001Sorzano_Uneven]]
| Free parameter selection under uneven angular distributions
|-

| Paper
| [[2005Sorzano_Parameters]]
| Free parameter selection for optimizing multiple tasks
|-

| Paper
| [[2008Sorzano_Constraints]]
| Mass, surface, positivity and symmetry constraints for real-space algorithms
|-

| Paper
| [[2009Bilbao_ParallelART]]
| Efficient parallelization of ART
|-

| Paper
| [[2011Li_GradientFlow]]
| Regularized 3D Reconstruction by Gradient Flow
|-

| Paper
| [[2011Vonesch_Wavelets]]
| Fast wavelet-based 3D reconstruction
|-

| Paper
| [[2012Gopinath_ShapeRegularization]]
| Regularized 3D Reconstruction by Shape information
|-

| Paper
| [[2012Kucukelbir_adaptiveBasis]]
| 3D reconstruction in an adaptive basis promoting sparsity
|-

| Paper
| [[2012Sindelar_NoiseReduction]]
| Optimal noise reduction in 3D reconstructions
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Lyumkis_Optimod]]
| Construction of initial volumes with Optimod
|-

| Paper
| [[2013Wang FIRM]]
| Fast 3D reconstruction in Fourier domain
|-

| Paper
| [[2014Kunz_SART_OS]]
| Simultaneous ART with OS
|-

| Paper
| [[2015Abrishami_Fourier]]
| 3D Reconstruction in Fourier space
|-

| Paper
| [[2015Dvornek_SubspaceEM]]
| Fast Maximum a posteriori
|-

| Paper
| [[2015Moriya_Bayesian]]
| Bayesian approach to suppress limited angular artifacts
|-

| Paper
| [[2015Xu_GeometricFlow]]
| Multi-scale geometric flow
|-

| Arxiv
| [[2016Ye_Cohomology]]
| Cohomology properties of 3D reconstruction
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

| Paper
| [[2017Punjani_CryoSPARCTheory]]
| Theory related to CryoSPARC
|-

|}

=== 3D Heterogeneity ===

{|

| Paper
| [[2004White_Size]]
| Heterogeneity classification of differently sized images
|-

| Paper
| [[2006Penczek_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Scheres_ML3D]]
| Maximum Likelihood alignment and classification in 3D
|-

| Paper
| [[2009Spahn_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2010Elmlund_AbInitio]]
| Solving the initial volume problem with multiple conformations
|-

| Paper
| [[2010Shatsky_MultiVariate]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2012Scheres_Bayesian]]
| A Bayesian view on cryo-EM structure determination
|-

| Paper
| [[2012Zheng_Covariance]]
| Estimation of the volume covariance
|-

| Paper
| [[2013Wang_MLVariance]]
| Maximum Likelihood estimate of the map variance
|-

| Paper
| [[2013Lyumkis D_FREALIGN]]
| Likelihood-based classification of cryo-EM images using FREALIGN.
|-

| Paper
| [[2014Jin_NMA]]
| Continuous heterogeneity through Normal Mode Analysis
|-

| Paper
| [[2014Dashti_Brownian]]
| Continuous heterogeneity through Brownian trajectories
|-

| Paper
| [[2014Chen_Migration]]
| Particle migration analysis in 3D classification
|-

| Paper
| [[2015Anden_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Bai_Focused]]
| Focused classification
|-

| Paper
| [[2015Katsevich_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Klaholz_MRA]]
| Multivariate Statistical Analysis of Jackknife and Bootstrapping on random subsets
|-

| Paper
| [[2015Liao_Covariance]]
| Estimation of the 3D covariance from 2D projections
|-

| Paper
| [[2015Tagare_Direct]]
| Direct reconstruction of PCA components
|-

| Paper
| [[2016Gong_Mechanical]]
| Mechanical model for macromolecules
|-

| Paper
| [[2016Rawson_Movement]]
| Movement and flexibility
|-

| Paper
| [[2016Sorzano_StructMap]]
| Sorting a discrete set of conformational states
|-

| Paper
| [[2016Sorzano_Strain]]
| Calculate local stretches, strains and rotations from two conformational states
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

|}

=== Validation ===

{|

| Paper
| [[2008Stagg_TestBed]]
| Effect of voltage, dosis, number of particles and Euler jumps on resolution
|-

| Paper
| [[2011Henderson]]
| Tilt Validation
|-

| Paper
| [[2011Read]]
| Validation of PDBs
|-

| Paper
| [[2012Henderson]]
| EM Map Validation
|-

| Paper
| [[2013Cossio_Bayesian]]
| EM Map Validation in a probabilistic setting
|-

| Paper
| [[2013Chen_NoiseSubstitution]]
| Noise substitution at high resolution for measuring overfitting
|-

| Paper
| [[2014Russo_StatisticalSignificance]]
| EM Map Validation through the statistical significance of the tilt-pair angular assignment
|-

| Paper
| [[2014Stagg_Reslog]]
| EM Map Validation through the resolution evolution with the number of particles
|-

| Paper
| [[2014Wasilewski_Tilt]]
| Web implementation of the tilt pair validation
|-

| Paper
| [[2015Heymann_Alignability]]
| EM Map Validation through the resolution of reconstructions from particles and noise
|-

| Paper
| [[2015Oliveira_FreqLimited]]
| Comparison of gold standard and frequency limited optimization
|-

| Paper
| [[2015Wriggers_Secondary]]
| Validation by secondary structure
|-

| Paper
| [[2016Kim_SAXS]]
| Comparison of SAXS data and EM projections
|-

| Paper
| [[2016Rosenthal_Review]]
| Review of validation methods
|-

| Paper
| [[2016Vargas_Alignability]]
| Validation by studying the tendency of an angular assignment to cluster in the projection space
|-

| Paper
| [[2017Monroe_PDBRefinement]]
| Validation by comparison to a refined PDB
|-

|}

=== Resolution ===

{|

| Paper
| [[1986Harauz_FBP]]
| Fourier Shell Correlation
|-

| Paper
| [[1987Unser_SSNR]]
| 2D Spectral Signal to Noise Ratio
|-

| Paper
| [[2002Penczek_SSNR]]
| 3D Spectral Signal to Noise Ratio for Fourier based algorithms
|-

| Paper
| [[2003Rosenthal_DPR]]
| Review of the FSC and establishment of a new threshold
|-

| Paper
| [[2005Unser_SSNR]]
| 3D Spectral Signal to Noise Ratio for any kind of algorithms
|-

| Paper
| [[2005VanHeel_FSC]]
| Establishment of a new threshold for FSC
|-

| Paper
| [[2007Sousa_AbInitio]]
| Resolution measurement on neighbour Fourier voxels
|-

| Paper
| [[2014Kucukelbir_Local]]
| Quantifying the local resolution of cryo-EM density maps
|-

| Paper
| [[2016Pintilie_Probabilistic]]
| Probabilistic models and resolution
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Statistical properties of resolution measures defined in Fourier space
|-

|}

=== Sharpening of high resolution information ===
{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast restoration and map sharpening
|-

| Paper
| [[2008Fernandez_Bfactor]]
| Bfactor determination and restoration
|-

| Paper
| [[2013Fiddy_SaxtonAlgorithm]]
| Phase retrieval or extension
|-

| Paper
| [[2014Kishchenko_SphericalDeconvolution]]
| Spherical deconvolution
|-

| Paper
| [[2015Spiegel_VISDEM]]
| Visualization improvement by the use of pseudoatomic profiles
|-

| Paper
| [[2016Jonic_Pseudoatoms]]
| Approximation with pseudoatoms
|-

| Paper
| [[2016Jonic_Denoising]]
| Denoising and high-frequency boosting by pseudoatom approximation
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[1982Schiske_Correction]]
| CTF correction for tilted objects
|-

| Paper
| [[1988Toyoshima_Model]]
| CTF estimation
|-

| Paper
| [[1995Frank_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1996Skoglund_MaxEnt]]
| CTF correction with Maximum Entropy
|-

| Paper
| [[1996Zhou_Model]]
| CTF model and user interface for manual fitting
|-

| Paper
| [[1997Fernandez_AR]]
| PSD estimation using periodogram averaging and AR models
|-

| Paper
| [[1997Penczek_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1997Stark_Deconvolution]]
| CTF correction using deconvolution
|-

| Paper
| [[1997Zhu_RecCTF]]
| CTF correction and reconstruction
|-

| Paper
| [[2000DeRosier_EwaldCorrection]]
| CTF correction considering the Ewald sphere
|-

| Paper
| [[2000Jensen_TiltedCorrection]]
| CTF correction considering tilt in backprojection
|-

| Paper
| [[2001Saad_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Huang_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Mindell_CTFTILT]]
| CTF estimation for tilted micrographs
|-

| Paper
| [[2003Sander_MSA]]
| CTF estimation through MSA classification of PSDs
|-

| Paper
| [[2003Velazquez_ARMA]]
| PSD and CTF estimation using ARMA models
|-

| Paper
| [[2004Sorzano_IDR]]
| CTF restoration and reconstruction with Iterative Data Refinement
|-

| Conference
| [[2004Wan_CTF]]
| Spatially variant CTF
|-

| Paper
| [[2004Zubelli_Chahine]]
| CTF restoration and reconstruction with Chahine's multiplicative method
|-

| Conference
| [[2005Dubowy_SpaceVariant]]
| CTF correction when this is space variant
|-

| Paper
| [[2005Mallick_ACE]]
| CTF estimation
|-

| Paper
| [[2006Wolf_Ewald]]
| CTF correction considering Ewald sphere
|-

| Paper
| [[2007Jonic_EnhancedPSD]]
| PSD enhancement for better identification of Thon rings; Vitreous ice diffracts in Thon rings
|-

| Paper
| [[2007Philippsen_Model]]
| CTF Model for tilted specimens
|-

| Paper
| [[2007Sorzano_CTF]]
| CTF estimation using enhanced PSDs
|-

| Paper
| [[2009Sorzano_Sensitivity]]
| Error sensitivity of the CTF models, non-uniqueness of the CTF parameters
|-

| Paper
| [[2010Jiang2010_CTFCorrection]]
| Amplitude correction method
|-

| Paper
| [[2010Kasantsev_CTFCorrection]]
| Mathematical foundations of Kornberg and Jensen method
|-

| Paper
| [[2010Leong_CTFCorrection]]
| Correction for spatially variant CTF
|-

| Paper
| [[2011Glaeser_Coma]]
| The effect of coma at high-resolution
|-

| Paper
| [[2011Mariani_Tilted]]
| CTF simulation and correction of tilted specimens
|-

| Paper
| [[2011Sindelar_Wiener]]
| CTF correction using a modified version of Wiener filter
|-

| Paper
| [[2011Voortman_Tilted]]
| CTF correction for tilted specimen
|-

| Paper
| [[2012Voortman_VaryingCTF]]
| Correcting a spatially varying CTF
|-

| Paper
| [[2013Vargas_FastDef]]
| Fast defocus
|-

| Paper
| [[2015Rohou_CTFFind4]]
| CTF Find 4
|-

| Paper
| [[2015Sheth_CTFquality]]
| Visualization and quality assessment of CTF
|-

| Paper
| [[2016Zhang_GCTF]]
| gCTF
|-

|}

=== Segmentation ===

{|

| Paper
| [[2006Baker_segmentation]]
| Segmentation of molecular subunits
|-

|}

=== Fitting and docking ===

{|

| Paper
| [[1999Volkmann_Fitting]]
| Fitting in real space
|-

| Paper
| [[2001Baker_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2001Jones_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2003Kovacs_FRM3D]]
| Fast Rotational Alignment of two EM maps
|-

| Paper
| [[2004Tama_NMA1]]
| Flexible fitting with Normal Modes (I)
|-

| Paper
| [[2004Tama_NMA2]]
| Flexible fitting with Normal Modes (II)
|-

| Paper
| [[2005Velazquez_Superfamilies]]
| Recognition of the superfamily folding in medium-high resolution volumes
|-

| Paper
| [[2007DeVries_Haddock]]
| Docking with Haddock 2.0
|-

| Paper
| [[2007Kleywegt_QualityControl]]
| Quality control and validation of fitting
|-

| Paper
| [[2012Biswas_Secondary]]
| Secondary structure determination in EM volumes
|-

| Paper
| [[2012Velazquez_Constraints]]
| Multicomponent fitting by using constraints from other information sources
|-

| Paper
| [[2013Chapman MS_Atomicmodeling]]
| Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters
|-

| Paper
| [[2013Esquivel_Modelling]]
| Review on modelling (secondary structure, fitting, ...)
|-

| Paper
| [[2013Lopez_Imodfit]]
| Fitting based on vibrational analysis
|-

| Paper
| [[2013Nogales_3DEMLoupe]]
| Normal Mode Analysis of reconstructed volumes
|-

| Paper
| [[2014AlNasr_Secondary]]
| Identification of secondary structure elements in EM volumes
|-

| Paper
| [[2014Politis_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Rey_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Villa_Review]]
| Review of atomic fitting into EM volumes
|-

| Paper
| [[2015Barad_EMRinger]]
| Validation of hybrid models
|-

| Paper
| [[2015Bettadapura_PF2Fit]]
| Fast rigid fitting of PDBs into EM maps
|-

| Paper
| [[2015Carrillo_CapsidMaps]]
| Analysis of virus capsids using Google Maps
|-

| Paper
| [[2015Schroeder_Hybrid]]
| Review on model building
|-

| Paper
| [[2015Tamo_Dynamics]]
| Dynamics in integrative modeling
|-

| Paper
| [[2015Sorzano_AtomsToVoxels]]
| Accurate conversion of an atomic model into a voxel density volume
|-

| Paper
| [[2016Joseph_Evolution]]
| Evolutionary constraints for the fitting of atomic models into density maps
|-

| Paper
| [[2016Segura_3Diana]]
| Validation of hybrid models
|-

| Paper
| [[2016Singharoy_MDFF]]
| Construction of hybrid models driven by EM density and molecular dynamics
|-

| Paper
| [[2016Wang_Rosetta]]
| Construction of hybrid models driven by EM density using Rosetta
|-

| Paper
| [[2017Hryc_WeightedAtoms]]
| Construction of hybrid models by locally weighting the different atoms
|-

| Paper
| [[2017Matsumoto_Distribution]]
| Estimating the distribution of conformations of atomic models
|-

| Paper
| [[2017Miyashita_EnsembleFitting]]
| Ensemble fitting using Molecular Dynamics
|-

|}

=== Books and reviews ===

{|

| Book
| [[1980Herman_Tomography]]
| General book on tomography
|-

| Book
| [[1988Kak_Tomography]]
| General book on tomography
|-

| Paper
| [[2000Tao_Review]]
| Review of single particles
|-

| Paper
| [[2000VanHeel_Review]]
| Review of single particles
|-

| Paper
| [[2002Frank_Review]]
| Review of single particles
|-

| Paper
| [[2002Schmid_Review]]
| Review of single particles
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2004Subramaniam_Review]]
| Review of single particles
|-

| Paper
| [[2005Steven_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_book]]
| Book covering all aspects of electron microscopy of single particles
|-

| Paper
| [[2006Sorzano_Review]]
| Review of optimization problems in electron microscopy
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems in Electron Tomography
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2008Mueller_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2008Taylor_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2010DeRosier_Review]]
| Personal account of how 3DEM developed in the early days
|-

| Chapter
| [[2012Sorzano_Review]]
| Review of single particle analysis using Xmipp
|-

| Chapter
| [[2012Devaux_Protocol]]
| Protocols for performing single particle analysis
|-

| Paper
| [[2014Bai_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Carazo_Review]]
| Review of the reconstruction process
|-

| Paper
| [[2015Cheng_Review]]
| A primer to Single Particle Cryo-EM
|-

| Paper
| [[2015Cheng_Reviewb]]
| Single Particle Cryo-EM at crystallographic resolution
|-

| Paper
| [[2015Elmlund_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Henderson_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Nogales_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Schroeder_Review]]
| Review of advances in the electron microscope
|-

| Paper
| [[2015Wu_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Carroni_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Egelman_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Eisenstein_CryoEM]]
| News feature on the Method of the Year
|-

| Paper
| [[2016FernandezLeiro_Review]]
| Review of EM
|-

| Paper
| [[2016Glaeser_HowGood]]
| How good can cryo-EM become?
|-

| Paper
| [[2016Jonic_PseudoAtoms]]
| Review of the applications of the use of pseudoatoms in EM
|-

| Chapter
| [[2016Mio_Review]]
| Overview of the process to obtain EM reconstructions
|-

| Paper
| [[2016Jonic_Review]]
| A review of computational ways to handle heterogeneity
|-

| Paper
| [[2016Nogales_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Subramaniam_Review]]
| Why cryo-EM is now suitable for crystallographic journals
|-

| Paper
| [[2016Vinothkumar_Review]]
| Historical review and current limitations
|-

| Paper
| [[2017Frank_Review]]
| Historical review of EM
|-

| Paper
| [[2017Jonic_Review]]
| Review of computational methods to analyze conformational variability
|-

| Paper
| [[2017Rawson_Limitations]]
| Limitations of EM for drug design
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Review of statistical properties of resolution measures defined in Fourier space
|-
|}

=== Software ===

{|

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[1999Lutdke_Eman]]
| Eman
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Baldwin_AngularTransformations]]
| The Transform Class in SPARX and EMAN2
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Grigorieff_Frealign]]
| Frealign
|-

| Paper
| [[2008Scheres_XmippProtocols]]
| Xmipp Protocols
|-

| Paper
| [[2008Shaikh_SpiderProtocols]]
| Spider Protocols
|-

| Paper
| [[2012Wriggers_SitusConventions]]
| Conventions and workflows in Situs
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2015Cianfrocco_Cloud]]
| Software execution in the cloud
|-

| Paper
| [[2015Cheng_MRC2014]]
| Extensions to MRC file format
|-

| Paper
| [[2013DeLaRosa_Scipion]]
| Scipion
|-

| Paper
| [[2016Scheres_Relion]]
| Tutorial on the use of Relion
|-

| Paper
| [[2016Grigorieff_Frealign]]
| Tutorial on the use of Frealign
|-

|}

== Electron tomography ==

=== Image preprocessing ===

{|

| Paper
| [[2015Yan_thickness]]
| Determination of thickness, tilt and electron mean free path
|-

|}

=== Image alignment ===

{|

| Paper
| [[1982Guckenberger_commonOrigin]]
| Determination of a common origin in the micrographs of titl series in three-dimensional electron microscopy
|-

| Paper
| [[1992Lawrence_leastSquares]]
| Least squares solution of the alignment problem
|-

| Paper
| [[1995Penczek_dual]]
| Dual tilt alignment
|-

| Paper
| [[1996Owen_alignmentQuality]]
| Automatic alignment without fiducial markers and evaluation of alignment quality
|-

| Paper
| [[1998Grimm_normalization]]
| Discussion of several gray level normalization methods for electron tomography
|-

| Paper
| [[2001Brandt_Automatic1]]
| Automatic alignment without fiducial markers
|-

| Paper
| [[2001Brandt_Automatic2]]
| Automatic alignment with fiducial markers
|-

| Paper
| [[2006Winkler_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2006Castano_alignment]]
| Alignment with non-perpendicularity
|-

| Paper
| [[2007Castano_alignment]]
| Fiducial-less alignment of cryo-sections
|-

| Paper
| [[2009Sorzano_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2010Cantele_dualAlignment]]
| Alignment of dual series
|-

| Paper
| [[2014Tomonaga_Automatic]]
| Automatic alignment of tilt series using the projection themselves
|-

| Paper
| [[2014Han_Automatic]]
| Automatic alignment of tilt series using SIFT features
|-

| Paper
| [[2015Han_Automatic]]
| Automatic alignment of tilt series using fiducials
|-

| Paper
| [[2017Mastronarde_Automatic]]
| Automatic alignment and reconstruction of tilt series in IMOD
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[2003Winkler_CTF]]
| Focus gradient correction in electron tomography
|-

| Paper
| [[2006Fernandez_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Zanetti_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Xiong_CTF]]
| CTF determination and correction for low dose tomographic tilt series
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2017Kunz_3DCTF]]
| 3D CTF Correction
|-

|}

=== 3D reconstruction ===

{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1992Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[1997Marabini_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2002Fernandez_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2007Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[2008Fernandez_CARP]]
| Component Averaged Row Projections (CARP)
|-

| Paper
| [[2012Herman General Superiorization]]
| Superiorization: an optimization heuristic for medical physics
|-

| Paper
| [[2012Zhang_IPET_FETR]]
| IPET and FETR, a reconstruction algorithm for single molecule tomography
|-

| Paper
| [[2013Goris_SIRT_TV_DART]]
| Combination of SIRT, Total Variation and Discrete ART to reconstruct and segment at the same time
|-

| Paper
| [[2013Briegel A_Challenge]]
| The challenge of determining handedness in electron tomography and the use of DNA origami gold nanoparticle helices as molecular standards
|-

| Paper
| [[2013Messaoudi_EnergyFiltered]]
| 3D Reconstruction of Energy-Filtered TEM
|-

| Paper
| [[2016Deng_ICON]]
| 3D Reconstruction with missing information restoration
|-

| Paper
| [[2016Guay_Compressed]]
| 3D Reconstruction using compressed sensing
|-

|}

=== Noise reduction ===
{|

| Paper
| [[2001Frangakis_NAD]]
| Noise reduction with Nonlinear Anisotropic Diffusion
|-

| Paper
| [[2003Fernandez_AND]]
| Anisotropic nonlinear diffusion for electron tomography
|-

| Paper
| [[2003Jiang_Bilateral]]
| Bilateral denoising filter in electron microscopy
|-

| Paper
| [[2005Fernandez_AND]]
| Anisotropic nonlinear denoising in electron tomography
|-

| Paper
| [[2007Heide_median]]
| Iterative median filtering in electron tomography
|-

| Paper
| [[2007Fernandez_autAND]]
| Anisotropic nonlinear diffusion with automated parameter tuning
|-

| Paper
| [[2009Fernandez_Beltrami]]
| Nonlinear filtering based on Beltrami flow
|-

| Paper
| [[2010Bilbao_MeanShift]]
| Mean Shift Filtering
|-

| Paper
| [[2014Kovacik_wedgeArtefacts]]
| Removal of wedge artefacts
|-

| Paper
| [[2014Maiorca_beadArtefacts]]
| Removal of gold bead artefacts
|-

|}

=== Segmentation ===

{|

| Paper
| [[2002Frangakis_Eigenanalysis]]
| Segmentation using eigenvector analysis.
|-

| Paper
| [[2002Volkmann_Watershed]]
| Segmentation using watershed transform.
|-

| Paper
| [[2003Bajaj_BoundarySegmentation]]
| Segmentation based on fast marching.
|-

| Paper
| [[2005Cyrklaff_Thresholding]]
| Segmentation using optimal thresholding.
|-

| Paper
| [[2007Lebbink_TemplateMatching]]
| Segmentation using template matching.
|-

| Paper
| [[2007Sandberg_OrientationFields]]
| Segmentation using orientation fields.
|-

| Paper
| [[2007Sandberg_SegmentationReview]]
| Review on segmentation in electron tomography.
|-

| Paper
| [[2008Garduno_FuzzySegmentation]]
| Segmentation using fuzzy set theory principles.
|-

| Paper
| [[2009Lebbink_TemplateMatching2]]
| Segmentation using template matching.
|-

| Paper
| [[2012RubbiyaAli_EdgeDetection]]
| Parameter-Free Segmentation of Macromolecular Structures.
|-

| Conference
| [[2015Xu_TemplateMatching]]
| Detection of macromolecular complexes with a reduced representation of the templates.
|-

|}

=== Resolution ===
{|

| Paper
| [[2005Cardone_Resolution]]
| Resolution criterion for electron tomography
|-

| Chapter
| [[2007Penczek_Resolution]]
| Review of resolution criteria for electron tomography
|-

| Paper
| [[2015Diebolder_ConicalFSC]]
| Conical Fourier Shell Correlation
|-

|}

=== Subtomogram analysis ===

{|

| Paper
| [[2000Bohm_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2002Frangakis_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2006Nickell_Review]]
| Review of macromolecule finding by template matching (Visual Proteomics)
|-

| Paper
| [[2007Best_Review]]
| Review of Localization of Protein Complexes by Pattern Recognition
|-

| Paper
| [[2007Forster_Review]]
| Review of structure determination by subtomogram averaging
|-

| Paper
| [[2008Forster_Classification]]
| Classification of subtomograms using constrained correlation
|-

| Paper
| [[2008Bartesaghi_Classification]]
| Classification and averaging of subtomograms
|-

| Paper
| [[2008Schmid_Averaging]]
| Alignment and averaging of subtomograms
|-

| Paper
| [[2010Amat_Averaging]]
| Alignment and averaging of subtomograms exploiting thresholding in Fourier space
|-

| Paper
| [[2013Chen_Averaging]]
| Fast alignment of subtomograms using spherical harmonics
|-

| Paper
| [[2013Kuybeda_Averaging]]
| Alignment and averaging of subtomograms using the nuclear norm of the cluster
|-

| Paper
| [[2013Shatsky_Averaging]]
| Alignment and averaging of subtomograms with constrained cross-correlation
|-

| Paper
| [[2014Chen_Autofocus]]
| Subtomogram averaging and classification with special attention to differences
|-

| Paper
| [[2014Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2014Voortman_LimitingFactors]]
| Limiting factors of subtomogram averaging
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2015Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2016Bharat_Relion]]
| Subtomogram averaging with Relion
|-

| Paper
| [[2016Song_MatrixNorm]]
| Matrix norm minimization for tomographic reconstruction and alignment
|-

| Paper
| [[2017Castano_ParticlePicking]]
| Particle picking in tomograms for subtomogram averaging
|-

|}

=== Single particle tomography ===

{|

| Paper
| [[2012Bartesaghi_Constrained]]
| 3D reconstruction by imposing geometrical constraints
|-

| Paper
| [[2015Galaz_SingleParticleTomography]]
| Set of tools for Single Particle Tomography in EMAN2
|-

| Paper
| [[2016Galaz_SingleParticleTomography]]
| Alignment algorithms and CTF correction
|-

|}

=== Books and reviews ===

{|

| Paper
| [[2000Baumeister_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Koster_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Sali_Review]]
| Review of electron tomography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2005Lucic_Review]]
| Review of electron tomography
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_TomoBook]]
| Electron Tomography
|-

| Book
| [[2007McIntosh_Book]]
| Cellular Electron Microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2012Kudryashev_Review]]
| Review of subtomogram averaging
|-

| Paper
| [[2016Beck_Review]]
| Review of molecular sociology
|-

|}

=== Software ===

{|

| Paper
| [[1996Kremer_IMOD]]
| IMOD
|-

| Paper
| [[1996Chen_Priism/IVE]]
| Priism/IVE
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2005Nickell_TOM]]
| TOM Toolbox
|-

| Paper
| [[2007Messaoudi_TomoJ]]
| TomoJ
|-

| Paper
| [[2008Heymann_BsoftTomo]]
| Bsoft
|-

| Paper
| [[2015Ding_CaltechTomography]]
| Caltech tomography database
|-

| Paper
| [[2015Noble_AppionProtomo]]
| Batch fiducial-less tilt-series alignment in Appion using Protomo
|-

| Paper
| [[2015vanAarle_Astra]]
| ASTRA Toolbox
|-

| Paper
| [[2017Wan_Simulator]]
| Electron Tomography Simulator
|-

|}

== 2D Crystals ==

=== 2D Preprocessing ===

{|

| Paper
| [[1986Henderson_Processing]]
| General 2D processing
|-

| Paper
| [[2000He_PhaseAlignment]]
| Phase consistency and Alignment
|-

| Paper
| [[2006Gil_Unbending]]
| Crystal unbending
|-

|}

=== Classification ===
{|

| Paper
| [[1988Frank_Classification]]
| MSA and classification in electron crystallography
|-

| Paper
| [[1996Fernandez_SOM]]
| Classification based on self organizing maps
|-

| Paper
| [[1998Sherman_MSA]]
| Classification based on MSA
|-

|}
=== 3D Reconstruction ===

{|

| Paper
| [[1985Wang_Solvent]]
| Solvent flattening
|-

| Paper
| [[1990Henderson_Processing]]
| General 3D processing
|-

| Paper
| [[2004Marabini_ART]]
| Algebraic Reconstruction Technique with blobs for crystals (Xmipp)
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1998Walz_Review]]
| Review of 2D crystallography
|-

| Paper
| [[1999Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Ellis_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of single particles, electron tomography and crystallography
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Gipson_2dx]]
| 2dx
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Philippsen_IPLT]]
| IPLT
|-

|}

== 3D Crystals - MicroED ==

=== Sample Preparation ===
{|
| Paper
| [[2016Shi_Preparation]]
| Sample Preparation
|}
=== Data Collection ===
{|
| Paper
| [[2014Nannenga_CR]]
| Continuous rotation

|}
=== Data Processing ===
{|

| Paper
| [[2011Wisedchaisri_PhaseExtension]]
| Fragment-based phase extension
|-

| Paper
| [[2015Hattne_Processing]]
| Data Processing
|-

| Paper
| [[2016Hattne_Correction]]
| Image correction
|}

=== Software ===
{|

| Paper
| [[2014Iadanza_Processing]]
| Data Processing of still diffraction data
|}

=== Books and Reviews ===
{|
| Paper
| [[2014Nannenga_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Liu_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Rodriguez_Review ]]
| Review of MicroED
|-

|}

== Helical particles ==

=== Filament corrections ===

{|

| Paper
| [[1986Egelman_Curved]]
| Algorithm for correcting curved filaments
|-

| Paper
| [[1988Bluemke_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2006Wang_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2016Yang_Flexible]]
| Algorithm for correcting filaments with flexible subunits
|-

|}

=== Reconstruction ===

{|

| Paper
| [[1952Cochran_Fourier]]
| Fourier Bessel transform of filamentous structures
|-

| Paper
| [[1958Klug_Fourier]]
| Fourier Bessel decomposition of the projection images
|-

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2005Wang_Iterative]]
| Iterative Fourier-Bessel algorithm
|-

| Paper
| [[2007Egelman_Iterative]]
| Iterative real-space algorithm
|-

| Paper
| [[2013Desfosses_Spring]]
| Helical processing with Spring
|-

| Paper
| [[2015Zhang_seam]]
| Workflow for the detection of the lattice seam
|-

| Paper
| [[2016Rohou_Frealix]]
| Helical processing with Frealix
|-

|}

=== Validation ===

{|

| Paper
| [[2014Egelman_ambiguity]]
| How to detect incorrect models
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Carragher_Phoelix]]
| Phoelix
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Owen_Brandeis]]
| Brandeis
|-

|}

== Icosahedral particles ==

=== Reconstruction ===

{|

| Paper
| [[1970Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1971Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1996Fuller_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1997Thuman_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

|}

=== Classification ===

{|

| Paper
| [[2005Scheres_Virus]]
| Classification of virus capsids in real space
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1999Baker_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[1999Conway_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2000Thuman_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Lee_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Navaza_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2006Grunewald_Review]]
| Review of reconstruction of icosahedral viruses
|-

|}

=== Software ===

{|

| Paper
| [[1996Baker_EMPFT]]
| EMPFT
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2013Morin_Sliz SBGrid]]
| SBGrid presentation for eLife
|-

|}

== Databases ==

{|

| Paper
| [[2003Boutselakis_EMSD]]
| EMSD database
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2011Kim_CDDB]]
| Conformational Dynamics Data Bank
|-

| Paper
| [[2011Lawson_EMDB]]
| Electron Microscopy Data Bank
|-

| Paper
| [[2013Ison_EDAM]]
| EDAM, an ontology of bioinformatics operations
|-

| Paper
| [[2016Iudin_EMPIAR]]
| EMPIAR raw data database
|-

| Paper
| [[2016Patwhardan_EMDB]]
| EMDB, PDB, ...
|-

| Paper
| [[2017Patwhardan_Trends]]
| Trends at EMDB
|-

| Paper
| [[2017Shao_PDBQuality]]
| Quality metrics in PDB
|-

| Blog
| http://www.mybiosoftware.com
| Huge list of bioinformatics programs (many of them structural bioinformatics)
|-

|}

== Relationship to other structural information sources ==

{|

| Paper
| [[2000Engel_AFM]]
| Review of Atomic Force Microscopy
|-

| Paper
| [[2001Dimmeler_AFM]]
| Constraints from Atomic Force Microscopy
|-

| Paper
| [[2003Mobus_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_Review]]
| Review on correlative microscopy
|-

| Paper
| [[2005Boudier_EFTETJ]]
| Software for Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2005Vestergaard_SAXS]]
| Example of comparison of 3DEM and Small-angle X-ray scattering
|-

| Paper
| [[2007Hamada_SAXS]]
| Constraints from Small-angle X-ray scattering
|-

| Paper
| [[2013Xu_FRET]]
| EM+FRET
|-

|}

== X-ray tomography ==

{|

| Paper
| [[2012Oton_ImageFormation]]
| Image formation model in X-ray cell microscopy
|-

|}

== Mathematical tools necessary ==

== People developing methods ==
Please, add yourself to this list (due to privacy reasons, please, do not add anyone else to the list without his/her explicit consent). Sort by first name alphabetical order.

[http://biocomp.cnb.csic.es/~coss Carlos Oscar S. Sorzano]: CSIC, Madrid, Spain 

[http://www.curie.fr/recherche/themes/detail_equipe.cfm/lang/_fr/id_equipe/241.htm Cédric Messaoudi]: Institute Curie, Paris, France 

[http://scholar.google.es/citations?user=_jNYGScAAAAJ&hl=en Javier Vargas]:[mailto:jvargas@cnb.csic.es mail]: CSIC, Madrid, Spain 

[http://scholar.google.es/citations?hl=es&user=g2ZJPIYAAAAJ Joaquín Otón]: CSIC, Madrid, Spain 

[mailto:jrbcast@gmail.com José Román Bilbao-Castro]: UAL, Almería, Spain; CSIC, Madrid, Spain 

[José Miguel de la Rosa Trevín]: Biocomputing Unit CNB-CSIC, Madrid, Spain 

[http://cryoem.janelia.org Tamir Gonen]: [mailto:gonent@janelia.hhmi.org mail]: Howard Hughes Medical Institute, Ashburn, VA, USA 

[mailto:vabrishami@cnb.csic.es Vahid Abrishami]: CSIC, Madrid, Spain 

== 3DEM sites ==
* [http://3dem.ucsd.edu/ 3DEM web site]

* [http://en.wikibooks.org/wiki/Software_Tools_For_Molecular_Microscopy Software tools for molecular microscopy]

* [http://www.emdatabank.org/ The Electron Microscopy Data Bank (EMDB)]

* [http://ccdb.ucsd.edu The Cell Centered Database (CCDB)]

* [http://conventions.cnb.csic.es The geometrical software conventions web page ]

== Editing useful links ==

* [http://www.mediawiki.org/wiki/Help:Formatting Text formatting in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Links Adding links in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Images Adding images in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Tables Making tables in Mediawiki]

2017Scapin Storage

2017-06-13T05:19:09Z

CoSS: Created page with "== Citation == Scapin, G.; Prosise, W. W.; Wismer, M. K. & Strickland, C. A novel storage system for cryoEM samples. Journal of structural biology, 2017, 199, 84-86 == Abstr..."

== Citation ==

Scapin, G.; Prosise, W. W.; Wismer, M. K. & Strickland, C. A novel storage system for cryoEM samples. Journal of structural biology, 2017, 199, 84-86

== Abstract ==

We present here a new CryoEM grid boxes storage system designed to simplify sample labeling, tracking and retrieval. The system is based on the crystal pucks widely used by the X-ray crystallographic community for storage and shipping of crystals. This system is suitable for any cryoEM laboratory, but especially for large facilities that will need accurate tracking of large numbers of samples coming from different sources.

== Keywords ==

== Links ==

https://www.ncbi.nlm.nih.gov/pubmed/28433496

== Related software ==

== Related methods ==

== Comments ==

Main Page

2017-06-13T05:18:22Z

CoSS: /* Sample preparation */

== Presentation ==

This web page is intended to be an extensive repository of three-dimensional electron microscopy (3DEM) methods. The advantages of having such a repository are

* You know which are the relevant articles in a particular topic, therefore, paper introductions, reviews, etc. are easier to write and you make sure you will cite all the related articles.
* You will be sure that your paper has more chances of being cited.
* You can add whatever information you find relevant to your method, external links, links to other papers, etc.
* You can link your method to a web page providing the corresponding software, so you know people can use your algorithms.
* You can use the Wiki search capabilities to locate relevant articles even if they are not at the topic you are looking at.
* As a community we will "reconstruct" our history.
* You can select the "watch" option above to receive notifications in case of further changes in the Main Page.

Developing image processing methods for 3DEM is not "[[well-paid]]" in terms of citations and impact factor. However, it is crucial for the advance of the field. Gathering methodological papers in a portal will help to increase the recognition of the field.

Please:

* Add your articles at the right place (you can add a single article in several topics if it is relevant to all of them). The easiest way to add an article is by editing the corresponding topic in the main page, adding your entry, then save the main page. Click on the red link that appears on your new entry, copy and paste the Wiki following code, add the information of your article

== Citation ==

== Abstract ==

== Keywords ==

== Links ==

== Related software ==

== Related methods ==

== Comments ==

* Maintain the information of each article as complete as possible.
* Sort articles by years and authors.
* Be respectful to other people's work.

== How to subscribe to this page ==

You may subscribe to this page so that you will be notified every time someone adds a new method. To do so, you have to register in the page, and edit your preferences ("my preferences"). Be sure that you have activated the option "E-mail me when a page on my watchlist is changed". Finally, click on the "Watch" tab at the top of this page.

You may subscribe to changes on this page on the mailing list 3demmethods@cnb.csic.es. To send a new method to this mail list just send a mail to 3demmethods@cnb.csic.es

To subscribe to this list, visit the web page

https://listas.csic.es/cnb/wws/subscribe/3demmethods

Alternatively, you may write a mail to sympa6@cnb.csic.es with the subject

<code>subscribe 3demmethods YourName YourFamilyName</code>

and an empty mail body.

To unsubscribe visit the page

https://listas.csic.es/cnb/wws/sigrequest/3demmethods

or write sympa6@cnb.csic.es with the subject

<code>unsubscribe 3demmethods</code>

and an empty mail body.

== Electron microscopy images ==

=== Online courses ===

CALTECH: http://cryo-em-course.caltech.edu/

MRC: ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/EM-course/

CNB-CSIC: http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/MadridJan2014EM

Workshop on Computational methods for CryoEM: https://www.youtube.com/watch?v=XdKO1iaPP8o

Workshop on Management of large CryoEM facilities: https://www.youtube.com/watch?v=as4seOPszL0

Icknield Course on Model Building and Refinement for High Resolution EM Maps: http://www.ccpem.ac.uk/training/icknield_2017/icknield_2017.php

=== Image formation ===

{|

| Paper
| [[1971Erickson_CTF]]
| CTF model
|-

| Paper
| [[1971Glaeser_Damage]]
| Radiation damage
|-

| Chapter
| [[1971Hanszen_CTF]]
| Image formation model
|-

| Paper
| [[1971Thon_Model]]
| CTF model
|-

| Paper
| [[1975Unwin_Imaging]]
| Radiation dose
|-

| Paper
| [[1977Wade_Model]]
| CTF model
|-

| Paper
| [[1978Wade_Model]]
| CTF model
|-

| Paper
| [[1979Hayward_Radiation]]
| Radiation damage
|-

| Paper
| [[1984Cohen_Validity]]
| Validity of the CTF model at high frequencies
|-

| Paper
| [[1988Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[1992Wade_Model]]
| CTF model
|-

| Paper
| [[1993Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2004Egerton_Damage]]
| Radiation damage
|-

| Paper
| [[2004Sorzano_Normalization]]
| Background noise is Gaussian
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2009Baxter_NoiseCharacterization]]
| Characterization of the different noise sources in cryo-EM
|-

| Paper
| [[2010Baker_Damage]]
| Radiation damage dependence on resolution
|-

| Paper
| [[2010Bammes_Damage]]
| Radiation damage dependence on temperature
|-

| Paper
| [[2010Gomez_Multislice]]
| Simulation of the multi slice model
|-

| Paper
| [[2010Zewail_FourDimensional]]
| Review on the use of ultrafast EM
|-

| Paper
| [[2011Bammes_CCD]]
| Performance of CCD cameras
|-

| Paper
| [[2011Glaeser_Coma]]
| Image formation model including coma
|-

| Paper
| [[2011Milazzo_DirectDetectors]]
| Evaluation of Direct Detectors
|-

| Paper
| [[2011Rullgard_ImageSimulation]]
| Accurate simulation of EM images
|-

| Paper
| [[2011Zhang LimitingFactors]]
| Limiting factor for atomic resolution in EM
|-

| Paper
| [[2012Bammes_DirectDetection]]
| Performance of Direct detectors
|-

| Paper
| [[2012Campbell_MotionCorrection]]
| Beam induced motion correction and direct detectors
|-

| Paper
| [[2012Shang_HydrationLayer]]
| Simulation of PDB volumes explicitly considering the hydration layer
|-

| Paper
| [[2013Egerton_RadiationDamage]]
| Review of TEM radiation damage and experimental ways of reducing it
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu H_Noisemodels]]
| Noise models and cryo-EM drift correction with a direct-electron camera
|-

| Paper
| [[2013Li X K2 noisemodels]]
| Influence of electron dose rate on electron counting images recorded with the K2 camera
|-

| Paper
| [[2013Vulovic_CTFApproximations]]
| When to use the different approximations performed so that a projection with linear CTF is valid
|-

| Thesis
| [[2013Vulovic_ImageFormation]]
| Ph.D. Thesis on the image formation in cryo-EM
|-

| Paper
| [[2014Danev_PhasePlate]]
| Volta potential phase plate
|-

| Paper
| [[2015Chiu_K2]]
| Characterization of K2
|-

| Paper
| [[2015Hawkes_AberrationCorrection]]
| Historical account of the development of lens corrections
|-

| Paper
| [[2015Koeck_Quadratic]]
| Limitations of the linear approximation and use of the quadratic terms
|-

| Paper
| [[2015Kuijper_FEI]]
| Description of the FEI Falcons
|-

| Paper
| [[2015Lobato_MULTEM]]
| Simulation of multislice diffraction
|-

| Paper
| [[2015McMullan_AmorphousIce]]
| Beam induced movement is caused by Brownian motion
|-

| Paper
| [[2016Koeck_ADF]]
| Simulations of Annular Dark Field TEM
|-

| Paper
| [[2017Mishyna_DNARadiation]]
| Review of radiation damage on DNA
|-

|}

=== Collection geometry ===

{|

| Chapter
| [[1980Hoppe_Wedge]]
| Missing wedge
|-

| Paper
| [[1987Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1995Penczek_Dual]]
| Dual axis tomography
|-

| Paper
| [[1997Mastronarde_Dual]]
| Dual axis tomography
|-

| Paper
| [[2003Ludtke_FocusPairs]]
| Focus pairs for single particles
|-

| Paper
| [[2005Lanzavecchia_Conical]]
| Conical tomography
|-

| Paper
| [[2005Zampighi_Conical]]
| Conical tomography
|-

| Paper
| [[2006Leschziner_OT]]
| Orthogonal Tilt
|-

| Paper
| [[2006Messaoudi_Multiple]]
| Multiple axis tomography
|-

| Paper
| [[2012Kudryashev_FocusPairs]]
| Focus pairs tomography
|-

| Paper
| [[2014Hovden_TiltFocus]]
| Combining tilt series with focus series
|-

| Paper
| [[2015Sorzano_RandomConicalTilt]]
| General formulation of Random Conical Tilt
|-

| Paper
| [[2017Hagen_DoseTomography]]
| Dose optimization for subtomogram averaging
|-

|}

=== Sample preparation ===

{|

| Paper
| [[1982Dubochet_Sample]]
| Vitreous ice
|-

| Paper
| [[1986Lepault_Sample]]
| Fast freezing
|-

| Paper
| [[1995Dubochet_Sample]]
| High-pressure freezing
|-

| Paper
| [[1995VanMarle_Sample]]
| Sample damages in resin
|-

| Paper
| [[1998Adrian_Sample]]
| Cryo negative staining
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2002Hsieh_Sample]]
| Cryofixation
|-

| Paper
| [[2004AlAmoudi_Sample]]
| CEMOVIS
|-

| Paper
| [[2008Studer_Sample]]
| Review on high pressure freezing
|-

| Paper
| [[2009Pierson_Sample]]
| Review on sample preparation for electron tomography
|-

| Paper
| [[2010Zhang_NegativeStaining]]
| Negative staining for small protein imaging
|-

| Paper
| [[2012Zhang_PositiveStaining]]
| Positive staining
|-

| Paper
| [[2014Rames_NegativeStaining]]
| Optimized negative staining
|-

| Paper
| [[2014Russo_GoldGrids]]
| Gold grids for single particles
|-

| Paper
| [[2015Cabra_Sample]]
| Review on sample preparation for single particles with videos
|-

| Paper
| [[2016Passmore_Review]]
| Tutorial chapter on sample preparation
|-

| Paper
| [[2016Razinkov_Vitrification]]
| New vitrification method
|-

| Paper
| [[2016Takizawa_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2016Thompson_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2017Arnold_BlottingFree]]
| Blotting-free preparation
|-

| Paper
| [[2017Feng_SprayingPlunging]]
| Spraying plunging
|-

| Paper
| [[2017Peitsch_Sample]]
| iMEM: Isolation of Plasma Membrane for Cryoelectron Microscopy
|-

| Paper
| [[2017Scapin_Storage]]
| Cryo storage of samples
|-

| Paper
| [[2017Schaffer_FocusedIonBeam]]
| Focused Ion Beam sample preparation for membrane proteins
|-

|}

=== Automated data collection ===

{|

| Paper
| [[1992Dierksen_Automatic]]
| Automated data collection
|-

| Paper
| [[1992Koster_Automatic]]
| Automated data collection
|-

| Paper
| [[1996Fung_Automatic]]
| Automated data collection for tomography
|-

| Paper
| [[2001Zhang_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2003Ziese_Automatic]]
| Automated autofocusing
|-

| Paper
| [[2004Potter_Automatic]]
| Automated sample loading
|-

| Paper
| [[2004Zheng_Automatic]]
| Automated data collection
|-

| Paper
| [[2005Lei_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2005Suloway_Automatic]]
| Automated data collection: Leginon
|-

| Paper
| [[2007Yoshioka_RCT]]
| Automated Random Conical Tilt
|-

| Paper
| [[2011Korinek_TOM2]]
| Automated acquisition with TOM2
|-

| Paper
| [[2015Li_UCSFImage]]
| Automated acquisition with UCSFImage
|-

| Paper
| [[2016Gil_Fuzzy]]
| Real time decisions during acquisition with neuro-fuzzy method
|-

| Paper
| [[2016Liu_TiltControl]]
| Accurate control of the tilt angle for electron tomography
|-

| Paper
| [[2016Vargas_FoilHole]]
| Determination of image quality at low magnification
|-

| Paper
| [[2017Biyani_Focus]]
| Automatic processing of micrographs
|-

|}

== Single particles ==

=== Automatic particle picking ===

{|

| Paper
| [[1982VanHeel_Detection]]
| Detection of particles in micrographs
|-

| Paper
| [[2001Nicholson_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2001Zhu_Filaments]]
| Automatic identification of filaments in micrographs
|-

| Paper
| [[2004Sigworth_Detection]]
| Classical detection theory and the cryo-EM particle selection problem
|-

| Paper
| [[2004Volkmann_ParticlePicking]]
| An approach to automated particle picking from electron micrographs based on reduced representation templates
|-

| Paper
| [[2004Wong_ParticlePicking]]
| Model-based particle picking for cryo-electron microscopy
|-

| Paper
| [[2004Zhu_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2007Chen_Signature]]
| Automatic particle picking program: Signature
|-

| Paper
| [[2007Woolford_SwarmPS]]
| Automatic particle picking with several criteria, implemented in EMAN Boxer
|-

| Paper
| [[2009Sorzano_MachineLearning]]
| Automatic particle picking based on machine learning of rotational invariants
|-

| Paper
| [[2011Arbelaez_Comparison]]
| Evaluation of the performance of software for automated particle-boxing
|-

| Paper
| [[2013Abrishami_MachineLearning]]
| A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs
|-

| Paper
| [[2013Hauer_2013]]
| Automatic tilt pair detection in Random Conical Tilt
|-

| Paper
| [[2013Shatsky_ParticlePicking]]
| Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Langlois_ParticlePicking]]
| Automatic particle picking
|-

| Paper
| [[2016Vilas_AutomaticTilt]]
| Automatic identification of image pairs in untilted-tilted micrograph pairs
|-

|}

=== 2D Preprocessing ===

{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast enhancement through DPR
|-

| Paper
| [[2004Sorzano_Normalization]]
| Normalization procedures and their statistical properties.
|-

| Paper
| [[2006Sorzano_Denoising]]
| Strong denoising in wavelet space
|-

| Conference
| [[2009Sorzano_Downsampling]]
| Differences between the different downsampling schemes
|-

| Paper
| [[2012Brilot_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Campbell_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Zhao_Denoising]]
| Denoising using an invariant Fourier-Bessel eigenspace
|-

| Paper
| [[2013Norousi_Screening]]
| Screening particles to identify outliers
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu_Movies]]
| Drift correction for movies considering dark field
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Scheres_Movies]]
| Beam induced motion correction
|-

| Paper
| [[2015Abrishami_Movies]]
| Alignment of direct detection device micrographs
|-

| Paper
| [[2015Grant_Anisotropic]]
| Automatic estimation and correction of anisotropic magnification
|-

| Paper
| [[2015Grant_OptimalExposure]]
| Filter movies according to the radiation damage
|-

| Paper
| [[2015Rubinstein_Alignment]]
| Frame alignment at the level of particle
|-

| Paper
| [[2015Spear_DoseCompensation]]
| Effect of dose compensation on resolution
|-

| Paper
| [[2015Zhao_AnisotropicMagnification]]
| Correction of anisotropic magnification
|-

| Conference
| [[2016Bajic_Denoising]]
| Denoising and deconvolution of micrographs
|-

| Paper
| [[2016Jensen_RemovalVesicles]]
| Removal of vesicles in membrane proteins
|-

| Paper
| [[2016Bhamre_Denoising]]
| Denoising by 2D covariance estimation
|-

| Paper
| [[2017McLeod_Zorro]]
| Movie alignment by Zorro
|-

| Paper
| [[2017Zheng_MotionCorr2]]
| Movie alignment by MotionCorr2
|-

|}

=== 2D Alignment ===

{|

| Paper
| [[1981Frank_Averaging]]
| 2D averaging and phase residual
|-

| Paper
| [[1982Saxton_Averaging]]
| 2D averaging using correlation
|-

| Paper
| [[1998Sigworth_ML2D]]
| Maximum likelihood alignment in 2D
|-

| Paper
| [[2003Cong_FRM2D]]
| Fast Rotational Matching in 2D
|-

| Paper
| [[2005Cong_FRM2D]]
| Fast Rotational Matching in 2D introduced in a 3D Alignment algorithm
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

|}

=== 2D Classification and clustering ===

{|

| Paper
| [[1981VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[1984VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2011Singer_DiffusionMaps]]
| Classification in 2D based on graph analysis of the projections
|-

| Paper
| [[2012Yang_ISAC]]
| Iterative Stable Alignment and clustering
|-

| Paper
| [[2014Sorzano_Outlier]]
| Outlier detection in 2D classifications.
|-

| Paper
| [[2014Zhao_Aspire]]
| Fast classification based on rotational invariants and vector diffusion maps
|-

| Paper
| [[2015Huang_Robust]]
| Robust w-estimators of 2D classes
|-

| Paper
| [[2016Reboul_Stochastic]]
| Stochastic Hill Climbing for calculating 2D classes
|-

| Conference
| [[2017Bhamre_Mahalanobis]]
| 2D classification using Mahalanobis distance
|-

|}

=== 3D Alignment ===

{|

| Paper
| [[1980Kam_AutoCorrelation]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[1986Goncharov_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1987VanHeel_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1988Provencher_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Vogel_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1990Gelfand_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Goncharov_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Harauz_Quaternions]]
| Use of quaternions to represent rotations
|-

| Paper
| [[1994Penczek_Real]]
| Angular assignment using projection matching in real space
|-

| Paper
| [[1994Radermacher_Radon]]
| Angular assignment in Radon space
|-

| Paper
| [[1996Penczek_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[2003Rosenthal_DPR]]
| Angular assignment using DPR
|-

| Paper
| [[2004Sorzano_Wavelet]]
| Angular assignment in the wavelet space.
|-

| Paper
| [[2005Jonic_Splines]]
| Angular assignment in Fourier space using spline interpolation.
|-

| Paper
| [[2005Yang_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[2006Ogura_SimulatedAnnealing]]
| Angular asignment by simulated annealing
|-

| Paper
| [[2007Grigorieff_Continuous]]
| Continuous angular assignment in Fourier space
|-

| Paper
| [[2010Jaitly_Bayesian]]
| Angular assignment by a Bayesian method and annealing
|-

| Paper
| [[2010Sanz_Random]]
| Random model method
|-

| Paper
| [[2010Singer_Voting]]
| Detecting consistent common lines by voting (reference free)
|-

| Paper
| [[2011Singer_SDP]]
| Angular assignment by semidefinite programming and eigenvectors (reference free)
|-

| Paper
| [[2012Giannakis_Scattering]]
| Construction of an initial volume, reference free, by graph analysis of the projections
|-

| Paper
| [[2012Shkolnisky_Sync]]
| Angular assignment by synchronization of rotations (reference free)
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Wang_LUD]]
| Angular assignment by least unsquared deviations (reference free)
|-

| Paper
| [[2014Vargas_RANSAC]]
| Initial model using RANSAC (reference free)
|-

| Paper
| [[2015Joubert_Pseudoatoms]]
| Initial model based on pseudo-atoms
|-

| Paper
| [[2015Singer_Kam]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[2015Sorzano_Significant]]
| Statistical approach to the initial volume estimation (reconstruct significant)
|-

| Conference
| [[2016Michels_Heterogeneous]]
| Initial volume in the presence of heterogeneity
|-

| Paper
| [[2016Cossio_BayesianGPU]]
| GPU implementation of the Bayesian 3D reconstruction approach
|-

|}

=== 3D Reconstruction ===
{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1986Harauz_FBP]]
| Exact filters for Filtered Back Projection
|-

| Chapter
| [[1992Radermacher_WBP]]
| Exact filters for Weighted Back Projection
|-

| Paper
| [[1997Zhu_RecCTF]]
| 3D Reconstruction (SIRT like) and simultaneous CTF correction
|-

| Paper
| [[1998Boisset_Uneven]]
| Artifacts in SIRT and WBP under uneven angular distributions
|-

| Paper
| [[1998Marabini_ART]]
| Algebraic Reconstruction Technique with blobs (Xmipp)
|-

| Paper
| [[2001Sorzano_Uneven]]
| Free parameter selection under uneven angular distributions
|-

| Paper
| [[2005Sorzano_Parameters]]
| Free parameter selection for optimizing multiple tasks
|-

| Paper
| [[2008Sorzano_Constraints]]
| Mass, surface, positivity and symmetry constraints for real-space algorithms
|-

| Paper
| [[2009Bilbao_ParallelART]]
| Efficient parallelization of ART
|-

| Paper
| [[2011Li_GradientFlow]]
| Regularized 3D Reconstruction by Gradient Flow
|-

| Paper
| [[2011Vonesch_Wavelets]]
| Fast wavelet-based 3D reconstruction
|-

| Paper
| [[2012Gopinath_ShapeRegularization]]
| Regularized 3D Reconstruction by Shape information
|-

| Paper
| [[2012Kucukelbir_adaptiveBasis]]
| 3D reconstruction in an adaptive basis promoting sparsity
|-

| Paper
| [[2012Sindelar_NoiseReduction]]
| Optimal noise reduction in 3D reconstructions
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Lyumkis_Optimod]]
| Construction of initial volumes with Optimod
|-

| Paper
| [[2013Wang FIRM]]
| Fast 3D reconstruction in Fourier domain
|-

| Paper
| [[2014Kunz_SART_OS]]
| Simultaneous ART with OS
|-

| Paper
| [[2015Abrishami_Fourier]]
| 3D Reconstruction in Fourier space
|-

| Paper
| [[2015Dvornek_SubspaceEM]]
| Fast Maximum a posteriori
|-

| Paper
| [[2015Moriya_Bayesian]]
| Bayesian approach to suppress limited angular artifacts
|-

| Paper
| [[2015Xu_GeometricFlow]]
| Multi-scale geometric flow
|-

| Arxiv
| [[2016Ye_Cohomology]]
| Cohomology properties of 3D reconstruction
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

|}

=== 3D Heterogeneity ===

{|

| Paper
| [[2004White_Size]]
| Heterogeneity classification of differently sized images
|-

| Paper
| [[2006Penczek_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Scheres_ML3D]]
| Maximum Likelihood alignment and classification in 3D
|-

| Paper
| [[2009Spahn_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2010Elmlund_AbInitio]]
| Solving the initial volume problem with multiple conformations
|-

| Paper
| [[2010Shatsky_MultiVariate]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2012Scheres_Bayesian]]
| A Bayesian view on cryo-EM structure determination
|-

| Paper
| [[2012Zheng_Covariance]]
| Estimation of the volume covariance
|-

| Paper
| [[2013Wang_MLVariance]]
| Maximum Likelihood estimate of the map variance
|-

| Paper
| [[2013Lyumkis D_FREALIGN]]
| Likelihood-based classification of cryo-EM images using FREALIGN.
|-

| Paper
| [[2014Jin_NMA]]
| Continuous heterogeneity through Normal Mode Analysis
|-

| Paper
| [[2014Dashti_Brownian]]
| Continuous heterogeneity through Brownian trajectories
|-

| Paper
| [[2014Chen_Migration]]
| Particle migration analysis in 3D classification
|-

| Paper
| [[2015Anden_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Bai_Focused]]
| Focused classification
|-

| Paper
| [[2015Katsevich_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Klaholz_MRA]]
| Multivariate Statistical Analysis of Jackknife and Bootstrapping on random subsets
|-

| Paper
| [[2015Liao_Covariance]]
| Estimation of the 3D covariance from 2D projections
|-

| Paper
| [[2015Tagare_Direct]]
| Direct reconstruction of PCA components
|-

| Paper
| [[2016Gong_Mechanical]]
| Mechanical model for macromolecules
|-

| Paper
| [[2016Rawson_Movement]]
| Movement and flexibility
|-

| Paper
| [[2016Sorzano_StructMap]]
| Sorting a discrete set of conformational states
|-

| Paper
| [[2016Sorzano_Strain]]
| Calculate local stretches, strains and rotations from two conformational states
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

|}

=== Validation ===

{|

| Paper
| [[2008Stagg_TestBed]]
| Effect of voltage, dosis, number of particles and Euler jumps on resolution
|-

| Paper
| [[2011Henderson]]
| Tilt Validation
|-

| Paper
| [[2011Read]]
| Validation of PDBs
|-

| Paper
| [[2012Henderson]]
| EM Map Validation
|-

| Paper
| [[2013Cossio_Bayesian]]
| EM Map Validation in a probabilistic setting
|-

| Paper
| [[2013Chen_NoiseSubstitution]]
| Noise substitution at high resolution for measuring overfitting
|-

| Paper
| [[2014Russo_StatisticalSignificance]]
| EM Map Validation through the statistical significance of the tilt-pair angular assignment
|-

| Paper
| [[2014Stagg_Reslog]]
| EM Map Validation through the resolution evolution with the number of particles
|-

| Paper
| [[2014Wasilewski_Tilt]]
| Web implementation of the tilt pair validation
|-

| Paper
| [[2015Heymann_Alignability]]
| EM Map Validation through the resolution of reconstructions from particles and noise
|-

| Paper
| [[2015Oliveira_FreqLimited]]
| Comparison of gold standard and frequency limited optimization
|-

| Paper
| [[2015Wriggers_Secondary]]
| Validation by secondary structure
|-

| Paper
| [[2016Kim_SAXS]]
| Comparison of SAXS data and EM projections
|-

| Paper
| [[2016Rosenthal_Review]]
| Review of validation methods
|-

| Paper
| [[2016Vargas_Alignability]]
| Validation by studying the tendency of an angular assignment to cluster in the projection space
|-

| Paper
| [[2017Monroe_PDBRefinement]]
| Validation by comparison to a refined PDB
|-

|}

=== Resolution ===

{|

| Paper
| [[1986Harauz_FBP]]
| Fourier Shell Correlation
|-

| Paper
| [[1987Unser_SSNR]]
| 2D Spectral Signal to Noise Ratio
|-

| Paper
| [[2002Penczek_SSNR]]
| 3D Spectral Signal to Noise Ratio for Fourier based algorithms
|-

| Paper
| [[2003Rosenthal_DPR]]
| Review of the FSC and establishment of a new threshold
|-

| Paper
| [[2005Unser_SSNR]]
| 3D Spectral Signal to Noise Ratio for any kind of algorithms
|-

| Paper
| [[2005VanHeel_FSC]]
| Establishment of a new threshold for FSC
|-

| Paper
| [[2007Sousa_AbInitio]]
| Resolution measurement on neighbour Fourier voxels
|-

| Paper
| [[2014Kucukelbir_Local]]
| Quantifying the local resolution of cryo-EM density maps
|-

| Paper
| [[2016Pintilie_Probabilistic]]
| Probabilistic models and resolution
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Statistical properties of resolution measures defined in Fourier space
|-

|}

=== Sharpening of high resolution information ===
{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast restoration and map sharpening
|-

| Paper
| [[2008Fernandez_Bfactor]]
| Bfactor determination and restoration
|-

| Paper
| [[2013Fiddy_SaxtonAlgorithm]]
| Phase retrieval or extension
|-

| Paper
| [[2014Kishchenko_SphericalDeconvolution]]
| Spherical deconvolution
|-

| Paper
| [[2015Spiegel_VISDEM]]
| Visualization improvement by the use of pseudoatomic profiles
|-

| Paper
| [[2016Jonic_Pseudoatoms]]
| Approximation with pseudoatoms
|-

| Paper
| [[2016Jonic_Denoising]]
| Denoising and high-frequency boosting by pseudoatom approximation
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[1982Schiske_Correction]]
| CTF correction for tilted objects
|-

| Paper
| [[1988Toyoshima_Model]]
| CTF estimation
|-

| Paper
| [[1995Frank_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1996Skoglund_MaxEnt]]
| CTF correction with Maximum Entropy
|-

| Paper
| [[1996Zhou_Model]]
| CTF model and user interface for manual fitting
|-

| Paper
| [[1997Fernandez_AR]]
| PSD estimation using periodogram averaging and AR models
|-

| Paper
| [[1997Penczek_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1997Stark_Deconvolution]]
| CTF correction using deconvolution
|-

| Paper
| [[1997Zhu_RecCTF]]
| CTF correction and reconstruction
|-

| Paper
| [[2000DeRosier_EwaldCorrection]]
| CTF correction considering the Ewald sphere
|-

| Paper
| [[2000Jensen_TiltedCorrection]]
| CTF correction considering tilt in backprojection
|-

| Paper
| [[2001Saad_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Huang_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Mindell_CTFTILT]]
| CTF estimation for tilted micrographs
|-

| Paper
| [[2003Sander_MSA]]
| CTF estimation through MSA classification of PSDs
|-

| Paper
| [[2003Velazquez_ARMA]]
| PSD and CTF estimation using ARMA models
|-

| Paper
| [[2004Sorzano_IDR]]
| CTF restoration and reconstruction with Iterative Data Refinement
|-

| Conference
| [[2004Wan_CTF]]
| Spatially variant CTF
|-

| Paper
| [[2004Zubelli_Chahine]]
| CTF restoration and reconstruction with Chahine's multiplicative method
|-

| Conference
| [[2005Dubowy_SpaceVariant]]
| CTF correction when this is space variant
|-

| Paper
| [[2005Mallick_ACE]]
| CTF estimation
|-

| Paper
| [[2006Wolf_Ewald]]
| CTF correction considering Ewald sphere
|-

| Paper
| [[2007Jonic_EnhancedPSD]]
| PSD enhancement for better identification of Thon rings; Vitreous ice diffracts in Thon rings
|-

| Paper
| [[2007Philippsen_Model]]
| CTF Model for tilted specimens
|-

| Paper
| [[2007Sorzano_CTF]]
| CTF estimation using enhanced PSDs
|-

| Paper
| [[2009Sorzano_Sensitivity]]
| Error sensitivity of the CTF models, non-uniqueness of the CTF parameters
|-

| Paper
| [[2010Jiang2010_CTFCorrection]]
| Amplitude correction method
|-

| Paper
| [[2010Kasantsev_CTFCorrection]]
| Mathematical foundations of Kornberg and Jensen method
|-

| Paper
| [[2010Leong_CTFCorrection]]
| Correction for spatially variant CTF
|-

| Paper
| [[2011Glaeser_Coma]]
| The effect of coma at high-resolution
|-

| Paper
| [[2011Mariani_Tilted]]
| CTF simulation and correction of tilted specimens
|-

| Paper
| [[2011Sindelar_Wiener]]
| CTF correction using a modified version of Wiener filter
|-

| Paper
| [[2011Voortman_Tilted]]
| CTF correction for tilted specimen
|-

| Paper
| [[2012Voortman_VaryingCTF]]
| Correcting a spatially varying CTF
|-

| Paper
| [[2013Vargas_FastDef]]
| Fast defocus
|-

| Paper
| [[2015Rohou_CTFFind4]]
| CTF Find 4
|-

| Paper
| [[2015Sheth_CTFquality]]
| Visualization and quality assessment of CTF
|-

| Paper
| [[2016Zhang_GCTF]]
| gCTF
|-

|}

=== Segmentation ===

{|

| Paper
| [[2006Baker_segmentation]]
| Segmentation of molecular subunits
|-

|}

=== Fitting and docking ===

{|

| Paper
| [[1999Volkmann_Fitting]]
| Fitting in real space
|-

| Paper
| [[2001Baker_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2001Jones_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2003Kovacs_FRM3D]]
| Fast Rotational Alignment of two EM maps
|-

| Paper
| [[2004Tama_NMA1]]
| Flexible fitting with Normal Modes (I)
|-

| Paper
| [[2004Tama_NMA2]]
| Flexible fitting with Normal Modes (II)
|-

| Paper
| [[2005Velazquez_Superfamilies]]
| Recognition of the superfamily folding in medium-high resolution volumes
|-

| Paper
| [[2007DeVries_Haddock]]
| Docking with Haddock 2.0
|-

| Paper
| [[2007Kleywegt_QualityControl]]
| Quality control and validation of fitting
|-

| Paper
| [[2012Biswas_Secondary]]
| Secondary structure determination in EM volumes
|-

| Paper
| [[2012Velazquez_Constraints]]
| Multicomponent fitting by using constraints from other information sources
|-

| Paper
| [[2013Chapman MS_Atomicmodeling]]
| Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters
|-

| Paper
| [[2013Esquivel_Modelling]]
| Review on modelling (secondary structure, fitting, ...)
|-

| Paper
| [[2013Lopez_Imodfit]]
| Fitting based on vibrational analysis
|-

| Paper
| [[2013Nogales_3DEMLoupe]]
| Normal Mode Analysis of reconstructed volumes
|-

| Paper
| [[2014AlNasr_Secondary]]
| Identification of secondary structure elements in EM volumes
|-

| Paper
| [[2014Politis_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Rey_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Villa_Review]]
| Review of atomic fitting into EM volumes
|-

| Paper
| [[2015Barad_EMRinger]]
| Validation of hybrid models
|-

| Paper
| [[2015Bettadapura_PF2Fit]]
| Fast rigid fitting of PDBs into EM maps
|-

| Paper
| [[2015Carrillo_CapsidMaps]]
| Analysis of virus capsids using Google Maps
|-

| Paper
| [[2015Schroeder_Hybrid]]
| Review on model building
|-

| Paper
| [[2015Tamo_Dynamics]]
| Dynamics in integrative modeling
|-

| Paper
| [[2015Sorzano_AtomsToVoxels]]
| Accurate conversion of an atomic model into a voxel density volume
|-

| Paper
| [[2016Joseph_Evolution]]
| Evolutionary constraints for the fitting of atomic models into density maps
|-

| Paper
| [[2016Segura_3Diana]]
| Validation of hybrid models
|-

| Paper
| [[2016Singharoy_MDFF]]
| Construction of hybrid models driven by EM density and molecular dynamics
|-

| Paper
| [[2016Wang_Rosetta]]
| Construction of hybrid models driven by EM density using Rosetta
|-

| Paper
| [[2017Hryc_WeightedAtoms]]
| Construction of hybrid models by locally weighting the different atoms
|-

| Paper
| [[2017Matsumoto_Distribution]]
| Estimating the distribution of conformations of atomic models
|-

| Paper
| [[2017Miyashita_EnsembleFitting]]
| Ensemble fitting using Molecular Dynamics
|-

|}

=== Books and reviews ===

{|

| Book
| [[1980Herman_Tomography]]
| General book on tomography
|-

| Book
| [[1988Kak_Tomography]]
| General book on tomography
|-

| Paper
| [[2000Tao_Review]]
| Review of single particles
|-

| Paper
| [[2000VanHeel_Review]]
| Review of single particles
|-

| Paper
| [[2002Frank_Review]]
| Review of single particles
|-

| Paper
| [[2002Schmid_Review]]
| Review of single particles
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2004Subramaniam_Review]]
| Review of single particles
|-

| Paper
| [[2005Steven_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_book]]
| Book covering all aspects of electron microscopy of single particles
|-

| Paper
| [[2006Sorzano_Review]]
| Review of optimization problems in electron microscopy
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems in Electron Tomography
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2008Mueller_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2008Taylor_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2010DeRosier_Review]]
| Personal account of how 3DEM developed in the early days
|-

| Chapter
| [[2012Sorzano_Review]]
| Review of single particle analysis using Xmipp
|-

| Chapter
| [[2012Devaux_Protocol]]
| Protocols for performing single particle analysis
|-

| Paper
| [[2014Bai_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Carazo_Review]]
| Review of the reconstruction process
|-

| Paper
| [[2015Cheng_Review]]
| A primer to Single Particle Cryo-EM
|-

| Paper
| [[2015Cheng_Reviewb]]
| Single Particle Cryo-EM at crystallographic resolution
|-

| Paper
| [[2015Elmlund_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Henderson_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Nogales_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Schroeder_Review]]
| Review of advances in the electron microscope
|-

| Paper
| [[2015Wu_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Carroni_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Egelman_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Eisenstein_CryoEM]]
| News feature on the Method of the Year
|-

| Paper
| [[2016FernandezLeiro_Review]]
| Review of EM
|-

| Paper
| [[2016Glaeser_HowGood]]
| How good can cryo-EM become?
|-

| Paper
| [[2016Jonic_PseudoAtoms]]
| Review of the applications of the use of pseudoatoms in EM
|-

| Chapter
| [[2016Mio_Review]]
| Overview of the process to obtain EM reconstructions
|-

| Paper
| [[2016Jonic_Review]]
| A review of computational ways to handle heterogeneity
|-

| Paper
| [[2016Nogales_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Subramaniam_Review]]
| Why cryo-EM is now suitable for crystallographic journals
|-

| Paper
| [[2016Vinothkumar_Review]]
| Historical review and current limitations
|-

| Paper
| [[2017Frank_Review]]
| Historical review of EM
|-

| Paper
| [[2017Jonic_Review]]
| Review of computational methods to analyze conformational variability
|-

| Paper
| [[2017Rawson_Limitations]]
| Limitations of EM for drug design
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Review of statistical properties of resolution measures defined in Fourier space
|-
|}

=== Software ===

{|

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[1999Lutdke_Eman]]
| Eman
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Baldwin_AngularTransformations]]
| The Transform Class in SPARX and EMAN2
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Grigorieff_Frealign]]
| Frealign
|-

| Paper
| [[2008Scheres_XmippProtocols]]
| Xmipp Protocols
|-

| Paper
| [[2008Shaikh_SpiderProtocols]]
| Spider Protocols
|-

| Paper
| [[2012Wriggers_SitusConventions]]
| Conventions and workflows in Situs
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2015Cianfrocco_Cloud]]
| Software execution in the cloud
|-

| Paper
| [[2015Cheng_MRC2014]]
| Extensions to MRC file format
|-

| Paper
| [[2013DeLaRosa_Scipion]]
| Scipion
|-

| Paper
| [[2016Scheres_Relion]]
| Tutorial on the use of Relion
|-

| Paper
| [[2016Grigorieff_Frealign]]
| Tutorial on the use of Frealign
|-

|}

== Electron tomography ==

=== Image preprocessing ===

{|

| Paper
| [[2015Yan_thickness]]
| Determination of thickness, tilt and electron mean free path
|-

|}

=== Image alignment ===

{|

| Paper
| [[1982Guckenberger_commonOrigin]]
| Determination of a common origin in the micrographs of titl series in three-dimensional electron microscopy
|-

| Paper
| [[1992Lawrence_leastSquares]]
| Least squares solution of the alignment problem
|-

| Paper
| [[1995Penczek_dual]]
| Dual tilt alignment
|-

| Paper
| [[1996Owen_alignmentQuality]]
| Automatic alignment without fiducial markers and evaluation of alignment quality
|-

| Paper
| [[1998Grimm_normalization]]
| Discussion of several gray level normalization methods for electron tomography
|-

| Paper
| [[2001Brandt_Automatic1]]
| Automatic alignment without fiducial markers
|-

| Paper
| [[2001Brandt_Automatic2]]
| Automatic alignment with fiducial markers
|-

| Paper
| [[2006Winkler_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2006Castano_alignment]]
| Alignment with non-perpendicularity
|-

| Paper
| [[2007Castano_alignment]]
| Fiducial-less alignment of cryo-sections
|-

| Paper
| [[2009Sorzano_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2010Cantele_dualAlignment]]
| Alignment of dual series
|-

| Paper
| [[2014Tomonaga_Automatic]]
| Automatic alignment of tilt series using the projection themselves
|-

| Paper
| [[2014Han_Automatic]]
| Automatic alignment of tilt series using SIFT features
|-

| Paper
| [[2015Han_Automatic]]
| Automatic alignment of tilt series using fiducials
|-

| Paper
| [[2017Mastronarde_Automatic]]
| Automatic alignment and reconstruction of tilt series in IMOD
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[2003Winkler_CTF]]
| Focus gradient correction in electron tomography
|-

| Paper
| [[2006Fernandez_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Zanetti_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Xiong_CTF]]
| CTF determination and correction for low dose tomographic tilt series
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2017Kunz_3DCTF]]
| 3D CTF Correction
|-

|}

=== 3D reconstruction ===

{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1992Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[1997Marabini_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2002Fernandez_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2007Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[2008Fernandez_CARP]]
| Component Averaged Row Projections (CARP)
|-

| Paper
| [[2012Herman General Superiorization]]
| Superiorization: an optimization heuristic for medical physics
|-

| Paper
| [[2012Zhang_IPET_FETR]]
| IPET and FETR, a reconstruction algorithm for single molecule tomography
|-

| Paper
| [[2013Goris_SIRT_TV_DART]]
| Combination of SIRT, Total Variation and Discrete ART to reconstruct and segment at the same time
|-

| Paper
| [[2013Briegel A_Challenge]]
| The challenge of determining handedness in electron tomography and the use of DNA origami gold nanoparticle helices as molecular standards
|-

| Paper
| [[2013Messaoudi_EnergyFiltered]]
| 3D Reconstruction of Energy-Filtered TEM
|-

| Paper
| [[2016Deng_ICON]]
| 3D Reconstruction with missing information restoration
|-

| Paper
| [[2016Guay_Compressed]]
| 3D Reconstruction using compressed sensing
|-

|}

=== Noise reduction ===
{|

| Paper
| [[2001Frangakis_NAD]]
| Noise reduction with Nonlinear Anisotropic Diffusion
|-

| Paper
| [[2003Fernandez_AND]]
| Anisotropic nonlinear diffusion for electron tomography
|-

| Paper
| [[2003Jiang_Bilateral]]
| Bilateral denoising filter in electron microscopy
|-

| Paper
| [[2005Fernandez_AND]]
| Anisotropic nonlinear denoising in electron tomography
|-

| Paper
| [[2007Heide_median]]
| Iterative median filtering in electron tomography
|-

| Paper
| [[2007Fernandez_autAND]]
| Anisotropic nonlinear diffusion with automated parameter tuning
|-

| Paper
| [[2009Fernandez_Beltrami]]
| Nonlinear filtering based on Beltrami flow
|-

| Paper
| [[2010Bilbao_MeanShift]]
| Mean Shift Filtering
|-

| Paper
| [[2014Kovacik_wedgeArtefacts]]
| Removal of wedge artefacts
|-

| Paper
| [[2014Maiorca_beadArtefacts]]
| Removal of gold bead artefacts
|-

|}

=== Segmentation ===

{|

| Paper
| [[2002Frangakis_Eigenanalysis]]
| Segmentation using eigenvector analysis.
|-

| Paper
| [[2002Volkmann_Watershed]]
| Segmentation using watershed transform.
|-

| Paper
| [[2003Bajaj_BoundarySegmentation]]
| Segmentation based on fast marching.
|-

| Paper
| [[2005Cyrklaff_Thresholding]]
| Segmentation using optimal thresholding.
|-

| Paper
| [[2007Lebbink_TemplateMatching]]
| Segmentation using template matching.
|-

| Paper
| [[2007Sandberg_OrientationFields]]
| Segmentation using orientation fields.
|-

| Paper
| [[2007Sandberg_SegmentationReview]]
| Review on segmentation in electron tomography.
|-

| Paper
| [[2008Garduno_FuzzySegmentation]]
| Segmentation using fuzzy set theory principles.
|-

| Paper
| [[2009Lebbink_TemplateMatching2]]
| Segmentation using template matching.
|-

| Paper
| [[2012RubbiyaAli_EdgeDetection]]
| Parameter-Free Segmentation of Macromolecular Structures.
|-

| Conference
| [[2015Xu_TemplateMatching]]
| Detection of macromolecular complexes with a reduced representation of the templates.
|-

|}

=== Resolution ===
{|

| Paper
| [[2005Cardone_Resolution]]
| Resolution criterion for electron tomography
|-

| Chapter
| [[2007Penczek_Resolution]]
| Review of resolution criteria for electron tomography
|-

| Paper
| [[2015Diebolder_ConicalFSC]]
| Conical Fourier Shell Correlation
|-

|}

=== Subtomogram analysis ===

{|

| Paper
| [[2000Bohm_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2002Frangakis_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2006Nickell_Review]]
| Review of macromolecule finding by template matching (Visual Proteomics)
|-

| Paper
| [[2007Best_Review]]
| Review of Localization of Protein Complexes by Pattern Recognition
|-

| Paper
| [[2007Forster_Review]]
| Review of structure determination by subtomogram averaging
|-

| Paper
| [[2008Forster_Classification]]
| Classification of subtomograms using constrained correlation
|-

| Paper
| [[2008Bartesaghi_Classification]]
| Classification and averaging of subtomograms
|-

| Paper
| [[2008Schmid_Averaging]]
| Alignment and averaging of subtomograms
|-

| Paper
| [[2010Amat_Averaging]]
| Alignment and averaging of subtomograms exploiting thresholding in Fourier space
|-

| Paper
| [[2013Chen_Averaging]]
| Fast alignment of subtomograms using spherical harmonics
|-

| Paper
| [[2013Kuybeda_Averaging]]
| Alignment and averaging of subtomograms using the nuclear norm of the cluster
|-

| Paper
| [[2013Shatsky_Averaging]]
| Alignment and averaging of subtomograms with constrained cross-correlation
|-

| Paper
| [[2014Chen_Autofocus]]
| Subtomogram averaging and classification with special attention to differences
|-

| Paper
| [[2014Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2014Voortman_LimitingFactors]]
| Limiting factors of subtomogram averaging
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2015Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2016Bharat_Relion]]
| Subtomogram averaging with Relion
|-

| Paper
| [[2016Song_MatrixNorm]]
| Matrix norm minimization for tomographic reconstruction and alignment
|-

| Paper
| [[2017Castano_ParticlePicking]]
| Particle picking in tomograms for subtomogram averaging
|-

|}

=== Single particle tomography ===

{|

| Paper
| [[2012Bartesaghi_Constrained]]
| 3D reconstruction by imposing geometrical constraints
|-

| Paper
| [[2015Galaz_SingleParticleTomography]]
| Set of tools for Single Particle Tomography in EMAN2
|-

| Paper
| [[2016Galaz_SingleParticleTomography]]
| Alignment algorithms and CTF correction
|-

|}

=== Books and reviews ===

{|

| Paper
| [[2000Baumeister_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Koster_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Sali_Review]]
| Review of electron tomography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2005Lucic_Review]]
| Review of electron tomography
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_TomoBook]]
| Electron Tomography
|-

| Book
| [[2007McIntosh_Book]]
| Cellular Electron Microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2012Kudryashev_Review]]
| Review of subtomogram averaging
|-

| Paper
| [[2016Beck_Review]]
| Review of molecular sociology
|-

|}

=== Software ===

{|

| Paper
| [[1996Kremer_IMOD]]
| IMOD
|-

| Paper
| [[1996Chen_Priism/IVE]]
| Priism/IVE
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2005Nickell_TOM]]
| TOM Toolbox
|-

| Paper
| [[2007Messaoudi_TomoJ]]
| TomoJ
|-

| Paper
| [[2008Heymann_BsoftTomo]]
| Bsoft
|-

| Paper
| [[2015Ding_CaltechTomography]]
| Caltech tomography database
|-

| Paper
| [[2015Noble_AppionProtomo]]
| Batch fiducial-less tilt-series alignment in Appion using Protomo
|-

| Paper
| [[2015vanAarle_Astra]]
| ASTRA Toolbox
|-

| Paper
| [[2017Wan_Simulator]]
| Electron Tomography Simulator
|-

|}

== 2D Crystals ==

=== 2D Preprocessing ===

{|

| Paper
| [[1986Henderson_Processing]]
| General 2D processing
|-

| Paper
| [[2000He_PhaseAlignment]]
| Phase consistency and Alignment
|-

| Paper
| [[2006Gil_Unbending]]
| Crystal unbending
|-

|}

=== Classification ===
{|

| Paper
| [[1988Frank_Classification]]
| MSA and classification in electron crystallography
|-

| Paper
| [[1996Fernandez_SOM]]
| Classification based on self organizing maps
|-

| Paper
| [[1998Sherman_MSA]]
| Classification based on MSA
|-

|}
=== 3D Reconstruction ===

{|

| Paper
| [[1985Wang_Solvent]]
| Solvent flattening
|-

| Paper
| [[1990Henderson_Processing]]
| General 3D processing
|-

| Paper
| [[2004Marabini_ART]]
| Algebraic Reconstruction Technique with blobs for crystals (Xmipp)
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1998Walz_Review]]
| Review of 2D crystallography
|-

| Paper
| [[1999Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Ellis_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of single particles, electron tomography and crystallography
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Gipson_2dx]]
| 2dx
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Philippsen_IPLT]]
| IPLT
|-

|}

== 3D Crystals - MicroED ==

=== Sample Preparation ===
{|
| Paper
| [[2016Shi_Preparation]]
| Sample Preparation
|}
=== Data Collection ===
{|
| Paper
| [[2014Nannenga_CR]]
| Continuous rotation

|}
=== Data Processing ===
{|

| Paper
| [[2011Wisedchaisri_PhaseExtension]]
| Fragment-based phase extension
|-

| Paper
| [[2015Hattne_Processing]]
| Data Processing
|-

| Paper
| [[2016Hattne_Correction]]
| Image correction
|}

=== Software ===
{|

| Paper
| [[2014Iadanza_Processing]]
| Data Processing of still diffraction data
|}

=== Books and Reviews ===
{|
| Paper
| [[2014Nannenga_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Liu_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Rodriguez_Review ]]
| Review of MicroED
|-

|}

== Helical particles ==

=== Filament corrections ===

{|

| Paper
| [[1986Egelman_Curved]]
| Algorithm for correcting curved filaments
|-

| Paper
| [[1988Bluemke_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2006Wang_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2016Yang_Flexible]]
| Algorithm for correcting filaments with flexible subunits
|-

|}

=== Reconstruction ===

{|

| Paper
| [[1952Cochran_Fourier]]
| Fourier Bessel transform of filamentous structures
|-

| Paper
| [[1958Klug_Fourier]]
| Fourier Bessel decomposition of the projection images
|-

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2005Wang_Iterative]]
| Iterative Fourier-Bessel algorithm
|-

| Paper
| [[2007Egelman_Iterative]]
| Iterative real-space algorithm
|-

| Paper
| [[2013Desfosses_Spring]]
| Helical processing with Spring
|-

| Paper
| [[2015Zhang_seam]]
| Workflow for the detection of the lattice seam
|-

| Paper
| [[2016Rohou_Frealix]]
| Helical processing with Frealix
|-

|}

=== Validation ===

{|

| Paper
| [[2014Egelman_ambiguity]]
| How to detect incorrect models
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Carragher_Phoelix]]
| Phoelix
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Owen_Brandeis]]
| Brandeis
|-

|}

== Icosahedral particles ==

=== Reconstruction ===

{|

| Paper
| [[1970Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1971Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1996Fuller_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1997Thuman_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

|}

=== Classification ===

{|

| Paper
| [[2005Scheres_Virus]]
| Classification of virus capsids in real space
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1999Baker_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[1999Conway_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2000Thuman_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Lee_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Navaza_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2006Grunewald_Review]]
| Review of reconstruction of icosahedral viruses
|-

|}

=== Software ===

{|

| Paper
| [[1996Baker_EMPFT]]
| EMPFT
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2013Morin_Sliz SBGrid]]
| SBGrid presentation for eLife
|-

|}

== Databases ==

{|

| Paper
| [[2003Boutselakis_EMSD]]
| EMSD database
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2011Kim_CDDB]]
| Conformational Dynamics Data Bank
|-

| Paper
| [[2011Lawson_EMDB]]
| Electron Microscopy Data Bank
|-

| Paper
| [[2013Ison_EDAM]]
| EDAM, an ontology of bioinformatics operations
|-

| Paper
| [[2016Iudin_EMPIAR]]
| EMPIAR raw data database
|-

| Paper
| [[2016Patwhardan_EMDB]]
| EMDB, PDB, ...
|-

| Paper
| [[2017Patwhardan_Trends]]
| Trends at EMDB
|-

| Paper
| [[2017Shao_PDBQuality]]
| Quality metrics in PDB
|-

| Blog
| http://www.mybiosoftware.com
| Huge list of bioinformatics programs (many of them structural bioinformatics)
|-

|}

== Relationship to other structural information sources ==

{|

| Paper
| [[2000Engel_AFM]]
| Review of Atomic Force Microscopy
|-

| Paper
| [[2001Dimmeler_AFM]]
| Constraints from Atomic Force Microscopy
|-

| Paper
| [[2003Mobus_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_Review]]
| Review on correlative microscopy
|-

| Paper
| [[2005Boudier_EFTETJ]]
| Software for Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2005Vestergaard_SAXS]]
| Example of comparison of 3DEM and Small-angle X-ray scattering
|-

| Paper
| [[2007Hamada_SAXS]]
| Constraints from Small-angle X-ray scattering
|-

| Paper
| [[2013Xu_FRET]]
| EM+FRET
|-

|}

== X-ray tomography ==

{|

| Paper
| [[2012Oton_ImageFormation]]
| Image formation model in X-ray cell microscopy
|-

|}

== Mathematical tools necessary ==

== People developing methods ==
Please, add yourself to this list (due to privacy reasons, please, do not add anyone else to the list without his/her explicit consent). Sort by first name alphabetical order.

[http://biocomp.cnb.csic.es/~coss Carlos Oscar S. Sorzano]: CSIC, Madrid, Spain 

[http://www.curie.fr/recherche/themes/detail_equipe.cfm/lang/_fr/id_equipe/241.htm Cédric Messaoudi]: Institute Curie, Paris, France 

[http://scholar.google.es/citations?user=_jNYGScAAAAJ&hl=en Javier Vargas]:[mailto:jvargas@cnb.csic.es mail]: CSIC, Madrid, Spain 

[http://scholar.google.es/citations?hl=es&user=g2ZJPIYAAAAJ Joaquín Otón]: CSIC, Madrid, Spain 

[mailto:jrbcast@gmail.com José Román Bilbao-Castro]: UAL, Almería, Spain; CSIC, Madrid, Spain 

[José Miguel de la Rosa Trevín]: Biocomputing Unit CNB-CSIC, Madrid, Spain 

[http://cryoem.janelia.org Tamir Gonen]: [mailto:gonent@janelia.hhmi.org mail]: Howard Hughes Medical Institute, Ashburn, VA, USA 

[mailto:vabrishami@cnb.csic.es Vahid Abrishami]: CSIC, Madrid, Spain 

== 3DEM sites ==
* [http://3dem.ucsd.edu/ 3DEM web site]

* [http://en.wikibooks.org/wiki/Software_Tools_For_Molecular_Microscopy Software tools for molecular microscopy]

* [http://www.emdatabank.org/ The Electron Microscopy Data Bank (EMDB)]

* [http://ccdb.ucsd.edu The Cell Centered Database (CCDB)]

* [http://conventions.cnb.csic.es The geometrical software conventions web page ]

== Editing useful links ==

* [http://www.mediawiki.org/wiki/Help:Formatting Text formatting in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Links Adding links in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Images Adding images in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Tables Making tables in Mediawiki]

2017Biyani Focus

2017-05-19T14:25:27Z

CoSS: Created page with "== Citation == Biyani, N.; Righetto, R. D.; McLeod, R.; Caujolle-Bert, D.; Castano-Diez, D.; Goldie, K. N. & Stahlberg, H. Focus: The interface between data collection and da..."

== Citation ==

Biyani, N.; Righetto, R. D.; McLeod, R.; Caujolle-Bert, D.; Castano-Diez, D.; Goldie, K. N. & Stahlberg, H. Focus: The interface between data collection and data processing in cryo-EM. Journal of structural biology, 2017, 198, 124-133

== Abstract ==

We present a new software package called Focus that interfaces cryo-transmission electron microscopy (cryo-EM) data collection with computer image processing. Focus creates a user-friendly environment to import and manage data recorded by direct electron detectors and perform elemental image processing tasks in a high-throughput manner while new data is being acquired at the microscope. It provides the functionality required to remotely monitor the progress of data collection and data processing, which is essential now that automation in cryo-EM allows a steady flow of images of single particles, two-dimensional crystals, or electron tomography data to be recorded in overnight sessions. The rapid detection of any errors that may occur greatly increases the productivity of recording sessions at the electron microscope.

== Keywords ==

== Links ==

http://www.sciencedirect.com/science/article/pii/S1047847717300515

== Related software ==

== Related methods ==

== Comments ==

Main Page

2017-05-19T14:23:18Z

CoSS: /* Automated data collection */

== Presentation ==

This web page is intended to be an extensive repository of three-dimensional electron microscopy (3DEM) methods. The advantages of having such a repository are

* You know which are the relevant articles in a particular topic, therefore, paper introductions, reviews, etc. are easier to write and you make sure you will cite all the related articles.
* You will be sure that your paper has more chances of being cited.
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== Electron microscopy images ==

=== Online courses ===

CALTECH: http://cryo-em-course.caltech.edu/

MRC: ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/EM-course/

CNB-CSIC: http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/MadridJan2014EM

Workshop on Computational methods for CryoEM: https://www.youtube.com/watch?v=XdKO1iaPP8o

Workshop on Management of large CryoEM facilities: https://www.youtube.com/watch?v=as4seOPszL0

Icknield Course on Model Building and Refinement for High Resolution EM Maps: http://www.ccpem.ac.uk/training/icknield_2017/icknield_2017.php

=== Image formation ===

{|

| Paper
| [[1971Erickson_CTF]]
| CTF model
|-

| Paper
| [[1971Glaeser_Damage]]
| Radiation damage
|-

| Chapter
| [[1971Hanszen_CTF]]
| Image formation model
|-

| Paper
| [[1971Thon_Model]]
| CTF model
|-

| Paper
| [[1975Unwin_Imaging]]
| Radiation dose
|-

| Paper
| [[1977Wade_Model]]
| CTF model
|-

| Paper
| [[1978Wade_Model]]
| CTF model
|-

| Paper
| [[1979Hayward_Radiation]]
| Radiation damage
|-

| Paper
| [[1984Cohen_Validity]]
| Validity of the CTF model at high frequencies
|-

| Paper
| [[1988Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[1992Wade_Model]]
| CTF model
|-

| Paper
| [[1993Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2004Egerton_Damage]]
| Radiation damage
|-

| Paper
| [[2004Sorzano_Normalization]]
| Background noise is Gaussian
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2009Baxter_NoiseCharacterization]]
| Characterization of the different noise sources in cryo-EM
|-

| Paper
| [[2010Baker_Damage]]
| Radiation damage dependence on resolution
|-

| Paper
| [[2010Bammes_Damage]]
| Radiation damage dependence on temperature
|-

| Paper
| [[2010Gomez_Multislice]]
| Simulation of the multi slice model
|-

| Paper
| [[2010Zewail_FourDimensional]]
| Review on the use of ultrafast EM
|-

| Paper
| [[2011Bammes_CCD]]
| Performance of CCD cameras
|-

| Paper
| [[2011Glaeser_Coma]]
| Image formation model including coma
|-

| Paper
| [[2011Milazzo_DirectDetectors]]
| Evaluation of Direct Detectors
|-

| Paper
| [[2011Rullgard_ImageSimulation]]
| Accurate simulation of EM images
|-

| Paper
| [[2011Zhang LimitingFactors]]
| Limiting factor for atomic resolution in EM
|-

| Paper
| [[2012Bammes_DirectDetection]]
| Performance of Direct detectors
|-

| Paper
| [[2012Campbell_MotionCorrection]]
| Beam induced motion correction and direct detectors
|-

| Paper
| [[2012Shang_HydrationLayer]]
| Simulation of PDB volumes explicitly considering the hydration layer
|-

| Paper
| [[2013Egerton_RadiationDamage]]
| Review of TEM radiation damage and experimental ways of reducing it
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu H_Noisemodels]]
| Noise models and cryo-EM drift correction with a direct-electron camera
|-

| Paper
| [[2013Li X K2 noisemodels]]
| Influence of electron dose rate on electron counting images recorded with the K2 camera
|-

| Paper
| [[2013Vulovic_CTFApproximations]]
| When to use the different approximations performed so that a projection with linear CTF is valid
|-

| Thesis
| [[2013Vulovic_ImageFormation]]
| Ph.D. Thesis on the image formation in cryo-EM
|-

| Paper
| [[2014Danev_PhasePlate]]
| Volta potential phase plate
|-

| Paper
| [[2015Chiu_K2]]
| Characterization of K2
|-

| Paper
| [[2015Hawkes_AberrationCorrection]]
| Historical account of the development of lens corrections
|-

| Paper
| [[2015Koeck_Quadratic]]
| Limitations of the linear approximation and use of the quadratic terms
|-

| Paper
| [[2015Kuijper_FEI]]
| Description of the FEI Falcons
|-

| Paper
| [[2015Lobato_MULTEM]]
| Simulation of multislice diffraction
|-

| Paper
| [[2015McMullan_AmorphousIce]]
| Beam induced movement is caused by Brownian motion
|-

| Paper
| [[2016Koeck_ADF]]
| Simulations of Annular Dark Field TEM
|-

| Paper
| [[2017Mishyna_DNARadiation]]
| Review of radiation damage on DNA
|-

|}

=== Collection geometry ===

{|

| Chapter
| [[1980Hoppe_Wedge]]
| Missing wedge
|-

| Paper
| [[1987Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1995Penczek_Dual]]
| Dual axis tomography
|-

| Paper
| [[1997Mastronarde_Dual]]
| Dual axis tomography
|-

| Paper
| [[2003Ludtke_FocusPairs]]
| Focus pairs for single particles
|-

| Paper
| [[2005Lanzavecchia_Conical]]
| Conical tomography
|-

| Paper
| [[2005Zampighi_Conical]]
| Conical tomography
|-

| Paper
| [[2006Leschziner_OT]]
| Orthogonal Tilt
|-

| Paper
| [[2006Messaoudi_Multiple]]
| Multiple axis tomography
|-

| Paper
| [[2012Kudryashev_FocusPairs]]
| Focus pairs tomography
|-

| Paper
| [[2014Hovden_TiltFocus]]
| Combining tilt series with focus series
|-

| Paper
| [[2015Sorzano_RandomConicalTilt]]
| General formulation of Random Conical Tilt
|-

| Paper
| [[2017Hagen_DoseTomography]]
| Dose optimization for subtomogram averaging
|-

|}

=== Sample preparation ===

{|

| Paper
| [[1982Dubochet_Sample]]
| Vitreous ice
|-

| Paper
| [[1986Lepault_Sample]]
| Fast freezing
|-

| Paper
| [[1995Dubochet_Sample]]
| High-pressure freezing
|-

| Paper
| [[1995VanMarle_Sample]]
| Sample damages in resin
|-

| Paper
| [[1998Adrian_Sample]]
| Cryo negative staining
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2002Hsieh_Sample]]
| Cryofixation
|-

| Paper
| [[2004AlAmoudi_Sample]]
| CEMOVIS
|-

| Paper
| [[2008Studer_Sample]]
| Review on high pressure freezing
|-

| Paper
| [[2009Pierson_Sample]]
| Review on sample preparation for electron tomography
|-

| Paper
| [[2010Zhang_NegativeStaining]]
| Negative staining for small protein imaging
|-

| Paper
| [[2012Zhang_PositiveStaining]]
| Positive staining
|-

| Paper
| [[2014Rames_NegativeStaining]]
| Optimized negative staining
|-

| Paper
| [[2014Russo_GoldGrids]]
| Gold grids for single particles
|-

| Paper
| [[2015Cabra_Sample]]
| Review on sample preparation for single particles with videos
|-

| Paper
| [[2016Passmore_Review]]
| Tutorial chapter on sample preparation
|-

| Paper
| [[2016Razinkov_Vitrification]]
| New vitrification method
|-

| Paper
| [[2016Takizawa_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2016Thompson_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2017Arnold_BlottingFree]]
| Blotting-free preparation
|-

| Paper
| [[2017Feng_SprayingPlunging]]
| Spraying plunging
|-

| Paper
| [[2017Peitsch_Sample]]
| iMEM: Isolation of Plasma Membrane for Cryoelectron Microscopy
|-

| Paper
| [[2017Schaffer_FocusedIonBeam]]
| Focused Ion Beam sample preparation for membrane proteins
|-

|}

=== Automated data collection ===

{|

| Paper
| [[1992Dierksen_Automatic]]
| Automated data collection
|-

| Paper
| [[1992Koster_Automatic]]
| Automated data collection
|-

| Paper
| [[1996Fung_Automatic]]
| Automated data collection for tomography
|-

| Paper
| [[2001Zhang_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2003Ziese_Automatic]]
| Automated autofocusing
|-

| Paper
| [[2004Potter_Automatic]]
| Automated sample loading
|-

| Paper
| [[2004Zheng_Automatic]]
| Automated data collection
|-

| Paper
| [[2005Lei_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2005Suloway_Automatic]]
| Automated data collection: Leginon
|-

| Paper
| [[2007Yoshioka_RCT]]
| Automated Random Conical Tilt
|-

| Paper
| [[2011Korinek_TOM2]]
| Automated acquisition with TOM2
|-

| Paper
| [[2015Li_UCSFImage]]
| Automated acquisition with UCSFImage
|-

| Paper
| [[2016Gil_Fuzzy]]
| Real time decisions during acquisition with neuro-fuzzy method
|-

| Paper
| [[2016Liu_TiltControl]]
| Accurate control of the tilt angle for electron tomography
|-

| Paper
| [[2016Vargas_FoilHole]]
| Determination of image quality at low magnification
|-

| Paper
| [[2017Biyani_Focus]]
| Automatic processing of micrographs
|-

|}

== Single particles ==

=== Automatic particle picking ===

{|

| Paper
| [[1982VanHeel_Detection]]
| Detection of particles in micrographs
|-

| Paper
| [[2001Nicholson_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2001Zhu_Filaments]]
| Automatic identification of filaments in micrographs
|-

| Paper
| [[2004Sigworth_Detection]]
| Classical detection theory and the cryo-EM particle selection problem
|-

| Paper
| [[2004Volkmann_ParticlePicking]]
| An approach to automated particle picking from electron micrographs based on reduced representation templates
|-

| Paper
| [[2004Wong_ParticlePicking]]
| Model-based particle picking for cryo-electron microscopy
|-

| Paper
| [[2004Zhu_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2007Chen_Signature]]
| Automatic particle picking program: Signature
|-

| Paper
| [[2007Woolford_SwarmPS]]
| Automatic particle picking with several criteria, implemented in EMAN Boxer
|-

| Paper
| [[2009Sorzano_MachineLearning]]
| Automatic particle picking based on machine learning of rotational invariants
|-

| Paper
| [[2011Arbelaez_Comparison]]
| Evaluation of the performance of software for automated particle-boxing
|-

| Paper
| [[2013Abrishami_MachineLearning]]
| A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs
|-

| Paper
| [[2013Hauer_2013]]
| Automatic tilt pair detection in Random Conical Tilt
|-

| Paper
| [[2013Shatsky_ParticlePicking]]
| Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Langlois_ParticlePicking]]
| Automatic particle picking
|-

| Paper
| [[2016Vilas_AutomaticTilt]]
| Automatic identification of image pairs in untilted-tilted micrograph pairs
|-

|}

=== 2D Preprocessing ===

{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast enhancement through DPR
|-

| Paper
| [[2004Sorzano_Normalization]]
| Normalization procedures and their statistical properties.
|-

| Paper
| [[2006Sorzano_Denoising]]
| Strong denoising in wavelet space
|-

| Conference
| [[2009Sorzano_Downsampling]]
| Differences between the different downsampling schemes
|-

| Paper
| [[2012Brilot_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Campbell_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Zhao_Denoising]]
| Denoising using an invariant Fourier-Bessel eigenspace
|-

| Paper
| [[2013Norousi_Screening]]
| Screening particles to identify outliers
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu_Movies]]
| Drift correction for movies considering dark field
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Scheres_Movies]]
| Beam induced motion correction
|-

| Paper
| [[2015Abrishami_Movies]]
| Alignment of direct detection device micrographs
|-

| Paper
| [[2015Grant_Anisotropic]]
| Automatic estimation and correction of anisotropic magnification
|-

| Paper
| [[2015Grant_OptimalExposure]]
| Filter movies according to the radiation damage
|-

| Paper
| [[2015Rubinstein_Alignment]]
| Frame alignment at the level of particle
|-

| Paper
| [[2015Spear_DoseCompensation]]
| Effect of dose compensation on resolution
|-

| Paper
| [[2015Zhao_AnisotropicMagnification]]
| Correction of anisotropic magnification
|-

| Conference
| [[2016Bajic_Denoising]]
| Denoising and deconvolution of micrographs
|-

| Paper
| [[2016Jensen_RemovalVesicles]]
| Removal of vesicles in membrane proteins
|-

| Paper
| [[2016Bhamre_Denoising]]
| Denoising by 2D covariance estimation
|-

| Paper
| [[2017McLeod_Zorro]]
| Movie alignment by Zorro
|-

| Paper
| [[2017Zheng_MotionCorr2]]
| Movie alignment by MotionCorr2
|-

|}

=== 2D Alignment ===

{|

| Paper
| [[1981Frank_Averaging]]
| 2D averaging and phase residual
|-

| Paper
| [[1982Saxton_Averaging]]
| 2D averaging using correlation
|-

| Paper
| [[1998Sigworth_ML2D]]
| Maximum likelihood alignment in 2D
|-

| Paper
| [[2003Cong_FRM2D]]
| Fast Rotational Matching in 2D
|-

| Paper
| [[2005Cong_FRM2D]]
| Fast Rotational Matching in 2D introduced in a 3D Alignment algorithm
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

|}

=== 2D Classification and clustering ===

{|

| Paper
| [[1981VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[1984VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2011Singer_DiffusionMaps]]
| Classification in 2D based on graph analysis of the projections
|-

| Paper
| [[2012Yang_ISAC]]
| Iterative Stable Alignment and clustering
|-

| Paper
| [[2014Sorzano_Outlier]]
| Outlier detection in 2D classifications.
|-

| Paper
| [[2014Zhao_Aspire]]
| Fast classification based on rotational invariants and vector diffusion maps
|-

| Paper
| [[2015Huang_Robust]]
| Robust w-estimators of 2D classes
|-

| Paper
| [[2016Reboul_Stochastic]]
| Stochastic Hill Climbing for calculating 2D classes
|-

| Conference
| [[2017Bhamre_Mahalanobis]]
| 2D classification using Mahalanobis distance
|-

|}

=== 3D Alignment ===

{|

| Paper
| [[1980Kam_AutoCorrelation]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[1986Goncharov_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1987VanHeel_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1988Provencher_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Vogel_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1990Gelfand_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Goncharov_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Harauz_Quaternions]]
| Use of quaternions to represent rotations
|-

| Paper
| [[1994Penczek_Real]]
| Angular assignment using projection matching in real space
|-

| Paper
| [[1994Radermacher_Radon]]
| Angular assignment in Radon space
|-

| Paper
| [[1996Penczek_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[2003Rosenthal_DPR]]
| Angular assignment using DPR
|-

| Paper
| [[2004Sorzano_Wavelet]]
| Angular assignment in the wavelet space.
|-

| Paper
| [[2005Jonic_Splines]]
| Angular assignment in Fourier space using spline interpolation.
|-

| Paper
| [[2005Yang_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[2006Ogura_SimulatedAnnealing]]
| Angular asignment by simulated annealing
|-

| Paper
| [[2007Grigorieff_Continuous]]
| Continuous angular assignment in Fourier space
|-

| Paper
| [[2010Jaitly_Bayesian]]
| Angular assignment by a Bayesian method and annealing
|-

| Paper
| [[2010Sanz_Random]]
| Random model method
|-

| Paper
| [[2010Singer_Voting]]
| Detecting consistent common lines by voting (reference free)
|-

| Paper
| [[2011Singer_SDP]]
| Angular assignment by semidefinite programming and eigenvectors (reference free)
|-

| Paper
| [[2012Giannakis_Scattering]]
| Construction of an initial volume, reference free, by graph analysis of the projections
|-

| Paper
| [[2012Shkolnisky_Sync]]
| Angular assignment by synchronization of rotations (reference free)
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Wang_LUD]]
| Angular assignment by least unsquared deviations (reference free)
|-

| Paper
| [[2014Vargas_RANSAC]]
| Initial model using RANSAC (reference free)
|-

| Paper
| [[2015Joubert_Pseudoatoms]]
| Initial model based on pseudo-atoms
|-

| Paper
| [[2015Singer_Kam]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[2015Sorzano_Significant]]
| Statistical approach to the initial volume estimation (reconstruct significant)
|-

| Conference
| [[2016Michels_Heterogeneous]]
| Initial volume in the presence of heterogeneity
|-

| Paper
| [[2016Cossio_BayesianGPU]]
| GPU implementation of the Bayesian 3D reconstruction approach
|-

|}

=== 3D Reconstruction ===
{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1986Harauz_FBP]]
| Exact filters for Filtered Back Projection
|-

| Chapter
| [[1992Radermacher_WBP]]
| Exact filters for Weighted Back Projection
|-

| Paper
| [[1997Zhu_RecCTF]]
| 3D Reconstruction (SIRT like) and simultaneous CTF correction
|-

| Paper
| [[1998Boisset_Uneven]]
| Artifacts in SIRT and WBP under uneven angular distributions
|-

| Paper
| [[1998Marabini_ART]]
| Algebraic Reconstruction Technique with blobs (Xmipp)
|-

| Paper
| [[2001Sorzano_Uneven]]
| Free parameter selection under uneven angular distributions
|-

| Paper
| [[2005Sorzano_Parameters]]
| Free parameter selection for optimizing multiple tasks
|-

| Paper
| [[2008Sorzano_Constraints]]
| Mass, surface, positivity and symmetry constraints for real-space algorithms
|-

| Paper
| [[2009Bilbao_ParallelART]]
| Efficient parallelization of ART
|-

| Paper
| [[2011Li_GradientFlow]]
| Regularized 3D Reconstruction by Gradient Flow
|-

| Paper
| [[2011Vonesch_Wavelets]]
| Fast wavelet-based 3D reconstruction
|-

| Paper
| [[2012Gopinath_ShapeRegularization]]
| Regularized 3D Reconstruction by Shape information
|-

| Paper
| [[2012Kucukelbir_adaptiveBasis]]
| 3D reconstruction in an adaptive basis promoting sparsity
|-

| Paper
| [[2012Sindelar_NoiseReduction]]
| Optimal noise reduction in 3D reconstructions
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Lyumkis_Optimod]]
| Construction of initial volumes with Optimod
|-

| Paper
| [[2013Wang FIRM]]
| Fast 3D reconstruction in Fourier domain
|-

| Paper
| [[2014Kunz_SART_OS]]
| Simultaneous ART with OS
|-

| Paper
| [[2015Abrishami_Fourier]]
| 3D Reconstruction in Fourier space
|-

| Paper
| [[2015Dvornek_SubspaceEM]]
| Fast Maximum a posteriori
|-

| Paper
| [[2015Moriya_Bayesian]]
| Bayesian approach to suppress limited angular artifacts
|-

| Paper
| [[2015Xu_GeometricFlow]]
| Multi-scale geometric flow
|-

| Arxiv
| [[2016Ye_Cohomology]]
| Cohomology properties of 3D reconstruction
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

|}

=== 3D Heterogeneity ===

{|

| Paper
| [[2004White_Size]]
| Heterogeneity classification of differently sized images
|-

| Paper
| [[2006Penczek_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Scheres_ML3D]]
| Maximum Likelihood alignment and classification in 3D
|-

| Paper
| [[2009Spahn_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2010Elmlund_AbInitio]]
| Solving the initial volume problem with multiple conformations
|-

| Paper
| [[2010Shatsky_MultiVariate]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2012Scheres_Bayesian]]
| A Bayesian view on cryo-EM structure determination
|-

| Paper
| [[2012Zheng_Covariance]]
| Estimation of the volume covariance
|-

| Paper
| [[2013Wang_MLVariance]]
| Maximum Likelihood estimate of the map variance
|-

| Paper
| [[2013Lyumkis D_FREALIGN]]
| Likelihood-based classification of cryo-EM images using FREALIGN.
|-

| Paper
| [[2014Jin_NMA]]
| Continuous heterogeneity through Normal Mode Analysis
|-

| Paper
| [[2014Dashti_Brownian]]
| Continuous heterogeneity through Brownian trajectories
|-

| Paper
| [[2014Chen_Migration]]
| Particle migration analysis in 3D classification
|-

| Paper
| [[2015Anden_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Bai_Focused]]
| Focused classification
|-

| Paper
| [[2015Katsevich_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Klaholz_MRA]]
| Multivariate Statistical Analysis of Jackknife and Bootstrapping on random subsets
|-

| Paper
| [[2015Liao_Covariance]]
| Estimation of the 3D covariance from 2D projections
|-

| Paper
| [[2015Tagare_Direct]]
| Direct reconstruction of PCA components
|-

| Paper
| [[2016Gong_Mechanical]]
| Mechanical model for macromolecules
|-

| Paper
| [[2016Rawson_Movement]]
| Movement and flexibility
|-

| Paper
| [[2016Sorzano_StructMap]]
| Sorting a discrete set of conformational states
|-

| Paper
| [[2016Sorzano_Strain]]
| Calculate local stretches, strains and rotations from two conformational states
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

|}

=== Validation ===

{|

| Paper
| [[2008Stagg_TestBed]]
| Effect of voltage, dosis, number of particles and Euler jumps on resolution
|-

| Paper
| [[2011Henderson]]
| Tilt Validation
|-

| Paper
| [[2011Read]]
| Validation of PDBs
|-

| Paper
| [[2012Henderson]]
| EM Map Validation
|-

| Paper
| [[2013Cossio_Bayesian]]
| EM Map Validation in a probabilistic setting
|-

| Paper
| [[2013Chen_NoiseSubstitution]]
| Noise substitution at high resolution for measuring overfitting
|-

| Paper
| [[2014Russo_StatisticalSignificance]]
| EM Map Validation through the statistical significance of the tilt-pair angular assignment
|-

| Paper
| [[2014Stagg_Reslog]]
| EM Map Validation through the resolution evolution with the number of particles
|-

| Paper
| [[2014Wasilewski_Tilt]]
| Web implementation of the tilt pair validation
|-

| Paper
| [[2015Heymann_Alignability]]
| EM Map Validation through the resolution of reconstructions from particles and noise
|-

| Paper
| [[2015Oliveira_FreqLimited]]
| Comparison of gold standard and frequency limited optimization
|-

| Paper
| [[2015Wriggers_Secondary]]
| Validation by secondary structure
|-

| Paper
| [[2016Kim_SAXS]]
| Comparison of SAXS data and EM projections
|-

| Paper
| [[2016Rosenthal_Review]]
| Review of validation methods
|-

| Paper
| [[2016Vargas_Alignability]]
| Validation by studying the tendency of an angular assignment to cluster in the projection space
|-

| Paper
| [[2017Monroe_PDBRefinement]]
| Validation by comparison to a refined PDB
|-

|}

=== Resolution ===

{|

| Paper
| [[1986Harauz_FBP]]
| Fourier Shell Correlation
|-

| Paper
| [[1987Unser_SSNR]]
| 2D Spectral Signal to Noise Ratio
|-

| Paper
| [[2002Penczek_SSNR]]
| 3D Spectral Signal to Noise Ratio for Fourier based algorithms
|-

| Paper
| [[2003Rosenthal_DPR]]
| Review of the FSC and establishment of a new threshold
|-

| Paper
| [[2005Unser_SSNR]]
| 3D Spectral Signal to Noise Ratio for any kind of algorithms
|-

| Paper
| [[2005VanHeel_FSC]]
| Establishment of a new threshold for FSC
|-

| Paper
| [[2007Sousa_AbInitio]]
| Resolution measurement on neighbour Fourier voxels
|-

| Paper
| [[2014Kucukelbir_Local]]
| Quantifying the local resolution of cryo-EM density maps
|-

| Paper
| [[2016Pintilie_Probabilistic]]
| Probabilistic models and resolution
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Statistical properties of resolution measures defined in Fourier space
|-

|}

=== Sharpening of high resolution information ===
{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast restoration and map sharpening
|-

| Paper
| [[2008Fernandez_Bfactor]]
| Bfactor determination and restoration
|-

| Paper
| [[2013Fiddy_SaxtonAlgorithm]]
| Phase retrieval or extension
|-

| Paper
| [[2014Kishchenko_SphericalDeconvolution]]
| Spherical deconvolution
|-

| Paper
| [[2015Spiegel_VISDEM]]
| Visualization improvement by the use of pseudoatomic profiles
|-

| Paper
| [[2016Jonic_Pseudoatoms]]
| Approximation with pseudoatoms
|-

| Paper
| [[2016Jonic_Denoising]]
| Denoising and high-frequency boosting by pseudoatom approximation
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[1982Schiske_Correction]]
| CTF correction for tilted objects
|-

| Paper
| [[1988Toyoshima_Model]]
| CTF estimation
|-

| Paper
| [[1995Frank_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1996Skoglund_MaxEnt]]
| CTF correction with Maximum Entropy
|-

| Paper
| [[1996Zhou_Model]]
| CTF model and user interface for manual fitting
|-

| Paper
| [[1997Fernandez_AR]]
| PSD estimation using periodogram averaging and AR models
|-

| Paper
| [[1997Penczek_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1997Stark_Deconvolution]]
| CTF correction using deconvolution
|-

| Paper
| [[1997Zhu_RecCTF]]
| CTF correction and reconstruction
|-

| Paper
| [[2000DeRosier_EwaldCorrection]]
| CTF correction considering the Ewald sphere
|-

| Paper
| [[2000Jensen_TiltedCorrection]]
| CTF correction considering tilt in backprojection
|-

| Paper
| [[2001Saad_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Huang_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Mindell_CTFTILT]]
| CTF estimation for tilted micrographs
|-

| Paper
| [[2003Sander_MSA]]
| CTF estimation through MSA classification of PSDs
|-

| Paper
| [[2003Velazquez_ARMA]]
| PSD and CTF estimation using ARMA models
|-

| Paper
| [[2004Sorzano_IDR]]
| CTF restoration and reconstruction with Iterative Data Refinement
|-

| Conference
| [[2004Wan_CTF]]
| Spatially variant CTF
|-

| Paper
| [[2004Zubelli_Chahine]]
| CTF restoration and reconstruction with Chahine's multiplicative method
|-

| Conference
| [[2005Dubowy_SpaceVariant]]
| CTF correction when this is space variant
|-

| Paper
| [[2005Mallick_ACE]]
| CTF estimation
|-

| Paper
| [[2006Wolf_Ewald]]
| CTF correction considering Ewald sphere
|-

| Paper
| [[2007Jonic_EnhancedPSD]]
| PSD enhancement for better identification of Thon rings; Vitreous ice diffracts in Thon rings
|-

| Paper
| [[2007Philippsen_Model]]
| CTF Model for tilted specimens
|-

| Paper
| [[2007Sorzano_CTF]]
| CTF estimation using enhanced PSDs
|-

| Paper
| [[2009Sorzano_Sensitivity]]
| Error sensitivity of the CTF models, non-uniqueness of the CTF parameters
|-

| Paper
| [[2010Jiang2010_CTFCorrection]]
| Amplitude correction method
|-

| Paper
| [[2010Kasantsev_CTFCorrection]]
| Mathematical foundations of Kornberg and Jensen method
|-

| Paper
| [[2010Leong_CTFCorrection]]
| Correction for spatially variant CTF
|-

| Paper
| [[2011Glaeser_Coma]]
| The effect of coma at high-resolution
|-

| Paper
| [[2011Mariani_Tilted]]
| CTF simulation and correction of tilted specimens
|-

| Paper
| [[2011Sindelar_Wiener]]
| CTF correction using a modified version of Wiener filter
|-

| Paper
| [[2011Voortman_Tilted]]
| CTF correction for tilted specimen
|-

| Paper
| [[2012Voortman_VaryingCTF]]
| Correcting a spatially varying CTF
|-

| Paper
| [[2013Vargas_FastDef]]
| Fast defocus
|-

| Paper
| [[2015Rohou_CTFFind4]]
| CTF Find 4
|-

| Paper
| [[2015Sheth_CTFquality]]
| Visualization and quality assessment of CTF
|-

| Paper
| [[2016Zhang_GCTF]]
| gCTF
|-

|}

=== Segmentation ===

{|

| Paper
| [[2006Baker_segmentation]]
| Segmentation of molecular subunits
|-

|}

=== Fitting and docking ===

{|

| Paper
| [[1999Volkmann_Fitting]]
| Fitting in real space
|-

| Paper
| [[2001Baker_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2001Jones_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2003Kovacs_FRM3D]]
| Fast Rotational Alignment of two EM maps
|-

| Paper
| [[2004Tama_NMA1]]
| Flexible fitting with Normal Modes (I)
|-

| Paper
| [[2004Tama_NMA2]]
| Flexible fitting with Normal Modes (II)
|-

| Paper
| [[2005Velazquez_Superfamilies]]
| Recognition of the superfamily folding in medium-high resolution volumes
|-

| Paper
| [[2007DeVries_Haddock]]
| Docking with Haddock 2.0
|-

| Paper
| [[2007Kleywegt_QualityControl]]
| Quality control and validation of fitting
|-

| Paper
| [[2012Biswas_Secondary]]
| Secondary structure determination in EM volumes
|-

| Paper
| [[2012Velazquez_Constraints]]
| Multicomponent fitting by using constraints from other information sources
|-

| Paper
| [[2013Chapman MS_Atomicmodeling]]
| Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters
|-

| Paper
| [[2013Esquivel_Modelling]]
| Review on modelling (secondary structure, fitting, ...)
|-

| Paper
| [[2013Lopez_Imodfit]]
| Fitting based on vibrational analysis
|-

| Paper
| [[2013Nogales_3DEMLoupe]]
| Normal Mode Analysis of reconstructed volumes
|-

| Paper
| [[2014AlNasr_Secondary]]
| Identification of secondary structure elements in EM volumes
|-

| Paper
| [[2014Politis_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Rey_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Villa_Review]]
| Review of atomic fitting into EM volumes
|-

| Paper
| [[2015Barad_EMRinger]]
| Validation of hybrid models
|-

| Paper
| [[2015Bettadapura_PF2Fit]]
| Fast rigid fitting of PDBs into EM maps
|-

| Paper
| [[2015Carrillo_CapsidMaps]]
| Analysis of virus capsids using Google Maps
|-

| Paper
| [[2015Schroeder_Hybrid]]
| Review on model building
|-

| Paper
| [[2015Tamo_Dynamics]]
| Dynamics in integrative modeling
|-

| Paper
| [[2015Sorzano_AtomsToVoxels]]
| Accurate conversion of an atomic model into a voxel density volume
|-

| Paper
| [[2016Joseph_Evolution]]
| Evolutionary constraints for the fitting of atomic models into density maps
|-

| Paper
| [[2016Segura_3Diana]]
| Validation of hybrid models
|-

| Paper
| [[2016Singharoy_MDFF]]
| Construction of hybrid models driven by EM density and molecular dynamics
|-

| Paper
| [[2016Wang_Rosetta]]
| Construction of hybrid models driven by EM density using Rosetta
|-

| Paper
| [[2017Hryc_WeightedAtoms]]
| Construction of hybrid models by locally weighting the different atoms
|-

| Paper
| [[2017Matsumoto_Distribution]]
| Estimating the distribution of conformations of atomic models
|-

| Paper
| [[2017Miyashita_EnsembleFitting]]
| Ensemble fitting using Molecular Dynamics
|-

|}

=== Books and reviews ===

{|

| Book
| [[1980Herman_Tomography]]
| General book on tomography
|-

| Book
| [[1988Kak_Tomography]]
| General book on tomography
|-

| Paper
| [[2000Tao_Review]]
| Review of single particles
|-

| Paper
| [[2000VanHeel_Review]]
| Review of single particles
|-

| Paper
| [[2002Frank_Review]]
| Review of single particles
|-

| Paper
| [[2002Schmid_Review]]
| Review of single particles
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2004Subramaniam_Review]]
| Review of single particles
|-

| Paper
| [[2005Steven_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_book]]
| Book covering all aspects of electron microscopy of single particles
|-

| Paper
| [[2006Sorzano_Review]]
| Review of optimization problems in electron microscopy
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems in Electron Tomography
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2008Mueller_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2008Taylor_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2010DeRosier_Review]]
| Personal account of how 3DEM developed in the early days
|-

| Chapter
| [[2012Sorzano_Review]]
| Review of single particle analysis using Xmipp
|-

| Chapter
| [[2012Devaux_Protocol]]
| Protocols for performing single particle analysis
|-

| Paper
| [[2014Bai_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Carazo_Review]]
| Review of the reconstruction process
|-

| Paper
| [[2015Cheng_Review]]
| A primer to Single Particle Cryo-EM
|-

| Paper
| [[2015Cheng_Reviewb]]
| Single Particle Cryo-EM at crystallographic resolution
|-

| Paper
| [[2015Elmlund_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Henderson_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Nogales_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Schroeder_Review]]
| Review of advances in the electron microscope
|-

| Paper
| [[2015Wu_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Carroni_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Egelman_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Eisenstein_CryoEM]]
| News feature on the Method of the Year
|-

| Paper
| [[2016FernandezLeiro_Review]]
| Review of EM
|-

| Paper
| [[2016Glaeser_HowGood]]
| How good can cryo-EM become?
|-

| Paper
| [[2016Jonic_PseudoAtoms]]
| Review of the applications of the use of pseudoatoms in EM
|-

| Chapter
| [[2016Mio_Review]]
| Overview of the process to obtain EM reconstructions
|-

| Paper
| [[2016Jonic_Review]]
| A review of computational ways to handle heterogeneity
|-

| Paper
| [[2016Nogales_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Subramaniam_Review]]
| Why cryo-EM is now suitable for crystallographic journals
|-

| Paper
| [[2016Vinothkumar_Review]]
| Historical review and current limitations
|-

| Paper
| [[2017Frank_Review]]
| Historical review of EM
|-

| Paper
| [[2017Jonic_Review]]
| Review of computational methods to analyze conformational variability
|-

| Paper
| [[2017Rawson_Limitations]]
| Limitations of EM for drug design
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Review of statistical properties of resolution measures defined in Fourier space
|-
|}

=== Software ===

{|

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[1999Lutdke_Eman]]
| Eman
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Baldwin_AngularTransformations]]
| The Transform Class in SPARX and EMAN2
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Grigorieff_Frealign]]
| Frealign
|-

| Paper
| [[2008Scheres_XmippProtocols]]
| Xmipp Protocols
|-

| Paper
| [[2008Shaikh_SpiderProtocols]]
| Spider Protocols
|-

| Paper
| [[2012Wriggers_SitusConventions]]
| Conventions and workflows in Situs
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2015Cianfrocco_Cloud]]
| Software execution in the cloud
|-

| Paper
| [[2015Cheng_MRC2014]]
| Extensions to MRC file format
|-

| Paper
| [[2013DeLaRosa_Scipion]]
| Scipion
|-

| Paper
| [[2016Scheres_Relion]]
| Tutorial on the use of Relion
|-

| Paper
| [[2016Grigorieff_Frealign]]
| Tutorial on the use of Frealign
|-

|}

== Electron tomography ==

=== Image preprocessing ===

{|

| Paper
| [[2015Yan_thickness]]
| Determination of thickness, tilt and electron mean free path
|-

|}

=== Image alignment ===

{|

| Paper
| [[1982Guckenberger_commonOrigin]]
| Determination of a common origin in the micrographs of titl series in three-dimensional electron microscopy
|-

| Paper
| [[1992Lawrence_leastSquares]]
| Least squares solution of the alignment problem
|-

| Paper
| [[1995Penczek_dual]]
| Dual tilt alignment
|-

| Paper
| [[1996Owen_alignmentQuality]]
| Automatic alignment without fiducial markers and evaluation of alignment quality
|-

| Paper
| [[1998Grimm_normalization]]
| Discussion of several gray level normalization methods for electron tomography
|-

| Paper
| [[2001Brandt_Automatic1]]
| Automatic alignment without fiducial markers
|-

| Paper
| [[2001Brandt_Automatic2]]
| Automatic alignment with fiducial markers
|-

| Paper
| [[2006Winkler_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2006Castano_alignment]]
| Alignment with non-perpendicularity
|-

| Paper
| [[2007Castano_alignment]]
| Fiducial-less alignment of cryo-sections
|-

| Paper
| [[2009Sorzano_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2010Cantele_dualAlignment]]
| Alignment of dual series
|-

| Paper
| [[2014Tomonaga_Automatic]]
| Automatic alignment of tilt series using the projection themselves
|-

| Paper
| [[2014Han_Automatic]]
| Automatic alignment of tilt series using SIFT features
|-

| Paper
| [[2015Han_Automatic]]
| Automatic alignment of tilt series using fiducials
|-

| Paper
| [[2017Mastronarde_Automatic]]
| Automatic alignment and reconstruction of tilt series in IMOD
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[2003Winkler_CTF]]
| Focus gradient correction in electron tomography
|-

| Paper
| [[2006Fernandez_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Zanetti_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Xiong_CTF]]
| CTF determination and correction for low dose tomographic tilt series
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2017Kunz_3DCTF]]
| 3D CTF Correction
|-

|}

=== 3D reconstruction ===

{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1992Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[1997Marabini_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2002Fernandez_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2007Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[2008Fernandez_CARP]]
| Component Averaged Row Projections (CARP)
|-

| Paper
| [[2012Herman General Superiorization]]
| Superiorization: an optimization heuristic for medical physics
|-

| Paper
| [[2012Zhang_IPET_FETR]]
| IPET and FETR, a reconstruction algorithm for single molecule tomography
|-

| Paper
| [[2013Goris_SIRT_TV_DART]]
| Combination of SIRT, Total Variation and Discrete ART to reconstruct and segment at the same time
|-

| Paper
| [[2013Briegel A_Challenge]]
| The challenge of determining handedness in electron tomography and the use of DNA origami gold nanoparticle helices as molecular standards
|-

| Paper
| [[2013Messaoudi_EnergyFiltered]]
| 3D Reconstruction of Energy-Filtered TEM
|-

| Paper
| [[2016Deng_ICON]]
| 3D Reconstruction with missing information restoration
|-

| Paper
| [[2016Guay_Compressed]]
| 3D Reconstruction using compressed sensing
|-

|}

=== Noise reduction ===
{|

| Paper
| [[2001Frangakis_NAD]]
| Noise reduction with Nonlinear Anisotropic Diffusion
|-

| Paper
| [[2003Fernandez_AND]]
| Anisotropic nonlinear diffusion for electron tomography
|-

| Paper
| [[2003Jiang_Bilateral]]
| Bilateral denoising filter in electron microscopy
|-

| Paper
| [[2005Fernandez_AND]]
| Anisotropic nonlinear denoising in electron tomography
|-

| Paper
| [[2007Heide_median]]
| Iterative median filtering in electron tomography
|-

| Paper
| [[2007Fernandez_autAND]]
| Anisotropic nonlinear diffusion with automated parameter tuning
|-

| Paper
| [[2009Fernandez_Beltrami]]
| Nonlinear filtering based on Beltrami flow
|-

| Paper
| [[2010Bilbao_MeanShift]]
| Mean Shift Filtering
|-

| Paper
| [[2014Kovacik_wedgeArtefacts]]
| Removal of wedge artefacts
|-

| Paper
| [[2014Maiorca_beadArtefacts]]
| Removal of gold bead artefacts
|-

|}

=== Segmentation ===

{|

| Paper
| [[2002Frangakis_Eigenanalysis]]
| Segmentation using eigenvector analysis.
|-

| Paper
| [[2002Volkmann_Watershed]]
| Segmentation using watershed transform.
|-

| Paper
| [[2003Bajaj_BoundarySegmentation]]
| Segmentation based on fast marching.
|-

| Paper
| [[2005Cyrklaff_Thresholding]]
| Segmentation using optimal thresholding.
|-

| Paper
| [[2007Lebbink_TemplateMatching]]
| Segmentation using template matching.
|-

| Paper
| [[2007Sandberg_OrientationFields]]
| Segmentation using orientation fields.
|-

| Paper
| [[2007Sandberg_SegmentationReview]]
| Review on segmentation in electron tomography.
|-

| Paper
| [[2008Garduno_FuzzySegmentation]]
| Segmentation using fuzzy set theory principles.
|-

| Paper
| [[2009Lebbink_TemplateMatching2]]
| Segmentation using template matching.
|-

| Paper
| [[2012RubbiyaAli_EdgeDetection]]
| Parameter-Free Segmentation of Macromolecular Structures.
|-

| Conference
| [[2015Xu_TemplateMatching]]
| Detection of macromolecular complexes with a reduced representation of the templates.
|-

|}

=== Resolution ===
{|

| Paper
| [[2005Cardone_Resolution]]
| Resolution criterion for electron tomography
|-

| Chapter
| [[2007Penczek_Resolution]]
| Review of resolution criteria for electron tomography
|-

| Paper
| [[2015Diebolder_ConicalFSC]]
| Conical Fourier Shell Correlation
|-

|}

=== Subtomogram analysis ===

{|

| Paper
| [[2000Bohm_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2002Frangakis_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2006Nickell_Review]]
| Review of macromolecule finding by template matching (Visual Proteomics)
|-

| Paper
| [[2007Best_Review]]
| Review of Localization of Protein Complexes by Pattern Recognition
|-

| Paper
| [[2007Forster_Review]]
| Review of structure determination by subtomogram averaging
|-

| Paper
| [[2008Forster_Classification]]
| Classification of subtomograms using constrained correlation
|-

| Paper
| [[2008Bartesaghi_Classification]]
| Classification and averaging of subtomograms
|-

| Paper
| [[2008Schmid_Averaging]]
| Alignment and averaging of subtomograms
|-

| Paper
| [[2010Amat_Averaging]]
| Alignment and averaging of subtomograms exploiting thresholding in Fourier space
|-

| Paper
| [[2013Chen_Averaging]]
| Fast alignment of subtomograms using spherical harmonics
|-

| Paper
| [[2013Kuybeda_Averaging]]
| Alignment and averaging of subtomograms using the nuclear norm of the cluster
|-

| Paper
| [[2013Shatsky_Averaging]]
| Alignment and averaging of subtomograms with constrained cross-correlation
|-

| Paper
| [[2014Chen_Autofocus]]
| Subtomogram averaging and classification with special attention to differences
|-

| Paper
| [[2014Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2014Voortman_LimitingFactors]]
| Limiting factors of subtomogram averaging
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2015Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2016Bharat_Relion]]
| Subtomogram averaging with Relion
|-

| Paper
| [[2016Song_MatrixNorm]]
| Matrix norm minimization for tomographic reconstruction and alignment
|-

| Paper
| [[2017Castano_ParticlePicking]]
| Particle picking in tomograms for subtomogram averaging
|-

|}

=== Single particle tomography ===

{|

| Paper
| [[2012Bartesaghi_Constrained]]
| 3D reconstruction by imposing geometrical constraints
|-

| Paper
| [[2015Galaz_SingleParticleTomography]]
| Set of tools for Single Particle Tomography in EMAN2
|-

| Paper
| [[2016Galaz_SingleParticleTomography]]
| Alignment algorithms and CTF correction
|-

|}

=== Books and reviews ===

{|

| Paper
| [[2000Baumeister_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Koster_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Sali_Review]]
| Review of electron tomography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2005Lucic_Review]]
| Review of electron tomography
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_TomoBook]]
| Electron Tomography
|-

| Book
| [[2007McIntosh_Book]]
| Cellular Electron Microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2012Kudryashev_Review]]
| Review of subtomogram averaging
|-

| Paper
| [[2016Beck_Review]]
| Review of molecular sociology
|-

|}

=== Software ===

{|

| Paper
| [[1996Kremer_IMOD]]
| IMOD
|-

| Paper
| [[1996Chen_Priism/IVE]]
| Priism/IVE
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2005Nickell_TOM]]
| TOM Toolbox
|-

| Paper
| [[2007Messaoudi_TomoJ]]
| TomoJ
|-

| Paper
| [[2008Heymann_BsoftTomo]]
| Bsoft
|-

| Paper
| [[2015Ding_CaltechTomography]]
| Caltech tomography database
|-

| Paper
| [[2015Noble_AppionProtomo]]
| Batch fiducial-less tilt-series alignment in Appion using Protomo
|-

| Paper
| [[2015vanAarle_Astra]]
| ASTRA Toolbox
|-

| Paper
| [[2017Wan_Simulator]]
| Electron Tomography Simulator
|-

|}

== 2D Crystals ==

=== 2D Preprocessing ===

{|

| Paper
| [[1986Henderson_Processing]]
| General 2D processing
|-

| Paper
| [[2000He_PhaseAlignment]]
| Phase consistency and Alignment
|-

| Paper
| [[2006Gil_Unbending]]
| Crystal unbending
|-

|}

=== Classification ===
{|

| Paper
| [[1988Frank_Classification]]
| MSA and classification in electron crystallography
|-

| Paper
| [[1996Fernandez_SOM]]
| Classification based on self organizing maps
|-

| Paper
| [[1998Sherman_MSA]]
| Classification based on MSA
|-

|}
=== 3D Reconstruction ===

{|

| Paper
| [[1985Wang_Solvent]]
| Solvent flattening
|-

| Paper
| [[1990Henderson_Processing]]
| General 3D processing
|-

| Paper
| [[2004Marabini_ART]]
| Algebraic Reconstruction Technique with blobs for crystals (Xmipp)
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1998Walz_Review]]
| Review of 2D crystallography
|-

| Paper
| [[1999Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Ellis_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of single particles, electron tomography and crystallography
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Gipson_2dx]]
| 2dx
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Philippsen_IPLT]]
| IPLT
|-

|}

== 3D Crystals - MicroED ==

=== Sample Preparation ===
{|
| Paper
| [[2016Shi_Preparation]]
| Sample Preparation
|}
=== Data Collection ===
{|
| Paper
| [[2014Nannenga_CR]]
| Continuous rotation

|}
=== Data Processing ===
{|

| Paper
| [[2011Wisedchaisri_PhaseExtension]]
| Fragment-based phase extension
|-

| Paper
| [[2015Hattne_Processing]]
| Data Processing
|-

| Paper
| [[2016Hattne_Correction]]
| Image correction
|}

=== Software ===
{|

| Paper
| [[2014Iadanza_Processing]]
| Data Processing of still diffraction data
|}

=== Books and Reviews ===
{|
| Paper
| [[2014Nannenga_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Liu_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Rodriguez_Review ]]
| Review of MicroED
|-

|}

== Helical particles ==

=== Filament corrections ===

{|

| Paper
| [[1986Egelman_Curved]]
| Algorithm for correcting curved filaments
|-

| Paper
| [[1988Bluemke_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2006Wang_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2016Yang_Flexible]]
| Algorithm for correcting filaments with flexible subunits
|-

|}

=== Reconstruction ===

{|

| Paper
| [[1952Cochran_Fourier]]
| Fourier Bessel transform of filamentous structures
|-

| Paper
| [[1958Klug_Fourier]]
| Fourier Bessel decomposition of the projection images
|-

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2005Wang_Iterative]]
| Iterative Fourier-Bessel algorithm
|-

| Paper
| [[2007Egelman_Iterative]]
| Iterative real-space algorithm
|-

| Paper
| [[2013Desfosses_Spring]]
| Helical processing with Spring
|-

| Paper
| [[2015Zhang_seam]]
| Workflow for the detection of the lattice seam
|-

| Paper
| [[2016Rohou_Frealix]]
| Helical processing with Frealix
|-

|}

=== Validation ===

{|

| Paper
| [[2014Egelman_ambiguity]]
| How to detect incorrect models
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Carragher_Phoelix]]
| Phoelix
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Owen_Brandeis]]
| Brandeis
|-

|}

== Icosahedral particles ==

=== Reconstruction ===

{|

| Paper
| [[1970Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1971Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1996Fuller_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1997Thuman_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

|}

=== Classification ===

{|

| Paper
| [[2005Scheres_Virus]]
| Classification of virus capsids in real space
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1999Baker_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[1999Conway_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2000Thuman_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Lee_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Navaza_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2006Grunewald_Review]]
| Review of reconstruction of icosahedral viruses
|-

|}

=== Software ===

{|

| Paper
| [[1996Baker_EMPFT]]
| EMPFT
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2013Morin_Sliz SBGrid]]
| SBGrid presentation for eLife
|-

|}

== Databases ==

{|

| Paper
| [[2003Boutselakis_EMSD]]
| EMSD database
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2011Kim_CDDB]]
| Conformational Dynamics Data Bank
|-

| Paper
| [[2011Lawson_EMDB]]
| Electron Microscopy Data Bank
|-

| Paper
| [[2013Ison_EDAM]]
| EDAM, an ontology of bioinformatics operations
|-

| Paper
| [[2016Iudin_EMPIAR]]
| EMPIAR raw data database
|-

| Paper
| [[2016Patwhardan_EMDB]]
| EMDB, PDB, ...
|-

| Paper
| [[2017Patwhardan_Trends]]
| Trends at EMDB
|-

| Paper
| [[2017Shao_PDBQuality]]
| Quality metrics in PDB
|-

| Blog
| http://www.mybiosoftware.com
| Huge list of bioinformatics programs (many of them structural bioinformatics)
|-

|}

== Relationship to other structural information sources ==

{|

| Paper
| [[2000Engel_AFM]]
| Review of Atomic Force Microscopy
|-

| Paper
| [[2001Dimmeler_AFM]]
| Constraints from Atomic Force Microscopy
|-

| Paper
| [[2003Mobus_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_Review]]
| Review on correlative microscopy
|-

| Paper
| [[2005Boudier_EFTETJ]]
| Software for Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2005Vestergaard_SAXS]]
| Example of comparison of 3DEM and Small-angle X-ray scattering
|-

| Paper
| [[2007Hamada_SAXS]]
| Constraints from Small-angle X-ray scattering
|-

| Paper
| [[2013Xu_FRET]]
| EM+FRET
|-

|}

== X-ray tomography ==

{|

| Paper
| [[2012Oton_ImageFormation]]
| Image formation model in X-ray cell microscopy
|-

|}

== Mathematical tools necessary ==

== People developing methods ==
Please, add yourself to this list (due to privacy reasons, please, do not add anyone else to the list without his/her explicit consent). Sort by first name alphabetical order.

[http://biocomp.cnb.csic.es/~coss Carlos Oscar S. Sorzano]: CSIC, Madrid, Spain 

[http://www.curie.fr/recherche/themes/detail_equipe.cfm/lang/_fr/id_equipe/241.htm Cédric Messaoudi]: Institute Curie, Paris, France 

[http://scholar.google.es/citations?user=_jNYGScAAAAJ&hl=en Javier Vargas]:[mailto:jvargas@cnb.csic.es mail]: CSIC, Madrid, Spain 

[http://scholar.google.es/citations?hl=es&user=g2ZJPIYAAAAJ Joaquín Otón]: CSIC, Madrid, Spain 

[mailto:jrbcast@gmail.com José Román Bilbao-Castro]: UAL, Almería, Spain; CSIC, Madrid, Spain 

[José Miguel de la Rosa Trevín]: Biocomputing Unit CNB-CSIC, Madrid, Spain 

[http://cryoem.janelia.org Tamir Gonen]: [mailto:gonent@janelia.hhmi.org mail]: Howard Hughes Medical Institute, Ashburn, VA, USA 

[mailto:vabrishami@cnb.csic.es Vahid Abrishami]: CSIC, Madrid, Spain 

== 3DEM sites ==
* [http://3dem.ucsd.edu/ 3DEM web site]

* [http://en.wikibooks.org/wiki/Software_Tools_For_Molecular_Microscopy Software tools for molecular microscopy]

* [http://www.emdatabank.org/ The Electron Microscopy Data Bank (EMDB)]

* [http://ccdb.ucsd.edu The Cell Centered Database (CCDB)]

* [http://conventions.cnb.csic.es The geometrical software conventions web page ]

== Editing useful links ==

* [http://www.mediawiki.org/wiki/Help:Formatting Text formatting in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Links Adding links in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Images Adding images in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Tables Making tables in Mediawiki]

2017Wan Simulator

2017-05-19T13:06:05Z

CoSS: Created page with "== Citation == Wan, X.; Katchalski, T.; Churas, C.; Ghosh, S.; Phan, S.; Lawrence, A.; Hao, Y.; Zhou, Z.; Chen, R.; Chen, Y.; Zhang, F. & Ellisman, M. H. Electron tomography..."

== Citation ==

Wan, X.; Katchalski, T.; Churas, C.; Ghosh, S.; Phan, S.; Lawrence, A.; Hao, Y.; Zhou, Z.; Chen, R.; Chen, Y.; Zhang, F. & Ellisman, M. H. Electron tomography simulator with realistic 3D phantom for evaluation of acquisition, alignment and reconstruction methods. Journal of structural biology, 2017, 198, 103-115

== Abstract ==

Because of the significance of electron microscope tomography in the investigation of biological structure at nanometer scales, ongoing improvement efforts have been continuous over recent years. This is particularly true in the case of software developments. Nevertheless, verification of improvements delivered by new algorithms and software remains difficult. Current analysis tools do not provide adaptable and consistent methods for quality assessment. This is particularly true with images of biological samples, due to image complexity, variability, low contrast and noise. We report an electron tomography (ET) simulator with accurate ray optics modeling of image formation that includes curvilinear trajectories through the sample, warping of the sample and noise. As a demonstration of the utility of our approach, we have concentrated on providing verification of the class of reconstruction methods applicable to wide field images of stained plastic-embedded samples. Accordingly, we have also constructed digital phantoms derived from serial block face scanning electron microscope images. These phantoms are also easily modified to include alignment features to test alignment algorithms. The combination of more realistic phantoms with more faithful simulations facilitates objective comparison of acquisition parameters, alignment and reconstruction algorithms and their range of applicability. With proper phantoms, this approach can also be modified to include more complex optical models, including distance-dependent blurring and phase contrast functions, such as may occur in cryotomography.

== Keywords ==

== Links ==

http://www.sciencedirect.com/science/article/pii/S1047847717300552

== Related software ==

== Related methods ==

== Comments ==

Main Page

2017-05-19T13:05:02Z

CoSS: /* Software */

== Presentation ==

This web page is intended to be an extensive repository of three-dimensional electron microscopy (3DEM) methods. The advantages of having such a repository are

* You know which are the relevant articles in a particular topic, therefore, paper introductions, reviews, etc. are easier to write and you make sure you will cite all the related articles.
* You will be sure that your paper has more chances of being cited.
* You can add whatever information you find relevant to your method, external links, links to other papers, etc.
* You can link your method to a web page providing the corresponding software, so you know people can use your algorithms.
* You can use the Wiki search capabilities to locate relevant articles even if they are not at the topic you are looking at.
* As a community we will "reconstruct" our history.
* You can select the "watch" option above to receive notifications in case of further changes in the Main Page.

Developing image processing methods for 3DEM is not "[[well-paid]]" in terms of citations and impact factor. However, it is crucial for the advance of the field. Gathering methodological papers in a portal will help to increase the recognition of the field.

Please:

* Add your articles at the right place (you can add a single article in several topics if it is relevant to all of them). The easiest way to add an article is by editing the corresponding topic in the main page, adding your entry, then save the main page. Click on the red link that appears on your new entry, copy and paste the Wiki following code, add the information of your article

== Citation ==

== Abstract ==

== Keywords ==

== Links ==

== Related software ==

== Related methods ==

== Comments ==

* Maintain the information of each article as complete as possible.
* Sort articles by years and authors.
* Be respectful to other people's work.

== How to subscribe to this page ==

You may subscribe to this page so that you will be notified every time someone adds a new method. To do so, you have to register in the page, and edit your preferences ("my preferences"). Be sure that you have activated the option "E-mail me when a page on my watchlist is changed". Finally, click on the "Watch" tab at the top of this page.

You may subscribe to changes on this page on the mailing list 3demmethods@cnb.csic.es. To send a new method to this mail list just send a mail to 3demmethods@cnb.csic.es

To subscribe to this list, visit the web page

https://listas.csic.es/cnb/wws/subscribe/3demmethods

Alternatively, you may write a mail to sympa6@cnb.csic.es with the subject

<code>subscribe 3demmethods YourName YourFamilyName</code>

and an empty mail body.

To unsubscribe visit the page

https://listas.csic.es/cnb/wws/sigrequest/3demmethods

or write sympa6@cnb.csic.es with the subject

<code>unsubscribe 3demmethods</code>

and an empty mail body.

== Electron microscopy images ==

=== Online courses ===

CALTECH: http://cryo-em-course.caltech.edu/

MRC: ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/EM-course/

CNB-CSIC: http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/MadridJan2014EM

Workshop on Computational methods for CryoEM: https://www.youtube.com/watch?v=XdKO1iaPP8o

Workshop on Management of large CryoEM facilities: https://www.youtube.com/watch?v=as4seOPszL0

Icknield Course on Model Building and Refinement for High Resolution EM Maps: http://www.ccpem.ac.uk/training/icknield_2017/icknield_2017.php

=== Image formation ===

{|

| Paper
| [[1971Erickson_CTF]]
| CTF model
|-

| Paper
| [[1971Glaeser_Damage]]
| Radiation damage
|-

| Chapter
| [[1971Hanszen_CTF]]
| Image formation model
|-

| Paper
| [[1971Thon_Model]]
| CTF model
|-

| Paper
| [[1975Unwin_Imaging]]
| Radiation dose
|-

| Paper
| [[1977Wade_Model]]
| CTF model
|-

| Paper
| [[1978Wade_Model]]
| CTF model
|-

| Paper
| [[1979Hayward_Radiation]]
| Radiation damage
|-

| Paper
| [[1984Cohen_Validity]]
| Validity of the CTF model at high frequencies
|-

| Paper
| [[1988Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[1992Wade_Model]]
| CTF model
|-

| Paper
| [[1993Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2004Egerton_Damage]]
| Radiation damage
|-

| Paper
| [[2004Sorzano_Normalization]]
| Background noise is Gaussian
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2009Baxter_NoiseCharacterization]]
| Characterization of the different noise sources in cryo-EM
|-

| Paper
| [[2010Baker_Damage]]
| Radiation damage dependence on resolution
|-

| Paper
| [[2010Bammes_Damage]]
| Radiation damage dependence on temperature
|-

| Paper
| [[2010Gomez_Multislice]]
| Simulation of the multi slice model
|-

| Paper
| [[2010Zewail_FourDimensional]]
| Review on the use of ultrafast EM
|-

| Paper
| [[2011Bammes_CCD]]
| Performance of CCD cameras
|-

| Paper
| [[2011Glaeser_Coma]]
| Image formation model including coma
|-

| Paper
| [[2011Milazzo_DirectDetectors]]
| Evaluation of Direct Detectors
|-

| Paper
| [[2011Rullgard_ImageSimulation]]
| Accurate simulation of EM images
|-

| Paper
| [[2011Zhang LimitingFactors]]
| Limiting factor for atomic resolution in EM
|-

| Paper
| [[2012Bammes_DirectDetection]]
| Performance of Direct detectors
|-

| Paper
| [[2012Campbell_MotionCorrection]]
| Beam induced motion correction and direct detectors
|-

| Paper
| [[2012Shang_HydrationLayer]]
| Simulation of PDB volumes explicitly considering the hydration layer
|-

| Paper
| [[2013Egerton_RadiationDamage]]
| Review of TEM radiation damage and experimental ways of reducing it
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu H_Noisemodels]]
| Noise models and cryo-EM drift correction with a direct-electron camera
|-

| Paper
| [[2013Li X K2 noisemodels]]
| Influence of electron dose rate on electron counting images recorded with the K2 camera
|-

| Paper
| [[2013Vulovic_CTFApproximations]]
| When to use the different approximations performed so that a projection with linear CTF is valid
|-

| Thesis
| [[2013Vulovic_ImageFormation]]
| Ph.D. Thesis on the image formation in cryo-EM
|-

| Paper
| [[2014Danev_PhasePlate]]
| Volta potential phase plate
|-

| Paper
| [[2015Chiu_K2]]
| Characterization of K2
|-

| Paper
| [[2015Hawkes_AberrationCorrection]]
| Historical account of the development of lens corrections
|-

| Paper
| [[2015Koeck_Quadratic]]
| Limitations of the linear approximation and use of the quadratic terms
|-

| Paper
| [[2015Kuijper_FEI]]
| Description of the FEI Falcons
|-

| Paper
| [[2015Lobato_MULTEM]]
| Simulation of multislice diffraction
|-

| Paper
| [[2015McMullan_AmorphousIce]]
| Beam induced movement is caused by Brownian motion
|-

| Paper
| [[2016Koeck_ADF]]
| Simulations of Annular Dark Field TEM
|-

| Paper
| [[2017Mishyna_DNARadiation]]
| Review of radiation damage on DNA
|-

|}

=== Collection geometry ===

{|

| Chapter
| [[1980Hoppe_Wedge]]
| Missing wedge
|-

| Paper
| [[1987Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1995Penczek_Dual]]
| Dual axis tomography
|-

| Paper
| [[1997Mastronarde_Dual]]
| Dual axis tomography
|-

| Paper
| [[2003Ludtke_FocusPairs]]
| Focus pairs for single particles
|-

| Paper
| [[2005Lanzavecchia_Conical]]
| Conical tomography
|-

| Paper
| [[2005Zampighi_Conical]]
| Conical tomography
|-

| Paper
| [[2006Leschziner_OT]]
| Orthogonal Tilt
|-

| Paper
| [[2006Messaoudi_Multiple]]
| Multiple axis tomography
|-

| Paper
| [[2012Kudryashev_FocusPairs]]
| Focus pairs tomography
|-

| Paper
| [[2014Hovden_TiltFocus]]
| Combining tilt series with focus series
|-

| Paper
| [[2015Sorzano_RandomConicalTilt]]
| General formulation of Random Conical Tilt
|-

| Paper
| [[2017Hagen_DoseTomography]]
| Dose optimization for subtomogram averaging
|-

|}

=== Sample preparation ===

{|

| Paper
| [[1982Dubochet_Sample]]
| Vitreous ice
|-

| Paper
| [[1986Lepault_Sample]]
| Fast freezing
|-

| Paper
| [[1995Dubochet_Sample]]
| High-pressure freezing
|-

| Paper
| [[1995VanMarle_Sample]]
| Sample damages in resin
|-

| Paper
| [[1998Adrian_Sample]]
| Cryo negative staining
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2002Hsieh_Sample]]
| Cryofixation
|-

| Paper
| [[2004AlAmoudi_Sample]]
| CEMOVIS
|-

| Paper
| [[2008Studer_Sample]]
| Review on high pressure freezing
|-

| Paper
| [[2009Pierson_Sample]]
| Review on sample preparation for electron tomography
|-

| Paper
| [[2010Zhang_NegativeStaining]]
| Negative staining for small protein imaging
|-

| Paper
| [[2012Zhang_PositiveStaining]]
| Positive staining
|-

| Paper
| [[2014Rames_NegativeStaining]]
| Optimized negative staining
|-

| Paper
| [[2014Russo_GoldGrids]]
| Gold grids for single particles
|-

| Paper
| [[2015Cabra_Sample]]
| Review on sample preparation for single particles with videos
|-

| Paper
| [[2016Passmore_Review]]
| Tutorial chapter on sample preparation
|-

| Paper
| [[2016Razinkov_Vitrification]]
| New vitrification method
|-

| Paper
| [[2016Takizawa_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2016Thompson_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2017Arnold_BlottingFree]]
| Blotting-free preparation
|-

| Paper
| [[2017Feng_SprayingPlunging]]
| Spraying plunging
|-

| Paper
| [[2017Peitsch_Sample]]
| iMEM: Isolation of Plasma Membrane for Cryoelectron Microscopy
|-

| Paper
| [[2017Schaffer_FocusedIonBeam]]
| Focused Ion Beam sample preparation for membrane proteins
|-

|}

=== Automated data collection ===

{|

| Paper
| [[1992Dierksen_Automatic]]
| Automated data collection
|-

| Paper
| [[1992Koster_Automatic]]
| Automated data collection
|-

| Paper
| [[1996Fung_Automatic]]
| Automated data collection for tomography
|-

| Paper
| [[2001Zhang_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2003Ziese_Automatic]]
| Automated autofocusing
|-

| Paper
| [[2004Potter_Automatic]]
| Automated sample loading
|-

| Paper
| [[2004Zheng_Automatic]]
| Automated data collection
|-

| Paper
| [[2005Lei_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2005Suloway_Automatic]]
| Automated data collection: Leginon
|-

| Paper
| [[2007Yoshioka_RCT]]
| Automated Random Conical Tilt
|-

| Paper
| [[2011Korinek_TOM2]]
| Automated acquisition with TOM2
|-

| Paper
| [[2015Li_UCSFImage]]
| Automated acquisition with UCSFImage
|-

| Paper
| [[2016Gil_Fuzzy]]
| Real time decisions during acquisition with neuro-fuzzy method
|-

| Paper
| [[2016Liu_TiltControl]]
| Accurate control of the tilt angle for electron tomography
|-

| Paper
| [[2016Vargas_FoilHole]]
| Determination of image quality at low magnification
|-

|}

== Single particles ==

=== Automatic particle picking ===

{|

| Paper
| [[1982VanHeel_Detection]]
| Detection of particles in micrographs
|-

| Paper
| [[2001Nicholson_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2001Zhu_Filaments]]
| Automatic identification of filaments in micrographs
|-

| Paper
| [[2004Sigworth_Detection]]
| Classical detection theory and the cryo-EM particle selection problem
|-

| Paper
| [[2004Volkmann_ParticlePicking]]
| An approach to automated particle picking from electron micrographs based on reduced representation templates
|-

| Paper
| [[2004Wong_ParticlePicking]]
| Model-based particle picking for cryo-electron microscopy
|-

| Paper
| [[2004Zhu_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2007Chen_Signature]]
| Automatic particle picking program: Signature
|-

| Paper
| [[2007Woolford_SwarmPS]]
| Automatic particle picking with several criteria, implemented in EMAN Boxer
|-

| Paper
| [[2009Sorzano_MachineLearning]]
| Automatic particle picking based on machine learning of rotational invariants
|-

| Paper
| [[2011Arbelaez_Comparison]]
| Evaluation of the performance of software for automated particle-boxing
|-

| Paper
| [[2013Abrishami_MachineLearning]]
| A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs
|-

| Paper
| [[2013Hauer_2013]]
| Automatic tilt pair detection in Random Conical Tilt
|-

| Paper
| [[2013Shatsky_ParticlePicking]]
| Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Langlois_ParticlePicking]]
| Automatic particle picking
|-

| Paper
| [[2016Vilas_AutomaticTilt]]
| Automatic identification of image pairs in untilted-tilted micrograph pairs
|-

|}

=== 2D Preprocessing ===

{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast enhancement through DPR
|-

| Paper
| [[2004Sorzano_Normalization]]
| Normalization procedures and their statistical properties.
|-

| Paper
| [[2006Sorzano_Denoising]]
| Strong denoising in wavelet space
|-

| Conference
| [[2009Sorzano_Downsampling]]
| Differences between the different downsampling schemes
|-

| Paper
| [[2012Brilot_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Campbell_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Zhao_Denoising]]
| Denoising using an invariant Fourier-Bessel eigenspace
|-

| Paper
| [[2013Norousi_Screening]]
| Screening particles to identify outliers
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu_Movies]]
| Drift correction for movies considering dark field
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Scheres_Movies]]
| Beam induced motion correction
|-

| Paper
| [[2015Abrishami_Movies]]
| Alignment of direct detection device micrographs
|-

| Paper
| [[2015Grant_Anisotropic]]
| Automatic estimation and correction of anisotropic magnification
|-

| Paper
| [[2015Grant_OptimalExposure]]
| Filter movies according to the radiation damage
|-

| Paper
| [[2015Rubinstein_Alignment]]
| Frame alignment at the level of particle
|-

| Paper
| [[2015Spear_DoseCompensation]]
| Effect of dose compensation on resolution
|-

| Paper
| [[2015Zhao_AnisotropicMagnification]]
| Correction of anisotropic magnification
|-

| Conference
| [[2016Bajic_Denoising]]
| Denoising and deconvolution of micrographs
|-

| Paper
| [[2016Jensen_RemovalVesicles]]
| Removal of vesicles in membrane proteins
|-

| Paper
| [[2016Bhamre_Denoising]]
| Denoising by 2D covariance estimation
|-

| Paper
| [[2017McLeod_Zorro]]
| Movie alignment by Zorro
|-

| Paper
| [[2017Zheng_MotionCorr2]]
| Movie alignment by MotionCorr2
|-

|}

=== 2D Alignment ===

{|

| Paper
| [[1981Frank_Averaging]]
| 2D averaging and phase residual
|-

| Paper
| [[1982Saxton_Averaging]]
| 2D averaging using correlation
|-

| Paper
| [[1998Sigworth_ML2D]]
| Maximum likelihood alignment in 2D
|-

| Paper
| [[2003Cong_FRM2D]]
| Fast Rotational Matching in 2D
|-

| Paper
| [[2005Cong_FRM2D]]
| Fast Rotational Matching in 2D introduced in a 3D Alignment algorithm
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

|}

=== 2D Classification and clustering ===

{|

| Paper
| [[1981VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[1984VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2011Singer_DiffusionMaps]]
| Classification in 2D based on graph analysis of the projections
|-

| Paper
| [[2012Yang_ISAC]]
| Iterative Stable Alignment and clustering
|-

| Paper
| [[2014Sorzano_Outlier]]
| Outlier detection in 2D classifications.
|-

| Paper
| [[2014Zhao_Aspire]]
| Fast classification based on rotational invariants and vector diffusion maps
|-

| Paper
| [[2015Huang_Robust]]
| Robust w-estimators of 2D classes
|-

| Paper
| [[2016Reboul_Stochastic]]
| Stochastic Hill Climbing for calculating 2D classes
|-

| Conference
| [[2017Bhamre_Mahalanobis]]
| 2D classification using Mahalanobis distance
|-

|}

=== 3D Alignment ===

{|

| Paper
| [[1980Kam_AutoCorrelation]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[1986Goncharov_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1987VanHeel_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1988Provencher_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Vogel_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1990Gelfand_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Goncharov_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Harauz_Quaternions]]
| Use of quaternions to represent rotations
|-

| Paper
| [[1994Penczek_Real]]
| Angular assignment using projection matching in real space
|-

| Paper
| [[1994Radermacher_Radon]]
| Angular assignment in Radon space
|-

| Paper
| [[1996Penczek_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[2003Rosenthal_DPR]]
| Angular assignment using DPR
|-

| Paper
| [[2004Sorzano_Wavelet]]
| Angular assignment in the wavelet space.
|-

| Paper
| [[2005Jonic_Splines]]
| Angular assignment in Fourier space using spline interpolation.
|-

| Paper
| [[2005Yang_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[2006Ogura_SimulatedAnnealing]]
| Angular asignment by simulated annealing
|-

| Paper
| [[2007Grigorieff_Continuous]]
| Continuous angular assignment in Fourier space
|-

| Paper
| [[2010Jaitly_Bayesian]]
| Angular assignment by a Bayesian method and annealing
|-

| Paper
| [[2010Sanz_Random]]
| Random model method
|-

| Paper
| [[2010Singer_Voting]]
| Detecting consistent common lines by voting (reference free)
|-

| Paper
| [[2011Singer_SDP]]
| Angular assignment by semidefinite programming and eigenvectors (reference free)
|-

| Paper
| [[2012Giannakis_Scattering]]
| Construction of an initial volume, reference free, by graph analysis of the projections
|-

| Paper
| [[2012Shkolnisky_Sync]]
| Angular assignment by synchronization of rotations (reference free)
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Wang_LUD]]
| Angular assignment by least unsquared deviations (reference free)
|-

| Paper
| [[2014Vargas_RANSAC]]
| Initial model using RANSAC (reference free)
|-

| Paper
| [[2015Joubert_Pseudoatoms]]
| Initial model based on pseudo-atoms
|-

| Paper
| [[2015Singer_Kam]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[2015Sorzano_Significant]]
| Statistical approach to the initial volume estimation (reconstruct significant)
|-

| Conference
| [[2016Michels_Heterogeneous]]
| Initial volume in the presence of heterogeneity
|-

| Paper
| [[2016Cossio_BayesianGPU]]
| GPU implementation of the Bayesian 3D reconstruction approach
|-

|}

=== 3D Reconstruction ===
{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1986Harauz_FBP]]
| Exact filters for Filtered Back Projection
|-

| Chapter
| [[1992Radermacher_WBP]]
| Exact filters for Weighted Back Projection
|-

| Paper
| [[1997Zhu_RecCTF]]
| 3D Reconstruction (SIRT like) and simultaneous CTF correction
|-

| Paper
| [[1998Boisset_Uneven]]
| Artifacts in SIRT and WBP under uneven angular distributions
|-

| Paper
| [[1998Marabini_ART]]
| Algebraic Reconstruction Technique with blobs (Xmipp)
|-

| Paper
| [[2001Sorzano_Uneven]]
| Free parameter selection under uneven angular distributions
|-

| Paper
| [[2005Sorzano_Parameters]]
| Free parameter selection for optimizing multiple tasks
|-

| Paper
| [[2008Sorzano_Constraints]]
| Mass, surface, positivity and symmetry constraints for real-space algorithms
|-

| Paper
| [[2009Bilbao_ParallelART]]
| Efficient parallelization of ART
|-

| Paper
| [[2011Li_GradientFlow]]
| Regularized 3D Reconstruction by Gradient Flow
|-

| Paper
| [[2011Vonesch_Wavelets]]
| Fast wavelet-based 3D reconstruction
|-

| Paper
| [[2012Gopinath_ShapeRegularization]]
| Regularized 3D Reconstruction by Shape information
|-

| Paper
| [[2012Kucukelbir_adaptiveBasis]]
| 3D reconstruction in an adaptive basis promoting sparsity
|-

| Paper
| [[2012Sindelar_NoiseReduction]]
| Optimal noise reduction in 3D reconstructions
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Lyumkis_Optimod]]
| Construction of initial volumes with Optimod
|-

| Paper
| [[2013Wang FIRM]]
| Fast 3D reconstruction in Fourier domain
|-

| Paper
| [[2014Kunz_SART_OS]]
| Simultaneous ART with OS
|-

| Paper
| [[2015Abrishami_Fourier]]
| 3D Reconstruction in Fourier space
|-

| Paper
| [[2015Dvornek_SubspaceEM]]
| Fast Maximum a posteriori
|-

| Paper
| [[2015Moriya_Bayesian]]
| Bayesian approach to suppress limited angular artifacts
|-

| Paper
| [[2015Xu_GeometricFlow]]
| Multi-scale geometric flow
|-

| Arxiv
| [[2016Ye_Cohomology]]
| Cohomology properties of 3D reconstruction
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

|}

=== 3D Heterogeneity ===

{|

| Paper
| [[2004White_Size]]
| Heterogeneity classification of differently sized images
|-

| Paper
| [[2006Penczek_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Scheres_ML3D]]
| Maximum Likelihood alignment and classification in 3D
|-

| Paper
| [[2009Spahn_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2010Elmlund_AbInitio]]
| Solving the initial volume problem with multiple conformations
|-

| Paper
| [[2010Shatsky_MultiVariate]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2012Scheres_Bayesian]]
| A Bayesian view on cryo-EM structure determination
|-

| Paper
| [[2012Zheng_Covariance]]
| Estimation of the volume covariance
|-

| Paper
| [[2013Wang_MLVariance]]
| Maximum Likelihood estimate of the map variance
|-

| Paper
| [[2013Lyumkis D_FREALIGN]]
| Likelihood-based classification of cryo-EM images using FREALIGN.
|-

| Paper
| [[2014Jin_NMA]]
| Continuous heterogeneity through Normal Mode Analysis
|-

| Paper
| [[2014Dashti_Brownian]]
| Continuous heterogeneity through Brownian trajectories
|-

| Paper
| [[2014Chen_Migration]]
| Particle migration analysis in 3D classification
|-

| Paper
| [[2015Anden_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Bai_Focused]]
| Focused classification
|-

| Paper
| [[2015Katsevich_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Klaholz_MRA]]
| Multivariate Statistical Analysis of Jackknife and Bootstrapping on random subsets
|-

| Paper
| [[2015Liao_Covariance]]
| Estimation of the 3D covariance from 2D projections
|-

| Paper
| [[2015Tagare_Direct]]
| Direct reconstruction of PCA components
|-

| Paper
| [[2016Gong_Mechanical]]
| Mechanical model for macromolecules
|-

| Paper
| [[2016Rawson_Movement]]
| Movement and flexibility
|-

| Paper
| [[2016Sorzano_StructMap]]
| Sorting a discrete set of conformational states
|-

| Paper
| [[2016Sorzano_Strain]]
| Calculate local stretches, strains and rotations from two conformational states
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

|}

=== Validation ===

{|

| Paper
| [[2008Stagg_TestBed]]
| Effect of voltage, dosis, number of particles and Euler jumps on resolution
|-

| Paper
| [[2011Henderson]]
| Tilt Validation
|-

| Paper
| [[2011Read]]
| Validation of PDBs
|-

| Paper
| [[2012Henderson]]
| EM Map Validation
|-

| Paper
| [[2013Cossio_Bayesian]]
| EM Map Validation in a probabilistic setting
|-

| Paper
| [[2013Chen_NoiseSubstitution]]
| Noise substitution at high resolution for measuring overfitting
|-

| Paper
| [[2014Russo_StatisticalSignificance]]
| EM Map Validation through the statistical significance of the tilt-pair angular assignment
|-

| Paper
| [[2014Stagg_Reslog]]
| EM Map Validation through the resolution evolution with the number of particles
|-

| Paper
| [[2014Wasilewski_Tilt]]
| Web implementation of the tilt pair validation
|-

| Paper
| [[2015Heymann_Alignability]]
| EM Map Validation through the resolution of reconstructions from particles and noise
|-

| Paper
| [[2015Oliveira_FreqLimited]]
| Comparison of gold standard and frequency limited optimization
|-

| Paper
| [[2015Wriggers_Secondary]]
| Validation by secondary structure
|-

| Paper
| [[2016Kim_SAXS]]
| Comparison of SAXS data and EM projections
|-

| Paper
| [[2016Rosenthal_Review]]
| Review of validation methods
|-

| Paper
| [[2016Vargas_Alignability]]
| Validation by studying the tendency of an angular assignment to cluster in the projection space
|-

| Paper
| [[2017Monroe_PDBRefinement]]
| Validation by comparison to a refined PDB
|-

|}

=== Resolution ===

{|

| Paper
| [[1986Harauz_FBP]]
| Fourier Shell Correlation
|-

| Paper
| [[1987Unser_SSNR]]
| 2D Spectral Signal to Noise Ratio
|-

| Paper
| [[2002Penczek_SSNR]]
| 3D Spectral Signal to Noise Ratio for Fourier based algorithms
|-

| Paper
| [[2003Rosenthal_DPR]]
| Review of the FSC and establishment of a new threshold
|-

| Paper
| [[2005Unser_SSNR]]
| 3D Spectral Signal to Noise Ratio for any kind of algorithms
|-

| Paper
| [[2005VanHeel_FSC]]
| Establishment of a new threshold for FSC
|-

| Paper
| [[2007Sousa_AbInitio]]
| Resolution measurement on neighbour Fourier voxels
|-

| Paper
| [[2014Kucukelbir_Local]]
| Quantifying the local resolution of cryo-EM density maps
|-

| Paper
| [[2016Pintilie_Probabilistic]]
| Probabilistic models and resolution
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Statistical properties of resolution measures defined in Fourier space
|-

|}

=== Sharpening of high resolution information ===
{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast restoration and map sharpening
|-

| Paper
| [[2008Fernandez_Bfactor]]
| Bfactor determination and restoration
|-

| Paper
| [[2013Fiddy_SaxtonAlgorithm]]
| Phase retrieval or extension
|-

| Paper
| [[2014Kishchenko_SphericalDeconvolution]]
| Spherical deconvolution
|-

| Paper
| [[2015Spiegel_VISDEM]]
| Visualization improvement by the use of pseudoatomic profiles
|-

| Paper
| [[2016Jonic_Pseudoatoms]]
| Approximation with pseudoatoms
|-

| Paper
| [[2016Jonic_Denoising]]
| Denoising and high-frequency boosting by pseudoatom approximation
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[1982Schiske_Correction]]
| CTF correction for tilted objects
|-

| Paper
| [[1988Toyoshima_Model]]
| CTF estimation
|-

| Paper
| [[1995Frank_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1996Skoglund_MaxEnt]]
| CTF correction with Maximum Entropy
|-

| Paper
| [[1996Zhou_Model]]
| CTF model and user interface for manual fitting
|-

| Paper
| [[1997Fernandez_AR]]
| PSD estimation using periodogram averaging and AR models
|-

| Paper
| [[1997Penczek_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1997Stark_Deconvolution]]
| CTF correction using deconvolution
|-

| Paper
| [[1997Zhu_RecCTF]]
| CTF correction and reconstruction
|-

| Paper
| [[2000DeRosier_EwaldCorrection]]
| CTF correction considering the Ewald sphere
|-

| Paper
| [[2000Jensen_TiltedCorrection]]
| CTF correction considering tilt in backprojection
|-

| Paper
| [[2001Saad_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Huang_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Mindell_CTFTILT]]
| CTF estimation for tilted micrographs
|-

| Paper
| [[2003Sander_MSA]]
| CTF estimation through MSA classification of PSDs
|-

| Paper
| [[2003Velazquez_ARMA]]
| PSD and CTF estimation using ARMA models
|-

| Paper
| [[2004Sorzano_IDR]]
| CTF restoration and reconstruction with Iterative Data Refinement
|-

| Conference
| [[2004Wan_CTF]]
| Spatially variant CTF
|-

| Paper
| [[2004Zubelli_Chahine]]
| CTF restoration and reconstruction with Chahine's multiplicative method
|-

| Conference
| [[2005Dubowy_SpaceVariant]]
| CTF correction when this is space variant
|-

| Paper
| [[2005Mallick_ACE]]
| CTF estimation
|-

| Paper
| [[2006Wolf_Ewald]]
| CTF correction considering Ewald sphere
|-

| Paper
| [[2007Jonic_EnhancedPSD]]
| PSD enhancement for better identification of Thon rings; Vitreous ice diffracts in Thon rings
|-

| Paper
| [[2007Philippsen_Model]]
| CTF Model for tilted specimens
|-

| Paper
| [[2007Sorzano_CTF]]
| CTF estimation using enhanced PSDs
|-

| Paper
| [[2009Sorzano_Sensitivity]]
| Error sensitivity of the CTF models, non-uniqueness of the CTF parameters
|-

| Paper
| [[2010Jiang2010_CTFCorrection]]
| Amplitude correction method
|-

| Paper
| [[2010Kasantsev_CTFCorrection]]
| Mathematical foundations of Kornberg and Jensen method
|-

| Paper
| [[2010Leong_CTFCorrection]]
| Correction for spatially variant CTF
|-

| Paper
| [[2011Glaeser_Coma]]
| The effect of coma at high-resolution
|-

| Paper
| [[2011Mariani_Tilted]]
| CTF simulation and correction of tilted specimens
|-

| Paper
| [[2011Sindelar_Wiener]]
| CTF correction using a modified version of Wiener filter
|-

| Paper
| [[2011Voortman_Tilted]]
| CTF correction for tilted specimen
|-

| Paper
| [[2012Voortman_VaryingCTF]]
| Correcting a spatially varying CTF
|-

| Paper
| [[2013Vargas_FastDef]]
| Fast defocus
|-

| Paper
| [[2015Rohou_CTFFind4]]
| CTF Find 4
|-

| Paper
| [[2015Sheth_CTFquality]]
| Visualization and quality assessment of CTF
|-

| Paper
| [[2016Zhang_GCTF]]
| gCTF
|-

|}

=== Segmentation ===

{|

| Paper
| [[2006Baker_segmentation]]
| Segmentation of molecular subunits
|-

|}

=== Fitting and docking ===

{|

| Paper
| [[1999Volkmann_Fitting]]
| Fitting in real space
|-

| Paper
| [[2001Baker_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2001Jones_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2003Kovacs_FRM3D]]
| Fast Rotational Alignment of two EM maps
|-

| Paper
| [[2004Tama_NMA1]]
| Flexible fitting with Normal Modes (I)
|-

| Paper
| [[2004Tama_NMA2]]
| Flexible fitting with Normal Modes (II)
|-

| Paper
| [[2005Velazquez_Superfamilies]]
| Recognition of the superfamily folding in medium-high resolution volumes
|-

| Paper
| [[2007DeVries_Haddock]]
| Docking with Haddock 2.0
|-

| Paper
| [[2007Kleywegt_QualityControl]]
| Quality control and validation of fitting
|-

| Paper
| [[2012Biswas_Secondary]]
| Secondary structure determination in EM volumes
|-

| Paper
| [[2012Velazquez_Constraints]]
| Multicomponent fitting by using constraints from other information sources
|-

| Paper
| [[2013Chapman MS_Atomicmodeling]]
| Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters
|-

| Paper
| [[2013Esquivel_Modelling]]
| Review on modelling (secondary structure, fitting, ...)
|-

| Paper
| [[2013Lopez_Imodfit]]
| Fitting based on vibrational analysis
|-

| Paper
| [[2013Nogales_3DEMLoupe]]
| Normal Mode Analysis of reconstructed volumes
|-

| Paper
| [[2014AlNasr_Secondary]]
| Identification of secondary structure elements in EM volumes
|-

| Paper
| [[2014Politis_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Rey_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Villa_Review]]
| Review of atomic fitting into EM volumes
|-

| Paper
| [[2015Barad_EMRinger]]
| Validation of hybrid models
|-

| Paper
| [[2015Bettadapura_PF2Fit]]
| Fast rigid fitting of PDBs into EM maps
|-

| Paper
| [[2015Carrillo_CapsidMaps]]
| Analysis of virus capsids using Google Maps
|-

| Paper
| [[2015Schroeder_Hybrid]]
| Review on model building
|-

| Paper
| [[2015Tamo_Dynamics]]
| Dynamics in integrative modeling
|-

| Paper
| [[2015Sorzano_AtomsToVoxels]]
| Accurate conversion of an atomic model into a voxel density volume
|-

| Paper
| [[2016Joseph_Evolution]]
| Evolutionary constraints for the fitting of atomic models into density maps
|-

| Paper
| [[2016Segura_3Diana]]
| Validation of hybrid models
|-

| Paper
| [[2016Singharoy_MDFF]]
| Construction of hybrid models driven by EM density and molecular dynamics
|-

| Paper
| [[2016Wang_Rosetta]]
| Construction of hybrid models driven by EM density using Rosetta
|-

| Paper
| [[2017Hryc_WeightedAtoms]]
| Construction of hybrid models by locally weighting the different atoms
|-

| Paper
| [[2017Matsumoto_Distribution]]
| Estimating the distribution of conformations of atomic models
|-

| Paper
| [[2017Miyashita_EnsembleFitting]]
| Ensemble fitting using Molecular Dynamics
|-

|}

=== Books and reviews ===

{|

| Book
| [[1980Herman_Tomography]]
| General book on tomography
|-

| Book
| [[1988Kak_Tomography]]
| General book on tomography
|-

| Paper
| [[2000Tao_Review]]
| Review of single particles
|-

| Paper
| [[2000VanHeel_Review]]
| Review of single particles
|-

| Paper
| [[2002Frank_Review]]
| Review of single particles
|-

| Paper
| [[2002Schmid_Review]]
| Review of single particles
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2004Subramaniam_Review]]
| Review of single particles
|-

| Paper
| [[2005Steven_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_book]]
| Book covering all aspects of electron microscopy of single particles
|-

| Paper
| [[2006Sorzano_Review]]
| Review of optimization problems in electron microscopy
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems in Electron Tomography
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2008Mueller_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2008Taylor_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2010DeRosier_Review]]
| Personal account of how 3DEM developed in the early days
|-

| Chapter
| [[2012Sorzano_Review]]
| Review of single particle analysis using Xmipp
|-

| Chapter
| [[2012Devaux_Protocol]]
| Protocols for performing single particle analysis
|-

| Paper
| [[2014Bai_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Carazo_Review]]
| Review of the reconstruction process
|-

| Paper
| [[2015Cheng_Review]]
| A primer to Single Particle Cryo-EM
|-

| Paper
| [[2015Cheng_Reviewb]]
| Single Particle Cryo-EM at crystallographic resolution
|-

| Paper
| [[2015Elmlund_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Henderson_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Nogales_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Schroeder_Review]]
| Review of advances in the electron microscope
|-

| Paper
| [[2015Wu_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Carroni_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Egelman_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Eisenstein_CryoEM]]
| News feature on the Method of the Year
|-

| Paper
| [[2016FernandezLeiro_Review]]
| Review of EM
|-

| Paper
| [[2016Glaeser_HowGood]]
| How good can cryo-EM become?
|-

| Paper
| [[2016Jonic_PseudoAtoms]]
| Review of the applications of the use of pseudoatoms in EM
|-

| Chapter
| [[2016Mio_Review]]
| Overview of the process to obtain EM reconstructions
|-

| Paper
| [[2016Jonic_Review]]
| A review of computational ways to handle heterogeneity
|-

| Paper
| [[2016Nogales_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Subramaniam_Review]]
| Why cryo-EM is now suitable for crystallographic journals
|-

| Paper
| [[2016Vinothkumar_Review]]
| Historical review and current limitations
|-

| Paper
| [[2017Frank_Review]]
| Historical review of EM
|-

| Paper
| [[2017Jonic_Review]]
| Review of computational methods to analyze conformational variability
|-

| Paper
| [[2017Rawson_Limitations]]
| Limitations of EM for drug design
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Review of statistical properties of resolution measures defined in Fourier space
|-
|}

=== Software ===

{|

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[1999Lutdke_Eman]]
| Eman
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Baldwin_AngularTransformations]]
| The Transform Class in SPARX and EMAN2
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Grigorieff_Frealign]]
| Frealign
|-

| Paper
| [[2008Scheres_XmippProtocols]]
| Xmipp Protocols
|-

| Paper
| [[2008Shaikh_SpiderProtocols]]
| Spider Protocols
|-

| Paper
| [[2012Wriggers_SitusConventions]]
| Conventions and workflows in Situs
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2015Cianfrocco_Cloud]]
| Software execution in the cloud
|-

| Paper
| [[2015Cheng_MRC2014]]
| Extensions to MRC file format
|-

| Paper
| [[2013DeLaRosa_Scipion]]
| Scipion
|-

| Paper
| [[2016Scheres_Relion]]
| Tutorial on the use of Relion
|-

| Paper
| [[2016Grigorieff_Frealign]]
| Tutorial on the use of Frealign
|-

|}

== Electron tomography ==

=== Image preprocessing ===

{|

| Paper
| [[2015Yan_thickness]]
| Determination of thickness, tilt and electron mean free path
|-

|}

=== Image alignment ===

{|

| Paper
| [[1982Guckenberger_commonOrigin]]
| Determination of a common origin in the micrographs of titl series in three-dimensional electron microscopy
|-

| Paper
| [[1992Lawrence_leastSquares]]
| Least squares solution of the alignment problem
|-

| Paper
| [[1995Penczek_dual]]
| Dual tilt alignment
|-

| Paper
| [[1996Owen_alignmentQuality]]
| Automatic alignment without fiducial markers and evaluation of alignment quality
|-

| Paper
| [[1998Grimm_normalization]]
| Discussion of several gray level normalization methods for electron tomography
|-

| Paper
| [[2001Brandt_Automatic1]]
| Automatic alignment without fiducial markers
|-

| Paper
| [[2001Brandt_Automatic2]]
| Automatic alignment with fiducial markers
|-

| Paper
| [[2006Winkler_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2006Castano_alignment]]
| Alignment with non-perpendicularity
|-

| Paper
| [[2007Castano_alignment]]
| Fiducial-less alignment of cryo-sections
|-

| Paper
| [[2009Sorzano_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2010Cantele_dualAlignment]]
| Alignment of dual series
|-

| Paper
| [[2014Tomonaga_Automatic]]
| Automatic alignment of tilt series using the projection themselves
|-

| Paper
| [[2014Han_Automatic]]
| Automatic alignment of tilt series using SIFT features
|-

| Paper
| [[2015Han_Automatic]]
| Automatic alignment of tilt series using fiducials
|-

| Paper
| [[2017Mastronarde_Automatic]]
| Automatic alignment and reconstruction of tilt series in IMOD
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[2003Winkler_CTF]]
| Focus gradient correction in electron tomography
|-

| Paper
| [[2006Fernandez_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Zanetti_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Xiong_CTF]]
| CTF determination and correction for low dose tomographic tilt series
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2017Kunz_3DCTF]]
| 3D CTF Correction
|-

|}

=== 3D reconstruction ===

{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1992Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[1997Marabini_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2002Fernandez_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2007Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[2008Fernandez_CARP]]
| Component Averaged Row Projections (CARP)
|-

| Paper
| [[2012Herman General Superiorization]]
| Superiorization: an optimization heuristic for medical physics
|-

| Paper
| [[2012Zhang_IPET_FETR]]
| IPET and FETR, a reconstruction algorithm for single molecule tomography
|-

| Paper
| [[2013Goris_SIRT_TV_DART]]
| Combination of SIRT, Total Variation and Discrete ART to reconstruct and segment at the same time
|-

| Paper
| [[2013Briegel A_Challenge]]
| The challenge of determining handedness in electron tomography and the use of DNA origami gold nanoparticle helices as molecular standards
|-

| Paper
| [[2013Messaoudi_EnergyFiltered]]
| 3D Reconstruction of Energy-Filtered TEM
|-

| Paper
| [[2016Deng_ICON]]
| 3D Reconstruction with missing information restoration
|-

| Paper
| [[2016Guay_Compressed]]
| 3D Reconstruction using compressed sensing
|-

|}

=== Noise reduction ===
{|

| Paper
| [[2001Frangakis_NAD]]
| Noise reduction with Nonlinear Anisotropic Diffusion
|-

| Paper
| [[2003Fernandez_AND]]
| Anisotropic nonlinear diffusion for electron tomography
|-

| Paper
| [[2003Jiang_Bilateral]]
| Bilateral denoising filter in electron microscopy
|-

| Paper
| [[2005Fernandez_AND]]
| Anisotropic nonlinear denoising in electron tomography
|-

| Paper
| [[2007Heide_median]]
| Iterative median filtering in electron tomography
|-

| Paper
| [[2007Fernandez_autAND]]
| Anisotropic nonlinear diffusion with automated parameter tuning
|-

| Paper
| [[2009Fernandez_Beltrami]]
| Nonlinear filtering based on Beltrami flow
|-

| Paper
| [[2010Bilbao_MeanShift]]
| Mean Shift Filtering
|-

| Paper
| [[2014Kovacik_wedgeArtefacts]]
| Removal of wedge artefacts
|-

| Paper
| [[2014Maiorca_beadArtefacts]]
| Removal of gold bead artefacts
|-

|}

=== Segmentation ===

{|

| Paper
| [[2002Frangakis_Eigenanalysis]]
| Segmentation using eigenvector analysis.
|-

| Paper
| [[2002Volkmann_Watershed]]
| Segmentation using watershed transform.
|-

| Paper
| [[2003Bajaj_BoundarySegmentation]]
| Segmentation based on fast marching.
|-

| Paper
| [[2005Cyrklaff_Thresholding]]
| Segmentation using optimal thresholding.
|-

| Paper
| [[2007Lebbink_TemplateMatching]]
| Segmentation using template matching.
|-

| Paper
| [[2007Sandberg_OrientationFields]]
| Segmentation using orientation fields.
|-

| Paper
| [[2007Sandberg_SegmentationReview]]
| Review on segmentation in electron tomography.
|-

| Paper
| [[2008Garduno_FuzzySegmentation]]
| Segmentation using fuzzy set theory principles.
|-

| Paper
| [[2009Lebbink_TemplateMatching2]]
| Segmentation using template matching.
|-

| Paper
| [[2012RubbiyaAli_EdgeDetection]]
| Parameter-Free Segmentation of Macromolecular Structures.
|-

| Conference
| [[2015Xu_TemplateMatching]]
| Detection of macromolecular complexes with a reduced representation of the templates.
|-

|}

=== Resolution ===
{|

| Paper
| [[2005Cardone_Resolution]]
| Resolution criterion for electron tomography
|-

| Chapter
| [[2007Penczek_Resolution]]
| Review of resolution criteria for electron tomography
|-

| Paper
| [[2015Diebolder_ConicalFSC]]
| Conical Fourier Shell Correlation
|-

|}

=== Subtomogram analysis ===

{|

| Paper
| [[2000Bohm_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2002Frangakis_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2006Nickell_Review]]
| Review of macromolecule finding by template matching (Visual Proteomics)
|-

| Paper
| [[2007Best_Review]]
| Review of Localization of Protein Complexes by Pattern Recognition
|-

| Paper
| [[2007Forster_Review]]
| Review of structure determination by subtomogram averaging
|-

| Paper
| [[2008Forster_Classification]]
| Classification of subtomograms using constrained correlation
|-

| Paper
| [[2008Bartesaghi_Classification]]
| Classification and averaging of subtomograms
|-

| Paper
| [[2008Schmid_Averaging]]
| Alignment and averaging of subtomograms
|-

| Paper
| [[2010Amat_Averaging]]
| Alignment and averaging of subtomograms exploiting thresholding in Fourier space
|-

| Paper
| [[2013Chen_Averaging]]
| Fast alignment of subtomograms using spherical harmonics
|-

| Paper
| [[2013Kuybeda_Averaging]]
| Alignment and averaging of subtomograms using the nuclear norm of the cluster
|-

| Paper
| [[2013Shatsky_Averaging]]
| Alignment and averaging of subtomograms with constrained cross-correlation
|-

| Paper
| [[2014Chen_Autofocus]]
| Subtomogram averaging and classification with special attention to differences
|-

| Paper
| [[2014Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2014Voortman_LimitingFactors]]
| Limiting factors of subtomogram averaging
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2015Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2016Bharat_Relion]]
| Subtomogram averaging with Relion
|-

| Paper
| [[2016Song_MatrixNorm]]
| Matrix norm minimization for tomographic reconstruction and alignment
|-

| Paper
| [[2017Castano_ParticlePicking]]
| Particle picking in tomograms for subtomogram averaging
|-

|}

=== Single particle tomography ===

{|

| Paper
| [[2012Bartesaghi_Constrained]]
| 3D reconstruction by imposing geometrical constraints
|-

| Paper
| [[2015Galaz_SingleParticleTomography]]
| Set of tools for Single Particle Tomography in EMAN2
|-

| Paper
| [[2016Galaz_SingleParticleTomography]]
| Alignment algorithms and CTF correction
|-

|}

=== Books and reviews ===

{|

| Paper
| [[2000Baumeister_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Koster_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Sali_Review]]
| Review of electron tomography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2005Lucic_Review]]
| Review of electron tomography
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_TomoBook]]
| Electron Tomography
|-

| Book
| [[2007McIntosh_Book]]
| Cellular Electron Microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2012Kudryashev_Review]]
| Review of subtomogram averaging
|-

| Paper
| [[2016Beck_Review]]
| Review of molecular sociology
|-

|}

=== Software ===

{|

| Paper
| [[1996Kremer_IMOD]]
| IMOD
|-

| Paper
| [[1996Chen_Priism/IVE]]
| Priism/IVE
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2005Nickell_TOM]]
| TOM Toolbox
|-

| Paper
| [[2007Messaoudi_TomoJ]]
| TomoJ
|-

| Paper
| [[2008Heymann_BsoftTomo]]
| Bsoft
|-

| Paper
| [[2015Ding_CaltechTomography]]
| Caltech tomography database
|-

| Paper
| [[2015Noble_AppionProtomo]]
| Batch fiducial-less tilt-series alignment in Appion using Protomo
|-

| Paper
| [[2015vanAarle_Astra]]
| ASTRA Toolbox
|-

| Paper
| [[2017Wan_Simulator]]
| Electron Tomography Simulator
|-

|}

== 2D Crystals ==

=== 2D Preprocessing ===

{|

| Paper
| [[1986Henderson_Processing]]
| General 2D processing
|-

| Paper
| [[2000He_PhaseAlignment]]
| Phase consistency and Alignment
|-

| Paper
| [[2006Gil_Unbending]]
| Crystal unbending
|-

|}

=== Classification ===
{|

| Paper
| [[1988Frank_Classification]]
| MSA and classification in electron crystallography
|-

| Paper
| [[1996Fernandez_SOM]]
| Classification based on self organizing maps
|-

| Paper
| [[1998Sherman_MSA]]
| Classification based on MSA
|-

|}
=== 3D Reconstruction ===

{|

| Paper
| [[1985Wang_Solvent]]
| Solvent flattening
|-

| Paper
| [[1990Henderson_Processing]]
| General 3D processing
|-

| Paper
| [[2004Marabini_ART]]
| Algebraic Reconstruction Technique with blobs for crystals (Xmipp)
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1998Walz_Review]]
| Review of 2D crystallography
|-

| Paper
| [[1999Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Ellis_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of single particles, electron tomography and crystallography
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Gipson_2dx]]
| 2dx
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Philippsen_IPLT]]
| IPLT
|-

|}

== 3D Crystals - MicroED ==

=== Sample Preparation ===
{|
| Paper
| [[2016Shi_Preparation]]
| Sample Preparation
|}
=== Data Collection ===
{|
| Paper
| [[2014Nannenga_CR]]
| Continuous rotation

|}
=== Data Processing ===
{|

| Paper
| [[2011Wisedchaisri_PhaseExtension]]
| Fragment-based phase extension
|-

| Paper
| [[2015Hattne_Processing]]
| Data Processing
|-

| Paper
| [[2016Hattne_Correction]]
| Image correction
|}

=== Software ===
{|

| Paper
| [[2014Iadanza_Processing]]
| Data Processing of still diffraction data
|}

=== Books and Reviews ===
{|
| Paper
| [[2014Nannenga_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Liu_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Rodriguez_Review ]]
| Review of MicroED
|-

|}

== Helical particles ==

=== Filament corrections ===

{|

| Paper
| [[1986Egelman_Curved]]
| Algorithm for correcting curved filaments
|-

| Paper
| [[1988Bluemke_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2006Wang_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2016Yang_Flexible]]
| Algorithm for correcting filaments with flexible subunits
|-

|}

=== Reconstruction ===

{|

| Paper
| [[1952Cochran_Fourier]]
| Fourier Bessel transform of filamentous structures
|-

| Paper
| [[1958Klug_Fourier]]
| Fourier Bessel decomposition of the projection images
|-

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2005Wang_Iterative]]
| Iterative Fourier-Bessel algorithm
|-

| Paper
| [[2007Egelman_Iterative]]
| Iterative real-space algorithm
|-

| Paper
| [[2013Desfosses_Spring]]
| Helical processing with Spring
|-

| Paper
| [[2015Zhang_seam]]
| Workflow for the detection of the lattice seam
|-

| Paper
| [[2016Rohou_Frealix]]
| Helical processing with Frealix
|-

|}

=== Validation ===

{|

| Paper
| [[2014Egelman_ambiguity]]
| How to detect incorrect models
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Carragher_Phoelix]]
| Phoelix
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Owen_Brandeis]]
| Brandeis
|-

|}

== Icosahedral particles ==

=== Reconstruction ===

{|

| Paper
| [[1970Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1971Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1996Fuller_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1997Thuman_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

|}

=== Classification ===

{|

| Paper
| [[2005Scheres_Virus]]
| Classification of virus capsids in real space
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1999Baker_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[1999Conway_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2000Thuman_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Lee_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Navaza_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2006Grunewald_Review]]
| Review of reconstruction of icosahedral viruses
|-

|}

=== Software ===

{|

| Paper
| [[1996Baker_EMPFT]]
| EMPFT
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2013Morin_Sliz SBGrid]]
| SBGrid presentation for eLife
|-

|}

== Databases ==

{|

| Paper
| [[2003Boutselakis_EMSD]]
| EMSD database
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2011Kim_CDDB]]
| Conformational Dynamics Data Bank
|-

| Paper
| [[2011Lawson_EMDB]]
| Electron Microscopy Data Bank
|-

| Paper
| [[2013Ison_EDAM]]
| EDAM, an ontology of bioinformatics operations
|-

| Paper
| [[2016Iudin_EMPIAR]]
| EMPIAR raw data database
|-

| Paper
| [[2016Patwhardan_EMDB]]
| EMDB, PDB, ...
|-

| Paper
| [[2017Patwhardan_Trends]]
| Trends at EMDB
|-

| Paper
| [[2017Shao_PDBQuality]]
| Quality metrics in PDB
|-

| Blog
| http://www.mybiosoftware.com
| Huge list of bioinformatics programs (many of them structural bioinformatics)
|-

|}

== Relationship to other structural information sources ==

{|

| Paper
| [[2000Engel_AFM]]
| Review of Atomic Force Microscopy
|-

| Paper
| [[2001Dimmeler_AFM]]
| Constraints from Atomic Force Microscopy
|-

| Paper
| [[2003Mobus_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_Review]]
| Review on correlative microscopy
|-

| Paper
| [[2005Boudier_EFTETJ]]
| Software for Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2005Vestergaard_SAXS]]
| Example of comparison of 3DEM and Small-angle X-ray scattering
|-

| Paper
| [[2007Hamada_SAXS]]
| Constraints from Small-angle X-ray scattering
|-

| Paper
| [[2013Xu_FRET]]
| EM+FRET
|-

|}

== X-ray tomography ==

{|

| Paper
| [[2012Oton_ImageFormation]]
| Image formation model in X-ray cell microscopy
|-

|}

== Mathematical tools necessary ==

== People developing methods ==
Please, add yourself to this list (due to privacy reasons, please, do not add anyone else to the list without his/her explicit consent). Sort by first name alphabetical order.

[http://biocomp.cnb.csic.es/~coss Carlos Oscar S. Sorzano]: CSIC, Madrid, Spain 

[http://www.curie.fr/recherche/themes/detail_equipe.cfm/lang/_fr/id_equipe/241.htm Cédric Messaoudi]: Institute Curie, Paris, France 

[http://scholar.google.es/citations?user=_jNYGScAAAAJ&hl=en Javier Vargas]:[mailto:jvargas@cnb.csic.es mail]: CSIC, Madrid, Spain 

[http://scholar.google.es/citations?hl=es&user=g2ZJPIYAAAAJ Joaquín Otón]: CSIC, Madrid, Spain 

[mailto:jrbcast@gmail.com José Román Bilbao-Castro]: UAL, Almería, Spain; CSIC, Madrid, Spain 

[José Miguel de la Rosa Trevín]: Biocomputing Unit CNB-CSIC, Madrid, Spain 

[http://cryoem.janelia.org Tamir Gonen]: [mailto:gonent@janelia.hhmi.org mail]: Howard Hughes Medical Institute, Ashburn, VA, USA 

[mailto:vabrishami@cnb.csic.es Vahid Abrishami]: CSIC, Madrid, Spain 

== 3DEM sites ==
* [http://3dem.ucsd.edu/ 3DEM web site]

* [http://en.wikibooks.org/wiki/Software_Tools_For_Molecular_Microscopy Software tools for molecular microscopy]

* [http://www.emdatabank.org/ The Electron Microscopy Data Bank (EMDB)]

* [http://ccdb.ucsd.edu The Cell Centered Database (CCDB)]

* [http://conventions.cnb.csic.es The geometrical software conventions web page ]

== Editing useful links ==

* [http://www.mediawiki.org/wiki/Help:Formatting Text formatting in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Links Adding links in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Images Adding images in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Tables Making tables in Mediawiki]

2017Rawson Limitations

2017-05-19T12:57:43Z

CoSS: Created page with "== Citation == Rawson, S.; McPhillie, M.; Johnson, R.; Fishwick, C. & Muench, S. The potential use of single-particle electron microscopy as a tool for structure-based inhibi..."

== Citation ==

Rawson, S.; McPhillie, M.; Johnson, R.; Fishwick, C. & Muench, S. The potential use of single-particle electron microscopy as a tool for structure-based inhibitor design. Acta Crystallographica Section D: Structural Biology, International Union of Crystallography, 2017, 73

== Abstract ==

Recent developments in electron microscopy (EM) have led to a step change in our ability to solve the structures of previously intractable systems, especially membrane proteins and large protein complexes. This has provided new opportunities in the field of structure-based drug design, with a number of high-profile publications resolving the binding sites of small molecules and peptide inhibitors. There are a number of advantages of EM over the more traditional X-ray crystallographic approach, such as resolving different conformational states and permitting the dynamics of a system to be better resolved when not constrained by a crystal lattice. There are still significant challenges to be overcome using an EM approach, not least the speed of structure determination, difficulties with low-occupancy ligands and the modest resolution that is available. However, with the anticipated developments in the field of EM, the potential of EM to become a key tool for structure-based drug design, often complementing X-ray and NMR studies, seems promising.

== Keywords ==

== Links ==

http://journals.iucr.org/d/issues/2017/06/00/id5001/

== Related software ==

== Related methods ==

== Comments ==

Main Page

2017-05-19T12:56:45Z

CoSS: /* Books and reviews */

== Presentation ==

This web page is intended to be an extensive repository of three-dimensional electron microscopy (3DEM) methods. The advantages of having such a repository are

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== Electron microscopy images ==

=== Online courses ===

CALTECH: http://cryo-em-course.caltech.edu/

MRC: ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/EM-course/

CNB-CSIC: http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/MadridJan2014EM

Workshop on Computational methods for CryoEM: https://www.youtube.com/watch?v=XdKO1iaPP8o

Workshop on Management of large CryoEM facilities: https://www.youtube.com/watch?v=as4seOPszL0

Icknield Course on Model Building and Refinement for High Resolution EM Maps: http://www.ccpem.ac.uk/training/icknield_2017/icknield_2017.php

=== Image formation ===

{|

| Paper
| [[1971Erickson_CTF]]
| CTF model
|-

| Paper
| [[1971Glaeser_Damage]]
| Radiation damage
|-

| Chapter
| [[1971Hanszen_CTF]]
| Image formation model
|-

| Paper
| [[1971Thon_Model]]
| CTF model
|-

| Paper
| [[1975Unwin_Imaging]]
| Radiation dose
|-

| Paper
| [[1977Wade_Model]]
| CTF model
|-

| Paper
| [[1978Wade_Model]]
| CTF model
|-

| Paper
| [[1979Hayward_Radiation]]
| Radiation damage
|-

| Paper
| [[1984Cohen_Validity]]
| Validity of the CTF model at high frequencies
|-

| Paper
| [[1988Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[1992Wade_Model]]
| CTF model
|-

| Paper
| [[1993Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2004Egerton_Damage]]
| Radiation damage
|-

| Paper
| [[2004Sorzano_Normalization]]
| Background noise is Gaussian
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2009Baxter_NoiseCharacterization]]
| Characterization of the different noise sources in cryo-EM
|-

| Paper
| [[2010Baker_Damage]]
| Radiation damage dependence on resolution
|-

| Paper
| [[2010Bammes_Damage]]
| Radiation damage dependence on temperature
|-

| Paper
| [[2010Gomez_Multislice]]
| Simulation of the multi slice model
|-

| Paper
| [[2010Zewail_FourDimensional]]
| Review on the use of ultrafast EM
|-

| Paper
| [[2011Bammes_CCD]]
| Performance of CCD cameras
|-

| Paper
| [[2011Glaeser_Coma]]
| Image formation model including coma
|-

| Paper
| [[2011Milazzo_DirectDetectors]]
| Evaluation of Direct Detectors
|-

| Paper
| [[2011Rullgard_ImageSimulation]]
| Accurate simulation of EM images
|-

| Paper
| [[2011Zhang LimitingFactors]]
| Limiting factor for atomic resolution in EM
|-

| Paper
| [[2012Bammes_DirectDetection]]
| Performance of Direct detectors
|-

| Paper
| [[2012Campbell_MotionCorrection]]
| Beam induced motion correction and direct detectors
|-

| Paper
| [[2012Shang_HydrationLayer]]
| Simulation of PDB volumes explicitly considering the hydration layer
|-

| Paper
| [[2013Egerton_RadiationDamage]]
| Review of TEM radiation damage and experimental ways of reducing it
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu H_Noisemodels]]
| Noise models and cryo-EM drift correction with a direct-electron camera
|-

| Paper
| [[2013Li X K2 noisemodels]]
| Influence of electron dose rate on electron counting images recorded with the K2 camera
|-

| Paper
| [[2013Vulovic_CTFApproximations]]
| When to use the different approximations performed so that a projection with linear CTF is valid
|-

| Thesis
| [[2013Vulovic_ImageFormation]]
| Ph.D. Thesis on the image formation in cryo-EM
|-

| Paper
| [[2014Danev_PhasePlate]]
| Volta potential phase plate
|-

| Paper
| [[2015Chiu_K2]]
| Characterization of K2
|-

| Paper
| [[2015Hawkes_AberrationCorrection]]
| Historical account of the development of lens corrections
|-

| Paper
| [[2015Koeck_Quadratic]]
| Limitations of the linear approximation and use of the quadratic terms
|-

| Paper
| [[2015Kuijper_FEI]]
| Description of the FEI Falcons
|-

| Paper
| [[2015Lobato_MULTEM]]
| Simulation of multislice diffraction
|-

| Paper
| [[2015McMullan_AmorphousIce]]
| Beam induced movement is caused by Brownian motion
|-

| Paper
| [[2016Koeck_ADF]]
| Simulations of Annular Dark Field TEM
|-

| Paper
| [[2017Mishyna_DNARadiation]]
| Review of radiation damage on DNA
|-

|}

=== Collection geometry ===

{|

| Chapter
| [[1980Hoppe_Wedge]]
| Missing wedge
|-

| Paper
| [[1987Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1995Penczek_Dual]]
| Dual axis tomography
|-

| Paper
| [[1997Mastronarde_Dual]]
| Dual axis tomography
|-

| Paper
| [[2003Ludtke_FocusPairs]]
| Focus pairs for single particles
|-

| Paper
| [[2005Lanzavecchia_Conical]]
| Conical tomography
|-

| Paper
| [[2005Zampighi_Conical]]
| Conical tomography
|-

| Paper
| [[2006Leschziner_OT]]
| Orthogonal Tilt
|-

| Paper
| [[2006Messaoudi_Multiple]]
| Multiple axis tomography
|-

| Paper
| [[2012Kudryashev_FocusPairs]]
| Focus pairs tomography
|-

| Paper
| [[2014Hovden_TiltFocus]]
| Combining tilt series with focus series
|-

| Paper
| [[2015Sorzano_RandomConicalTilt]]
| General formulation of Random Conical Tilt
|-

| Paper
| [[2017Hagen_DoseTomography]]
| Dose optimization for subtomogram averaging
|-

|}

=== Sample preparation ===

{|

| Paper
| [[1982Dubochet_Sample]]
| Vitreous ice
|-

| Paper
| [[1986Lepault_Sample]]
| Fast freezing
|-

| Paper
| [[1995Dubochet_Sample]]
| High-pressure freezing
|-

| Paper
| [[1995VanMarle_Sample]]
| Sample damages in resin
|-

| Paper
| [[1998Adrian_Sample]]
| Cryo negative staining
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2002Hsieh_Sample]]
| Cryofixation
|-

| Paper
| [[2004AlAmoudi_Sample]]
| CEMOVIS
|-

| Paper
| [[2008Studer_Sample]]
| Review on high pressure freezing
|-

| Paper
| [[2009Pierson_Sample]]
| Review on sample preparation for electron tomography
|-

| Paper
| [[2010Zhang_NegativeStaining]]
| Negative staining for small protein imaging
|-

| Paper
| [[2012Zhang_PositiveStaining]]
| Positive staining
|-

| Paper
| [[2014Rames_NegativeStaining]]
| Optimized negative staining
|-

| Paper
| [[2014Russo_GoldGrids]]
| Gold grids for single particles
|-

| Paper
| [[2015Cabra_Sample]]
| Review on sample preparation for single particles with videos
|-

| Paper
| [[2016Passmore_Review]]
| Tutorial chapter on sample preparation
|-

| Paper
| [[2016Razinkov_Vitrification]]
| New vitrification method
|-

| Paper
| [[2016Takizawa_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2016Thompson_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2017Arnold_BlottingFree]]
| Blotting-free preparation
|-

| Paper
| [[2017Feng_SprayingPlunging]]
| Spraying plunging
|-

| Paper
| [[2017Peitsch_Sample]]
| iMEM: Isolation of Plasma Membrane for Cryoelectron Microscopy
|-

| Paper
| [[2017Schaffer_FocusedIonBeam]]
| Focused Ion Beam sample preparation for membrane proteins
|-

|}

=== Automated data collection ===

{|

| Paper
| [[1992Dierksen_Automatic]]
| Automated data collection
|-

| Paper
| [[1992Koster_Automatic]]
| Automated data collection
|-

| Paper
| [[1996Fung_Automatic]]
| Automated data collection for tomography
|-

| Paper
| [[2001Zhang_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2003Ziese_Automatic]]
| Automated autofocusing
|-

| Paper
| [[2004Potter_Automatic]]
| Automated sample loading
|-

| Paper
| [[2004Zheng_Automatic]]
| Automated data collection
|-

| Paper
| [[2005Lei_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2005Suloway_Automatic]]
| Automated data collection: Leginon
|-

| Paper
| [[2007Yoshioka_RCT]]
| Automated Random Conical Tilt
|-

| Paper
| [[2011Korinek_TOM2]]
| Automated acquisition with TOM2
|-

| Paper
| [[2015Li_UCSFImage]]
| Automated acquisition with UCSFImage
|-

| Paper
| [[2016Gil_Fuzzy]]
| Real time decisions during acquisition with neuro-fuzzy method
|-

| Paper
| [[2016Liu_TiltControl]]
| Accurate control of the tilt angle for electron tomography
|-

| Paper
| [[2016Vargas_FoilHole]]
| Determination of image quality at low magnification
|-

|}

== Single particles ==

=== Automatic particle picking ===

{|

| Paper
| [[1982VanHeel_Detection]]
| Detection of particles in micrographs
|-

| Paper
| [[2001Nicholson_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2001Zhu_Filaments]]
| Automatic identification of filaments in micrographs
|-

| Paper
| [[2004Sigworth_Detection]]
| Classical detection theory and the cryo-EM particle selection problem
|-

| Paper
| [[2004Volkmann_ParticlePicking]]
| An approach to automated particle picking from electron micrographs based on reduced representation templates
|-

| Paper
| [[2004Wong_ParticlePicking]]
| Model-based particle picking for cryo-electron microscopy
|-

| Paper
| [[2004Zhu_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2007Chen_Signature]]
| Automatic particle picking program: Signature
|-

| Paper
| [[2007Woolford_SwarmPS]]
| Automatic particle picking with several criteria, implemented in EMAN Boxer
|-

| Paper
| [[2009Sorzano_MachineLearning]]
| Automatic particle picking based on machine learning of rotational invariants
|-

| Paper
| [[2011Arbelaez_Comparison]]
| Evaluation of the performance of software for automated particle-boxing
|-

| Paper
| [[2013Abrishami_MachineLearning]]
| A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs
|-

| Paper
| [[2013Hauer_2013]]
| Automatic tilt pair detection in Random Conical Tilt
|-

| Paper
| [[2013Shatsky_ParticlePicking]]
| Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Langlois_ParticlePicking]]
| Automatic particle picking
|-

| Paper
| [[2016Vilas_AutomaticTilt]]
| Automatic identification of image pairs in untilted-tilted micrograph pairs
|-

|}

=== 2D Preprocessing ===

{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast enhancement through DPR
|-

| Paper
| [[2004Sorzano_Normalization]]
| Normalization procedures and their statistical properties.
|-

| Paper
| [[2006Sorzano_Denoising]]
| Strong denoising in wavelet space
|-

| Conference
| [[2009Sorzano_Downsampling]]
| Differences between the different downsampling schemes
|-

| Paper
| [[2012Brilot_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Campbell_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Zhao_Denoising]]
| Denoising using an invariant Fourier-Bessel eigenspace
|-

| Paper
| [[2013Norousi_Screening]]
| Screening particles to identify outliers
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu_Movies]]
| Drift correction for movies considering dark field
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Scheres_Movies]]
| Beam induced motion correction
|-

| Paper
| [[2015Abrishami_Movies]]
| Alignment of direct detection device micrographs
|-

| Paper
| [[2015Grant_Anisotropic]]
| Automatic estimation and correction of anisotropic magnification
|-

| Paper
| [[2015Grant_OptimalExposure]]
| Filter movies according to the radiation damage
|-

| Paper
| [[2015Rubinstein_Alignment]]
| Frame alignment at the level of particle
|-

| Paper
| [[2015Spear_DoseCompensation]]
| Effect of dose compensation on resolution
|-

| Paper
| [[2015Zhao_AnisotropicMagnification]]
| Correction of anisotropic magnification
|-

| Conference
| [[2016Bajic_Denoising]]
| Denoising and deconvolution of micrographs
|-

| Paper
| [[2016Jensen_RemovalVesicles]]
| Removal of vesicles in membrane proteins
|-

| Paper
| [[2016Bhamre_Denoising]]
| Denoising by 2D covariance estimation
|-

| Paper
| [[2017McLeod_Zorro]]
| Movie alignment by Zorro
|-

| Paper
| [[2017Zheng_MotionCorr2]]
| Movie alignment by MotionCorr2
|-

|}

=== 2D Alignment ===

{|

| Paper
| [[1981Frank_Averaging]]
| 2D averaging and phase residual
|-

| Paper
| [[1982Saxton_Averaging]]
| 2D averaging using correlation
|-

| Paper
| [[1998Sigworth_ML2D]]
| Maximum likelihood alignment in 2D
|-

| Paper
| [[2003Cong_FRM2D]]
| Fast Rotational Matching in 2D
|-

| Paper
| [[2005Cong_FRM2D]]
| Fast Rotational Matching in 2D introduced in a 3D Alignment algorithm
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

|}

=== 2D Classification and clustering ===

{|

| Paper
| [[1981VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[1984VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2011Singer_DiffusionMaps]]
| Classification in 2D based on graph analysis of the projections
|-

| Paper
| [[2012Yang_ISAC]]
| Iterative Stable Alignment and clustering
|-

| Paper
| [[2014Sorzano_Outlier]]
| Outlier detection in 2D classifications.
|-

| Paper
| [[2014Zhao_Aspire]]
| Fast classification based on rotational invariants and vector diffusion maps
|-

| Paper
| [[2015Huang_Robust]]
| Robust w-estimators of 2D classes
|-

| Paper
| [[2016Reboul_Stochastic]]
| Stochastic Hill Climbing for calculating 2D classes
|-

| Conference
| [[2017Bhamre_Mahalanobis]]
| 2D classification using Mahalanobis distance
|-

|}

=== 3D Alignment ===

{|

| Paper
| [[1980Kam_AutoCorrelation]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[1986Goncharov_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1987VanHeel_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1988Provencher_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Vogel_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1990Gelfand_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Goncharov_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Harauz_Quaternions]]
| Use of quaternions to represent rotations
|-

| Paper
| [[1994Penczek_Real]]
| Angular assignment using projection matching in real space
|-

| Paper
| [[1994Radermacher_Radon]]
| Angular assignment in Radon space
|-

| Paper
| [[1996Penczek_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[2003Rosenthal_DPR]]
| Angular assignment using DPR
|-

| Paper
| [[2004Sorzano_Wavelet]]
| Angular assignment in the wavelet space.
|-

| Paper
| [[2005Jonic_Splines]]
| Angular assignment in Fourier space using spline interpolation.
|-

| Paper
| [[2005Yang_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[2006Ogura_SimulatedAnnealing]]
| Angular asignment by simulated annealing
|-

| Paper
| [[2007Grigorieff_Continuous]]
| Continuous angular assignment in Fourier space
|-

| Paper
| [[2010Jaitly_Bayesian]]
| Angular assignment by a Bayesian method and annealing
|-

| Paper
| [[2010Sanz_Random]]
| Random model method
|-

| Paper
| [[2010Singer_Voting]]
| Detecting consistent common lines by voting (reference free)
|-

| Paper
| [[2011Singer_SDP]]
| Angular assignment by semidefinite programming and eigenvectors (reference free)
|-

| Paper
| [[2012Giannakis_Scattering]]
| Construction of an initial volume, reference free, by graph analysis of the projections
|-

| Paper
| [[2012Shkolnisky_Sync]]
| Angular assignment by synchronization of rotations (reference free)
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Wang_LUD]]
| Angular assignment by least unsquared deviations (reference free)
|-

| Paper
| [[2014Vargas_RANSAC]]
| Initial model using RANSAC (reference free)
|-

| Paper
| [[2015Joubert_Pseudoatoms]]
| Initial model based on pseudo-atoms
|-

| Paper
| [[2015Singer_Kam]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[2015Sorzano_Significant]]
| Statistical approach to the initial volume estimation (reconstruct significant)
|-

| Conference
| [[2016Michels_Heterogeneous]]
| Initial volume in the presence of heterogeneity
|-

| Paper
| [[2016Cossio_BayesianGPU]]
| GPU implementation of the Bayesian 3D reconstruction approach
|-

|}

=== 3D Reconstruction ===
{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1986Harauz_FBP]]
| Exact filters for Filtered Back Projection
|-

| Chapter
| [[1992Radermacher_WBP]]
| Exact filters for Weighted Back Projection
|-

| Paper
| [[1997Zhu_RecCTF]]
| 3D Reconstruction (SIRT like) and simultaneous CTF correction
|-

| Paper
| [[1998Boisset_Uneven]]
| Artifacts in SIRT and WBP under uneven angular distributions
|-

| Paper
| [[1998Marabini_ART]]
| Algebraic Reconstruction Technique with blobs (Xmipp)
|-

| Paper
| [[2001Sorzano_Uneven]]
| Free parameter selection under uneven angular distributions
|-

| Paper
| [[2005Sorzano_Parameters]]
| Free parameter selection for optimizing multiple tasks
|-

| Paper
| [[2008Sorzano_Constraints]]
| Mass, surface, positivity and symmetry constraints for real-space algorithms
|-

| Paper
| [[2009Bilbao_ParallelART]]
| Efficient parallelization of ART
|-

| Paper
| [[2011Li_GradientFlow]]
| Regularized 3D Reconstruction by Gradient Flow
|-

| Paper
| [[2011Vonesch_Wavelets]]
| Fast wavelet-based 3D reconstruction
|-

| Paper
| [[2012Gopinath_ShapeRegularization]]
| Regularized 3D Reconstruction by Shape information
|-

| Paper
| [[2012Kucukelbir_adaptiveBasis]]
| 3D reconstruction in an adaptive basis promoting sparsity
|-

| Paper
| [[2012Sindelar_NoiseReduction]]
| Optimal noise reduction in 3D reconstructions
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Lyumkis_Optimod]]
| Construction of initial volumes with Optimod
|-

| Paper
| [[2013Wang FIRM]]
| Fast 3D reconstruction in Fourier domain
|-

| Paper
| [[2014Kunz_SART_OS]]
| Simultaneous ART with OS
|-

| Paper
| [[2015Abrishami_Fourier]]
| 3D Reconstruction in Fourier space
|-

| Paper
| [[2015Dvornek_SubspaceEM]]
| Fast Maximum a posteriori
|-

| Paper
| [[2015Moriya_Bayesian]]
| Bayesian approach to suppress limited angular artifacts
|-

| Paper
| [[2015Xu_GeometricFlow]]
| Multi-scale geometric flow
|-

| Arxiv
| [[2016Ye_Cohomology]]
| Cohomology properties of 3D reconstruction
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

|}

=== 3D Heterogeneity ===

{|

| Paper
| [[2004White_Size]]
| Heterogeneity classification of differently sized images
|-

| Paper
| [[2006Penczek_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Scheres_ML3D]]
| Maximum Likelihood alignment and classification in 3D
|-

| Paper
| [[2009Spahn_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2010Elmlund_AbInitio]]
| Solving the initial volume problem with multiple conformations
|-

| Paper
| [[2010Shatsky_MultiVariate]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2012Scheres_Bayesian]]
| A Bayesian view on cryo-EM structure determination
|-

| Paper
| [[2012Zheng_Covariance]]
| Estimation of the volume covariance
|-

| Paper
| [[2013Wang_MLVariance]]
| Maximum Likelihood estimate of the map variance
|-

| Paper
| [[2013Lyumkis D_FREALIGN]]
| Likelihood-based classification of cryo-EM images using FREALIGN.
|-

| Paper
| [[2014Jin_NMA]]
| Continuous heterogeneity through Normal Mode Analysis
|-

| Paper
| [[2014Dashti_Brownian]]
| Continuous heterogeneity through Brownian trajectories
|-

| Paper
| [[2014Chen_Migration]]
| Particle migration analysis in 3D classification
|-

| Paper
| [[2015Anden_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Bai_Focused]]
| Focused classification
|-

| Paper
| [[2015Katsevich_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Klaholz_MRA]]
| Multivariate Statistical Analysis of Jackknife and Bootstrapping on random subsets
|-

| Paper
| [[2015Liao_Covariance]]
| Estimation of the 3D covariance from 2D projections
|-

| Paper
| [[2015Tagare_Direct]]
| Direct reconstruction of PCA components
|-

| Paper
| [[2016Gong_Mechanical]]
| Mechanical model for macromolecules
|-

| Paper
| [[2016Rawson_Movement]]
| Movement and flexibility
|-

| Paper
| [[2016Sorzano_StructMap]]
| Sorting a discrete set of conformational states
|-

| Paper
| [[2016Sorzano_Strain]]
| Calculate local stretches, strains and rotations from two conformational states
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

|}

=== Validation ===

{|

| Paper
| [[2008Stagg_TestBed]]
| Effect of voltage, dosis, number of particles and Euler jumps on resolution
|-

| Paper
| [[2011Henderson]]
| Tilt Validation
|-

| Paper
| [[2011Read]]
| Validation of PDBs
|-

| Paper
| [[2012Henderson]]
| EM Map Validation
|-

| Paper
| [[2013Cossio_Bayesian]]
| EM Map Validation in a probabilistic setting
|-

| Paper
| [[2013Chen_NoiseSubstitution]]
| Noise substitution at high resolution for measuring overfitting
|-

| Paper
| [[2014Russo_StatisticalSignificance]]
| EM Map Validation through the statistical significance of the tilt-pair angular assignment
|-

| Paper
| [[2014Stagg_Reslog]]
| EM Map Validation through the resolution evolution with the number of particles
|-

| Paper
| [[2014Wasilewski_Tilt]]
| Web implementation of the tilt pair validation
|-

| Paper
| [[2015Heymann_Alignability]]
| EM Map Validation through the resolution of reconstructions from particles and noise
|-

| Paper
| [[2015Oliveira_FreqLimited]]
| Comparison of gold standard and frequency limited optimization
|-

| Paper
| [[2015Wriggers_Secondary]]
| Validation by secondary structure
|-

| Paper
| [[2016Kim_SAXS]]
| Comparison of SAXS data and EM projections
|-

| Paper
| [[2016Rosenthal_Review]]
| Review of validation methods
|-

| Paper
| [[2016Vargas_Alignability]]
| Validation by studying the tendency of an angular assignment to cluster in the projection space
|-

| Paper
| [[2017Monroe_PDBRefinement]]
| Validation by comparison to a refined PDB
|-

|}

=== Resolution ===

{|

| Paper
| [[1986Harauz_FBP]]
| Fourier Shell Correlation
|-

| Paper
| [[1987Unser_SSNR]]
| 2D Spectral Signal to Noise Ratio
|-

| Paper
| [[2002Penczek_SSNR]]
| 3D Spectral Signal to Noise Ratio for Fourier based algorithms
|-

| Paper
| [[2003Rosenthal_DPR]]
| Review of the FSC and establishment of a new threshold
|-

| Paper
| [[2005Unser_SSNR]]
| 3D Spectral Signal to Noise Ratio for any kind of algorithms
|-

| Paper
| [[2005VanHeel_FSC]]
| Establishment of a new threshold for FSC
|-

| Paper
| [[2007Sousa_AbInitio]]
| Resolution measurement on neighbour Fourier voxels
|-

| Paper
| [[2014Kucukelbir_Local]]
| Quantifying the local resolution of cryo-EM density maps
|-

| Paper
| [[2016Pintilie_Probabilistic]]
| Probabilistic models and resolution
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Statistical properties of resolution measures defined in Fourier space
|-

|}

=== Sharpening of high resolution information ===
{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast restoration and map sharpening
|-

| Paper
| [[2008Fernandez_Bfactor]]
| Bfactor determination and restoration
|-

| Paper
| [[2013Fiddy_SaxtonAlgorithm]]
| Phase retrieval or extension
|-

| Paper
| [[2014Kishchenko_SphericalDeconvolution]]
| Spherical deconvolution
|-

| Paper
| [[2015Spiegel_VISDEM]]
| Visualization improvement by the use of pseudoatomic profiles
|-

| Paper
| [[2016Jonic_Pseudoatoms]]
| Approximation with pseudoatoms
|-

| Paper
| [[2016Jonic_Denoising]]
| Denoising and high-frequency boosting by pseudoatom approximation
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[1982Schiske_Correction]]
| CTF correction for tilted objects
|-

| Paper
| [[1988Toyoshima_Model]]
| CTF estimation
|-

| Paper
| [[1995Frank_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1996Skoglund_MaxEnt]]
| CTF correction with Maximum Entropy
|-

| Paper
| [[1996Zhou_Model]]
| CTF model and user interface for manual fitting
|-

| Paper
| [[1997Fernandez_AR]]
| PSD estimation using periodogram averaging and AR models
|-

| Paper
| [[1997Penczek_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1997Stark_Deconvolution]]
| CTF correction using deconvolution
|-

| Paper
| [[1997Zhu_RecCTF]]
| CTF correction and reconstruction
|-

| Paper
| [[2000DeRosier_EwaldCorrection]]
| CTF correction considering the Ewald sphere
|-

| Paper
| [[2000Jensen_TiltedCorrection]]
| CTF correction considering tilt in backprojection
|-

| Paper
| [[2001Saad_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Huang_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Mindell_CTFTILT]]
| CTF estimation for tilted micrographs
|-

| Paper
| [[2003Sander_MSA]]
| CTF estimation through MSA classification of PSDs
|-

| Paper
| [[2003Velazquez_ARMA]]
| PSD and CTF estimation using ARMA models
|-

| Paper
| [[2004Sorzano_IDR]]
| CTF restoration and reconstruction with Iterative Data Refinement
|-

| Conference
| [[2004Wan_CTF]]
| Spatially variant CTF
|-

| Paper
| [[2004Zubelli_Chahine]]
| CTF restoration and reconstruction with Chahine's multiplicative method
|-

| Conference
| [[2005Dubowy_SpaceVariant]]
| CTF correction when this is space variant
|-

| Paper
| [[2005Mallick_ACE]]
| CTF estimation
|-

| Paper
| [[2006Wolf_Ewald]]
| CTF correction considering Ewald sphere
|-

| Paper
| [[2007Jonic_EnhancedPSD]]
| PSD enhancement for better identification of Thon rings; Vitreous ice diffracts in Thon rings
|-

| Paper
| [[2007Philippsen_Model]]
| CTF Model for tilted specimens
|-

| Paper
| [[2007Sorzano_CTF]]
| CTF estimation using enhanced PSDs
|-

| Paper
| [[2009Sorzano_Sensitivity]]
| Error sensitivity of the CTF models, non-uniqueness of the CTF parameters
|-

| Paper
| [[2010Jiang2010_CTFCorrection]]
| Amplitude correction method
|-

| Paper
| [[2010Kasantsev_CTFCorrection]]
| Mathematical foundations of Kornberg and Jensen method
|-

| Paper
| [[2010Leong_CTFCorrection]]
| Correction for spatially variant CTF
|-

| Paper
| [[2011Glaeser_Coma]]
| The effect of coma at high-resolution
|-

| Paper
| [[2011Mariani_Tilted]]
| CTF simulation and correction of tilted specimens
|-

| Paper
| [[2011Sindelar_Wiener]]
| CTF correction using a modified version of Wiener filter
|-

| Paper
| [[2011Voortman_Tilted]]
| CTF correction for tilted specimen
|-

| Paper
| [[2012Voortman_VaryingCTF]]
| Correcting a spatially varying CTF
|-

| Paper
| [[2013Vargas_FastDef]]
| Fast defocus
|-

| Paper
| [[2015Rohou_CTFFind4]]
| CTF Find 4
|-

| Paper
| [[2015Sheth_CTFquality]]
| Visualization and quality assessment of CTF
|-

| Paper
| [[2016Zhang_GCTF]]
| gCTF
|-

|}

=== Segmentation ===

{|

| Paper
| [[2006Baker_segmentation]]
| Segmentation of molecular subunits
|-

|}

=== Fitting and docking ===

{|

| Paper
| [[1999Volkmann_Fitting]]
| Fitting in real space
|-

| Paper
| [[2001Baker_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2001Jones_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2003Kovacs_FRM3D]]
| Fast Rotational Alignment of two EM maps
|-

| Paper
| [[2004Tama_NMA1]]
| Flexible fitting with Normal Modes (I)
|-

| Paper
| [[2004Tama_NMA2]]
| Flexible fitting with Normal Modes (II)
|-

| Paper
| [[2005Velazquez_Superfamilies]]
| Recognition of the superfamily folding in medium-high resolution volumes
|-

| Paper
| [[2007DeVries_Haddock]]
| Docking with Haddock 2.0
|-

| Paper
| [[2007Kleywegt_QualityControl]]
| Quality control and validation of fitting
|-

| Paper
| [[2012Biswas_Secondary]]
| Secondary structure determination in EM volumes
|-

| Paper
| [[2012Velazquez_Constraints]]
| Multicomponent fitting by using constraints from other information sources
|-

| Paper
| [[2013Chapman MS_Atomicmodeling]]
| Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters
|-

| Paper
| [[2013Esquivel_Modelling]]
| Review on modelling (secondary structure, fitting, ...)
|-

| Paper
| [[2013Lopez_Imodfit]]
| Fitting based on vibrational analysis
|-

| Paper
| [[2013Nogales_3DEMLoupe]]
| Normal Mode Analysis of reconstructed volumes
|-

| Paper
| [[2014AlNasr_Secondary]]
| Identification of secondary structure elements in EM volumes
|-

| Paper
| [[2014Politis_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Rey_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Villa_Review]]
| Review of atomic fitting into EM volumes
|-

| Paper
| [[2015Barad_EMRinger]]
| Validation of hybrid models
|-

| Paper
| [[2015Bettadapura_PF2Fit]]
| Fast rigid fitting of PDBs into EM maps
|-

| Paper
| [[2015Carrillo_CapsidMaps]]
| Analysis of virus capsids using Google Maps
|-

| Paper
| [[2015Schroeder_Hybrid]]
| Review on model building
|-

| Paper
| [[2015Tamo_Dynamics]]
| Dynamics in integrative modeling
|-

| Paper
| [[2015Sorzano_AtomsToVoxels]]
| Accurate conversion of an atomic model into a voxel density volume
|-

| Paper
| [[2016Joseph_Evolution]]
| Evolutionary constraints for the fitting of atomic models into density maps
|-

| Paper
| [[2016Segura_3Diana]]
| Validation of hybrid models
|-

| Paper
| [[2016Singharoy_MDFF]]
| Construction of hybrid models driven by EM density and molecular dynamics
|-

| Paper
| [[2016Wang_Rosetta]]
| Construction of hybrid models driven by EM density using Rosetta
|-

| Paper
| [[2017Hryc_WeightedAtoms]]
| Construction of hybrid models by locally weighting the different atoms
|-

| Paper
| [[2017Matsumoto_Distribution]]
| Estimating the distribution of conformations of atomic models
|-

| Paper
| [[2017Miyashita_EnsembleFitting]]
| Ensemble fitting using Molecular Dynamics
|-

|}

=== Books and reviews ===

{|

| Book
| [[1980Herman_Tomography]]
| General book on tomography
|-

| Book
| [[1988Kak_Tomography]]
| General book on tomography
|-

| Paper
| [[2000Tao_Review]]
| Review of single particles
|-

| Paper
| [[2000VanHeel_Review]]
| Review of single particles
|-

| Paper
| [[2002Frank_Review]]
| Review of single particles
|-

| Paper
| [[2002Schmid_Review]]
| Review of single particles
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2004Subramaniam_Review]]
| Review of single particles
|-

| Paper
| [[2005Steven_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_book]]
| Book covering all aspects of electron microscopy of single particles
|-

| Paper
| [[2006Sorzano_Review]]
| Review of optimization problems in electron microscopy
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems in Electron Tomography
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2008Mueller_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2008Taylor_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2010DeRosier_Review]]
| Personal account of how 3DEM developed in the early days
|-

| Chapter
| [[2012Sorzano_Review]]
| Review of single particle analysis using Xmipp
|-

| Chapter
| [[2012Devaux_Protocol]]
| Protocols for performing single particle analysis
|-

| Paper
| [[2014Bai_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Carazo_Review]]
| Review of the reconstruction process
|-

| Paper
| [[2015Cheng_Review]]
| A primer to Single Particle Cryo-EM
|-

| Paper
| [[2015Cheng_Reviewb]]
| Single Particle Cryo-EM at crystallographic resolution
|-

| Paper
| [[2015Elmlund_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Henderson_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Nogales_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Schroeder_Review]]
| Review of advances in the electron microscope
|-

| Paper
| [[2015Wu_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Carroni_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Egelman_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Eisenstein_CryoEM]]
| News feature on the Method of the Year
|-

| Paper
| [[2016FernandezLeiro_Review]]
| Review of EM
|-

| Paper
| [[2016Glaeser_HowGood]]
| How good can cryo-EM become?
|-

| Paper
| [[2016Jonic_PseudoAtoms]]
| Review of the applications of the use of pseudoatoms in EM
|-

| Chapter
| [[2016Mio_Review]]
| Overview of the process to obtain EM reconstructions
|-

| Paper
| [[2016Jonic_Review]]
| A review of computational ways to handle heterogeneity
|-

| Paper
| [[2016Nogales_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Subramaniam_Review]]
| Why cryo-EM is now suitable for crystallographic journals
|-

| Paper
| [[2016Vinothkumar_Review]]
| Historical review and current limitations
|-

| Paper
| [[2017Frank_Review]]
| Historical review of EM
|-

| Paper
| [[2017Jonic_Review]]
| Review of computational methods to analyze conformational variability
|-

| Paper
| [[2017Rawson_Limitations]]
| Limitations of EM for drug design
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Review of statistical properties of resolution measures defined in Fourier space
|-
|}

=== Software ===

{|

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[1999Lutdke_Eman]]
| Eman
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Baldwin_AngularTransformations]]
| The Transform Class in SPARX and EMAN2
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Grigorieff_Frealign]]
| Frealign
|-

| Paper
| [[2008Scheres_XmippProtocols]]
| Xmipp Protocols
|-

| Paper
| [[2008Shaikh_SpiderProtocols]]
| Spider Protocols
|-

| Paper
| [[2012Wriggers_SitusConventions]]
| Conventions and workflows in Situs
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2015Cianfrocco_Cloud]]
| Software execution in the cloud
|-

| Paper
| [[2015Cheng_MRC2014]]
| Extensions to MRC file format
|-

| Paper
| [[2013DeLaRosa_Scipion]]
| Scipion
|-

| Paper
| [[2016Scheres_Relion]]
| Tutorial on the use of Relion
|-

| Paper
| [[2016Grigorieff_Frealign]]
| Tutorial on the use of Frealign
|-

|}

== Electron tomography ==

=== Image preprocessing ===

{|

| Paper
| [[2015Yan_thickness]]
| Determination of thickness, tilt and electron mean free path
|-

|}

=== Image alignment ===

{|

| Paper
| [[1982Guckenberger_commonOrigin]]
| Determination of a common origin in the micrographs of titl series in three-dimensional electron microscopy
|-

| Paper
| [[1992Lawrence_leastSquares]]
| Least squares solution of the alignment problem
|-

| Paper
| [[1995Penczek_dual]]
| Dual tilt alignment
|-

| Paper
| [[1996Owen_alignmentQuality]]
| Automatic alignment without fiducial markers and evaluation of alignment quality
|-

| Paper
| [[1998Grimm_normalization]]
| Discussion of several gray level normalization methods for electron tomography
|-

| Paper
| [[2001Brandt_Automatic1]]
| Automatic alignment without fiducial markers
|-

| Paper
| [[2001Brandt_Automatic2]]
| Automatic alignment with fiducial markers
|-

| Paper
| [[2006Winkler_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2006Castano_alignment]]
| Alignment with non-perpendicularity
|-

| Paper
| [[2007Castano_alignment]]
| Fiducial-less alignment of cryo-sections
|-

| Paper
| [[2009Sorzano_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2010Cantele_dualAlignment]]
| Alignment of dual series
|-

| Paper
| [[2014Tomonaga_Automatic]]
| Automatic alignment of tilt series using the projection themselves
|-

| Paper
| [[2014Han_Automatic]]
| Automatic alignment of tilt series using SIFT features
|-

| Paper
| [[2015Han_Automatic]]
| Automatic alignment of tilt series using fiducials
|-

| Paper
| [[2017Mastronarde_Automatic]]
| Automatic alignment and reconstruction of tilt series in IMOD
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[2003Winkler_CTF]]
| Focus gradient correction in electron tomography
|-

| Paper
| [[2006Fernandez_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Zanetti_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Xiong_CTF]]
| CTF determination and correction for low dose tomographic tilt series
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2017Kunz_3DCTF]]
| 3D CTF Correction
|-

|}

=== 3D reconstruction ===

{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1992Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[1997Marabini_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2002Fernandez_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2007Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[2008Fernandez_CARP]]
| Component Averaged Row Projections (CARP)
|-

| Paper
| [[2012Herman General Superiorization]]
| Superiorization: an optimization heuristic for medical physics
|-

| Paper
| [[2012Zhang_IPET_FETR]]
| IPET and FETR, a reconstruction algorithm for single molecule tomography
|-

| Paper
| [[2013Goris_SIRT_TV_DART]]
| Combination of SIRT, Total Variation and Discrete ART to reconstruct and segment at the same time
|-

| Paper
| [[2013Briegel A_Challenge]]
| The challenge of determining handedness in electron tomography and the use of DNA origami gold nanoparticle helices as molecular standards
|-

| Paper
| [[2013Messaoudi_EnergyFiltered]]
| 3D Reconstruction of Energy-Filtered TEM
|-

| Paper
| [[2016Deng_ICON]]
| 3D Reconstruction with missing information restoration
|-

| Paper
| [[2016Guay_Compressed]]
| 3D Reconstruction using compressed sensing
|-

|}

=== Noise reduction ===
{|

| Paper
| [[2001Frangakis_NAD]]
| Noise reduction with Nonlinear Anisotropic Diffusion
|-

| Paper
| [[2003Fernandez_AND]]
| Anisotropic nonlinear diffusion for electron tomography
|-

| Paper
| [[2003Jiang_Bilateral]]
| Bilateral denoising filter in electron microscopy
|-

| Paper
| [[2005Fernandez_AND]]
| Anisotropic nonlinear denoising in electron tomography
|-

| Paper
| [[2007Heide_median]]
| Iterative median filtering in electron tomography
|-

| Paper
| [[2007Fernandez_autAND]]
| Anisotropic nonlinear diffusion with automated parameter tuning
|-

| Paper
| [[2009Fernandez_Beltrami]]
| Nonlinear filtering based on Beltrami flow
|-

| Paper
| [[2010Bilbao_MeanShift]]
| Mean Shift Filtering
|-

| Paper
| [[2014Kovacik_wedgeArtefacts]]
| Removal of wedge artefacts
|-

| Paper
| [[2014Maiorca_beadArtefacts]]
| Removal of gold bead artefacts
|-

|}

=== Segmentation ===

{|

| Paper
| [[2002Frangakis_Eigenanalysis]]
| Segmentation using eigenvector analysis.
|-

| Paper
| [[2002Volkmann_Watershed]]
| Segmentation using watershed transform.
|-

| Paper
| [[2003Bajaj_BoundarySegmentation]]
| Segmentation based on fast marching.
|-

| Paper
| [[2005Cyrklaff_Thresholding]]
| Segmentation using optimal thresholding.
|-

| Paper
| [[2007Lebbink_TemplateMatching]]
| Segmentation using template matching.
|-

| Paper
| [[2007Sandberg_OrientationFields]]
| Segmentation using orientation fields.
|-

| Paper
| [[2007Sandberg_SegmentationReview]]
| Review on segmentation in electron tomography.
|-

| Paper
| [[2008Garduno_FuzzySegmentation]]
| Segmentation using fuzzy set theory principles.
|-

| Paper
| [[2009Lebbink_TemplateMatching2]]
| Segmentation using template matching.
|-

| Paper
| [[2012RubbiyaAli_EdgeDetection]]
| Parameter-Free Segmentation of Macromolecular Structures.
|-

| Conference
| [[2015Xu_TemplateMatching]]
| Detection of macromolecular complexes with a reduced representation of the templates.
|-

|}

=== Resolution ===
{|

| Paper
| [[2005Cardone_Resolution]]
| Resolution criterion for electron tomography
|-

| Chapter
| [[2007Penczek_Resolution]]
| Review of resolution criteria for electron tomography
|-

| Paper
| [[2015Diebolder_ConicalFSC]]
| Conical Fourier Shell Correlation
|-

|}

=== Subtomogram analysis ===

{|

| Paper
| [[2000Bohm_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2002Frangakis_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2006Nickell_Review]]
| Review of macromolecule finding by template matching (Visual Proteomics)
|-

| Paper
| [[2007Best_Review]]
| Review of Localization of Protein Complexes by Pattern Recognition
|-

| Paper
| [[2007Forster_Review]]
| Review of structure determination by subtomogram averaging
|-

| Paper
| [[2008Forster_Classification]]
| Classification of subtomograms using constrained correlation
|-

| Paper
| [[2008Bartesaghi_Classification]]
| Classification and averaging of subtomograms
|-

| Paper
| [[2008Schmid_Averaging]]
| Alignment and averaging of subtomograms
|-

| Paper
| [[2010Amat_Averaging]]
| Alignment and averaging of subtomograms exploiting thresholding in Fourier space
|-

| Paper
| [[2013Chen_Averaging]]
| Fast alignment of subtomograms using spherical harmonics
|-

| Paper
| [[2013Kuybeda_Averaging]]
| Alignment and averaging of subtomograms using the nuclear norm of the cluster
|-

| Paper
| [[2013Shatsky_Averaging]]
| Alignment and averaging of subtomograms with constrained cross-correlation
|-

| Paper
| [[2014Chen_Autofocus]]
| Subtomogram averaging and classification with special attention to differences
|-

| Paper
| [[2014Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2014Voortman_LimitingFactors]]
| Limiting factors of subtomogram averaging
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2015Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2016Bharat_Relion]]
| Subtomogram averaging with Relion
|-

| Paper
| [[2016Song_MatrixNorm]]
| Matrix norm minimization for tomographic reconstruction and alignment
|-

| Paper
| [[2017Castano_ParticlePicking]]
| Particle picking in tomograms for subtomogram averaging
|-

|}

=== Single particle tomography ===

{|

| Paper
| [[2012Bartesaghi_Constrained]]
| 3D reconstruction by imposing geometrical constraints
|-

| Paper
| [[2015Galaz_SingleParticleTomography]]
| Set of tools for Single Particle Tomography in EMAN2
|-

| Paper
| [[2016Galaz_SingleParticleTomography]]
| Alignment algorithms and CTF correction
|-

|}

=== Books and reviews ===

{|

| Paper
| [[2000Baumeister_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Koster_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Sali_Review]]
| Review of electron tomography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2005Lucic_Review]]
| Review of electron tomography
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_TomoBook]]
| Electron Tomography
|-

| Book
| [[2007McIntosh_Book]]
| Cellular Electron Microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2012Kudryashev_Review]]
| Review of subtomogram averaging
|-

| Paper
| [[2016Beck_Review]]
| Review of molecular sociology
|-

|}

=== Software ===

{|

| Paper
| [[1996Kremer_IMOD]]
| IMOD
|-

| Paper
| [[1996Chen_Priism/IVE]]
| Priism/IVE
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2005Nickell_TOM]]
| TOM Toolbox
|-

| Paper
| [[2007Messaoudi_TomoJ]]
| TomoJ
|-

| Paper
| [[2008Heymann_BsoftTomo]]
| Bsoft
|-

| Paper
| [[2015Ding_CaltechTomography]]
| Caltech tomography database
|-

| Paper
| [[2015Noble_AppionProtomo]]
| Batch fiducial-less tilt-series alignment in Appion using Protomo
|-

| Paper
| [[2015vanAarle_Astra]]
| ASTRA Toolbox
|-

|}

== 2D Crystals ==

=== 2D Preprocessing ===

{|

| Paper
| [[1986Henderson_Processing]]
| General 2D processing
|-

| Paper
| [[2000He_PhaseAlignment]]
| Phase consistency and Alignment
|-

| Paper
| [[2006Gil_Unbending]]
| Crystal unbending
|-

|}

=== Classification ===
{|

| Paper
| [[1988Frank_Classification]]
| MSA and classification in electron crystallography
|-

| Paper
| [[1996Fernandez_SOM]]
| Classification based on self organizing maps
|-

| Paper
| [[1998Sherman_MSA]]
| Classification based on MSA
|-

|}
=== 3D Reconstruction ===

{|

| Paper
| [[1985Wang_Solvent]]
| Solvent flattening
|-

| Paper
| [[1990Henderson_Processing]]
| General 3D processing
|-

| Paper
| [[2004Marabini_ART]]
| Algebraic Reconstruction Technique with blobs for crystals (Xmipp)
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1998Walz_Review]]
| Review of 2D crystallography
|-

| Paper
| [[1999Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Ellis_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of single particles, electron tomography and crystallography
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Gipson_2dx]]
| 2dx
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Philippsen_IPLT]]
| IPLT
|-

|}

== 3D Crystals - MicroED ==

=== Sample Preparation ===
{|
| Paper
| [[2016Shi_Preparation]]
| Sample Preparation
|}
=== Data Collection ===
{|
| Paper
| [[2014Nannenga_CR]]
| Continuous rotation

|}
=== Data Processing ===
{|

| Paper
| [[2011Wisedchaisri_PhaseExtension]]
| Fragment-based phase extension
|-

| Paper
| [[2015Hattne_Processing]]
| Data Processing
|-

| Paper
| [[2016Hattne_Correction]]
| Image correction
|}

=== Software ===
{|

| Paper
| [[2014Iadanza_Processing]]
| Data Processing of still diffraction data
|}

=== Books and Reviews ===
{|
| Paper
| [[2014Nannenga_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Liu_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Rodriguez_Review ]]
| Review of MicroED
|-

|}

== Helical particles ==

=== Filament corrections ===

{|

| Paper
| [[1986Egelman_Curved]]
| Algorithm for correcting curved filaments
|-

| Paper
| [[1988Bluemke_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2006Wang_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2016Yang_Flexible]]
| Algorithm for correcting filaments with flexible subunits
|-

|}

=== Reconstruction ===

{|

| Paper
| [[1952Cochran_Fourier]]
| Fourier Bessel transform of filamentous structures
|-

| Paper
| [[1958Klug_Fourier]]
| Fourier Bessel decomposition of the projection images
|-

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2005Wang_Iterative]]
| Iterative Fourier-Bessel algorithm
|-

| Paper
| [[2007Egelman_Iterative]]
| Iterative real-space algorithm
|-

| Paper
| [[2013Desfosses_Spring]]
| Helical processing with Spring
|-

| Paper
| [[2015Zhang_seam]]
| Workflow for the detection of the lattice seam
|-

| Paper
| [[2016Rohou_Frealix]]
| Helical processing with Frealix
|-

|}

=== Validation ===

{|

| Paper
| [[2014Egelman_ambiguity]]
| How to detect incorrect models
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Carragher_Phoelix]]
| Phoelix
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Owen_Brandeis]]
| Brandeis
|-

|}

== Icosahedral particles ==

=== Reconstruction ===

{|

| Paper
| [[1970Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1971Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1996Fuller_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1997Thuman_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

|}

=== Classification ===

{|

| Paper
| [[2005Scheres_Virus]]
| Classification of virus capsids in real space
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1999Baker_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[1999Conway_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2000Thuman_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Lee_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Navaza_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2006Grunewald_Review]]
| Review of reconstruction of icosahedral viruses
|-

|}

=== Software ===

{|

| Paper
| [[1996Baker_EMPFT]]
| EMPFT
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2013Morin_Sliz SBGrid]]
| SBGrid presentation for eLife
|-

|}

== Databases ==

{|

| Paper
| [[2003Boutselakis_EMSD]]
| EMSD database
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2011Kim_CDDB]]
| Conformational Dynamics Data Bank
|-

| Paper
| [[2011Lawson_EMDB]]
| Electron Microscopy Data Bank
|-

| Paper
| [[2013Ison_EDAM]]
| EDAM, an ontology of bioinformatics operations
|-

| Paper
| [[2016Iudin_EMPIAR]]
| EMPIAR raw data database
|-

| Paper
| [[2016Patwhardan_EMDB]]
| EMDB, PDB, ...
|-

| Paper
| [[2017Patwhardan_Trends]]
| Trends at EMDB
|-

| Paper
| [[2017Shao_PDBQuality]]
| Quality metrics in PDB
|-

| Blog
| http://www.mybiosoftware.com
| Huge list of bioinformatics programs (many of them structural bioinformatics)
|-

|}

== Relationship to other structural information sources ==

{|

| Paper
| [[2000Engel_AFM]]
| Review of Atomic Force Microscopy
|-

| Paper
| [[2001Dimmeler_AFM]]
| Constraints from Atomic Force Microscopy
|-

| Paper
| [[2003Mobus_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_Review]]
| Review on correlative microscopy
|-

| Paper
| [[2005Boudier_EFTETJ]]
| Software for Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2005Vestergaard_SAXS]]
| Example of comparison of 3DEM and Small-angle X-ray scattering
|-

| Paper
| [[2007Hamada_SAXS]]
| Constraints from Small-angle X-ray scattering
|-

| Paper
| [[2013Xu_FRET]]
| EM+FRET
|-

|}

== X-ray tomography ==

{|

| Paper
| [[2012Oton_ImageFormation]]
| Image formation model in X-ray cell microscopy
|-

|}

== Mathematical tools necessary ==

== People developing methods ==
Please, add yourself to this list (due to privacy reasons, please, do not add anyone else to the list without his/her explicit consent). Sort by first name alphabetical order.

[http://biocomp.cnb.csic.es/~coss Carlos Oscar S. Sorzano]: CSIC, Madrid, Spain 

[http://www.curie.fr/recherche/themes/detail_equipe.cfm/lang/_fr/id_equipe/241.htm Cédric Messaoudi]: Institute Curie, Paris, France 

[http://scholar.google.es/citations?user=_jNYGScAAAAJ&hl=en Javier Vargas]:[mailto:jvargas@cnb.csic.es mail]: CSIC, Madrid, Spain 

[http://scholar.google.es/citations?hl=es&user=g2ZJPIYAAAAJ Joaquín Otón]: CSIC, Madrid, Spain 

[mailto:jrbcast@gmail.com José Román Bilbao-Castro]: UAL, Almería, Spain; CSIC, Madrid, Spain 

[José Miguel de la Rosa Trevín]: Biocomputing Unit CNB-CSIC, Madrid, Spain 

[http://cryoem.janelia.org Tamir Gonen]: [mailto:gonent@janelia.hhmi.org mail]: Howard Hughes Medical Institute, Ashburn, VA, USA 

[mailto:vabrishami@cnb.csic.es Vahid Abrishami]: CSIC, Madrid, Spain 

== 3DEM sites ==
* [http://3dem.ucsd.edu/ 3DEM web site]

* [http://en.wikibooks.org/wiki/Software_Tools_For_Molecular_Microscopy Software tools for molecular microscopy]

* [http://www.emdatabank.org/ The Electron Microscopy Data Bank (EMDB)]

* [http://ccdb.ucsd.edu The Cell Centered Database (CCDB)]

* [http://conventions.cnb.csic.es The geometrical software conventions web page ]

== Editing useful links ==

* [http://www.mediawiki.org/wiki/Help:Formatting Text formatting in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Links Adding links in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Images Adding images in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Tables Making tables in Mediawiki]

2017Miyashita EnsembleFitting

2017-05-17T07:54:22Z

CoSS: Created page with "== Citation == Miyashita, O.; Kobayashi, C.; Mori, T.; Sugita, Y. & Tama, F. Flexible fitting to cryo-EM density map using ensemble molecular dynamics simulations. Journal of..."

== Citation ==

Miyashita, O.; Kobayashi, C.; Mori, T.; Sugita, Y. & Tama, F. Flexible fitting to cryo-EM density map using ensemble molecular dynamics simulations. Journal of computational chemistry, 2017, 38, 1447-1461

== Abstract ==

Flexible fitting is a computational algorithm to derive a new conformational model that conforms to low-resolution experimental data by transforming a known structure. A common application is against data from cryo-electron microscopy to obtain conformational models in new functional states. The conventional flexible fitting algorithms cannot derive correct structures in some cases due to the complexity of conformational transitions. In this study, we show the importance of conformational ensemble in the refinement process by performing multiple fittings trials using a variety of different force constants. Application to simulated maps of Ca(2+) ATPase and diphtheria toxin as well as experimental data of release factor 2 revealed that for these systems, multiple conformations with similar agreement with the density map exist and a large number of fitting trials are necessary to generate good models. Clustering analysis can be an effective approach to avoid over-fitting models. In addition, we show that an automatic adjustment of the biasing force constants during the fitting process, implemented as replica-exchange scheme, can improve the success rate.

== Keywords ==

== Links ==

https://www.ncbi.nlm.nih.gov/pubmed/28370077

== Related software ==

== Related methods ==

== Comments ==

Main Page

2017-05-17T07:53:33Z

CoSS: /* Fitting and docking */

== Presentation ==

This web page is intended to be an extensive repository of three-dimensional electron microscopy (3DEM) methods. The advantages of having such a repository are

* You know which are the relevant articles in a particular topic, therefore, paper introductions, reviews, etc. are easier to write and you make sure you will cite all the related articles.
* You will be sure that your paper has more chances of being cited.
* You can add whatever information you find relevant to your method, external links, links to other papers, etc.
* You can link your method to a web page providing the corresponding software, so you know people can use your algorithms.
* You can use the Wiki search capabilities to locate relevant articles even if they are not at the topic you are looking at.
* As a community we will "reconstruct" our history.
* You can select the "watch" option above to receive notifications in case of further changes in the Main Page.

Developing image processing methods for 3DEM is not "[[well-paid]]" in terms of citations and impact factor. However, it is crucial for the advance of the field. Gathering methodological papers in a portal will help to increase the recognition of the field.

Please:

* Add your articles at the right place (you can add a single article in several topics if it is relevant to all of them). The easiest way to add an article is by editing the corresponding topic in the main page, adding your entry, then save the main page. Click on the red link that appears on your new entry, copy and paste the Wiki following code, add the information of your article

== Citation ==

== Abstract ==

== Keywords ==

== Links ==

== Related software ==

== Related methods ==

== Comments ==

* Maintain the information of each article as complete as possible.
* Sort articles by years and authors.
* Be respectful to other people's work.

== How to subscribe to this page ==

You may subscribe to this page so that you will be notified every time someone adds a new method. To do so, you have to register in the page, and edit your preferences ("my preferences"). Be sure that you have activated the option "E-mail me when a page on my watchlist is changed". Finally, click on the "Watch" tab at the top of this page.

You may subscribe to changes on this page on the mailing list 3demmethods@cnb.csic.es. To send a new method to this mail list just send a mail to 3demmethods@cnb.csic.es

To subscribe to this list, visit the web page

https://listas.csic.es/cnb/wws/subscribe/3demmethods

Alternatively, you may write a mail to sympa6@cnb.csic.es with the subject

<code>subscribe 3demmethods YourName YourFamilyName</code>

and an empty mail body.

To unsubscribe visit the page

https://listas.csic.es/cnb/wws/sigrequest/3demmethods

or write sympa6@cnb.csic.es with the subject

<code>unsubscribe 3demmethods</code>

and an empty mail body.

== Electron microscopy images ==

=== Online courses ===

CALTECH: http://cryo-em-course.caltech.edu/

MRC: ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/EM-course/

CNB-CSIC: http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/MadridJan2014EM

Workshop on Computational methods for CryoEM: https://www.youtube.com/watch?v=XdKO1iaPP8o

Workshop on Management of large CryoEM facilities: https://www.youtube.com/watch?v=as4seOPszL0

Icknield Course on Model Building and Refinement for High Resolution EM Maps: http://www.ccpem.ac.uk/training/icknield_2017/icknield_2017.php

=== Image formation ===

{|

| Paper
| [[1971Erickson_CTF]]
| CTF model
|-

| Paper
| [[1971Glaeser_Damage]]
| Radiation damage
|-

| Chapter
| [[1971Hanszen_CTF]]
| Image formation model
|-

| Paper
| [[1971Thon_Model]]
| CTF model
|-

| Paper
| [[1975Unwin_Imaging]]
| Radiation dose
|-

| Paper
| [[1977Wade_Model]]
| CTF model
|-

| Paper
| [[1978Wade_Model]]
| CTF model
|-

| Paper
| [[1979Hayward_Radiation]]
| Radiation damage
|-

| Paper
| [[1984Cohen_Validity]]
| Validity of the CTF model at high frequencies
|-

| Paper
| [[1988Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[1992Wade_Model]]
| CTF model
|-

| Paper
| [[1993Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2004Egerton_Damage]]
| Radiation damage
|-

| Paper
| [[2004Sorzano_Normalization]]
| Background noise is Gaussian
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2009Baxter_NoiseCharacterization]]
| Characterization of the different noise sources in cryo-EM
|-

| Paper
| [[2010Baker_Damage]]
| Radiation damage dependence on resolution
|-

| Paper
| [[2010Bammes_Damage]]
| Radiation damage dependence on temperature
|-

| Paper
| [[2010Gomez_Multislice]]
| Simulation of the multi slice model
|-

| Paper
| [[2010Zewail_FourDimensional]]
| Review on the use of ultrafast EM
|-

| Paper
| [[2011Bammes_CCD]]
| Performance of CCD cameras
|-

| Paper
| [[2011Glaeser_Coma]]
| Image formation model including coma
|-

| Paper
| [[2011Milazzo_DirectDetectors]]
| Evaluation of Direct Detectors
|-

| Paper
| [[2011Rullgard_ImageSimulation]]
| Accurate simulation of EM images
|-

| Paper
| [[2011Zhang LimitingFactors]]
| Limiting factor for atomic resolution in EM
|-

| Paper
| [[2012Bammes_DirectDetection]]
| Performance of Direct detectors
|-

| Paper
| [[2012Campbell_MotionCorrection]]
| Beam induced motion correction and direct detectors
|-

| Paper
| [[2012Shang_HydrationLayer]]
| Simulation of PDB volumes explicitly considering the hydration layer
|-

| Paper
| [[2013Egerton_RadiationDamage]]
| Review of TEM radiation damage and experimental ways of reducing it
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu H_Noisemodels]]
| Noise models and cryo-EM drift correction with a direct-electron camera
|-

| Paper
| [[2013Li X K2 noisemodels]]
| Influence of electron dose rate on electron counting images recorded with the K2 camera
|-

| Paper
| [[2013Vulovic_CTFApproximations]]
| When to use the different approximations performed so that a projection with linear CTF is valid
|-

| Thesis
| [[2013Vulovic_ImageFormation]]
| Ph.D. Thesis on the image formation in cryo-EM
|-

| Paper
| [[2014Danev_PhasePlate]]
| Volta potential phase plate
|-

| Paper
| [[2015Chiu_K2]]
| Characterization of K2
|-

| Paper
| [[2015Hawkes_AberrationCorrection]]
| Historical account of the development of lens corrections
|-

| Paper
| [[2015Koeck_Quadratic]]
| Limitations of the linear approximation and use of the quadratic terms
|-

| Paper
| [[2015Kuijper_FEI]]
| Description of the FEI Falcons
|-

| Paper
| [[2015Lobato_MULTEM]]
| Simulation of multislice diffraction
|-

| Paper
| [[2015McMullan_AmorphousIce]]
| Beam induced movement is caused by Brownian motion
|-

| Paper
| [[2016Koeck_ADF]]
| Simulations of Annular Dark Field TEM
|-

| Paper
| [[2017Mishyna_DNARadiation]]
| Review of radiation damage on DNA
|-

|}

=== Collection geometry ===

{|

| Chapter
| [[1980Hoppe_Wedge]]
| Missing wedge
|-

| Paper
| [[1987Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1995Penczek_Dual]]
| Dual axis tomography
|-

| Paper
| [[1997Mastronarde_Dual]]
| Dual axis tomography
|-

| Paper
| [[2003Ludtke_FocusPairs]]
| Focus pairs for single particles
|-

| Paper
| [[2005Lanzavecchia_Conical]]
| Conical tomography
|-

| Paper
| [[2005Zampighi_Conical]]
| Conical tomography
|-

| Paper
| [[2006Leschziner_OT]]
| Orthogonal Tilt
|-

| Paper
| [[2006Messaoudi_Multiple]]
| Multiple axis tomography
|-

| Paper
| [[2012Kudryashev_FocusPairs]]
| Focus pairs tomography
|-

| Paper
| [[2014Hovden_TiltFocus]]
| Combining tilt series with focus series
|-

| Paper
| [[2015Sorzano_RandomConicalTilt]]
| General formulation of Random Conical Tilt
|-

| Paper
| [[2017Hagen_DoseTomography]]
| Dose optimization for subtomogram averaging
|-

|}

=== Sample preparation ===

{|

| Paper
| [[1982Dubochet_Sample]]
| Vitreous ice
|-

| Paper
| [[1986Lepault_Sample]]
| Fast freezing
|-

| Paper
| [[1995Dubochet_Sample]]
| High-pressure freezing
|-

| Paper
| [[1995VanMarle_Sample]]
| Sample damages in resin
|-

| Paper
| [[1998Adrian_Sample]]
| Cryo negative staining
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2002Hsieh_Sample]]
| Cryofixation
|-

| Paper
| [[2004AlAmoudi_Sample]]
| CEMOVIS
|-

| Paper
| [[2008Studer_Sample]]
| Review on high pressure freezing
|-

| Paper
| [[2009Pierson_Sample]]
| Review on sample preparation for electron tomography
|-

| Paper
| [[2010Zhang_NegativeStaining]]
| Negative staining for small protein imaging
|-

| Paper
| [[2012Zhang_PositiveStaining]]
| Positive staining
|-

| Paper
| [[2014Rames_NegativeStaining]]
| Optimized negative staining
|-

| Paper
| [[2014Russo_GoldGrids]]
| Gold grids for single particles
|-

| Paper
| [[2015Cabra_Sample]]
| Review on sample preparation for single particles with videos
|-

| Paper
| [[2016Passmore_Review]]
| Tutorial chapter on sample preparation
|-

| Paper
| [[2016Razinkov_Vitrification]]
| New vitrification method
|-

| Paper
| [[2016Takizawa_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2016Thompson_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2017Arnold_BlottingFree]]
| Blotting-free preparation
|-

| Paper
| [[2017Feng_SprayingPlunging]]
| Spraying plunging
|-

| Paper
| [[2017Peitsch_Sample]]
| iMEM: Isolation of Plasma Membrane for Cryoelectron Microscopy
|-

| Paper
| [[2017Schaffer_FocusedIonBeam]]
| Focused Ion Beam sample preparation for membrane proteins
|-

|}

=== Automated data collection ===

{|

| Paper
| [[1992Dierksen_Automatic]]
| Automated data collection
|-

| Paper
| [[1992Koster_Automatic]]
| Automated data collection
|-

| Paper
| [[1996Fung_Automatic]]
| Automated data collection for tomography
|-

| Paper
| [[2001Zhang_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2003Ziese_Automatic]]
| Automated autofocusing
|-

| Paper
| [[2004Potter_Automatic]]
| Automated sample loading
|-

| Paper
| [[2004Zheng_Automatic]]
| Automated data collection
|-

| Paper
| [[2005Lei_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2005Suloway_Automatic]]
| Automated data collection: Leginon
|-

| Paper
| [[2007Yoshioka_RCT]]
| Automated Random Conical Tilt
|-

| Paper
| [[2011Korinek_TOM2]]
| Automated acquisition with TOM2
|-

| Paper
| [[2015Li_UCSFImage]]
| Automated acquisition with UCSFImage
|-

| Paper
| [[2016Gil_Fuzzy]]
| Real time decisions during acquisition with neuro-fuzzy method
|-

| Paper
| [[2016Liu_TiltControl]]
| Accurate control of the tilt angle for electron tomography
|-

| Paper
| [[2016Vargas_FoilHole]]
| Determination of image quality at low magnification
|-

|}

== Single particles ==

=== Automatic particle picking ===

{|

| Paper
| [[1982VanHeel_Detection]]
| Detection of particles in micrographs
|-

| Paper
| [[2001Nicholson_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2001Zhu_Filaments]]
| Automatic identification of filaments in micrographs
|-

| Paper
| [[2004Sigworth_Detection]]
| Classical detection theory and the cryo-EM particle selection problem
|-

| Paper
| [[2004Volkmann_ParticlePicking]]
| An approach to automated particle picking from electron micrographs based on reduced representation templates
|-

| Paper
| [[2004Wong_ParticlePicking]]
| Model-based particle picking for cryo-electron microscopy
|-

| Paper
| [[2004Zhu_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2007Chen_Signature]]
| Automatic particle picking program: Signature
|-

| Paper
| [[2007Woolford_SwarmPS]]
| Automatic particle picking with several criteria, implemented in EMAN Boxer
|-

| Paper
| [[2009Sorzano_MachineLearning]]
| Automatic particle picking based on machine learning of rotational invariants
|-

| Paper
| [[2011Arbelaez_Comparison]]
| Evaluation of the performance of software for automated particle-boxing
|-

| Paper
| [[2013Abrishami_MachineLearning]]
| A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs
|-

| Paper
| [[2013Hauer_2013]]
| Automatic tilt pair detection in Random Conical Tilt
|-

| Paper
| [[2013Shatsky_ParticlePicking]]
| Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Langlois_ParticlePicking]]
| Automatic particle picking
|-

| Paper
| [[2016Vilas_AutomaticTilt]]
| Automatic identification of image pairs in untilted-tilted micrograph pairs
|-

|}

=== 2D Preprocessing ===

{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast enhancement through DPR
|-

| Paper
| [[2004Sorzano_Normalization]]
| Normalization procedures and their statistical properties.
|-

| Paper
| [[2006Sorzano_Denoising]]
| Strong denoising in wavelet space
|-

| Conference
| [[2009Sorzano_Downsampling]]
| Differences between the different downsampling schemes
|-

| Paper
| [[2012Brilot_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Campbell_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Zhao_Denoising]]
| Denoising using an invariant Fourier-Bessel eigenspace
|-

| Paper
| [[2013Norousi_Screening]]
| Screening particles to identify outliers
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu_Movies]]
| Drift correction for movies considering dark field
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Scheres_Movies]]
| Beam induced motion correction
|-

| Paper
| [[2015Abrishami_Movies]]
| Alignment of direct detection device micrographs
|-

| Paper
| [[2015Grant_Anisotropic]]
| Automatic estimation and correction of anisotropic magnification
|-

| Paper
| [[2015Grant_OptimalExposure]]
| Filter movies according to the radiation damage
|-

| Paper
| [[2015Rubinstein_Alignment]]
| Frame alignment at the level of particle
|-

| Paper
| [[2015Spear_DoseCompensation]]
| Effect of dose compensation on resolution
|-

| Paper
| [[2015Zhao_AnisotropicMagnification]]
| Correction of anisotropic magnification
|-

| Conference
| [[2016Bajic_Denoising]]
| Denoising and deconvolution of micrographs
|-

| Paper
| [[2016Jensen_RemovalVesicles]]
| Removal of vesicles in membrane proteins
|-

| Paper
| [[2016Bhamre_Denoising]]
| Denoising by 2D covariance estimation
|-

| Paper
| [[2017McLeod_Zorro]]
| Movie alignment by Zorro
|-

| Paper
| [[2017Zheng_MotionCorr2]]
| Movie alignment by MotionCorr2
|-

|}

=== 2D Alignment ===

{|

| Paper
| [[1981Frank_Averaging]]
| 2D averaging and phase residual
|-

| Paper
| [[1982Saxton_Averaging]]
| 2D averaging using correlation
|-

| Paper
| [[1998Sigworth_ML2D]]
| Maximum likelihood alignment in 2D
|-

| Paper
| [[2003Cong_FRM2D]]
| Fast Rotational Matching in 2D
|-

| Paper
| [[2005Cong_FRM2D]]
| Fast Rotational Matching in 2D introduced in a 3D Alignment algorithm
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

|}

=== 2D Classification and clustering ===

{|

| Paper
| [[1981VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[1984VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2011Singer_DiffusionMaps]]
| Classification in 2D based on graph analysis of the projections
|-

| Paper
| [[2012Yang_ISAC]]
| Iterative Stable Alignment and clustering
|-

| Paper
| [[2014Sorzano_Outlier]]
| Outlier detection in 2D classifications.
|-

| Paper
| [[2014Zhao_Aspire]]
| Fast classification based on rotational invariants and vector diffusion maps
|-

| Paper
| [[2015Huang_Robust]]
| Robust w-estimators of 2D classes
|-

| Paper
| [[2016Reboul_Stochastic]]
| Stochastic Hill Climbing for calculating 2D classes
|-

| Conference
| [[2017Bhamre_Mahalanobis]]
| 2D classification using Mahalanobis distance
|-

|}

=== 3D Alignment ===

{|

| Paper
| [[1980Kam_AutoCorrelation]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[1986Goncharov_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1987VanHeel_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1988Provencher_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Vogel_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1990Gelfand_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Goncharov_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Harauz_Quaternions]]
| Use of quaternions to represent rotations
|-

| Paper
| [[1994Penczek_Real]]
| Angular assignment using projection matching in real space
|-

| Paper
| [[1994Radermacher_Radon]]
| Angular assignment in Radon space
|-

| Paper
| [[1996Penczek_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[2003Rosenthal_DPR]]
| Angular assignment using DPR
|-

| Paper
| [[2004Sorzano_Wavelet]]
| Angular assignment in the wavelet space.
|-

| Paper
| [[2005Jonic_Splines]]
| Angular assignment in Fourier space using spline interpolation.
|-

| Paper
| [[2005Yang_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[2006Ogura_SimulatedAnnealing]]
| Angular asignment by simulated annealing
|-

| Paper
| [[2007Grigorieff_Continuous]]
| Continuous angular assignment in Fourier space
|-

| Paper
| [[2010Jaitly_Bayesian]]
| Angular assignment by a Bayesian method and annealing
|-

| Paper
| [[2010Sanz_Random]]
| Random model method
|-

| Paper
| [[2010Singer_Voting]]
| Detecting consistent common lines by voting (reference free)
|-

| Paper
| [[2011Singer_SDP]]
| Angular assignment by semidefinite programming and eigenvectors (reference free)
|-

| Paper
| [[2012Giannakis_Scattering]]
| Construction of an initial volume, reference free, by graph analysis of the projections
|-

| Paper
| [[2012Shkolnisky_Sync]]
| Angular assignment by synchronization of rotations (reference free)
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Wang_LUD]]
| Angular assignment by least unsquared deviations (reference free)
|-

| Paper
| [[2014Vargas_RANSAC]]
| Initial model using RANSAC (reference free)
|-

| Paper
| [[2015Joubert_Pseudoatoms]]
| Initial model based on pseudo-atoms
|-

| Paper
| [[2015Singer_Kam]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[2015Sorzano_Significant]]
| Statistical approach to the initial volume estimation (reconstruct significant)
|-

| Conference
| [[2016Michels_Heterogeneous]]
| Initial volume in the presence of heterogeneity
|-

| Paper
| [[2016Cossio_BayesianGPU]]
| GPU implementation of the Bayesian 3D reconstruction approach
|-

|}

=== 3D Reconstruction ===
{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1986Harauz_FBP]]
| Exact filters for Filtered Back Projection
|-

| Chapter
| [[1992Radermacher_WBP]]
| Exact filters for Weighted Back Projection
|-

| Paper
| [[1997Zhu_RecCTF]]
| 3D Reconstruction (SIRT like) and simultaneous CTF correction
|-

| Paper
| [[1998Boisset_Uneven]]
| Artifacts in SIRT and WBP under uneven angular distributions
|-

| Paper
| [[1998Marabini_ART]]
| Algebraic Reconstruction Technique with blobs (Xmipp)
|-

| Paper
| [[2001Sorzano_Uneven]]
| Free parameter selection under uneven angular distributions
|-

| Paper
| [[2005Sorzano_Parameters]]
| Free parameter selection for optimizing multiple tasks
|-

| Paper
| [[2008Sorzano_Constraints]]
| Mass, surface, positivity and symmetry constraints for real-space algorithms
|-

| Paper
| [[2009Bilbao_ParallelART]]
| Efficient parallelization of ART
|-

| Paper
| [[2011Li_GradientFlow]]
| Regularized 3D Reconstruction by Gradient Flow
|-

| Paper
| [[2011Vonesch_Wavelets]]
| Fast wavelet-based 3D reconstruction
|-

| Paper
| [[2012Gopinath_ShapeRegularization]]
| Regularized 3D Reconstruction by Shape information
|-

| Paper
| [[2012Kucukelbir_adaptiveBasis]]
| 3D reconstruction in an adaptive basis promoting sparsity
|-

| Paper
| [[2012Sindelar_NoiseReduction]]
| Optimal noise reduction in 3D reconstructions
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Lyumkis_Optimod]]
| Construction of initial volumes with Optimod
|-

| Paper
| [[2013Wang FIRM]]
| Fast 3D reconstruction in Fourier domain
|-

| Paper
| [[2014Kunz_SART_OS]]
| Simultaneous ART with OS
|-

| Paper
| [[2015Abrishami_Fourier]]
| 3D Reconstruction in Fourier space
|-

| Paper
| [[2015Dvornek_SubspaceEM]]
| Fast Maximum a posteriori
|-

| Paper
| [[2015Moriya_Bayesian]]
| Bayesian approach to suppress limited angular artifacts
|-

| Paper
| [[2015Xu_GeometricFlow]]
| Multi-scale geometric flow
|-

| Arxiv
| [[2016Ye_Cohomology]]
| Cohomology properties of 3D reconstruction
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

|}

=== 3D Heterogeneity ===

{|

| Paper
| [[2004White_Size]]
| Heterogeneity classification of differently sized images
|-

| Paper
| [[2006Penczek_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Scheres_ML3D]]
| Maximum Likelihood alignment and classification in 3D
|-

| Paper
| [[2009Spahn_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2010Elmlund_AbInitio]]
| Solving the initial volume problem with multiple conformations
|-

| Paper
| [[2010Shatsky_MultiVariate]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2012Scheres_Bayesian]]
| A Bayesian view on cryo-EM structure determination
|-

| Paper
| [[2012Zheng_Covariance]]
| Estimation of the volume covariance
|-

| Paper
| [[2013Wang_MLVariance]]
| Maximum Likelihood estimate of the map variance
|-

| Paper
| [[2013Lyumkis D_FREALIGN]]
| Likelihood-based classification of cryo-EM images using FREALIGN.
|-

| Paper
| [[2014Jin_NMA]]
| Continuous heterogeneity through Normal Mode Analysis
|-

| Paper
| [[2014Dashti_Brownian]]
| Continuous heterogeneity through Brownian trajectories
|-

| Paper
| [[2014Chen_Migration]]
| Particle migration analysis in 3D classification
|-

| Paper
| [[2015Anden_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Bai_Focused]]
| Focused classification
|-

| Paper
| [[2015Katsevich_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Klaholz_MRA]]
| Multivariate Statistical Analysis of Jackknife and Bootstrapping on random subsets
|-

| Paper
| [[2015Liao_Covariance]]
| Estimation of the 3D covariance from 2D projections
|-

| Paper
| [[2015Tagare_Direct]]
| Direct reconstruction of PCA components
|-

| Paper
| [[2016Gong_Mechanical]]
| Mechanical model for macromolecules
|-

| Paper
| [[2016Rawson_Movement]]
| Movement and flexibility
|-

| Paper
| [[2016Sorzano_StructMap]]
| Sorting a discrete set of conformational states
|-

| Paper
| [[2016Sorzano_Strain]]
| Calculate local stretches, strains and rotations from two conformational states
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

|}

=== Validation ===

{|

| Paper
| [[2008Stagg_TestBed]]
| Effect of voltage, dosis, number of particles and Euler jumps on resolution
|-

| Paper
| [[2011Henderson]]
| Tilt Validation
|-

| Paper
| [[2011Read]]
| Validation of PDBs
|-

| Paper
| [[2012Henderson]]
| EM Map Validation
|-

| Paper
| [[2013Cossio_Bayesian]]
| EM Map Validation in a probabilistic setting
|-

| Paper
| [[2013Chen_NoiseSubstitution]]
| Noise substitution at high resolution for measuring overfitting
|-

| Paper
| [[2014Russo_StatisticalSignificance]]
| EM Map Validation through the statistical significance of the tilt-pair angular assignment
|-

| Paper
| [[2014Stagg_Reslog]]
| EM Map Validation through the resolution evolution with the number of particles
|-

| Paper
| [[2014Wasilewski_Tilt]]
| Web implementation of the tilt pair validation
|-

| Paper
| [[2015Heymann_Alignability]]
| EM Map Validation through the resolution of reconstructions from particles and noise
|-

| Paper
| [[2015Oliveira_FreqLimited]]
| Comparison of gold standard and frequency limited optimization
|-

| Paper
| [[2015Wriggers_Secondary]]
| Validation by secondary structure
|-

| Paper
| [[2016Kim_SAXS]]
| Comparison of SAXS data and EM projections
|-

| Paper
| [[2016Rosenthal_Review]]
| Review of validation methods
|-

| Paper
| [[2016Vargas_Alignability]]
| Validation by studying the tendency of an angular assignment to cluster in the projection space
|-

| Paper
| [[2017Monroe_PDBRefinement]]
| Validation by comparison to a refined PDB
|-

|}

=== Resolution ===

{|

| Paper
| [[1986Harauz_FBP]]
| Fourier Shell Correlation
|-

| Paper
| [[1987Unser_SSNR]]
| 2D Spectral Signal to Noise Ratio
|-

| Paper
| [[2002Penczek_SSNR]]
| 3D Spectral Signal to Noise Ratio for Fourier based algorithms
|-

| Paper
| [[2003Rosenthal_DPR]]
| Review of the FSC and establishment of a new threshold
|-

| Paper
| [[2005Unser_SSNR]]
| 3D Spectral Signal to Noise Ratio for any kind of algorithms
|-

| Paper
| [[2005VanHeel_FSC]]
| Establishment of a new threshold for FSC
|-

| Paper
| [[2007Sousa_AbInitio]]
| Resolution measurement on neighbour Fourier voxels
|-

| Paper
| [[2014Kucukelbir_Local]]
| Quantifying the local resolution of cryo-EM density maps
|-

| Paper
| [[2016Pintilie_Probabilistic]]
| Probabilistic models and resolution
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Statistical properties of resolution measures defined in Fourier space
|-

|}

=== Sharpening of high resolution information ===
{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast restoration and map sharpening
|-

| Paper
| [[2008Fernandez_Bfactor]]
| Bfactor determination and restoration
|-

| Paper
| [[2013Fiddy_SaxtonAlgorithm]]
| Phase retrieval or extension
|-

| Paper
| [[2014Kishchenko_SphericalDeconvolution]]
| Spherical deconvolution
|-

| Paper
| [[2015Spiegel_VISDEM]]
| Visualization improvement by the use of pseudoatomic profiles
|-

| Paper
| [[2016Jonic_Pseudoatoms]]
| Approximation with pseudoatoms
|-

| Paper
| [[2016Jonic_Denoising]]
| Denoising and high-frequency boosting by pseudoatom approximation
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[1982Schiske_Correction]]
| CTF correction for tilted objects
|-

| Paper
| [[1988Toyoshima_Model]]
| CTF estimation
|-

| Paper
| [[1995Frank_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1996Skoglund_MaxEnt]]
| CTF correction with Maximum Entropy
|-

| Paper
| [[1996Zhou_Model]]
| CTF model and user interface for manual fitting
|-

| Paper
| [[1997Fernandez_AR]]
| PSD estimation using periodogram averaging and AR models
|-

| Paper
| [[1997Penczek_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1997Stark_Deconvolution]]
| CTF correction using deconvolution
|-

| Paper
| [[1997Zhu_RecCTF]]
| CTF correction and reconstruction
|-

| Paper
| [[2000DeRosier_EwaldCorrection]]
| CTF correction considering the Ewald sphere
|-

| Paper
| [[2000Jensen_TiltedCorrection]]
| CTF correction considering tilt in backprojection
|-

| Paper
| [[2001Saad_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Huang_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Mindell_CTFTILT]]
| CTF estimation for tilted micrographs
|-

| Paper
| [[2003Sander_MSA]]
| CTF estimation through MSA classification of PSDs
|-

| Paper
| [[2003Velazquez_ARMA]]
| PSD and CTF estimation using ARMA models
|-

| Paper
| [[2004Sorzano_IDR]]
| CTF restoration and reconstruction with Iterative Data Refinement
|-

| Conference
| [[2004Wan_CTF]]
| Spatially variant CTF
|-

| Paper
| [[2004Zubelli_Chahine]]
| CTF restoration and reconstruction with Chahine's multiplicative method
|-

| Conference
| [[2005Dubowy_SpaceVariant]]
| CTF correction when this is space variant
|-

| Paper
| [[2005Mallick_ACE]]
| CTF estimation
|-

| Paper
| [[2006Wolf_Ewald]]
| CTF correction considering Ewald sphere
|-

| Paper
| [[2007Jonic_EnhancedPSD]]
| PSD enhancement for better identification of Thon rings; Vitreous ice diffracts in Thon rings
|-

| Paper
| [[2007Philippsen_Model]]
| CTF Model for tilted specimens
|-

| Paper
| [[2007Sorzano_CTF]]
| CTF estimation using enhanced PSDs
|-

| Paper
| [[2009Sorzano_Sensitivity]]
| Error sensitivity of the CTF models, non-uniqueness of the CTF parameters
|-

| Paper
| [[2010Jiang2010_CTFCorrection]]
| Amplitude correction method
|-

| Paper
| [[2010Kasantsev_CTFCorrection]]
| Mathematical foundations of Kornberg and Jensen method
|-

| Paper
| [[2010Leong_CTFCorrection]]
| Correction for spatially variant CTF
|-

| Paper
| [[2011Glaeser_Coma]]
| The effect of coma at high-resolution
|-

| Paper
| [[2011Mariani_Tilted]]
| CTF simulation and correction of tilted specimens
|-

| Paper
| [[2011Sindelar_Wiener]]
| CTF correction using a modified version of Wiener filter
|-

| Paper
| [[2011Voortman_Tilted]]
| CTF correction for tilted specimen
|-

| Paper
| [[2012Voortman_VaryingCTF]]
| Correcting a spatially varying CTF
|-

| Paper
| [[2013Vargas_FastDef]]
| Fast defocus
|-

| Paper
| [[2015Rohou_CTFFind4]]
| CTF Find 4
|-

| Paper
| [[2015Sheth_CTFquality]]
| Visualization and quality assessment of CTF
|-

| Paper
| [[2016Zhang_GCTF]]
| gCTF
|-

|}

=== Segmentation ===

{|

| Paper
| [[2006Baker_segmentation]]
| Segmentation of molecular subunits
|-

|}

=== Fitting and docking ===

{|

| Paper
| [[1999Volkmann_Fitting]]
| Fitting in real space
|-

| Paper
| [[2001Baker_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2001Jones_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2003Kovacs_FRM3D]]
| Fast Rotational Alignment of two EM maps
|-

| Paper
| [[2004Tama_NMA1]]
| Flexible fitting with Normal Modes (I)
|-

| Paper
| [[2004Tama_NMA2]]
| Flexible fitting with Normal Modes (II)
|-

| Paper
| [[2005Velazquez_Superfamilies]]
| Recognition of the superfamily folding in medium-high resolution volumes
|-

| Paper
| [[2007DeVries_Haddock]]
| Docking with Haddock 2.0
|-

| Paper
| [[2007Kleywegt_QualityControl]]
| Quality control and validation of fitting
|-

| Paper
| [[2012Biswas_Secondary]]
| Secondary structure determination in EM volumes
|-

| Paper
| [[2012Velazquez_Constraints]]
| Multicomponent fitting by using constraints from other information sources
|-

| Paper
| [[2013Chapman MS_Atomicmodeling]]
| Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters
|-

| Paper
| [[2013Esquivel_Modelling]]
| Review on modelling (secondary structure, fitting, ...)
|-

| Paper
| [[2013Lopez_Imodfit]]
| Fitting based on vibrational analysis
|-

| Paper
| [[2013Nogales_3DEMLoupe]]
| Normal Mode Analysis of reconstructed volumes
|-

| Paper
| [[2014AlNasr_Secondary]]
| Identification of secondary structure elements in EM volumes
|-

| Paper
| [[2014Politis_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Rey_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Villa_Review]]
| Review of atomic fitting into EM volumes
|-

| Paper
| [[2015Barad_EMRinger]]
| Validation of hybrid models
|-

| Paper
| [[2015Bettadapura_PF2Fit]]
| Fast rigid fitting of PDBs into EM maps
|-

| Paper
| [[2015Carrillo_CapsidMaps]]
| Analysis of virus capsids using Google Maps
|-

| Paper
| [[2015Schroeder_Hybrid]]
| Review on model building
|-

| Paper
| [[2015Tamo_Dynamics]]
| Dynamics in integrative modeling
|-

| Paper
| [[2015Sorzano_AtomsToVoxels]]
| Accurate conversion of an atomic model into a voxel density volume
|-

| Paper
| [[2016Joseph_Evolution]]
| Evolutionary constraints for the fitting of atomic models into density maps
|-

| Paper
| [[2016Segura_3Diana]]
| Validation of hybrid models
|-

| Paper
| [[2016Singharoy_MDFF]]
| Construction of hybrid models driven by EM density and molecular dynamics
|-

| Paper
| [[2016Wang_Rosetta]]
| Construction of hybrid models driven by EM density using Rosetta
|-

| Paper
| [[2017Hryc_WeightedAtoms]]
| Construction of hybrid models by locally weighting the different atoms
|-

| Paper
| [[2017Matsumoto_Distribution]]
| Estimating the distribution of conformations of atomic models
|-

| Paper
| [[2017Miyashita_EnsembleFitting]]
| Ensemble fitting using Molecular Dynamics
|-

|}

=== Books and reviews ===

{|

| Book
| [[1980Herman_Tomography]]
| General book on tomography
|-

| Book
| [[1988Kak_Tomography]]
| General book on tomography
|-

| Paper
| [[2000Tao_Review]]
| Review of single particles
|-

| Paper
| [[2000VanHeel_Review]]
| Review of single particles
|-

| Paper
| [[2002Frank_Review]]
| Review of single particles
|-

| Paper
| [[2002Schmid_Review]]
| Review of single particles
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2004Subramaniam_Review]]
| Review of single particles
|-

| Paper
| [[2005Steven_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_book]]
| Book covering all aspects of electron microscopy of single particles
|-

| Paper
| [[2006Sorzano_Review]]
| Review of optimization problems in electron microscopy
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems in Electron Tomography
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2008Mueller_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2008Taylor_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2010DeRosier_Review]]
| Personal account of how 3DEM developed in the early days
|-

| Chapter
| [[2012Sorzano_Review]]
| Review of single particle analysis using Xmipp
|-

| Chapter
| [[2012Devaux_Protocol]]
| Protocols for performing single particle analysis
|-

| Paper
| [[2014Bai_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Carazo_Review]]
| Review of the reconstruction process
|-

| Paper
| [[2015Cheng_Review]]
| A primer to Single Particle Cryo-EM
|-

| Paper
| [[2015Cheng_Reviewb]]
| Single Particle Cryo-EM at crystallographic resolution
|-

| Paper
| [[2015Elmlund_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Henderson_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Nogales_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Schroeder_Review]]
| Review of advances in the electron microscope
|-

| Paper
| [[2015Wu_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Carroni_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Egelman_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Eisenstein_CryoEM]]
| News feature on the Method of the Year
|-

| Paper
| [[2016FernandezLeiro_Review]]
| Review of EM
|-

| Paper
| [[2016Glaeser_HowGood]]
| How good can cryo-EM become?
|-

| Paper
| [[2016Jonic_PseudoAtoms]]
| Review of the applications of the use of pseudoatoms in EM
|-

| Chapter
| [[2016Mio_Review]]
| Overview of the process to obtain EM reconstructions
|-

| Paper
| [[2016Jonic_Review]]
| A review of computational ways to handle heterogeneity
|-

| Paper
| [[2016Nogales_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Subramaniam_Review]]
| Why cryo-EM is now suitable for crystallographic journals
|-

| Paper
| [[2016Vinothkumar_Review]]
| Historical review and current limitations
|-

| Paper
| [[2017Frank_Review]]
| Historical review of EM
|-

| Paper
| [[2017Jonic_Review]]
| Review of computational methods to analyze conformational variability
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Review of statistical properties of resolution measures defined in Fourier space
|-
|}

=== Software ===

{|

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[1999Lutdke_Eman]]
| Eman
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Baldwin_AngularTransformations]]
| The Transform Class in SPARX and EMAN2
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Grigorieff_Frealign]]
| Frealign
|-

| Paper
| [[2008Scheres_XmippProtocols]]
| Xmipp Protocols
|-

| Paper
| [[2008Shaikh_SpiderProtocols]]
| Spider Protocols
|-

| Paper
| [[2012Wriggers_SitusConventions]]
| Conventions and workflows in Situs
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2015Cianfrocco_Cloud]]
| Software execution in the cloud
|-

| Paper
| [[2015Cheng_MRC2014]]
| Extensions to MRC file format
|-

| Paper
| [[2013DeLaRosa_Scipion]]
| Scipion
|-

| Paper
| [[2016Scheres_Relion]]
| Tutorial on the use of Relion
|-

| Paper
| [[2016Grigorieff_Frealign]]
| Tutorial on the use of Frealign
|-

|}

== Electron tomography ==

=== Image preprocessing ===

{|

| Paper
| [[2015Yan_thickness]]
| Determination of thickness, tilt and electron mean free path
|-

|}

=== Image alignment ===

{|

| Paper
| [[1982Guckenberger_commonOrigin]]
| Determination of a common origin in the micrographs of titl series in three-dimensional electron microscopy
|-

| Paper
| [[1992Lawrence_leastSquares]]
| Least squares solution of the alignment problem
|-

| Paper
| [[1995Penczek_dual]]
| Dual tilt alignment
|-

| Paper
| [[1996Owen_alignmentQuality]]
| Automatic alignment without fiducial markers and evaluation of alignment quality
|-

| Paper
| [[1998Grimm_normalization]]
| Discussion of several gray level normalization methods for electron tomography
|-

| Paper
| [[2001Brandt_Automatic1]]
| Automatic alignment without fiducial markers
|-

| Paper
| [[2001Brandt_Automatic2]]
| Automatic alignment with fiducial markers
|-

| Paper
| [[2006Winkler_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2006Castano_alignment]]
| Alignment with non-perpendicularity
|-

| Paper
| [[2007Castano_alignment]]
| Fiducial-less alignment of cryo-sections
|-

| Paper
| [[2009Sorzano_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2010Cantele_dualAlignment]]
| Alignment of dual series
|-

| Paper
| [[2014Tomonaga_Automatic]]
| Automatic alignment of tilt series using the projection themselves
|-

| Paper
| [[2014Han_Automatic]]
| Automatic alignment of tilt series using SIFT features
|-

| Paper
| [[2015Han_Automatic]]
| Automatic alignment of tilt series using fiducials
|-

| Paper
| [[2017Mastronarde_Automatic]]
| Automatic alignment and reconstruction of tilt series in IMOD
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[2003Winkler_CTF]]
| Focus gradient correction in electron tomography
|-

| Paper
| [[2006Fernandez_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Zanetti_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Xiong_CTF]]
| CTF determination and correction for low dose tomographic tilt series
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2017Kunz_3DCTF]]
| 3D CTF Correction
|-

|}

=== 3D reconstruction ===

{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1992Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[1997Marabini_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2002Fernandez_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2007Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[2008Fernandez_CARP]]
| Component Averaged Row Projections (CARP)
|-

| Paper
| [[2012Herman General Superiorization]]
| Superiorization: an optimization heuristic for medical physics
|-

| Paper
| [[2012Zhang_IPET_FETR]]
| IPET and FETR, a reconstruction algorithm for single molecule tomography
|-

| Paper
| [[2013Goris_SIRT_TV_DART]]
| Combination of SIRT, Total Variation and Discrete ART to reconstruct and segment at the same time
|-

| Paper
| [[2013Briegel A_Challenge]]
| The challenge of determining handedness in electron tomography and the use of DNA origami gold nanoparticle helices as molecular standards
|-

| Paper
| [[2013Messaoudi_EnergyFiltered]]
| 3D Reconstruction of Energy-Filtered TEM
|-

| Paper
| [[2016Deng_ICON]]
| 3D Reconstruction with missing information restoration
|-

| Paper
| [[2016Guay_Compressed]]
| 3D Reconstruction using compressed sensing
|-

|}

=== Noise reduction ===
{|

| Paper
| [[2001Frangakis_NAD]]
| Noise reduction with Nonlinear Anisotropic Diffusion
|-

| Paper
| [[2003Fernandez_AND]]
| Anisotropic nonlinear diffusion for electron tomography
|-

| Paper
| [[2003Jiang_Bilateral]]
| Bilateral denoising filter in electron microscopy
|-

| Paper
| [[2005Fernandez_AND]]
| Anisotropic nonlinear denoising in electron tomography
|-

| Paper
| [[2007Heide_median]]
| Iterative median filtering in electron tomography
|-

| Paper
| [[2007Fernandez_autAND]]
| Anisotropic nonlinear diffusion with automated parameter tuning
|-

| Paper
| [[2009Fernandez_Beltrami]]
| Nonlinear filtering based on Beltrami flow
|-

| Paper
| [[2010Bilbao_MeanShift]]
| Mean Shift Filtering
|-

| Paper
| [[2014Kovacik_wedgeArtefacts]]
| Removal of wedge artefacts
|-

| Paper
| [[2014Maiorca_beadArtefacts]]
| Removal of gold bead artefacts
|-

|}

=== Segmentation ===

{|

| Paper
| [[2002Frangakis_Eigenanalysis]]
| Segmentation using eigenvector analysis.
|-

| Paper
| [[2002Volkmann_Watershed]]
| Segmentation using watershed transform.
|-

| Paper
| [[2003Bajaj_BoundarySegmentation]]
| Segmentation based on fast marching.
|-

| Paper
| [[2005Cyrklaff_Thresholding]]
| Segmentation using optimal thresholding.
|-

| Paper
| [[2007Lebbink_TemplateMatching]]
| Segmentation using template matching.
|-

| Paper
| [[2007Sandberg_OrientationFields]]
| Segmentation using orientation fields.
|-

| Paper
| [[2007Sandberg_SegmentationReview]]
| Review on segmentation in electron tomography.
|-

| Paper
| [[2008Garduno_FuzzySegmentation]]
| Segmentation using fuzzy set theory principles.
|-

| Paper
| [[2009Lebbink_TemplateMatching2]]
| Segmentation using template matching.
|-

| Paper
| [[2012RubbiyaAli_EdgeDetection]]
| Parameter-Free Segmentation of Macromolecular Structures.
|-

| Conference
| [[2015Xu_TemplateMatching]]
| Detection of macromolecular complexes with a reduced representation of the templates.
|-

|}

=== Resolution ===
{|

| Paper
| [[2005Cardone_Resolution]]
| Resolution criterion for electron tomography
|-

| Chapter
| [[2007Penczek_Resolution]]
| Review of resolution criteria for electron tomography
|-

| Paper
| [[2015Diebolder_ConicalFSC]]
| Conical Fourier Shell Correlation
|-

|}

=== Subtomogram analysis ===

{|

| Paper
| [[2000Bohm_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2002Frangakis_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2006Nickell_Review]]
| Review of macromolecule finding by template matching (Visual Proteomics)
|-

| Paper
| [[2007Best_Review]]
| Review of Localization of Protein Complexes by Pattern Recognition
|-

| Paper
| [[2007Forster_Review]]
| Review of structure determination by subtomogram averaging
|-

| Paper
| [[2008Forster_Classification]]
| Classification of subtomograms using constrained correlation
|-

| Paper
| [[2008Bartesaghi_Classification]]
| Classification and averaging of subtomograms
|-

| Paper
| [[2008Schmid_Averaging]]
| Alignment and averaging of subtomograms
|-

| Paper
| [[2010Amat_Averaging]]
| Alignment and averaging of subtomograms exploiting thresholding in Fourier space
|-

| Paper
| [[2013Chen_Averaging]]
| Fast alignment of subtomograms using spherical harmonics
|-

| Paper
| [[2013Kuybeda_Averaging]]
| Alignment and averaging of subtomograms using the nuclear norm of the cluster
|-

| Paper
| [[2013Shatsky_Averaging]]
| Alignment and averaging of subtomograms with constrained cross-correlation
|-

| Paper
| [[2014Chen_Autofocus]]
| Subtomogram averaging and classification with special attention to differences
|-

| Paper
| [[2014Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2014Voortman_LimitingFactors]]
| Limiting factors of subtomogram averaging
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2015Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2016Bharat_Relion]]
| Subtomogram averaging with Relion
|-

| Paper
| [[2016Song_MatrixNorm]]
| Matrix norm minimization for tomographic reconstruction and alignment
|-

| Paper
| [[2017Castano_ParticlePicking]]
| Particle picking in tomograms for subtomogram averaging
|-

|}

=== Single particle tomography ===

{|

| Paper
| [[2012Bartesaghi_Constrained]]
| 3D reconstruction by imposing geometrical constraints
|-

| Paper
| [[2015Galaz_SingleParticleTomography]]
| Set of tools for Single Particle Tomography in EMAN2
|-

| Paper
| [[2016Galaz_SingleParticleTomography]]
| Alignment algorithms and CTF correction
|-

|}

=== Books and reviews ===

{|

| Paper
| [[2000Baumeister_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Koster_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Sali_Review]]
| Review of electron tomography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2005Lucic_Review]]
| Review of electron tomography
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_TomoBook]]
| Electron Tomography
|-

| Book
| [[2007McIntosh_Book]]
| Cellular Electron Microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2012Kudryashev_Review]]
| Review of subtomogram averaging
|-

| Paper
| [[2016Beck_Review]]
| Review of molecular sociology
|-

|}

=== Software ===

{|

| Paper
| [[1996Kremer_IMOD]]
| IMOD
|-

| Paper
| [[1996Chen_Priism/IVE]]
| Priism/IVE
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2005Nickell_TOM]]
| TOM Toolbox
|-

| Paper
| [[2007Messaoudi_TomoJ]]
| TomoJ
|-

| Paper
| [[2008Heymann_BsoftTomo]]
| Bsoft
|-

| Paper
| [[2015Ding_CaltechTomography]]
| Caltech tomography database
|-

| Paper
| [[2015Noble_AppionProtomo]]
| Batch fiducial-less tilt-series alignment in Appion using Protomo
|-

| Paper
| [[2015vanAarle_Astra]]
| ASTRA Toolbox
|-

|}

== 2D Crystals ==

=== 2D Preprocessing ===

{|

| Paper
| [[1986Henderson_Processing]]
| General 2D processing
|-

| Paper
| [[2000He_PhaseAlignment]]
| Phase consistency and Alignment
|-

| Paper
| [[2006Gil_Unbending]]
| Crystal unbending
|-

|}

=== Classification ===
{|

| Paper
| [[1988Frank_Classification]]
| MSA and classification in electron crystallography
|-

| Paper
| [[1996Fernandez_SOM]]
| Classification based on self organizing maps
|-

| Paper
| [[1998Sherman_MSA]]
| Classification based on MSA
|-

|}
=== 3D Reconstruction ===

{|

| Paper
| [[1985Wang_Solvent]]
| Solvent flattening
|-

| Paper
| [[1990Henderson_Processing]]
| General 3D processing
|-

| Paper
| [[2004Marabini_ART]]
| Algebraic Reconstruction Technique with blobs for crystals (Xmipp)
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1998Walz_Review]]
| Review of 2D crystallography
|-

| Paper
| [[1999Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Ellis_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of single particles, electron tomography and crystallography
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Gipson_2dx]]
| 2dx
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Philippsen_IPLT]]
| IPLT
|-

|}

== 3D Crystals - MicroED ==

=== Sample Preparation ===
{|
| Paper
| [[2016Shi_Preparation]]
| Sample Preparation
|}
=== Data Collection ===
{|
| Paper
| [[2014Nannenga_CR]]
| Continuous rotation

|}
=== Data Processing ===
{|

| Paper
| [[2011Wisedchaisri_PhaseExtension]]
| Fragment-based phase extension
|-

| Paper
| [[2015Hattne_Processing]]
| Data Processing
|-

| Paper
| [[2016Hattne_Correction]]
| Image correction
|}

=== Software ===
{|

| Paper
| [[2014Iadanza_Processing]]
| Data Processing of still diffraction data
|}

=== Books and Reviews ===
{|
| Paper
| [[2014Nannenga_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Liu_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Rodriguez_Review ]]
| Review of MicroED
|-

|}

== Helical particles ==

=== Filament corrections ===

{|

| Paper
| [[1986Egelman_Curved]]
| Algorithm for correcting curved filaments
|-

| Paper
| [[1988Bluemke_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2006Wang_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2016Yang_Flexible]]
| Algorithm for correcting filaments with flexible subunits
|-

|}

=== Reconstruction ===

{|

| Paper
| [[1952Cochran_Fourier]]
| Fourier Bessel transform of filamentous structures
|-

| Paper
| [[1958Klug_Fourier]]
| Fourier Bessel decomposition of the projection images
|-

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2005Wang_Iterative]]
| Iterative Fourier-Bessel algorithm
|-

| Paper
| [[2007Egelman_Iterative]]
| Iterative real-space algorithm
|-

| Paper
| [[2013Desfosses_Spring]]
| Helical processing with Spring
|-

| Paper
| [[2015Zhang_seam]]
| Workflow for the detection of the lattice seam
|-

| Paper
| [[2016Rohou_Frealix]]
| Helical processing with Frealix
|-

|}

=== Validation ===

{|

| Paper
| [[2014Egelman_ambiguity]]
| How to detect incorrect models
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Carragher_Phoelix]]
| Phoelix
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Owen_Brandeis]]
| Brandeis
|-

|}

== Icosahedral particles ==

=== Reconstruction ===

{|

| Paper
| [[1970Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1971Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1996Fuller_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1997Thuman_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

|}

=== Classification ===

{|

| Paper
| [[2005Scheres_Virus]]
| Classification of virus capsids in real space
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1999Baker_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[1999Conway_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2000Thuman_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Lee_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Navaza_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2006Grunewald_Review]]
| Review of reconstruction of icosahedral viruses
|-

|}

=== Software ===

{|

| Paper
| [[1996Baker_EMPFT]]
| EMPFT
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2013Morin_Sliz SBGrid]]
| SBGrid presentation for eLife
|-

|}

== Databases ==

{|

| Paper
| [[2003Boutselakis_EMSD]]
| EMSD database
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2011Kim_CDDB]]
| Conformational Dynamics Data Bank
|-

| Paper
| [[2011Lawson_EMDB]]
| Electron Microscopy Data Bank
|-

| Paper
| [[2013Ison_EDAM]]
| EDAM, an ontology of bioinformatics operations
|-

| Paper
| [[2016Iudin_EMPIAR]]
| EMPIAR raw data database
|-

| Paper
| [[2016Patwhardan_EMDB]]
| EMDB, PDB, ...
|-

| Paper
| [[2017Patwhardan_Trends]]
| Trends at EMDB
|-

| Paper
| [[2017Shao_PDBQuality]]
| Quality metrics in PDB
|-

| Blog
| http://www.mybiosoftware.com
| Huge list of bioinformatics programs (many of them structural bioinformatics)
|-

|}

== Relationship to other structural information sources ==

{|

| Paper
| [[2000Engel_AFM]]
| Review of Atomic Force Microscopy
|-

| Paper
| [[2001Dimmeler_AFM]]
| Constraints from Atomic Force Microscopy
|-

| Paper
| [[2003Mobus_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_Review]]
| Review on correlative microscopy
|-

| Paper
| [[2005Boudier_EFTETJ]]
| Software for Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2005Vestergaard_SAXS]]
| Example of comparison of 3DEM and Small-angle X-ray scattering
|-

| Paper
| [[2007Hamada_SAXS]]
| Constraints from Small-angle X-ray scattering
|-

| Paper
| [[2013Xu_FRET]]
| EM+FRET
|-

|}

== X-ray tomography ==

{|

| Paper
| [[2012Oton_ImageFormation]]
| Image formation model in X-ray cell microscopy
|-

|}

== Mathematical tools necessary ==

== People developing methods ==
Please, add yourself to this list (due to privacy reasons, please, do not add anyone else to the list without his/her explicit consent). Sort by first name alphabetical order.

[http://biocomp.cnb.csic.es/~coss Carlos Oscar S. Sorzano]: CSIC, Madrid, Spain 

[http://www.curie.fr/recherche/themes/detail_equipe.cfm/lang/_fr/id_equipe/241.htm Cédric Messaoudi]: Institute Curie, Paris, France 

[http://scholar.google.es/citations?user=_jNYGScAAAAJ&hl=en Javier Vargas]:[mailto:jvargas@cnb.csic.es mail]: CSIC, Madrid, Spain 

[http://scholar.google.es/citations?hl=es&user=g2ZJPIYAAAAJ Joaquín Otón]: CSIC, Madrid, Spain 

[mailto:jrbcast@gmail.com José Román Bilbao-Castro]: UAL, Almería, Spain; CSIC, Madrid, Spain 

[José Miguel de la Rosa Trevín]: Biocomputing Unit CNB-CSIC, Madrid, Spain 

[http://cryoem.janelia.org Tamir Gonen]: [mailto:gonent@janelia.hhmi.org mail]: Howard Hughes Medical Institute, Ashburn, VA, USA 

[mailto:vabrishami@cnb.csic.es Vahid Abrishami]: CSIC, Madrid, Spain 

== 3DEM sites ==
* [http://3dem.ucsd.edu/ 3DEM web site]

* [http://en.wikibooks.org/wiki/Software_Tools_For_Molecular_Microscopy Software tools for molecular microscopy]

* [http://www.emdatabank.org/ The Electron Microscopy Data Bank (EMDB)]

* [http://ccdb.ucsd.edu The Cell Centered Database (CCDB)]

* [http://conventions.cnb.csic.es The geometrical software conventions web page ]

== Editing useful links ==

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2017Feng SprayingPlunging

2017-05-17T06:16:48Z

CoSS: Created page with "== Citation == Feng, X.; Fu, Z.; Kaledhonkar, S.; Jia, Y.; Shah, B.; Jin, A.; Liu, Z.; Sun, M.; Chen, B.; Grassucci, R. A.; Ren, Y.; Jiang, H.; Frank, J. & Lin, Q. A Fast and..."

== Citation ==

Feng, X.; Fu, Z.; Kaledhonkar, S.; Jia, Y.; Shah, B.; Jin, A.; Liu, Z.; Sun, M.; Chen, B.; Grassucci, R. A.; Ren, Y.; Jiang, H.; Frank, J. & Lin, Q. A Fast and Effective Microfluidic Spraying-Plunging Method for High-Resolution Single-Particle Cryo-EM. Structure, 2017, 25, 663-670.e3

== Abstract ==

We describe a spraying-plunging method for preparing cryoelectron microscopy (cryo-EM) grids with vitreous ice of controllable, highly consistent thickness using a microfluidic device. The new polydimethylsiloxane (PDMS)-based sprayer was tested with apoferritin. We demonstrate that the structure can be solved to high resolution with this method of sample preparation. Besides replacing the conventional pipetting-blotting-plunging method, one of many potential applications of the new sprayer is in time-resolved cryo-EM, as part of a PDMS-based microfluidic reaction channel to study short-lived intermediates on the timescale of 10-1,000 ms.

== Keywords ==

== Links ==

https://www.ncbi.nlm.nih.gov/pubmed/28286002

== Related software ==

== Related methods ==

== Comments ==

Main Page

2017-05-17T06:15:59Z

CoSS: /* Sample preparation */

== Presentation ==

This web page is intended to be an extensive repository of three-dimensional electron microscopy (3DEM) methods. The advantages of having such a repository are

* You know which are the relevant articles in a particular topic, therefore, paper introductions, reviews, etc. are easier to write and you make sure you will cite all the related articles.
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Developing image processing methods for 3DEM is not "[[well-paid]]" in terms of citations and impact factor. However, it is crucial for the advance of the field. Gathering methodological papers in a portal will help to increase the recognition of the field.

Please:

* Add your articles at the right place (you can add a single article in several topics if it is relevant to all of them). The easiest way to add an article is by editing the corresponding topic in the main page, adding your entry, then save the main page. Click on the red link that appears on your new entry, copy and paste the Wiki following code, add the information of your article

== Citation ==

== Abstract ==

== Keywords ==

== Links ==

== Related software ==

== Related methods ==

== Comments ==

* Maintain the information of each article as complete as possible.
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== Electron microscopy images ==

=== Online courses ===

CALTECH: http://cryo-em-course.caltech.edu/

MRC: ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/EM-course/

CNB-CSIC: http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/MadridJan2014EM

Workshop on Computational methods for CryoEM: https://www.youtube.com/watch?v=XdKO1iaPP8o

Workshop on Management of large CryoEM facilities: https://www.youtube.com/watch?v=as4seOPszL0

Icknield Course on Model Building and Refinement for High Resolution EM Maps: http://www.ccpem.ac.uk/training/icknield_2017/icknield_2017.php

=== Image formation ===

{|

| Paper
| [[1971Erickson_CTF]]
| CTF model
|-

| Paper
| [[1971Glaeser_Damage]]
| Radiation damage
|-

| Chapter
| [[1971Hanszen_CTF]]
| Image formation model
|-

| Paper
| [[1971Thon_Model]]
| CTF model
|-

| Paper
| [[1975Unwin_Imaging]]
| Radiation dose
|-

| Paper
| [[1977Wade_Model]]
| CTF model
|-

| Paper
| [[1978Wade_Model]]
| CTF model
|-

| Paper
| [[1979Hayward_Radiation]]
| Radiation damage
|-

| Paper
| [[1984Cohen_Validity]]
| Validity of the CTF model at high frequencies
|-

| Paper
| [[1988Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[1992Wade_Model]]
| CTF model
|-

| Paper
| [[1993Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2004Egerton_Damage]]
| Radiation damage
|-

| Paper
| [[2004Sorzano_Normalization]]
| Background noise is Gaussian
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2009Baxter_NoiseCharacterization]]
| Characterization of the different noise sources in cryo-EM
|-

| Paper
| [[2010Baker_Damage]]
| Radiation damage dependence on resolution
|-

| Paper
| [[2010Bammes_Damage]]
| Radiation damage dependence on temperature
|-

| Paper
| [[2010Gomez_Multislice]]
| Simulation of the multi slice model
|-

| Paper
| [[2010Zewail_FourDimensional]]
| Review on the use of ultrafast EM
|-

| Paper
| [[2011Bammes_CCD]]
| Performance of CCD cameras
|-

| Paper
| [[2011Glaeser_Coma]]
| Image formation model including coma
|-

| Paper
| [[2011Milazzo_DirectDetectors]]
| Evaluation of Direct Detectors
|-

| Paper
| [[2011Rullgard_ImageSimulation]]
| Accurate simulation of EM images
|-

| Paper
| [[2011Zhang LimitingFactors]]
| Limiting factor for atomic resolution in EM
|-

| Paper
| [[2012Bammes_DirectDetection]]
| Performance of Direct detectors
|-

| Paper
| [[2012Campbell_MotionCorrection]]
| Beam induced motion correction and direct detectors
|-

| Paper
| [[2012Shang_HydrationLayer]]
| Simulation of PDB volumes explicitly considering the hydration layer
|-

| Paper
| [[2013Egerton_RadiationDamage]]
| Review of TEM radiation damage and experimental ways of reducing it
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu H_Noisemodels]]
| Noise models and cryo-EM drift correction with a direct-electron camera
|-

| Paper
| [[2013Li X K2 noisemodels]]
| Influence of electron dose rate on electron counting images recorded with the K2 camera
|-

| Paper
| [[2013Vulovic_CTFApproximations]]
| When to use the different approximations performed so that a projection with linear CTF is valid
|-

| Thesis
| [[2013Vulovic_ImageFormation]]
| Ph.D. Thesis on the image formation in cryo-EM
|-

| Paper
| [[2014Danev_PhasePlate]]
| Volta potential phase plate
|-

| Paper
| [[2015Chiu_K2]]
| Characterization of K2
|-

| Paper
| [[2015Hawkes_AberrationCorrection]]
| Historical account of the development of lens corrections
|-

| Paper
| [[2015Koeck_Quadratic]]
| Limitations of the linear approximation and use of the quadratic terms
|-

| Paper
| [[2015Kuijper_FEI]]
| Description of the FEI Falcons
|-

| Paper
| [[2015Lobato_MULTEM]]
| Simulation of multislice diffraction
|-

| Paper
| [[2015McMullan_AmorphousIce]]
| Beam induced movement is caused by Brownian motion
|-

| Paper
| [[2016Koeck_ADF]]
| Simulations of Annular Dark Field TEM
|-

| Paper
| [[2017Mishyna_DNARadiation]]
| Review of radiation damage on DNA
|-

|}

=== Collection geometry ===

{|

| Chapter
| [[1980Hoppe_Wedge]]
| Missing wedge
|-

| Paper
| [[1987Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1995Penczek_Dual]]
| Dual axis tomography
|-

| Paper
| [[1997Mastronarde_Dual]]
| Dual axis tomography
|-

| Paper
| [[2003Ludtke_FocusPairs]]
| Focus pairs for single particles
|-

| Paper
| [[2005Lanzavecchia_Conical]]
| Conical tomography
|-

| Paper
| [[2005Zampighi_Conical]]
| Conical tomography
|-

| Paper
| [[2006Leschziner_OT]]
| Orthogonal Tilt
|-

| Paper
| [[2006Messaoudi_Multiple]]
| Multiple axis tomography
|-

| Paper
| [[2012Kudryashev_FocusPairs]]
| Focus pairs tomography
|-

| Paper
| [[2014Hovden_TiltFocus]]
| Combining tilt series with focus series
|-

| Paper
| [[2015Sorzano_RandomConicalTilt]]
| General formulation of Random Conical Tilt
|-

| Paper
| [[2017Hagen_DoseTomography]]
| Dose optimization for subtomogram averaging
|-

|}

=== Sample preparation ===

{|

| Paper
| [[1982Dubochet_Sample]]
| Vitreous ice
|-

| Paper
| [[1986Lepault_Sample]]
| Fast freezing
|-

| Paper
| [[1995Dubochet_Sample]]
| High-pressure freezing
|-

| Paper
| [[1995VanMarle_Sample]]
| Sample damages in resin
|-

| Paper
| [[1998Adrian_Sample]]
| Cryo negative staining
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2002Hsieh_Sample]]
| Cryofixation
|-

| Paper
| [[2004AlAmoudi_Sample]]
| CEMOVIS
|-

| Paper
| [[2008Studer_Sample]]
| Review on high pressure freezing
|-

| Paper
| [[2009Pierson_Sample]]
| Review on sample preparation for electron tomography
|-

| Paper
| [[2010Zhang_NegativeStaining]]
| Negative staining for small protein imaging
|-

| Paper
| [[2012Zhang_PositiveStaining]]
| Positive staining
|-

| Paper
| [[2014Rames_NegativeStaining]]
| Optimized negative staining
|-

| Paper
| [[2014Russo_GoldGrids]]
| Gold grids for single particles
|-

| Paper
| [[2015Cabra_Sample]]
| Review on sample preparation for single particles with videos
|-

| Paper
| [[2016Passmore_Review]]
| Tutorial chapter on sample preparation
|-

| Paper
| [[2016Razinkov_Vitrification]]
| New vitrification method
|-

| Paper
| [[2016Takizawa_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2016Thompson_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2017Arnold_BlottingFree]]
| Blotting-free preparation
|-

| Paper
| [[2017Feng_SprayingPlunging]]
| Spraying plunging
|-

| Paper
| [[2017Peitsch_Sample]]
| iMEM: Isolation of Plasma Membrane for Cryoelectron Microscopy
|-

| Paper
| [[2017Schaffer_FocusedIonBeam]]
| Focused Ion Beam sample preparation for membrane proteins
|-

|}

=== Automated data collection ===

{|

| Paper
| [[1992Dierksen_Automatic]]
| Automated data collection
|-

| Paper
| [[1992Koster_Automatic]]
| Automated data collection
|-

| Paper
| [[1996Fung_Automatic]]
| Automated data collection for tomography
|-

| Paper
| [[2001Zhang_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2003Ziese_Automatic]]
| Automated autofocusing
|-

| Paper
| [[2004Potter_Automatic]]
| Automated sample loading
|-

| Paper
| [[2004Zheng_Automatic]]
| Automated data collection
|-

| Paper
| [[2005Lei_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2005Suloway_Automatic]]
| Automated data collection: Leginon
|-

| Paper
| [[2007Yoshioka_RCT]]
| Automated Random Conical Tilt
|-

| Paper
| [[2011Korinek_TOM2]]
| Automated acquisition with TOM2
|-

| Paper
| [[2015Li_UCSFImage]]
| Automated acquisition with UCSFImage
|-

| Paper
| [[2016Gil_Fuzzy]]
| Real time decisions during acquisition with neuro-fuzzy method
|-

| Paper
| [[2016Liu_TiltControl]]
| Accurate control of the tilt angle for electron tomography
|-

| Paper
| [[2016Vargas_FoilHole]]
| Determination of image quality at low magnification
|-

|}

== Single particles ==

=== Automatic particle picking ===

{|

| Paper
| [[1982VanHeel_Detection]]
| Detection of particles in micrographs
|-

| Paper
| [[2001Nicholson_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2001Zhu_Filaments]]
| Automatic identification of filaments in micrographs
|-

| Paper
| [[2004Sigworth_Detection]]
| Classical detection theory and the cryo-EM particle selection problem
|-

| Paper
| [[2004Volkmann_ParticlePicking]]
| An approach to automated particle picking from electron micrographs based on reduced representation templates
|-

| Paper
| [[2004Wong_ParticlePicking]]
| Model-based particle picking for cryo-electron microscopy
|-

| Paper
| [[2004Zhu_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2007Chen_Signature]]
| Automatic particle picking program: Signature
|-

| Paper
| [[2007Woolford_SwarmPS]]
| Automatic particle picking with several criteria, implemented in EMAN Boxer
|-

| Paper
| [[2009Sorzano_MachineLearning]]
| Automatic particle picking based on machine learning of rotational invariants
|-

| Paper
| [[2011Arbelaez_Comparison]]
| Evaluation of the performance of software for automated particle-boxing
|-

| Paper
| [[2013Abrishami_MachineLearning]]
| A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs
|-

| Paper
| [[2013Hauer_2013]]
| Automatic tilt pair detection in Random Conical Tilt
|-

| Paper
| [[2013Shatsky_ParticlePicking]]
| Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Langlois_ParticlePicking]]
| Automatic particle picking
|-

| Paper
| [[2016Vilas_AutomaticTilt]]
| Automatic identification of image pairs in untilted-tilted micrograph pairs
|-

|}

=== 2D Preprocessing ===

{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast enhancement through DPR
|-

| Paper
| [[2004Sorzano_Normalization]]
| Normalization procedures and their statistical properties.
|-

| Paper
| [[2006Sorzano_Denoising]]
| Strong denoising in wavelet space
|-

| Conference
| [[2009Sorzano_Downsampling]]
| Differences between the different downsampling schemes
|-

| Paper
| [[2012Brilot_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Campbell_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Zhao_Denoising]]
| Denoising using an invariant Fourier-Bessel eigenspace
|-

| Paper
| [[2013Norousi_Screening]]
| Screening particles to identify outliers
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu_Movies]]
| Drift correction for movies considering dark field
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Scheres_Movies]]
| Beam induced motion correction
|-

| Paper
| [[2015Abrishami_Movies]]
| Alignment of direct detection device micrographs
|-

| Paper
| [[2015Grant_Anisotropic]]
| Automatic estimation and correction of anisotropic magnification
|-

| Paper
| [[2015Grant_OptimalExposure]]
| Filter movies according to the radiation damage
|-

| Paper
| [[2015Rubinstein_Alignment]]
| Frame alignment at the level of particle
|-

| Paper
| [[2015Spear_DoseCompensation]]
| Effect of dose compensation on resolution
|-

| Paper
| [[2015Zhao_AnisotropicMagnification]]
| Correction of anisotropic magnification
|-

| Conference
| [[2016Bajic_Denoising]]
| Denoising and deconvolution of micrographs
|-

| Paper
| [[2016Jensen_RemovalVesicles]]
| Removal of vesicles in membrane proteins
|-

| Paper
| [[2016Bhamre_Denoising]]
| Denoising by 2D covariance estimation
|-

| Paper
| [[2017McLeod_Zorro]]
| Movie alignment by Zorro
|-

| Paper
| [[2017Zheng_MotionCorr2]]
| Movie alignment by MotionCorr2
|-

|}

=== 2D Alignment ===

{|

| Paper
| [[1981Frank_Averaging]]
| 2D averaging and phase residual
|-

| Paper
| [[1982Saxton_Averaging]]
| 2D averaging using correlation
|-

| Paper
| [[1998Sigworth_ML2D]]
| Maximum likelihood alignment in 2D
|-

| Paper
| [[2003Cong_FRM2D]]
| Fast Rotational Matching in 2D
|-

| Paper
| [[2005Cong_FRM2D]]
| Fast Rotational Matching in 2D introduced in a 3D Alignment algorithm
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

|}

=== 2D Classification and clustering ===

{|

| Paper
| [[1981VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[1984VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2011Singer_DiffusionMaps]]
| Classification in 2D based on graph analysis of the projections
|-

| Paper
| [[2012Yang_ISAC]]
| Iterative Stable Alignment and clustering
|-

| Paper
| [[2014Sorzano_Outlier]]
| Outlier detection in 2D classifications.
|-

| Paper
| [[2014Zhao_Aspire]]
| Fast classification based on rotational invariants and vector diffusion maps
|-

| Paper
| [[2015Huang_Robust]]
| Robust w-estimators of 2D classes
|-

| Paper
| [[2016Reboul_Stochastic]]
| Stochastic Hill Climbing for calculating 2D classes
|-

| Conference
| [[2017Bhamre_Mahalanobis]]
| 2D classification using Mahalanobis distance
|-

|}

=== 3D Alignment ===

{|

| Paper
| [[1980Kam_AutoCorrelation]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[1986Goncharov_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1987VanHeel_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1988Provencher_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Vogel_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1990Gelfand_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Goncharov_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Harauz_Quaternions]]
| Use of quaternions to represent rotations
|-

| Paper
| [[1994Penczek_Real]]
| Angular assignment using projection matching in real space
|-

| Paper
| [[1994Radermacher_Radon]]
| Angular assignment in Radon space
|-

| Paper
| [[1996Penczek_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[2003Rosenthal_DPR]]
| Angular assignment using DPR
|-

| Paper
| [[2004Sorzano_Wavelet]]
| Angular assignment in the wavelet space.
|-

| Paper
| [[2005Jonic_Splines]]
| Angular assignment in Fourier space using spline interpolation.
|-

| Paper
| [[2005Yang_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[2006Ogura_SimulatedAnnealing]]
| Angular asignment by simulated annealing
|-

| Paper
| [[2007Grigorieff_Continuous]]
| Continuous angular assignment in Fourier space
|-

| Paper
| [[2010Jaitly_Bayesian]]
| Angular assignment by a Bayesian method and annealing
|-

| Paper
| [[2010Sanz_Random]]
| Random model method
|-

| Paper
| [[2010Singer_Voting]]
| Detecting consistent common lines by voting (reference free)
|-

| Paper
| [[2011Singer_SDP]]
| Angular assignment by semidefinite programming and eigenvectors (reference free)
|-

| Paper
| [[2012Giannakis_Scattering]]
| Construction of an initial volume, reference free, by graph analysis of the projections
|-

| Paper
| [[2012Shkolnisky_Sync]]
| Angular assignment by synchronization of rotations (reference free)
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Wang_LUD]]
| Angular assignment by least unsquared deviations (reference free)
|-

| Paper
| [[2014Vargas_RANSAC]]
| Initial model using RANSAC (reference free)
|-

| Paper
| [[2015Joubert_Pseudoatoms]]
| Initial model based on pseudo-atoms
|-

| Paper
| [[2015Singer_Kam]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[2015Sorzano_Significant]]
| Statistical approach to the initial volume estimation (reconstruct significant)
|-

| Conference
| [[2016Michels_Heterogeneous]]
| Initial volume in the presence of heterogeneity
|-

| Paper
| [[2016Cossio_BayesianGPU]]
| GPU implementation of the Bayesian 3D reconstruction approach
|-

|}

=== 3D Reconstruction ===
{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1986Harauz_FBP]]
| Exact filters for Filtered Back Projection
|-

| Chapter
| [[1992Radermacher_WBP]]
| Exact filters for Weighted Back Projection
|-

| Paper
| [[1997Zhu_RecCTF]]
| 3D Reconstruction (SIRT like) and simultaneous CTF correction
|-

| Paper
| [[1998Boisset_Uneven]]
| Artifacts in SIRT and WBP under uneven angular distributions
|-

| Paper
| [[1998Marabini_ART]]
| Algebraic Reconstruction Technique with blobs (Xmipp)
|-

| Paper
| [[2001Sorzano_Uneven]]
| Free parameter selection under uneven angular distributions
|-

| Paper
| [[2005Sorzano_Parameters]]
| Free parameter selection for optimizing multiple tasks
|-

| Paper
| [[2008Sorzano_Constraints]]
| Mass, surface, positivity and symmetry constraints for real-space algorithms
|-

| Paper
| [[2009Bilbao_ParallelART]]
| Efficient parallelization of ART
|-

| Paper
| [[2011Li_GradientFlow]]
| Regularized 3D Reconstruction by Gradient Flow
|-

| Paper
| [[2011Vonesch_Wavelets]]
| Fast wavelet-based 3D reconstruction
|-

| Paper
| [[2012Gopinath_ShapeRegularization]]
| Regularized 3D Reconstruction by Shape information
|-

| Paper
| [[2012Kucukelbir_adaptiveBasis]]
| 3D reconstruction in an adaptive basis promoting sparsity
|-

| Paper
| [[2012Sindelar_NoiseReduction]]
| Optimal noise reduction in 3D reconstructions
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Lyumkis_Optimod]]
| Construction of initial volumes with Optimod
|-

| Paper
| [[2013Wang FIRM]]
| Fast 3D reconstruction in Fourier domain
|-

| Paper
| [[2014Kunz_SART_OS]]
| Simultaneous ART with OS
|-

| Paper
| [[2015Abrishami_Fourier]]
| 3D Reconstruction in Fourier space
|-

| Paper
| [[2015Dvornek_SubspaceEM]]
| Fast Maximum a posteriori
|-

| Paper
| [[2015Moriya_Bayesian]]
| Bayesian approach to suppress limited angular artifacts
|-

| Paper
| [[2015Xu_GeometricFlow]]
| Multi-scale geometric flow
|-

| Arxiv
| [[2016Ye_Cohomology]]
| Cohomology properties of 3D reconstruction
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

|}

=== 3D Heterogeneity ===

{|

| Paper
| [[2004White_Size]]
| Heterogeneity classification of differently sized images
|-

| Paper
| [[2006Penczek_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Scheres_ML3D]]
| Maximum Likelihood alignment and classification in 3D
|-

| Paper
| [[2009Spahn_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2010Elmlund_AbInitio]]
| Solving the initial volume problem with multiple conformations
|-

| Paper
| [[2010Shatsky_MultiVariate]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2012Scheres_Bayesian]]
| A Bayesian view on cryo-EM structure determination
|-

| Paper
| [[2012Zheng_Covariance]]
| Estimation of the volume covariance
|-

| Paper
| [[2013Wang_MLVariance]]
| Maximum Likelihood estimate of the map variance
|-

| Paper
| [[2013Lyumkis D_FREALIGN]]
| Likelihood-based classification of cryo-EM images using FREALIGN.
|-

| Paper
| [[2014Jin_NMA]]
| Continuous heterogeneity through Normal Mode Analysis
|-

| Paper
| [[2014Dashti_Brownian]]
| Continuous heterogeneity through Brownian trajectories
|-

| Paper
| [[2014Chen_Migration]]
| Particle migration analysis in 3D classification
|-

| Paper
| [[2015Anden_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Bai_Focused]]
| Focused classification
|-

| Paper
| [[2015Katsevich_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Klaholz_MRA]]
| Multivariate Statistical Analysis of Jackknife and Bootstrapping on random subsets
|-

| Paper
| [[2015Liao_Covariance]]
| Estimation of the 3D covariance from 2D projections
|-

| Paper
| [[2015Tagare_Direct]]
| Direct reconstruction of PCA components
|-

| Paper
| [[2016Gong_Mechanical]]
| Mechanical model for macromolecules
|-

| Paper
| [[2016Rawson_Movement]]
| Movement and flexibility
|-

| Paper
| [[2016Sorzano_StructMap]]
| Sorting a discrete set of conformational states
|-

| Paper
| [[2016Sorzano_Strain]]
| Calculate local stretches, strains and rotations from two conformational states
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

|}

=== Validation ===

{|

| Paper
| [[2008Stagg_TestBed]]
| Effect of voltage, dosis, number of particles and Euler jumps on resolution
|-

| Paper
| [[2011Henderson]]
| Tilt Validation
|-

| Paper
| [[2011Read]]
| Validation of PDBs
|-

| Paper
| [[2012Henderson]]
| EM Map Validation
|-

| Paper
| [[2013Cossio_Bayesian]]
| EM Map Validation in a probabilistic setting
|-

| Paper
| [[2013Chen_NoiseSubstitution]]
| Noise substitution at high resolution for measuring overfitting
|-

| Paper
| [[2014Russo_StatisticalSignificance]]
| EM Map Validation through the statistical significance of the tilt-pair angular assignment
|-

| Paper
| [[2014Stagg_Reslog]]
| EM Map Validation through the resolution evolution with the number of particles
|-

| Paper
| [[2014Wasilewski_Tilt]]
| Web implementation of the tilt pair validation
|-

| Paper
| [[2015Heymann_Alignability]]
| EM Map Validation through the resolution of reconstructions from particles and noise
|-

| Paper
| [[2015Oliveira_FreqLimited]]
| Comparison of gold standard and frequency limited optimization
|-

| Paper
| [[2015Wriggers_Secondary]]
| Validation by secondary structure
|-

| Paper
| [[2016Kim_SAXS]]
| Comparison of SAXS data and EM projections
|-

| Paper
| [[2016Rosenthal_Review]]
| Review of validation methods
|-

| Paper
| [[2016Vargas_Alignability]]
| Validation by studying the tendency of an angular assignment to cluster in the projection space
|-

| Paper
| [[2017Monroe_PDBRefinement]]
| Validation by comparison to a refined PDB
|-

|}

=== Resolution ===

{|

| Paper
| [[1986Harauz_FBP]]
| Fourier Shell Correlation
|-

| Paper
| [[1987Unser_SSNR]]
| 2D Spectral Signal to Noise Ratio
|-

| Paper
| [[2002Penczek_SSNR]]
| 3D Spectral Signal to Noise Ratio for Fourier based algorithms
|-

| Paper
| [[2003Rosenthal_DPR]]
| Review of the FSC and establishment of a new threshold
|-

| Paper
| [[2005Unser_SSNR]]
| 3D Spectral Signal to Noise Ratio for any kind of algorithms
|-

| Paper
| [[2005VanHeel_FSC]]
| Establishment of a new threshold for FSC
|-

| Paper
| [[2007Sousa_AbInitio]]
| Resolution measurement on neighbour Fourier voxels
|-

| Paper
| [[2014Kucukelbir_Local]]
| Quantifying the local resolution of cryo-EM density maps
|-

| Paper
| [[2016Pintilie_Probabilistic]]
| Probabilistic models and resolution
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Statistical properties of resolution measures defined in Fourier space
|-

|}

=== Sharpening of high resolution information ===
{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast restoration and map sharpening
|-

| Paper
| [[2008Fernandez_Bfactor]]
| Bfactor determination and restoration
|-

| Paper
| [[2013Fiddy_SaxtonAlgorithm]]
| Phase retrieval or extension
|-

| Paper
| [[2014Kishchenko_SphericalDeconvolution]]
| Spherical deconvolution
|-

| Paper
| [[2015Spiegel_VISDEM]]
| Visualization improvement by the use of pseudoatomic profiles
|-

| Paper
| [[2016Jonic_Pseudoatoms]]
| Approximation with pseudoatoms
|-

| Paper
| [[2016Jonic_Denoising]]
| Denoising and high-frequency boosting by pseudoatom approximation
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[1982Schiske_Correction]]
| CTF correction for tilted objects
|-

| Paper
| [[1988Toyoshima_Model]]
| CTF estimation
|-

| Paper
| [[1995Frank_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1996Skoglund_MaxEnt]]
| CTF correction with Maximum Entropy
|-

| Paper
| [[1996Zhou_Model]]
| CTF model and user interface for manual fitting
|-

| Paper
| [[1997Fernandez_AR]]
| PSD estimation using periodogram averaging and AR models
|-

| Paper
| [[1997Penczek_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1997Stark_Deconvolution]]
| CTF correction using deconvolution
|-

| Paper
| [[1997Zhu_RecCTF]]
| CTF correction and reconstruction
|-

| Paper
| [[2000DeRosier_EwaldCorrection]]
| CTF correction considering the Ewald sphere
|-

| Paper
| [[2000Jensen_TiltedCorrection]]
| CTF correction considering tilt in backprojection
|-

| Paper
| [[2001Saad_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Huang_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Mindell_CTFTILT]]
| CTF estimation for tilted micrographs
|-

| Paper
| [[2003Sander_MSA]]
| CTF estimation through MSA classification of PSDs
|-

| Paper
| [[2003Velazquez_ARMA]]
| PSD and CTF estimation using ARMA models
|-

| Paper
| [[2004Sorzano_IDR]]
| CTF restoration and reconstruction with Iterative Data Refinement
|-

| Conference
| [[2004Wan_CTF]]
| Spatially variant CTF
|-

| Paper
| [[2004Zubelli_Chahine]]
| CTF restoration and reconstruction with Chahine's multiplicative method
|-

| Conference
| [[2005Dubowy_SpaceVariant]]
| CTF correction when this is space variant
|-

| Paper
| [[2005Mallick_ACE]]
| CTF estimation
|-

| Paper
| [[2006Wolf_Ewald]]
| CTF correction considering Ewald sphere
|-

| Paper
| [[2007Jonic_EnhancedPSD]]
| PSD enhancement for better identification of Thon rings; Vitreous ice diffracts in Thon rings
|-

| Paper
| [[2007Philippsen_Model]]
| CTF Model for tilted specimens
|-

| Paper
| [[2007Sorzano_CTF]]
| CTF estimation using enhanced PSDs
|-

| Paper
| [[2009Sorzano_Sensitivity]]
| Error sensitivity of the CTF models, non-uniqueness of the CTF parameters
|-

| Paper
| [[2010Jiang2010_CTFCorrection]]
| Amplitude correction method
|-

| Paper
| [[2010Kasantsev_CTFCorrection]]
| Mathematical foundations of Kornberg and Jensen method
|-

| Paper
| [[2010Leong_CTFCorrection]]
| Correction for spatially variant CTF
|-

| Paper
| [[2011Glaeser_Coma]]
| The effect of coma at high-resolution
|-

| Paper
| [[2011Mariani_Tilted]]
| CTF simulation and correction of tilted specimens
|-

| Paper
| [[2011Sindelar_Wiener]]
| CTF correction using a modified version of Wiener filter
|-

| Paper
| [[2011Voortman_Tilted]]
| CTF correction for tilted specimen
|-

| Paper
| [[2012Voortman_VaryingCTF]]
| Correcting a spatially varying CTF
|-

| Paper
| [[2013Vargas_FastDef]]
| Fast defocus
|-

| Paper
| [[2015Rohou_CTFFind4]]
| CTF Find 4
|-

| Paper
| [[2015Sheth_CTFquality]]
| Visualization and quality assessment of CTF
|-

| Paper
| [[2016Zhang_GCTF]]
| gCTF
|-

|}

=== Segmentation ===

{|

| Paper
| [[2006Baker_segmentation]]
| Segmentation of molecular subunits
|-

|}

=== Fitting and docking ===

{|

| Paper
| [[1999Volkmann_Fitting]]
| Fitting in real space
|-

| Paper
| [[2001Baker_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2001Jones_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2003Kovacs_FRM3D]]
| Fast Rotational Alignment of two EM maps
|-

| Paper
| [[2004Tama_NMA1]]
| Flexible fitting with Normal Modes (I)
|-

| Paper
| [[2004Tama_NMA2]]
| Flexible fitting with Normal Modes (II)
|-

| Paper
| [[2005Velazquez_Superfamilies]]
| Recognition of the superfamily folding in medium-high resolution volumes
|-

| Paper
| [[2007DeVries_Haddock]]
| Docking with Haddock 2.0
|-

| Paper
| [[2007Kleywegt_QualityControl]]
| Quality control and validation of fitting
|-

| Paper
| [[2012Biswas_Secondary]]
| Secondary structure determination in EM volumes
|-

| Paper
| [[2012Velazquez_Constraints]]
| Multicomponent fitting by using constraints from other information sources
|-

| Paper
| [[2013Chapman MS_Atomicmodeling]]
| Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters
|-

| Paper
| [[2013Esquivel_Modelling]]
| Review on modelling (secondary structure, fitting, ...)
|-

| Paper
| [[2013Lopez_Imodfit]]
| Fitting based on vibrational analysis
|-

| Paper
| [[2013Nogales_3DEMLoupe]]
| Normal Mode Analysis of reconstructed volumes
|-

| Paper
| [[2014AlNasr_Secondary]]
| Identification of secondary structure elements in EM volumes
|-

| Paper
| [[2014Politis_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Rey_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Villa_Review]]
| Review of atomic fitting into EM volumes
|-

| Paper
| [[2015Barad_EMRinger]]
| Validation of hybrid models
|-

| Paper
| [[2015Bettadapura_PF2Fit]]
| Fast rigid fitting of PDBs into EM maps
|-

| Paper
| [[2015Carrillo_CapsidMaps]]
| Analysis of virus capsids using Google Maps
|-

| Paper
| [[2015Schroeder_Hybrid]]
| Review on model building
|-

| Paper
| [[2015Tamo_Dynamics]]
| Dynamics in integrative modeling
|-

| Paper
| [[2015Sorzano_AtomsToVoxels]]
| Accurate conversion of an atomic model into a voxel density volume
|-

| Paper
| [[2016Joseph_Evolution]]
| Evolutionary constraints for the fitting of atomic models into density maps
|-

| Paper
| [[2016Segura_3Diana]]
| Validation of hybrid models
|-

| Paper
| [[2016Singharoy_MDFF]]
| Construction of hybrid models driven by EM density and molecular dynamics
|-

| Paper
| [[2016Wang_Rosetta]]
| Construction of hybrid models driven by EM density using Rosetta
|-

| Paper
| [[2017Hryc_WeightedAtoms]]
| Construction of hybrid models by locally weighting the different atoms
|-

| Paper
| [[2017Matsumoto_Distribution]]
| Estimating the distribution of conformations of atomic models
|-

|}

=== Books and reviews ===

{|

| Book
| [[1980Herman_Tomography]]
| General book on tomography
|-

| Book
| [[1988Kak_Tomography]]
| General book on tomography
|-

| Paper
| [[2000Tao_Review]]
| Review of single particles
|-

| Paper
| [[2000VanHeel_Review]]
| Review of single particles
|-

| Paper
| [[2002Frank_Review]]
| Review of single particles
|-

| Paper
| [[2002Schmid_Review]]
| Review of single particles
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2004Subramaniam_Review]]
| Review of single particles
|-

| Paper
| [[2005Steven_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_book]]
| Book covering all aspects of electron microscopy of single particles
|-

| Paper
| [[2006Sorzano_Review]]
| Review of optimization problems in electron microscopy
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems in Electron Tomography
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2008Mueller_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2008Taylor_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2010DeRosier_Review]]
| Personal account of how 3DEM developed in the early days
|-

| Chapter
| [[2012Sorzano_Review]]
| Review of single particle analysis using Xmipp
|-

| Chapter
| [[2012Devaux_Protocol]]
| Protocols for performing single particle analysis
|-

| Paper
| [[2014Bai_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Carazo_Review]]
| Review of the reconstruction process
|-

| Paper
| [[2015Cheng_Review]]
| A primer to Single Particle Cryo-EM
|-

| Paper
| [[2015Cheng_Reviewb]]
| Single Particle Cryo-EM at crystallographic resolution
|-

| Paper
| [[2015Elmlund_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Henderson_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Nogales_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Schroeder_Review]]
| Review of advances in the electron microscope
|-

| Paper
| [[2015Wu_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Carroni_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Egelman_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Eisenstein_CryoEM]]
| News feature on the Method of the Year
|-

| Paper
| [[2016FernandezLeiro_Review]]
| Review of EM
|-

| Paper
| [[2016Glaeser_HowGood]]
| How good can cryo-EM become?
|-

| Paper
| [[2016Jonic_PseudoAtoms]]
| Review of the applications of the use of pseudoatoms in EM
|-

| Chapter
| [[2016Mio_Review]]
| Overview of the process to obtain EM reconstructions
|-

| Paper
| [[2016Jonic_Review]]
| A review of computational ways to handle heterogeneity
|-

| Paper
| [[2016Nogales_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Subramaniam_Review]]
| Why cryo-EM is now suitable for crystallographic journals
|-

| Paper
| [[2016Vinothkumar_Review]]
| Historical review and current limitations
|-

| Paper
| [[2017Frank_Review]]
| Historical review of EM
|-

| Paper
| [[2017Jonic_Review]]
| Review of computational methods to analyze conformational variability
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Review of statistical properties of resolution measures defined in Fourier space
|-
|}

=== Software ===

{|

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[1999Lutdke_Eman]]
| Eman
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Baldwin_AngularTransformations]]
| The Transform Class in SPARX and EMAN2
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Grigorieff_Frealign]]
| Frealign
|-

| Paper
| [[2008Scheres_XmippProtocols]]
| Xmipp Protocols
|-

| Paper
| [[2008Shaikh_SpiderProtocols]]
| Spider Protocols
|-

| Paper
| [[2012Wriggers_SitusConventions]]
| Conventions and workflows in Situs
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2015Cianfrocco_Cloud]]
| Software execution in the cloud
|-

| Paper
| [[2015Cheng_MRC2014]]
| Extensions to MRC file format
|-

| Paper
| [[2013DeLaRosa_Scipion]]
| Scipion
|-

| Paper
| [[2016Scheres_Relion]]
| Tutorial on the use of Relion
|-

| Paper
| [[2016Grigorieff_Frealign]]
| Tutorial on the use of Frealign
|-

|}

== Electron tomography ==

=== Image preprocessing ===

{|

| Paper
| [[2015Yan_thickness]]
| Determination of thickness, tilt and electron mean free path
|-

|}

=== Image alignment ===

{|

| Paper
| [[1982Guckenberger_commonOrigin]]
| Determination of a common origin in the micrographs of titl series in three-dimensional electron microscopy
|-

| Paper
| [[1992Lawrence_leastSquares]]
| Least squares solution of the alignment problem
|-

| Paper
| [[1995Penczek_dual]]
| Dual tilt alignment
|-

| Paper
| [[1996Owen_alignmentQuality]]
| Automatic alignment without fiducial markers and evaluation of alignment quality
|-

| Paper
| [[1998Grimm_normalization]]
| Discussion of several gray level normalization methods for electron tomography
|-

| Paper
| [[2001Brandt_Automatic1]]
| Automatic alignment without fiducial markers
|-

| Paper
| [[2001Brandt_Automatic2]]
| Automatic alignment with fiducial markers
|-

| Paper
| [[2006Winkler_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2006Castano_alignment]]
| Alignment with non-perpendicularity
|-

| Paper
| [[2007Castano_alignment]]
| Fiducial-less alignment of cryo-sections
|-

| Paper
| [[2009Sorzano_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2010Cantele_dualAlignment]]
| Alignment of dual series
|-

| Paper
| [[2014Tomonaga_Automatic]]
| Automatic alignment of tilt series using the projection themselves
|-

| Paper
| [[2014Han_Automatic]]
| Automatic alignment of tilt series using SIFT features
|-

| Paper
| [[2015Han_Automatic]]
| Automatic alignment of tilt series using fiducials
|-

| Paper
| [[2017Mastronarde_Automatic]]
| Automatic alignment and reconstruction of tilt series in IMOD
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[2003Winkler_CTF]]
| Focus gradient correction in electron tomography
|-

| Paper
| [[2006Fernandez_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Zanetti_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Xiong_CTF]]
| CTF determination and correction for low dose tomographic tilt series
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2017Kunz_3DCTF]]
| 3D CTF Correction
|-

|}

=== 3D reconstruction ===

{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1992Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[1997Marabini_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2002Fernandez_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2007Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[2008Fernandez_CARP]]
| Component Averaged Row Projections (CARP)
|-

| Paper
| [[2012Herman General Superiorization]]
| Superiorization: an optimization heuristic for medical physics
|-

| Paper
| [[2012Zhang_IPET_FETR]]
| IPET and FETR, a reconstruction algorithm for single molecule tomography
|-

| Paper
| [[2013Goris_SIRT_TV_DART]]
| Combination of SIRT, Total Variation and Discrete ART to reconstruct and segment at the same time
|-

| Paper
| [[2013Briegel A_Challenge]]
| The challenge of determining handedness in electron tomography and the use of DNA origami gold nanoparticle helices as molecular standards
|-

| Paper
| [[2013Messaoudi_EnergyFiltered]]
| 3D Reconstruction of Energy-Filtered TEM
|-

| Paper
| [[2016Deng_ICON]]
| 3D Reconstruction with missing information restoration
|-

| Paper
| [[2016Guay_Compressed]]
| 3D Reconstruction using compressed sensing
|-

|}

=== Noise reduction ===
{|

| Paper
| [[2001Frangakis_NAD]]
| Noise reduction with Nonlinear Anisotropic Diffusion
|-

| Paper
| [[2003Fernandez_AND]]
| Anisotropic nonlinear diffusion for electron tomography
|-

| Paper
| [[2003Jiang_Bilateral]]
| Bilateral denoising filter in electron microscopy
|-

| Paper
| [[2005Fernandez_AND]]
| Anisotropic nonlinear denoising in electron tomography
|-

| Paper
| [[2007Heide_median]]
| Iterative median filtering in electron tomography
|-

| Paper
| [[2007Fernandez_autAND]]
| Anisotropic nonlinear diffusion with automated parameter tuning
|-

| Paper
| [[2009Fernandez_Beltrami]]
| Nonlinear filtering based on Beltrami flow
|-

| Paper
| [[2010Bilbao_MeanShift]]
| Mean Shift Filtering
|-

| Paper
| [[2014Kovacik_wedgeArtefacts]]
| Removal of wedge artefacts
|-

| Paper
| [[2014Maiorca_beadArtefacts]]
| Removal of gold bead artefacts
|-

|}

=== Segmentation ===

{|

| Paper
| [[2002Frangakis_Eigenanalysis]]
| Segmentation using eigenvector analysis.
|-

| Paper
| [[2002Volkmann_Watershed]]
| Segmentation using watershed transform.
|-

| Paper
| [[2003Bajaj_BoundarySegmentation]]
| Segmentation based on fast marching.
|-

| Paper
| [[2005Cyrklaff_Thresholding]]
| Segmentation using optimal thresholding.
|-

| Paper
| [[2007Lebbink_TemplateMatching]]
| Segmentation using template matching.
|-

| Paper
| [[2007Sandberg_OrientationFields]]
| Segmentation using orientation fields.
|-

| Paper
| [[2007Sandberg_SegmentationReview]]
| Review on segmentation in electron tomography.
|-

| Paper
| [[2008Garduno_FuzzySegmentation]]
| Segmentation using fuzzy set theory principles.
|-

| Paper
| [[2009Lebbink_TemplateMatching2]]
| Segmentation using template matching.
|-

| Paper
| [[2012RubbiyaAli_EdgeDetection]]
| Parameter-Free Segmentation of Macromolecular Structures.
|-

| Conference
| [[2015Xu_TemplateMatching]]
| Detection of macromolecular complexes with a reduced representation of the templates.
|-

|}

=== Resolution ===
{|

| Paper
| [[2005Cardone_Resolution]]
| Resolution criterion for electron tomography
|-

| Chapter
| [[2007Penczek_Resolution]]
| Review of resolution criteria for electron tomography
|-

| Paper
| [[2015Diebolder_ConicalFSC]]
| Conical Fourier Shell Correlation
|-

|}

=== Subtomogram analysis ===

{|

| Paper
| [[2000Bohm_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2002Frangakis_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2006Nickell_Review]]
| Review of macromolecule finding by template matching (Visual Proteomics)
|-

| Paper
| [[2007Best_Review]]
| Review of Localization of Protein Complexes by Pattern Recognition
|-

| Paper
| [[2007Forster_Review]]
| Review of structure determination by subtomogram averaging
|-

| Paper
| [[2008Forster_Classification]]
| Classification of subtomograms using constrained correlation
|-

| Paper
| [[2008Bartesaghi_Classification]]
| Classification and averaging of subtomograms
|-

| Paper
| [[2008Schmid_Averaging]]
| Alignment and averaging of subtomograms
|-

| Paper
| [[2010Amat_Averaging]]
| Alignment and averaging of subtomograms exploiting thresholding in Fourier space
|-

| Paper
| [[2013Chen_Averaging]]
| Fast alignment of subtomograms using spherical harmonics
|-

| Paper
| [[2013Kuybeda_Averaging]]
| Alignment and averaging of subtomograms using the nuclear norm of the cluster
|-

| Paper
| [[2013Shatsky_Averaging]]
| Alignment and averaging of subtomograms with constrained cross-correlation
|-

| Paper
| [[2014Chen_Autofocus]]
| Subtomogram averaging and classification with special attention to differences
|-

| Paper
| [[2014Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2014Voortman_LimitingFactors]]
| Limiting factors of subtomogram averaging
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2015Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2016Bharat_Relion]]
| Subtomogram averaging with Relion
|-

| Paper
| [[2016Song_MatrixNorm]]
| Matrix norm minimization for tomographic reconstruction and alignment
|-

| Paper
| [[2017Castano_ParticlePicking]]
| Particle picking in tomograms for subtomogram averaging
|-

|}

=== Single particle tomography ===

{|

| Paper
| [[2012Bartesaghi_Constrained]]
| 3D reconstruction by imposing geometrical constraints
|-

| Paper
| [[2015Galaz_SingleParticleTomography]]
| Set of tools for Single Particle Tomography in EMAN2
|-

| Paper
| [[2016Galaz_SingleParticleTomography]]
| Alignment algorithms and CTF correction
|-

|}

=== Books and reviews ===

{|

| Paper
| [[2000Baumeister_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Koster_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Sali_Review]]
| Review of electron tomography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2005Lucic_Review]]
| Review of electron tomography
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_TomoBook]]
| Electron Tomography
|-

| Book
| [[2007McIntosh_Book]]
| Cellular Electron Microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2012Kudryashev_Review]]
| Review of subtomogram averaging
|-

| Paper
| [[2016Beck_Review]]
| Review of molecular sociology
|-

|}

=== Software ===

{|

| Paper
| [[1996Kremer_IMOD]]
| IMOD
|-

| Paper
| [[1996Chen_Priism/IVE]]
| Priism/IVE
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2005Nickell_TOM]]
| TOM Toolbox
|-

| Paper
| [[2007Messaoudi_TomoJ]]
| TomoJ
|-

| Paper
| [[2008Heymann_BsoftTomo]]
| Bsoft
|-

| Paper
| [[2015Ding_CaltechTomography]]
| Caltech tomography database
|-

| Paper
| [[2015Noble_AppionProtomo]]
| Batch fiducial-less tilt-series alignment in Appion using Protomo
|-

| Paper
| [[2015vanAarle_Astra]]
| ASTRA Toolbox
|-

|}

== 2D Crystals ==

=== 2D Preprocessing ===

{|

| Paper
| [[1986Henderson_Processing]]
| General 2D processing
|-

| Paper
| [[2000He_PhaseAlignment]]
| Phase consistency and Alignment
|-

| Paper
| [[2006Gil_Unbending]]
| Crystal unbending
|-

|}

=== Classification ===
{|

| Paper
| [[1988Frank_Classification]]
| MSA and classification in electron crystallography
|-

| Paper
| [[1996Fernandez_SOM]]
| Classification based on self organizing maps
|-

| Paper
| [[1998Sherman_MSA]]
| Classification based on MSA
|-

|}
=== 3D Reconstruction ===

{|

| Paper
| [[1985Wang_Solvent]]
| Solvent flattening
|-

| Paper
| [[1990Henderson_Processing]]
| General 3D processing
|-

| Paper
| [[2004Marabini_ART]]
| Algebraic Reconstruction Technique with blobs for crystals (Xmipp)
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1998Walz_Review]]
| Review of 2D crystallography
|-

| Paper
| [[1999Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Ellis_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of single particles, electron tomography and crystallography
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Gipson_2dx]]
| 2dx
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Philippsen_IPLT]]
| IPLT
|-

|}

== 3D Crystals - MicroED ==

=== Sample Preparation ===
{|
| Paper
| [[2016Shi_Preparation]]
| Sample Preparation
|}
=== Data Collection ===
{|
| Paper
| [[2014Nannenga_CR]]
| Continuous rotation

|}
=== Data Processing ===
{|

| Paper
| [[2011Wisedchaisri_PhaseExtension]]
| Fragment-based phase extension
|-

| Paper
| [[2015Hattne_Processing]]
| Data Processing
|-

| Paper
| [[2016Hattne_Correction]]
| Image correction
|}

=== Software ===
{|

| Paper
| [[2014Iadanza_Processing]]
| Data Processing of still diffraction data
|}

=== Books and Reviews ===
{|
| Paper
| [[2014Nannenga_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Liu_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Rodriguez_Review ]]
| Review of MicroED
|-

|}

== Helical particles ==

=== Filament corrections ===

{|

| Paper
| [[1986Egelman_Curved]]
| Algorithm for correcting curved filaments
|-

| Paper
| [[1988Bluemke_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2006Wang_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2016Yang_Flexible]]
| Algorithm for correcting filaments with flexible subunits
|-

|}

=== Reconstruction ===

{|

| Paper
| [[1952Cochran_Fourier]]
| Fourier Bessel transform of filamentous structures
|-

| Paper
| [[1958Klug_Fourier]]
| Fourier Bessel decomposition of the projection images
|-

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2005Wang_Iterative]]
| Iterative Fourier-Bessel algorithm
|-

| Paper
| [[2007Egelman_Iterative]]
| Iterative real-space algorithm
|-

| Paper
| [[2013Desfosses_Spring]]
| Helical processing with Spring
|-

| Paper
| [[2015Zhang_seam]]
| Workflow for the detection of the lattice seam
|-

| Paper
| [[2016Rohou_Frealix]]
| Helical processing with Frealix
|-

|}

=== Validation ===

{|

| Paper
| [[2014Egelman_ambiguity]]
| How to detect incorrect models
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Carragher_Phoelix]]
| Phoelix
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Owen_Brandeis]]
| Brandeis
|-

|}

== Icosahedral particles ==

=== Reconstruction ===

{|

| Paper
| [[1970Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1971Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1996Fuller_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1997Thuman_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

|}

=== Classification ===

{|

| Paper
| [[2005Scheres_Virus]]
| Classification of virus capsids in real space
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1999Baker_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[1999Conway_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2000Thuman_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Lee_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Navaza_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2006Grunewald_Review]]
| Review of reconstruction of icosahedral viruses
|-

|}

=== Software ===

{|

| Paper
| [[1996Baker_EMPFT]]
| EMPFT
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2013Morin_Sliz SBGrid]]
| SBGrid presentation for eLife
|-

|}

== Databases ==

{|

| Paper
| [[2003Boutselakis_EMSD]]
| EMSD database
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2011Kim_CDDB]]
| Conformational Dynamics Data Bank
|-

| Paper
| [[2011Lawson_EMDB]]
| Electron Microscopy Data Bank
|-

| Paper
| [[2013Ison_EDAM]]
| EDAM, an ontology of bioinformatics operations
|-

| Paper
| [[2016Iudin_EMPIAR]]
| EMPIAR raw data database
|-

| Paper
| [[2016Patwhardan_EMDB]]
| EMDB, PDB, ...
|-

| Paper
| [[2017Patwhardan_Trends]]
| Trends at EMDB
|-

| Paper
| [[2017Shao_PDBQuality]]
| Quality metrics in PDB
|-

| Blog
| http://www.mybiosoftware.com
| Huge list of bioinformatics programs (many of them structural bioinformatics)
|-

|}

== Relationship to other structural information sources ==

{|

| Paper
| [[2000Engel_AFM]]
| Review of Atomic Force Microscopy
|-

| Paper
| [[2001Dimmeler_AFM]]
| Constraints from Atomic Force Microscopy
|-

| Paper
| [[2003Mobus_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_Review]]
| Review on correlative microscopy
|-

| Paper
| [[2005Boudier_EFTETJ]]
| Software for Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2005Vestergaard_SAXS]]
| Example of comparison of 3DEM and Small-angle X-ray scattering
|-

| Paper
| [[2007Hamada_SAXS]]
| Constraints from Small-angle X-ray scattering
|-

| Paper
| [[2013Xu_FRET]]
| EM+FRET
|-

|}

== X-ray tomography ==

{|

| Paper
| [[2012Oton_ImageFormation]]
| Image formation model in X-ray cell microscopy
|-

|}

== Mathematical tools necessary ==

== People developing methods ==
Please, add yourself to this list (due to privacy reasons, please, do not add anyone else to the list without his/her explicit consent). Sort by first name alphabetical order.

[http://biocomp.cnb.csic.es/~coss Carlos Oscar S. Sorzano]: CSIC, Madrid, Spain 

[http://www.curie.fr/recherche/themes/detail_equipe.cfm/lang/_fr/id_equipe/241.htm Cédric Messaoudi]: Institute Curie, Paris, France 

[http://scholar.google.es/citations?user=_jNYGScAAAAJ&hl=en Javier Vargas]:[mailto:jvargas@cnb.csic.es mail]: CSIC, Madrid, Spain 

[http://scholar.google.es/citations?hl=es&user=g2ZJPIYAAAAJ Joaquín Otón]: CSIC, Madrid, Spain 

[mailto:jrbcast@gmail.com José Román Bilbao-Castro]: UAL, Almería, Spain; CSIC, Madrid, Spain 

[José Miguel de la Rosa Trevín]: Biocomputing Unit CNB-CSIC, Madrid, Spain 

[http://cryoem.janelia.org Tamir Gonen]: [mailto:gonent@janelia.hhmi.org mail]: Howard Hughes Medical Institute, Ashburn, VA, USA 

[mailto:vabrishami@cnb.csic.es Vahid Abrishami]: CSIC, Madrid, Spain 

== 3DEM sites ==
* [http://3dem.ucsd.edu/ 3DEM web site]

* [http://en.wikibooks.org/wiki/Software_Tools_For_Molecular_Microscopy Software tools for molecular microscopy]

* [http://www.emdatabank.org/ The Electron Microscopy Data Bank (EMDB)]

* [http://ccdb.ucsd.edu The Cell Centered Database (CCDB)]

* [http://conventions.cnb.csic.es The geometrical software conventions web page ]

== Editing useful links ==

* [http://www.mediawiki.org/wiki/Help:Formatting Text formatting in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Links Adding links in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Images Adding images in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Tables Making tables in Mediawiki]

2017Matsumoto Distribution

2017-05-17T06:12:49Z

CoSS: Created page with "== Citation == Matsumoto, A.; Miyazaki, N.; Takagi, J. & Iwasaki, K. 2D hybrid analysis: Approach for building three-dimensional atomic model by electron microscopy image mat..."

== Citation ==

Matsumoto, A.; Miyazaki, N.; Takagi, J. & Iwasaki, K. 2D hybrid analysis: Approach for building three-dimensional atomic model by electron microscopy image matching. Scientific reports, 2017, 7, 377

== Abstract ==

In this study, we develop an approach termed "2D hybrid analysis" for building atomic models by image matching from electron microscopy (EM) images of biological molecules. The key advantage is that it is applicable to flexible molecules, which are difficult to analyze by 3DEM approach. In the proposed approach, first, a lot of atomic models with different conformations are built by computer simulation. Then, simulated EM images are built from each atomic model. Finally, they are compared with the experimental EM image. Two kinds of models are used as simulated EM images: the negative stain model and the simple projection model. Although the former is more realistic, the latter is adopted to perform faster computations. The use of the negative stain model enables decomposition of the averaged EM images into multiple projection images, each of which originated from a different conformation or orientation. We apply this approach to the EM images of integrin to obtain the distribution of the conformations, from which the pathway of the conformational change of the protein is deduced.

== Keywords ==

== Links ==

https://www.ncbi.nlm.nih.gov/pubmed/28336911

== Related software ==

== Related methods ==

== Comments ==

Main Page

2017-05-17T06:11:55Z

CoSS: /* Fitting and docking */

== Presentation ==

This web page is intended to be an extensive repository of three-dimensional electron microscopy (3DEM) methods. The advantages of having such a repository are

* You know which are the relevant articles in a particular topic, therefore, paper introductions, reviews, etc. are easier to write and you make sure you will cite all the related articles.
* You will be sure that your paper has more chances of being cited.
* You can add whatever information you find relevant to your method, external links, links to other papers, etc.
* You can link your method to a web page providing the corresponding software, so you know people can use your algorithms.
* You can use the Wiki search capabilities to locate relevant articles even if they are not at the topic you are looking at.
* As a community we will "reconstruct" our history.
* You can select the "watch" option above to receive notifications in case of further changes in the Main Page.

Developing image processing methods for 3DEM is not "[[well-paid]]" in terms of citations and impact factor. However, it is crucial for the advance of the field. Gathering methodological papers in a portal will help to increase the recognition of the field.

Please:

* Add your articles at the right place (you can add a single article in several topics if it is relevant to all of them). The easiest way to add an article is by editing the corresponding topic in the main page, adding your entry, then save the main page. Click on the red link that appears on your new entry, copy and paste the Wiki following code, add the information of your article

== Citation ==

== Abstract ==

== Keywords ==

== Links ==

== Related software ==

== Related methods ==

== Comments ==

* Maintain the information of each article as complete as possible.
* Sort articles by years and authors.
* Be respectful to other people's work.

== How to subscribe to this page ==

You may subscribe to this page so that you will be notified every time someone adds a new method. To do so, you have to register in the page, and edit your preferences ("my preferences"). Be sure that you have activated the option "E-mail me when a page on my watchlist is changed". Finally, click on the "Watch" tab at the top of this page.

You may subscribe to changes on this page on the mailing list 3demmethods@cnb.csic.es. To send a new method to this mail list just send a mail to 3demmethods@cnb.csic.es

To subscribe to this list, visit the web page

https://listas.csic.es/cnb/wws/subscribe/3demmethods

Alternatively, you may write a mail to sympa6@cnb.csic.es with the subject

<code>subscribe 3demmethods YourName YourFamilyName</code>

and an empty mail body.

To unsubscribe visit the page

https://listas.csic.es/cnb/wws/sigrequest/3demmethods

or write sympa6@cnb.csic.es with the subject

<code>unsubscribe 3demmethods</code>

and an empty mail body.

== Electron microscopy images ==

=== Online courses ===

CALTECH: http://cryo-em-course.caltech.edu/

MRC: ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/EM-course/

CNB-CSIC: http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/MadridJan2014EM

Workshop on Computational methods for CryoEM: https://www.youtube.com/watch?v=XdKO1iaPP8o

Workshop on Management of large CryoEM facilities: https://www.youtube.com/watch?v=as4seOPszL0

Icknield Course on Model Building and Refinement for High Resolution EM Maps: http://www.ccpem.ac.uk/training/icknield_2017/icknield_2017.php

=== Image formation ===

{|

| Paper
| [[1971Erickson_CTF]]
| CTF model
|-

| Paper
| [[1971Glaeser_Damage]]
| Radiation damage
|-

| Chapter
| [[1971Hanszen_CTF]]
| Image formation model
|-

| Paper
| [[1971Thon_Model]]
| CTF model
|-

| Paper
| [[1975Unwin_Imaging]]
| Radiation dose
|-

| Paper
| [[1977Wade_Model]]
| CTF model
|-

| Paper
| [[1978Wade_Model]]
| CTF model
|-

| Paper
| [[1979Hayward_Radiation]]
| Radiation damage
|-

| Paper
| [[1984Cohen_Validity]]
| Validity of the CTF model at high frequencies
|-

| Paper
| [[1988Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[1992Wade_Model]]
| CTF model
|-

| Paper
| [[1993Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2004Egerton_Damage]]
| Radiation damage
|-

| Paper
| [[2004Sorzano_Normalization]]
| Background noise is Gaussian
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2009Baxter_NoiseCharacterization]]
| Characterization of the different noise sources in cryo-EM
|-

| Paper
| [[2010Baker_Damage]]
| Radiation damage dependence on resolution
|-

| Paper
| [[2010Bammes_Damage]]
| Radiation damage dependence on temperature
|-

| Paper
| [[2010Gomez_Multislice]]
| Simulation of the multi slice model
|-

| Paper
| [[2010Zewail_FourDimensional]]
| Review on the use of ultrafast EM
|-

| Paper
| [[2011Bammes_CCD]]
| Performance of CCD cameras
|-

| Paper
| [[2011Glaeser_Coma]]
| Image formation model including coma
|-

| Paper
| [[2011Milazzo_DirectDetectors]]
| Evaluation of Direct Detectors
|-

| Paper
| [[2011Rullgard_ImageSimulation]]
| Accurate simulation of EM images
|-

| Paper
| [[2011Zhang LimitingFactors]]
| Limiting factor for atomic resolution in EM
|-

| Paper
| [[2012Bammes_DirectDetection]]
| Performance of Direct detectors
|-

| Paper
| [[2012Campbell_MotionCorrection]]
| Beam induced motion correction and direct detectors
|-

| Paper
| [[2012Shang_HydrationLayer]]
| Simulation of PDB volumes explicitly considering the hydration layer
|-

| Paper
| [[2013Egerton_RadiationDamage]]
| Review of TEM radiation damage and experimental ways of reducing it
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu H_Noisemodels]]
| Noise models and cryo-EM drift correction with a direct-electron camera
|-

| Paper
| [[2013Li X K2 noisemodels]]
| Influence of electron dose rate on electron counting images recorded with the K2 camera
|-

| Paper
| [[2013Vulovic_CTFApproximations]]
| When to use the different approximations performed so that a projection with linear CTF is valid
|-

| Thesis
| [[2013Vulovic_ImageFormation]]
| Ph.D. Thesis on the image formation in cryo-EM
|-

| Paper
| [[2014Danev_PhasePlate]]
| Volta potential phase plate
|-

| Paper
| [[2015Chiu_K2]]
| Characterization of K2
|-

| Paper
| [[2015Hawkes_AberrationCorrection]]
| Historical account of the development of lens corrections
|-

| Paper
| [[2015Koeck_Quadratic]]
| Limitations of the linear approximation and use of the quadratic terms
|-

| Paper
| [[2015Kuijper_FEI]]
| Description of the FEI Falcons
|-

| Paper
| [[2015Lobato_MULTEM]]
| Simulation of multislice diffraction
|-

| Paper
| [[2015McMullan_AmorphousIce]]
| Beam induced movement is caused by Brownian motion
|-

| Paper
| [[2016Koeck_ADF]]
| Simulations of Annular Dark Field TEM
|-

| Paper
| [[2017Mishyna_DNARadiation]]
| Review of radiation damage on DNA
|-

|}

=== Collection geometry ===

{|

| Chapter
| [[1980Hoppe_Wedge]]
| Missing wedge
|-

| Paper
| [[1987Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1995Penczek_Dual]]
| Dual axis tomography
|-

| Paper
| [[1997Mastronarde_Dual]]
| Dual axis tomography
|-

| Paper
| [[2003Ludtke_FocusPairs]]
| Focus pairs for single particles
|-

| Paper
| [[2005Lanzavecchia_Conical]]
| Conical tomography
|-

| Paper
| [[2005Zampighi_Conical]]
| Conical tomography
|-

| Paper
| [[2006Leschziner_OT]]
| Orthogonal Tilt
|-

| Paper
| [[2006Messaoudi_Multiple]]
| Multiple axis tomography
|-

| Paper
| [[2012Kudryashev_FocusPairs]]
| Focus pairs tomography
|-

| Paper
| [[2014Hovden_TiltFocus]]
| Combining tilt series with focus series
|-

| Paper
| [[2015Sorzano_RandomConicalTilt]]
| General formulation of Random Conical Tilt
|-

| Paper
| [[2017Hagen_DoseTomography]]
| Dose optimization for subtomogram averaging
|-

|}

=== Sample preparation ===

{|

| Paper
| [[1982Dubochet_Sample]]
| Vitreous ice
|-

| Paper
| [[1986Lepault_Sample]]
| Fast freezing
|-

| Paper
| [[1995Dubochet_Sample]]
| High-pressure freezing
|-

| Paper
| [[1995VanMarle_Sample]]
| Sample damages in resin
|-

| Paper
| [[1998Adrian_Sample]]
| Cryo negative staining
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2002Hsieh_Sample]]
| Cryofixation
|-

| Paper
| [[2004AlAmoudi_Sample]]
| CEMOVIS
|-

| Paper
| [[2008Studer_Sample]]
| Review on high pressure freezing
|-

| Paper
| [[2009Pierson_Sample]]
| Review on sample preparation for electron tomography
|-

| Paper
| [[2010Zhang_NegativeStaining]]
| Negative staining for small protein imaging
|-

| Paper
| [[2012Zhang_PositiveStaining]]
| Positive staining
|-

| Paper
| [[2014Rames_NegativeStaining]]
| Optimized negative staining
|-

| Paper
| [[2014Russo_GoldGrids]]
| Gold grids for single particles
|-

| Paper
| [[2015Cabra_Sample]]
| Review on sample preparation for single particles with videos
|-

| Paper
| [[2016Passmore_Review]]
| Tutorial chapter on sample preparation
|-

| Paper
| [[2016Razinkov_Vitrification]]
| New vitrification method
|-

| Paper
| [[2016Takizawa_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2016Thompson_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2017Arnold_BlottingFree]]
| Blotting-free preparation
|-

| Paper
| [[2017Peitsch_Sample]]
| iMEM: Isolation of Plasma Membrane for Cryoelectron Microscopy
|-

| Paper
| [[2017Schaffer_FocusedIonBeam]]
| Focused Ion Beam sample preparation for membrane proteins
|-

|}

=== Automated data collection ===

{|

| Paper
| [[1992Dierksen_Automatic]]
| Automated data collection
|-

| Paper
| [[1992Koster_Automatic]]
| Automated data collection
|-

| Paper
| [[1996Fung_Automatic]]
| Automated data collection for tomography
|-

| Paper
| [[2001Zhang_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2003Ziese_Automatic]]
| Automated autofocusing
|-

| Paper
| [[2004Potter_Automatic]]
| Automated sample loading
|-

| Paper
| [[2004Zheng_Automatic]]
| Automated data collection
|-

| Paper
| [[2005Lei_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2005Suloway_Automatic]]
| Automated data collection: Leginon
|-

| Paper
| [[2007Yoshioka_RCT]]
| Automated Random Conical Tilt
|-

| Paper
| [[2011Korinek_TOM2]]
| Automated acquisition with TOM2
|-

| Paper
| [[2015Li_UCSFImage]]
| Automated acquisition with UCSFImage
|-

| Paper
| [[2016Gil_Fuzzy]]
| Real time decisions during acquisition with neuro-fuzzy method
|-

| Paper
| [[2016Liu_TiltControl]]
| Accurate control of the tilt angle for electron tomography
|-

| Paper
| [[2016Vargas_FoilHole]]
| Determination of image quality at low magnification
|-

|}

== Single particles ==

=== Automatic particle picking ===

{|

| Paper
| [[1982VanHeel_Detection]]
| Detection of particles in micrographs
|-

| Paper
| [[2001Nicholson_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2001Zhu_Filaments]]
| Automatic identification of filaments in micrographs
|-

| Paper
| [[2004Sigworth_Detection]]
| Classical detection theory and the cryo-EM particle selection problem
|-

| Paper
| [[2004Volkmann_ParticlePicking]]
| An approach to automated particle picking from electron micrographs based on reduced representation templates
|-

| Paper
| [[2004Wong_ParticlePicking]]
| Model-based particle picking for cryo-electron microscopy
|-

| Paper
| [[2004Zhu_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2007Chen_Signature]]
| Automatic particle picking program: Signature
|-

| Paper
| [[2007Woolford_SwarmPS]]
| Automatic particle picking with several criteria, implemented in EMAN Boxer
|-

| Paper
| [[2009Sorzano_MachineLearning]]
| Automatic particle picking based on machine learning of rotational invariants
|-

| Paper
| [[2011Arbelaez_Comparison]]
| Evaluation of the performance of software for automated particle-boxing
|-

| Paper
| [[2013Abrishami_MachineLearning]]
| A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs
|-

| Paper
| [[2013Hauer_2013]]
| Automatic tilt pair detection in Random Conical Tilt
|-

| Paper
| [[2013Shatsky_ParticlePicking]]
| Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Langlois_ParticlePicking]]
| Automatic particle picking
|-

| Paper
| [[2016Vilas_AutomaticTilt]]
| Automatic identification of image pairs in untilted-tilted micrograph pairs
|-

|}

=== 2D Preprocessing ===

{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast enhancement through DPR
|-

| Paper
| [[2004Sorzano_Normalization]]
| Normalization procedures and their statistical properties.
|-

| Paper
| [[2006Sorzano_Denoising]]
| Strong denoising in wavelet space
|-

| Conference
| [[2009Sorzano_Downsampling]]
| Differences between the different downsampling schemes
|-

| Paper
| [[2012Brilot_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Campbell_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Zhao_Denoising]]
| Denoising using an invariant Fourier-Bessel eigenspace
|-

| Paper
| [[2013Norousi_Screening]]
| Screening particles to identify outliers
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu_Movies]]
| Drift correction for movies considering dark field
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Scheres_Movies]]
| Beam induced motion correction
|-

| Paper
| [[2015Abrishami_Movies]]
| Alignment of direct detection device micrographs
|-

| Paper
| [[2015Grant_Anisotropic]]
| Automatic estimation and correction of anisotropic magnification
|-

| Paper
| [[2015Grant_OptimalExposure]]
| Filter movies according to the radiation damage
|-

| Paper
| [[2015Rubinstein_Alignment]]
| Frame alignment at the level of particle
|-

| Paper
| [[2015Spear_DoseCompensation]]
| Effect of dose compensation on resolution
|-

| Paper
| [[2015Zhao_AnisotropicMagnification]]
| Correction of anisotropic magnification
|-

| Conference
| [[2016Bajic_Denoising]]
| Denoising and deconvolution of micrographs
|-

| Paper
| [[2016Jensen_RemovalVesicles]]
| Removal of vesicles in membrane proteins
|-

| Paper
| [[2016Bhamre_Denoising]]
| Denoising by 2D covariance estimation
|-

| Paper
| [[2017McLeod_Zorro]]
| Movie alignment by Zorro
|-

| Paper
| [[2017Zheng_MotionCorr2]]
| Movie alignment by MotionCorr2
|-

|}

=== 2D Alignment ===

{|

| Paper
| [[1981Frank_Averaging]]
| 2D averaging and phase residual
|-

| Paper
| [[1982Saxton_Averaging]]
| 2D averaging using correlation
|-

| Paper
| [[1998Sigworth_ML2D]]
| Maximum likelihood alignment in 2D
|-

| Paper
| [[2003Cong_FRM2D]]
| Fast Rotational Matching in 2D
|-

| Paper
| [[2005Cong_FRM2D]]
| Fast Rotational Matching in 2D introduced in a 3D Alignment algorithm
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

|}

=== 2D Classification and clustering ===

{|

| Paper
| [[1981VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[1984VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2011Singer_DiffusionMaps]]
| Classification in 2D based on graph analysis of the projections
|-

| Paper
| [[2012Yang_ISAC]]
| Iterative Stable Alignment and clustering
|-

| Paper
| [[2014Sorzano_Outlier]]
| Outlier detection in 2D classifications.
|-

| Paper
| [[2014Zhao_Aspire]]
| Fast classification based on rotational invariants and vector diffusion maps
|-

| Paper
| [[2015Huang_Robust]]
| Robust w-estimators of 2D classes
|-

| Paper
| [[2016Reboul_Stochastic]]
| Stochastic Hill Climbing for calculating 2D classes
|-

| Conference
| [[2017Bhamre_Mahalanobis]]
| 2D classification using Mahalanobis distance
|-

|}

=== 3D Alignment ===

{|

| Paper
| [[1980Kam_AutoCorrelation]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[1986Goncharov_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1987VanHeel_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1988Provencher_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Vogel_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1990Gelfand_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Goncharov_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Harauz_Quaternions]]
| Use of quaternions to represent rotations
|-

| Paper
| [[1994Penczek_Real]]
| Angular assignment using projection matching in real space
|-

| Paper
| [[1994Radermacher_Radon]]
| Angular assignment in Radon space
|-

| Paper
| [[1996Penczek_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[2003Rosenthal_DPR]]
| Angular assignment using DPR
|-

| Paper
| [[2004Sorzano_Wavelet]]
| Angular assignment in the wavelet space.
|-

| Paper
| [[2005Jonic_Splines]]
| Angular assignment in Fourier space using spline interpolation.
|-

| Paper
| [[2005Yang_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[2006Ogura_SimulatedAnnealing]]
| Angular asignment by simulated annealing
|-

| Paper
| [[2007Grigorieff_Continuous]]
| Continuous angular assignment in Fourier space
|-

| Paper
| [[2010Jaitly_Bayesian]]
| Angular assignment by a Bayesian method and annealing
|-

| Paper
| [[2010Sanz_Random]]
| Random model method
|-

| Paper
| [[2010Singer_Voting]]
| Detecting consistent common lines by voting (reference free)
|-

| Paper
| [[2011Singer_SDP]]
| Angular assignment by semidefinite programming and eigenvectors (reference free)
|-

| Paper
| [[2012Giannakis_Scattering]]
| Construction of an initial volume, reference free, by graph analysis of the projections
|-

| Paper
| [[2012Shkolnisky_Sync]]
| Angular assignment by synchronization of rotations (reference free)
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Wang_LUD]]
| Angular assignment by least unsquared deviations (reference free)
|-

| Paper
| [[2014Vargas_RANSAC]]
| Initial model using RANSAC (reference free)
|-

| Paper
| [[2015Joubert_Pseudoatoms]]
| Initial model based on pseudo-atoms
|-

| Paper
| [[2015Singer_Kam]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[2015Sorzano_Significant]]
| Statistical approach to the initial volume estimation (reconstruct significant)
|-

| Conference
| [[2016Michels_Heterogeneous]]
| Initial volume in the presence of heterogeneity
|-

| Paper
| [[2016Cossio_BayesianGPU]]
| GPU implementation of the Bayesian 3D reconstruction approach
|-

|}

=== 3D Reconstruction ===
{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1986Harauz_FBP]]
| Exact filters for Filtered Back Projection
|-

| Chapter
| [[1992Radermacher_WBP]]
| Exact filters for Weighted Back Projection
|-

| Paper
| [[1997Zhu_RecCTF]]
| 3D Reconstruction (SIRT like) and simultaneous CTF correction
|-

| Paper
| [[1998Boisset_Uneven]]
| Artifacts in SIRT and WBP under uneven angular distributions
|-

| Paper
| [[1998Marabini_ART]]
| Algebraic Reconstruction Technique with blobs (Xmipp)
|-

| Paper
| [[2001Sorzano_Uneven]]
| Free parameter selection under uneven angular distributions
|-

| Paper
| [[2005Sorzano_Parameters]]
| Free parameter selection for optimizing multiple tasks
|-

| Paper
| [[2008Sorzano_Constraints]]
| Mass, surface, positivity and symmetry constraints for real-space algorithms
|-

| Paper
| [[2009Bilbao_ParallelART]]
| Efficient parallelization of ART
|-

| Paper
| [[2011Li_GradientFlow]]
| Regularized 3D Reconstruction by Gradient Flow
|-

| Paper
| [[2011Vonesch_Wavelets]]
| Fast wavelet-based 3D reconstruction
|-

| Paper
| [[2012Gopinath_ShapeRegularization]]
| Regularized 3D Reconstruction by Shape information
|-

| Paper
| [[2012Kucukelbir_adaptiveBasis]]
| 3D reconstruction in an adaptive basis promoting sparsity
|-

| Paper
| [[2012Sindelar_NoiseReduction]]
| Optimal noise reduction in 3D reconstructions
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Lyumkis_Optimod]]
| Construction of initial volumes with Optimod
|-

| Paper
| [[2013Wang FIRM]]
| Fast 3D reconstruction in Fourier domain
|-

| Paper
| [[2014Kunz_SART_OS]]
| Simultaneous ART with OS
|-

| Paper
| [[2015Abrishami_Fourier]]
| 3D Reconstruction in Fourier space
|-

| Paper
| [[2015Dvornek_SubspaceEM]]
| Fast Maximum a posteriori
|-

| Paper
| [[2015Moriya_Bayesian]]
| Bayesian approach to suppress limited angular artifacts
|-

| Paper
| [[2015Xu_GeometricFlow]]
| Multi-scale geometric flow
|-

| Arxiv
| [[2016Ye_Cohomology]]
| Cohomology properties of 3D reconstruction
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

|}

=== 3D Heterogeneity ===

{|

| Paper
| [[2004White_Size]]
| Heterogeneity classification of differently sized images
|-

| Paper
| [[2006Penczek_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Scheres_ML3D]]
| Maximum Likelihood alignment and classification in 3D
|-

| Paper
| [[2009Spahn_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2010Elmlund_AbInitio]]
| Solving the initial volume problem with multiple conformations
|-

| Paper
| [[2010Shatsky_MultiVariate]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2012Scheres_Bayesian]]
| A Bayesian view on cryo-EM structure determination
|-

| Paper
| [[2012Zheng_Covariance]]
| Estimation of the volume covariance
|-

| Paper
| [[2013Wang_MLVariance]]
| Maximum Likelihood estimate of the map variance
|-

| Paper
| [[2013Lyumkis D_FREALIGN]]
| Likelihood-based classification of cryo-EM images using FREALIGN.
|-

| Paper
| [[2014Jin_NMA]]
| Continuous heterogeneity through Normal Mode Analysis
|-

| Paper
| [[2014Dashti_Brownian]]
| Continuous heterogeneity through Brownian trajectories
|-

| Paper
| [[2014Chen_Migration]]
| Particle migration analysis in 3D classification
|-

| Paper
| [[2015Anden_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Bai_Focused]]
| Focused classification
|-

| Paper
| [[2015Katsevich_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Klaholz_MRA]]
| Multivariate Statistical Analysis of Jackknife and Bootstrapping on random subsets
|-

| Paper
| [[2015Liao_Covariance]]
| Estimation of the 3D covariance from 2D projections
|-

| Paper
| [[2015Tagare_Direct]]
| Direct reconstruction of PCA components
|-

| Paper
| [[2016Gong_Mechanical]]
| Mechanical model for macromolecules
|-

| Paper
| [[2016Rawson_Movement]]
| Movement and flexibility
|-

| Paper
| [[2016Sorzano_StructMap]]
| Sorting a discrete set of conformational states
|-

| Paper
| [[2016Sorzano_Strain]]
| Calculate local stretches, strains and rotations from two conformational states
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

|}

=== Validation ===

{|

| Paper
| [[2008Stagg_TestBed]]
| Effect of voltage, dosis, number of particles and Euler jumps on resolution
|-

| Paper
| [[2011Henderson]]
| Tilt Validation
|-

| Paper
| [[2011Read]]
| Validation of PDBs
|-

| Paper
| [[2012Henderson]]
| EM Map Validation
|-

| Paper
| [[2013Cossio_Bayesian]]
| EM Map Validation in a probabilistic setting
|-

| Paper
| [[2013Chen_NoiseSubstitution]]
| Noise substitution at high resolution for measuring overfitting
|-

| Paper
| [[2014Russo_StatisticalSignificance]]
| EM Map Validation through the statistical significance of the tilt-pair angular assignment
|-

| Paper
| [[2014Stagg_Reslog]]
| EM Map Validation through the resolution evolution with the number of particles
|-

| Paper
| [[2014Wasilewski_Tilt]]
| Web implementation of the tilt pair validation
|-

| Paper
| [[2015Heymann_Alignability]]
| EM Map Validation through the resolution of reconstructions from particles and noise
|-

| Paper
| [[2015Oliveira_FreqLimited]]
| Comparison of gold standard and frequency limited optimization
|-

| Paper
| [[2015Wriggers_Secondary]]
| Validation by secondary structure
|-

| Paper
| [[2016Kim_SAXS]]
| Comparison of SAXS data and EM projections
|-

| Paper
| [[2016Rosenthal_Review]]
| Review of validation methods
|-

| Paper
| [[2016Vargas_Alignability]]
| Validation by studying the tendency of an angular assignment to cluster in the projection space
|-

| Paper
| [[2017Monroe_PDBRefinement]]
| Validation by comparison to a refined PDB
|-

|}

=== Resolution ===

{|

| Paper
| [[1986Harauz_FBP]]
| Fourier Shell Correlation
|-

| Paper
| [[1987Unser_SSNR]]
| 2D Spectral Signal to Noise Ratio
|-

| Paper
| [[2002Penczek_SSNR]]
| 3D Spectral Signal to Noise Ratio for Fourier based algorithms
|-

| Paper
| [[2003Rosenthal_DPR]]
| Review of the FSC and establishment of a new threshold
|-

| Paper
| [[2005Unser_SSNR]]
| 3D Spectral Signal to Noise Ratio for any kind of algorithms
|-

| Paper
| [[2005VanHeel_FSC]]
| Establishment of a new threshold for FSC
|-

| Paper
| [[2007Sousa_AbInitio]]
| Resolution measurement on neighbour Fourier voxels
|-

| Paper
| [[2014Kucukelbir_Local]]
| Quantifying the local resolution of cryo-EM density maps
|-

| Paper
| [[2016Pintilie_Probabilistic]]
| Probabilistic models and resolution
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Statistical properties of resolution measures defined in Fourier space
|-

|}

=== Sharpening of high resolution information ===
{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast restoration and map sharpening
|-

| Paper
| [[2008Fernandez_Bfactor]]
| Bfactor determination and restoration
|-

| Paper
| [[2013Fiddy_SaxtonAlgorithm]]
| Phase retrieval or extension
|-

| Paper
| [[2014Kishchenko_SphericalDeconvolution]]
| Spherical deconvolution
|-

| Paper
| [[2015Spiegel_VISDEM]]
| Visualization improvement by the use of pseudoatomic profiles
|-

| Paper
| [[2016Jonic_Pseudoatoms]]
| Approximation with pseudoatoms
|-

| Paper
| [[2016Jonic_Denoising]]
| Denoising and high-frequency boosting by pseudoatom approximation
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[1982Schiske_Correction]]
| CTF correction for tilted objects
|-

| Paper
| [[1988Toyoshima_Model]]
| CTF estimation
|-

| Paper
| [[1995Frank_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1996Skoglund_MaxEnt]]
| CTF correction with Maximum Entropy
|-

| Paper
| [[1996Zhou_Model]]
| CTF model and user interface for manual fitting
|-

| Paper
| [[1997Fernandez_AR]]
| PSD estimation using periodogram averaging and AR models
|-

| Paper
| [[1997Penczek_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1997Stark_Deconvolution]]
| CTF correction using deconvolution
|-

| Paper
| [[1997Zhu_RecCTF]]
| CTF correction and reconstruction
|-

| Paper
| [[2000DeRosier_EwaldCorrection]]
| CTF correction considering the Ewald sphere
|-

| Paper
| [[2000Jensen_TiltedCorrection]]
| CTF correction considering tilt in backprojection
|-

| Paper
| [[2001Saad_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Huang_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Mindell_CTFTILT]]
| CTF estimation for tilted micrographs
|-

| Paper
| [[2003Sander_MSA]]
| CTF estimation through MSA classification of PSDs
|-

| Paper
| [[2003Velazquez_ARMA]]
| PSD and CTF estimation using ARMA models
|-

| Paper
| [[2004Sorzano_IDR]]
| CTF restoration and reconstruction with Iterative Data Refinement
|-

| Conference
| [[2004Wan_CTF]]
| Spatially variant CTF
|-

| Paper
| [[2004Zubelli_Chahine]]
| CTF restoration and reconstruction with Chahine's multiplicative method
|-

| Conference
| [[2005Dubowy_SpaceVariant]]
| CTF correction when this is space variant
|-

| Paper
| [[2005Mallick_ACE]]
| CTF estimation
|-

| Paper
| [[2006Wolf_Ewald]]
| CTF correction considering Ewald sphere
|-

| Paper
| [[2007Jonic_EnhancedPSD]]
| PSD enhancement for better identification of Thon rings; Vitreous ice diffracts in Thon rings
|-

| Paper
| [[2007Philippsen_Model]]
| CTF Model for tilted specimens
|-

| Paper
| [[2007Sorzano_CTF]]
| CTF estimation using enhanced PSDs
|-

| Paper
| [[2009Sorzano_Sensitivity]]
| Error sensitivity of the CTF models, non-uniqueness of the CTF parameters
|-

| Paper
| [[2010Jiang2010_CTFCorrection]]
| Amplitude correction method
|-

| Paper
| [[2010Kasantsev_CTFCorrection]]
| Mathematical foundations of Kornberg and Jensen method
|-

| Paper
| [[2010Leong_CTFCorrection]]
| Correction for spatially variant CTF
|-

| Paper
| [[2011Glaeser_Coma]]
| The effect of coma at high-resolution
|-

| Paper
| [[2011Mariani_Tilted]]
| CTF simulation and correction of tilted specimens
|-

| Paper
| [[2011Sindelar_Wiener]]
| CTF correction using a modified version of Wiener filter
|-

| Paper
| [[2011Voortman_Tilted]]
| CTF correction for tilted specimen
|-

| Paper
| [[2012Voortman_VaryingCTF]]
| Correcting a spatially varying CTF
|-

| Paper
| [[2013Vargas_FastDef]]
| Fast defocus
|-

| Paper
| [[2015Rohou_CTFFind4]]
| CTF Find 4
|-

| Paper
| [[2015Sheth_CTFquality]]
| Visualization and quality assessment of CTF
|-

| Paper
| [[2016Zhang_GCTF]]
| gCTF
|-

|}

=== Segmentation ===

{|

| Paper
| [[2006Baker_segmentation]]
| Segmentation of molecular subunits
|-

|}

=== Fitting and docking ===

{|

| Paper
| [[1999Volkmann_Fitting]]
| Fitting in real space
|-

| Paper
| [[2001Baker_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2001Jones_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2003Kovacs_FRM3D]]
| Fast Rotational Alignment of two EM maps
|-

| Paper
| [[2004Tama_NMA1]]
| Flexible fitting with Normal Modes (I)
|-

| Paper
| [[2004Tama_NMA2]]
| Flexible fitting with Normal Modes (II)
|-

| Paper
| [[2005Velazquez_Superfamilies]]
| Recognition of the superfamily folding in medium-high resolution volumes
|-

| Paper
| [[2007DeVries_Haddock]]
| Docking with Haddock 2.0
|-

| Paper
| [[2007Kleywegt_QualityControl]]
| Quality control and validation of fitting
|-

| Paper
| [[2012Biswas_Secondary]]
| Secondary structure determination in EM volumes
|-

| Paper
| [[2012Velazquez_Constraints]]
| Multicomponent fitting by using constraints from other information sources
|-

| Paper
| [[2013Chapman MS_Atomicmodeling]]
| Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters
|-

| Paper
| [[2013Esquivel_Modelling]]
| Review on modelling (secondary structure, fitting, ...)
|-

| Paper
| [[2013Lopez_Imodfit]]
| Fitting based on vibrational analysis
|-

| Paper
| [[2013Nogales_3DEMLoupe]]
| Normal Mode Analysis of reconstructed volumes
|-

| Paper
| [[2014AlNasr_Secondary]]
| Identification of secondary structure elements in EM volumes
|-

| Paper
| [[2014Politis_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Rey_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Villa_Review]]
| Review of atomic fitting into EM volumes
|-

| Paper
| [[2015Barad_EMRinger]]
| Validation of hybrid models
|-

| Paper
| [[2015Bettadapura_PF2Fit]]
| Fast rigid fitting of PDBs into EM maps
|-

| Paper
| [[2015Carrillo_CapsidMaps]]
| Analysis of virus capsids using Google Maps
|-

| Paper
| [[2015Schroeder_Hybrid]]
| Review on model building
|-

| Paper
| [[2015Tamo_Dynamics]]
| Dynamics in integrative modeling
|-

| Paper
| [[2015Sorzano_AtomsToVoxels]]
| Accurate conversion of an atomic model into a voxel density volume
|-

| Paper
| [[2016Joseph_Evolution]]
| Evolutionary constraints for the fitting of atomic models into density maps
|-

| Paper
| [[2016Segura_3Diana]]
| Validation of hybrid models
|-

| Paper
| [[2016Singharoy_MDFF]]
| Construction of hybrid models driven by EM density and molecular dynamics
|-

| Paper
| [[2016Wang_Rosetta]]
| Construction of hybrid models driven by EM density using Rosetta
|-

| Paper
| [[2017Hryc_WeightedAtoms]]
| Construction of hybrid models by locally weighting the different atoms
|-

| Paper
| [[2017Matsumoto_Distribution]]
| Estimating the distribution of conformations of atomic models
|-

|}

=== Books and reviews ===

{|

| Book
| [[1980Herman_Tomography]]
| General book on tomography
|-

| Book
| [[1988Kak_Tomography]]
| General book on tomography
|-

| Paper
| [[2000Tao_Review]]
| Review of single particles
|-

| Paper
| [[2000VanHeel_Review]]
| Review of single particles
|-

| Paper
| [[2002Frank_Review]]
| Review of single particles
|-

| Paper
| [[2002Schmid_Review]]
| Review of single particles
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2004Subramaniam_Review]]
| Review of single particles
|-

| Paper
| [[2005Steven_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_book]]
| Book covering all aspects of electron microscopy of single particles
|-

| Paper
| [[2006Sorzano_Review]]
| Review of optimization problems in electron microscopy
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems in Electron Tomography
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2008Mueller_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2008Taylor_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2010DeRosier_Review]]
| Personal account of how 3DEM developed in the early days
|-

| Chapter
| [[2012Sorzano_Review]]
| Review of single particle analysis using Xmipp
|-

| Chapter
| [[2012Devaux_Protocol]]
| Protocols for performing single particle analysis
|-

| Paper
| [[2014Bai_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Carazo_Review]]
| Review of the reconstruction process
|-

| Paper
| [[2015Cheng_Review]]
| A primer to Single Particle Cryo-EM
|-

| Paper
| [[2015Cheng_Reviewb]]
| Single Particle Cryo-EM at crystallographic resolution
|-

| Paper
| [[2015Elmlund_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Henderson_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Nogales_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Schroeder_Review]]
| Review of advances in the electron microscope
|-

| Paper
| [[2015Wu_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Carroni_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Egelman_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Eisenstein_CryoEM]]
| News feature on the Method of the Year
|-

| Paper
| [[2016FernandezLeiro_Review]]
| Review of EM
|-

| Paper
| [[2016Glaeser_HowGood]]
| How good can cryo-EM become?
|-

| Paper
| [[2016Jonic_PseudoAtoms]]
| Review of the applications of the use of pseudoatoms in EM
|-

| Chapter
| [[2016Mio_Review]]
| Overview of the process to obtain EM reconstructions
|-

| Paper
| [[2016Jonic_Review]]
| A review of computational ways to handle heterogeneity
|-

| Paper
| [[2016Nogales_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Subramaniam_Review]]
| Why cryo-EM is now suitable for crystallographic journals
|-

| Paper
| [[2016Vinothkumar_Review]]
| Historical review and current limitations
|-

| Paper
| [[2017Frank_Review]]
| Historical review of EM
|-

| Paper
| [[2017Jonic_Review]]
| Review of computational methods to analyze conformational variability
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Review of statistical properties of resolution measures defined in Fourier space
|-
|}

=== Software ===

{|

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[1999Lutdke_Eman]]
| Eman
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Baldwin_AngularTransformations]]
| The Transform Class in SPARX and EMAN2
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Grigorieff_Frealign]]
| Frealign
|-

| Paper
| [[2008Scheres_XmippProtocols]]
| Xmipp Protocols
|-

| Paper
| [[2008Shaikh_SpiderProtocols]]
| Spider Protocols
|-

| Paper
| [[2012Wriggers_SitusConventions]]
| Conventions and workflows in Situs
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2015Cianfrocco_Cloud]]
| Software execution in the cloud
|-

| Paper
| [[2015Cheng_MRC2014]]
| Extensions to MRC file format
|-

| Paper
| [[2013DeLaRosa_Scipion]]
| Scipion
|-

| Paper
| [[2016Scheres_Relion]]
| Tutorial on the use of Relion
|-

| Paper
| [[2016Grigorieff_Frealign]]
| Tutorial on the use of Frealign
|-

|}

== Electron tomography ==

=== Image preprocessing ===

{|

| Paper
| [[2015Yan_thickness]]
| Determination of thickness, tilt and electron mean free path
|-

|}

=== Image alignment ===

{|

| Paper
| [[1982Guckenberger_commonOrigin]]
| Determination of a common origin in the micrographs of titl series in three-dimensional electron microscopy
|-

| Paper
| [[1992Lawrence_leastSquares]]
| Least squares solution of the alignment problem
|-

| Paper
| [[1995Penczek_dual]]
| Dual tilt alignment
|-

| Paper
| [[1996Owen_alignmentQuality]]
| Automatic alignment without fiducial markers and evaluation of alignment quality
|-

| Paper
| [[1998Grimm_normalization]]
| Discussion of several gray level normalization methods for electron tomography
|-

| Paper
| [[2001Brandt_Automatic1]]
| Automatic alignment without fiducial markers
|-

| Paper
| [[2001Brandt_Automatic2]]
| Automatic alignment with fiducial markers
|-

| Paper
| [[2006Winkler_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2006Castano_alignment]]
| Alignment with non-perpendicularity
|-

| Paper
| [[2007Castano_alignment]]
| Fiducial-less alignment of cryo-sections
|-

| Paper
| [[2009Sorzano_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2010Cantele_dualAlignment]]
| Alignment of dual series
|-

| Paper
| [[2014Tomonaga_Automatic]]
| Automatic alignment of tilt series using the projection themselves
|-

| Paper
| [[2014Han_Automatic]]
| Automatic alignment of tilt series using SIFT features
|-

| Paper
| [[2015Han_Automatic]]
| Automatic alignment of tilt series using fiducials
|-

| Paper
| [[2017Mastronarde_Automatic]]
| Automatic alignment and reconstruction of tilt series in IMOD
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[2003Winkler_CTF]]
| Focus gradient correction in electron tomography
|-

| Paper
| [[2006Fernandez_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Zanetti_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Xiong_CTF]]
| CTF determination and correction for low dose tomographic tilt series
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2017Kunz_3DCTF]]
| 3D CTF Correction
|-

|}

=== 3D reconstruction ===

{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1992Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[1997Marabini_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2002Fernandez_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2007Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[2008Fernandez_CARP]]
| Component Averaged Row Projections (CARP)
|-

| Paper
| [[2012Herman General Superiorization]]
| Superiorization: an optimization heuristic for medical physics
|-

| Paper
| [[2012Zhang_IPET_FETR]]
| IPET and FETR, a reconstruction algorithm for single molecule tomography
|-

| Paper
| [[2013Goris_SIRT_TV_DART]]
| Combination of SIRT, Total Variation and Discrete ART to reconstruct and segment at the same time
|-

| Paper
| [[2013Briegel A_Challenge]]
| The challenge of determining handedness in electron tomography and the use of DNA origami gold nanoparticle helices as molecular standards
|-

| Paper
| [[2013Messaoudi_EnergyFiltered]]
| 3D Reconstruction of Energy-Filtered TEM
|-

| Paper
| [[2016Deng_ICON]]
| 3D Reconstruction with missing information restoration
|-

| Paper
| [[2016Guay_Compressed]]
| 3D Reconstruction using compressed sensing
|-

|}

=== Noise reduction ===
{|

| Paper
| [[2001Frangakis_NAD]]
| Noise reduction with Nonlinear Anisotropic Diffusion
|-

| Paper
| [[2003Fernandez_AND]]
| Anisotropic nonlinear diffusion for electron tomography
|-

| Paper
| [[2003Jiang_Bilateral]]
| Bilateral denoising filter in electron microscopy
|-

| Paper
| [[2005Fernandez_AND]]
| Anisotropic nonlinear denoising in electron tomography
|-

| Paper
| [[2007Heide_median]]
| Iterative median filtering in electron tomography
|-

| Paper
| [[2007Fernandez_autAND]]
| Anisotropic nonlinear diffusion with automated parameter tuning
|-

| Paper
| [[2009Fernandez_Beltrami]]
| Nonlinear filtering based on Beltrami flow
|-

| Paper
| [[2010Bilbao_MeanShift]]
| Mean Shift Filtering
|-

| Paper
| [[2014Kovacik_wedgeArtefacts]]
| Removal of wedge artefacts
|-

| Paper
| [[2014Maiorca_beadArtefacts]]
| Removal of gold bead artefacts
|-

|}

=== Segmentation ===

{|

| Paper
| [[2002Frangakis_Eigenanalysis]]
| Segmentation using eigenvector analysis.
|-

| Paper
| [[2002Volkmann_Watershed]]
| Segmentation using watershed transform.
|-

| Paper
| [[2003Bajaj_BoundarySegmentation]]
| Segmentation based on fast marching.
|-

| Paper
| [[2005Cyrklaff_Thresholding]]
| Segmentation using optimal thresholding.
|-

| Paper
| [[2007Lebbink_TemplateMatching]]
| Segmentation using template matching.
|-

| Paper
| [[2007Sandberg_OrientationFields]]
| Segmentation using orientation fields.
|-

| Paper
| [[2007Sandberg_SegmentationReview]]
| Review on segmentation in electron tomography.
|-

| Paper
| [[2008Garduno_FuzzySegmentation]]
| Segmentation using fuzzy set theory principles.
|-

| Paper
| [[2009Lebbink_TemplateMatching2]]
| Segmentation using template matching.
|-

| Paper
| [[2012RubbiyaAli_EdgeDetection]]
| Parameter-Free Segmentation of Macromolecular Structures.
|-

| Conference
| [[2015Xu_TemplateMatching]]
| Detection of macromolecular complexes with a reduced representation of the templates.
|-

|}

=== Resolution ===
{|

| Paper
| [[2005Cardone_Resolution]]
| Resolution criterion for electron tomography
|-

| Chapter
| [[2007Penczek_Resolution]]
| Review of resolution criteria for electron tomography
|-

| Paper
| [[2015Diebolder_ConicalFSC]]
| Conical Fourier Shell Correlation
|-

|}

=== Subtomogram analysis ===

{|

| Paper
| [[2000Bohm_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2002Frangakis_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2006Nickell_Review]]
| Review of macromolecule finding by template matching (Visual Proteomics)
|-

| Paper
| [[2007Best_Review]]
| Review of Localization of Protein Complexes by Pattern Recognition
|-

| Paper
| [[2007Forster_Review]]
| Review of structure determination by subtomogram averaging
|-

| Paper
| [[2008Forster_Classification]]
| Classification of subtomograms using constrained correlation
|-

| Paper
| [[2008Bartesaghi_Classification]]
| Classification and averaging of subtomograms
|-

| Paper
| [[2008Schmid_Averaging]]
| Alignment and averaging of subtomograms
|-

| Paper
| [[2010Amat_Averaging]]
| Alignment and averaging of subtomograms exploiting thresholding in Fourier space
|-

| Paper
| [[2013Chen_Averaging]]
| Fast alignment of subtomograms using spherical harmonics
|-

| Paper
| [[2013Kuybeda_Averaging]]
| Alignment and averaging of subtomograms using the nuclear norm of the cluster
|-

| Paper
| [[2013Shatsky_Averaging]]
| Alignment and averaging of subtomograms with constrained cross-correlation
|-

| Paper
| [[2014Chen_Autofocus]]
| Subtomogram averaging and classification with special attention to differences
|-

| Paper
| [[2014Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2014Voortman_LimitingFactors]]
| Limiting factors of subtomogram averaging
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2015Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2016Bharat_Relion]]
| Subtomogram averaging with Relion
|-

| Paper
| [[2016Song_MatrixNorm]]
| Matrix norm minimization for tomographic reconstruction and alignment
|-

| Paper
| [[2017Castano_ParticlePicking]]
| Particle picking in tomograms for subtomogram averaging
|-

|}

=== Single particle tomography ===

{|

| Paper
| [[2012Bartesaghi_Constrained]]
| 3D reconstruction by imposing geometrical constraints
|-

| Paper
| [[2015Galaz_SingleParticleTomography]]
| Set of tools for Single Particle Tomography in EMAN2
|-

| Paper
| [[2016Galaz_SingleParticleTomography]]
| Alignment algorithms and CTF correction
|-

|}

=== Books and reviews ===

{|

| Paper
| [[2000Baumeister_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Koster_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Sali_Review]]
| Review of electron tomography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2005Lucic_Review]]
| Review of electron tomography
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_TomoBook]]
| Electron Tomography
|-

| Book
| [[2007McIntosh_Book]]
| Cellular Electron Microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2012Kudryashev_Review]]
| Review of subtomogram averaging
|-

| Paper
| [[2016Beck_Review]]
| Review of molecular sociology
|-

|}

=== Software ===

{|

| Paper
| [[1996Kremer_IMOD]]
| IMOD
|-

| Paper
| [[1996Chen_Priism/IVE]]
| Priism/IVE
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2005Nickell_TOM]]
| TOM Toolbox
|-

| Paper
| [[2007Messaoudi_TomoJ]]
| TomoJ
|-

| Paper
| [[2008Heymann_BsoftTomo]]
| Bsoft
|-

| Paper
| [[2015Ding_CaltechTomography]]
| Caltech tomography database
|-

| Paper
| [[2015Noble_AppionProtomo]]
| Batch fiducial-less tilt-series alignment in Appion using Protomo
|-

| Paper
| [[2015vanAarle_Astra]]
| ASTRA Toolbox
|-

|}

== 2D Crystals ==

=== 2D Preprocessing ===

{|

| Paper
| [[1986Henderson_Processing]]
| General 2D processing
|-

| Paper
| [[2000He_PhaseAlignment]]
| Phase consistency and Alignment
|-

| Paper
| [[2006Gil_Unbending]]
| Crystal unbending
|-

|}

=== Classification ===
{|

| Paper
| [[1988Frank_Classification]]
| MSA and classification in electron crystallography
|-

| Paper
| [[1996Fernandez_SOM]]
| Classification based on self organizing maps
|-

| Paper
| [[1998Sherman_MSA]]
| Classification based on MSA
|-

|}
=== 3D Reconstruction ===

{|

| Paper
| [[1985Wang_Solvent]]
| Solvent flattening
|-

| Paper
| [[1990Henderson_Processing]]
| General 3D processing
|-

| Paper
| [[2004Marabini_ART]]
| Algebraic Reconstruction Technique with blobs for crystals (Xmipp)
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1998Walz_Review]]
| Review of 2D crystallography
|-

| Paper
| [[1999Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Ellis_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of single particles, electron tomography and crystallography
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Gipson_2dx]]
| 2dx
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Philippsen_IPLT]]
| IPLT
|-

|}

== 3D Crystals - MicroED ==

=== Sample Preparation ===
{|
| Paper
| [[2016Shi_Preparation]]
| Sample Preparation
|}
=== Data Collection ===
{|
| Paper
| [[2014Nannenga_CR]]
| Continuous rotation

|}
=== Data Processing ===
{|

| Paper
| [[2011Wisedchaisri_PhaseExtension]]
| Fragment-based phase extension
|-

| Paper
| [[2015Hattne_Processing]]
| Data Processing
|-

| Paper
| [[2016Hattne_Correction]]
| Image correction
|}

=== Software ===
{|

| Paper
| [[2014Iadanza_Processing]]
| Data Processing of still diffraction data
|}

=== Books and Reviews ===
{|
| Paper
| [[2014Nannenga_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Liu_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Rodriguez_Review ]]
| Review of MicroED
|-

|}

== Helical particles ==

=== Filament corrections ===

{|

| Paper
| [[1986Egelman_Curved]]
| Algorithm for correcting curved filaments
|-

| Paper
| [[1988Bluemke_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2006Wang_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2016Yang_Flexible]]
| Algorithm for correcting filaments with flexible subunits
|-

|}

=== Reconstruction ===

{|

| Paper
| [[1952Cochran_Fourier]]
| Fourier Bessel transform of filamentous structures
|-

| Paper
| [[1958Klug_Fourier]]
| Fourier Bessel decomposition of the projection images
|-

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2005Wang_Iterative]]
| Iterative Fourier-Bessel algorithm
|-

| Paper
| [[2007Egelman_Iterative]]
| Iterative real-space algorithm
|-

| Paper
| [[2013Desfosses_Spring]]
| Helical processing with Spring
|-

| Paper
| [[2015Zhang_seam]]
| Workflow for the detection of the lattice seam
|-

| Paper
| [[2016Rohou_Frealix]]
| Helical processing with Frealix
|-

|}

=== Validation ===

{|

| Paper
| [[2014Egelman_ambiguity]]
| How to detect incorrect models
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Carragher_Phoelix]]
| Phoelix
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Owen_Brandeis]]
| Brandeis
|-

|}

== Icosahedral particles ==

=== Reconstruction ===

{|

| Paper
| [[1970Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1971Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1996Fuller_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1997Thuman_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

|}

=== Classification ===

{|

| Paper
| [[2005Scheres_Virus]]
| Classification of virus capsids in real space
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1999Baker_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[1999Conway_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2000Thuman_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Lee_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Navaza_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2006Grunewald_Review]]
| Review of reconstruction of icosahedral viruses
|-

|}

=== Software ===

{|

| Paper
| [[1996Baker_EMPFT]]
| EMPFT
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2013Morin_Sliz SBGrid]]
| SBGrid presentation for eLife
|-

|}

== Databases ==

{|

| Paper
| [[2003Boutselakis_EMSD]]
| EMSD database
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2011Kim_CDDB]]
| Conformational Dynamics Data Bank
|-

| Paper
| [[2011Lawson_EMDB]]
| Electron Microscopy Data Bank
|-

| Paper
| [[2013Ison_EDAM]]
| EDAM, an ontology of bioinformatics operations
|-

| Paper
| [[2016Iudin_EMPIAR]]
| EMPIAR raw data database
|-

| Paper
| [[2016Patwhardan_EMDB]]
| EMDB, PDB, ...
|-

| Paper
| [[2017Patwhardan_Trends]]
| Trends at EMDB
|-

| Paper
| [[2017Shao_PDBQuality]]
| Quality metrics in PDB
|-

| Blog
| http://www.mybiosoftware.com
| Huge list of bioinformatics programs (many of them structural bioinformatics)
|-

|}

== Relationship to other structural information sources ==

{|

| Paper
| [[2000Engel_AFM]]
| Review of Atomic Force Microscopy
|-

| Paper
| [[2001Dimmeler_AFM]]
| Constraints from Atomic Force Microscopy
|-

| Paper
| [[2003Mobus_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_Review]]
| Review on correlative microscopy
|-

| Paper
| [[2005Boudier_EFTETJ]]
| Software for Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2005Vestergaard_SAXS]]
| Example of comparison of 3DEM and Small-angle X-ray scattering
|-

| Paper
| [[2007Hamada_SAXS]]
| Constraints from Small-angle X-ray scattering
|-

| Paper
| [[2013Xu_FRET]]
| EM+FRET
|-

|}

== X-ray tomography ==

{|

| Paper
| [[2012Oton_ImageFormation]]
| Image formation model in X-ray cell microscopy
|-

|}

== Mathematical tools necessary ==

== People developing methods ==
Please, add yourself to this list (due to privacy reasons, please, do not add anyone else to the list without his/her explicit consent). Sort by first name alphabetical order.

[http://biocomp.cnb.csic.es/~coss Carlos Oscar S. Sorzano]: CSIC, Madrid, Spain 

[http://www.curie.fr/recherche/themes/detail_equipe.cfm/lang/_fr/id_equipe/241.htm Cédric Messaoudi]: Institute Curie, Paris, France 

[http://scholar.google.es/citations?user=_jNYGScAAAAJ&hl=en Javier Vargas]:[mailto:jvargas@cnb.csic.es mail]: CSIC, Madrid, Spain 

[http://scholar.google.es/citations?hl=es&user=g2ZJPIYAAAAJ Joaquín Otón]: CSIC, Madrid, Spain 

[mailto:jrbcast@gmail.com José Román Bilbao-Castro]: UAL, Almería, Spain; CSIC, Madrid, Spain 

[José Miguel de la Rosa Trevín]: Biocomputing Unit CNB-CSIC, Madrid, Spain 

[http://cryoem.janelia.org Tamir Gonen]: [mailto:gonent@janelia.hhmi.org mail]: Howard Hughes Medical Institute, Ashburn, VA, USA 

[mailto:vabrishami@cnb.csic.es Vahid Abrishami]: CSIC, Madrid, Spain 

== 3DEM sites ==
* [http://3dem.ucsd.edu/ 3DEM web site]

* [http://en.wikibooks.org/wiki/Software_Tools_For_Molecular_Microscopy Software tools for molecular microscopy]

* [http://www.emdatabank.org/ The Electron Microscopy Data Bank (EMDB)]

* [http://ccdb.ucsd.edu The Cell Centered Database (CCDB)]

* [http://conventions.cnb.csic.es The geometrical software conventions web page ]

== Editing useful links ==

* [http://www.mediawiki.org/wiki/Help:Formatting Text formatting in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Links Adding links in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Images Adding images in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Tables Making tables in Mediawiki]

2017Patwhardan Trends

2017-05-17T06:08:29Z

CoSS: Created page with "== Citation == Patwardhan, A. Trends in the Electron Microscopy Data Bank (EMDB) Acta Crystallographica Section D: Structural Biology, International Union of Crystallography,..."

== Citation ==

Patwardhan, A. Trends in the Electron Microscopy Data Bank (EMDB) Acta Crystallographica Section D: Structural Biology, International Union of Crystallography, 2017, 73

== Abstract ==

Recent technological advances, such as the introduction of the direct electron detector, have transformed the field of cryo-EM and the landscape of molecular and cellular structural biology. This study analyses these trends from the vantage point of the Electron Microscopy Data Bank (EMDB), the public archive for three-dimensional EM reconstructions. Over 1000 entries were released in 2016, representing almost a quarter of the total number of entries (4431). Structures at better than 6 Å resolution now represent one of the fastest-growing categories, while the share of annually released tomography-related structures is approaching 20%. The use of direct electron detectors is growing very rapidly: they were used for 70% of the structures released in 2016, in contrast to none before 2011. Microscopes from FEI have an overwhelming lead in terms of usage, and the use of the RELION software package continues to grow rapidly after having attained a leading position in the field. China is rapidly emerging as a major player in the field, supplementing the US, Germany and the UK as the big four. Similarly, Tsinghua University ranks only second to the MRC Laboratory for Molecular Biology in terms of involvement in publications associated with cryo-EM structures at better than 4 Å resolution. Overall, the numbers point to a rapid democratization of the field, with more countries and institutes becoming involved.

== Keywords ==

== Links ==

http://scripts.iucr.org/cgi-bin/paper?S2059798317004181

== Related software ==

== Related methods ==

== Comments ==

Main Page

2017-05-17T06:07:39Z

CoSS: /* Databases */

== Presentation ==

This web page is intended to be an extensive repository of three-dimensional electron microscopy (3DEM) methods. The advantages of having such a repository are

* You know which are the relevant articles in a particular topic, therefore, paper introductions, reviews, etc. are easier to write and you make sure you will cite all the related articles.
* You will be sure that your paper has more chances of being cited.
* You can add whatever information you find relevant to your method, external links, links to other papers, etc.
* You can link your method to a web page providing the corresponding software, so you know people can use your algorithms.
* You can use the Wiki search capabilities to locate relevant articles even if they are not at the topic you are looking at.
* As a community we will "reconstruct" our history.
* You can select the "watch" option above to receive notifications in case of further changes in the Main Page.

Developing image processing methods for 3DEM is not "[[well-paid]]" in terms of citations and impact factor. However, it is crucial for the advance of the field. Gathering methodological papers in a portal will help to increase the recognition of the field.

Please:

* Add your articles at the right place (you can add a single article in several topics if it is relevant to all of them). The easiest way to add an article is by editing the corresponding topic in the main page, adding your entry, then save the main page. Click on the red link that appears on your new entry, copy and paste the Wiki following code, add the information of your article

== Citation ==

== Abstract ==

== Keywords ==

== Links ==

== Related software ==

== Related methods ==

== Comments ==

* Maintain the information of each article as complete as possible.
* Sort articles by years and authors.
* Be respectful to other people's work.

== How to subscribe to this page ==

You may subscribe to this page so that you will be notified every time someone adds a new method. To do so, you have to register in the page, and edit your preferences ("my preferences"). Be sure that you have activated the option "E-mail me when a page on my watchlist is changed". Finally, click on the "Watch" tab at the top of this page.

You may subscribe to changes on this page on the mailing list 3demmethods@cnb.csic.es. To send a new method to this mail list just send a mail to 3demmethods@cnb.csic.es

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== Electron microscopy images ==

=== Online courses ===

CALTECH: http://cryo-em-course.caltech.edu/

MRC: ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/EM-course/

CNB-CSIC: http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/MadridJan2014EM

Workshop on Computational methods for CryoEM: https://www.youtube.com/watch?v=XdKO1iaPP8o

Workshop on Management of large CryoEM facilities: https://www.youtube.com/watch?v=as4seOPszL0

Icknield Course on Model Building and Refinement for High Resolution EM Maps: http://www.ccpem.ac.uk/training/icknield_2017/icknield_2017.php

=== Image formation ===

{|

| Paper
| [[1971Erickson_CTF]]
| CTF model
|-

| Paper
| [[1971Glaeser_Damage]]
| Radiation damage
|-

| Chapter
| [[1971Hanszen_CTF]]
| Image formation model
|-

| Paper
| [[1971Thon_Model]]
| CTF model
|-

| Paper
| [[1975Unwin_Imaging]]
| Radiation dose
|-

| Paper
| [[1977Wade_Model]]
| CTF model
|-

| Paper
| [[1978Wade_Model]]
| CTF model
|-

| Paper
| [[1979Hayward_Radiation]]
| Radiation damage
|-

| Paper
| [[1984Cohen_Validity]]
| Validity of the CTF model at high frequencies
|-

| Paper
| [[1988Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[1992Wade_Model]]
| CTF model
|-

| Paper
| [[1993Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2004Egerton_Damage]]
| Radiation damage
|-

| Paper
| [[2004Sorzano_Normalization]]
| Background noise is Gaussian
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2009Baxter_NoiseCharacterization]]
| Characterization of the different noise sources in cryo-EM
|-

| Paper
| [[2010Baker_Damage]]
| Radiation damage dependence on resolution
|-

| Paper
| [[2010Bammes_Damage]]
| Radiation damage dependence on temperature
|-

| Paper
| [[2010Gomez_Multislice]]
| Simulation of the multi slice model
|-

| Paper
| [[2010Zewail_FourDimensional]]
| Review on the use of ultrafast EM
|-

| Paper
| [[2011Bammes_CCD]]
| Performance of CCD cameras
|-

| Paper
| [[2011Glaeser_Coma]]
| Image formation model including coma
|-

| Paper
| [[2011Milazzo_DirectDetectors]]
| Evaluation of Direct Detectors
|-

| Paper
| [[2011Rullgard_ImageSimulation]]
| Accurate simulation of EM images
|-

| Paper
| [[2011Zhang LimitingFactors]]
| Limiting factor for atomic resolution in EM
|-

| Paper
| [[2012Bammes_DirectDetection]]
| Performance of Direct detectors
|-

| Paper
| [[2012Campbell_MotionCorrection]]
| Beam induced motion correction and direct detectors
|-

| Paper
| [[2012Shang_HydrationLayer]]
| Simulation of PDB volumes explicitly considering the hydration layer
|-

| Paper
| [[2013Egerton_RadiationDamage]]
| Review of TEM radiation damage and experimental ways of reducing it
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu H_Noisemodels]]
| Noise models and cryo-EM drift correction with a direct-electron camera
|-

| Paper
| [[2013Li X K2 noisemodels]]
| Influence of electron dose rate on electron counting images recorded with the K2 camera
|-

| Paper
| [[2013Vulovic_CTFApproximations]]
| When to use the different approximations performed so that a projection with linear CTF is valid
|-

| Thesis
| [[2013Vulovic_ImageFormation]]
| Ph.D. Thesis on the image formation in cryo-EM
|-

| Paper
| [[2014Danev_PhasePlate]]
| Volta potential phase plate
|-

| Paper
| [[2015Chiu_K2]]
| Characterization of K2
|-

| Paper
| [[2015Hawkes_AberrationCorrection]]
| Historical account of the development of lens corrections
|-

| Paper
| [[2015Koeck_Quadratic]]
| Limitations of the linear approximation and use of the quadratic terms
|-

| Paper
| [[2015Kuijper_FEI]]
| Description of the FEI Falcons
|-

| Paper
| [[2015Lobato_MULTEM]]
| Simulation of multislice diffraction
|-

| Paper
| [[2015McMullan_AmorphousIce]]
| Beam induced movement is caused by Brownian motion
|-

| Paper
| [[2016Koeck_ADF]]
| Simulations of Annular Dark Field TEM
|-

| Paper
| [[2017Mishyna_DNARadiation]]
| Review of radiation damage on DNA
|-

|}

=== Collection geometry ===

{|

| Chapter
| [[1980Hoppe_Wedge]]
| Missing wedge
|-

| Paper
| [[1987Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1995Penczek_Dual]]
| Dual axis tomography
|-

| Paper
| [[1997Mastronarde_Dual]]
| Dual axis tomography
|-

| Paper
| [[2003Ludtke_FocusPairs]]
| Focus pairs for single particles
|-

| Paper
| [[2005Lanzavecchia_Conical]]
| Conical tomography
|-

| Paper
| [[2005Zampighi_Conical]]
| Conical tomography
|-

| Paper
| [[2006Leschziner_OT]]
| Orthogonal Tilt
|-

| Paper
| [[2006Messaoudi_Multiple]]
| Multiple axis tomography
|-

| Paper
| [[2012Kudryashev_FocusPairs]]
| Focus pairs tomography
|-

| Paper
| [[2014Hovden_TiltFocus]]
| Combining tilt series with focus series
|-

| Paper
| [[2015Sorzano_RandomConicalTilt]]
| General formulation of Random Conical Tilt
|-

| Paper
| [[2017Hagen_DoseTomography]]
| Dose optimization for subtomogram averaging
|-

|}

=== Sample preparation ===

{|

| Paper
| [[1982Dubochet_Sample]]
| Vitreous ice
|-

| Paper
| [[1986Lepault_Sample]]
| Fast freezing
|-

| Paper
| [[1995Dubochet_Sample]]
| High-pressure freezing
|-

| Paper
| [[1995VanMarle_Sample]]
| Sample damages in resin
|-

| Paper
| [[1998Adrian_Sample]]
| Cryo negative staining
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2002Hsieh_Sample]]
| Cryofixation
|-

| Paper
| [[2004AlAmoudi_Sample]]
| CEMOVIS
|-

| Paper
| [[2008Studer_Sample]]
| Review on high pressure freezing
|-

| Paper
| [[2009Pierson_Sample]]
| Review on sample preparation for electron tomography
|-

| Paper
| [[2010Zhang_NegativeStaining]]
| Negative staining for small protein imaging
|-

| Paper
| [[2012Zhang_PositiveStaining]]
| Positive staining
|-

| Paper
| [[2014Rames_NegativeStaining]]
| Optimized negative staining
|-

| Paper
| [[2014Russo_GoldGrids]]
| Gold grids for single particles
|-

| Paper
| [[2015Cabra_Sample]]
| Review on sample preparation for single particles with videos
|-

| Paper
| [[2016Passmore_Review]]
| Tutorial chapter on sample preparation
|-

| Paper
| [[2016Razinkov_Vitrification]]
| New vitrification method
|-

| Paper
| [[2016Takizawa_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2016Thompson_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2017Arnold_BlottingFree]]
| Blotting-free preparation
|-

| Paper
| [[2017Peitsch_Sample]]
| iMEM: Isolation of Plasma Membrane for Cryoelectron Microscopy
|-

| Paper
| [[2017Schaffer_FocusedIonBeam]]
| Focused Ion Beam sample preparation for membrane proteins
|-

|}

=== Automated data collection ===

{|

| Paper
| [[1992Dierksen_Automatic]]
| Automated data collection
|-

| Paper
| [[1992Koster_Automatic]]
| Automated data collection
|-

| Paper
| [[1996Fung_Automatic]]
| Automated data collection for tomography
|-

| Paper
| [[2001Zhang_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2003Ziese_Automatic]]
| Automated autofocusing
|-

| Paper
| [[2004Potter_Automatic]]
| Automated sample loading
|-

| Paper
| [[2004Zheng_Automatic]]
| Automated data collection
|-

| Paper
| [[2005Lei_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2005Suloway_Automatic]]
| Automated data collection: Leginon
|-

| Paper
| [[2007Yoshioka_RCT]]
| Automated Random Conical Tilt
|-

| Paper
| [[2011Korinek_TOM2]]
| Automated acquisition with TOM2
|-

| Paper
| [[2015Li_UCSFImage]]
| Automated acquisition with UCSFImage
|-

| Paper
| [[2016Gil_Fuzzy]]
| Real time decisions during acquisition with neuro-fuzzy method
|-

| Paper
| [[2016Liu_TiltControl]]
| Accurate control of the tilt angle for electron tomography
|-

| Paper
| [[2016Vargas_FoilHole]]
| Determination of image quality at low magnification
|-

|}

== Single particles ==

=== Automatic particle picking ===

{|

| Paper
| [[1982VanHeel_Detection]]
| Detection of particles in micrographs
|-

| Paper
| [[2001Nicholson_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2001Zhu_Filaments]]
| Automatic identification of filaments in micrographs
|-

| Paper
| [[2004Sigworth_Detection]]
| Classical detection theory and the cryo-EM particle selection problem
|-

| Paper
| [[2004Volkmann_ParticlePicking]]
| An approach to automated particle picking from electron micrographs based on reduced representation templates
|-

| Paper
| [[2004Wong_ParticlePicking]]
| Model-based particle picking for cryo-electron microscopy
|-

| Paper
| [[2004Zhu_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2007Chen_Signature]]
| Automatic particle picking program: Signature
|-

| Paper
| [[2007Woolford_SwarmPS]]
| Automatic particle picking with several criteria, implemented in EMAN Boxer
|-

| Paper
| [[2009Sorzano_MachineLearning]]
| Automatic particle picking based on machine learning of rotational invariants
|-

| Paper
| [[2011Arbelaez_Comparison]]
| Evaluation of the performance of software for automated particle-boxing
|-

| Paper
| [[2013Abrishami_MachineLearning]]
| A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs
|-

| Paper
| [[2013Hauer_2013]]
| Automatic tilt pair detection in Random Conical Tilt
|-

| Paper
| [[2013Shatsky_ParticlePicking]]
| Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Langlois_ParticlePicking]]
| Automatic particle picking
|-

| Paper
| [[2016Vilas_AutomaticTilt]]
| Automatic identification of image pairs in untilted-tilted micrograph pairs
|-

|}

=== 2D Preprocessing ===

{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast enhancement through DPR
|-

| Paper
| [[2004Sorzano_Normalization]]
| Normalization procedures and their statistical properties.
|-

| Paper
| [[2006Sorzano_Denoising]]
| Strong denoising in wavelet space
|-

| Conference
| [[2009Sorzano_Downsampling]]
| Differences between the different downsampling schemes
|-

| Paper
| [[2012Brilot_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Campbell_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Zhao_Denoising]]
| Denoising using an invariant Fourier-Bessel eigenspace
|-

| Paper
| [[2013Norousi_Screening]]
| Screening particles to identify outliers
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu_Movies]]
| Drift correction for movies considering dark field
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Scheres_Movies]]
| Beam induced motion correction
|-

| Paper
| [[2015Abrishami_Movies]]
| Alignment of direct detection device micrographs
|-

| Paper
| [[2015Grant_Anisotropic]]
| Automatic estimation and correction of anisotropic magnification
|-

| Paper
| [[2015Grant_OptimalExposure]]
| Filter movies according to the radiation damage
|-

| Paper
| [[2015Rubinstein_Alignment]]
| Frame alignment at the level of particle
|-

| Paper
| [[2015Spear_DoseCompensation]]
| Effect of dose compensation on resolution
|-

| Paper
| [[2015Zhao_AnisotropicMagnification]]
| Correction of anisotropic magnification
|-

| Conference
| [[2016Bajic_Denoising]]
| Denoising and deconvolution of micrographs
|-

| Paper
| [[2016Jensen_RemovalVesicles]]
| Removal of vesicles in membrane proteins
|-

| Paper
| [[2016Bhamre_Denoising]]
| Denoising by 2D covariance estimation
|-

| Paper
| [[2017McLeod_Zorro]]
| Movie alignment by Zorro
|-

| Paper
| [[2017Zheng_MotionCorr2]]
| Movie alignment by MotionCorr2
|-

|}

=== 2D Alignment ===

{|

| Paper
| [[1981Frank_Averaging]]
| 2D averaging and phase residual
|-

| Paper
| [[1982Saxton_Averaging]]
| 2D averaging using correlation
|-

| Paper
| [[1998Sigworth_ML2D]]
| Maximum likelihood alignment in 2D
|-

| Paper
| [[2003Cong_FRM2D]]
| Fast Rotational Matching in 2D
|-

| Paper
| [[2005Cong_FRM2D]]
| Fast Rotational Matching in 2D introduced in a 3D Alignment algorithm
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

|}

=== 2D Classification and clustering ===

{|

| Paper
| [[1981VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[1984VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2011Singer_DiffusionMaps]]
| Classification in 2D based on graph analysis of the projections
|-

| Paper
| [[2012Yang_ISAC]]
| Iterative Stable Alignment and clustering
|-

| Paper
| [[2014Sorzano_Outlier]]
| Outlier detection in 2D classifications.
|-

| Paper
| [[2014Zhao_Aspire]]
| Fast classification based on rotational invariants and vector diffusion maps
|-

| Paper
| [[2015Huang_Robust]]
| Robust w-estimators of 2D classes
|-

| Paper
| [[2016Reboul_Stochastic]]
| Stochastic Hill Climbing for calculating 2D classes
|-

| Conference
| [[2017Bhamre_Mahalanobis]]
| 2D classification using Mahalanobis distance
|-

|}

=== 3D Alignment ===

{|

| Paper
| [[1980Kam_AutoCorrelation]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[1986Goncharov_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1987VanHeel_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1988Provencher_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Vogel_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1990Gelfand_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Goncharov_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Harauz_Quaternions]]
| Use of quaternions to represent rotations
|-

| Paper
| [[1994Penczek_Real]]
| Angular assignment using projection matching in real space
|-

| Paper
| [[1994Radermacher_Radon]]
| Angular assignment in Radon space
|-

| Paper
| [[1996Penczek_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[2003Rosenthal_DPR]]
| Angular assignment using DPR
|-

| Paper
| [[2004Sorzano_Wavelet]]
| Angular assignment in the wavelet space.
|-

| Paper
| [[2005Jonic_Splines]]
| Angular assignment in Fourier space using spline interpolation.
|-

| Paper
| [[2005Yang_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[2006Ogura_SimulatedAnnealing]]
| Angular asignment by simulated annealing
|-

| Paper
| [[2007Grigorieff_Continuous]]
| Continuous angular assignment in Fourier space
|-

| Paper
| [[2010Jaitly_Bayesian]]
| Angular assignment by a Bayesian method and annealing
|-

| Paper
| [[2010Sanz_Random]]
| Random model method
|-

| Paper
| [[2010Singer_Voting]]
| Detecting consistent common lines by voting (reference free)
|-

| Paper
| [[2011Singer_SDP]]
| Angular assignment by semidefinite programming and eigenvectors (reference free)
|-

| Paper
| [[2012Giannakis_Scattering]]
| Construction of an initial volume, reference free, by graph analysis of the projections
|-

| Paper
| [[2012Shkolnisky_Sync]]
| Angular assignment by synchronization of rotations (reference free)
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Wang_LUD]]
| Angular assignment by least unsquared deviations (reference free)
|-

| Paper
| [[2014Vargas_RANSAC]]
| Initial model using RANSAC (reference free)
|-

| Paper
| [[2015Joubert_Pseudoatoms]]
| Initial model based on pseudo-atoms
|-

| Paper
| [[2015Singer_Kam]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[2015Sorzano_Significant]]
| Statistical approach to the initial volume estimation (reconstruct significant)
|-

| Conference
| [[2016Michels_Heterogeneous]]
| Initial volume in the presence of heterogeneity
|-

| Paper
| [[2016Cossio_BayesianGPU]]
| GPU implementation of the Bayesian 3D reconstruction approach
|-

|}

=== 3D Reconstruction ===
{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1986Harauz_FBP]]
| Exact filters for Filtered Back Projection
|-

| Chapter
| [[1992Radermacher_WBP]]
| Exact filters for Weighted Back Projection
|-

| Paper
| [[1997Zhu_RecCTF]]
| 3D Reconstruction (SIRT like) and simultaneous CTF correction
|-

| Paper
| [[1998Boisset_Uneven]]
| Artifacts in SIRT and WBP under uneven angular distributions
|-

| Paper
| [[1998Marabini_ART]]
| Algebraic Reconstruction Technique with blobs (Xmipp)
|-

| Paper
| [[2001Sorzano_Uneven]]
| Free parameter selection under uneven angular distributions
|-

| Paper
| [[2005Sorzano_Parameters]]
| Free parameter selection for optimizing multiple tasks
|-

| Paper
| [[2008Sorzano_Constraints]]
| Mass, surface, positivity and symmetry constraints for real-space algorithms
|-

| Paper
| [[2009Bilbao_ParallelART]]
| Efficient parallelization of ART
|-

| Paper
| [[2011Li_GradientFlow]]
| Regularized 3D Reconstruction by Gradient Flow
|-

| Paper
| [[2011Vonesch_Wavelets]]
| Fast wavelet-based 3D reconstruction
|-

| Paper
| [[2012Gopinath_ShapeRegularization]]
| Regularized 3D Reconstruction by Shape information
|-

| Paper
| [[2012Kucukelbir_adaptiveBasis]]
| 3D reconstruction in an adaptive basis promoting sparsity
|-

| Paper
| [[2012Sindelar_NoiseReduction]]
| Optimal noise reduction in 3D reconstructions
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Lyumkis_Optimod]]
| Construction of initial volumes with Optimod
|-

| Paper
| [[2013Wang FIRM]]
| Fast 3D reconstruction in Fourier domain
|-

| Paper
| [[2014Kunz_SART_OS]]
| Simultaneous ART with OS
|-

| Paper
| [[2015Abrishami_Fourier]]
| 3D Reconstruction in Fourier space
|-

| Paper
| [[2015Dvornek_SubspaceEM]]
| Fast Maximum a posteriori
|-

| Paper
| [[2015Moriya_Bayesian]]
| Bayesian approach to suppress limited angular artifacts
|-

| Paper
| [[2015Xu_GeometricFlow]]
| Multi-scale geometric flow
|-

| Arxiv
| [[2016Ye_Cohomology]]
| Cohomology properties of 3D reconstruction
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

|}

=== 3D Heterogeneity ===

{|

| Paper
| [[2004White_Size]]
| Heterogeneity classification of differently sized images
|-

| Paper
| [[2006Penczek_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Scheres_ML3D]]
| Maximum Likelihood alignment and classification in 3D
|-

| Paper
| [[2009Spahn_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2010Elmlund_AbInitio]]
| Solving the initial volume problem with multiple conformations
|-

| Paper
| [[2010Shatsky_MultiVariate]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2012Scheres_Bayesian]]
| A Bayesian view on cryo-EM structure determination
|-

| Paper
| [[2012Zheng_Covariance]]
| Estimation of the volume covariance
|-

| Paper
| [[2013Wang_MLVariance]]
| Maximum Likelihood estimate of the map variance
|-

| Paper
| [[2013Lyumkis D_FREALIGN]]
| Likelihood-based classification of cryo-EM images using FREALIGN.
|-

| Paper
| [[2014Jin_NMA]]
| Continuous heterogeneity through Normal Mode Analysis
|-

| Paper
| [[2014Dashti_Brownian]]
| Continuous heterogeneity through Brownian trajectories
|-

| Paper
| [[2014Chen_Migration]]
| Particle migration analysis in 3D classification
|-

| Paper
| [[2015Anden_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Bai_Focused]]
| Focused classification
|-

| Paper
| [[2015Katsevich_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Klaholz_MRA]]
| Multivariate Statistical Analysis of Jackknife and Bootstrapping on random subsets
|-

| Paper
| [[2015Liao_Covariance]]
| Estimation of the 3D covariance from 2D projections
|-

| Paper
| [[2015Tagare_Direct]]
| Direct reconstruction of PCA components
|-

| Paper
| [[2016Gong_Mechanical]]
| Mechanical model for macromolecules
|-

| Paper
| [[2016Rawson_Movement]]
| Movement and flexibility
|-

| Paper
| [[2016Sorzano_StructMap]]
| Sorting a discrete set of conformational states
|-

| Paper
| [[2016Sorzano_Strain]]
| Calculate local stretches, strains and rotations from two conformational states
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

|}

=== Validation ===

{|

| Paper
| [[2008Stagg_TestBed]]
| Effect of voltage, dosis, number of particles and Euler jumps on resolution
|-

| Paper
| [[2011Henderson]]
| Tilt Validation
|-

| Paper
| [[2011Read]]
| Validation of PDBs
|-

| Paper
| [[2012Henderson]]
| EM Map Validation
|-

| Paper
| [[2013Cossio_Bayesian]]
| EM Map Validation in a probabilistic setting
|-

| Paper
| [[2013Chen_NoiseSubstitution]]
| Noise substitution at high resolution for measuring overfitting
|-

| Paper
| [[2014Russo_StatisticalSignificance]]
| EM Map Validation through the statistical significance of the tilt-pair angular assignment
|-

| Paper
| [[2014Stagg_Reslog]]
| EM Map Validation through the resolution evolution with the number of particles
|-

| Paper
| [[2014Wasilewski_Tilt]]
| Web implementation of the tilt pair validation
|-

| Paper
| [[2015Heymann_Alignability]]
| EM Map Validation through the resolution of reconstructions from particles and noise
|-

| Paper
| [[2015Oliveira_FreqLimited]]
| Comparison of gold standard and frequency limited optimization
|-

| Paper
| [[2015Wriggers_Secondary]]
| Validation by secondary structure
|-

| Paper
| [[2016Kim_SAXS]]
| Comparison of SAXS data and EM projections
|-

| Paper
| [[2016Rosenthal_Review]]
| Review of validation methods
|-

| Paper
| [[2016Vargas_Alignability]]
| Validation by studying the tendency of an angular assignment to cluster in the projection space
|-

| Paper
| [[2017Monroe_PDBRefinement]]
| Validation by comparison to a refined PDB
|-

|}

=== Resolution ===

{|

| Paper
| [[1986Harauz_FBP]]
| Fourier Shell Correlation
|-

| Paper
| [[1987Unser_SSNR]]
| 2D Spectral Signal to Noise Ratio
|-

| Paper
| [[2002Penczek_SSNR]]
| 3D Spectral Signal to Noise Ratio for Fourier based algorithms
|-

| Paper
| [[2003Rosenthal_DPR]]
| Review of the FSC and establishment of a new threshold
|-

| Paper
| [[2005Unser_SSNR]]
| 3D Spectral Signal to Noise Ratio for any kind of algorithms
|-

| Paper
| [[2005VanHeel_FSC]]
| Establishment of a new threshold for FSC
|-

| Paper
| [[2007Sousa_AbInitio]]
| Resolution measurement on neighbour Fourier voxels
|-

| Paper
| [[2014Kucukelbir_Local]]
| Quantifying the local resolution of cryo-EM density maps
|-

| Paper
| [[2016Pintilie_Probabilistic]]
| Probabilistic models and resolution
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Statistical properties of resolution measures defined in Fourier space
|-

|}

=== Sharpening of high resolution information ===
{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast restoration and map sharpening
|-

| Paper
| [[2008Fernandez_Bfactor]]
| Bfactor determination and restoration
|-

| Paper
| [[2013Fiddy_SaxtonAlgorithm]]
| Phase retrieval or extension
|-

| Paper
| [[2014Kishchenko_SphericalDeconvolution]]
| Spherical deconvolution
|-

| Paper
| [[2015Spiegel_VISDEM]]
| Visualization improvement by the use of pseudoatomic profiles
|-

| Paper
| [[2016Jonic_Pseudoatoms]]
| Approximation with pseudoatoms
|-

| Paper
| [[2016Jonic_Denoising]]
| Denoising and high-frequency boosting by pseudoatom approximation
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[1982Schiske_Correction]]
| CTF correction for tilted objects
|-

| Paper
| [[1988Toyoshima_Model]]
| CTF estimation
|-

| Paper
| [[1995Frank_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1996Skoglund_MaxEnt]]
| CTF correction with Maximum Entropy
|-

| Paper
| [[1996Zhou_Model]]
| CTF model and user interface for manual fitting
|-

| Paper
| [[1997Fernandez_AR]]
| PSD estimation using periodogram averaging and AR models
|-

| Paper
| [[1997Penczek_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1997Stark_Deconvolution]]
| CTF correction using deconvolution
|-

| Paper
| [[1997Zhu_RecCTF]]
| CTF correction and reconstruction
|-

| Paper
| [[2000DeRosier_EwaldCorrection]]
| CTF correction considering the Ewald sphere
|-

| Paper
| [[2000Jensen_TiltedCorrection]]
| CTF correction considering tilt in backprojection
|-

| Paper
| [[2001Saad_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Huang_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Mindell_CTFTILT]]
| CTF estimation for tilted micrographs
|-

| Paper
| [[2003Sander_MSA]]
| CTF estimation through MSA classification of PSDs
|-

| Paper
| [[2003Velazquez_ARMA]]
| PSD and CTF estimation using ARMA models
|-

| Paper
| [[2004Sorzano_IDR]]
| CTF restoration and reconstruction with Iterative Data Refinement
|-

| Conference
| [[2004Wan_CTF]]
| Spatially variant CTF
|-

| Paper
| [[2004Zubelli_Chahine]]
| CTF restoration and reconstruction with Chahine's multiplicative method
|-

| Conference
| [[2005Dubowy_SpaceVariant]]
| CTF correction when this is space variant
|-

| Paper
| [[2005Mallick_ACE]]
| CTF estimation
|-

| Paper
| [[2006Wolf_Ewald]]
| CTF correction considering Ewald sphere
|-

| Paper
| [[2007Jonic_EnhancedPSD]]
| PSD enhancement for better identification of Thon rings; Vitreous ice diffracts in Thon rings
|-

| Paper
| [[2007Philippsen_Model]]
| CTF Model for tilted specimens
|-

| Paper
| [[2007Sorzano_CTF]]
| CTF estimation using enhanced PSDs
|-

| Paper
| [[2009Sorzano_Sensitivity]]
| Error sensitivity of the CTF models, non-uniqueness of the CTF parameters
|-

| Paper
| [[2010Jiang2010_CTFCorrection]]
| Amplitude correction method
|-

| Paper
| [[2010Kasantsev_CTFCorrection]]
| Mathematical foundations of Kornberg and Jensen method
|-

| Paper
| [[2010Leong_CTFCorrection]]
| Correction for spatially variant CTF
|-

| Paper
| [[2011Glaeser_Coma]]
| The effect of coma at high-resolution
|-

| Paper
| [[2011Mariani_Tilted]]
| CTF simulation and correction of tilted specimens
|-

| Paper
| [[2011Sindelar_Wiener]]
| CTF correction using a modified version of Wiener filter
|-

| Paper
| [[2011Voortman_Tilted]]
| CTF correction for tilted specimen
|-

| Paper
| [[2012Voortman_VaryingCTF]]
| Correcting a spatially varying CTF
|-

| Paper
| [[2013Vargas_FastDef]]
| Fast defocus
|-

| Paper
| [[2015Rohou_CTFFind4]]
| CTF Find 4
|-

| Paper
| [[2015Sheth_CTFquality]]
| Visualization and quality assessment of CTF
|-

| Paper
| [[2016Zhang_GCTF]]
| gCTF
|-

|}

=== Segmentation ===

{|

| Paper
| [[2006Baker_segmentation]]
| Segmentation of molecular subunits
|-

|}

=== Fitting and docking ===

{|

| Paper
| [[1999Volkmann_Fitting]]
| Fitting in real space
|-

| Paper
| [[2001Baker_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2001Jones_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2003Kovacs_FRM3D]]
| Fast Rotational Alignment of two EM maps
|-

| Paper
| [[2004Tama_NMA1]]
| Flexible fitting with Normal Modes (I)
|-

| Paper
| [[2004Tama_NMA2]]
| Flexible fitting with Normal Modes (II)
|-

| Paper
| [[2005Velazquez_Superfamilies]]
| Recognition of the superfamily folding in medium-high resolution volumes
|-

| Paper
| [[2007DeVries_Haddock]]
| Docking with Haddock 2.0
|-

| Paper
| [[2007Kleywegt_QualityControl]]
| Quality control and validation of fitting
|-

| Paper
| [[2012Biswas_Secondary]]
| Secondary structure determination in EM volumes
|-

| Paper
| [[2012Velazquez_Constraints]]
| Multicomponent fitting by using constraints from other information sources
|-

| Paper
| [[2013Chapman MS_Atomicmodeling]]
| Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters
|-

| Paper
| [[2013Esquivel_Modelling]]
| Review on modelling (secondary structure, fitting, ...)
|-

| Paper
| [[2013Lopez_Imodfit]]
| Fitting based on vibrational analysis
|-

| Paper
| [[2013Nogales_3DEMLoupe]]
| Normal Mode Analysis of reconstructed volumes
|-

| Paper
| [[2014AlNasr_Secondary]]
| Identification of secondary structure elements in EM volumes
|-

| Paper
| [[2014Politis_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Rey_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Villa_Review]]
| Review of atomic fitting into EM volumes
|-

| Paper
| [[2015Barad_EMRinger]]
| Validation of hybrid models
|-

| Paper
| [[2015Bettadapura_PF2Fit]]
| Fast rigid fitting of PDBs into EM maps
|-

| Paper
| [[2015Carrillo_CapsidMaps]]
| Analysis of virus capsids using Google Maps
|-

| Paper
| [[2015Schroeder_Hybrid]]
| Review on model building
|-

| Paper
| [[2015Tamo_Dynamics]]
| Dynamics in integrative modeling
|-

| Paper
| [[2015Sorzano_AtomsToVoxels]]
| Accurate conversion of an atomic model into a voxel density volume
|-

| Paper
| [[2016Joseph_Evolution]]
| Evolutionary constraints for the fitting of atomic models into density maps
|-

| Paper
| [[2016Segura_3Diana]]
| Validation of hybrid models
|-

| Paper
| [[2016Singharoy_MDFF]]
| Construction of hybrid models driven by EM density and molecular dynamics
|-

| Paper
| [[2016Wang_Rosetta]]
| Construction of hybrid models driven by EM density using Rosetta
|-

| Paper
| [[2017Hryc_WeightedAtoms]]
| Construction of hybrid models by locally weighting the different atoms
|-

|}

=== Books and reviews ===

{|

| Book
| [[1980Herman_Tomography]]
| General book on tomography
|-

| Book
| [[1988Kak_Tomography]]
| General book on tomography
|-

| Paper
| [[2000Tao_Review]]
| Review of single particles
|-

| Paper
| [[2000VanHeel_Review]]
| Review of single particles
|-

| Paper
| [[2002Frank_Review]]
| Review of single particles
|-

| Paper
| [[2002Schmid_Review]]
| Review of single particles
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2004Subramaniam_Review]]
| Review of single particles
|-

| Paper
| [[2005Steven_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_book]]
| Book covering all aspects of electron microscopy of single particles
|-

| Paper
| [[2006Sorzano_Review]]
| Review of optimization problems in electron microscopy
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems in Electron Tomography
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2008Mueller_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2008Taylor_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2010DeRosier_Review]]
| Personal account of how 3DEM developed in the early days
|-

| Chapter
| [[2012Sorzano_Review]]
| Review of single particle analysis using Xmipp
|-

| Chapter
| [[2012Devaux_Protocol]]
| Protocols for performing single particle analysis
|-

| Paper
| [[2014Bai_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Carazo_Review]]
| Review of the reconstruction process
|-

| Paper
| [[2015Cheng_Review]]
| A primer to Single Particle Cryo-EM
|-

| Paper
| [[2015Cheng_Reviewb]]
| Single Particle Cryo-EM at crystallographic resolution
|-

| Paper
| [[2015Elmlund_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Henderson_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Nogales_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Schroeder_Review]]
| Review of advances in the electron microscope
|-

| Paper
| [[2015Wu_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Carroni_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Egelman_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Eisenstein_CryoEM]]
| News feature on the Method of the Year
|-

| Paper
| [[2016FernandezLeiro_Review]]
| Review of EM
|-

| Paper
| [[2016Glaeser_HowGood]]
| How good can cryo-EM become?
|-

| Paper
| [[2016Jonic_PseudoAtoms]]
| Review of the applications of the use of pseudoatoms in EM
|-

| Chapter
| [[2016Mio_Review]]
| Overview of the process to obtain EM reconstructions
|-

| Paper
| [[2016Jonic_Review]]
| A review of computational ways to handle heterogeneity
|-

| Paper
| [[2016Nogales_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Subramaniam_Review]]
| Why cryo-EM is now suitable for crystallographic journals
|-

| Paper
| [[2016Vinothkumar_Review]]
| Historical review and current limitations
|-

| Paper
| [[2017Frank_Review]]
| Historical review of EM
|-

| Paper
| [[2017Jonic_Review]]
| Review of computational methods to analyze conformational variability
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Review of statistical properties of resolution measures defined in Fourier space
|-
|}

=== Software ===

{|

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[1999Lutdke_Eman]]
| Eman
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Baldwin_AngularTransformations]]
| The Transform Class in SPARX and EMAN2
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Grigorieff_Frealign]]
| Frealign
|-

| Paper
| [[2008Scheres_XmippProtocols]]
| Xmipp Protocols
|-

| Paper
| [[2008Shaikh_SpiderProtocols]]
| Spider Protocols
|-

| Paper
| [[2012Wriggers_SitusConventions]]
| Conventions and workflows in Situs
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2015Cianfrocco_Cloud]]
| Software execution in the cloud
|-

| Paper
| [[2015Cheng_MRC2014]]
| Extensions to MRC file format
|-

| Paper
| [[2013DeLaRosa_Scipion]]
| Scipion
|-

| Paper
| [[2016Scheres_Relion]]
| Tutorial on the use of Relion
|-

| Paper
| [[2016Grigorieff_Frealign]]
| Tutorial on the use of Frealign
|-

|}

== Electron tomography ==

=== Image preprocessing ===

{|

| Paper
| [[2015Yan_thickness]]
| Determination of thickness, tilt and electron mean free path
|-

|}

=== Image alignment ===

{|

| Paper
| [[1982Guckenberger_commonOrigin]]
| Determination of a common origin in the micrographs of titl series in three-dimensional electron microscopy
|-

| Paper
| [[1992Lawrence_leastSquares]]
| Least squares solution of the alignment problem
|-

| Paper
| [[1995Penczek_dual]]
| Dual tilt alignment
|-

| Paper
| [[1996Owen_alignmentQuality]]
| Automatic alignment without fiducial markers and evaluation of alignment quality
|-

| Paper
| [[1998Grimm_normalization]]
| Discussion of several gray level normalization methods for electron tomography
|-

| Paper
| [[2001Brandt_Automatic1]]
| Automatic alignment without fiducial markers
|-

| Paper
| [[2001Brandt_Automatic2]]
| Automatic alignment with fiducial markers
|-

| Paper
| [[2006Winkler_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2006Castano_alignment]]
| Alignment with non-perpendicularity
|-

| Paper
| [[2007Castano_alignment]]
| Fiducial-less alignment of cryo-sections
|-

| Paper
| [[2009Sorzano_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2010Cantele_dualAlignment]]
| Alignment of dual series
|-

| Paper
| [[2014Tomonaga_Automatic]]
| Automatic alignment of tilt series using the projection themselves
|-

| Paper
| [[2014Han_Automatic]]
| Automatic alignment of tilt series using SIFT features
|-

| Paper
| [[2015Han_Automatic]]
| Automatic alignment of tilt series using fiducials
|-

| Paper
| [[2017Mastronarde_Automatic]]
| Automatic alignment and reconstruction of tilt series in IMOD
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[2003Winkler_CTF]]
| Focus gradient correction in electron tomography
|-

| Paper
| [[2006Fernandez_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Zanetti_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Xiong_CTF]]
| CTF determination and correction for low dose tomographic tilt series
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2017Kunz_3DCTF]]
| 3D CTF Correction
|-

|}

=== 3D reconstruction ===

{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1992Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[1997Marabini_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2002Fernandez_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2007Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[2008Fernandez_CARP]]
| Component Averaged Row Projections (CARP)
|-

| Paper
| [[2012Herman General Superiorization]]
| Superiorization: an optimization heuristic for medical physics
|-

| Paper
| [[2012Zhang_IPET_FETR]]
| IPET and FETR, a reconstruction algorithm for single molecule tomography
|-

| Paper
| [[2013Goris_SIRT_TV_DART]]
| Combination of SIRT, Total Variation and Discrete ART to reconstruct and segment at the same time
|-

| Paper
| [[2013Briegel A_Challenge]]
| The challenge of determining handedness in electron tomography and the use of DNA origami gold nanoparticle helices as molecular standards
|-

| Paper
| [[2013Messaoudi_EnergyFiltered]]
| 3D Reconstruction of Energy-Filtered TEM
|-

| Paper
| [[2016Deng_ICON]]
| 3D Reconstruction with missing information restoration
|-

| Paper
| [[2016Guay_Compressed]]
| 3D Reconstruction using compressed sensing
|-

|}

=== Noise reduction ===
{|

| Paper
| [[2001Frangakis_NAD]]
| Noise reduction with Nonlinear Anisotropic Diffusion
|-

| Paper
| [[2003Fernandez_AND]]
| Anisotropic nonlinear diffusion for electron tomography
|-

| Paper
| [[2003Jiang_Bilateral]]
| Bilateral denoising filter in electron microscopy
|-

| Paper
| [[2005Fernandez_AND]]
| Anisotropic nonlinear denoising in electron tomography
|-

| Paper
| [[2007Heide_median]]
| Iterative median filtering in electron tomography
|-

| Paper
| [[2007Fernandez_autAND]]
| Anisotropic nonlinear diffusion with automated parameter tuning
|-

| Paper
| [[2009Fernandez_Beltrami]]
| Nonlinear filtering based on Beltrami flow
|-

| Paper
| [[2010Bilbao_MeanShift]]
| Mean Shift Filtering
|-

| Paper
| [[2014Kovacik_wedgeArtefacts]]
| Removal of wedge artefacts
|-

| Paper
| [[2014Maiorca_beadArtefacts]]
| Removal of gold bead artefacts
|-

|}

=== Segmentation ===

{|

| Paper
| [[2002Frangakis_Eigenanalysis]]
| Segmentation using eigenvector analysis.
|-

| Paper
| [[2002Volkmann_Watershed]]
| Segmentation using watershed transform.
|-

| Paper
| [[2003Bajaj_BoundarySegmentation]]
| Segmentation based on fast marching.
|-

| Paper
| [[2005Cyrklaff_Thresholding]]
| Segmentation using optimal thresholding.
|-

| Paper
| [[2007Lebbink_TemplateMatching]]
| Segmentation using template matching.
|-

| Paper
| [[2007Sandberg_OrientationFields]]
| Segmentation using orientation fields.
|-

| Paper
| [[2007Sandberg_SegmentationReview]]
| Review on segmentation in electron tomography.
|-

| Paper
| [[2008Garduno_FuzzySegmentation]]
| Segmentation using fuzzy set theory principles.
|-

| Paper
| [[2009Lebbink_TemplateMatching2]]
| Segmentation using template matching.
|-

| Paper
| [[2012RubbiyaAli_EdgeDetection]]
| Parameter-Free Segmentation of Macromolecular Structures.
|-

| Conference
| [[2015Xu_TemplateMatching]]
| Detection of macromolecular complexes with a reduced representation of the templates.
|-

|}

=== Resolution ===
{|

| Paper
| [[2005Cardone_Resolution]]
| Resolution criterion for electron tomography
|-

| Chapter
| [[2007Penczek_Resolution]]
| Review of resolution criteria for electron tomography
|-

| Paper
| [[2015Diebolder_ConicalFSC]]
| Conical Fourier Shell Correlation
|-

|}

=== Subtomogram analysis ===

{|

| Paper
| [[2000Bohm_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2002Frangakis_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2006Nickell_Review]]
| Review of macromolecule finding by template matching (Visual Proteomics)
|-

| Paper
| [[2007Best_Review]]
| Review of Localization of Protein Complexes by Pattern Recognition
|-

| Paper
| [[2007Forster_Review]]
| Review of structure determination by subtomogram averaging
|-

| Paper
| [[2008Forster_Classification]]
| Classification of subtomograms using constrained correlation
|-

| Paper
| [[2008Bartesaghi_Classification]]
| Classification and averaging of subtomograms
|-

| Paper
| [[2008Schmid_Averaging]]
| Alignment and averaging of subtomograms
|-

| Paper
| [[2010Amat_Averaging]]
| Alignment and averaging of subtomograms exploiting thresholding in Fourier space
|-

| Paper
| [[2013Chen_Averaging]]
| Fast alignment of subtomograms using spherical harmonics
|-

| Paper
| [[2013Kuybeda_Averaging]]
| Alignment and averaging of subtomograms using the nuclear norm of the cluster
|-

| Paper
| [[2013Shatsky_Averaging]]
| Alignment and averaging of subtomograms with constrained cross-correlation
|-

| Paper
| [[2014Chen_Autofocus]]
| Subtomogram averaging and classification with special attention to differences
|-

| Paper
| [[2014Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2014Voortman_LimitingFactors]]
| Limiting factors of subtomogram averaging
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2015Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2016Bharat_Relion]]
| Subtomogram averaging with Relion
|-

| Paper
| [[2016Song_MatrixNorm]]
| Matrix norm minimization for tomographic reconstruction and alignment
|-

| Paper
| [[2017Castano_ParticlePicking]]
| Particle picking in tomograms for subtomogram averaging
|-

|}

=== Single particle tomography ===

{|

| Paper
| [[2012Bartesaghi_Constrained]]
| 3D reconstruction by imposing geometrical constraints
|-

| Paper
| [[2015Galaz_SingleParticleTomography]]
| Set of tools for Single Particle Tomography in EMAN2
|-

| Paper
| [[2016Galaz_SingleParticleTomography]]
| Alignment algorithms and CTF correction
|-

|}

=== Books and reviews ===

{|

| Paper
| [[2000Baumeister_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Koster_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Sali_Review]]
| Review of electron tomography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2005Lucic_Review]]
| Review of electron tomography
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_TomoBook]]
| Electron Tomography
|-

| Book
| [[2007McIntosh_Book]]
| Cellular Electron Microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2012Kudryashev_Review]]
| Review of subtomogram averaging
|-

| Paper
| [[2016Beck_Review]]
| Review of molecular sociology
|-

|}

=== Software ===

{|

| Paper
| [[1996Kremer_IMOD]]
| IMOD
|-

| Paper
| [[1996Chen_Priism/IVE]]
| Priism/IVE
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2005Nickell_TOM]]
| TOM Toolbox
|-

| Paper
| [[2007Messaoudi_TomoJ]]
| TomoJ
|-

| Paper
| [[2008Heymann_BsoftTomo]]
| Bsoft
|-

| Paper
| [[2015Ding_CaltechTomography]]
| Caltech tomography database
|-

| Paper
| [[2015Noble_AppionProtomo]]
| Batch fiducial-less tilt-series alignment in Appion using Protomo
|-

| Paper
| [[2015vanAarle_Astra]]
| ASTRA Toolbox
|-

|}

== 2D Crystals ==

=== 2D Preprocessing ===

{|

| Paper
| [[1986Henderson_Processing]]
| General 2D processing
|-

| Paper
| [[2000He_PhaseAlignment]]
| Phase consistency and Alignment
|-

| Paper
| [[2006Gil_Unbending]]
| Crystal unbending
|-

|}

=== Classification ===
{|

| Paper
| [[1988Frank_Classification]]
| MSA and classification in electron crystallography
|-

| Paper
| [[1996Fernandez_SOM]]
| Classification based on self organizing maps
|-

| Paper
| [[1998Sherman_MSA]]
| Classification based on MSA
|-

|}
=== 3D Reconstruction ===

{|

| Paper
| [[1985Wang_Solvent]]
| Solvent flattening
|-

| Paper
| [[1990Henderson_Processing]]
| General 3D processing
|-

| Paper
| [[2004Marabini_ART]]
| Algebraic Reconstruction Technique with blobs for crystals (Xmipp)
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1998Walz_Review]]
| Review of 2D crystallography
|-

| Paper
| [[1999Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Ellis_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of single particles, electron tomography and crystallography
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Gipson_2dx]]
| 2dx
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Philippsen_IPLT]]
| IPLT
|-

|}

== 3D Crystals - MicroED ==

=== Sample Preparation ===
{|
| Paper
| [[2016Shi_Preparation]]
| Sample Preparation
|}
=== Data Collection ===
{|
| Paper
| [[2014Nannenga_CR]]
| Continuous rotation

|}
=== Data Processing ===
{|

| Paper
| [[2011Wisedchaisri_PhaseExtension]]
| Fragment-based phase extension
|-

| Paper
| [[2015Hattne_Processing]]
| Data Processing
|-

| Paper
| [[2016Hattne_Correction]]
| Image correction
|}

=== Software ===
{|

| Paper
| [[2014Iadanza_Processing]]
| Data Processing of still diffraction data
|}

=== Books and Reviews ===
{|
| Paper
| [[2014Nannenga_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Liu_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Rodriguez_Review ]]
| Review of MicroED
|-

|}

== Helical particles ==

=== Filament corrections ===

{|

| Paper
| [[1986Egelman_Curved]]
| Algorithm for correcting curved filaments
|-

| Paper
| [[1988Bluemke_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2006Wang_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2016Yang_Flexible]]
| Algorithm for correcting filaments with flexible subunits
|-

|}

=== Reconstruction ===

{|

| Paper
| [[1952Cochran_Fourier]]
| Fourier Bessel transform of filamentous structures
|-

| Paper
| [[1958Klug_Fourier]]
| Fourier Bessel decomposition of the projection images
|-

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2005Wang_Iterative]]
| Iterative Fourier-Bessel algorithm
|-

| Paper
| [[2007Egelman_Iterative]]
| Iterative real-space algorithm
|-

| Paper
| [[2013Desfosses_Spring]]
| Helical processing with Spring
|-

| Paper
| [[2015Zhang_seam]]
| Workflow for the detection of the lattice seam
|-

| Paper
| [[2016Rohou_Frealix]]
| Helical processing with Frealix
|-

|}

=== Validation ===

{|

| Paper
| [[2014Egelman_ambiguity]]
| How to detect incorrect models
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Carragher_Phoelix]]
| Phoelix
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Owen_Brandeis]]
| Brandeis
|-

|}

== Icosahedral particles ==

=== Reconstruction ===

{|

| Paper
| [[1970Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1971Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1996Fuller_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1997Thuman_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

|}

=== Classification ===

{|

| Paper
| [[2005Scheres_Virus]]
| Classification of virus capsids in real space
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1999Baker_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[1999Conway_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2000Thuman_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Lee_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Navaza_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2006Grunewald_Review]]
| Review of reconstruction of icosahedral viruses
|-

|}

=== Software ===

{|

| Paper
| [[1996Baker_EMPFT]]
| EMPFT
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2013Morin_Sliz SBGrid]]
| SBGrid presentation for eLife
|-

|}

== Databases ==

{|

| Paper
| [[2003Boutselakis_EMSD]]
| EMSD database
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2011Kim_CDDB]]
| Conformational Dynamics Data Bank
|-

| Paper
| [[2011Lawson_EMDB]]
| Electron Microscopy Data Bank
|-

| Paper
| [[2013Ison_EDAM]]
| EDAM, an ontology of bioinformatics operations
|-

| Paper
| [[2016Iudin_EMPIAR]]
| EMPIAR raw data database
|-

| Paper
| [[2016Patwhardan_EMDB]]
| EMDB, PDB, ...
|-

| Paper
| [[2017Patwhardan_Trends]]
| Trends at EMDB
|-

| Paper
| [[2017Shao_PDBQuality]]
| Quality metrics in PDB
|-

| Blog
| http://www.mybiosoftware.com
| Huge list of bioinformatics programs (many of them structural bioinformatics)
|-

|}

== Relationship to other structural information sources ==

{|

| Paper
| [[2000Engel_AFM]]
| Review of Atomic Force Microscopy
|-

| Paper
| [[2001Dimmeler_AFM]]
| Constraints from Atomic Force Microscopy
|-

| Paper
| [[2003Mobus_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_Review]]
| Review on correlative microscopy
|-

| Paper
| [[2005Boudier_EFTETJ]]
| Software for Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2005Vestergaard_SAXS]]
| Example of comparison of 3DEM and Small-angle X-ray scattering
|-

| Paper
| [[2007Hamada_SAXS]]
| Constraints from Small-angle X-ray scattering
|-

| Paper
| [[2013Xu_FRET]]
| EM+FRET
|-

|}

== X-ray tomography ==

{|

| Paper
| [[2012Oton_ImageFormation]]
| Image formation model in X-ray cell microscopy
|-

|}

== Mathematical tools necessary ==

== People developing methods ==
Please, add yourself to this list (due to privacy reasons, please, do not add anyone else to the list without his/her explicit consent). Sort by first name alphabetical order.

[http://biocomp.cnb.csic.es/~coss Carlos Oscar S. Sorzano]: CSIC, Madrid, Spain 

[http://www.curie.fr/recherche/themes/detail_equipe.cfm/lang/_fr/id_equipe/241.htm Cédric Messaoudi]: Institute Curie, Paris, France 

[http://scholar.google.es/citations?user=_jNYGScAAAAJ&hl=en Javier Vargas]:[mailto:jvargas@cnb.csic.es mail]: CSIC, Madrid, Spain 

[http://scholar.google.es/citations?hl=es&user=g2ZJPIYAAAAJ Joaquín Otón]: CSIC, Madrid, Spain 

[mailto:jrbcast@gmail.com José Román Bilbao-Castro]: UAL, Almería, Spain; CSIC, Madrid, Spain 

[José Miguel de la Rosa Trevín]: Biocomputing Unit CNB-CSIC, Madrid, Spain 

[http://cryoem.janelia.org Tamir Gonen]: [mailto:gonent@janelia.hhmi.org mail]: Howard Hughes Medical Institute, Ashburn, VA, USA 

[mailto:vabrishami@cnb.csic.es Vahid Abrishami]: CSIC, Madrid, Spain 

== 3DEM sites ==
* [http://3dem.ucsd.edu/ 3DEM web site]

* [http://en.wikibooks.org/wiki/Software_Tools_For_Molecular_Microscopy Software tools for molecular microscopy]

* [http://www.emdatabank.org/ The Electron Microscopy Data Bank (EMDB)]

* [http://ccdb.ucsd.edu The Cell Centered Database (CCDB)]

* [http://conventions.cnb.csic.es The geometrical software conventions web page ]

== Editing useful links ==

* [http://www.mediawiki.org/wiki/Help:Formatting Text formatting in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Links Adding links in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Images Adding images in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Tables Making tables in Mediawiki]

2013Ison EDAM

2017-05-11T21:37:59Z

CoSS: Created page with "== Citation == Ison, J.; Kalas, M.; Jonassen, I.; Bolser, D.; Uludag, M.; McWilliam, H.; Malone, J.; Lopez, R.; Pettifer, S. & Rice, P. EDAM: an ontology of bioinformatics op..."

== Citation ==

Ison, J.; Kalas, M.; Jonassen, I.; Bolser, D.; Uludag, M.; McWilliam, H.; Malone, J.; Lopez, R.; Pettifer, S. & Rice, P. EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats. Bioinformatics, 2013, 29, 1325-1332

== Abstract ==

Advancing the search, publication and integration of bioinformatics tools and resources demands consistent machine-understandable descriptions. A comprehensive ontology allowing such descriptions is therefore required. EDAM is an ontology of bioinformatics operations (tool or workflow functions), types of data and identifiers, application domains and data formats. EDAM supports semantic annotation of diverse entities such as Web services, databases, programmatic libraries, standalone tools, interactive applications, data schemas, datasets and publications within bioinformatics. EDAM applies to organizing and finding suitable tools and data and to automating their integration into complex applications or workflows. It includes over 2200 defined concepts and has successfully been used for annotations and implementations. The latest stable version of EDAM is available in OWL format from http://edamontology.org/EDAM.owl and in OBO format from http://edamontology.org/EDAM.obo. It can be viewed online at the NCBO BioPortal and the EBI Ontology Lookup Service. For documentation and license please refer to http://edamontology.org. This article describes version 1.2 available at http://edamontology.org/EDAM_1.2.owl. jison@ebi.ac.uk.

== Keywords ==

== Links ==

https://www.ncbi.nlm.nih.gov/pubmed/23479348

== Related software ==

== Related methods ==

== Comments ==

Main Page

2017-05-11T21:37:09Z

CoSS: /* Databases */

== Presentation ==

This web page is intended to be an extensive repository of three-dimensional electron microscopy (3DEM) methods. The advantages of having such a repository are

* You know which are the relevant articles in a particular topic, therefore, paper introductions, reviews, etc. are easier to write and you make sure you will cite all the related articles.
* You will be sure that your paper has more chances of being cited.
* You can add whatever information you find relevant to your method, external links, links to other papers, etc.
* You can link your method to a web page providing the corresponding software, so you know people can use your algorithms.
* You can use the Wiki search capabilities to locate relevant articles even if they are not at the topic you are looking at.
* As a community we will "reconstruct" our history.
* You can select the "watch" option above to receive notifications in case of further changes in the Main Page.

Developing image processing methods for 3DEM is not "[[well-paid]]" in terms of citations and impact factor. However, it is crucial for the advance of the field. Gathering methodological papers in a portal will help to increase the recognition of the field.

Please:

* Add your articles at the right place (you can add a single article in several topics if it is relevant to all of them). The easiest way to add an article is by editing the corresponding topic in the main page, adding your entry, then save the main page. Click on the red link that appears on your new entry, copy and paste the Wiki following code, add the information of your article

== Citation ==

== Abstract ==

== Keywords ==

== Links ==

== Related software ==

== Related methods ==

== Comments ==

* Maintain the information of each article as complete as possible.
* Sort articles by years and authors.
* Be respectful to other people's work.

== How to subscribe to this page ==

You may subscribe to this page so that you will be notified every time someone adds a new method. To do so, you have to register in the page, and edit your preferences ("my preferences"). Be sure that you have activated the option "E-mail me when a page on my watchlist is changed". Finally, click on the "Watch" tab at the top of this page.

You may subscribe to changes on this page on the mailing list 3demmethods@cnb.csic.es. To send a new method to this mail list just send a mail to 3demmethods@cnb.csic.es

To subscribe to this list, visit the web page

https://listas.csic.es/cnb/wws/subscribe/3demmethods

Alternatively, you may write a mail to sympa6@cnb.csic.es with the subject

<code>subscribe 3demmethods YourName YourFamilyName</code>

and an empty mail body.

To unsubscribe visit the page

https://listas.csic.es/cnb/wws/sigrequest/3demmethods

or write sympa6@cnb.csic.es with the subject

<code>unsubscribe 3demmethods</code>

and an empty mail body.

== Electron microscopy images ==

=== Online courses ===

CALTECH: http://cryo-em-course.caltech.edu/

MRC: ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/EM-course/

CNB-CSIC: http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/MadridJan2014EM

Workshop on Computational methods for CryoEM: https://www.youtube.com/watch?v=XdKO1iaPP8o

Workshop on Management of large CryoEM facilities: https://www.youtube.com/watch?v=as4seOPszL0

Icknield Course on Model Building and Refinement for High Resolution EM Maps: http://www.ccpem.ac.uk/training/icknield_2017/icknield_2017.php

=== Image formation ===

{|

| Paper
| [[1971Erickson_CTF]]
| CTF model
|-

| Paper
| [[1971Glaeser_Damage]]
| Radiation damage
|-

| Chapter
| [[1971Hanszen_CTF]]
| Image formation model
|-

| Paper
| [[1971Thon_Model]]
| CTF model
|-

| Paper
| [[1975Unwin_Imaging]]
| Radiation dose
|-

| Paper
| [[1977Wade_Model]]
| CTF model
|-

| Paper
| [[1978Wade_Model]]
| CTF model
|-

| Paper
| [[1979Hayward_Radiation]]
| Radiation damage
|-

| Paper
| [[1984Cohen_Validity]]
| Validity of the CTF model at high frequencies
|-

| Paper
| [[1988Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[1992Wade_Model]]
| CTF model
|-

| Paper
| [[1993Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2004Egerton_Damage]]
| Radiation damage
|-

| Paper
| [[2004Sorzano_Normalization]]
| Background noise is Gaussian
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2009Baxter_NoiseCharacterization]]
| Characterization of the different noise sources in cryo-EM
|-

| Paper
| [[2010Baker_Damage]]
| Radiation damage dependence on resolution
|-

| Paper
| [[2010Bammes_Damage]]
| Radiation damage dependence on temperature
|-

| Paper
| [[2010Gomez_Multislice]]
| Simulation of the multi slice model
|-

| Paper
| [[2010Zewail_FourDimensional]]
| Review on the use of ultrafast EM
|-

| Paper
| [[2011Bammes_CCD]]
| Performance of CCD cameras
|-

| Paper
| [[2011Glaeser_Coma]]
| Image formation model including coma
|-

| Paper
| [[2011Milazzo_DirectDetectors]]
| Evaluation of Direct Detectors
|-

| Paper
| [[2011Rullgard_ImageSimulation]]
| Accurate simulation of EM images
|-

| Paper
| [[2011Zhang LimitingFactors]]
| Limiting factor for atomic resolution in EM
|-

| Paper
| [[2012Bammes_DirectDetection]]
| Performance of Direct detectors
|-

| Paper
| [[2012Campbell_MotionCorrection]]
| Beam induced motion correction and direct detectors
|-

| Paper
| [[2012Shang_HydrationLayer]]
| Simulation of PDB volumes explicitly considering the hydration layer
|-

| Paper
| [[2013Egerton_RadiationDamage]]
| Review of TEM radiation damage and experimental ways of reducing it
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu H_Noisemodels]]
| Noise models and cryo-EM drift correction with a direct-electron camera
|-

| Paper
| [[2013Li X K2 noisemodels]]
| Influence of electron dose rate on electron counting images recorded with the K2 camera
|-

| Paper
| [[2013Vulovic_CTFApproximations]]
| When to use the different approximations performed so that a projection with linear CTF is valid
|-

| Thesis
| [[2013Vulovic_ImageFormation]]
| Ph.D. Thesis on the image formation in cryo-EM
|-

| Paper
| [[2014Danev_PhasePlate]]
| Volta potential phase plate
|-

| Paper
| [[2015Chiu_K2]]
| Characterization of K2
|-

| Paper
| [[2015Hawkes_AberrationCorrection]]
| Historical account of the development of lens corrections
|-

| Paper
| [[2015Koeck_Quadratic]]
| Limitations of the linear approximation and use of the quadratic terms
|-

| Paper
| [[2015Kuijper_FEI]]
| Description of the FEI Falcons
|-

| Paper
| [[2015Lobato_MULTEM]]
| Simulation of multislice diffraction
|-

| Paper
| [[2015McMullan_AmorphousIce]]
| Beam induced movement is caused by Brownian motion
|-

| Paper
| [[2016Koeck_ADF]]
| Simulations of Annular Dark Field TEM
|-

| Paper
| [[2017Mishyna_DNARadiation]]
| Review of radiation damage on DNA
|-

|}

=== Collection geometry ===

{|

| Chapter
| [[1980Hoppe_Wedge]]
| Missing wedge
|-

| Paper
| [[1987Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1995Penczek_Dual]]
| Dual axis tomography
|-

| Paper
| [[1997Mastronarde_Dual]]
| Dual axis tomography
|-

| Paper
| [[2003Ludtke_FocusPairs]]
| Focus pairs for single particles
|-

| Paper
| [[2005Lanzavecchia_Conical]]
| Conical tomography
|-

| Paper
| [[2005Zampighi_Conical]]
| Conical tomography
|-

| Paper
| [[2006Leschziner_OT]]
| Orthogonal Tilt
|-

| Paper
| [[2006Messaoudi_Multiple]]
| Multiple axis tomography
|-

| Paper
| [[2012Kudryashev_FocusPairs]]
| Focus pairs tomography
|-

| Paper
| [[2014Hovden_TiltFocus]]
| Combining tilt series with focus series
|-

| Paper
| [[2015Sorzano_RandomConicalTilt]]
| General formulation of Random Conical Tilt
|-

| Paper
| [[2017Hagen_DoseTomography]]
| Dose optimization for subtomogram averaging
|-

|}

=== Sample preparation ===

{|

| Paper
| [[1982Dubochet_Sample]]
| Vitreous ice
|-

| Paper
| [[1986Lepault_Sample]]
| Fast freezing
|-

| Paper
| [[1995Dubochet_Sample]]
| High-pressure freezing
|-

| Paper
| [[1995VanMarle_Sample]]
| Sample damages in resin
|-

| Paper
| [[1998Adrian_Sample]]
| Cryo negative staining
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2002Hsieh_Sample]]
| Cryofixation
|-

| Paper
| [[2004AlAmoudi_Sample]]
| CEMOVIS
|-

| Paper
| [[2008Studer_Sample]]
| Review on high pressure freezing
|-

| Paper
| [[2009Pierson_Sample]]
| Review on sample preparation for electron tomography
|-

| Paper
| [[2010Zhang_NegativeStaining]]
| Negative staining for small protein imaging
|-

| Paper
| [[2012Zhang_PositiveStaining]]
| Positive staining
|-

| Paper
| [[2014Rames_NegativeStaining]]
| Optimized negative staining
|-

| Paper
| [[2014Russo_GoldGrids]]
| Gold grids for single particles
|-

| Paper
| [[2015Cabra_Sample]]
| Review on sample preparation for single particles with videos
|-

| Paper
| [[2016Passmore_Review]]
| Tutorial chapter on sample preparation
|-

| Paper
| [[2016Razinkov_Vitrification]]
| New vitrification method
|-

| Paper
| [[2016Takizawa_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2016Thompson_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2017Arnold_BlottingFree]]
| Blotting-free preparation
|-

| Paper
| [[2017Peitsch_Sample]]
| iMEM: Isolation of Plasma Membrane for Cryoelectron Microscopy
|-

| Paper
| [[2017Schaffer_FocusedIonBeam]]
| Focused Ion Beam sample preparation for membrane proteins
|-

|}

=== Automated data collection ===

{|

| Paper
| [[1992Dierksen_Automatic]]
| Automated data collection
|-

| Paper
| [[1992Koster_Automatic]]
| Automated data collection
|-

| Paper
| [[1996Fung_Automatic]]
| Automated data collection for tomography
|-

| Paper
| [[2001Zhang_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2003Ziese_Automatic]]
| Automated autofocusing
|-

| Paper
| [[2004Potter_Automatic]]
| Automated sample loading
|-

| Paper
| [[2004Zheng_Automatic]]
| Automated data collection
|-

| Paper
| [[2005Lei_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2005Suloway_Automatic]]
| Automated data collection: Leginon
|-

| Paper
| [[2007Yoshioka_RCT]]
| Automated Random Conical Tilt
|-

| Paper
| [[2011Korinek_TOM2]]
| Automated acquisition with TOM2
|-

| Paper
| [[2015Li_UCSFImage]]
| Automated acquisition with UCSFImage
|-

| Paper
| [[2016Gil_Fuzzy]]
| Real time decisions during acquisition with neuro-fuzzy method
|-

| Paper
| [[2016Liu_TiltControl]]
| Accurate control of the tilt angle for electron tomography
|-

| Paper
| [[2016Vargas_FoilHole]]
| Determination of image quality at low magnification
|-

|}

== Single particles ==

=== Automatic particle picking ===

{|

| Paper
| [[1982VanHeel_Detection]]
| Detection of particles in micrographs
|-

| Paper
| [[2001Nicholson_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2001Zhu_Filaments]]
| Automatic identification of filaments in micrographs
|-

| Paper
| [[2004Sigworth_Detection]]
| Classical detection theory and the cryo-EM particle selection problem
|-

| Paper
| [[2004Volkmann_ParticlePicking]]
| An approach to automated particle picking from electron micrographs based on reduced representation templates
|-

| Paper
| [[2004Wong_ParticlePicking]]
| Model-based particle picking for cryo-electron microscopy
|-

| Paper
| [[2004Zhu_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2007Chen_Signature]]
| Automatic particle picking program: Signature
|-

| Paper
| [[2007Woolford_SwarmPS]]
| Automatic particle picking with several criteria, implemented in EMAN Boxer
|-

| Paper
| [[2009Sorzano_MachineLearning]]
| Automatic particle picking based on machine learning of rotational invariants
|-

| Paper
| [[2011Arbelaez_Comparison]]
| Evaluation of the performance of software for automated particle-boxing
|-

| Paper
| [[2013Abrishami_MachineLearning]]
| A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs
|-

| Paper
| [[2013Hauer_2013]]
| Automatic tilt pair detection in Random Conical Tilt
|-

| Paper
| [[2013Shatsky_ParticlePicking]]
| Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Langlois_ParticlePicking]]
| Automatic particle picking
|-

| Paper
| [[2016Vilas_AutomaticTilt]]
| Automatic identification of image pairs in untilted-tilted micrograph pairs
|-

|}

=== 2D Preprocessing ===

{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast enhancement through DPR
|-

| Paper
| [[2004Sorzano_Normalization]]
| Normalization procedures and their statistical properties.
|-

| Paper
| [[2006Sorzano_Denoising]]
| Strong denoising in wavelet space
|-

| Conference
| [[2009Sorzano_Downsampling]]
| Differences between the different downsampling schemes
|-

| Paper
| [[2012Brilot_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Campbell_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Zhao_Denoising]]
| Denoising using an invariant Fourier-Bessel eigenspace
|-

| Paper
| [[2013Norousi_Screening]]
| Screening particles to identify outliers
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu_Movies]]
| Drift correction for movies considering dark field
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Scheres_Movies]]
| Beam induced motion correction
|-

| Paper
| [[2015Abrishami_Movies]]
| Alignment of direct detection device micrographs
|-

| Paper
| [[2015Grant_Anisotropic]]
| Automatic estimation and correction of anisotropic magnification
|-

| Paper
| [[2015Grant_OptimalExposure]]
| Filter movies according to the radiation damage
|-

| Paper
| [[2015Rubinstein_Alignment]]
| Frame alignment at the level of particle
|-

| Paper
| [[2015Spear_DoseCompensation]]
| Effect of dose compensation on resolution
|-

| Paper
| [[2015Zhao_AnisotropicMagnification]]
| Correction of anisotropic magnification
|-

| Conference
| [[2016Bajic_Denoising]]
| Denoising and deconvolution of micrographs
|-

| Paper
| [[2016Jensen_RemovalVesicles]]
| Removal of vesicles in membrane proteins
|-

| Paper
| [[2016Bhamre_Denoising]]
| Denoising by 2D covariance estimation
|-

| Paper
| [[2017McLeod_Zorro]]
| Movie alignment by Zorro
|-

| Paper
| [[2017Zheng_MotionCorr2]]
| Movie alignment by MotionCorr2
|-

|}

=== 2D Alignment ===

{|

| Paper
| [[1981Frank_Averaging]]
| 2D averaging and phase residual
|-

| Paper
| [[1982Saxton_Averaging]]
| 2D averaging using correlation
|-

| Paper
| [[1998Sigworth_ML2D]]
| Maximum likelihood alignment in 2D
|-

| Paper
| [[2003Cong_FRM2D]]
| Fast Rotational Matching in 2D
|-

| Paper
| [[2005Cong_FRM2D]]
| Fast Rotational Matching in 2D introduced in a 3D Alignment algorithm
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

|}

=== 2D Classification and clustering ===

{|

| Paper
| [[1981VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[1984VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2011Singer_DiffusionMaps]]
| Classification in 2D based on graph analysis of the projections
|-

| Paper
| [[2012Yang_ISAC]]
| Iterative Stable Alignment and clustering
|-

| Paper
| [[2014Sorzano_Outlier]]
| Outlier detection in 2D classifications.
|-

| Paper
| [[2014Zhao_Aspire]]
| Fast classification based on rotational invariants and vector diffusion maps
|-

| Paper
| [[2015Huang_Robust]]
| Robust w-estimators of 2D classes
|-

| Paper
| [[2016Reboul_Stochastic]]
| Stochastic Hill Climbing for calculating 2D classes
|-

| Conference
| [[2017Bhamre_Mahalanobis]]
| 2D classification using Mahalanobis distance
|-

|}

=== 3D Alignment ===

{|

| Paper
| [[1980Kam_AutoCorrelation]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[1986Goncharov_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1987VanHeel_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1988Provencher_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Vogel_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1990Gelfand_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Goncharov_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Harauz_Quaternions]]
| Use of quaternions to represent rotations
|-

| Paper
| [[1994Penczek_Real]]
| Angular assignment using projection matching in real space
|-

| Paper
| [[1994Radermacher_Radon]]
| Angular assignment in Radon space
|-

| Paper
| [[1996Penczek_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[2003Rosenthal_DPR]]
| Angular assignment using DPR
|-

| Paper
| [[2004Sorzano_Wavelet]]
| Angular assignment in the wavelet space.
|-

| Paper
| [[2005Jonic_Splines]]
| Angular assignment in Fourier space using spline interpolation.
|-

| Paper
| [[2005Yang_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[2006Ogura_SimulatedAnnealing]]
| Angular asignment by simulated annealing
|-

| Paper
| [[2007Grigorieff_Continuous]]
| Continuous angular assignment in Fourier space
|-

| Paper
| [[2010Jaitly_Bayesian]]
| Angular assignment by a Bayesian method and annealing
|-

| Paper
| [[2010Sanz_Random]]
| Random model method
|-

| Paper
| [[2010Singer_Voting]]
| Detecting consistent common lines by voting (reference free)
|-

| Paper
| [[2011Singer_SDP]]
| Angular assignment by semidefinite programming and eigenvectors (reference free)
|-

| Paper
| [[2012Giannakis_Scattering]]
| Construction of an initial volume, reference free, by graph analysis of the projections
|-

| Paper
| [[2012Shkolnisky_Sync]]
| Angular assignment by synchronization of rotations (reference free)
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Wang_LUD]]
| Angular assignment by least unsquared deviations (reference free)
|-

| Paper
| [[2014Vargas_RANSAC]]
| Initial model using RANSAC (reference free)
|-

| Paper
| [[2015Joubert_Pseudoatoms]]
| Initial model based on pseudo-atoms
|-

| Paper
| [[2015Singer_Kam]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[2015Sorzano_Significant]]
| Statistical approach to the initial volume estimation (reconstruct significant)
|-

| Conference
| [[2016Michels_Heterogeneous]]
| Initial volume in the presence of heterogeneity
|-

| Paper
| [[2016Cossio_BayesianGPU]]
| GPU implementation of the Bayesian 3D reconstruction approach
|-

|}

=== 3D Reconstruction ===
{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1986Harauz_FBP]]
| Exact filters for Filtered Back Projection
|-

| Chapter
| [[1992Radermacher_WBP]]
| Exact filters for Weighted Back Projection
|-

| Paper
| [[1997Zhu_RecCTF]]
| 3D Reconstruction (SIRT like) and simultaneous CTF correction
|-

| Paper
| [[1998Boisset_Uneven]]
| Artifacts in SIRT and WBP under uneven angular distributions
|-

| Paper
| [[1998Marabini_ART]]
| Algebraic Reconstruction Technique with blobs (Xmipp)
|-

| Paper
| [[2001Sorzano_Uneven]]
| Free parameter selection under uneven angular distributions
|-

| Paper
| [[2005Sorzano_Parameters]]
| Free parameter selection for optimizing multiple tasks
|-

| Paper
| [[2008Sorzano_Constraints]]
| Mass, surface, positivity and symmetry constraints for real-space algorithms
|-

| Paper
| [[2009Bilbao_ParallelART]]
| Efficient parallelization of ART
|-

| Paper
| [[2011Li_GradientFlow]]
| Regularized 3D Reconstruction by Gradient Flow
|-

| Paper
| [[2011Vonesch_Wavelets]]
| Fast wavelet-based 3D reconstruction
|-

| Paper
| [[2012Gopinath_ShapeRegularization]]
| Regularized 3D Reconstruction by Shape information
|-

| Paper
| [[2012Kucukelbir_adaptiveBasis]]
| 3D reconstruction in an adaptive basis promoting sparsity
|-

| Paper
| [[2012Sindelar_NoiseReduction]]
| Optimal noise reduction in 3D reconstructions
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Lyumkis_Optimod]]
| Construction of initial volumes with Optimod
|-

| Paper
| [[2013Wang FIRM]]
| Fast 3D reconstruction in Fourier domain
|-

| Paper
| [[2014Kunz_SART_OS]]
| Simultaneous ART with OS
|-

| Paper
| [[2015Abrishami_Fourier]]
| 3D Reconstruction in Fourier space
|-

| Paper
| [[2015Dvornek_SubspaceEM]]
| Fast Maximum a posteriori
|-

| Paper
| [[2015Moriya_Bayesian]]
| Bayesian approach to suppress limited angular artifacts
|-

| Paper
| [[2015Xu_GeometricFlow]]
| Multi-scale geometric flow
|-

| Arxiv
| [[2016Ye_Cohomology]]
| Cohomology properties of 3D reconstruction
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

|}

=== 3D Heterogeneity ===

{|

| Paper
| [[2004White_Size]]
| Heterogeneity classification of differently sized images
|-

| Paper
| [[2006Penczek_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Scheres_ML3D]]
| Maximum Likelihood alignment and classification in 3D
|-

| Paper
| [[2009Spahn_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2010Elmlund_AbInitio]]
| Solving the initial volume problem with multiple conformations
|-

| Paper
| [[2010Shatsky_MultiVariate]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2012Scheres_Bayesian]]
| A Bayesian view on cryo-EM structure determination
|-

| Paper
| [[2012Zheng_Covariance]]
| Estimation of the volume covariance
|-

| Paper
| [[2013Wang_MLVariance]]
| Maximum Likelihood estimate of the map variance
|-

| Paper
| [[2013Lyumkis D_FREALIGN]]
| Likelihood-based classification of cryo-EM images using FREALIGN.
|-

| Paper
| [[2014Jin_NMA]]
| Continuous heterogeneity through Normal Mode Analysis
|-

| Paper
| [[2014Dashti_Brownian]]
| Continuous heterogeneity through Brownian trajectories
|-

| Paper
| [[2014Chen_Migration]]
| Particle migration analysis in 3D classification
|-

| Paper
| [[2015Anden_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Bai_Focused]]
| Focused classification
|-

| Paper
| [[2015Katsevich_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Klaholz_MRA]]
| Multivariate Statistical Analysis of Jackknife and Bootstrapping on random subsets
|-

| Paper
| [[2015Liao_Covariance]]
| Estimation of the 3D covariance from 2D projections
|-

| Paper
| [[2015Tagare_Direct]]
| Direct reconstruction of PCA components
|-

| Paper
| [[2016Gong_Mechanical]]
| Mechanical model for macromolecules
|-

| Paper
| [[2016Rawson_Movement]]
| Movement and flexibility
|-

| Paper
| [[2016Sorzano_StructMap]]
| Sorting a discrete set of conformational states
|-

| Paper
| [[2016Sorzano_Strain]]
| Calculate local stretches, strains and rotations from two conformational states
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

|}

=== Validation ===

{|

| Paper
| [[2008Stagg_TestBed]]
| Effect of voltage, dosis, number of particles and Euler jumps on resolution
|-

| Paper
| [[2011Henderson]]
| Tilt Validation
|-

| Paper
| [[2011Read]]
| Validation of PDBs
|-

| Paper
| [[2012Henderson]]
| EM Map Validation
|-

| Paper
| [[2013Cossio_Bayesian]]
| EM Map Validation in a probabilistic setting
|-

| Paper
| [[2013Chen_NoiseSubstitution]]
| Noise substitution at high resolution for measuring overfitting
|-

| Paper
| [[2014Russo_StatisticalSignificance]]
| EM Map Validation through the statistical significance of the tilt-pair angular assignment
|-

| Paper
| [[2014Stagg_Reslog]]
| EM Map Validation through the resolution evolution with the number of particles
|-

| Paper
| [[2014Wasilewski_Tilt]]
| Web implementation of the tilt pair validation
|-

| Paper
| [[2015Heymann_Alignability]]
| EM Map Validation through the resolution of reconstructions from particles and noise
|-

| Paper
| [[2015Oliveira_FreqLimited]]
| Comparison of gold standard and frequency limited optimization
|-

| Paper
| [[2015Wriggers_Secondary]]
| Validation by secondary structure
|-

| Paper
| [[2016Kim_SAXS]]
| Comparison of SAXS data and EM projections
|-

| Paper
| [[2016Rosenthal_Review]]
| Review of validation methods
|-

| Paper
| [[2016Vargas_Alignability]]
| Validation by studying the tendency of an angular assignment to cluster in the projection space
|-

| Paper
| [[2017Monroe_PDBRefinement]]
| Validation by comparison to a refined PDB
|-

|}

=== Resolution ===

{|

| Paper
| [[1986Harauz_FBP]]
| Fourier Shell Correlation
|-

| Paper
| [[1987Unser_SSNR]]
| 2D Spectral Signal to Noise Ratio
|-

| Paper
| [[2002Penczek_SSNR]]
| 3D Spectral Signal to Noise Ratio for Fourier based algorithms
|-

| Paper
| [[2003Rosenthal_DPR]]
| Review of the FSC and establishment of a new threshold
|-

| Paper
| [[2005Unser_SSNR]]
| 3D Spectral Signal to Noise Ratio for any kind of algorithms
|-

| Paper
| [[2005VanHeel_FSC]]
| Establishment of a new threshold for FSC
|-

| Paper
| [[2007Sousa_AbInitio]]
| Resolution measurement on neighbour Fourier voxels
|-

| Paper
| [[2014Kucukelbir_Local]]
| Quantifying the local resolution of cryo-EM density maps
|-

| Paper
| [[2016Pintilie_Probabilistic]]
| Probabilistic models and resolution
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Statistical properties of resolution measures defined in Fourier space
|-

|}

=== Sharpening of high resolution information ===
{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast restoration and map sharpening
|-

| Paper
| [[2008Fernandez_Bfactor]]
| Bfactor determination and restoration
|-

| Paper
| [[2013Fiddy_SaxtonAlgorithm]]
| Phase retrieval or extension
|-

| Paper
| [[2014Kishchenko_SphericalDeconvolution]]
| Spherical deconvolution
|-

| Paper
| [[2015Spiegel_VISDEM]]
| Visualization improvement by the use of pseudoatomic profiles
|-

| Paper
| [[2016Jonic_Pseudoatoms]]
| Approximation with pseudoatoms
|-

| Paper
| [[2016Jonic_Denoising]]
| Denoising and high-frequency boosting by pseudoatom approximation
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[1982Schiske_Correction]]
| CTF correction for tilted objects
|-

| Paper
| [[1988Toyoshima_Model]]
| CTF estimation
|-

| Paper
| [[1995Frank_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1996Skoglund_MaxEnt]]
| CTF correction with Maximum Entropy
|-

| Paper
| [[1996Zhou_Model]]
| CTF model and user interface for manual fitting
|-

| Paper
| [[1997Fernandez_AR]]
| PSD estimation using periodogram averaging and AR models
|-

| Paper
| [[1997Penczek_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1997Stark_Deconvolution]]
| CTF correction using deconvolution
|-

| Paper
| [[1997Zhu_RecCTF]]
| CTF correction and reconstruction
|-

| Paper
| [[2000DeRosier_EwaldCorrection]]
| CTF correction considering the Ewald sphere
|-

| Paper
| [[2000Jensen_TiltedCorrection]]
| CTF correction considering tilt in backprojection
|-

| Paper
| [[2001Saad_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Huang_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Mindell_CTFTILT]]
| CTF estimation for tilted micrographs
|-

| Paper
| [[2003Sander_MSA]]
| CTF estimation through MSA classification of PSDs
|-

| Paper
| [[2003Velazquez_ARMA]]
| PSD and CTF estimation using ARMA models
|-

| Paper
| [[2004Sorzano_IDR]]
| CTF restoration and reconstruction with Iterative Data Refinement
|-

| Conference
| [[2004Wan_CTF]]
| Spatially variant CTF
|-

| Paper
| [[2004Zubelli_Chahine]]
| CTF restoration and reconstruction with Chahine's multiplicative method
|-

| Conference
| [[2005Dubowy_SpaceVariant]]
| CTF correction when this is space variant
|-

| Paper
| [[2005Mallick_ACE]]
| CTF estimation
|-

| Paper
| [[2006Wolf_Ewald]]
| CTF correction considering Ewald sphere
|-

| Paper
| [[2007Jonic_EnhancedPSD]]
| PSD enhancement for better identification of Thon rings; Vitreous ice diffracts in Thon rings
|-

| Paper
| [[2007Philippsen_Model]]
| CTF Model for tilted specimens
|-

| Paper
| [[2007Sorzano_CTF]]
| CTF estimation using enhanced PSDs
|-

| Paper
| [[2009Sorzano_Sensitivity]]
| Error sensitivity of the CTF models, non-uniqueness of the CTF parameters
|-

| Paper
| [[2010Jiang2010_CTFCorrection]]
| Amplitude correction method
|-

| Paper
| [[2010Kasantsev_CTFCorrection]]
| Mathematical foundations of Kornberg and Jensen method
|-

| Paper
| [[2010Leong_CTFCorrection]]
| Correction for spatially variant CTF
|-

| Paper
| [[2011Glaeser_Coma]]
| The effect of coma at high-resolution
|-

| Paper
| [[2011Mariani_Tilted]]
| CTF simulation and correction of tilted specimens
|-

| Paper
| [[2011Sindelar_Wiener]]
| CTF correction using a modified version of Wiener filter
|-

| Paper
| [[2011Voortman_Tilted]]
| CTF correction for tilted specimen
|-

| Paper
| [[2012Voortman_VaryingCTF]]
| Correcting a spatially varying CTF
|-

| Paper
| [[2013Vargas_FastDef]]
| Fast defocus
|-

| Paper
| [[2015Rohou_CTFFind4]]
| CTF Find 4
|-

| Paper
| [[2015Sheth_CTFquality]]
| Visualization and quality assessment of CTF
|-

| Paper
| [[2016Zhang_GCTF]]
| gCTF
|-

|}

=== Segmentation ===

{|

| Paper
| [[2006Baker_segmentation]]
| Segmentation of molecular subunits
|-

|}

=== Fitting and docking ===

{|

| Paper
| [[1999Volkmann_Fitting]]
| Fitting in real space
|-

| Paper
| [[2001Baker_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2001Jones_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2003Kovacs_FRM3D]]
| Fast Rotational Alignment of two EM maps
|-

| Paper
| [[2004Tama_NMA1]]
| Flexible fitting with Normal Modes (I)
|-

| Paper
| [[2004Tama_NMA2]]
| Flexible fitting with Normal Modes (II)
|-

| Paper
| [[2005Velazquez_Superfamilies]]
| Recognition of the superfamily folding in medium-high resolution volumes
|-

| Paper
| [[2007DeVries_Haddock]]
| Docking with Haddock 2.0
|-

| Paper
| [[2007Kleywegt_QualityControl]]
| Quality control and validation of fitting
|-

| Paper
| [[2012Biswas_Secondary]]
| Secondary structure determination in EM volumes
|-

| Paper
| [[2012Velazquez_Constraints]]
| Multicomponent fitting by using constraints from other information sources
|-

| Paper
| [[2013Chapman MS_Atomicmodeling]]
| Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters
|-

| Paper
| [[2013Esquivel_Modelling]]
| Review on modelling (secondary structure, fitting, ...)
|-

| Paper
| [[2013Lopez_Imodfit]]
| Fitting based on vibrational analysis
|-

| Paper
| [[2013Nogales_3DEMLoupe]]
| Normal Mode Analysis of reconstructed volumes
|-

| Paper
| [[2014AlNasr_Secondary]]
| Identification of secondary structure elements in EM volumes
|-

| Paper
| [[2014Politis_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Rey_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Villa_Review]]
| Review of atomic fitting into EM volumes
|-

| Paper
| [[2015Barad_EMRinger]]
| Validation of hybrid models
|-

| Paper
| [[2015Bettadapura_PF2Fit]]
| Fast rigid fitting of PDBs into EM maps
|-

| Paper
| [[2015Carrillo_CapsidMaps]]
| Analysis of virus capsids using Google Maps
|-

| Paper
| [[2015Schroeder_Hybrid]]
| Review on model building
|-

| Paper
| [[2015Tamo_Dynamics]]
| Dynamics in integrative modeling
|-

| Paper
| [[2015Sorzano_AtomsToVoxels]]
| Accurate conversion of an atomic model into a voxel density volume
|-

| Paper
| [[2016Joseph_Evolution]]
| Evolutionary constraints for the fitting of atomic models into density maps
|-

| Paper
| [[2016Segura_3Diana]]
| Validation of hybrid models
|-

| Paper
| [[2016Singharoy_MDFF]]
| Construction of hybrid models driven by EM density and molecular dynamics
|-

| Paper
| [[2016Wang_Rosetta]]
| Construction of hybrid models driven by EM density using Rosetta
|-

| Paper
| [[2017Hryc_WeightedAtoms]]
| Construction of hybrid models by locally weighting the different atoms
|-

|}

=== Books and reviews ===

{|

| Book
| [[1980Herman_Tomography]]
| General book on tomography
|-

| Book
| [[1988Kak_Tomography]]
| General book on tomography
|-

| Paper
| [[2000Tao_Review]]
| Review of single particles
|-

| Paper
| [[2000VanHeel_Review]]
| Review of single particles
|-

| Paper
| [[2002Frank_Review]]
| Review of single particles
|-

| Paper
| [[2002Schmid_Review]]
| Review of single particles
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2004Subramaniam_Review]]
| Review of single particles
|-

| Paper
| [[2005Steven_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_book]]
| Book covering all aspects of electron microscopy of single particles
|-

| Paper
| [[2006Sorzano_Review]]
| Review of optimization problems in electron microscopy
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems in Electron Tomography
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2008Mueller_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2008Taylor_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2010DeRosier_Review]]
| Personal account of how 3DEM developed in the early days
|-

| Chapter
| [[2012Sorzano_Review]]
| Review of single particle analysis using Xmipp
|-

| Chapter
| [[2012Devaux_Protocol]]
| Protocols for performing single particle analysis
|-

| Paper
| [[2014Bai_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Carazo_Review]]
| Review of the reconstruction process
|-

| Paper
| [[2015Cheng_Review]]
| A primer to Single Particle Cryo-EM
|-

| Paper
| [[2015Cheng_Reviewb]]
| Single Particle Cryo-EM at crystallographic resolution
|-

| Paper
| [[2015Elmlund_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Henderson_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Nogales_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Schroeder_Review]]
| Review of advances in the electron microscope
|-

| Paper
| [[2015Wu_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Carroni_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Egelman_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Eisenstein_CryoEM]]
| News feature on the Method of the Year
|-

| Paper
| [[2016FernandezLeiro_Review]]
| Review of EM
|-

| Paper
| [[2016Glaeser_HowGood]]
| How good can cryo-EM become?
|-

| Paper
| [[2016Jonic_PseudoAtoms]]
| Review of the applications of the use of pseudoatoms in EM
|-

| Chapter
| [[2016Mio_Review]]
| Overview of the process to obtain EM reconstructions
|-

| Paper
| [[2016Jonic_Review]]
| A review of computational ways to handle heterogeneity
|-

| Paper
| [[2016Nogales_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Subramaniam_Review]]
| Why cryo-EM is now suitable for crystallographic journals
|-

| Paper
| [[2016Vinothkumar_Review]]
| Historical review and current limitations
|-

| Paper
| [[2017Frank_Review]]
| Historical review of EM
|-

| Paper
| [[2017Jonic_Review]]
| Review of computational methods to analyze conformational variability
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Review of statistical properties of resolution measures defined in Fourier space
|-
|}

=== Software ===

{|

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[1999Lutdke_Eman]]
| Eman
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Baldwin_AngularTransformations]]
| The Transform Class in SPARX and EMAN2
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Grigorieff_Frealign]]
| Frealign
|-

| Paper
| [[2008Scheres_XmippProtocols]]
| Xmipp Protocols
|-

| Paper
| [[2008Shaikh_SpiderProtocols]]
| Spider Protocols
|-

| Paper
| [[2012Wriggers_SitusConventions]]
| Conventions and workflows in Situs
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2015Cianfrocco_Cloud]]
| Software execution in the cloud
|-

| Paper
| [[2015Cheng_MRC2014]]
| Extensions to MRC file format
|-

| Paper
| [[2013DeLaRosa_Scipion]]
| Scipion
|-

| Paper
| [[2016Scheres_Relion]]
| Tutorial on the use of Relion
|-

| Paper
| [[2016Grigorieff_Frealign]]
| Tutorial on the use of Frealign
|-

|}

== Electron tomography ==

=== Image preprocessing ===

{|

| Paper
| [[2015Yan_thickness]]
| Determination of thickness, tilt and electron mean free path
|-

|}

=== Image alignment ===

{|

| Paper
| [[1982Guckenberger_commonOrigin]]
| Determination of a common origin in the micrographs of titl series in three-dimensional electron microscopy
|-

| Paper
| [[1992Lawrence_leastSquares]]
| Least squares solution of the alignment problem
|-

| Paper
| [[1995Penczek_dual]]
| Dual tilt alignment
|-

| Paper
| [[1996Owen_alignmentQuality]]
| Automatic alignment without fiducial markers and evaluation of alignment quality
|-

| Paper
| [[1998Grimm_normalization]]
| Discussion of several gray level normalization methods for electron tomography
|-

| Paper
| [[2001Brandt_Automatic1]]
| Automatic alignment without fiducial markers
|-

| Paper
| [[2001Brandt_Automatic2]]
| Automatic alignment with fiducial markers
|-

| Paper
| [[2006Winkler_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2006Castano_alignment]]
| Alignment with non-perpendicularity
|-

| Paper
| [[2007Castano_alignment]]
| Fiducial-less alignment of cryo-sections
|-

| Paper
| [[2009Sorzano_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2010Cantele_dualAlignment]]
| Alignment of dual series
|-

| Paper
| [[2014Tomonaga_Automatic]]
| Automatic alignment of tilt series using the projection themselves
|-

| Paper
| [[2014Han_Automatic]]
| Automatic alignment of tilt series using SIFT features
|-

| Paper
| [[2015Han_Automatic]]
| Automatic alignment of tilt series using fiducials
|-

| Paper
| [[2017Mastronarde_Automatic]]
| Automatic alignment and reconstruction of tilt series in IMOD
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[2003Winkler_CTF]]
| Focus gradient correction in electron tomography
|-

| Paper
| [[2006Fernandez_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Zanetti_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Xiong_CTF]]
| CTF determination and correction for low dose tomographic tilt series
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2017Kunz_3DCTF]]
| 3D CTF Correction
|-

|}

=== 3D reconstruction ===

{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1992Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[1997Marabini_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2002Fernandez_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2007Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[2008Fernandez_CARP]]
| Component Averaged Row Projections (CARP)
|-

| Paper
| [[2012Herman General Superiorization]]
| Superiorization: an optimization heuristic for medical physics
|-

| Paper
| [[2012Zhang_IPET_FETR]]
| IPET and FETR, a reconstruction algorithm for single molecule tomography
|-

| Paper
| [[2013Goris_SIRT_TV_DART]]
| Combination of SIRT, Total Variation and Discrete ART to reconstruct and segment at the same time
|-

| Paper
| [[2013Briegel A_Challenge]]
| The challenge of determining handedness in electron tomography and the use of DNA origami gold nanoparticle helices as molecular standards
|-

| Paper
| [[2013Messaoudi_EnergyFiltered]]
| 3D Reconstruction of Energy-Filtered TEM
|-

| Paper
| [[2016Deng_ICON]]
| 3D Reconstruction with missing information restoration
|-

| Paper
| [[2016Guay_Compressed]]
| 3D Reconstruction using compressed sensing
|-

|}

=== Noise reduction ===
{|

| Paper
| [[2001Frangakis_NAD]]
| Noise reduction with Nonlinear Anisotropic Diffusion
|-

| Paper
| [[2003Fernandez_AND]]
| Anisotropic nonlinear diffusion for electron tomography
|-

| Paper
| [[2003Jiang_Bilateral]]
| Bilateral denoising filter in electron microscopy
|-

| Paper
| [[2005Fernandez_AND]]
| Anisotropic nonlinear denoising in electron tomography
|-

| Paper
| [[2007Heide_median]]
| Iterative median filtering in electron tomography
|-

| Paper
| [[2007Fernandez_autAND]]
| Anisotropic nonlinear diffusion with automated parameter tuning
|-

| Paper
| [[2009Fernandez_Beltrami]]
| Nonlinear filtering based on Beltrami flow
|-

| Paper
| [[2010Bilbao_MeanShift]]
| Mean Shift Filtering
|-

| Paper
| [[2014Kovacik_wedgeArtefacts]]
| Removal of wedge artefacts
|-

| Paper
| [[2014Maiorca_beadArtefacts]]
| Removal of gold bead artefacts
|-

|}

=== Segmentation ===

{|

| Paper
| [[2002Frangakis_Eigenanalysis]]
| Segmentation using eigenvector analysis.
|-

| Paper
| [[2002Volkmann_Watershed]]
| Segmentation using watershed transform.
|-

| Paper
| [[2003Bajaj_BoundarySegmentation]]
| Segmentation based on fast marching.
|-

| Paper
| [[2005Cyrklaff_Thresholding]]
| Segmentation using optimal thresholding.
|-

| Paper
| [[2007Lebbink_TemplateMatching]]
| Segmentation using template matching.
|-

| Paper
| [[2007Sandberg_OrientationFields]]
| Segmentation using orientation fields.
|-

| Paper
| [[2007Sandberg_SegmentationReview]]
| Review on segmentation in electron tomography.
|-

| Paper
| [[2008Garduno_FuzzySegmentation]]
| Segmentation using fuzzy set theory principles.
|-

| Paper
| [[2009Lebbink_TemplateMatching2]]
| Segmentation using template matching.
|-

| Paper
| [[2012RubbiyaAli_EdgeDetection]]
| Parameter-Free Segmentation of Macromolecular Structures.
|-

| Conference
| [[2015Xu_TemplateMatching]]
| Detection of macromolecular complexes with a reduced representation of the templates.
|-

|}

=== Resolution ===
{|

| Paper
| [[2005Cardone_Resolution]]
| Resolution criterion for electron tomography
|-

| Chapter
| [[2007Penczek_Resolution]]
| Review of resolution criteria for electron tomography
|-

| Paper
| [[2015Diebolder_ConicalFSC]]
| Conical Fourier Shell Correlation
|-

|}

=== Subtomogram analysis ===

{|

| Paper
| [[2000Bohm_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2002Frangakis_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2006Nickell_Review]]
| Review of macromolecule finding by template matching (Visual Proteomics)
|-

| Paper
| [[2007Best_Review]]
| Review of Localization of Protein Complexes by Pattern Recognition
|-

| Paper
| [[2007Forster_Review]]
| Review of structure determination by subtomogram averaging
|-

| Paper
| [[2008Forster_Classification]]
| Classification of subtomograms using constrained correlation
|-

| Paper
| [[2008Bartesaghi_Classification]]
| Classification and averaging of subtomograms
|-

| Paper
| [[2008Schmid_Averaging]]
| Alignment and averaging of subtomograms
|-

| Paper
| [[2010Amat_Averaging]]
| Alignment and averaging of subtomograms exploiting thresholding in Fourier space
|-

| Paper
| [[2013Chen_Averaging]]
| Fast alignment of subtomograms using spherical harmonics
|-

| Paper
| [[2013Kuybeda_Averaging]]
| Alignment and averaging of subtomograms using the nuclear norm of the cluster
|-

| Paper
| [[2013Shatsky_Averaging]]
| Alignment and averaging of subtomograms with constrained cross-correlation
|-

| Paper
| [[2014Chen_Autofocus]]
| Subtomogram averaging and classification with special attention to differences
|-

| Paper
| [[2014Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2014Voortman_LimitingFactors]]
| Limiting factors of subtomogram averaging
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2015Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2016Bharat_Relion]]
| Subtomogram averaging with Relion
|-

| Paper
| [[2016Song_MatrixNorm]]
| Matrix norm minimization for tomographic reconstruction and alignment
|-

| Paper
| [[2017Castano_ParticlePicking]]
| Particle picking in tomograms for subtomogram averaging
|-

|}

=== Single particle tomography ===

{|

| Paper
| [[2012Bartesaghi_Constrained]]
| 3D reconstruction by imposing geometrical constraints
|-

| Paper
| [[2015Galaz_SingleParticleTomography]]
| Set of tools for Single Particle Tomography in EMAN2
|-

| Paper
| [[2016Galaz_SingleParticleTomography]]
| Alignment algorithms and CTF correction
|-

|}

=== Books and reviews ===

{|

| Paper
| [[2000Baumeister_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Koster_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Sali_Review]]
| Review of electron tomography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2005Lucic_Review]]
| Review of electron tomography
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_TomoBook]]
| Electron Tomography
|-

| Book
| [[2007McIntosh_Book]]
| Cellular Electron Microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2012Kudryashev_Review]]
| Review of subtomogram averaging
|-

| Paper
| [[2016Beck_Review]]
| Review of molecular sociology
|-

|}

=== Software ===

{|

| Paper
| [[1996Kremer_IMOD]]
| IMOD
|-

| Paper
| [[1996Chen_Priism/IVE]]
| Priism/IVE
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2005Nickell_TOM]]
| TOM Toolbox
|-

| Paper
| [[2007Messaoudi_TomoJ]]
| TomoJ
|-

| Paper
| [[2008Heymann_BsoftTomo]]
| Bsoft
|-

| Paper
| [[2015Ding_CaltechTomography]]
| Caltech tomography database
|-

| Paper
| [[2015Noble_AppionProtomo]]
| Batch fiducial-less tilt-series alignment in Appion using Protomo
|-

| Paper
| [[2015vanAarle_Astra]]
| ASTRA Toolbox
|-

|}

== 2D Crystals ==

=== 2D Preprocessing ===

{|

| Paper
| [[1986Henderson_Processing]]
| General 2D processing
|-

| Paper
| [[2000He_PhaseAlignment]]
| Phase consistency and Alignment
|-

| Paper
| [[2006Gil_Unbending]]
| Crystal unbending
|-

|}

=== Classification ===
{|

| Paper
| [[1988Frank_Classification]]
| MSA and classification in electron crystallography
|-

| Paper
| [[1996Fernandez_SOM]]
| Classification based on self organizing maps
|-

| Paper
| [[1998Sherman_MSA]]
| Classification based on MSA
|-

|}
=== 3D Reconstruction ===

{|

| Paper
| [[1985Wang_Solvent]]
| Solvent flattening
|-

| Paper
| [[1990Henderson_Processing]]
| General 3D processing
|-

| Paper
| [[2004Marabini_ART]]
| Algebraic Reconstruction Technique with blobs for crystals (Xmipp)
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1998Walz_Review]]
| Review of 2D crystallography
|-

| Paper
| [[1999Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Ellis_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of single particles, electron tomography and crystallography
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Gipson_2dx]]
| 2dx
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Philippsen_IPLT]]
| IPLT
|-

|}

== 3D Crystals - MicroED ==

=== Sample Preparation ===
{|
| Paper
| [[2016Shi_Preparation]]
| Sample Preparation
|}
=== Data Collection ===
{|
| Paper
| [[2014Nannenga_CR]]
| Continuous rotation

|}
=== Data Processing ===
{|

| Paper
| [[2011Wisedchaisri_PhaseExtension]]
| Fragment-based phase extension
|-

| Paper
| [[2015Hattne_Processing]]
| Data Processing
|-

| Paper
| [[2016Hattne_Correction]]
| Image correction
|}

=== Software ===
{|

| Paper
| [[2014Iadanza_Processing]]
| Data Processing of still diffraction data
|}

=== Books and Reviews ===
{|
| Paper
| [[2014Nannenga_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Liu_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Rodriguez_Review ]]
| Review of MicroED
|-

|}

== Helical particles ==

=== Filament corrections ===

{|

| Paper
| [[1986Egelman_Curved]]
| Algorithm for correcting curved filaments
|-

| Paper
| [[1988Bluemke_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2006Wang_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2016Yang_Flexible]]
| Algorithm for correcting filaments with flexible subunits
|-

|}

=== Reconstruction ===

{|

| Paper
| [[1952Cochran_Fourier]]
| Fourier Bessel transform of filamentous structures
|-

| Paper
| [[1958Klug_Fourier]]
| Fourier Bessel decomposition of the projection images
|-

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2005Wang_Iterative]]
| Iterative Fourier-Bessel algorithm
|-

| Paper
| [[2007Egelman_Iterative]]
| Iterative real-space algorithm
|-

| Paper
| [[2013Desfosses_Spring]]
| Helical processing with Spring
|-

| Paper
| [[2015Zhang_seam]]
| Workflow for the detection of the lattice seam
|-

| Paper
| [[2016Rohou_Frealix]]
| Helical processing with Frealix
|-

|}

=== Validation ===

{|

| Paper
| [[2014Egelman_ambiguity]]
| How to detect incorrect models
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Carragher_Phoelix]]
| Phoelix
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Owen_Brandeis]]
| Brandeis
|-

|}

== Icosahedral particles ==

=== Reconstruction ===

{|

| Paper
| [[1970Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1971Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1996Fuller_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1997Thuman_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

|}

=== Classification ===

{|

| Paper
| [[2005Scheres_Virus]]
| Classification of virus capsids in real space
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1999Baker_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[1999Conway_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2000Thuman_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Lee_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Navaza_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2006Grunewald_Review]]
| Review of reconstruction of icosahedral viruses
|-

|}

=== Software ===

{|

| Paper
| [[1996Baker_EMPFT]]
| EMPFT
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2013Morin_Sliz SBGrid]]
| SBGrid presentation for eLife
|-

|}

== Databases ==

{|

| Paper
| [[2003Boutselakis_EMSD]]
| EMSD database
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2011Kim_CDDB]]
| Conformational Dynamics Data Bank
|-

| Paper
| [[2011Lawson_EMDB]]
| Electron Microscopy Data Bank
|-

| Paper
| [[2013Ison_EDAM]]
| EDAM, an ontology of bioinformatics operations
|-

| Paper
| [[2016Iudin_EMPIAR]]
| EMPIAR raw data database
|-

| Paper
| [[2016Patwhardan_EMDB]]
| EMDB, PDB, ...
|-

| Paper
| [[2017Shao_PDBQuality]]
| Quality metrics in PDB
|-

| Blog
| http://www.mybiosoftware.com
| Huge list of bioinformatics programs (many of them structural bioinformatics)
|-

|}

== Relationship to other structural information sources ==

{|

| Paper
| [[2000Engel_AFM]]
| Review of Atomic Force Microscopy
|-

| Paper
| [[2001Dimmeler_AFM]]
| Constraints from Atomic Force Microscopy
|-

| Paper
| [[2003Mobus_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_Review]]
| Review on correlative microscopy
|-

| Paper
| [[2005Boudier_EFTETJ]]
| Software for Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2005Vestergaard_SAXS]]
| Example of comparison of 3DEM and Small-angle X-ray scattering
|-

| Paper
| [[2007Hamada_SAXS]]
| Constraints from Small-angle X-ray scattering
|-

| Paper
| [[2013Xu_FRET]]
| EM+FRET
|-

|}

== X-ray tomography ==

{|

| Paper
| [[2012Oton_ImageFormation]]
| Image formation model in X-ray cell microscopy
|-

|}

== Mathematical tools necessary ==

== People developing methods ==
Please, add yourself to this list (due to privacy reasons, please, do not add anyone else to the list without his/her explicit consent). Sort by first name alphabetical order.

[http://biocomp.cnb.csic.es/~coss Carlos Oscar S. Sorzano]: CSIC, Madrid, Spain 

[http://www.curie.fr/recherche/themes/detail_equipe.cfm/lang/_fr/id_equipe/241.htm Cédric Messaoudi]: Institute Curie, Paris, France 

[http://scholar.google.es/citations?user=_jNYGScAAAAJ&hl=en Javier Vargas]:[mailto:jvargas@cnb.csic.es mail]: CSIC, Madrid, Spain 

[http://scholar.google.es/citations?hl=es&user=g2ZJPIYAAAAJ Joaquín Otón]: CSIC, Madrid, Spain 

[mailto:jrbcast@gmail.com José Román Bilbao-Castro]: UAL, Almería, Spain; CSIC, Madrid, Spain 

[José Miguel de la Rosa Trevín]: Biocomputing Unit CNB-CSIC, Madrid, Spain 

[http://cryoem.janelia.org Tamir Gonen]: [mailto:gonent@janelia.hhmi.org mail]: Howard Hughes Medical Institute, Ashburn, VA, USA 

[mailto:vabrishami@cnb.csic.es Vahid Abrishami]: CSIC, Madrid, Spain 

== 3DEM sites ==
* [http://3dem.ucsd.edu/ 3DEM web site]

* [http://en.wikibooks.org/wiki/Software_Tools_For_Molecular_Microscopy Software tools for molecular microscopy]

* [http://www.emdatabank.org/ The Electron Microscopy Data Bank (EMDB)]

* [http://ccdb.ucsd.edu The Cell Centered Database (CCDB)]

* [http://conventions.cnb.csic.es The geometrical software conventions web page ]

== Editing useful links ==

* [http://www.mediawiki.org/wiki/Help:Formatting Text formatting in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Links Adding links in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Images Adding images in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Tables Making tables in Mediawiki]

2017Zheng MotionCorr2

2017-05-11T21:04:10Z

CoSS: Created page with "== Citation == Zheng, S. Q.; Palovcak, E.; Armache, J.-P.; Verba, K. A.; Cheng, Y. & Agard, D. A. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-..."

== Citation ==

Zheng, S. Q.; Palovcak, E.; Armache, J.-P.; Verba, K. A.; Cheng, Y. & Agard, D. A. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nature methods, 2017, 14, 331-332

== Abstract ==

In recent years single-particle cryo-electron microscopy (cryo-EM) has enabled groundbreaking advancements in obtaining atomic-resolution structures of macromolecules1, 2. Central to this success has been the broad application of direct electron detector cameras with high output frame rates, which has enabled the recording of images of frozen hydrated biological samples as dose-fractionated stacks of subframes (movies). Beam-induced sample motion that blurs the captured images can then be corrected by registering identical features in the subframes, followed by summing the registered subframes to produce a motion-corrected image3. Here we describe MotionCor2, a software tool for anisotropic correction of beam-induced motion

== Keywords ==

== Links ==

http://www.nature.com/nmeth/journal/v14/n4/full/nmeth.4193.html

== Related software ==

== Related methods ==

== Comments ==

Main Page

2017-05-11T21:00:24Z

CoSS: /* 2D Preprocessing */

== Presentation ==

This web page is intended to be an extensive repository of three-dimensional electron microscopy (3DEM) methods. The advantages of having such a repository are

* You know which are the relevant articles in a particular topic, therefore, paper introductions, reviews, etc. are easier to write and you make sure you will cite all the related articles.
* You will be sure that your paper has more chances of being cited.
* You can add whatever information you find relevant to your method, external links, links to other papers, etc.
* You can link your method to a web page providing the corresponding software, so you know people can use your algorithms.
* You can use the Wiki search capabilities to locate relevant articles even if they are not at the topic you are looking at.
* As a community we will "reconstruct" our history.
* You can select the "watch" option above to receive notifications in case of further changes in the Main Page.

Developing image processing methods for 3DEM is not "[[well-paid]]" in terms of citations and impact factor. However, it is crucial for the advance of the field. Gathering methodological papers in a portal will help to increase the recognition of the field.

Please:

* Add your articles at the right place (you can add a single article in several topics if it is relevant to all of them). The easiest way to add an article is by editing the corresponding topic in the main page, adding your entry, then save the main page. Click on the red link that appears on your new entry, copy and paste the Wiki following code, add the information of your article

== Citation ==

== Abstract ==

== Keywords ==

== Links ==

== Related software ==

== Related methods ==

== Comments ==

* Maintain the information of each article as complete as possible.
* Sort articles by years and authors.
* Be respectful to other people's work.

== How to subscribe to this page ==

You may subscribe to this page so that you will be notified every time someone adds a new method. To do so, you have to register in the page, and edit your preferences ("my preferences"). Be sure that you have activated the option "E-mail me when a page on my watchlist is changed". Finally, click on the "Watch" tab at the top of this page.

You may subscribe to changes on this page on the mailing list 3demmethods@cnb.csic.es. To send a new method to this mail list just send a mail to 3demmethods@cnb.csic.es

To subscribe to this list, visit the web page

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Alternatively, you may write a mail to sympa6@cnb.csic.es with the subject

<code>subscribe 3demmethods YourName YourFamilyName</code>

and an empty mail body.

To unsubscribe visit the page

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or write sympa6@cnb.csic.es with the subject

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and an empty mail body.

== Electron microscopy images ==

=== Online courses ===

CALTECH: http://cryo-em-course.caltech.edu/

MRC: ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/EM-course/

CNB-CSIC: http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/MadridJan2014EM

Workshop on Computational methods for CryoEM: https://www.youtube.com/watch?v=XdKO1iaPP8o

Workshop on Management of large CryoEM facilities: https://www.youtube.com/watch?v=as4seOPszL0

Icknield Course on Model Building and Refinement for High Resolution EM Maps: http://www.ccpem.ac.uk/training/icknield_2017/icknield_2017.php

=== Image formation ===

{|

| Paper
| [[1971Erickson_CTF]]
| CTF model
|-

| Paper
| [[1971Glaeser_Damage]]
| Radiation damage
|-

| Chapter
| [[1971Hanszen_CTF]]
| Image formation model
|-

| Paper
| [[1971Thon_Model]]
| CTF model
|-

| Paper
| [[1975Unwin_Imaging]]
| Radiation dose
|-

| Paper
| [[1977Wade_Model]]
| CTF model
|-

| Paper
| [[1978Wade_Model]]
| CTF model
|-

| Paper
| [[1979Hayward_Radiation]]
| Radiation damage
|-

| Paper
| [[1984Cohen_Validity]]
| Validity of the CTF model at high frequencies
|-

| Paper
| [[1988Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[1992Wade_Model]]
| CTF model
|-

| Paper
| [[1993Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2004Egerton_Damage]]
| Radiation damage
|-

| Paper
| [[2004Sorzano_Normalization]]
| Background noise is Gaussian
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2009Baxter_NoiseCharacterization]]
| Characterization of the different noise sources in cryo-EM
|-

| Paper
| [[2010Baker_Damage]]
| Radiation damage dependence on resolution
|-

| Paper
| [[2010Bammes_Damage]]
| Radiation damage dependence on temperature
|-

| Paper
| [[2010Gomez_Multislice]]
| Simulation of the multi slice model
|-

| Paper
| [[2010Zewail_FourDimensional]]
| Review on the use of ultrafast EM
|-

| Paper
| [[2011Bammes_CCD]]
| Performance of CCD cameras
|-

| Paper
| [[2011Glaeser_Coma]]
| Image formation model including coma
|-

| Paper
| [[2011Milazzo_DirectDetectors]]
| Evaluation of Direct Detectors
|-

| Paper
| [[2011Rullgard_ImageSimulation]]
| Accurate simulation of EM images
|-

| Paper
| [[2011Zhang LimitingFactors]]
| Limiting factor for atomic resolution in EM
|-

| Paper
| [[2012Bammes_DirectDetection]]
| Performance of Direct detectors
|-

| Paper
| [[2012Campbell_MotionCorrection]]
| Beam induced motion correction and direct detectors
|-

| Paper
| [[2012Shang_HydrationLayer]]
| Simulation of PDB volumes explicitly considering the hydration layer
|-

| Paper
| [[2013Egerton_RadiationDamage]]
| Review of TEM radiation damage and experimental ways of reducing it
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu H_Noisemodels]]
| Noise models and cryo-EM drift correction with a direct-electron camera
|-

| Paper
| [[2013Li X K2 noisemodels]]
| Influence of electron dose rate on electron counting images recorded with the K2 camera
|-

| Paper
| [[2013Vulovic_CTFApproximations]]
| When to use the different approximations performed so that a projection with linear CTF is valid
|-

| Thesis
| [[2013Vulovic_ImageFormation]]
| Ph.D. Thesis on the image formation in cryo-EM
|-

| Paper
| [[2014Danev_PhasePlate]]
| Volta potential phase plate
|-

| Paper
| [[2015Chiu_K2]]
| Characterization of K2
|-

| Paper
| [[2015Hawkes_AberrationCorrection]]
| Historical account of the development of lens corrections
|-

| Paper
| [[2015Koeck_Quadratic]]
| Limitations of the linear approximation and use of the quadratic terms
|-

| Paper
| [[2015Kuijper_FEI]]
| Description of the FEI Falcons
|-

| Paper
| [[2015Lobato_MULTEM]]
| Simulation of multislice diffraction
|-

| Paper
| [[2015McMullan_AmorphousIce]]
| Beam induced movement is caused by Brownian motion
|-

| Paper
| [[2016Koeck_ADF]]
| Simulations of Annular Dark Field TEM
|-

| Paper
| [[2017Mishyna_DNARadiation]]
| Review of radiation damage on DNA
|-

|}

=== Collection geometry ===

{|

| Chapter
| [[1980Hoppe_Wedge]]
| Missing wedge
|-

| Paper
| [[1987Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1995Penczek_Dual]]
| Dual axis tomography
|-

| Paper
| [[1997Mastronarde_Dual]]
| Dual axis tomography
|-

| Paper
| [[2003Ludtke_FocusPairs]]
| Focus pairs for single particles
|-

| Paper
| [[2005Lanzavecchia_Conical]]
| Conical tomography
|-

| Paper
| [[2005Zampighi_Conical]]
| Conical tomography
|-

| Paper
| [[2006Leschziner_OT]]
| Orthogonal Tilt
|-

| Paper
| [[2006Messaoudi_Multiple]]
| Multiple axis tomography
|-

| Paper
| [[2012Kudryashev_FocusPairs]]
| Focus pairs tomography
|-

| Paper
| [[2014Hovden_TiltFocus]]
| Combining tilt series with focus series
|-

| Paper
| [[2015Sorzano_RandomConicalTilt]]
| General formulation of Random Conical Tilt
|-

| Paper
| [[2017Hagen_DoseTomography]]
| Dose optimization for subtomogram averaging
|-

|}

=== Sample preparation ===

{|

| Paper
| [[1982Dubochet_Sample]]
| Vitreous ice
|-

| Paper
| [[1986Lepault_Sample]]
| Fast freezing
|-

| Paper
| [[1995Dubochet_Sample]]
| High-pressure freezing
|-

| Paper
| [[1995VanMarle_Sample]]
| Sample damages in resin
|-

| Paper
| [[1998Adrian_Sample]]
| Cryo negative staining
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2002Hsieh_Sample]]
| Cryofixation
|-

| Paper
| [[2004AlAmoudi_Sample]]
| CEMOVIS
|-

| Paper
| [[2008Studer_Sample]]
| Review on high pressure freezing
|-

| Paper
| [[2009Pierson_Sample]]
| Review on sample preparation for electron tomography
|-

| Paper
| [[2010Zhang_NegativeStaining]]
| Negative staining for small protein imaging
|-

| Paper
| [[2012Zhang_PositiveStaining]]
| Positive staining
|-

| Paper
| [[2014Rames_NegativeStaining]]
| Optimized negative staining
|-

| Paper
| [[2014Russo_GoldGrids]]
| Gold grids for single particles
|-

| Paper
| [[2015Cabra_Sample]]
| Review on sample preparation for single particles with videos
|-

| Paper
| [[2016Passmore_Review]]
| Tutorial chapter on sample preparation
|-

| Paper
| [[2016Razinkov_Vitrification]]
| New vitrification method
|-

| Paper
| [[2016Takizawa_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2016Thompson_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2017Arnold_BlottingFree]]
| Blotting-free preparation
|-

| Paper
| [[2017Peitsch_Sample]]
| iMEM: Isolation of Plasma Membrane for Cryoelectron Microscopy
|-

| Paper
| [[2017Schaffer_FocusedIonBeam]]
| Focused Ion Beam sample preparation for membrane proteins
|-

|}

=== Automated data collection ===

{|

| Paper
| [[1992Dierksen_Automatic]]
| Automated data collection
|-

| Paper
| [[1992Koster_Automatic]]
| Automated data collection
|-

| Paper
| [[1996Fung_Automatic]]
| Automated data collection for tomography
|-

| Paper
| [[2001Zhang_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2003Ziese_Automatic]]
| Automated autofocusing
|-

| Paper
| [[2004Potter_Automatic]]
| Automated sample loading
|-

| Paper
| [[2004Zheng_Automatic]]
| Automated data collection
|-

| Paper
| [[2005Lei_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2005Suloway_Automatic]]
| Automated data collection: Leginon
|-

| Paper
| [[2007Yoshioka_RCT]]
| Automated Random Conical Tilt
|-

| Paper
| [[2011Korinek_TOM2]]
| Automated acquisition with TOM2
|-

| Paper
| [[2015Li_UCSFImage]]
| Automated acquisition with UCSFImage
|-

| Paper
| [[2016Gil_Fuzzy]]
| Real time decisions during acquisition with neuro-fuzzy method
|-

| Paper
| [[2016Liu_TiltControl]]
| Accurate control of the tilt angle for electron tomography
|-

| Paper
| [[2016Vargas_FoilHole]]
| Determination of image quality at low magnification
|-

|}

== Single particles ==

=== Automatic particle picking ===

{|

| Paper
| [[1982VanHeel_Detection]]
| Detection of particles in micrographs
|-

| Paper
| [[2001Nicholson_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2001Zhu_Filaments]]
| Automatic identification of filaments in micrographs
|-

| Paper
| [[2004Sigworth_Detection]]
| Classical detection theory and the cryo-EM particle selection problem
|-

| Paper
| [[2004Volkmann_ParticlePicking]]
| An approach to automated particle picking from electron micrographs based on reduced representation templates
|-

| Paper
| [[2004Wong_ParticlePicking]]
| Model-based particle picking for cryo-electron microscopy
|-

| Paper
| [[2004Zhu_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2007Chen_Signature]]
| Automatic particle picking program: Signature
|-

| Paper
| [[2007Woolford_SwarmPS]]
| Automatic particle picking with several criteria, implemented in EMAN Boxer
|-

| Paper
| [[2009Sorzano_MachineLearning]]
| Automatic particle picking based on machine learning of rotational invariants
|-

| Paper
| [[2011Arbelaez_Comparison]]
| Evaluation of the performance of software for automated particle-boxing
|-

| Paper
| [[2013Abrishami_MachineLearning]]
| A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs
|-

| Paper
| [[2013Hauer_2013]]
| Automatic tilt pair detection in Random Conical Tilt
|-

| Paper
| [[2013Shatsky_ParticlePicking]]
| Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Langlois_ParticlePicking]]
| Automatic particle picking
|-

| Paper
| [[2016Vilas_AutomaticTilt]]
| Automatic identification of image pairs in untilted-tilted micrograph pairs
|-

|}

=== 2D Preprocessing ===

{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast enhancement through DPR
|-

| Paper
| [[2004Sorzano_Normalization]]
| Normalization procedures and their statistical properties.
|-

| Paper
| [[2006Sorzano_Denoising]]
| Strong denoising in wavelet space
|-

| Conference
| [[2009Sorzano_Downsampling]]
| Differences between the different downsampling schemes
|-

| Paper
| [[2012Brilot_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Campbell_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Zhao_Denoising]]
| Denoising using an invariant Fourier-Bessel eigenspace
|-

| Paper
| [[2013Norousi_Screening]]
| Screening particles to identify outliers
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu_Movies]]
| Drift correction for movies considering dark field
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Scheres_Movies]]
| Beam induced motion correction
|-

| Paper
| [[2015Abrishami_Movies]]
| Alignment of direct detection device micrographs
|-

| Paper
| [[2015Grant_Anisotropic]]
| Automatic estimation and correction of anisotropic magnification
|-

| Paper
| [[2015Grant_OptimalExposure]]
| Filter movies according to the radiation damage
|-

| Paper
| [[2015Rubinstein_Alignment]]
| Frame alignment at the level of particle
|-

| Paper
| [[2015Spear_DoseCompensation]]
| Effect of dose compensation on resolution
|-

| Paper
| [[2015Zhao_AnisotropicMagnification]]
| Correction of anisotropic magnification
|-

| Conference
| [[2016Bajic_Denoising]]
| Denoising and deconvolution of micrographs
|-

| Paper
| [[2016Jensen_RemovalVesicles]]
| Removal of vesicles in membrane proteins
|-

| Paper
| [[2016Bhamre_Denoising]]
| Denoising by 2D covariance estimation
|-

| Paper
| [[2017McLeod_Zorro]]
| Movie alignment by Zorro
|-

| Paper
| [[2017Zheng_MotionCorr2]]
| Movie alignment by MotionCorr2
|-

|}

=== 2D Alignment ===

{|

| Paper
| [[1981Frank_Averaging]]
| 2D averaging and phase residual
|-

| Paper
| [[1982Saxton_Averaging]]
| 2D averaging using correlation
|-

| Paper
| [[1998Sigworth_ML2D]]
| Maximum likelihood alignment in 2D
|-

| Paper
| [[2003Cong_FRM2D]]
| Fast Rotational Matching in 2D
|-

| Paper
| [[2005Cong_FRM2D]]
| Fast Rotational Matching in 2D introduced in a 3D Alignment algorithm
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

|}

=== 2D Classification and clustering ===

{|

| Paper
| [[1981VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[1984VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2011Singer_DiffusionMaps]]
| Classification in 2D based on graph analysis of the projections
|-

| Paper
| [[2012Yang_ISAC]]
| Iterative Stable Alignment and clustering
|-

| Paper
| [[2014Sorzano_Outlier]]
| Outlier detection in 2D classifications.
|-

| Paper
| [[2014Zhao_Aspire]]
| Fast classification based on rotational invariants and vector diffusion maps
|-

| Paper
| [[2015Huang_Robust]]
| Robust w-estimators of 2D classes
|-

| Paper
| [[2016Reboul_Stochastic]]
| Stochastic Hill Climbing for calculating 2D classes
|-

| Conference
| [[2017Bhamre_Mahalanobis]]
| 2D classification using Mahalanobis distance
|-

|}

=== 3D Alignment ===

{|

| Paper
| [[1980Kam_AutoCorrelation]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[1986Goncharov_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1987VanHeel_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1988Provencher_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Vogel_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1990Gelfand_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Goncharov_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Harauz_Quaternions]]
| Use of quaternions to represent rotations
|-

| Paper
| [[1994Penczek_Real]]
| Angular assignment using projection matching in real space
|-

| Paper
| [[1994Radermacher_Radon]]
| Angular assignment in Radon space
|-

| Paper
| [[1996Penczek_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[2003Rosenthal_DPR]]
| Angular assignment using DPR
|-

| Paper
| [[2004Sorzano_Wavelet]]
| Angular assignment in the wavelet space.
|-

| Paper
| [[2005Jonic_Splines]]
| Angular assignment in Fourier space using spline interpolation.
|-

| Paper
| [[2005Yang_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[2006Ogura_SimulatedAnnealing]]
| Angular asignment by simulated annealing
|-

| Paper
| [[2007Grigorieff_Continuous]]
| Continuous angular assignment in Fourier space
|-

| Paper
| [[2010Jaitly_Bayesian]]
| Angular assignment by a Bayesian method and annealing
|-

| Paper
| [[2010Sanz_Random]]
| Random model method
|-

| Paper
| [[2010Singer_Voting]]
| Detecting consistent common lines by voting (reference free)
|-

| Paper
| [[2011Singer_SDP]]
| Angular assignment by semidefinite programming and eigenvectors (reference free)
|-

| Paper
| [[2012Giannakis_Scattering]]
| Construction of an initial volume, reference free, by graph analysis of the projections
|-

| Paper
| [[2012Shkolnisky_Sync]]
| Angular assignment by synchronization of rotations (reference free)
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Wang_LUD]]
| Angular assignment by least unsquared deviations (reference free)
|-

| Paper
| [[2014Vargas_RANSAC]]
| Initial model using RANSAC (reference free)
|-

| Paper
| [[2015Joubert_Pseudoatoms]]
| Initial model based on pseudo-atoms
|-

| Paper
| [[2015Singer_Kam]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[2015Sorzano_Significant]]
| Statistical approach to the initial volume estimation (reconstruct significant)
|-

| Conference
| [[2016Michels_Heterogeneous]]
| Initial volume in the presence of heterogeneity
|-

| Paper
| [[2016Cossio_BayesianGPU]]
| GPU implementation of the Bayesian 3D reconstruction approach
|-

|}

=== 3D Reconstruction ===
{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1986Harauz_FBP]]
| Exact filters for Filtered Back Projection
|-

| Chapter
| [[1992Radermacher_WBP]]
| Exact filters for Weighted Back Projection
|-

| Paper
| [[1997Zhu_RecCTF]]
| 3D Reconstruction (SIRT like) and simultaneous CTF correction
|-

| Paper
| [[1998Boisset_Uneven]]
| Artifacts in SIRT and WBP under uneven angular distributions
|-

| Paper
| [[1998Marabini_ART]]
| Algebraic Reconstruction Technique with blobs (Xmipp)
|-

| Paper
| [[2001Sorzano_Uneven]]
| Free parameter selection under uneven angular distributions
|-

| Paper
| [[2005Sorzano_Parameters]]
| Free parameter selection for optimizing multiple tasks
|-

| Paper
| [[2008Sorzano_Constraints]]
| Mass, surface, positivity and symmetry constraints for real-space algorithms
|-

| Paper
| [[2009Bilbao_ParallelART]]
| Efficient parallelization of ART
|-

| Paper
| [[2011Li_GradientFlow]]
| Regularized 3D Reconstruction by Gradient Flow
|-

| Paper
| [[2011Vonesch_Wavelets]]
| Fast wavelet-based 3D reconstruction
|-

| Paper
| [[2012Gopinath_ShapeRegularization]]
| Regularized 3D Reconstruction by Shape information
|-

| Paper
| [[2012Kucukelbir_adaptiveBasis]]
| 3D reconstruction in an adaptive basis promoting sparsity
|-

| Paper
| [[2012Sindelar_NoiseReduction]]
| Optimal noise reduction in 3D reconstructions
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Lyumkis_Optimod]]
| Construction of initial volumes with Optimod
|-

| Paper
| [[2013Wang FIRM]]
| Fast 3D reconstruction in Fourier domain
|-

| Paper
| [[2014Kunz_SART_OS]]
| Simultaneous ART with OS
|-

| Paper
| [[2015Abrishami_Fourier]]
| 3D Reconstruction in Fourier space
|-

| Paper
| [[2015Dvornek_SubspaceEM]]
| Fast Maximum a posteriori
|-

| Paper
| [[2015Moriya_Bayesian]]
| Bayesian approach to suppress limited angular artifacts
|-

| Paper
| [[2015Xu_GeometricFlow]]
| Multi-scale geometric flow
|-

| Arxiv
| [[2016Ye_Cohomology]]
| Cohomology properties of 3D reconstruction
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

|}

=== 3D Heterogeneity ===

{|

| Paper
| [[2004White_Size]]
| Heterogeneity classification of differently sized images
|-

| Paper
| [[2006Penczek_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Scheres_ML3D]]
| Maximum Likelihood alignment and classification in 3D
|-

| Paper
| [[2009Spahn_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2010Elmlund_AbInitio]]
| Solving the initial volume problem with multiple conformations
|-

| Paper
| [[2010Shatsky_MultiVariate]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2012Scheres_Bayesian]]
| A Bayesian view on cryo-EM structure determination
|-

| Paper
| [[2012Zheng_Covariance]]
| Estimation of the volume covariance
|-

| Paper
| [[2013Wang_MLVariance]]
| Maximum Likelihood estimate of the map variance
|-

| Paper
| [[2013Lyumkis D_FREALIGN]]
| Likelihood-based classification of cryo-EM images using FREALIGN.
|-

| Paper
| [[2014Jin_NMA]]
| Continuous heterogeneity through Normal Mode Analysis
|-

| Paper
| [[2014Dashti_Brownian]]
| Continuous heterogeneity through Brownian trajectories
|-

| Paper
| [[2014Chen_Migration]]
| Particle migration analysis in 3D classification
|-

| Paper
| [[2015Anden_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Bai_Focused]]
| Focused classification
|-

| Paper
| [[2015Katsevich_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Klaholz_MRA]]
| Multivariate Statistical Analysis of Jackknife and Bootstrapping on random subsets
|-

| Paper
| [[2015Liao_Covariance]]
| Estimation of the 3D covariance from 2D projections
|-

| Paper
| [[2015Tagare_Direct]]
| Direct reconstruction of PCA components
|-

| Paper
| [[2016Gong_Mechanical]]
| Mechanical model for macromolecules
|-

| Paper
| [[2016Rawson_Movement]]
| Movement and flexibility
|-

| Paper
| [[2016Sorzano_StructMap]]
| Sorting a discrete set of conformational states
|-

| Paper
| [[2016Sorzano_Strain]]
| Calculate local stretches, strains and rotations from two conformational states
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

|}

=== Validation ===

{|

| Paper
| [[2008Stagg_TestBed]]
| Effect of voltage, dosis, number of particles and Euler jumps on resolution
|-

| Paper
| [[2011Henderson]]
| Tilt Validation
|-

| Paper
| [[2011Read]]
| Validation of PDBs
|-

| Paper
| [[2012Henderson]]
| EM Map Validation
|-

| Paper
| [[2013Cossio_Bayesian]]
| EM Map Validation in a probabilistic setting
|-

| Paper
| [[2013Chen_NoiseSubstitution]]
| Noise substitution at high resolution for measuring overfitting
|-

| Paper
| [[2014Russo_StatisticalSignificance]]
| EM Map Validation through the statistical significance of the tilt-pair angular assignment
|-

| Paper
| [[2014Stagg_Reslog]]
| EM Map Validation through the resolution evolution with the number of particles
|-

| Paper
| [[2014Wasilewski_Tilt]]
| Web implementation of the tilt pair validation
|-

| Paper
| [[2015Heymann_Alignability]]
| EM Map Validation through the resolution of reconstructions from particles and noise
|-

| Paper
| [[2015Oliveira_FreqLimited]]
| Comparison of gold standard and frequency limited optimization
|-

| Paper
| [[2015Wriggers_Secondary]]
| Validation by secondary structure
|-

| Paper
| [[2016Kim_SAXS]]
| Comparison of SAXS data and EM projections
|-

| Paper
| [[2016Rosenthal_Review]]
| Review of validation methods
|-

| Paper
| [[2016Vargas_Alignability]]
| Validation by studying the tendency of an angular assignment to cluster in the projection space
|-

| Paper
| [[2017Monroe_PDBRefinement]]
| Validation by comparison to a refined PDB
|-

|}

=== Resolution ===

{|

| Paper
| [[1986Harauz_FBP]]
| Fourier Shell Correlation
|-

| Paper
| [[1987Unser_SSNR]]
| 2D Spectral Signal to Noise Ratio
|-

| Paper
| [[2002Penczek_SSNR]]
| 3D Spectral Signal to Noise Ratio for Fourier based algorithms
|-

| Paper
| [[2003Rosenthal_DPR]]
| Review of the FSC and establishment of a new threshold
|-

| Paper
| [[2005Unser_SSNR]]
| 3D Spectral Signal to Noise Ratio for any kind of algorithms
|-

| Paper
| [[2005VanHeel_FSC]]
| Establishment of a new threshold for FSC
|-

| Paper
| [[2007Sousa_AbInitio]]
| Resolution measurement on neighbour Fourier voxels
|-

| Paper
| [[2014Kucukelbir_Local]]
| Quantifying the local resolution of cryo-EM density maps
|-

| Paper
| [[2016Pintilie_Probabilistic]]
| Probabilistic models and resolution
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Statistical properties of resolution measures defined in Fourier space
|-

|}

=== Sharpening of high resolution information ===
{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast restoration and map sharpening
|-

| Paper
| [[2008Fernandez_Bfactor]]
| Bfactor determination and restoration
|-

| Paper
| [[2013Fiddy_SaxtonAlgorithm]]
| Phase retrieval or extension
|-

| Paper
| [[2014Kishchenko_SphericalDeconvolution]]
| Spherical deconvolution
|-

| Paper
| [[2015Spiegel_VISDEM]]
| Visualization improvement by the use of pseudoatomic profiles
|-

| Paper
| [[2016Jonic_Pseudoatoms]]
| Approximation with pseudoatoms
|-

| Paper
| [[2016Jonic_Denoising]]
| Denoising and high-frequency boosting by pseudoatom approximation
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[1982Schiske_Correction]]
| CTF correction for tilted objects
|-

| Paper
| [[1988Toyoshima_Model]]
| CTF estimation
|-

| Paper
| [[1995Frank_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1996Skoglund_MaxEnt]]
| CTF correction with Maximum Entropy
|-

| Paper
| [[1996Zhou_Model]]
| CTF model and user interface for manual fitting
|-

| Paper
| [[1997Fernandez_AR]]
| PSD estimation using periodogram averaging and AR models
|-

| Paper
| [[1997Penczek_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1997Stark_Deconvolution]]
| CTF correction using deconvolution
|-

| Paper
| [[1997Zhu_RecCTF]]
| CTF correction and reconstruction
|-

| Paper
| [[2000DeRosier_EwaldCorrection]]
| CTF correction considering the Ewald sphere
|-

| Paper
| [[2000Jensen_TiltedCorrection]]
| CTF correction considering tilt in backprojection
|-

| Paper
| [[2001Saad_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Huang_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Mindell_CTFTILT]]
| CTF estimation for tilted micrographs
|-

| Paper
| [[2003Sander_MSA]]
| CTF estimation through MSA classification of PSDs
|-

| Paper
| [[2003Velazquez_ARMA]]
| PSD and CTF estimation using ARMA models
|-

| Paper
| [[2004Sorzano_IDR]]
| CTF restoration and reconstruction with Iterative Data Refinement
|-

| Conference
| [[2004Wan_CTF]]
| Spatially variant CTF
|-

| Paper
| [[2004Zubelli_Chahine]]
| CTF restoration and reconstruction with Chahine's multiplicative method
|-

| Conference
| [[2005Dubowy_SpaceVariant]]
| CTF correction when this is space variant
|-

| Paper
| [[2005Mallick_ACE]]
| CTF estimation
|-

| Paper
| [[2006Wolf_Ewald]]
| CTF correction considering Ewald sphere
|-

| Paper
| [[2007Jonic_EnhancedPSD]]
| PSD enhancement for better identification of Thon rings; Vitreous ice diffracts in Thon rings
|-

| Paper
| [[2007Philippsen_Model]]
| CTF Model for tilted specimens
|-

| Paper
| [[2007Sorzano_CTF]]
| CTF estimation using enhanced PSDs
|-

| Paper
| [[2009Sorzano_Sensitivity]]
| Error sensitivity of the CTF models, non-uniqueness of the CTF parameters
|-

| Paper
| [[2010Jiang2010_CTFCorrection]]
| Amplitude correction method
|-

| Paper
| [[2010Kasantsev_CTFCorrection]]
| Mathematical foundations of Kornberg and Jensen method
|-

| Paper
| [[2010Leong_CTFCorrection]]
| Correction for spatially variant CTF
|-

| Paper
| [[2011Glaeser_Coma]]
| The effect of coma at high-resolution
|-

| Paper
| [[2011Mariani_Tilted]]
| CTF simulation and correction of tilted specimens
|-

| Paper
| [[2011Sindelar_Wiener]]
| CTF correction using a modified version of Wiener filter
|-

| Paper
| [[2011Voortman_Tilted]]
| CTF correction for tilted specimen
|-

| Paper
| [[2012Voortman_VaryingCTF]]
| Correcting a spatially varying CTF
|-

| Paper
| [[2013Vargas_FastDef]]
| Fast defocus
|-

| Paper
| [[2015Rohou_CTFFind4]]
| CTF Find 4
|-

| Paper
| [[2015Sheth_CTFquality]]
| Visualization and quality assessment of CTF
|-

| Paper
| [[2016Zhang_GCTF]]
| gCTF
|-

|}

=== Segmentation ===

{|

| Paper
| [[2006Baker_segmentation]]
| Segmentation of molecular subunits
|-

|}

=== Fitting and docking ===

{|

| Paper
| [[1999Volkmann_Fitting]]
| Fitting in real space
|-

| Paper
| [[2001Baker_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2001Jones_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2003Kovacs_FRM3D]]
| Fast Rotational Alignment of two EM maps
|-

| Paper
| [[2004Tama_NMA1]]
| Flexible fitting with Normal Modes (I)
|-

| Paper
| [[2004Tama_NMA2]]
| Flexible fitting with Normal Modes (II)
|-

| Paper
| [[2005Velazquez_Superfamilies]]
| Recognition of the superfamily folding in medium-high resolution volumes
|-

| Paper
| [[2007DeVries_Haddock]]
| Docking with Haddock 2.0
|-

| Paper
| [[2007Kleywegt_QualityControl]]
| Quality control and validation of fitting
|-

| Paper
| [[2012Biswas_Secondary]]
| Secondary structure determination in EM volumes
|-

| Paper
| [[2012Velazquez_Constraints]]
| Multicomponent fitting by using constraints from other information sources
|-

| Paper
| [[2013Chapman MS_Atomicmodeling]]
| Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters
|-

| Paper
| [[2013Esquivel_Modelling]]
| Review on modelling (secondary structure, fitting, ...)
|-

| Paper
| [[2013Lopez_Imodfit]]
| Fitting based on vibrational analysis
|-

| Paper
| [[2013Nogales_3DEMLoupe]]
| Normal Mode Analysis of reconstructed volumes
|-

| Paper
| [[2014AlNasr_Secondary]]
| Identification of secondary structure elements in EM volumes
|-

| Paper
| [[2014Politis_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Rey_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Villa_Review]]
| Review of atomic fitting into EM volumes
|-

| Paper
| [[2015Barad_EMRinger]]
| Validation of hybrid models
|-

| Paper
| [[2015Bettadapura_PF2Fit]]
| Fast rigid fitting of PDBs into EM maps
|-

| Paper
| [[2015Carrillo_CapsidMaps]]
| Analysis of virus capsids using Google Maps
|-

| Paper
| [[2015Schroeder_Hybrid]]
| Review on model building
|-

| Paper
| [[2015Tamo_Dynamics]]
| Dynamics in integrative modeling
|-

| Paper
| [[2015Sorzano_AtomsToVoxels]]
| Accurate conversion of an atomic model into a voxel density volume
|-

| Paper
| [[2016Joseph_Evolution]]
| Evolutionary constraints for the fitting of atomic models into density maps
|-

| Paper
| [[2016Segura_3Diana]]
| Validation of hybrid models
|-

| Paper
| [[2016Singharoy_MDFF]]
| Construction of hybrid models driven by EM density and molecular dynamics
|-

| Paper
| [[2016Wang_Rosetta]]
| Construction of hybrid models driven by EM density using Rosetta
|-

| Paper
| [[2017Hryc_WeightedAtoms]]
| Construction of hybrid models by locally weighting the different atoms
|-

|}

=== Books and reviews ===

{|

| Book
| [[1980Herman_Tomography]]
| General book on tomography
|-

| Book
| [[1988Kak_Tomography]]
| General book on tomography
|-

| Paper
| [[2000Tao_Review]]
| Review of single particles
|-

| Paper
| [[2000VanHeel_Review]]
| Review of single particles
|-

| Paper
| [[2002Frank_Review]]
| Review of single particles
|-

| Paper
| [[2002Schmid_Review]]
| Review of single particles
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2004Subramaniam_Review]]
| Review of single particles
|-

| Paper
| [[2005Steven_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_book]]
| Book covering all aspects of electron microscopy of single particles
|-

| Paper
| [[2006Sorzano_Review]]
| Review of optimization problems in electron microscopy
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems in Electron Tomography
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2008Mueller_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2008Taylor_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2010DeRosier_Review]]
| Personal account of how 3DEM developed in the early days
|-

| Chapter
| [[2012Sorzano_Review]]
| Review of single particle analysis using Xmipp
|-

| Chapter
| [[2012Devaux_Protocol]]
| Protocols for performing single particle analysis
|-

| Paper
| [[2014Bai_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Carazo_Review]]
| Review of the reconstruction process
|-

| Paper
| [[2015Cheng_Review]]
| A primer to Single Particle Cryo-EM
|-

| Paper
| [[2015Cheng_Reviewb]]
| Single Particle Cryo-EM at crystallographic resolution
|-

| Paper
| [[2015Elmlund_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Henderson_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Nogales_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Schroeder_Review]]
| Review of advances in the electron microscope
|-

| Paper
| [[2015Wu_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Carroni_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Egelman_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Eisenstein_CryoEM]]
| News feature on the Method of the Year
|-

| Paper
| [[2016FernandezLeiro_Review]]
| Review of EM
|-

| Paper
| [[2016Glaeser_HowGood]]
| How good can cryo-EM become?
|-

| Paper
| [[2016Jonic_PseudoAtoms]]
| Review of the applications of the use of pseudoatoms in EM
|-

| Chapter
| [[2016Mio_Review]]
| Overview of the process to obtain EM reconstructions
|-

| Paper
| [[2016Jonic_Review]]
| A review of computational ways to handle heterogeneity
|-

| Paper
| [[2016Nogales_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Subramaniam_Review]]
| Why cryo-EM is now suitable for crystallographic journals
|-

| Paper
| [[2016Vinothkumar_Review]]
| Historical review and current limitations
|-

| Paper
| [[2017Frank_Review]]
| Historical review of EM
|-

| Paper
| [[2017Jonic_Review]]
| Review of computational methods to analyze conformational variability
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Review of statistical properties of resolution measures defined in Fourier space
|-
|}

=== Software ===

{|

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[1999Lutdke_Eman]]
| Eman
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Baldwin_AngularTransformations]]
| The Transform Class in SPARX and EMAN2
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Grigorieff_Frealign]]
| Frealign
|-

| Paper
| [[2008Scheres_XmippProtocols]]
| Xmipp Protocols
|-

| Paper
| [[2008Shaikh_SpiderProtocols]]
| Spider Protocols
|-

| Paper
| [[2012Wriggers_SitusConventions]]
| Conventions and workflows in Situs
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2015Cianfrocco_Cloud]]
| Software execution in the cloud
|-

| Paper
| [[2015Cheng_MRC2014]]
| Extensions to MRC file format
|-

| Paper
| [[2013DeLaRosa_Scipion]]
| Scipion
|-

| Paper
| [[2016Scheres_Relion]]
| Tutorial on the use of Relion
|-

| Paper
| [[2016Grigorieff_Frealign]]
| Tutorial on the use of Frealign
|-

|}

== Electron tomography ==

=== Image preprocessing ===

{|

| Paper
| [[2015Yan_thickness]]
| Determination of thickness, tilt and electron mean free path
|-

|}

=== Image alignment ===

{|

| Paper
| [[1982Guckenberger_commonOrigin]]
| Determination of a common origin in the micrographs of titl series in three-dimensional electron microscopy
|-

| Paper
| [[1992Lawrence_leastSquares]]
| Least squares solution of the alignment problem
|-

| Paper
| [[1995Penczek_dual]]
| Dual tilt alignment
|-

| Paper
| [[1996Owen_alignmentQuality]]
| Automatic alignment without fiducial markers and evaluation of alignment quality
|-

| Paper
| [[1998Grimm_normalization]]
| Discussion of several gray level normalization methods for electron tomography
|-

| Paper
| [[2001Brandt_Automatic1]]
| Automatic alignment without fiducial markers
|-

| Paper
| [[2001Brandt_Automatic2]]
| Automatic alignment with fiducial markers
|-

| Paper
| [[2006Winkler_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2006Castano_alignment]]
| Alignment with non-perpendicularity
|-

| Paper
| [[2007Castano_alignment]]
| Fiducial-less alignment of cryo-sections
|-

| Paper
| [[2009Sorzano_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2010Cantele_dualAlignment]]
| Alignment of dual series
|-

| Paper
| [[2014Tomonaga_Automatic]]
| Automatic alignment of tilt series using the projection themselves
|-

| Paper
| [[2014Han_Automatic]]
| Automatic alignment of tilt series using SIFT features
|-

| Paper
| [[2015Han_Automatic]]
| Automatic alignment of tilt series using fiducials
|-

| Paper
| [[2017Mastronarde_Automatic]]
| Automatic alignment and reconstruction of tilt series in IMOD
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[2003Winkler_CTF]]
| Focus gradient correction in electron tomography
|-

| Paper
| [[2006Fernandez_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Zanetti_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Xiong_CTF]]
| CTF determination and correction for low dose tomographic tilt series
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2017Kunz_3DCTF]]
| 3D CTF Correction
|-

|}

=== 3D reconstruction ===

{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1992Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[1997Marabini_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2002Fernandez_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2007Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[2008Fernandez_CARP]]
| Component Averaged Row Projections (CARP)
|-

| Paper
| [[2012Herman General Superiorization]]
| Superiorization: an optimization heuristic for medical physics
|-

| Paper
| [[2012Zhang_IPET_FETR]]
| IPET and FETR, a reconstruction algorithm for single molecule tomography
|-

| Paper
| [[2013Goris_SIRT_TV_DART]]
| Combination of SIRT, Total Variation and Discrete ART to reconstruct and segment at the same time
|-

| Paper
| [[2013Briegel A_Challenge]]
| The challenge of determining handedness in electron tomography and the use of DNA origami gold nanoparticle helices as molecular standards
|-

| Paper
| [[2013Messaoudi_EnergyFiltered]]
| 3D Reconstruction of Energy-Filtered TEM
|-

| Paper
| [[2016Deng_ICON]]
| 3D Reconstruction with missing information restoration
|-

| Paper
| [[2016Guay_Compressed]]
| 3D Reconstruction using compressed sensing
|-

|}

=== Noise reduction ===
{|

| Paper
| [[2001Frangakis_NAD]]
| Noise reduction with Nonlinear Anisotropic Diffusion
|-

| Paper
| [[2003Fernandez_AND]]
| Anisotropic nonlinear diffusion for electron tomography
|-

| Paper
| [[2003Jiang_Bilateral]]
| Bilateral denoising filter in electron microscopy
|-

| Paper
| [[2005Fernandez_AND]]
| Anisotropic nonlinear denoising in electron tomography
|-

| Paper
| [[2007Heide_median]]
| Iterative median filtering in electron tomography
|-

| Paper
| [[2007Fernandez_autAND]]
| Anisotropic nonlinear diffusion with automated parameter tuning
|-

| Paper
| [[2009Fernandez_Beltrami]]
| Nonlinear filtering based on Beltrami flow
|-

| Paper
| [[2010Bilbao_MeanShift]]
| Mean Shift Filtering
|-

| Paper
| [[2014Kovacik_wedgeArtefacts]]
| Removal of wedge artefacts
|-

| Paper
| [[2014Maiorca_beadArtefacts]]
| Removal of gold bead artefacts
|-

|}

=== Segmentation ===

{|

| Paper
| [[2002Frangakis_Eigenanalysis]]
| Segmentation using eigenvector analysis.
|-

| Paper
| [[2002Volkmann_Watershed]]
| Segmentation using watershed transform.
|-

| Paper
| [[2003Bajaj_BoundarySegmentation]]
| Segmentation based on fast marching.
|-

| Paper
| [[2005Cyrklaff_Thresholding]]
| Segmentation using optimal thresholding.
|-

| Paper
| [[2007Lebbink_TemplateMatching]]
| Segmentation using template matching.
|-

| Paper
| [[2007Sandberg_OrientationFields]]
| Segmentation using orientation fields.
|-

| Paper
| [[2007Sandberg_SegmentationReview]]
| Review on segmentation in electron tomography.
|-

| Paper
| [[2008Garduno_FuzzySegmentation]]
| Segmentation using fuzzy set theory principles.
|-

| Paper
| [[2009Lebbink_TemplateMatching2]]
| Segmentation using template matching.
|-

| Paper
| [[2012RubbiyaAli_EdgeDetection]]
| Parameter-Free Segmentation of Macromolecular Structures.
|-

| Conference
| [[2015Xu_TemplateMatching]]
| Detection of macromolecular complexes with a reduced representation of the templates.
|-

|}

=== Resolution ===
{|

| Paper
| [[2005Cardone_Resolution]]
| Resolution criterion for electron tomography
|-

| Chapter
| [[2007Penczek_Resolution]]
| Review of resolution criteria for electron tomography
|-

| Paper
| [[2015Diebolder_ConicalFSC]]
| Conical Fourier Shell Correlation
|-

|}

=== Subtomogram analysis ===

{|

| Paper
| [[2000Bohm_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2002Frangakis_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2006Nickell_Review]]
| Review of macromolecule finding by template matching (Visual Proteomics)
|-

| Paper
| [[2007Best_Review]]
| Review of Localization of Protein Complexes by Pattern Recognition
|-

| Paper
| [[2007Forster_Review]]
| Review of structure determination by subtomogram averaging
|-

| Paper
| [[2008Forster_Classification]]
| Classification of subtomograms using constrained correlation
|-

| Paper
| [[2008Bartesaghi_Classification]]
| Classification and averaging of subtomograms
|-

| Paper
| [[2008Schmid_Averaging]]
| Alignment and averaging of subtomograms
|-

| Paper
| [[2010Amat_Averaging]]
| Alignment and averaging of subtomograms exploiting thresholding in Fourier space
|-

| Paper
| [[2013Chen_Averaging]]
| Fast alignment of subtomograms using spherical harmonics
|-

| Paper
| [[2013Kuybeda_Averaging]]
| Alignment and averaging of subtomograms using the nuclear norm of the cluster
|-

| Paper
| [[2013Shatsky_Averaging]]
| Alignment and averaging of subtomograms with constrained cross-correlation
|-

| Paper
| [[2014Chen_Autofocus]]
| Subtomogram averaging and classification with special attention to differences
|-

| Paper
| [[2014Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2014Voortman_LimitingFactors]]
| Limiting factors of subtomogram averaging
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2015Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2016Bharat_Relion]]
| Subtomogram averaging with Relion
|-

| Paper
| [[2016Song_MatrixNorm]]
| Matrix norm minimization for tomographic reconstruction and alignment
|-

| Paper
| [[2017Castano_ParticlePicking]]
| Particle picking in tomograms for subtomogram averaging
|-

|}

=== Single particle tomography ===

{|

| Paper
| [[2012Bartesaghi_Constrained]]
| 3D reconstruction by imposing geometrical constraints
|-

| Paper
| [[2015Galaz_SingleParticleTomography]]
| Set of tools for Single Particle Tomography in EMAN2
|-

| Paper
| [[2016Galaz_SingleParticleTomography]]
| Alignment algorithms and CTF correction
|-

|}

=== Books and reviews ===

{|

| Paper
| [[2000Baumeister_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Koster_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Sali_Review]]
| Review of electron tomography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2005Lucic_Review]]
| Review of electron tomography
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_TomoBook]]
| Electron Tomography
|-

| Book
| [[2007McIntosh_Book]]
| Cellular Electron Microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2012Kudryashev_Review]]
| Review of subtomogram averaging
|-

| Paper
| [[2016Beck_Review]]
| Review of molecular sociology
|-

|}

=== Software ===

{|

| Paper
| [[1996Kremer_IMOD]]
| IMOD
|-

| Paper
| [[1996Chen_Priism/IVE]]
| Priism/IVE
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2005Nickell_TOM]]
| TOM Toolbox
|-

| Paper
| [[2007Messaoudi_TomoJ]]
| TomoJ
|-

| Paper
| [[2008Heymann_BsoftTomo]]
| Bsoft
|-

| Paper
| [[2015Ding_CaltechTomography]]
| Caltech tomography database
|-

| Paper
| [[2015Noble_AppionProtomo]]
| Batch fiducial-less tilt-series alignment in Appion using Protomo
|-

| Paper
| [[2015vanAarle_Astra]]
| ASTRA Toolbox
|-

|}

== 2D Crystals ==

=== 2D Preprocessing ===

{|

| Paper
| [[1986Henderson_Processing]]
| General 2D processing
|-

| Paper
| [[2000He_PhaseAlignment]]
| Phase consistency and Alignment
|-

| Paper
| [[2006Gil_Unbending]]
| Crystal unbending
|-

|}

=== Classification ===
{|

| Paper
| [[1988Frank_Classification]]
| MSA and classification in electron crystallography
|-

| Paper
| [[1996Fernandez_SOM]]
| Classification based on self organizing maps
|-

| Paper
| [[1998Sherman_MSA]]
| Classification based on MSA
|-

|}
=== 3D Reconstruction ===

{|

| Paper
| [[1985Wang_Solvent]]
| Solvent flattening
|-

| Paper
| [[1990Henderson_Processing]]
| General 3D processing
|-

| Paper
| [[2004Marabini_ART]]
| Algebraic Reconstruction Technique with blobs for crystals (Xmipp)
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1998Walz_Review]]
| Review of 2D crystallography
|-

| Paper
| [[1999Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Ellis_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of single particles, electron tomography and crystallography
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Gipson_2dx]]
| 2dx
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Philippsen_IPLT]]
| IPLT
|-

|}

== 3D Crystals - MicroED ==

=== Sample Preparation ===
{|
| Paper
| [[2016Shi_Preparation]]
| Sample Preparation
|}
=== Data Collection ===
{|
| Paper
| [[2014Nannenga_CR]]
| Continuous rotation

|}
=== Data Processing ===
{|

| Paper
| [[2011Wisedchaisri_PhaseExtension]]
| Fragment-based phase extension
|-

| Paper
| [[2015Hattne_Processing]]
| Data Processing
|-

| Paper
| [[2016Hattne_Correction]]
| Image correction
|}

=== Software ===
{|

| Paper
| [[2014Iadanza_Processing]]
| Data Processing of still diffraction data
|}

=== Books and Reviews ===
{|
| Paper
| [[2014Nannenga_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Liu_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Rodriguez_Review ]]
| Review of MicroED
|-

|}

== Helical particles ==

=== Filament corrections ===

{|

| Paper
| [[1986Egelman_Curved]]
| Algorithm for correcting curved filaments
|-

| Paper
| [[1988Bluemke_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2006Wang_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2016Yang_Flexible]]
| Algorithm for correcting filaments with flexible subunits
|-

|}

=== Reconstruction ===

{|

| Paper
| [[1952Cochran_Fourier]]
| Fourier Bessel transform of filamentous structures
|-

| Paper
| [[1958Klug_Fourier]]
| Fourier Bessel decomposition of the projection images
|-

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2005Wang_Iterative]]
| Iterative Fourier-Bessel algorithm
|-

| Paper
| [[2007Egelman_Iterative]]
| Iterative real-space algorithm
|-

| Paper
| [[2013Desfosses_Spring]]
| Helical processing with Spring
|-

| Paper
| [[2015Zhang_seam]]
| Workflow for the detection of the lattice seam
|-

| Paper
| [[2016Rohou_Frealix]]
| Helical processing with Frealix
|-

|}

=== Validation ===

{|

| Paper
| [[2014Egelman_ambiguity]]
| How to detect incorrect models
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Carragher_Phoelix]]
| Phoelix
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Owen_Brandeis]]
| Brandeis
|-

|}

== Icosahedral particles ==

=== Reconstruction ===

{|

| Paper
| [[1970Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1971Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1996Fuller_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1997Thuman_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

|}

=== Classification ===

{|

| Paper
| [[2005Scheres_Virus]]
| Classification of virus capsids in real space
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1999Baker_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[1999Conway_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2000Thuman_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Lee_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Navaza_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2006Grunewald_Review]]
| Review of reconstruction of icosahedral viruses
|-

|}

=== Software ===

{|

| Paper
| [[1996Baker_EMPFT]]
| EMPFT
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2013Morin_Sliz SBGrid]]
| SBGrid presentation for eLife
|-

|}

== Databases ==

{|

| Paper
| [[2003Boutselakis_EMSD]]
| EMSD database
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2011Kim_CDDB]]
| Conformational Dynamics Data Bank
|-

| Paper
| [[2011Lawson_EMDB]]
| Electron Microscopy Data Bank
|-

| Paper
| [[2016Iudin_EMPIAR]]
| EMPIAR raw data database
|-

| Paper
| [[2016Patwhardan_EMDB]]
| EMDB, PDB, ...
|-

| Paper
| [[2017Shao_PDBQuality]]
| Quality metrics in PDB
|-

| Blog
| http://www.mybiosoftware.com
| Huge list of bioinformatics programs (many of them structural bioinformatics)
|-

|}

== Relationship to other structural information sources ==

{|

| Paper
| [[2000Engel_AFM]]
| Review of Atomic Force Microscopy
|-

| Paper
| [[2001Dimmeler_AFM]]
| Constraints from Atomic Force Microscopy
|-

| Paper
| [[2003Mobus_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_Review]]
| Review on correlative microscopy
|-

| Paper
| [[2005Boudier_EFTETJ]]
| Software for Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2005Vestergaard_SAXS]]
| Example of comparison of 3DEM and Small-angle X-ray scattering
|-

| Paper
| [[2007Hamada_SAXS]]
| Constraints from Small-angle X-ray scattering
|-

| Paper
| [[2013Xu_FRET]]
| EM+FRET
|-

|}

== X-ray tomography ==

{|

| Paper
| [[2012Oton_ImageFormation]]
| Image formation model in X-ray cell microscopy
|-

|}

== Mathematical tools necessary ==

== People developing methods ==
Please, add yourself to this list (due to privacy reasons, please, do not add anyone else to the list without his/her explicit consent). Sort by first name alphabetical order.

[http://biocomp.cnb.csic.es/~coss Carlos Oscar S. Sorzano]: CSIC, Madrid, Spain 

[http://www.curie.fr/recherche/themes/detail_equipe.cfm/lang/_fr/id_equipe/241.htm Cédric Messaoudi]: Institute Curie, Paris, France 

[http://scholar.google.es/citations?user=_jNYGScAAAAJ&hl=en Javier Vargas]:[mailto:jvargas@cnb.csic.es mail]: CSIC, Madrid, Spain 

[http://scholar.google.es/citations?hl=es&user=g2ZJPIYAAAAJ Joaquín Otón]: CSIC, Madrid, Spain 

[mailto:jrbcast@gmail.com José Román Bilbao-Castro]: UAL, Almería, Spain; CSIC, Madrid, Spain 

[José Miguel de la Rosa Trevín]: Biocomputing Unit CNB-CSIC, Madrid, Spain 

[http://cryoem.janelia.org Tamir Gonen]: [mailto:gonent@janelia.hhmi.org mail]: Howard Hughes Medical Institute, Ashburn, VA, USA 

[mailto:vabrishami@cnb.csic.es Vahid Abrishami]: CSIC, Madrid, Spain 

== 3DEM sites ==
* [http://3dem.ucsd.edu/ 3DEM web site]

* [http://en.wikibooks.org/wiki/Software_Tools_For_Molecular_Microscopy Software tools for molecular microscopy]

* [http://www.emdatabank.org/ The Electron Microscopy Data Bank (EMDB)]

* [http://ccdb.ucsd.edu The Cell Centered Database (CCDB)]

* [http://conventions.cnb.csic.es The geometrical software conventions web page ]

== Editing useful links ==

* [http://www.mediawiki.org/wiki/Help:Formatting Text formatting in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Links Adding links in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Images Adding images in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Tables Making tables in Mediawiki]

2017Arnold BlottingFree

2017-05-11T20:53:55Z

CoSS: Created page with "== Citation == Arnold, S. A.; Albiez, S.; Bieri, A.; Syntychaki, A.; Adaixo, R.; McLeod, R. A.; Goldie, K. N.; Stahlberg, H. & Braun, T. Blotting-free and lossless cryo-elect..."

== Citation ==

Arnold, S. A.; Albiez, S.; Bieri, A.; Syntychaki, A.; Adaixo, R.; McLeod, R. A.; Goldie, K. N.; Stahlberg, H. & Braun, T. Blotting-free and lossless cryo-electron microscopy grid preparation from nanoliter-sized protein samples and single-cell extracts. Journal of structural biology, 2017, 197, 220-226

== Abstract ==

We present a sample preparation method for cryo-electron microscopy (cryo-EM) that requires only 3-20nL of sample to prepare a cryo-EM grid, depending on the protocol used. The sample is applied and spread on the grid by a microcapillary. The procedure does not involve any blotting steps, and real-time monitoring allows the water film thickness to be assessed and decreased to an optimum value prior to vitrification. We demonstrate that the method is suitable for high-resolution cryo-EM and will enable alternative electron microscopy approaches, such as single-cell visual proteomics.

== Keywords ==

== Links ==

http://www.sciencedirect.com/science/article/pii/S104784771630243X

== Related software ==

== Related methods ==

== Comments ==

Main Page

2017-05-11T20:53:04Z

CoSS: /* Sample preparation */

== Presentation ==

This web page is intended to be an extensive repository of three-dimensional electron microscopy (3DEM) methods. The advantages of having such a repository are

* You know which are the relevant articles in a particular topic, therefore, paper introductions, reviews, etc. are easier to write and you make sure you will cite all the related articles.
* You will be sure that your paper has more chances of being cited.
* You can add whatever information you find relevant to your method, external links, links to other papers, etc.
* You can link your method to a web page providing the corresponding software, so you know people can use your algorithms.
* You can use the Wiki search capabilities to locate relevant articles even if they are not at the topic you are looking at.
* As a community we will "reconstruct" our history.
* You can select the "watch" option above to receive notifications in case of further changes in the Main Page.

Developing image processing methods for 3DEM is not "[[well-paid]]" in terms of citations and impact factor. However, it is crucial for the advance of the field. Gathering methodological papers in a portal will help to increase the recognition of the field.

Please:

* Add your articles at the right place (you can add a single article in several topics if it is relevant to all of them). The easiest way to add an article is by editing the corresponding topic in the main page, adding your entry, then save the main page. Click on the red link that appears on your new entry, copy and paste the Wiki following code, add the information of your article

== Citation ==

== Abstract ==

== Keywords ==

== Links ==

== Related software ==

== Related methods ==

== Comments ==

* Maintain the information of each article as complete as possible.
* Sort articles by years and authors.
* Be respectful to other people's work.

== How to subscribe to this page ==

You may subscribe to this page so that you will be notified every time someone adds a new method. To do so, you have to register in the page, and edit your preferences ("my preferences"). Be sure that you have activated the option "E-mail me when a page on my watchlist is changed". Finally, click on the "Watch" tab at the top of this page.

You may subscribe to changes on this page on the mailing list 3demmethods@cnb.csic.es. To send a new method to this mail list just send a mail to 3demmethods@cnb.csic.es

To subscribe to this list, visit the web page

https://listas.csic.es/cnb/wws/subscribe/3demmethods

Alternatively, you may write a mail to sympa6@cnb.csic.es with the subject

<code>subscribe 3demmethods YourName YourFamilyName</code>

and an empty mail body.

To unsubscribe visit the page

https://listas.csic.es/cnb/wws/sigrequest/3demmethods

or write sympa6@cnb.csic.es with the subject

<code>unsubscribe 3demmethods</code>

and an empty mail body.

== Electron microscopy images ==

=== Online courses ===

CALTECH: http://cryo-em-course.caltech.edu/

MRC: ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/EM-course/

CNB-CSIC: http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/MadridJan2014EM

Workshop on Computational methods for CryoEM: https://www.youtube.com/watch?v=XdKO1iaPP8o

Workshop on Management of large CryoEM facilities: https://www.youtube.com/watch?v=as4seOPszL0

Icknield Course on Model Building and Refinement for High Resolution EM Maps: http://www.ccpem.ac.uk/training/icknield_2017/icknield_2017.php

=== Image formation ===

{|

| Paper
| [[1971Erickson_CTF]]
| CTF model
|-

| Paper
| [[1971Glaeser_Damage]]
| Radiation damage
|-

| Chapter
| [[1971Hanszen_CTF]]
| Image formation model
|-

| Paper
| [[1971Thon_Model]]
| CTF model
|-

| Paper
| [[1975Unwin_Imaging]]
| Radiation dose
|-

| Paper
| [[1977Wade_Model]]
| CTF model
|-

| Paper
| [[1978Wade_Model]]
| CTF model
|-

| Paper
| [[1979Hayward_Radiation]]
| Radiation damage
|-

| Paper
| [[1984Cohen_Validity]]
| Validity of the CTF model at high frequencies
|-

| Paper
| [[1988Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[1992Wade_Model]]
| CTF model
|-

| Paper
| [[1993Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2004Egerton_Damage]]
| Radiation damage
|-

| Paper
| [[2004Sorzano_Normalization]]
| Background noise is Gaussian
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2009Baxter_NoiseCharacterization]]
| Characterization of the different noise sources in cryo-EM
|-

| Paper
| [[2010Baker_Damage]]
| Radiation damage dependence on resolution
|-

| Paper
| [[2010Bammes_Damage]]
| Radiation damage dependence on temperature
|-

| Paper
| [[2010Gomez_Multislice]]
| Simulation of the multi slice model
|-

| Paper
| [[2010Zewail_FourDimensional]]
| Review on the use of ultrafast EM
|-

| Paper
| [[2011Bammes_CCD]]
| Performance of CCD cameras
|-

| Paper
| [[2011Glaeser_Coma]]
| Image formation model including coma
|-

| Paper
| [[2011Milazzo_DirectDetectors]]
| Evaluation of Direct Detectors
|-

| Paper
| [[2011Rullgard_ImageSimulation]]
| Accurate simulation of EM images
|-

| Paper
| [[2011Zhang LimitingFactors]]
| Limiting factor for atomic resolution in EM
|-

| Paper
| [[2012Bammes_DirectDetection]]
| Performance of Direct detectors
|-

| Paper
| [[2012Campbell_MotionCorrection]]
| Beam induced motion correction and direct detectors
|-

| Paper
| [[2012Shang_HydrationLayer]]
| Simulation of PDB volumes explicitly considering the hydration layer
|-

| Paper
| [[2013Egerton_RadiationDamage]]
| Review of TEM radiation damage and experimental ways of reducing it
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu H_Noisemodels]]
| Noise models and cryo-EM drift correction with a direct-electron camera
|-

| Paper
| [[2013Li X K2 noisemodels]]
| Influence of electron dose rate on electron counting images recorded with the K2 camera
|-

| Paper
| [[2013Vulovic_CTFApproximations]]
| When to use the different approximations performed so that a projection with linear CTF is valid
|-

| Thesis
| [[2013Vulovic_ImageFormation]]
| Ph.D. Thesis on the image formation in cryo-EM
|-

| Paper
| [[2014Danev_PhasePlate]]
| Volta potential phase plate
|-

| Paper
| [[2015Chiu_K2]]
| Characterization of K2
|-

| Paper
| [[2015Hawkes_AberrationCorrection]]
| Historical account of the development of lens corrections
|-

| Paper
| [[2015Koeck_Quadratic]]
| Limitations of the linear approximation and use of the quadratic terms
|-

| Paper
| [[2015Kuijper_FEI]]
| Description of the FEI Falcons
|-

| Paper
| [[2015Lobato_MULTEM]]
| Simulation of multislice diffraction
|-

| Paper
| [[2015McMullan_AmorphousIce]]
| Beam induced movement is caused by Brownian motion
|-

| Paper
| [[2016Koeck_ADF]]
| Simulations of Annular Dark Field TEM
|-

| Paper
| [[2017Mishyna_DNARadiation]]
| Review of radiation damage on DNA
|-

|}

=== Collection geometry ===

{|

| Chapter
| [[1980Hoppe_Wedge]]
| Missing wedge
|-

| Paper
| [[1987Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1995Penczek_Dual]]
| Dual axis tomography
|-

| Paper
| [[1997Mastronarde_Dual]]
| Dual axis tomography
|-

| Paper
| [[2003Ludtke_FocusPairs]]
| Focus pairs for single particles
|-

| Paper
| [[2005Lanzavecchia_Conical]]
| Conical tomography
|-

| Paper
| [[2005Zampighi_Conical]]
| Conical tomography
|-

| Paper
| [[2006Leschziner_OT]]
| Orthogonal Tilt
|-

| Paper
| [[2006Messaoudi_Multiple]]
| Multiple axis tomography
|-

| Paper
| [[2012Kudryashev_FocusPairs]]
| Focus pairs tomography
|-

| Paper
| [[2014Hovden_TiltFocus]]
| Combining tilt series with focus series
|-

| Paper
| [[2015Sorzano_RandomConicalTilt]]
| General formulation of Random Conical Tilt
|-

| Paper
| [[2017Hagen_DoseTomography]]
| Dose optimization for subtomogram averaging
|-

|}

=== Sample preparation ===

{|

| Paper
| [[1982Dubochet_Sample]]
| Vitreous ice
|-

| Paper
| [[1986Lepault_Sample]]
| Fast freezing
|-

| Paper
| [[1995Dubochet_Sample]]
| High-pressure freezing
|-

| Paper
| [[1995VanMarle_Sample]]
| Sample damages in resin
|-

| Paper
| [[1998Adrian_Sample]]
| Cryo negative staining
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2002Hsieh_Sample]]
| Cryofixation
|-

| Paper
| [[2004AlAmoudi_Sample]]
| CEMOVIS
|-

| Paper
| [[2008Studer_Sample]]
| Review on high pressure freezing
|-

| Paper
| [[2009Pierson_Sample]]
| Review on sample preparation for electron tomography
|-

| Paper
| [[2010Zhang_NegativeStaining]]
| Negative staining for small protein imaging
|-

| Paper
| [[2012Zhang_PositiveStaining]]
| Positive staining
|-

| Paper
| [[2014Rames_NegativeStaining]]
| Optimized negative staining
|-

| Paper
| [[2014Russo_GoldGrids]]
| Gold grids for single particles
|-

| Paper
| [[2015Cabra_Sample]]
| Review on sample preparation for single particles with videos
|-

| Paper
| [[2016Passmore_Review]]
| Tutorial chapter on sample preparation
|-

| Paper
| [[2016Razinkov_Vitrification]]
| New vitrification method
|-

| Paper
| [[2016Takizawa_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2016Thompson_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2017Arnold_BlottingFree]]
| Blotting-free preparation
|-

| Paper
| [[2017Peitsch_Sample]]
| iMEM: Isolation of Plasma Membrane for Cryoelectron Microscopy
|-

| Paper
| [[2017Schaffer_FocusedIonBeam]]
| Focused Ion Beam sample preparation for membrane proteins
|-

|}

=== Automated data collection ===

{|

| Paper
| [[1992Dierksen_Automatic]]
| Automated data collection
|-

| Paper
| [[1992Koster_Automatic]]
| Automated data collection
|-

| Paper
| [[1996Fung_Automatic]]
| Automated data collection for tomography
|-

| Paper
| [[2001Zhang_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2003Ziese_Automatic]]
| Automated autofocusing
|-

| Paper
| [[2004Potter_Automatic]]
| Automated sample loading
|-

| Paper
| [[2004Zheng_Automatic]]
| Automated data collection
|-

| Paper
| [[2005Lei_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2005Suloway_Automatic]]
| Automated data collection: Leginon
|-

| Paper
| [[2007Yoshioka_RCT]]
| Automated Random Conical Tilt
|-

| Paper
| [[2011Korinek_TOM2]]
| Automated acquisition with TOM2
|-

| Paper
| [[2015Li_UCSFImage]]
| Automated acquisition with UCSFImage
|-

| Paper
| [[2016Gil_Fuzzy]]
| Real time decisions during acquisition with neuro-fuzzy method
|-

| Paper
| [[2016Liu_TiltControl]]
| Accurate control of the tilt angle for electron tomography
|-

| Paper
| [[2016Vargas_FoilHole]]
| Determination of image quality at low magnification
|-

|}

== Single particles ==

=== Automatic particle picking ===

{|

| Paper
| [[1982VanHeel_Detection]]
| Detection of particles in micrographs
|-

| Paper
| [[2001Nicholson_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2001Zhu_Filaments]]
| Automatic identification of filaments in micrographs
|-

| Paper
| [[2004Sigworth_Detection]]
| Classical detection theory and the cryo-EM particle selection problem
|-

| Paper
| [[2004Volkmann_ParticlePicking]]
| An approach to automated particle picking from electron micrographs based on reduced representation templates
|-

| Paper
| [[2004Wong_ParticlePicking]]
| Model-based particle picking for cryo-electron microscopy
|-

| Paper
| [[2004Zhu_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2007Chen_Signature]]
| Automatic particle picking program: Signature
|-

| Paper
| [[2007Woolford_SwarmPS]]
| Automatic particle picking with several criteria, implemented in EMAN Boxer
|-

| Paper
| [[2009Sorzano_MachineLearning]]
| Automatic particle picking based on machine learning of rotational invariants
|-

| Paper
| [[2011Arbelaez_Comparison]]
| Evaluation of the performance of software for automated particle-boxing
|-

| Paper
| [[2013Abrishami_MachineLearning]]
| A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs
|-

| Paper
| [[2013Hauer_2013]]
| Automatic tilt pair detection in Random Conical Tilt
|-

| Paper
| [[2013Shatsky_ParticlePicking]]
| Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Langlois_ParticlePicking]]
| Automatic particle picking
|-

| Paper
| [[2016Vilas_AutomaticTilt]]
| Automatic identification of image pairs in untilted-tilted micrograph pairs
|-

|}

=== 2D Preprocessing ===

{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast enhancement through DPR
|-

| Paper
| [[2004Sorzano_Normalization]]
| Normalization procedures and their statistical properties.
|-

| Paper
| [[2006Sorzano_Denoising]]
| Strong denoising in wavelet space
|-

| Conference
| [[2009Sorzano_Downsampling]]
| Differences between the different downsampling schemes
|-

| Paper
| [[2012Brilot_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Campbell_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Zhao_Denoising]]
| Denoising using an invariant Fourier-Bessel eigenspace
|-

| Paper
| [[2013Norousi_Screening]]
| Screening particles to identify outliers
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu_Movies]]
| Drift correction for movies considering dark field
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Scheres_Movies]]
| Beam induced motion correction
|-

| Paper
| [[2015Abrishami_Movies]]
| Alignment of direct detection device micrographs
|-

| Paper
| [[2015Grant_Anisotropic]]
| Automatic estimation and correction of anisotropic magnification
|-

| Paper
| [[2015Grant_OptimalExposure]]
| Filter movies according to the radiation damage
|-

| Paper
| [[2015Rubinstein_Alignment]]
| Frame alignment at the level of particle
|-

| Paper
| [[2015Spear_DoseCompensation]]
| Effect of dose compensation on resolution
|-

| Paper
| [[2015Zhao_AnisotropicMagnification]]
| Correction of anisotropic magnification
|-

| Conference
| [[2016Bajic_Denoising]]
| Denoising and deconvolution of micrographs
|-

| Paper
| [[2016Jensen_RemovalVesicles]]
| Removal of vesicles in membrane proteins
|-

| Paper
| [[2016Bhamre_Denoising]]
| Denoising by 2D covariance estimation
|-

| Paper
| [[2017McLeod_Zorro]]
| Movie alignment by Zorro
|-

|}

=== 2D Alignment ===

{|

| Paper
| [[1981Frank_Averaging]]
| 2D averaging and phase residual
|-

| Paper
| [[1982Saxton_Averaging]]
| 2D averaging using correlation
|-

| Paper
| [[1998Sigworth_ML2D]]
| Maximum likelihood alignment in 2D
|-

| Paper
| [[2003Cong_FRM2D]]
| Fast Rotational Matching in 2D
|-

| Paper
| [[2005Cong_FRM2D]]
| Fast Rotational Matching in 2D introduced in a 3D Alignment algorithm
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

|}

=== 2D Classification and clustering ===

{|

| Paper
| [[1981VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[1984VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2011Singer_DiffusionMaps]]
| Classification in 2D based on graph analysis of the projections
|-

| Paper
| [[2012Yang_ISAC]]
| Iterative Stable Alignment and clustering
|-

| Paper
| [[2014Sorzano_Outlier]]
| Outlier detection in 2D classifications.
|-

| Paper
| [[2014Zhao_Aspire]]
| Fast classification based on rotational invariants and vector diffusion maps
|-

| Paper
| [[2015Huang_Robust]]
| Robust w-estimators of 2D classes
|-

| Paper
| [[2016Reboul_Stochastic]]
| Stochastic Hill Climbing for calculating 2D classes
|-

| Conference
| [[2017Bhamre_Mahalanobis]]
| 2D classification using Mahalanobis distance
|-

|}

=== 3D Alignment ===

{|

| Paper
| [[1980Kam_AutoCorrelation]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[1986Goncharov_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1987VanHeel_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1988Provencher_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Vogel_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1990Gelfand_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Goncharov_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Harauz_Quaternions]]
| Use of quaternions to represent rotations
|-

| Paper
| [[1994Penczek_Real]]
| Angular assignment using projection matching in real space
|-

| Paper
| [[1994Radermacher_Radon]]
| Angular assignment in Radon space
|-

| Paper
| [[1996Penczek_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[2003Rosenthal_DPR]]
| Angular assignment using DPR
|-

| Paper
| [[2004Sorzano_Wavelet]]
| Angular assignment in the wavelet space.
|-

| Paper
| [[2005Jonic_Splines]]
| Angular assignment in Fourier space using spline interpolation.
|-

| Paper
| [[2005Yang_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[2006Ogura_SimulatedAnnealing]]
| Angular asignment by simulated annealing
|-

| Paper
| [[2007Grigorieff_Continuous]]
| Continuous angular assignment in Fourier space
|-

| Paper
| [[2010Jaitly_Bayesian]]
| Angular assignment by a Bayesian method and annealing
|-

| Paper
| [[2010Sanz_Random]]
| Random model method
|-

| Paper
| [[2010Singer_Voting]]
| Detecting consistent common lines by voting (reference free)
|-

| Paper
| [[2011Singer_SDP]]
| Angular assignment by semidefinite programming and eigenvectors (reference free)
|-

| Paper
| [[2012Giannakis_Scattering]]
| Construction of an initial volume, reference free, by graph analysis of the projections
|-

| Paper
| [[2012Shkolnisky_Sync]]
| Angular assignment by synchronization of rotations (reference free)
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Wang_LUD]]
| Angular assignment by least unsquared deviations (reference free)
|-

| Paper
| [[2014Vargas_RANSAC]]
| Initial model using RANSAC (reference free)
|-

| Paper
| [[2015Joubert_Pseudoatoms]]
| Initial model based on pseudo-atoms
|-

| Paper
| [[2015Singer_Kam]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[2015Sorzano_Significant]]
| Statistical approach to the initial volume estimation (reconstruct significant)
|-

| Conference
| [[2016Michels_Heterogeneous]]
| Initial volume in the presence of heterogeneity
|-

| Paper
| [[2016Cossio_BayesianGPU]]
| GPU implementation of the Bayesian 3D reconstruction approach
|-

|}

=== 3D Reconstruction ===
{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1986Harauz_FBP]]
| Exact filters for Filtered Back Projection
|-

| Chapter
| [[1992Radermacher_WBP]]
| Exact filters for Weighted Back Projection
|-

| Paper
| [[1997Zhu_RecCTF]]
| 3D Reconstruction (SIRT like) and simultaneous CTF correction
|-

| Paper
| [[1998Boisset_Uneven]]
| Artifacts in SIRT and WBP under uneven angular distributions
|-

| Paper
| [[1998Marabini_ART]]
| Algebraic Reconstruction Technique with blobs (Xmipp)
|-

| Paper
| [[2001Sorzano_Uneven]]
| Free parameter selection under uneven angular distributions
|-

| Paper
| [[2005Sorzano_Parameters]]
| Free parameter selection for optimizing multiple tasks
|-

| Paper
| [[2008Sorzano_Constraints]]
| Mass, surface, positivity and symmetry constraints for real-space algorithms
|-

| Paper
| [[2009Bilbao_ParallelART]]
| Efficient parallelization of ART
|-

| Paper
| [[2011Li_GradientFlow]]
| Regularized 3D Reconstruction by Gradient Flow
|-

| Paper
| [[2011Vonesch_Wavelets]]
| Fast wavelet-based 3D reconstruction
|-

| Paper
| [[2012Gopinath_ShapeRegularization]]
| Regularized 3D Reconstruction by Shape information
|-

| Paper
| [[2012Kucukelbir_adaptiveBasis]]
| 3D reconstruction in an adaptive basis promoting sparsity
|-

| Paper
| [[2012Sindelar_NoiseReduction]]
| Optimal noise reduction in 3D reconstructions
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Lyumkis_Optimod]]
| Construction of initial volumes with Optimod
|-

| Paper
| [[2013Wang FIRM]]
| Fast 3D reconstruction in Fourier domain
|-

| Paper
| [[2014Kunz_SART_OS]]
| Simultaneous ART with OS
|-

| Paper
| [[2015Abrishami_Fourier]]
| 3D Reconstruction in Fourier space
|-

| Paper
| [[2015Dvornek_SubspaceEM]]
| Fast Maximum a posteriori
|-

| Paper
| [[2015Moriya_Bayesian]]
| Bayesian approach to suppress limited angular artifacts
|-

| Paper
| [[2015Xu_GeometricFlow]]
| Multi-scale geometric flow
|-

| Arxiv
| [[2016Ye_Cohomology]]
| Cohomology properties of 3D reconstruction
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

|}

=== 3D Heterogeneity ===

{|

| Paper
| [[2004White_Size]]
| Heterogeneity classification of differently sized images
|-

| Paper
| [[2006Penczek_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Scheres_ML3D]]
| Maximum Likelihood alignment and classification in 3D
|-

| Paper
| [[2009Spahn_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2010Elmlund_AbInitio]]
| Solving the initial volume problem with multiple conformations
|-

| Paper
| [[2010Shatsky_MultiVariate]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2012Scheres_Bayesian]]
| A Bayesian view on cryo-EM structure determination
|-

| Paper
| [[2012Zheng_Covariance]]
| Estimation of the volume covariance
|-

| Paper
| [[2013Wang_MLVariance]]
| Maximum Likelihood estimate of the map variance
|-

| Paper
| [[2013Lyumkis D_FREALIGN]]
| Likelihood-based classification of cryo-EM images using FREALIGN.
|-

| Paper
| [[2014Jin_NMA]]
| Continuous heterogeneity through Normal Mode Analysis
|-

| Paper
| [[2014Dashti_Brownian]]
| Continuous heterogeneity through Brownian trajectories
|-

| Paper
| [[2014Chen_Migration]]
| Particle migration analysis in 3D classification
|-

| Paper
| [[2015Anden_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Bai_Focused]]
| Focused classification
|-

| Paper
| [[2015Katsevich_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Klaholz_MRA]]
| Multivariate Statistical Analysis of Jackknife and Bootstrapping on random subsets
|-

| Paper
| [[2015Liao_Covariance]]
| Estimation of the 3D covariance from 2D projections
|-

| Paper
| [[2015Tagare_Direct]]
| Direct reconstruction of PCA components
|-

| Paper
| [[2016Gong_Mechanical]]
| Mechanical model for macromolecules
|-

| Paper
| [[2016Rawson_Movement]]
| Movement and flexibility
|-

| Paper
| [[2016Sorzano_StructMap]]
| Sorting a discrete set of conformational states
|-

| Paper
| [[2016Sorzano_Strain]]
| Calculate local stretches, strains and rotations from two conformational states
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

|}

=== Validation ===

{|

| Paper
| [[2008Stagg_TestBed]]
| Effect of voltage, dosis, number of particles and Euler jumps on resolution
|-

| Paper
| [[2011Henderson]]
| Tilt Validation
|-

| Paper
| [[2011Read]]
| Validation of PDBs
|-

| Paper
| [[2012Henderson]]
| EM Map Validation
|-

| Paper
| [[2013Cossio_Bayesian]]
| EM Map Validation in a probabilistic setting
|-

| Paper
| [[2013Chen_NoiseSubstitution]]
| Noise substitution at high resolution for measuring overfitting
|-

| Paper
| [[2014Russo_StatisticalSignificance]]
| EM Map Validation through the statistical significance of the tilt-pair angular assignment
|-

| Paper
| [[2014Stagg_Reslog]]
| EM Map Validation through the resolution evolution with the number of particles
|-

| Paper
| [[2014Wasilewski_Tilt]]
| Web implementation of the tilt pair validation
|-

| Paper
| [[2015Heymann_Alignability]]
| EM Map Validation through the resolution of reconstructions from particles and noise
|-

| Paper
| [[2015Oliveira_FreqLimited]]
| Comparison of gold standard and frequency limited optimization
|-

| Paper
| [[2015Wriggers_Secondary]]
| Validation by secondary structure
|-

| Paper
| [[2016Kim_SAXS]]
| Comparison of SAXS data and EM projections
|-

| Paper
| [[2016Rosenthal_Review]]
| Review of validation methods
|-

| Paper
| [[2016Vargas_Alignability]]
| Validation by studying the tendency of an angular assignment to cluster in the projection space
|-

| Paper
| [[2017Monroe_PDBRefinement]]
| Validation by comparison to a refined PDB
|-

|}

=== Resolution ===

{|

| Paper
| [[1986Harauz_FBP]]
| Fourier Shell Correlation
|-

| Paper
| [[1987Unser_SSNR]]
| 2D Spectral Signal to Noise Ratio
|-

| Paper
| [[2002Penczek_SSNR]]
| 3D Spectral Signal to Noise Ratio for Fourier based algorithms
|-

| Paper
| [[2003Rosenthal_DPR]]
| Review of the FSC and establishment of a new threshold
|-

| Paper
| [[2005Unser_SSNR]]
| 3D Spectral Signal to Noise Ratio for any kind of algorithms
|-

| Paper
| [[2005VanHeel_FSC]]
| Establishment of a new threshold for FSC
|-

| Paper
| [[2007Sousa_AbInitio]]
| Resolution measurement on neighbour Fourier voxels
|-

| Paper
| [[2014Kucukelbir_Local]]
| Quantifying the local resolution of cryo-EM density maps
|-

| Paper
| [[2016Pintilie_Probabilistic]]
| Probabilistic models and resolution
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Statistical properties of resolution measures defined in Fourier space
|-

|}

=== Sharpening of high resolution information ===
{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast restoration and map sharpening
|-

| Paper
| [[2008Fernandez_Bfactor]]
| Bfactor determination and restoration
|-

| Paper
| [[2013Fiddy_SaxtonAlgorithm]]
| Phase retrieval or extension
|-

| Paper
| [[2014Kishchenko_SphericalDeconvolution]]
| Spherical deconvolution
|-

| Paper
| [[2015Spiegel_VISDEM]]
| Visualization improvement by the use of pseudoatomic profiles
|-

| Paper
| [[2016Jonic_Pseudoatoms]]
| Approximation with pseudoatoms
|-

| Paper
| [[2016Jonic_Denoising]]
| Denoising and high-frequency boosting by pseudoatom approximation
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[1982Schiske_Correction]]
| CTF correction for tilted objects
|-

| Paper
| [[1988Toyoshima_Model]]
| CTF estimation
|-

| Paper
| [[1995Frank_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1996Skoglund_MaxEnt]]
| CTF correction with Maximum Entropy
|-

| Paper
| [[1996Zhou_Model]]
| CTF model and user interface for manual fitting
|-

| Paper
| [[1997Fernandez_AR]]
| PSD estimation using periodogram averaging and AR models
|-

| Paper
| [[1997Penczek_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1997Stark_Deconvolution]]
| CTF correction using deconvolution
|-

| Paper
| [[1997Zhu_RecCTF]]
| CTF correction and reconstruction
|-

| Paper
| [[2000DeRosier_EwaldCorrection]]
| CTF correction considering the Ewald sphere
|-

| Paper
| [[2000Jensen_TiltedCorrection]]
| CTF correction considering tilt in backprojection
|-

| Paper
| [[2001Saad_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Huang_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Mindell_CTFTILT]]
| CTF estimation for tilted micrographs
|-

| Paper
| [[2003Sander_MSA]]
| CTF estimation through MSA classification of PSDs
|-

| Paper
| [[2003Velazquez_ARMA]]
| PSD and CTF estimation using ARMA models
|-

| Paper
| [[2004Sorzano_IDR]]
| CTF restoration and reconstruction with Iterative Data Refinement
|-

| Conference
| [[2004Wan_CTF]]
| Spatially variant CTF
|-

| Paper
| [[2004Zubelli_Chahine]]
| CTF restoration and reconstruction with Chahine's multiplicative method
|-

| Conference
| [[2005Dubowy_SpaceVariant]]
| CTF correction when this is space variant
|-

| Paper
| [[2005Mallick_ACE]]
| CTF estimation
|-

| Paper
| [[2006Wolf_Ewald]]
| CTF correction considering Ewald sphere
|-

| Paper
| [[2007Jonic_EnhancedPSD]]
| PSD enhancement for better identification of Thon rings; Vitreous ice diffracts in Thon rings
|-

| Paper
| [[2007Philippsen_Model]]
| CTF Model for tilted specimens
|-

| Paper
| [[2007Sorzano_CTF]]
| CTF estimation using enhanced PSDs
|-

| Paper
| [[2009Sorzano_Sensitivity]]
| Error sensitivity of the CTF models, non-uniqueness of the CTF parameters
|-

| Paper
| [[2010Jiang2010_CTFCorrection]]
| Amplitude correction method
|-

| Paper
| [[2010Kasantsev_CTFCorrection]]
| Mathematical foundations of Kornberg and Jensen method
|-

| Paper
| [[2010Leong_CTFCorrection]]
| Correction for spatially variant CTF
|-

| Paper
| [[2011Glaeser_Coma]]
| The effect of coma at high-resolution
|-

| Paper
| [[2011Mariani_Tilted]]
| CTF simulation and correction of tilted specimens
|-

| Paper
| [[2011Sindelar_Wiener]]
| CTF correction using a modified version of Wiener filter
|-

| Paper
| [[2011Voortman_Tilted]]
| CTF correction for tilted specimen
|-

| Paper
| [[2012Voortman_VaryingCTF]]
| Correcting a spatially varying CTF
|-

| Paper
| [[2013Vargas_FastDef]]
| Fast defocus
|-

| Paper
| [[2015Rohou_CTFFind4]]
| CTF Find 4
|-

| Paper
| [[2015Sheth_CTFquality]]
| Visualization and quality assessment of CTF
|-

| Paper
| [[2016Zhang_GCTF]]
| gCTF
|-

|}

=== Segmentation ===

{|

| Paper
| [[2006Baker_segmentation]]
| Segmentation of molecular subunits
|-

|}

=== Fitting and docking ===

{|

| Paper
| [[1999Volkmann_Fitting]]
| Fitting in real space
|-

| Paper
| [[2001Baker_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2001Jones_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2003Kovacs_FRM3D]]
| Fast Rotational Alignment of two EM maps
|-

| Paper
| [[2004Tama_NMA1]]
| Flexible fitting with Normal Modes (I)
|-

| Paper
| [[2004Tama_NMA2]]
| Flexible fitting with Normal Modes (II)
|-

| Paper
| [[2005Velazquez_Superfamilies]]
| Recognition of the superfamily folding in medium-high resolution volumes
|-

| Paper
| [[2007DeVries_Haddock]]
| Docking with Haddock 2.0
|-

| Paper
| [[2007Kleywegt_QualityControl]]
| Quality control and validation of fitting
|-

| Paper
| [[2012Biswas_Secondary]]
| Secondary structure determination in EM volumes
|-

| Paper
| [[2012Velazquez_Constraints]]
| Multicomponent fitting by using constraints from other information sources
|-

| Paper
| [[2013Chapman MS_Atomicmodeling]]
| Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters
|-

| Paper
| [[2013Esquivel_Modelling]]
| Review on modelling (secondary structure, fitting, ...)
|-

| Paper
| [[2013Lopez_Imodfit]]
| Fitting based on vibrational analysis
|-

| Paper
| [[2013Nogales_3DEMLoupe]]
| Normal Mode Analysis of reconstructed volumes
|-

| Paper
| [[2014AlNasr_Secondary]]
| Identification of secondary structure elements in EM volumes
|-

| Paper
| [[2014Politis_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Rey_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Villa_Review]]
| Review of atomic fitting into EM volumes
|-

| Paper
| [[2015Barad_EMRinger]]
| Validation of hybrid models
|-

| Paper
| [[2015Bettadapura_PF2Fit]]
| Fast rigid fitting of PDBs into EM maps
|-

| Paper
| [[2015Carrillo_CapsidMaps]]
| Analysis of virus capsids using Google Maps
|-

| Paper
| [[2015Schroeder_Hybrid]]
| Review on model building
|-

| Paper
| [[2015Tamo_Dynamics]]
| Dynamics in integrative modeling
|-

| Paper
| [[2015Sorzano_AtomsToVoxels]]
| Accurate conversion of an atomic model into a voxel density volume
|-

| Paper
| [[2016Joseph_Evolution]]
| Evolutionary constraints for the fitting of atomic models into density maps
|-

| Paper
| [[2016Segura_3Diana]]
| Validation of hybrid models
|-

| Paper
| [[2016Singharoy_MDFF]]
| Construction of hybrid models driven by EM density and molecular dynamics
|-

| Paper
| [[2016Wang_Rosetta]]
| Construction of hybrid models driven by EM density using Rosetta
|-

| Paper
| [[2017Hryc_WeightedAtoms]]
| Construction of hybrid models by locally weighting the different atoms
|-

|}

=== Books and reviews ===

{|

| Book
| [[1980Herman_Tomography]]
| General book on tomography
|-

| Book
| [[1988Kak_Tomography]]
| General book on tomography
|-

| Paper
| [[2000Tao_Review]]
| Review of single particles
|-

| Paper
| [[2000VanHeel_Review]]
| Review of single particles
|-

| Paper
| [[2002Frank_Review]]
| Review of single particles
|-

| Paper
| [[2002Schmid_Review]]
| Review of single particles
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2004Subramaniam_Review]]
| Review of single particles
|-

| Paper
| [[2005Steven_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_book]]
| Book covering all aspects of electron microscopy of single particles
|-

| Paper
| [[2006Sorzano_Review]]
| Review of optimization problems in electron microscopy
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems in Electron Tomography
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2008Mueller_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2008Taylor_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2010DeRosier_Review]]
| Personal account of how 3DEM developed in the early days
|-

| Chapter
| [[2012Sorzano_Review]]
| Review of single particle analysis using Xmipp
|-

| Chapter
| [[2012Devaux_Protocol]]
| Protocols for performing single particle analysis
|-

| Paper
| [[2014Bai_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Carazo_Review]]
| Review of the reconstruction process
|-

| Paper
| [[2015Cheng_Review]]
| A primer to Single Particle Cryo-EM
|-

| Paper
| [[2015Cheng_Reviewb]]
| Single Particle Cryo-EM at crystallographic resolution
|-

| Paper
| [[2015Elmlund_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Henderson_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Nogales_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Schroeder_Review]]
| Review of advances in the electron microscope
|-

| Paper
| [[2015Wu_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Carroni_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Egelman_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Eisenstein_CryoEM]]
| News feature on the Method of the Year
|-

| Paper
| [[2016FernandezLeiro_Review]]
| Review of EM
|-

| Paper
| [[2016Glaeser_HowGood]]
| How good can cryo-EM become?
|-

| Paper
| [[2016Jonic_PseudoAtoms]]
| Review of the applications of the use of pseudoatoms in EM
|-

| Chapter
| [[2016Mio_Review]]
| Overview of the process to obtain EM reconstructions
|-

| Paper
| [[2016Jonic_Review]]
| A review of computational ways to handle heterogeneity
|-

| Paper
| [[2016Nogales_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Subramaniam_Review]]
| Why cryo-EM is now suitable for crystallographic journals
|-

| Paper
| [[2016Vinothkumar_Review]]
| Historical review and current limitations
|-

| Paper
| [[2017Frank_Review]]
| Historical review of EM
|-

| Paper
| [[2017Jonic_Review]]
| Review of computational methods to analyze conformational variability
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Review of statistical properties of resolution measures defined in Fourier space
|-
|}

=== Software ===

{|

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[1999Lutdke_Eman]]
| Eman
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Baldwin_AngularTransformations]]
| The Transform Class in SPARX and EMAN2
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Grigorieff_Frealign]]
| Frealign
|-

| Paper
| [[2008Scheres_XmippProtocols]]
| Xmipp Protocols
|-

| Paper
| [[2008Shaikh_SpiderProtocols]]
| Spider Protocols
|-

| Paper
| [[2012Wriggers_SitusConventions]]
| Conventions and workflows in Situs
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2015Cianfrocco_Cloud]]
| Software execution in the cloud
|-

| Paper
| [[2015Cheng_MRC2014]]
| Extensions to MRC file format
|-

| Paper
| [[2013DeLaRosa_Scipion]]
| Scipion
|-

| Paper
| [[2016Scheres_Relion]]
| Tutorial on the use of Relion
|-

| Paper
| [[2016Grigorieff_Frealign]]
| Tutorial on the use of Frealign
|-

|}

== Electron tomography ==

=== Image preprocessing ===

{|

| Paper
| [[2015Yan_thickness]]
| Determination of thickness, tilt and electron mean free path
|-

|}

=== Image alignment ===

{|

| Paper
| [[1982Guckenberger_commonOrigin]]
| Determination of a common origin in the micrographs of titl series in three-dimensional electron microscopy
|-

| Paper
| [[1992Lawrence_leastSquares]]
| Least squares solution of the alignment problem
|-

| Paper
| [[1995Penczek_dual]]
| Dual tilt alignment
|-

| Paper
| [[1996Owen_alignmentQuality]]
| Automatic alignment without fiducial markers and evaluation of alignment quality
|-

| Paper
| [[1998Grimm_normalization]]
| Discussion of several gray level normalization methods for electron tomography
|-

| Paper
| [[2001Brandt_Automatic1]]
| Automatic alignment without fiducial markers
|-

| Paper
| [[2001Brandt_Automatic2]]
| Automatic alignment with fiducial markers
|-

| Paper
| [[2006Winkler_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2006Castano_alignment]]
| Alignment with non-perpendicularity
|-

| Paper
| [[2007Castano_alignment]]
| Fiducial-less alignment of cryo-sections
|-

| Paper
| [[2009Sorzano_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2010Cantele_dualAlignment]]
| Alignment of dual series
|-

| Paper
| [[2014Tomonaga_Automatic]]
| Automatic alignment of tilt series using the projection themselves
|-

| Paper
| [[2014Han_Automatic]]
| Automatic alignment of tilt series using SIFT features
|-

| Paper
| [[2015Han_Automatic]]
| Automatic alignment of tilt series using fiducials
|-

| Paper
| [[2017Mastronarde_Automatic]]
| Automatic alignment and reconstruction of tilt series in IMOD
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[2003Winkler_CTF]]
| Focus gradient correction in electron tomography
|-

| Paper
| [[2006Fernandez_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Zanetti_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Xiong_CTF]]
| CTF determination and correction for low dose tomographic tilt series
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2017Kunz_3DCTF]]
| 3D CTF Correction
|-

|}

=== 3D reconstruction ===

{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1992Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[1997Marabini_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2002Fernandez_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2007Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[2008Fernandez_CARP]]
| Component Averaged Row Projections (CARP)
|-

| Paper
| [[2012Herman General Superiorization]]
| Superiorization: an optimization heuristic for medical physics
|-

| Paper
| [[2012Zhang_IPET_FETR]]
| IPET and FETR, a reconstruction algorithm for single molecule tomography
|-

| Paper
| [[2013Goris_SIRT_TV_DART]]
| Combination of SIRT, Total Variation and Discrete ART to reconstruct and segment at the same time
|-

| Paper
| [[2013Briegel A_Challenge]]
| The challenge of determining handedness in electron tomography and the use of DNA origami gold nanoparticle helices as molecular standards
|-

| Paper
| [[2013Messaoudi_EnergyFiltered]]
| 3D Reconstruction of Energy-Filtered TEM
|-

| Paper
| [[2016Deng_ICON]]
| 3D Reconstruction with missing information restoration
|-

| Paper
| [[2016Guay_Compressed]]
| 3D Reconstruction using compressed sensing
|-

|}

=== Noise reduction ===
{|

| Paper
| [[2001Frangakis_NAD]]
| Noise reduction with Nonlinear Anisotropic Diffusion
|-

| Paper
| [[2003Fernandez_AND]]
| Anisotropic nonlinear diffusion for electron tomography
|-

| Paper
| [[2003Jiang_Bilateral]]
| Bilateral denoising filter in electron microscopy
|-

| Paper
| [[2005Fernandez_AND]]
| Anisotropic nonlinear denoising in electron tomography
|-

| Paper
| [[2007Heide_median]]
| Iterative median filtering in electron tomography
|-

| Paper
| [[2007Fernandez_autAND]]
| Anisotropic nonlinear diffusion with automated parameter tuning
|-

| Paper
| [[2009Fernandez_Beltrami]]
| Nonlinear filtering based on Beltrami flow
|-

| Paper
| [[2010Bilbao_MeanShift]]
| Mean Shift Filtering
|-

| Paper
| [[2014Kovacik_wedgeArtefacts]]
| Removal of wedge artefacts
|-

| Paper
| [[2014Maiorca_beadArtefacts]]
| Removal of gold bead artefacts
|-

|}

=== Segmentation ===

{|

| Paper
| [[2002Frangakis_Eigenanalysis]]
| Segmentation using eigenvector analysis.
|-

| Paper
| [[2002Volkmann_Watershed]]
| Segmentation using watershed transform.
|-

| Paper
| [[2003Bajaj_BoundarySegmentation]]
| Segmentation based on fast marching.
|-

| Paper
| [[2005Cyrklaff_Thresholding]]
| Segmentation using optimal thresholding.
|-

| Paper
| [[2007Lebbink_TemplateMatching]]
| Segmentation using template matching.
|-

| Paper
| [[2007Sandberg_OrientationFields]]
| Segmentation using orientation fields.
|-

| Paper
| [[2007Sandberg_SegmentationReview]]
| Review on segmentation in electron tomography.
|-

| Paper
| [[2008Garduno_FuzzySegmentation]]
| Segmentation using fuzzy set theory principles.
|-

| Paper
| [[2009Lebbink_TemplateMatching2]]
| Segmentation using template matching.
|-

| Paper
| [[2012RubbiyaAli_EdgeDetection]]
| Parameter-Free Segmentation of Macromolecular Structures.
|-

| Conference
| [[2015Xu_TemplateMatching]]
| Detection of macromolecular complexes with a reduced representation of the templates.
|-

|}

=== Resolution ===
{|

| Paper
| [[2005Cardone_Resolution]]
| Resolution criterion for electron tomography
|-

| Chapter
| [[2007Penczek_Resolution]]
| Review of resolution criteria for electron tomography
|-

| Paper
| [[2015Diebolder_ConicalFSC]]
| Conical Fourier Shell Correlation
|-

|}

=== Subtomogram analysis ===

{|

| Paper
| [[2000Bohm_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2002Frangakis_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2006Nickell_Review]]
| Review of macromolecule finding by template matching (Visual Proteomics)
|-

| Paper
| [[2007Best_Review]]
| Review of Localization of Protein Complexes by Pattern Recognition
|-

| Paper
| [[2007Forster_Review]]
| Review of structure determination by subtomogram averaging
|-

| Paper
| [[2008Forster_Classification]]
| Classification of subtomograms using constrained correlation
|-

| Paper
| [[2008Bartesaghi_Classification]]
| Classification and averaging of subtomograms
|-

| Paper
| [[2008Schmid_Averaging]]
| Alignment and averaging of subtomograms
|-

| Paper
| [[2010Amat_Averaging]]
| Alignment and averaging of subtomograms exploiting thresholding in Fourier space
|-

| Paper
| [[2013Chen_Averaging]]
| Fast alignment of subtomograms using spherical harmonics
|-

| Paper
| [[2013Kuybeda_Averaging]]
| Alignment and averaging of subtomograms using the nuclear norm of the cluster
|-

| Paper
| [[2013Shatsky_Averaging]]
| Alignment and averaging of subtomograms with constrained cross-correlation
|-

| Paper
| [[2014Chen_Autofocus]]
| Subtomogram averaging and classification with special attention to differences
|-

| Paper
| [[2014Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2014Voortman_LimitingFactors]]
| Limiting factors of subtomogram averaging
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2015Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2016Bharat_Relion]]
| Subtomogram averaging with Relion
|-

| Paper
| [[2016Song_MatrixNorm]]
| Matrix norm minimization for tomographic reconstruction and alignment
|-

| Paper
| [[2017Castano_ParticlePicking]]
| Particle picking in tomograms for subtomogram averaging
|-

|}

=== Single particle tomography ===

{|

| Paper
| [[2012Bartesaghi_Constrained]]
| 3D reconstruction by imposing geometrical constraints
|-

| Paper
| [[2015Galaz_SingleParticleTomography]]
| Set of tools for Single Particle Tomography in EMAN2
|-

| Paper
| [[2016Galaz_SingleParticleTomography]]
| Alignment algorithms and CTF correction
|-

|}

=== Books and reviews ===

{|

| Paper
| [[2000Baumeister_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Koster_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Sali_Review]]
| Review of electron tomography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2005Lucic_Review]]
| Review of electron tomography
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_TomoBook]]
| Electron Tomography
|-

| Book
| [[2007McIntosh_Book]]
| Cellular Electron Microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2012Kudryashev_Review]]
| Review of subtomogram averaging
|-

| Paper
| [[2016Beck_Review]]
| Review of molecular sociology
|-

|}

=== Software ===

{|

| Paper
| [[1996Kremer_IMOD]]
| IMOD
|-

| Paper
| [[1996Chen_Priism/IVE]]
| Priism/IVE
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2005Nickell_TOM]]
| TOM Toolbox
|-

| Paper
| [[2007Messaoudi_TomoJ]]
| TomoJ
|-

| Paper
| [[2008Heymann_BsoftTomo]]
| Bsoft
|-

| Paper
| [[2015Ding_CaltechTomography]]
| Caltech tomography database
|-

| Paper
| [[2015Noble_AppionProtomo]]
| Batch fiducial-less tilt-series alignment in Appion using Protomo
|-

| Paper
| [[2015vanAarle_Astra]]
| ASTRA Toolbox
|-

|}

== 2D Crystals ==

=== 2D Preprocessing ===

{|

| Paper
| [[1986Henderson_Processing]]
| General 2D processing
|-

| Paper
| [[2000He_PhaseAlignment]]
| Phase consistency and Alignment
|-

| Paper
| [[2006Gil_Unbending]]
| Crystal unbending
|-

|}

=== Classification ===
{|

| Paper
| [[1988Frank_Classification]]
| MSA and classification in electron crystallography
|-

| Paper
| [[1996Fernandez_SOM]]
| Classification based on self organizing maps
|-

| Paper
| [[1998Sherman_MSA]]
| Classification based on MSA
|-

|}
=== 3D Reconstruction ===

{|

| Paper
| [[1985Wang_Solvent]]
| Solvent flattening
|-

| Paper
| [[1990Henderson_Processing]]
| General 3D processing
|-

| Paper
| [[2004Marabini_ART]]
| Algebraic Reconstruction Technique with blobs for crystals (Xmipp)
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1998Walz_Review]]
| Review of 2D crystallography
|-

| Paper
| [[1999Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Ellis_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of single particles, electron tomography and crystallography
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Gipson_2dx]]
| 2dx
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Philippsen_IPLT]]
| IPLT
|-

|}

== 3D Crystals - MicroED ==

=== Sample Preparation ===
{|
| Paper
| [[2016Shi_Preparation]]
| Sample Preparation
|}
=== Data Collection ===
{|
| Paper
| [[2014Nannenga_CR]]
| Continuous rotation

|}
=== Data Processing ===
{|

| Paper
| [[2011Wisedchaisri_PhaseExtension]]
| Fragment-based phase extension
|-

| Paper
| [[2015Hattne_Processing]]
| Data Processing
|-

| Paper
| [[2016Hattne_Correction]]
| Image correction
|}

=== Software ===
{|

| Paper
| [[2014Iadanza_Processing]]
| Data Processing of still diffraction data
|}

=== Books and Reviews ===
{|
| Paper
| [[2014Nannenga_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Liu_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Rodriguez_Review ]]
| Review of MicroED
|-

|}

== Helical particles ==

=== Filament corrections ===

{|

| Paper
| [[1986Egelman_Curved]]
| Algorithm for correcting curved filaments
|-

| Paper
| [[1988Bluemke_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2006Wang_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2016Yang_Flexible]]
| Algorithm for correcting filaments with flexible subunits
|-

|}

=== Reconstruction ===

{|

| Paper
| [[1952Cochran_Fourier]]
| Fourier Bessel transform of filamentous structures
|-

| Paper
| [[1958Klug_Fourier]]
| Fourier Bessel decomposition of the projection images
|-

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2005Wang_Iterative]]
| Iterative Fourier-Bessel algorithm
|-

| Paper
| [[2007Egelman_Iterative]]
| Iterative real-space algorithm
|-

| Paper
| [[2013Desfosses_Spring]]
| Helical processing with Spring
|-

| Paper
| [[2015Zhang_seam]]
| Workflow for the detection of the lattice seam
|-

| Paper
| [[2016Rohou_Frealix]]
| Helical processing with Frealix
|-

|}

=== Validation ===

{|

| Paper
| [[2014Egelman_ambiguity]]
| How to detect incorrect models
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Carragher_Phoelix]]
| Phoelix
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Owen_Brandeis]]
| Brandeis
|-

|}

== Icosahedral particles ==

=== Reconstruction ===

{|

| Paper
| [[1970Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1971Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1996Fuller_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1997Thuman_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

|}

=== Classification ===

{|

| Paper
| [[2005Scheres_Virus]]
| Classification of virus capsids in real space
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1999Baker_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[1999Conway_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2000Thuman_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Lee_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Navaza_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2006Grunewald_Review]]
| Review of reconstruction of icosahedral viruses
|-

|}

=== Software ===

{|

| Paper
| [[1996Baker_EMPFT]]
| EMPFT
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2013Morin_Sliz SBGrid]]
| SBGrid presentation for eLife
|-

|}

== Databases ==

{|

| Paper
| [[2003Boutselakis_EMSD]]
| EMSD database
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2011Kim_CDDB]]
| Conformational Dynamics Data Bank
|-

| Paper
| [[2011Lawson_EMDB]]
| Electron Microscopy Data Bank
|-

| Paper
| [[2016Iudin_EMPIAR]]
| EMPIAR raw data database
|-

| Paper
| [[2016Patwhardan_EMDB]]
| EMDB, PDB, ...
|-

| Paper
| [[2017Shao_PDBQuality]]
| Quality metrics in PDB
|-

| Blog
| http://www.mybiosoftware.com
| Huge list of bioinformatics programs (many of them structural bioinformatics)
|-

|}

== Relationship to other structural information sources ==

{|

| Paper
| [[2000Engel_AFM]]
| Review of Atomic Force Microscopy
|-

| Paper
| [[2001Dimmeler_AFM]]
| Constraints from Atomic Force Microscopy
|-

| Paper
| [[2003Mobus_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_Review]]
| Review on correlative microscopy
|-

| Paper
| [[2005Boudier_EFTETJ]]
| Software for Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2005Vestergaard_SAXS]]
| Example of comparison of 3DEM and Small-angle X-ray scattering
|-

| Paper
| [[2007Hamada_SAXS]]
| Constraints from Small-angle X-ray scattering
|-

| Paper
| [[2013Xu_FRET]]
| EM+FRET
|-

|}

== X-ray tomography ==

{|

| Paper
| [[2012Oton_ImageFormation]]
| Image formation model in X-ray cell microscopy
|-

|}

== Mathematical tools necessary ==

== People developing methods ==
Please, add yourself to this list (due to privacy reasons, please, do not add anyone else to the list without his/her explicit consent). Sort by first name alphabetical order.

[http://biocomp.cnb.csic.es/~coss Carlos Oscar S. Sorzano]: CSIC, Madrid, Spain 

[http://www.curie.fr/recherche/themes/detail_equipe.cfm/lang/_fr/id_equipe/241.htm Cédric Messaoudi]: Institute Curie, Paris, France 

[http://scholar.google.es/citations?user=_jNYGScAAAAJ&hl=en Javier Vargas]:[mailto:jvargas@cnb.csic.es mail]: CSIC, Madrid, Spain 

[http://scholar.google.es/citations?hl=es&user=g2ZJPIYAAAAJ Joaquín Otón]: CSIC, Madrid, Spain 

[mailto:jrbcast@gmail.com José Román Bilbao-Castro]: UAL, Almería, Spain; CSIC, Madrid, Spain 

[José Miguel de la Rosa Trevín]: Biocomputing Unit CNB-CSIC, Madrid, Spain 

[http://cryoem.janelia.org Tamir Gonen]: [mailto:gonent@janelia.hhmi.org mail]: Howard Hughes Medical Institute, Ashburn, VA, USA 

[mailto:vabrishami@cnb.csic.es Vahid Abrishami]: CSIC, Madrid, Spain 

== 3DEM sites ==
* [http://3dem.ucsd.edu/ 3DEM web site]

* [http://en.wikibooks.org/wiki/Software_Tools_For_Molecular_Microscopy Software tools for molecular microscopy]

* [http://www.emdatabank.org/ The Electron Microscopy Data Bank (EMDB)]

* [http://ccdb.ucsd.edu The Cell Centered Database (CCDB)]

* [http://conventions.cnb.csic.es The geometrical software conventions web page ]

== Editing useful links ==

* [http://www.mediawiki.org/wiki/Help:Formatting Text formatting in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Links Adding links in Mediawiki]
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* [http://www.mediawiki.org/wiki/Help:Tables Making tables in Mediawiki]

2017Mastronarde Automatic

2017-05-11T20:49:09Z

CoSS: Created page with "== Citation == Mastronarde, D. N. & Held, S. R. Automated tilt series alignment and tomographic reconstruction in IMOD. Journal of structural biology, 2017, 197, 102-113 ==..."

== Citation ==

Mastronarde, D. N. & Held, S. R. Automated tilt series alignment and tomographic reconstruction in IMOD. Journal of structural biology, 2017, 197, 102-113

== Abstract ==

Automated tomographic reconstruction is now possible in the IMOD software package, including the merging of tomograms taken around two orthogonal axes. Several developments enable the production of high-quality tomograms. When using fiducial markers for alignment, the markers to be tracked through the series are chosen automatically; if there is an excess of markers available, a well-distributed subset is selected that is most likely to track well. Marker positions are refined by applying an edge-enhancing Sobel filter, which results in a 20% improvement in alignment error for plastic-embedded samples and 10% for frozen-hydrated samples. Robust fitting, in which outlying points are given less or no weight in computing the fitting error, is used to obtain an alignment solution, so that aberrant points from the automated tracking can have little effect on the alignment. When merging two dual-axis tomograms, the alignment between them is refined from correlations between local patches; a measure of structure was developed so that patches with insufficient structure to give accurate correlations can now be excluded automatically. We have also developed a script for running all steps in the reconstruction process with a flexible mechanism for setting parameters, and we have added a user interface for batch processing of tilt series to the Etomo program in IMOD. Batch processing is fully compatible with interactive processing and can increase efficiency even when the automation is not fully successful, because users can focus their effort on the steps that require manual intervention.

== Keywords ==

== Links ==

http://www.sciencedirect.com/science/article/pii/S1047847716301526

== Related software ==

== Related methods ==

== Comments ==

Main Page

2017-05-11T20:48:20Z

CoSS: /* Image alignment */

== Presentation ==

This web page is intended to be an extensive repository of three-dimensional electron microscopy (3DEM) methods. The advantages of having such a repository are

* You know which are the relevant articles in a particular topic, therefore, paper introductions, reviews, etc. are easier to write and you make sure you will cite all the related articles.
* You will be sure that your paper has more chances of being cited.
* You can add whatever information you find relevant to your method, external links, links to other papers, etc.
* You can link your method to a web page providing the corresponding software, so you know people can use your algorithms.
* You can use the Wiki search capabilities to locate relevant articles even if they are not at the topic you are looking at.
* As a community we will "reconstruct" our history.
* You can select the "watch" option above to receive notifications in case of further changes in the Main Page.

Developing image processing methods for 3DEM is not "[[well-paid]]" in terms of citations and impact factor. However, it is crucial for the advance of the field. Gathering methodological papers in a portal will help to increase the recognition of the field.

Please:

* Add your articles at the right place (you can add a single article in several topics if it is relevant to all of them). The easiest way to add an article is by editing the corresponding topic in the main page, adding your entry, then save the main page. Click on the red link that appears on your new entry, copy and paste the Wiki following code, add the information of your article

== Citation ==

== Abstract ==

== Keywords ==

== Links ==

== Related software ==

== Related methods ==

== Comments ==

* Maintain the information of each article as complete as possible.
* Sort articles by years and authors.
* Be respectful to other people's work.

== How to subscribe to this page ==

You may subscribe to this page so that you will be notified every time someone adds a new method. To do so, you have to register in the page, and edit your preferences ("my preferences"). Be sure that you have activated the option "E-mail me when a page on my watchlist is changed". Finally, click on the "Watch" tab at the top of this page.

You may subscribe to changes on this page on the mailing list 3demmethods@cnb.csic.es. To send a new method to this mail list just send a mail to 3demmethods@cnb.csic.es

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== Electron microscopy images ==

=== Online courses ===

CALTECH: http://cryo-em-course.caltech.edu/

MRC: ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/EM-course/

CNB-CSIC: http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/MadridJan2014EM

Workshop on Computational methods for CryoEM: https://www.youtube.com/watch?v=XdKO1iaPP8o

Workshop on Management of large CryoEM facilities: https://www.youtube.com/watch?v=as4seOPszL0

Icknield Course on Model Building and Refinement for High Resolution EM Maps: http://www.ccpem.ac.uk/training/icknield_2017/icknield_2017.php

=== Image formation ===

{|

| Paper
| [[1971Erickson_CTF]]
| CTF model
|-

| Paper
| [[1971Glaeser_Damage]]
| Radiation damage
|-

| Chapter
| [[1971Hanszen_CTF]]
| Image formation model
|-

| Paper
| [[1971Thon_Model]]
| CTF model
|-

| Paper
| [[1975Unwin_Imaging]]
| Radiation dose
|-

| Paper
| [[1977Wade_Model]]
| CTF model
|-

| Paper
| [[1978Wade_Model]]
| CTF model
|-

| Paper
| [[1979Hayward_Radiation]]
| Radiation damage
|-

| Paper
| [[1984Cohen_Validity]]
| Validity of the CTF model at high frequencies
|-

| Paper
| [[1988Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[1992Wade_Model]]
| CTF model
|-

| Paper
| [[1993Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2004Egerton_Damage]]
| Radiation damage
|-

| Paper
| [[2004Sorzano_Normalization]]
| Background noise is Gaussian
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2009Baxter_NoiseCharacterization]]
| Characterization of the different noise sources in cryo-EM
|-

| Paper
| [[2010Baker_Damage]]
| Radiation damage dependence on resolution
|-

| Paper
| [[2010Bammes_Damage]]
| Radiation damage dependence on temperature
|-

| Paper
| [[2010Gomez_Multislice]]
| Simulation of the multi slice model
|-

| Paper
| [[2010Zewail_FourDimensional]]
| Review on the use of ultrafast EM
|-

| Paper
| [[2011Bammes_CCD]]
| Performance of CCD cameras
|-

| Paper
| [[2011Glaeser_Coma]]
| Image formation model including coma
|-

| Paper
| [[2011Milazzo_DirectDetectors]]
| Evaluation of Direct Detectors
|-

| Paper
| [[2011Rullgard_ImageSimulation]]
| Accurate simulation of EM images
|-

| Paper
| [[2011Zhang LimitingFactors]]
| Limiting factor for atomic resolution in EM
|-

| Paper
| [[2012Bammes_DirectDetection]]
| Performance of Direct detectors
|-

| Paper
| [[2012Campbell_MotionCorrection]]
| Beam induced motion correction and direct detectors
|-

| Paper
| [[2012Shang_HydrationLayer]]
| Simulation of PDB volumes explicitly considering the hydration layer
|-

| Paper
| [[2013Egerton_RadiationDamage]]
| Review of TEM radiation damage and experimental ways of reducing it
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu H_Noisemodels]]
| Noise models and cryo-EM drift correction with a direct-electron camera
|-

| Paper
| [[2013Li X K2 noisemodels]]
| Influence of electron dose rate on electron counting images recorded with the K2 camera
|-

| Paper
| [[2013Vulovic_CTFApproximations]]
| When to use the different approximations performed so that a projection with linear CTF is valid
|-

| Thesis
| [[2013Vulovic_ImageFormation]]
| Ph.D. Thesis on the image formation in cryo-EM
|-

| Paper
| [[2014Danev_PhasePlate]]
| Volta potential phase plate
|-

| Paper
| [[2015Chiu_K2]]
| Characterization of K2
|-

| Paper
| [[2015Hawkes_AberrationCorrection]]
| Historical account of the development of lens corrections
|-

| Paper
| [[2015Koeck_Quadratic]]
| Limitations of the linear approximation and use of the quadratic terms
|-

| Paper
| [[2015Kuijper_FEI]]
| Description of the FEI Falcons
|-

| Paper
| [[2015Lobato_MULTEM]]
| Simulation of multislice diffraction
|-

| Paper
| [[2015McMullan_AmorphousIce]]
| Beam induced movement is caused by Brownian motion
|-

| Paper
| [[2016Koeck_ADF]]
| Simulations of Annular Dark Field TEM
|-

| Paper
| [[2017Mishyna_DNARadiation]]
| Review of radiation damage on DNA
|-

|}

=== Collection geometry ===

{|

| Chapter
| [[1980Hoppe_Wedge]]
| Missing wedge
|-

| Paper
| [[1987Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1995Penczek_Dual]]
| Dual axis tomography
|-

| Paper
| [[1997Mastronarde_Dual]]
| Dual axis tomography
|-

| Paper
| [[2003Ludtke_FocusPairs]]
| Focus pairs for single particles
|-

| Paper
| [[2005Lanzavecchia_Conical]]
| Conical tomography
|-

| Paper
| [[2005Zampighi_Conical]]
| Conical tomography
|-

| Paper
| [[2006Leschziner_OT]]
| Orthogonal Tilt
|-

| Paper
| [[2006Messaoudi_Multiple]]
| Multiple axis tomography
|-

| Paper
| [[2012Kudryashev_FocusPairs]]
| Focus pairs tomography
|-

| Paper
| [[2014Hovden_TiltFocus]]
| Combining tilt series with focus series
|-

| Paper
| [[2015Sorzano_RandomConicalTilt]]
| General formulation of Random Conical Tilt
|-

| Paper
| [[2017Hagen_DoseTomography]]
| Dose optimization for subtomogram averaging
|-

|}

=== Sample preparation ===

{|

| Paper
| [[1982Dubochet_Sample]]
| Vitreous ice
|-

| Paper
| [[1986Lepault_Sample]]
| Fast freezing
|-

| Paper
| [[1995Dubochet_Sample]]
| High-pressure freezing
|-

| Paper
| [[1995VanMarle_Sample]]
| Sample damages in resin
|-

| Paper
| [[1998Adrian_Sample]]
| Cryo negative staining
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2002Hsieh_Sample]]
| Cryofixation
|-

| Paper
| [[2004AlAmoudi_Sample]]
| CEMOVIS
|-

| Paper
| [[2008Studer_Sample]]
| Review on high pressure freezing
|-

| Paper
| [[2009Pierson_Sample]]
| Review on sample preparation for electron tomography
|-

| Paper
| [[2010Zhang_NegativeStaining]]
| Negative staining for small protein imaging
|-

| Paper
| [[2012Zhang_PositiveStaining]]
| Positive staining
|-

| Paper
| [[2014Rames_NegativeStaining]]
| Optimized negative staining
|-

| Paper
| [[2014Russo_GoldGrids]]
| Gold grids for single particles
|-

| Paper
| [[2015Cabra_Sample]]
| Review on sample preparation for single particles with videos
|-

| Paper
| [[2016Passmore_Review]]
| Tutorial chapter on sample preparation
|-

| Paper
| [[2016Razinkov_Vitrification]]
| New vitrification method
|-

| Paper
| [[2016Takizawa_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2016Thompson_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2017Peitsch_Sample]]
| iMEM: Isolation of Plasma Membrane for Cryoelectron Microscopy
|-

| Paper
| [[2017Schaffer_FocusedIonBeam]]
| Focused Ion Beam sample preparation for membrane proteins
|-

|}

=== Automated data collection ===

{|

| Paper
| [[1992Dierksen_Automatic]]
| Automated data collection
|-

| Paper
| [[1992Koster_Automatic]]
| Automated data collection
|-

| Paper
| [[1996Fung_Automatic]]
| Automated data collection for tomography
|-

| Paper
| [[2001Zhang_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2003Ziese_Automatic]]
| Automated autofocusing
|-

| Paper
| [[2004Potter_Automatic]]
| Automated sample loading
|-

| Paper
| [[2004Zheng_Automatic]]
| Automated data collection
|-

| Paper
| [[2005Lei_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2005Suloway_Automatic]]
| Automated data collection: Leginon
|-

| Paper
| [[2007Yoshioka_RCT]]
| Automated Random Conical Tilt
|-

| Paper
| [[2011Korinek_TOM2]]
| Automated acquisition with TOM2
|-

| Paper
| [[2015Li_UCSFImage]]
| Automated acquisition with UCSFImage
|-

| Paper
| [[2016Gil_Fuzzy]]
| Real time decisions during acquisition with neuro-fuzzy method
|-

| Paper
| [[2016Liu_TiltControl]]
| Accurate control of the tilt angle for electron tomography
|-

| Paper
| [[2016Vargas_FoilHole]]
| Determination of image quality at low magnification
|-

|}

== Single particles ==

=== Automatic particle picking ===

{|

| Paper
| [[1982VanHeel_Detection]]
| Detection of particles in micrographs
|-

| Paper
| [[2001Nicholson_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2001Zhu_Filaments]]
| Automatic identification of filaments in micrographs
|-

| Paper
| [[2004Sigworth_Detection]]
| Classical detection theory and the cryo-EM particle selection problem
|-

| Paper
| [[2004Volkmann_ParticlePicking]]
| An approach to automated particle picking from electron micrographs based on reduced representation templates
|-

| Paper
| [[2004Wong_ParticlePicking]]
| Model-based particle picking for cryo-electron microscopy
|-

| Paper
| [[2004Zhu_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2007Chen_Signature]]
| Automatic particle picking program: Signature
|-

| Paper
| [[2007Woolford_SwarmPS]]
| Automatic particle picking with several criteria, implemented in EMAN Boxer
|-

| Paper
| [[2009Sorzano_MachineLearning]]
| Automatic particle picking based on machine learning of rotational invariants
|-

| Paper
| [[2011Arbelaez_Comparison]]
| Evaluation of the performance of software for automated particle-boxing
|-

| Paper
| [[2013Abrishami_MachineLearning]]
| A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs
|-

| Paper
| [[2013Hauer_2013]]
| Automatic tilt pair detection in Random Conical Tilt
|-

| Paper
| [[2013Shatsky_ParticlePicking]]
| Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Langlois_ParticlePicking]]
| Automatic particle picking
|-

| Paper
| [[2016Vilas_AutomaticTilt]]
| Automatic identification of image pairs in untilted-tilted micrograph pairs
|-

|}

=== 2D Preprocessing ===

{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast enhancement through DPR
|-

| Paper
| [[2004Sorzano_Normalization]]
| Normalization procedures and their statistical properties.
|-

| Paper
| [[2006Sorzano_Denoising]]
| Strong denoising in wavelet space
|-

| Conference
| [[2009Sorzano_Downsampling]]
| Differences between the different downsampling schemes
|-

| Paper
| [[2012Brilot_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Campbell_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Zhao_Denoising]]
| Denoising using an invariant Fourier-Bessel eigenspace
|-

| Paper
| [[2013Norousi_Screening]]
| Screening particles to identify outliers
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu_Movies]]
| Drift correction for movies considering dark field
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Scheres_Movies]]
| Beam induced motion correction
|-

| Paper
| [[2015Abrishami_Movies]]
| Alignment of direct detection device micrographs
|-

| Paper
| [[2015Grant_Anisotropic]]
| Automatic estimation and correction of anisotropic magnification
|-

| Paper
| [[2015Grant_OptimalExposure]]
| Filter movies according to the radiation damage
|-

| Paper
| [[2015Rubinstein_Alignment]]
| Frame alignment at the level of particle
|-

| Paper
| [[2015Spear_DoseCompensation]]
| Effect of dose compensation on resolution
|-

| Paper
| [[2015Zhao_AnisotropicMagnification]]
| Correction of anisotropic magnification
|-

| Conference
| [[2016Bajic_Denoising]]
| Denoising and deconvolution of micrographs
|-

| Paper
| [[2016Jensen_RemovalVesicles]]
| Removal of vesicles in membrane proteins
|-

| Paper
| [[2016Bhamre_Denoising]]
| Denoising by 2D covariance estimation
|-

| Paper
| [[2017McLeod_Zorro]]
| Movie alignment by Zorro
|-

|}

=== 2D Alignment ===

{|

| Paper
| [[1981Frank_Averaging]]
| 2D averaging and phase residual
|-

| Paper
| [[1982Saxton_Averaging]]
| 2D averaging using correlation
|-

| Paper
| [[1998Sigworth_ML2D]]
| Maximum likelihood alignment in 2D
|-

| Paper
| [[2003Cong_FRM2D]]
| Fast Rotational Matching in 2D
|-

| Paper
| [[2005Cong_FRM2D]]
| Fast Rotational Matching in 2D introduced in a 3D Alignment algorithm
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

|}

=== 2D Classification and clustering ===

{|

| Paper
| [[1981VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[1984VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2011Singer_DiffusionMaps]]
| Classification in 2D based on graph analysis of the projections
|-

| Paper
| [[2012Yang_ISAC]]
| Iterative Stable Alignment and clustering
|-

| Paper
| [[2014Sorzano_Outlier]]
| Outlier detection in 2D classifications.
|-

| Paper
| [[2014Zhao_Aspire]]
| Fast classification based on rotational invariants and vector diffusion maps
|-

| Paper
| [[2015Huang_Robust]]
| Robust w-estimators of 2D classes
|-

| Paper
| [[2016Reboul_Stochastic]]
| Stochastic Hill Climbing for calculating 2D classes
|-

| Conference
| [[2017Bhamre_Mahalanobis]]
| 2D classification using Mahalanobis distance
|-

|}

=== 3D Alignment ===

{|

| Paper
| [[1980Kam_AutoCorrelation]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[1986Goncharov_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1987VanHeel_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1988Provencher_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Vogel_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1990Gelfand_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Goncharov_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Harauz_Quaternions]]
| Use of quaternions to represent rotations
|-

| Paper
| [[1994Penczek_Real]]
| Angular assignment using projection matching in real space
|-

| Paper
| [[1994Radermacher_Radon]]
| Angular assignment in Radon space
|-

| Paper
| [[1996Penczek_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[2003Rosenthal_DPR]]
| Angular assignment using DPR
|-

| Paper
| [[2004Sorzano_Wavelet]]
| Angular assignment in the wavelet space.
|-

| Paper
| [[2005Jonic_Splines]]
| Angular assignment in Fourier space using spline interpolation.
|-

| Paper
| [[2005Yang_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[2006Ogura_SimulatedAnnealing]]
| Angular asignment by simulated annealing
|-

| Paper
| [[2007Grigorieff_Continuous]]
| Continuous angular assignment in Fourier space
|-

| Paper
| [[2010Jaitly_Bayesian]]
| Angular assignment by a Bayesian method and annealing
|-

| Paper
| [[2010Sanz_Random]]
| Random model method
|-

| Paper
| [[2010Singer_Voting]]
| Detecting consistent common lines by voting (reference free)
|-

| Paper
| [[2011Singer_SDP]]
| Angular assignment by semidefinite programming and eigenvectors (reference free)
|-

| Paper
| [[2012Giannakis_Scattering]]
| Construction of an initial volume, reference free, by graph analysis of the projections
|-

| Paper
| [[2012Shkolnisky_Sync]]
| Angular assignment by synchronization of rotations (reference free)
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Wang_LUD]]
| Angular assignment by least unsquared deviations (reference free)
|-

| Paper
| [[2014Vargas_RANSAC]]
| Initial model using RANSAC (reference free)
|-

| Paper
| [[2015Joubert_Pseudoatoms]]
| Initial model based on pseudo-atoms
|-

| Paper
| [[2015Singer_Kam]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[2015Sorzano_Significant]]
| Statistical approach to the initial volume estimation (reconstruct significant)
|-

| Conference
| [[2016Michels_Heterogeneous]]
| Initial volume in the presence of heterogeneity
|-

| Paper
| [[2016Cossio_BayesianGPU]]
| GPU implementation of the Bayesian 3D reconstruction approach
|-

|}

=== 3D Reconstruction ===
{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1986Harauz_FBP]]
| Exact filters for Filtered Back Projection
|-

| Chapter
| [[1992Radermacher_WBP]]
| Exact filters for Weighted Back Projection
|-

| Paper
| [[1997Zhu_RecCTF]]
| 3D Reconstruction (SIRT like) and simultaneous CTF correction
|-

| Paper
| [[1998Boisset_Uneven]]
| Artifacts in SIRT and WBP under uneven angular distributions
|-

| Paper
| [[1998Marabini_ART]]
| Algebraic Reconstruction Technique with blobs (Xmipp)
|-

| Paper
| [[2001Sorzano_Uneven]]
| Free parameter selection under uneven angular distributions
|-

| Paper
| [[2005Sorzano_Parameters]]
| Free parameter selection for optimizing multiple tasks
|-

| Paper
| [[2008Sorzano_Constraints]]
| Mass, surface, positivity and symmetry constraints for real-space algorithms
|-

| Paper
| [[2009Bilbao_ParallelART]]
| Efficient parallelization of ART
|-

| Paper
| [[2011Li_GradientFlow]]
| Regularized 3D Reconstruction by Gradient Flow
|-

| Paper
| [[2011Vonesch_Wavelets]]
| Fast wavelet-based 3D reconstruction
|-

| Paper
| [[2012Gopinath_ShapeRegularization]]
| Regularized 3D Reconstruction by Shape information
|-

| Paper
| [[2012Kucukelbir_adaptiveBasis]]
| 3D reconstruction in an adaptive basis promoting sparsity
|-

| Paper
| [[2012Sindelar_NoiseReduction]]
| Optimal noise reduction in 3D reconstructions
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Lyumkis_Optimod]]
| Construction of initial volumes with Optimod
|-

| Paper
| [[2013Wang FIRM]]
| Fast 3D reconstruction in Fourier domain
|-

| Paper
| [[2014Kunz_SART_OS]]
| Simultaneous ART with OS
|-

| Paper
| [[2015Abrishami_Fourier]]
| 3D Reconstruction in Fourier space
|-

| Paper
| [[2015Dvornek_SubspaceEM]]
| Fast Maximum a posteriori
|-

| Paper
| [[2015Moriya_Bayesian]]
| Bayesian approach to suppress limited angular artifacts
|-

| Paper
| [[2015Xu_GeometricFlow]]
| Multi-scale geometric flow
|-

| Arxiv
| [[2016Ye_Cohomology]]
| Cohomology properties of 3D reconstruction
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

|}

=== 3D Heterogeneity ===

{|

| Paper
| [[2004White_Size]]
| Heterogeneity classification of differently sized images
|-

| Paper
| [[2006Penczek_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Scheres_ML3D]]
| Maximum Likelihood alignment and classification in 3D
|-

| Paper
| [[2009Spahn_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2010Elmlund_AbInitio]]
| Solving the initial volume problem with multiple conformations
|-

| Paper
| [[2010Shatsky_MultiVariate]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2012Scheres_Bayesian]]
| A Bayesian view on cryo-EM structure determination
|-

| Paper
| [[2012Zheng_Covariance]]
| Estimation of the volume covariance
|-

| Paper
| [[2013Wang_MLVariance]]
| Maximum Likelihood estimate of the map variance
|-

| Paper
| [[2013Lyumkis D_FREALIGN]]
| Likelihood-based classification of cryo-EM images using FREALIGN.
|-

| Paper
| [[2014Jin_NMA]]
| Continuous heterogeneity through Normal Mode Analysis
|-

| Paper
| [[2014Dashti_Brownian]]
| Continuous heterogeneity through Brownian trajectories
|-

| Paper
| [[2014Chen_Migration]]
| Particle migration analysis in 3D classification
|-

| Paper
| [[2015Anden_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Bai_Focused]]
| Focused classification
|-

| Paper
| [[2015Katsevich_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Klaholz_MRA]]
| Multivariate Statistical Analysis of Jackknife and Bootstrapping on random subsets
|-

| Paper
| [[2015Liao_Covariance]]
| Estimation of the 3D covariance from 2D projections
|-

| Paper
| [[2015Tagare_Direct]]
| Direct reconstruction of PCA components
|-

| Paper
| [[2016Gong_Mechanical]]
| Mechanical model for macromolecules
|-

| Paper
| [[2016Rawson_Movement]]
| Movement and flexibility
|-

| Paper
| [[2016Sorzano_StructMap]]
| Sorting a discrete set of conformational states
|-

| Paper
| [[2016Sorzano_Strain]]
| Calculate local stretches, strains and rotations from two conformational states
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

|}

=== Validation ===

{|

| Paper
| [[2008Stagg_TestBed]]
| Effect of voltage, dosis, number of particles and Euler jumps on resolution
|-

| Paper
| [[2011Henderson]]
| Tilt Validation
|-

| Paper
| [[2011Read]]
| Validation of PDBs
|-

| Paper
| [[2012Henderson]]
| EM Map Validation
|-

| Paper
| [[2013Cossio_Bayesian]]
| EM Map Validation in a probabilistic setting
|-

| Paper
| [[2013Chen_NoiseSubstitution]]
| Noise substitution at high resolution for measuring overfitting
|-

| Paper
| [[2014Russo_StatisticalSignificance]]
| EM Map Validation through the statistical significance of the tilt-pair angular assignment
|-

| Paper
| [[2014Stagg_Reslog]]
| EM Map Validation through the resolution evolution with the number of particles
|-

| Paper
| [[2014Wasilewski_Tilt]]
| Web implementation of the tilt pair validation
|-

| Paper
| [[2015Heymann_Alignability]]
| EM Map Validation through the resolution of reconstructions from particles and noise
|-

| Paper
| [[2015Oliveira_FreqLimited]]
| Comparison of gold standard and frequency limited optimization
|-

| Paper
| [[2015Wriggers_Secondary]]
| Validation by secondary structure
|-

| Paper
| [[2016Kim_SAXS]]
| Comparison of SAXS data and EM projections
|-

| Paper
| [[2016Rosenthal_Review]]
| Review of validation methods
|-

| Paper
| [[2016Vargas_Alignability]]
| Validation by studying the tendency of an angular assignment to cluster in the projection space
|-

| Paper
| [[2017Monroe_PDBRefinement]]
| Validation by comparison to a refined PDB
|-

|}

=== Resolution ===

{|

| Paper
| [[1986Harauz_FBP]]
| Fourier Shell Correlation
|-

| Paper
| [[1987Unser_SSNR]]
| 2D Spectral Signal to Noise Ratio
|-

| Paper
| [[2002Penczek_SSNR]]
| 3D Spectral Signal to Noise Ratio for Fourier based algorithms
|-

| Paper
| [[2003Rosenthal_DPR]]
| Review of the FSC and establishment of a new threshold
|-

| Paper
| [[2005Unser_SSNR]]
| 3D Spectral Signal to Noise Ratio for any kind of algorithms
|-

| Paper
| [[2005VanHeel_FSC]]
| Establishment of a new threshold for FSC
|-

| Paper
| [[2007Sousa_AbInitio]]
| Resolution measurement on neighbour Fourier voxels
|-

| Paper
| [[2014Kucukelbir_Local]]
| Quantifying the local resolution of cryo-EM density maps
|-

| Paper
| [[2016Pintilie_Probabilistic]]
| Probabilistic models and resolution
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Statistical properties of resolution measures defined in Fourier space
|-

|}

=== Sharpening of high resolution information ===
{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast restoration and map sharpening
|-

| Paper
| [[2008Fernandez_Bfactor]]
| Bfactor determination and restoration
|-

| Paper
| [[2013Fiddy_SaxtonAlgorithm]]
| Phase retrieval or extension
|-

| Paper
| [[2014Kishchenko_SphericalDeconvolution]]
| Spherical deconvolution
|-

| Paper
| [[2015Spiegel_VISDEM]]
| Visualization improvement by the use of pseudoatomic profiles
|-

| Paper
| [[2016Jonic_Pseudoatoms]]
| Approximation with pseudoatoms
|-

| Paper
| [[2016Jonic_Denoising]]
| Denoising and high-frequency boosting by pseudoatom approximation
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[1982Schiske_Correction]]
| CTF correction for tilted objects
|-

| Paper
| [[1988Toyoshima_Model]]
| CTF estimation
|-

| Paper
| [[1995Frank_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1996Skoglund_MaxEnt]]
| CTF correction with Maximum Entropy
|-

| Paper
| [[1996Zhou_Model]]
| CTF model and user interface for manual fitting
|-

| Paper
| [[1997Fernandez_AR]]
| PSD estimation using periodogram averaging and AR models
|-

| Paper
| [[1997Penczek_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1997Stark_Deconvolution]]
| CTF correction using deconvolution
|-

| Paper
| [[1997Zhu_RecCTF]]
| CTF correction and reconstruction
|-

| Paper
| [[2000DeRosier_EwaldCorrection]]
| CTF correction considering the Ewald sphere
|-

| Paper
| [[2000Jensen_TiltedCorrection]]
| CTF correction considering tilt in backprojection
|-

| Paper
| [[2001Saad_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Huang_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Mindell_CTFTILT]]
| CTF estimation for tilted micrographs
|-

| Paper
| [[2003Sander_MSA]]
| CTF estimation through MSA classification of PSDs
|-

| Paper
| [[2003Velazquez_ARMA]]
| PSD and CTF estimation using ARMA models
|-

| Paper
| [[2004Sorzano_IDR]]
| CTF restoration and reconstruction with Iterative Data Refinement
|-

| Conference
| [[2004Wan_CTF]]
| Spatially variant CTF
|-

| Paper
| [[2004Zubelli_Chahine]]
| CTF restoration and reconstruction with Chahine's multiplicative method
|-

| Conference
| [[2005Dubowy_SpaceVariant]]
| CTF correction when this is space variant
|-

| Paper
| [[2005Mallick_ACE]]
| CTF estimation
|-

| Paper
| [[2006Wolf_Ewald]]
| CTF correction considering Ewald sphere
|-

| Paper
| [[2007Jonic_EnhancedPSD]]
| PSD enhancement for better identification of Thon rings; Vitreous ice diffracts in Thon rings
|-

| Paper
| [[2007Philippsen_Model]]
| CTF Model for tilted specimens
|-

| Paper
| [[2007Sorzano_CTF]]
| CTF estimation using enhanced PSDs
|-

| Paper
| [[2009Sorzano_Sensitivity]]
| Error sensitivity of the CTF models, non-uniqueness of the CTF parameters
|-

| Paper
| [[2010Jiang2010_CTFCorrection]]
| Amplitude correction method
|-

| Paper
| [[2010Kasantsev_CTFCorrection]]
| Mathematical foundations of Kornberg and Jensen method
|-

| Paper
| [[2010Leong_CTFCorrection]]
| Correction for spatially variant CTF
|-

| Paper
| [[2011Glaeser_Coma]]
| The effect of coma at high-resolution
|-

| Paper
| [[2011Mariani_Tilted]]
| CTF simulation and correction of tilted specimens
|-

| Paper
| [[2011Sindelar_Wiener]]
| CTF correction using a modified version of Wiener filter
|-

| Paper
| [[2011Voortman_Tilted]]
| CTF correction for tilted specimen
|-

| Paper
| [[2012Voortman_VaryingCTF]]
| Correcting a spatially varying CTF
|-

| Paper
| [[2013Vargas_FastDef]]
| Fast defocus
|-

| Paper
| [[2015Rohou_CTFFind4]]
| CTF Find 4
|-

| Paper
| [[2015Sheth_CTFquality]]
| Visualization and quality assessment of CTF
|-

| Paper
| [[2016Zhang_GCTF]]
| gCTF
|-

|}

=== Segmentation ===

{|

| Paper
| [[2006Baker_segmentation]]
| Segmentation of molecular subunits
|-

|}

=== Fitting and docking ===

{|

| Paper
| [[1999Volkmann_Fitting]]
| Fitting in real space
|-

| Paper
| [[2001Baker_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2001Jones_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2003Kovacs_FRM3D]]
| Fast Rotational Alignment of two EM maps
|-

| Paper
| [[2004Tama_NMA1]]
| Flexible fitting with Normal Modes (I)
|-

| Paper
| [[2004Tama_NMA2]]
| Flexible fitting with Normal Modes (II)
|-

| Paper
| [[2005Velazquez_Superfamilies]]
| Recognition of the superfamily folding in medium-high resolution volumes
|-

| Paper
| [[2007DeVries_Haddock]]
| Docking with Haddock 2.0
|-

| Paper
| [[2007Kleywegt_QualityControl]]
| Quality control and validation of fitting
|-

| Paper
| [[2012Biswas_Secondary]]
| Secondary structure determination in EM volumes
|-

| Paper
| [[2012Velazquez_Constraints]]
| Multicomponent fitting by using constraints from other information sources
|-

| Paper
| [[2013Chapman MS_Atomicmodeling]]
| Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters
|-

| Paper
| [[2013Esquivel_Modelling]]
| Review on modelling (secondary structure, fitting, ...)
|-

| Paper
| [[2013Lopez_Imodfit]]
| Fitting based on vibrational analysis
|-

| Paper
| [[2013Nogales_3DEMLoupe]]
| Normal Mode Analysis of reconstructed volumes
|-

| Paper
| [[2014AlNasr_Secondary]]
| Identification of secondary structure elements in EM volumes
|-

| Paper
| [[2014Politis_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Rey_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Villa_Review]]
| Review of atomic fitting into EM volumes
|-

| Paper
| [[2015Barad_EMRinger]]
| Validation of hybrid models
|-

| Paper
| [[2015Bettadapura_PF2Fit]]
| Fast rigid fitting of PDBs into EM maps
|-

| Paper
| [[2015Carrillo_CapsidMaps]]
| Analysis of virus capsids using Google Maps
|-

| Paper
| [[2015Schroeder_Hybrid]]
| Review on model building
|-

| Paper
| [[2015Tamo_Dynamics]]
| Dynamics in integrative modeling
|-

| Paper
| [[2015Sorzano_AtomsToVoxels]]
| Accurate conversion of an atomic model into a voxel density volume
|-

| Paper
| [[2016Joseph_Evolution]]
| Evolutionary constraints for the fitting of atomic models into density maps
|-

| Paper
| [[2016Segura_3Diana]]
| Validation of hybrid models
|-

| Paper
| [[2016Singharoy_MDFF]]
| Construction of hybrid models driven by EM density and molecular dynamics
|-

| Paper
| [[2016Wang_Rosetta]]
| Construction of hybrid models driven by EM density using Rosetta
|-

| Paper
| [[2017Hryc_WeightedAtoms]]
| Construction of hybrid models by locally weighting the different atoms
|-

|}

=== Books and reviews ===

{|

| Book
| [[1980Herman_Tomography]]
| General book on tomography
|-

| Book
| [[1988Kak_Tomography]]
| General book on tomography
|-

| Paper
| [[2000Tao_Review]]
| Review of single particles
|-

| Paper
| [[2000VanHeel_Review]]
| Review of single particles
|-

| Paper
| [[2002Frank_Review]]
| Review of single particles
|-

| Paper
| [[2002Schmid_Review]]
| Review of single particles
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2004Subramaniam_Review]]
| Review of single particles
|-

| Paper
| [[2005Steven_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_book]]
| Book covering all aspects of electron microscopy of single particles
|-

| Paper
| [[2006Sorzano_Review]]
| Review of optimization problems in electron microscopy
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems in Electron Tomography
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2008Mueller_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2008Taylor_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2010DeRosier_Review]]
| Personal account of how 3DEM developed in the early days
|-

| Chapter
| [[2012Sorzano_Review]]
| Review of single particle analysis using Xmipp
|-

| Chapter
| [[2012Devaux_Protocol]]
| Protocols for performing single particle analysis
|-

| Paper
| [[2014Bai_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Carazo_Review]]
| Review of the reconstruction process
|-

| Paper
| [[2015Cheng_Review]]
| A primer to Single Particle Cryo-EM
|-

| Paper
| [[2015Cheng_Reviewb]]
| Single Particle Cryo-EM at crystallographic resolution
|-

| Paper
| [[2015Elmlund_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Henderson_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Nogales_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Schroeder_Review]]
| Review of advances in the electron microscope
|-

| Paper
| [[2015Wu_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Carroni_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Egelman_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Eisenstein_CryoEM]]
| News feature on the Method of the Year
|-

| Paper
| [[2016FernandezLeiro_Review]]
| Review of EM
|-

| Paper
| [[2016Glaeser_HowGood]]
| How good can cryo-EM become?
|-

| Paper
| [[2016Jonic_PseudoAtoms]]
| Review of the applications of the use of pseudoatoms in EM
|-

| Chapter
| [[2016Mio_Review]]
| Overview of the process to obtain EM reconstructions
|-

| Paper
| [[2016Jonic_Review]]
| A review of computational ways to handle heterogeneity
|-

| Paper
| [[2016Nogales_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Subramaniam_Review]]
| Why cryo-EM is now suitable for crystallographic journals
|-

| Paper
| [[2016Vinothkumar_Review]]
| Historical review and current limitations
|-

| Paper
| [[2017Frank_Review]]
| Historical review of EM
|-

| Paper
| [[2017Jonic_Review]]
| Review of computational methods to analyze conformational variability
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Review of statistical properties of resolution measures defined in Fourier space
|-
|}

=== Software ===

{|

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[1999Lutdke_Eman]]
| Eman
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Baldwin_AngularTransformations]]
| The Transform Class in SPARX and EMAN2
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Grigorieff_Frealign]]
| Frealign
|-

| Paper
| [[2008Scheres_XmippProtocols]]
| Xmipp Protocols
|-

| Paper
| [[2008Shaikh_SpiderProtocols]]
| Spider Protocols
|-

| Paper
| [[2012Wriggers_SitusConventions]]
| Conventions and workflows in Situs
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2015Cianfrocco_Cloud]]
| Software execution in the cloud
|-

| Paper
| [[2015Cheng_MRC2014]]
| Extensions to MRC file format
|-

| Paper
| [[2013DeLaRosa_Scipion]]
| Scipion
|-

| Paper
| [[2016Scheres_Relion]]
| Tutorial on the use of Relion
|-

| Paper
| [[2016Grigorieff_Frealign]]
| Tutorial on the use of Frealign
|-

|}

== Electron tomography ==

=== Image preprocessing ===

{|

| Paper
| [[2015Yan_thickness]]
| Determination of thickness, tilt and electron mean free path
|-

|}

=== Image alignment ===

{|

| Paper
| [[1982Guckenberger_commonOrigin]]
| Determination of a common origin in the micrographs of titl series in three-dimensional electron microscopy
|-

| Paper
| [[1992Lawrence_leastSquares]]
| Least squares solution of the alignment problem
|-

| Paper
| [[1995Penczek_dual]]
| Dual tilt alignment
|-

| Paper
| [[1996Owen_alignmentQuality]]
| Automatic alignment without fiducial markers and evaluation of alignment quality
|-

| Paper
| [[1998Grimm_normalization]]
| Discussion of several gray level normalization methods for electron tomography
|-

| Paper
| [[2001Brandt_Automatic1]]
| Automatic alignment without fiducial markers
|-

| Paper
| [[2001Brandt_Automatic2]]
| Automatic alignment with fiducial markers
|-

| Paper
| [[2006Winkler_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2006Castano_alignment]]
| Alignment with non-perpendicularity
|-

| Paper
| [[2007Castano_alignment]]
| Fiducial-less alignment of cryo-sections
|-

| Paper
| [[2009Sorzano_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2010Cantele_dualAlignment]]
| Alignment of dual series
|-

| Paper
| [[2014Tomonaga_Automatic]]
| Automatic alignment of tilt series using the projection themselves
|-

| Paper
| [[2014Han_Automatic]]
| Automatic alignment of tilt series using SIFT features
|-

| Paper
| [[2015Han_Automatic]]
| Automatic alignment of tilt series using fiducials
|-

| Paper
| [[2017Mastronarde_Automatic]]
| Automatic alignment and reconstruction of tilt series in IMOD
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[2003Winkler_CTF]]
| Focus gradient correction in electron tomography
|-

| Paper
| [[2006Fernandez_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Zanetti_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Xiong_CTF]]
| CTF determination and correction for low dose tomographic tilt series
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2017Kunz_3DCTF]]
| 3D CTF Correction
|-

|}

=== 3D reconstruction ===

{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1992Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[1997Marabini_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2002Fernandez_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2007Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[2008Fernandez_CARP]]
| Component Averaged Row Projections (CARP)
|-

| Paper
| [[2012Herman General Superiorization]]
| Superiorization: an optimization heuristic for medical physics
|-

| Paper
| [[2012Zhang_IPET_FETR]]
| IPET and FETR, a reconstruction algorithm for single molecule tomography
|-

| Paper
| [[2013Goris_SIRT_TV_DART]]
| Combination of SIRT, Total Variation and Discrete ART to reconstruct and segment at the same time
|-

| Paper
| [[2013Briegel A_Challenge]]
| The challenge of determining handedness in electron tomography and the use of DNA origami gold nanoparticle helices as molecular standards
|-

| Paper
| [[2013Messaoudi_EnergyFiltered]]
| 3D Reconstruction of Energy-Filtered TEM
|-

| Paper
| [[2016Deng_ICON]]
| 3D Reconstruction with missing information restoration
|-

| Paper
| [[2016Guay_Compressed]]
| 3D Reconstruction using compressed sensing
|-

|}

=== Noise reduction ===
{|

| Paper
| [[2001Frangakis_NAD]]
| Noise reduction with Nonlinear Anisotropic Diffusion
|-

| Paper
| [[2003Fernandez_AND]]
| Anisotropic nonlinear diffusion for electron tomography
|-

| Paper
| [[2003Jiang_Bilateral]]
| Bilateral denoising filter in electron microscopy
|-

| Paper
| [[2005Fernandez_AND]]
| Anisotropic nonlinear denoising in electron tomography
|-

| Paper
| [[2007Heide_median]]
| Iterative median filtering in electron tomography
|-

| Paper
| [[2007Fernandez_autAND]]
| Anisotropic nonlinear diffusion with automated parameter tuning
|-

| Paper
| [[2009Fernandez_Beltrami]]
| Nonlinear filtering based on Beltrami flow
|-

| Paper
| [[2010Bilbao_MeanShift]]
| Mean Shift Filtering
|-

| Paper
| [[2014Kovacik_wedgeArtefacts]]
| Removal of wedge artefacts
|-

| Paper
| [[2014Maiorca_beadArtefacts]]
| Removal of gold bead artefacts
|-

|}

=== Segmentation ===

{|

| Paper
| [[2002Frangakis_Eigenanalysis]]
| Segmentation using eigenvector analysis.
|-

| Paper
| [[2002Volkmann_Watershed]]
| Segmentation using watershed transform.
|-

| Paper
| [[2003Bajaj_BoundarySegmentation]]
| Segmentation based on fast marching.
|-

| Paper
| [[2005Cyrklaff_Thresholding]]
| Segmentation using optimal thresholding.
|-

| Paper
| [[2007Lebbink_TemplateMatching]]
| Segmentation using template matching.
|-

| Paper
| [[2007Sandberg_OrientationFields]]
| Segmentation using orientation fields.
|-

| Paper
| [[2007Sandberg_SegmentationReview]]
| Review on segmentation in electron tomography.
|-

| Paper
| [[2008Garduno_FuzzySegmentation]]
| Segmentation using fuzzy set theory principles.
|-

| Paper
| [[2009Lebbink_TemplateMatching2]]
| Segmentation using template matching.
|-

| Paper
| [[2012RubbiyaAli_EdgeDetection]]
| Parameter-Free Segmentation of Macromolecular Structures.
|-

| Conference
| [[2015Xu_TemplateMatching]]
| Detection of macromolecular complexes with a reduced representation of the templates.
|-

|}

=== Resolution ===
{|

| Paper
| [[2005Cardone_Resolution]]
| Resolution criterion for electron tomography
|-

| Chapter
| [[2007Penczek_Resolution]]
| Review of resolution criteria for electron tomography
|-

| Paper
| [[2015Diebolder_ConicalFSC]]
| Conical Fourier Shell Correlation
|-

|}

=== Subtomogram analysis ===

{|

| Paper
| [[2000Bohm_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2002Frangakis_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2006Nickell_Review]]
| Review of macromolecule finding by template matching (Visual Proteomics)
|-

| Paper
| [[2007Best_Review]]
| Review of Localization of Protein Complexes by Pattern Recognition
|-

| Paper
| [[2007Forster_Review]]
| Review of structure determination by subtomogram averaging
|-

| Paper
| [[2008Forster_Classification]]
| Classification of subtomograms using constrained correlation
|-

| Paper
| [[2008Bartesaghi_Classification]]
| Classification and averaging of subtomograms
|-

| Paper
| [[2008Schmid_Averaging]]
| Alignment and averaging of subtomograms
|-

| Paper
| [[2010Amat_Averaging]]
| Alignment and averaging of subtomograms exploiting thresholding in Fourier space
|-

| Paper
| [[2013Chen_Averaging]]
| Fast alignment of subtomograms using spherical harmonics
|-

| Paper
| [[2013Kuybeda_Averaging]]
| Alignment and averaging of subtomograms using the nuclear norm of the cluster
|-

| Paper
| [[2013Shatsky_Averaging]]
| Alignment and averaging of subtomograms with constrained cross-correlation
|-

| Paper
| [[2014Chen_Autofocus]]
| Subtomogram averaging and classification with special attention to differences
|-

| Paper
| [[2014Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2014Voortman_LimitingFactors]]
| Limiting factors of subtomogram averaging
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2015Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2016Bharat_Relion]]
| Subtomogram averaging with Relion
|-

| Paper
| [[2016Song_MatrixNorm]]
| Matrix norm minimization for tomographic reconstruction and alignment
|-

| Paper
| [[2017Castano_ParticlePicking]]
| Particle picking in tomograms for subtomogram averaging
|-

|}

=== Single particle tomography ===

{|

| Paper
| [[2012Bartesaghi_Constrained]]
| 3D reconstruction by imposing geometrical constraints
|-

| Paper
| [[2015Galaz_SingleParticleTomography]]
| Set of tools for Single Particle Tomography in EMAN2
|-

| Paper
| [[2016Galaz_SingleParticleTomography]]
| Alignment algorithms and CTF correction
|-

|}

=== Books and reviews ===

{|

| Paper
| [[2000Baumeister_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Koster_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Sali_Review]]
| Review of electron tomography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2005Lucic_Review]]
| Review of electron tomography
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_TomoBook]]
| Electron Tomography
|-

| Book
| [[2007McIntosh_Book]]
| Cellular Electron Microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2012Kudryashev_Review]]
| Review of subtomogram averaging
|-

| Paper
| [[2016Beck_Review]]
| Review of molecular sociology
|-

|}

=== Software ===

{|

| Paper
| [[1996Kremer_IMOD]]
| IMOD
|-

| Paper
| [[1996Chen_Priism/IVE]]
| Priism/IVE
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2005Nickell_TOM]]
| TOM Toolbox
|-

| Paper
| [[2007Messaoudi_TomoJ]]
| TomoJ
|-

| Paper
| [[2008Heymann_BsoftTomo]]
| Bsoft
|-

| Paper
| [[2015Ding_CaltechTomography]]
| Caltech tomography database
|-

| Paper
| [[2015Noble_AppionProtomo]]
| Batch fiducial-less tilt-series alignment in Appion using Protomo
|-

| Paper
| [[2015vanAarle_Astra]]
| ASTRA Toolbox
|-

|}

== 2D Crystals ==

=== 2D Preprocessing ===

{|

| Paper
| [[1986Henderson_Processing]]
| General 2D processing
|-

| Paper
| [[2000He_PhaseAlignment]]
| Phase consistency and Alignment
|-

| Paper
| [[2006Gil_Unbending]]
| Crystal unbending
|-

|}

=== Classification ===
{|

| Paper
| [[1988Frank_Classification]]
| MSA and classification in electron crystallography
|-

| Paper
| [[1996Fernandez_SOM]]
| Classification based on self organizing maps
|-

| Paper
| [[1998Sherman_MSA]]
| Classification based on MSA
|-

|}
=== 3D Reconstruction ===

{|

| Paper
| [[1985Wang_Solvent]]
| Solvent flattening
|-

| Paper
| [[1990Henderson_Processing]]
| General 3D processing
|-

| Paper
| [[2004Marabini_ART]]
| Algebraic Reconstruction Technique with blobs for crystals (Xmipp)
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1998Walz_Review]]
| Review of 2D crystallography
|-

| Paper
| [[1999Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Ellis_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of single particles, electron tomography and crystallography
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Gipson_2dx]]
| 2dx
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Philippsen_IPLT]]
| IPLT
|-

|}

== 3D Crystals - MicroED ==

=== Sample Preparation ===
{|
| Paper
| [[2016Shi_Preparation]]
| Sample Preparation
|}
=== Data Collection ===
{|
| Paper
| [[2014Nannenga_CR]]
| Continuous rotation

|}
=== Data Processing ===
{|

| Paper
| [[2011Wisedchaisri_PhaseExtension]]
| Fragment-based phase extension
|-

| Paper
| [[2015Hattne_Processing]]
| Data Processing
|-

| Paper
| [[2016Hattne_Correction]]
| Image correction
|}

=== Software ===
{|

| Paper
| [[2014Iadanza_Processing]]
| Data Processing of still diffraction data
|}

=== Books and Reviews ===
{|
| Paper
| [[2014Nannenga_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Liu_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Rodriguez_Review ]]
| Review of MicroED
|-

|}

== Helical particles ==

=== Filament corrections ===

{|

| Paper
| [[1986Egelman_Curved]]
| Algorithm for correcting curved filaments
|-

| Paper
| [[1988Bluemke_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2006Wang_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2016Yang_Flexible]]
| Algorithm for correcting filaments with flexible subunits
|-

|}

=== Reconstruction ===

{|

| Paper
| [[1952Cochran_Fourier]]
| Fourier Bessel transform of filamentous structures
|-

| Paper
| [[1958Klug_Fourier]]
| Fourier Bessel decomposition of the projection images
|-

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2005Wang_Iterative]]
| Iterative Fourier-Bessel algorithm
|-

| Paper
| [[2007Egelman_Iterative]]
| Iterative real-space algorithm
|-

| Paper
| [[2013Desfosses_Spring]]
| Helical processing with Spring
|-

| Paper
| [[2015Zhang_seam]]
| Workflow for the detection of the lattice seam
|-

| Paper
| [[2016Rohou_Frealix]]
| Helical processing with Frealix
|-

|}

=== Validation ===

{|

| Paper
| [[2014Egelman_ambiguity]]
| How to detect incorrect models
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Carragher_Phoelix]]
| Phoelix
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Owen_Brandeis]]
| Brandeis
|-

|}

== Icosahedral particles ==

=== Reconstruction ===

{|

| Paper
| [[1970Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1971Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1996Fuller_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1997Thuman_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

|}

=== Classification ===

{|

| Paper
| [[2005Scheres_Virus]]
| Classification of virus capsids in real space
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1999Baker_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[1999Conway_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2000Thuman_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Lee_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Navaza_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2006Grunewald_Review]]
| Review of reconstruction of icosahedral viruses
|-

|}

=== Software ===

{|

| Paper
| [[1996Baker_EMPFT]]
| EMPFT
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2013Morin_Sliz SBGrid]]
| SBGrid presentation for eLife
|-

|}

== Databases ==

{|

| Paper
| [[2003Boutselakis_EMSD]]
| EMSD database
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2011Kim_CDDB]]
| Conformational Dynamics Data Bank
|-

| Paper
| [[2011Lawson_EMDB]]
| Electron Microscopy Data Bank
|-

| Paper
| [[2016Iudin_EMPIAR]]
| EMPIAR raw data database
|-

| Paper
| [[2016Patwhardan_EMDB]]
| EMDB, PDB, ...
|-

| Paper
| [[2017Shao_PDBQuality]]
| Quality metrics in PDB
|-

| Blog
| http://www.mybiosoftware.com
| Huge list of bioinformatics programs (many of them structural bioinformatics)
|-

|}

== Relationship to other structural information sources ==

{|

| Paper
| [[2000Engel_AFM]]
| Review of Atomic Force Microscopy
|-

| Paper
| [[2001Dimmeler_AFM]]
| Constraints from Atomic Force Microscopy
|-

| Paper
| [[2003Mobus_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_Review]]
| Review on correlative microscopy
|-

| Paper
| [[2005Boudier_EFTETJ]]
| Software for Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2005Vestergaard_SAXS]]
| Example of comparison of 3DEM and Small-angle X-ray scattering
|-

| Paper
| [[2007Hamada_SAXS]]
| Constraints from Small-angle X-ray scattering
|-

| Paper
| [[2013Xu_FRET]]
| EM+FRET
|-

|}

== X-ray tomography ==

{|

| Paper
| [[2012Oton_ImageFormation]]
| Image formation model in X-ray cell microscopy
|-

|}

== Mathematical tools necessary ==

== People developing methods ==
Please, add yourself to this list (due to privacy reasons, please, do not add anyone else to the list without his/her explicit consent). Sort by first name alphabetical order.

[http://biocomp.cnb.csic.es/~coss Carlos Oscar S. Sorzano]: CSIC, Madrid, Spain 

[http://www.curie.fr/recherche/themes/detail_equipe.cfm/lang/_fr/id_equipe/241.htm Cédric Messaoudi]: Institute Curie, Paris, France 

[http://scholar.google.es/citations?user=_jNYGScAAAAJ&hl=en Javier Vargas]:[mailto:jvargas@cnb.csic.es mail]: CSIC, Madrid, Spain 

[http://scholar.google.es/citations?hl=es&user=g2ZJPIYAAAAJ Joaquín Otón]: CSIC, Madrid, Spain 

[mailto:jrbcast@gmail.com José Román Bilbao-Castro]: UAL, Almería, Spain; CSIC, Madrid, Spain 

[José Miguel de la Rosa Trevín]: Biocomputing Unit CNB-CSIC, Madrid, Spain 

[http://cryoem.janelia.org Tamir Gonen]: [mailto:gonent@janelia.hhmi.org mail]: Howard Hughes Medical Institute, Ashburn, VA, USA 

[mailto:vabrishami@cnb.csic.es Vahid Abrishami]: CSIC, Madrid, Spain 

== 3DEM sites ==
* [http://3dem.ucsd.edu/ 3DEM web site]

* [http://en.wikibooks.org/wiki/Software_Tools_For_Molecular_Microscopy Software tools for molecular microscopy]

* [http://www.emdatabank.org/ The Electron Microscopy Data Bank (EMDB)]

* [http://ccdb.ucsd.edu The Cell Centered Database (CCDB)]

* [http://conventions.cnb.csic.es The geometrical software conventions web page ]

== Editing useful links ==

* [http://www.mediawiki.org/wiki/Help:Formatting Text formatting in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Links Adding links in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Images Adding images in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Tables Making tables in Mediawiki]

2017Schaffer FocusedIonBeam

2017-05-11T20:44:31Z

CoSS: /* Links */

== Citation ==

Schaffer, M.; Mahamid, J.; Engel, B. D.; Laugks, T.; Baumeister, W. & Plitzko, J. M. Optimized cryo-focused ion beam sample preparation aimed at in situ structural studies of membrane proteins. Journal of structural biology, 2017, 197, 73-82

== Abstract ==

While cryo-electron tomography (cryo-ET) can reveal biological structures in their native state within the cellular environment, it requires the production of high-quality frozen-hydrated sections that are thinner than 300nm. Sample requirements are even more stringent for the visualization of membrane-bound protein complexes within dense cellular regions. Focused ion beam (FIB) sample preparation for transmission electron microscopy (TEM) is a well-established technique in material science, but there are only few examples of biological samples exhibiting sufficient quality for high-resolution in situ investigation by cryo-ET. In this work, we present a comprehensive description of a cryo-sample preparation workflow incorporating additional conductive-coating procedures. These coating steps eliminate the adverse effects of sample charging on imaging with the Volta phase plate, allowing data acquisition with improved contrast. We discuss optimized FIB milling strategies adapted from material science and each critical step required to produce homogeneously thin, non-charging FIB lamellas that make large areas of unperturbed HeLa and Chlamydomonas cells accessible for cryo-ET at molecular resolution.

== Keywords ==

== Links ==

http://www.sciencedirect.com/science/article/pii/S1047847716301514

== Related software ==

== Related methods ==

== Comments ==

2017Schaffer FocusedIonBeam

2017-05-11T20:43:44Z

CoSS: Created page with "== Citation == Schaffer, M.; Mahamid, J.; Engel, B. D.; Laugks, T.; Baumeister, W. & Plitzko, J. M. Optimized cryo-focused ion beam sample preparation aimed at in situ struct..."

== Citation ==

Schaffer, M.; Mahamid, J.; Engel, B. D.; Laugks, T.; Baumeister, W. & Plitzko, J. M. Optimized cryo-focused ion beam sample preparation aimed at in situ structural studies of membrane proteins. Journal of structural biology, 2017, 197, 73-82

== Abstract ==

While cryo-electron tomography (cryo-ET) can reveal biological structures in their native state within the cellular environment, it requires the production of high-quality frozen-hydrated sections that are thinner than 300nm. Sample requirements are even more stringent for the visualization of membrane-bound protein complexes within dense cellular regions. Focused ion beam (FIB) sample preparation for transmission electron microscopy (TEM) is a well-established technique in material science, but there are only few examples of biological samples exhibiting sufficient quality for high-resolution in situ investigation by cryo-ET. In this work, we present a comprehensive description of a cryo-sample preparation workflow incorporating additional conductive-coating procedures. These coating steps eliminate the adverse effects of sample charging on imaging with the Volta phase plate, allowing data acquisition with improved contrast. We discuss optimized FIB milling strategies adapted from material science and each critical step required to produce homogeneously thin, non-charging FIB lamellas that make large areas of unperturbed HeLa and Chlamydomonas cells accessible for cryo-ET at molecular resolution.

== Keywords ==

== Links ==

Optimized cryo-focused ion beam sample preparation aimed at in situ structural studies of membrane proteins

== Related software ==

== Related methods ==

== Comments ==

Main Page

2017-05-11T20:42:54Z

CoSS: /* Sample preparation */

== Presentation ==

This web page is intended to be an extensive repository of three-dimensional electron microscopy (3DEM) methods. The advantages of having such a repository are

* You know which are the relevant articles in a particular topic, therefore, paper introductions, reviews, etc. are easier to write and you make sure you will cite all the related articles.
* You will be sure that your paper has more chances of being cited.
* You can add whatever information you find relevant to your method, external links, links to other papers, etc.
* You can link your method to a web page providing the corresponding software, so you know people can use your algorithms.
* You can use the Wiki search capabilities to locate relevant articles even if they are not at the topic you are looking at.
* As a community we will "reconstruct" our history.
* You can select the "watch" option above to receive notifications in case of further changes in the Main Page.

Developing image processing methods for 3DEM is not "[[well-paid]]" in terms of citations and impact factor. However, it is crucial for the advance of the field. Gathering methodological papers in a portal will help to increase the recognition of the field.

Please:

* Add your articles at the right place (you can add a single article in several topics if it is relevant to all of them). The easiest way to add an article is by editing the corresponding topic in the main page, adding your entry, then save the main page. Click on the red link that appears on your new entry, copy and paste the Wiki following code, add the information of your article

== Citation ==

== Abstract ==

== Keywords ==

== Links ==

== Related software ==

== Related methods ==

== Comments ==

* Maintain the information of each article as complete as possible.
* Sort articles by years and authors.
* Be respectful to other people's work.

== How to subscribe to this page ==

You may subscribe to this page so that you will be notified every time someone adds a new method. To do so, you have to register in the page, and edit your preferences ("my preferences"). Be sure that you have activated the option "E-mail me when a page on my watchlist is changed". Finally, click on the "Watch" tab at the top of this page.

You may subscribe to changes on this page on the mailing list 3demmethods@cnb.csic.es. To send a new method to this mail list just send a mail to 3demmethods@cnb.csic.es

To subscribe to this list, visit the web page

https://listas.csic.es/cnb/wws/subscribe/3demmethods

Alternatively, you may write a mail to sympa6@cnb.csic.es with the subject

<code>subscribe 3demmethods YourName YourFamilyName</code>

and an empty mail body.

To unsubscribe visit the page

https://listas.csic.es/cnb/wws/sigrequest/3demmethods

or write sympa6@cnb.csic.es with the subject

<code>unsubscribe 3demmethods</code>

and an empty mail body.

== Electron microscopy images ==

=== Online courses ===

CALTECH: http://cryo-em-course.caltech.edu/

MRC: ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/EM-course/

CNB-CSIC: http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/MadridJan2014EM

Workshop on Computational methods for CryoEM: https://www.youtube.com/watch?v=XdKO1iaPP8o

Workshop on Management of large CryoEM facilities: https://www.youtube.com/watch?v=as4seOPszL0

Icknield Course on Model Building and Refinement for High Resolution EM Maps: http://www.ccpem.ac.uk/training/icknield_2017/icknield_2017.php

=== Image formation ===

{|

| Paper
| [[1971Erickson_CTF]]
| CTF model
|-

| Paper
| [[1971Glaeser_Damage]]
| Radiation damage
|-

| Chapter
| [[1971Hanszen_CTF]]
| Image formation model
|-

| Paper
| [[1971Thon_Model]]
| CTF model
|-

| Paper
| [[1975Unwin_Imaging]]
| Radiation dose
|-

| Paper
| [[1977Wade_Model]]
| CTF model
|-

| Paper
| [[1978Wade_Model]]
| CTF model
|-

| Paper
| [[1979Hayward_Radiation]]
| Radiation damage
|-

| Paper
| [[1984Cohen_Validity]]
| Validity of the CTF model at high frequencies
|-

| Paper
| [[1988Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[1992Wade_Model]]
| CTF model
|-

| Paper
| [[1993Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2004Egerton_Damage]]
| Radiation damage
|-

| Paper
| [[2004Sorzano_Normalization]]
| Background noise is Gaussian
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2009Baxter_NoiseCharacterization]]
| Characterization of the different noise sources in cryo-EM
|-

| Paper
| [[2010Baker_Damage]]
| Radiation damage dependence on resolution
|-

| Paper
| [[2010Bammes_Damage]]
| Radiation damage dependence on temperature
|-

| Paper
| [[2010Gomez_Multislice]]
| Simulation of the multi slice model
|-

| Paper
| [[2010Zewail_FourDimensional]]
| Review on the use of ultrafast EM
|-

| Paper
| [[2011Bammes_CCD]]
| Performance of CCD cameras
|-

| Paper
| [[2011Glaeser_Coma]]
| Image formation model including coma
|-

| Paper
| [[2011Milazzo_DirectDetectors]]
| Evaluation of Direct Detectors
|-

| Paper
| [[2011Rullgard_ImageSimulation]]
| Accurate simulation of EM images
|-

| Paper
| [[2011Zhang LimitingFactors]]
| Limiting factor for atomic resolution in EM
|-

| Paper
| [[2012Bammes_DirectDetection]]
| Performance of Direct detectors
|-

| Paper
| [[2012Campbell_MotionCorrection]]
| Beam induced motion correction and direct detectors
|-

| Paper
| [[2012Shang_HydrationLayer]]
| Simulation of PDB volumes explicitly considering the hydration layer
|-

| Paper
| [[2013Egerton_RadiationDamage]]
| Review of TEM radiation damage and experimental ways of reducing it
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu H_Noisemodels]]
| Noise models and cryo-EM drift correction with a direct-electron camera
|-

| Paper
| [[2013Li X K2 noisemodels]]
| Influence of electron dose rate on electron counting images recorded with the K2 camera
|-

| Paper
| [[2013Vulovic_CTFApproximations]]
| When to use the different approximations performed so that a projection with linear CTF is valid
|-

| Thesis
| [[2013Vulovic_ImageFormation]]
| Ph.D. Thesis on the image formation in cryo-EM
|-

| Paper
| [[2014Danev_PhasePlate]]
| Volta potential phase plate
|-

| Paper
| [[2015Chiu_K2]]
| Characterization of K2
|-

| Paper
| [[2015Hawkes_AberrationCorrection]]
| Historical account of the development of lens corrections
|-

| Paper
| [[2015Koeck_Quadratic]]
| Limitations of the linear approximation and use of the quadratic terms
|-

| Paper
| [[2015Kuijper_FEI]]
| Description of the FEI Falcons
|-

| Paper
| [[2015Lobato_MULTEM]]
| Simulation of multislice diffraction
|-

| Paper
| [[2015McMullan_AmorphousIce]]
| Beam induced movement is caused by Brownian motion
|-

| Paper
| [[2016Koeck_ADF]]
| Simulations of Annular Dark Field TEM
|-

| Paper
| [[2017Mishyna_DNARadiation]]
| Review of radiation damage on DNA
|-

|}

=== Collection geometry ===

{|

| Chapter
| [[1980Hoppe_Wedge]]
| Missing wedge
|-

| Paper
| [[1987Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1995Penczek_Dual]]
| Dual axis tomography
|-

| Paper
| [[1997Mastronarde_Dual]]
| Dual axis tomography
|-

| Paper
| [[2003Ludtke_FocusPairs]]
| Focus pairs for single particles
|-

| Paper
| [[2005Lanzavecchia_Conical]]
| Conical tomography
|-

| Paper
| [[2005Zampighi_Conical]]
| Conical tomography
|-

| Paper
| [[2006Leschziner_OT]]
| Orthogonal Tilt
|-

| Paper
| [[2006Messaoudi_Multiple]]
| Multiple axis tomography
|-

| Paper
| [[2012Kudryashev_FocusPairs]]
| Focus pairs tomography
|-

| Paper
| [[2014Hovden_TiltFocus]]
| Combining tilt series with focus series
|-

| Paper
| [[2015Sorzano_RandomConicalTilt]]
| General formulation of Random Conical Tilt
|-

| Paper
| [[2017Hagen_DoseTomography]]
| Dose optimization for subtomogram averaging
|-

|}

=== Sample preparation ===

{|

| Paper
| [[1982Dubochet_Sample]]
| Vitreous ice
|-

| Paper
| [[1986Lepault_Sample]]
| Fast freezing
|-

| Paper
| [[1995Dubochet_Sample]]
| High-pressure freezing
|-

| Paper
| [[1995VanMarle_Sample]]
| Sample damages in resin
|-

| Paper
| [[1998Adrian_Sample]]
| Cryo negative staining
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2002Hsieh_Sample]]
| Cryofixation
|-

| Paper
| [[2004AlAmoudi_Sample]]
| CEMOVIS
|-

| Paper
| [[2008Studer_Sample]]
| Review on high pressure freezing
|-

| Paper
| [[2009Pierson_Sample]]
| Review on sample preparation for electron tomography
|-

| Paper
| [[2010Zhang_NegativeStaining]]
| Negative staining for small protein imaging
|-

| Paper
| [[2012Zhang_PositiveStaining]]
| Positive staining
|-

| Paper
| [[2014Rames_NegativeStaining]]
| Optimized negative staining
|-

| Paper
| [[2014Russo_GoldGrids]]
| Gold grids for single particles
|-

| Paper
| [[2015Cabra_Sample]]
| Review on sample preparation for single particles with videos
|-

| Paper
| [[2016Passmore_Review]]
| Tutorial chapter on sample preparation
|-

| Paper
| [[2016Razinkov_Vitrification]]
| New vitrification method
|-

| Paper
| [[2016Takizawa_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2016Thompson_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2017Peitsch_Sample]]
| iMEM: Isolation of Plasma Membrane for Cryoelectron Microscopy
|-

| Paper
| [[2017Schaffer_FocusedIonBeam]]
| Focused Ion Beam sample preparation for membrane proteins
|-

|}

=== Automated data collection ===

{|

| Paper
| [[1992Dierksen_Automatic]]
| Automated data collection
|-

| Paper
| [[1992Koster_Automatic]]
| Automated data collection
|-

| Paper
| [[1996Fung_Automatic]]
| Automated data collection for tomography
|-

| Paper
| [[2001Zhang_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2003Ziese_Automatic]]
| Automated autofocusing
|-

| Paper
| [[2004Potter_Automatic]]
| Automated sample loading
|-

| Paper
| [[2004Zheng_Automatic]]
| Automated data collection
|-

| Paper
| [[2005Lei_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2005Suloway_Automatic]]
| Automated data collection: Leginon
|-

| Paper
| [[2007Yoshioka_RCT]]
| Automated Random Conical Tilt
|-

| Paper
| [[2011Korinek_TOM2]]
| Automated acquisition with TOM2
|-

| Paper
| [[2015Li_UCSFImage]]
| Automated acquisition with UCSFImage
|-

| Paper
| [[2016Gil_Fuzzy]]
| Real time decisions during acquisition with neuro-fuzzy method
|-

| Paper
| [[2016Liu_TiltControl]]
| Accurate control of the tilt angle for electron tomography
|-

| Paper
| [[2016Vargas_FoilHole]]
| Determination of image quality at low magnification
|-

|}

== Single particles ==

=== Automatic particle picking ===

{|

| Paper
| [[1982VanHeel_Detection]]
| Detection of particles in micrographs
|-

| Paper
| [[2001Nicholson_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2001Zhu_Filaments]]
| Automatic identification of filaments in micrographs
|-

| Paper
| [[2004Sigworth_Detection]]
| Classical detection theory and the cryo-EM particle selection problem
|-

| Paper
| [[2004Volkmann_ParticlePicking]]
| An approach to automated particle picking from electron micrographs based on reduced representation templates
|-

| Paper
| [[2004Wong_ParticlePicking]]
| Model-based particle picking for cryo-electron microscopy
|-

| Paper
| [[2004Zhu_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2007Chen_Signature]]
| Automatic particle picking program: Signature
|-

| Paper
| [[2007Woolford_SwarmPS]]
| Automatic particle picking with several criteria, implemented in EMAN Boxer
|-

| Paper
| [[2009Sorzano_MachineLearning]]
| Automatic particle picking based on machine learning of rotational invariants
|-

| Paper
| [[2011Arbelaez_Comparison]]
| Evaluation of the performance of software for automated particle-boxing
|-

| Paper
| [[2013Abrishami_MachineLearning]]
| A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs
|-

| Paper
| [[2013Hauer_2013]]
| Automatic tilt pair detection in Random Conical Tilt
|-

| Paper
| [[2013Shatsky_ParticlePicking]]
| Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Langlois_ParticlePicking]]
| Automatic particle picking
|-

| Paper
| [[2016Vilas_AutomaticTilt]]
| Automatic identification of image pairs in untilted-tilted micrograph pairs
|-

|}

=== 2D Preprocessing ===

{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast enhancement through DPR
|-

| Paper
| [[2004Sorzano_Normalization]]
| Normalization procedures and their statistical properties.
|-

| Paper
| [[2006Sorzano_Denoising]]
| Strong denoising in wavelet space
|-

| Conference
| [[2009Sorzano_Downsampling]]
| Differences between the different downsampling schemes
|-

| Paper
| [[2012Brilot_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Campbell_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Zhao_Denoising]]
| Denoising using an invariant Fourier-Bessel eigenspace
|-

| Paper
| [[2013Norousi_Screening]]
| Screening particles to identify outliers
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu_Movies]]
| Drift correction for movies considering dark field
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Scheres_Movies]]
| Beam induced motion correction
|-

| Paper
| [[2015Abrishami_Movies]]
| Alignment of direct detection device micrographs
|-

| Paper
| [[2015Grant_Anisotropic]]
| Automatic estimation and correction of anisotropic magnification
|-

| Paper
| [[2015Grant_OptimalExposure]]
| Filter movies according to the radiation damage
|-

| Paper
| [[2015Rubinstein_Alignment]]
| Frame alignment at the level of particle
|-

| Paper
| [[2015Spear_DoseCompensation]]
| Effect of dose compensation on resolution
|-

| Paper
| [[2015Zhao_AnisotropicMagnification]]
| Correction of anisotropic magnification
|-

| Conference
| [[2016Bajic_Denoising]]
| Denoising and deconvolution of micrographs
|-

| Paper
| [[2016Jensen_RemovalVesicles]]
| Removal of vesicles in membrane proteins
|-

| Paper
| [[2016Bhamre_Denoising]]
| Denoising by 2D covariance estimation
|-

| Paper
| [[2017McLeod_Zorro]]
| Movie alignment by Zorro
|-

|}

=== 2D Alignment ===

{|

| Paper
| [[1981Frank_Averaging]]
| 2D averaging and phase residual
|-

| Paper
| [[1982Saxton_Averaging]]
| 2D averaging using correlation
|-

| Paper
| [[1998Sigworth_ML2D]]
| Maximum likelihood alignment in 2D
|-

| Paper
| [[2003Cong_FRM2D]]
| Fast Rotational Matching in 2D
|-

| Paper
| [[2005Cong_FRM2D]]
| Fast Rotational Matching in 2D introduced in a 3D Alignment algorithm
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

|}

=== 2D Classification and clustering ===

{|

| Paper
| [[1981VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[1984VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2011Singer_DiffusionMaps]]
| Classification in 2D based on graph analysis of the projections
|-

| Paper
| [[2012Yang_ISAC]]
| Iterative Stable Alignment and clustering
|-

| Paper
| [[2014Sorzano_Outlier]]
| Outlier detection in 2D classifications.
|-

| Paper
| [[2014Zhao_Aspire]]
| Fast classification based on rotational invariants and vector diffusion maps
|-

| Paper
| [[2015Huang_Robust]]
| Robust w-estimators of 2D classes
|-

| Paper
| [[2016Reboul_Stochastic]]
| Stochastic Hill Climbing for calculating 2D classes
|-

| Conference
| [[2017Bhamre_Mahalanobis]]
| 2D classification using Mahalanobis distance
|-

|}

=== 3D Alignment ===

{|

| Paper
| [[1980Kam_AutoCorrelation]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[1986Goncharov_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1987VanHeel_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1988Provencher_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Vogel_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1990Gelfand_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Goncharov_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Harauz_Quaternions]]
| Use of quaternions to represent rotations
|-

| Paper
| [[1994Penczek_Real]]
| Angular assignment using projection matching in real space
|-

| Paper
| [[1994Radermacher_Radon]]
| Angular assignment in Radon space
|-

| Paper
| [[1996Penczek_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[2003Rosenthal_DPR]]
| Angular assignment using DPR
|-

| Paper
| [[2004Sorzano_Wavelet]]
| Angular assignment in the wavelet space.
|-

| Paper
| [[2005Jonic_Splines]]
| Angular assignment in Fourier space using spline interpolation.
|-

| Paper
| [[2005Yang_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[2006Ogura_SimulatedAnnealing]]
| Angular asignment by simulated annealing
|-

| Paper
| [[2007Grigorieff_Continuous]]
| Continuous angular assignment in Fourier space
|-

| Paper
| [[2010Jaitly_Bayesian]]
| Angular assignment by a Bayesian method and annealing
|-

| Paper
| [[2010Sanz_Random]]
| Random model method
|-

| Paper
| [[2010Singer_Voting]]
| Detecting consistent common lines by voting (reference free)
|-

| Paper
| [[2011Singer_SDP]]
| Angular assignment by semidefinite programming and eigenvectors (reference free)
|-

| Paper
| [[2012Giannakis_Scattering]]
| Construction of an initial volume, reference free, by graph analysis of the projections
|-

| Paper
| [[2012Shkolnisky_Sync]]
| Angular assignment by synchronization of rotations (reference free)
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Wang_LUD]]
| Angular assignment by least unsquared deviations (reference free)
|-

| Paper
| [[2014Vargas_RANSAC]]
| Initial model using RANSAC (reference free)
|-

| Paper
| [[2015Joubert_Pseudoatoms]]
| Initial model based on pseudo-atoms
|-

| Paper
| [[2015Singer_Kam]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[2015Sorzano_Significant]]
| Statistical approach to the initial volume estimation (reconstruct significant)
|-

| Conference
| [[2016Michels_Heterogeneous]]
| Initial volume in the presence of heterogeneity
|-

| Paper
| [[2016Cossio_BayesianGPU]]
| GPU implementation of the Bayesian 3D reconstruction approach
|-

|}

=== 3D Reconstruction ===
{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1986Harauz_FBP]]
| Exact filters for Filtered Back Projection
|-

| Chapter
| [[1992Radermacher_WBP]]
| Exact filters for Weighted Back Projection
|-

| Paper
| [[1997Zhu_RecCTF]]
| 3D Reconstruction (SIRT like) and simultaneous CTF correction
|-

| Paper
| [[1998Boisset_Uneven]]
| Artifacts in SIRT and WBP under uneven angular distributions
|-

| Paper
| [[1998Marabini_ART]]
| Algebraic Reconstruction Technique with blobs (Xmipp)
|-

| Paper
| [[2001Sorzano_Uneven]]
| Free parameter selection under uneven angular distributions
|-

| Paper
| [[2005Sorzano_Parameters]]
| Free parameter selection for optimizing multiple tasks
|-

| Paper
| [[2008Sorzano_Constraints]]
| Mass, surface, positivity and symmetry constraints for real-space algorithms
|-

| Paper
| [[2009Bilbao_ParallelART]]
| Efficient parallelization of ART
|-

| Paper
| [[2011Li_GradientFlow]]
| Regularized 3D Reconstruction by Gradient Flow
|-

| Paper
| [[2011Vonesch_Wavelets]]
| Fast wavelet-based 3D reconstruction
|-

| Paper
| [[2012Gopinath_ShapeRegularization]]
| Regularized 3D Reconstruction by Shape information
|-

| Paper
| [[2012Kucukelbir_adaptiveBasis]]
| 3D reconstruction in an adaptive basis promoting sparsity
|-

| Paper
| [[2012Sindelar_NoiseReduction]]
| Optimal noise reduction in 3D reconstructions
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Lyumkis_Optimod]]
| Construction of initial volumes with Optimod
|-

| Paper
| [[2013Wang FIRM]]
| Fast 3D reconstruction in Fourier domain
|-

| Paper
| [[2014Kunz_SART_OS]]
| Simultaneous ART with OS
|-

| Paper
| [[2015Abrishami_Fourier]]
| 3D Reconstruction in Fourier space
|-

| Paper
| [[2015Dvornek_SubspaceEM]]
| Fast Maximum a posteriori
|-

| Paper
| [[2015Moriya_Bayesian]]
| Bayesian approach to suppress limited angular artifacts
|-

| Paper
| [[2015Xu_GeometricFlow]]
| Multi-scale geometric flow
|-

| Arxiv
| [[2016Ye_Cohomology]]
| Cohomology properties of 3D reconstruction
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

|}

=== 3D Heterogeneity ===

{|

| Paper
| [[2004White_Size]]
| Heterogeneity classification of differently sized images
|-

| Paper
| [[2006Penczek_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Scheres_ML3D]]
| Maximum Likelihood alignment and classification in 3D
|-

| Paper
| [[2009Spahn_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2010Elmlund_AbInitio]]
| Solving the initial volume problem with multiple conformations
|-

| Paper
| [[2010Shatsky_MultiVariate]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2012Scheres_Bayesian]]
| A Bayesian view on cryo-EM structure determination
|-

| Paper
| [[2012Zheng_Covariance]]
| Estimation of the volume covariance
|-

| Paper
| [[2013Wang_MLVariance]]
| Maximum Likelihood estimate of the map variance
|-

| Paper
| [[2013Lyumkis D_FREALIGN]]
| Likelihood-based classification of cryo-EM images using FREALIGN.
|-

| Paper
| [[2014Jin_NMA]]
| Continuous heterogeneity through Normal Mode Analysis
|-

| Paper
| [[2014Dashti_Brownian]]
| Continuous heterogeneity through Brownian trajectories
|-

| Paper
| [[2014Chen_Migration]]
| Particle migration analysis in 3D classification
|-

| Paper
| [[2015Anden_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Bai_Focused]]
| Focused classification
|-

| Paper
| [[2015Katsevich_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Klaholz_MRA]]
| Multivariate Statistical Analysis of Jackknife and Bootstrapping on random subsets
|-

| Paper
| [[2015Liao_Covariance]]
| Estimation of the 3D covariance from 2D projections
|-

| Paper
| [[2015Tagare_Direct]]
| Direct reconstruction of PCA components
|-

| Paper
| [[2016Gong_Mechanical]]
| Mechanical model for macromolecules
|-

| Paper
| [[2016Rawson_Movement]]
| Movement and flexibility
|-

| Paper
| [[2016Sorzano_StructMap]]
| Sorting a discrete set of conformational states
|-

| Paper
| [[2016Sorzano_Strain]]
| Calculate local stretches, strains and rotations from two conformational states
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

|}

=== Validation ===

{|

| Paper
| [[2008Stagg_TestBed]]
| Effect of voltage, dosis, number of particles and Euler jumps on resolution
|-

| Paper
| [[2011Henderson]]
| Tilt Validation
|-

| Paper
| [[2011Read]]
| Validation of PDBs
|-

| Paper
| [[2012Henderson]]
| EM Map Validation
|-

| Paper
| [[2013Cossio_Bayesian]]
| EM Map Validation in a probabilistic setting
|-

| Paper
| [[2013Chen_NoiseSubstitution]]
| Noise substitution at high resolution for measuring overfitting
|-

| Paper
| [[2014Russo_StatisticalSignificance]]
| EM Map Validation through the statistical significance of the tilt-pair angular assignment
|-

| Paper
| [[2014Stagg_Reslog]]
| EM Map Validation through the resolution evolution with the number of particles
|-

| Paper
| [[2014Wasilewski_Tilt]]
| Web implementation of the tilt pair validation
|-

| Paper
| [[2015Heymann_Alignability]]
| EM Map Validation through the resolution of reconstructions from particles and noise
|-

| Paper
| [[2015Oliveira_FreqLimited]]
| Comparison of gold standard and frequency limited optimization
|-

| Paper
| [[2015Wriggers_Secondary]]
| Validation by secondary structure
|-

| Paper
| [[2016Kim_SAXS]]
| Comparison of SAXS data and EM projections
|-

| Paper
| [[2016Rosenthal_Review]]
| Review of validation methods
|-

| Paper
| [[2016Vargas_Alignability]]
| Validation by studying the tendency of an angular assignment to cluster in the projection space
|-

| Paper
| [[2017Monroe_PDBRefinement]]
| Validation by comparison to a refined PDB
|-

|}

=== Resolution ===

{|

| Paper
| [[1986Harauz_FBP]]
| Fourier Shell Correlation
|-

| Paper
| [[1987Unser_SSNR]]
| 2D Spectral Signal to Noise Ratio
|-

| Paper
| [[2002Penczek_SSNR]]
| 3D Spectral Signal to Noise Ratio for Fourier based algorithms
|-

| Paper
| [[2003Rosenthal_DPR]]
| Review of the FSC and establishment of a new threshold
|-

| Paper
| [[2005Unser_SSNR]]
| 3D Spectral Signal to Noise Ratio for any kind of algorithms
|-

| Paper
| [[2005VanHeel_FSC]]
| Establishment of a new threshold for FSC
|-

| Paper
| [[2007Sousa_AbInitio]]
| Resolution measurement on neighbour Fourier voxels
|-

| Paper
| [[2014Kucukelbir_Local]]
| Quantifying the local resolution of cryo-EM density maps
|-

| Paper
| [[2016Pintilie_Probabilistic]]
| Probabilistic models and resolution
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Statistical properties of resolution measures defined in Fourier space
|-

|}

=== Sharpening of high resolution information ===
{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast restoration and map sharpening
|-

| Paper
| [[2008Fernandez_Bfactor]]
| Bfactor determination and restoration
|-

| Paper
| [[2013Fiddy_SaxtonAlgorithm]]
| Phase retrieval or extension
|-

| Paper
| [[2014Kishchenko_SphericalDeconvolution]]
| Spherical deconvolution
|-

| Paper
| [[2015Spiegel_VISDEM]]
| Visualization improvement by the use of pseudoatomic profiles
|-

| Paper
| [[2016Jonic_Pseudoatoms]]
| Approximation with pseudoatoms
|-

| Paper
| [[2016Jonic_Denoising]]
| Denoising and high-frequency boosting by pseudoatom approximation
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[1982Schiske_Correction]]
| CTF correction for tilted objects
|-

| Paper
| [[1988Toyoshima_Model]]
| CTF estimation
|-

| Paper
| [[1995Frank_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1996Skoglund_MaxEnt]]
| CTF correction with Maximum Entropy
|-

| Paper
| [[1996Zhou_Model]]
| CTF model and user interface for manual fitting
|-

| Paper
| [[1997Fernandez_AR]]
| PSD estimation using periodogram averaging and AR models
|-

| Paper
| [[1997Penczek_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1997Stark_Deconvolution]]
| CTF correction using deconvolution
|-

| Paper
| [[1997Zhu_RecCTF]]
| CTF correction and reconstruction
|-

| Paper
| [[2000DeRosier_EwaldCorrection]]
| CTF correction considering the Ewald sphere
|-

| Paper
| [[2000Jensen_TiltedCorrection]]
| CTF correction considering tilt in backprojection
|-

| Paper
| [[2001Saad_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Huang_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Mindell_CTFTILT]]
| CTF estimation for tilted micrographs
|-

| Paper
| [[2003Sander_MSA]]
| CTF estimation through MSA classification of PSDs
|-

| Paper
| [[2003Velazquez_ARMA]]
| PSD and CTF estimation using ARMA models
|-

| Paper
| [[2004Sorzano_IDR]]
| CTF restoration and reconstruction with Iterative Data Refinement
|-

| Conference
| [[2004Wan_CTF]]
| Spatially variant CTF
|-

| Paper
| [[2004Zubelli_Chahine]]
| CTF restoration and reconstruction with Chahine's multiplicative method
|-

| Conference
| [[2005Dubowy_SpaceVariant]]
| CTF correction when this is space variant
|-

| Paper
| [[2005Mallick_ACE]]
| CTF estimation
|-

| Paper
| [[2006Wolf_Ewald]]
| CTF correction considering Ewald sphere
|-

| Paper
| [[2007Jonic_EnhancedPSD]]
| PSD enhancement for better identification of Thon rings; Vitreous ice diffracts in Thon rings
|-

| Paper
| [[2007Philippsen_Model]]
| CTF Model for tilted specimens
|-

| Paper
| [[2007Sorzano_CTF]]
| CTF estimation using enhanced PSDs
|-

| Paper
| [[2009Sorzano_Sensitivity]]
| Error sensitivity of the CTF models, non-uniqueness of the CTF parameters
|-

| Paper
| [[2010Jiang2010_CTFCorrection]]
| Amplitude correction method
|-

| Paper
| [[2010Kasantsev_CTFCorrection]]
| Mathematical foundations of Kornberg and Jensen method
|-

| Paper
| [[2010Leong_CTFCorrection]]
| Correction for spatially variant CTF
|-

| Paper
| [[2011Glaeser_Coma]]
| The effect of coma at high-resolution
|-

| Paper
| [[2011Mariani_Tilted]]
| CTF simulation and correction of tilted specimens
|-

| Paper
| [[2011Sindelar_Wiener]]
| CTF correction using a modified version of Wiener filter
|-

| Paper
| [[2011Voortman_Tilted]]
| CTF correction for tilted specimen
|-

| Paper
| [[2012Voortman_VaryingCTF]]
| Correcting a spatially varying CTF
|-

| Paper
| [[2013Vargas_FastDef]]
| Fast defocus
|-

| Paper
| [[2015Rohou_CTFFind4]]
| CTF Find 4
|-

| Paper
| [[2015Sheth_CTFquality]]
| Visualization and quality assessment of CTF
|-

| Paper
| [[2016Zhang_GCTF]]
| gCTF
|-

|}

=== Segmentation ===

{|

| Paper
| [[2006Baker_segmentation]]
| Segmentation of molecular subunits
|-

|}

=== Fitting and docking ===

{|

| Paper
| [[1999Volkmann_Fitting]]
| Fitting in real space
|-

| Paper
| [[2001Baker_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2001Jones_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2003Kovacs_FRM3D]]
| Fast Rotational Alignment of two EM maps
|-

| Paper
| [[2004Tama_NMA1]]
| Flexible fitting with Normal Modes (I)
|-

| Paper
| [[2004Tama_NMA2]]
| Flexible fitting with Normal Modes (II)
|-

| Paper
| [[2005Velazquez_Superfamilies]]
| Recognition of the superfamily folding in medium-high resolution volumes
|-

| Paper
| [[2007DeVries_Haddock]]
| Docking with Haddock 2.0
|-

| Paper
| [[2007Kleywegt_QualityControl]]
| Quality control and validation of fitting
|-

| Paper
| [[2012Biswas_Secondary]]
| Secondary structure determination in EM volumes
|-

| Paper
| [[2012Velazquez_Constraints]]
| Multicomponent fitting by using constraints from other information sources
|-

| Paper
| [[2013Chapman MS_Atomicmodeling]]
| Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters
|-

| Paper
| [[2013Esquivel_Modelling]]
| Review on modelling (secondary structure, fitting, ...)
|-

| Paper
| [[2013Lopez_Imodfit]]
| Fitting based on vibrational analysis
|-

| Paper
| [[2013Nogales_3DEMLoupe]]
| Normal Mode Analysis of reconstructed volumes
|-

| Paper
| [[2014AlNasr_Secondary]]
| Identification of secondary structure elements in EM volumes
|-

| Paper
| [[2014Politis_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Rey_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Villa_Review]]
| Review of atomic fitting into EM volumes
|-

| Paper
| [[2015Barad_EMRinger]]
| Validation of hybrid models
|-

| Paper
| [[2015Bettadapura_PF2Fit]]
| Fast rigid fitting of PDBs into EM maps
|-

| Paper
| [[2015Carrillo_CapsidMaps]]
| Analysis of virus capsids using Google Maps
|-

| Paper
| [[2015Schroeder_Hybrid]]
| Review on model building
|-

| Paper
| [[2015Tamo_Dynamics]]
| Dynamics in integrative modeling
|-

| Paper
| [[2015Sorzano_AtomsToVoxels]]
| Accurate conversion of an atomic model into a voxel density volume
|-

| Paper
| [[2016Joseph_Evolution]]
| Evolutionary constraints for the fitting of atomic models into density maps
|-

| Paper
| [[2016Segura_3Diana]]
| Validation of hybrid models
|-

| Paper
| [[2016Singharoy_MDFF]]
| Construction of hybrid models driven by EM density and molecular dynamics
|-

| Paper
| [[2016Wang_Rosetta]]
| Construction of hybrid models driven by EM density using Rosetta
|-

| Paper
| [[2017Hryc_WeightedAtoms]]
| Construction of hybrid models by locally weighting the different atoms
|-

|}

=== Books and reviews ===

{|

| Book
| [[1980Herman_Tomography]]
| General book on tomography
|-

| Book
| [[1988Kak_Tomography]]
| General book on tomography
|-

| Paper
| [[2000Tao_Review]]
| Review of single particles
|-

| Paper
| [[2000VanHeel_Review]]
| Review of single particles
|-

| Paper
| [[2002Frank_Review]]
| Review of single particles
|-

| Paper
| [[2002Schmid_Review]]
| Review of single particles
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2004Subramaniam_Review]]
| Review of single particles
|-

| Paper
| [[2005Steven_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_book]]
| Book covering all aspects of electron microscopy of single particles
|-

| Paper
| [[2006Sorzano_Review]]
| Review of optimization problems in electron microscopy
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems in Electron Tomography
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2008Mueller_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2008Taylor_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2010DeRosier_Review]]
| Personal account of how 3DEM developed in the early days
|-

| Chapter
| [[2012Sorzano_Review]]
| Review of single particle analysis using Xmipp
|-

| Chapter
| [[2012Devaux_Protocol]]
| Protocols for performing single particle analysis
|-

| Paper
| [[2014Bai_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Carazo_Review]]
| Review of the reconstruction process
|-

| Paper
| [[2015Cheng_Review]]
| A primer to Single Particle Cryo-EM
|-

| Paper
| [[2015Cheng_Reviewb]]
| Single Particle Cryo-EM at crystallographic resolution
|-

| Paper
| [[2015Elmlund_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Henderson_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Nogales_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Schroeder_Review]]
| Review of advances in the electron microscope
|-

| Paper
| [[2015Wu_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Carroni_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Egelman_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Eisenstein_CryoEM]]
| News feature on the Method of the Year
|-

| Paper
| [[2016FernandezLeiro_Review]]
| Review of EM
|-

| Paper
| [[2016Glaeser_HowGood]]
| How good can cryo-EM become?
|-

| Paper
| [[2016Jonic_PseudoAtoms]]
| Review of the applications of the use of pseudoatoms in EM
|-

| Chapter
| [[2016Mio_Review]]
| Overview of the process to obtain EM reconstructions
|-

| Paper
| [[2016Jonic_Review]]
| A review of computational ways to handle heterogeneity
|-

| Paper
| [[2016Nogales_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Subramaniam_Review]]
| Why cryo-EM is now suitable for crystallographic journals
|-

| Paper
| [[2016Vinothkumar_Review]]
| Historical review and current limitations
|-

| Paper
| [[2017Frank_Review]]
| Historical review of EM
|-

| Paper
| [[2017Jonic_Review]]
| Review of computational methods to analyze conformational variability
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Review of statistical properties of resolution measures defined in Fourier space
|-
|}

=== Software ===

{|

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[1999Lutdke_Eman]]
| Eman
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Baldwin_AngularTransformations]]
| The Transform Class in SPARX and EMAN2
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Grigorieff_Frealign]]
| Frealign
|-

| Paper
| [[2008Scheres_XmippProtocols]]
| Xmipp Protocols
|-

| Paper
| [[2008Shaikh_SpiderProtocols]]
| Spider Protocols
|-

| Paper
| [[2012Wriggers_SitusConventions]]
| Conventions and workflows in Situs
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2015Cianfrocco_Cloud]]
| Software execution in the cloud
|-

| Paper
| [[2015Cheng_MRC2014]]
| Extensions to MRC file format
|-

| Paper
| [[2013DeLaRosa_Scipion]]
| Scipion
|-

| Paper
| [[2016Scheres_Relion]]
| Tutorial on the use of Relion
|-

| Paper
| [[2016Grigorieff_Frealign]]
| Tutorial on the use of Frealign
|-

|}

== Electron tomography ==

=== Image preprocessing ===

{|

| Paper
| [[2015Yan_thickness]]
| Determination of thickness, tilt and electron mean free path
|-

|}

=== Image alignment ===

{|

| Paper
| [[1982Guckenberger_commonOrigin]]
| Determination of a common origin in the micrographs of titl series in three-dimensional electron microscopy
|-

| Paper
| [[1992Lawrence_leastSquares]]
| Least squares solution of the alignment problem
|-

| Paper
| [[1995Penczek_dual]]
| Dual tilt alignment
|-

| Paper
| [[1996Owen_alignmentQuality]]
| Automatic alignment without fiducial markers and evaluation of alignment quality
|-

| Paper
| [[1998Grimm_normalization]]
| Discussion of several gray level normalization methods for electron tomography
|-

| Paper
| [[2001Brandt_Automatic1]]
| Automatic alignment without fiducial markers
|-

| Paper
| [[2001Brandt_Automatic2]]
| Automatic alignment with fiducial markers
|-

| Paper
| [[2006Winkler_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2006Castano_alignment]]
| Alignment with non-perpendicularity
|-

| Paper
| [[2007Castano_alignment]]
| Fiducial-less alignment of cryo-sections
|-

| Paper
| [[2009Sorzano_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2010Cantele_dualAlignment]]
| Alignment of dual series
|-

| Paper
| [[2014Tomonaga_Automatic]]
| Automatic alignment of tilt series using the projection themselves
|-

| Paper
| [[2014Han_Automatic]]
| Automatic alignment of tilt series using SIFT features
|-

| Paper
| [[2015Han_Automatic]]
| Automatic alignment of tilt series using fiducials
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[2003Winkler_CTF]]
| Focus gradient correction in electron tomography
|-

| Paper
| [[2006Fernandez_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Zanetti_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Xiong_CTF]]
| CTF determination and correction for low dose tomographic tilt series
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2017Kunz_3DCTF]]
| 3D CTF Correction
|-

|}

=== 3D reconstruction ===

{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1992Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[1997Marabini_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2002Fernandez_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2007Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[2008Fernandez_CARP]]
| Component Averaged Row Projections (CARP)
|-

| Paper
| [[2012Herman General Superiorization]]
| Superiorization: an optimization heuristic for medical physics
|-

| Paper
| [[2012Zhang_IPET_FETR]]
| IPET and FETR, a reconstruction algorithm for single molecule tomography
|-

| Paper
| [[2013Goris_SIRT_TV_DART]]
| Combination of SIRT, Total Variation and Discrete ART to reconstruct and segment at the same time
|-

| Paper
| [[2013Briegel A_Challenge]]
| The challenge of determining handedness in electron tomography and the use of DNA origami gold nanoparticle helices as molecular standards
|-

| Paper
| [[2013Messaoudi_EnergyFiltered]]
| 3D Reconstruction of Energy-Filtered TEM
|-

| Paper
| [[2016Deng_ICON]]
| 3D Reconstruction with missing information restoration
|-

| Paper
| [[2016Guay_Compressed]]
| 3D Reconstruction using compressed sensing
|-

|}

=== Noise reduction ===
{|

| Paper
| [[2001Frangakis_NAD]]
| Noise reduction with Nonlinear Anisotropic Diffusion
|-

| Paper
| [[2003Fernandez_AND]]
| Anisotropic nonlinear diffusion for electron tomography
|-

| Paper
| [[2003Jiang_Bilateral]]
| Bilateral denoising filter in electron microscopy
|-

| Paper
| [[2005Fernandez_AND]]
| Anisotropic nonlinear denoising in electron tomography
|-

| Paper
| [[2007Heide_median]]
| Iterative median filtering in electron tomography
|-

| Paper
| [[2007Fernandez_autAND]]
| Anisotropic nonlinear diffusion with automated parameter tuning
|-

| Paper
| [[2009Fernandez_Beltrami]]
| Nonlinear filtering based on Beltrami flow
|-

| Paper
| [[2010Bilbao_MeanShift]]
| Mean Shift Filtering
|-

| Paper
| [[2014Kovacik_wedgeArtefacts]]
| Removal of wedge artefacts
|-

| Paper
| [[2014Maiorca_beadArtefacts]]
| Removal of gold bead artefacts
|-

|}

=== Segmentation ===

{|

| Paper
| [[2002Frangakis_Eigenanalysis]]
| Segmentation using eigenvector analysis.
|-

| Paper
| [[2002Volkmann_Watershed]]
| Segmentation using watershed transform.
|-

| Paper
| [[2003Bajaj_BoundarySegmentation]]
| Segmentation based on fast marching.
|-

| Paper
| [[2005Cyrklaff_Thresholding]]
| Segmentation using optimal thresholding.
|-

| Paper
| [[2007Lebbink_TemplateMatching]]
| Segmentation using template matching.
|-

| Paper
| [[2007Sandberg_OrientationFields]]
| Segmentation using orientation fields.
|-

| Paper
| [[2007Sandberg_SegmentationReview]]
| Review on segmentation in electron tomography.
|-

| Paper
| [[2008Garduno_FuzzySegmentation]]
| Segmentation using fuzzy set theory principles.
|-

| Paper
| [[2009Lebbink_TemplateMatching2]]
| Segmentation using template matching.
|-

| Paper
| [[2012RubbiyaAli_EdgeDetection]]
| Parameter-Free Segmentation of Macromolecular Structures.
|-

| Conference
| [[2015Xu_TemplateMatching]]
| Detection of macromolecular complexes with a reduced representation of the templates.
|-

|}

=== Resolution ===
{|

| Paper
| [[2005Cardone_Resolution]]
| Resolution criterion for electron tomography
|-

| Chapter
| [[2007Penczek_Resolution]]
| Review of resolution criteria for electron tomography
|-

| Paper
| [[2015Diebolder_ConicalFSC]]
| Conical Fourier Shell Correlation
|-

|}

=== Subtomogram analysis ===

{|

| Paper
| [[2000Bohm_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2002Frangakis_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2006Nickell_Review]]
| Review of macromolecule finding by template matching (Visual Proteomics)
|-

| Paper
| [[2007Best_Review]]
| Review of Localization of Protein Complexes by Pattern Recognition
|-

| Paper
| [[2007Forster_Review]]
| Review of structure determination by subtomogram averaging
|-

| Paper
| [[2008Forster_Classification]]
| Classification of subtomograms using constrained correlation
|-

| Paper
| [[2008Bartesaghi_Classification]]
| Classification and averaging of subtomograms
|-

| Paper
| [[2008Schmid_Averaging]]
| Alignment and averaging of subtomograms
|-

| Paper
| [[2010Amat_Averaging]]
| Alignment and averaging of subtomograms exploiting thresholding in Fourier space
|-

| Paper
| [[2013Chen_Averaging]]
| Fast alignment of subtomograms using spherical harmonics
|-

| Paper
| [[2013Kuybeda_Averaging]]
| Alignment and averaging of subtomograms using the nuclear norm of the cluster
|-

| Paper
| [[2013Shatsky_Averaging]]
| Alignment and averaging of subtomograms with constrained cross-correlation
|-

| Paper
| [[2014Chen_Autofocus]]
| Subtomogram averaging and classification with special attention to differences
|-

| Paper
| [[2014Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2014Voortman_LimitingFactors]]
| Limiting factors of subtomogram averaging
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2015Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2016Bharat_Relion]]
| Subtomogram averaging with Relion
|-

| Paper
| [[2016Song_MatrixNorm]]
| Matrix norm minimization for tomographic reconstruction and alignment
|-

| Paper
| [[2017Castano_ParticlePicking]]
| Particle picking in tomograms for subtomogram averaging
|-

|}

=== Single particle tomography ===

{|

| Paper
| [[2012Bartesaghi_Constrained]]
| 3D reconstruction by imposing geometrical constraints
|-

| Paper
| [[2015Galaz_SingleParticleTomography]]
| Set of tools for Single Particle Tomography in EMAN2
|-

| Paper
| [[2016Galaz_SingleParticleTomography]]
| Alignment algorithms and CTF correction
|-

|}

=== Books and reviews ===

{|

| Paper
| [[2000Baumeister_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Koster_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Sali_Review]]
| Review of electron tomography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2005Lucic_Review]]
| Review of electron tomography
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_TomoBook]]
| Electron Tomography
|-

| Book
| [[2007McIntosh_Book]]
| Cellular Electron Microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2012Kudryashev_Review]]
| Review of subtomogram averaging
|-

| Paper
| [[2016Beck_Review]]
| Review of molecular sociology
|-

|}

=== Software ===

{|

| Paper
| [[1996Kremer_IMOD]]
| IMOD
|-

| Paper
| [[1996Chen_Priism/IVE]]
| Priism/IVE
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2005Nickell_TOM]]
| TOM Toolbox
|-

| Paper
| [[2007Messaoudi_TomoJ]]
| TomoJ
|-

| Paper
| [[2008Heymann_BsoftTomo]]
| Bsoft
|-

| Paper
| [[2015Ding_CaltechTomography]]
| Caltech tomography database
|-

| Paper
| [[2015Noble_AppionProtomo]]
| Batch fiducial-less tilt-series alignment in Appion using Protomo
|-

| Paper
| [[2015vanAarle_Astra]]
| ASTRA Toolbox
|-

|}

== 2D Crystals ==

=== 2D Preprocessing ===

{|

| Paper
| [[1986Henderson_Processing]]
| General 2D processing
|-

| Paper
| [[2000He_PhaseAlignment]]
| Phase consistency and Alignment
|-

| Paper
| [[2006Gil_Unbending]]
| Crystal unbending
|-

|}

=== Classification ===
{|

| Paper
| [[1988Frank_Classification]]
| MSA and classification in electron crystallography
|-

| Paper
| [[1996Fernandez_SOM]]
| Classification based on self organizing maps
|-

| Paper
| [[1998Sherman_MSA]]
| Classification based on MSA
|-

|}
=== 3D Reconstruction ===

{|

| Paper
| [[1985Wang_Solvent]]
| Solvent flattening
|-

| Paper
| [[1990Henderson_Processing]]
| General 3D processing
|-

| Paper
| [[2004Marabini_ART]]
| Algebraic Reconstruction Technique with blobs for crystals (Xmipp)
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1998Walz_Review]]
| Review of 2D crystallography
|-

| Paper
| [[1999Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Ellis_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of single particles, electron tomography and crystallography
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Gipson_2dx]]
| 2dx
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Philippsen_IPLT]]
| IPLT
|-

|}

== 3D Crystals - MicroED ==

=== Sample Preparation ===
{|
| Paper
| [[2016Shi_Preparation]]
| Sample Preparation
|}
=== Data Collection ===
{|
| Paper
| [[2014Nannenga_CR]]
| Continuous rotation

|}
=== Data Processing ===
{|

| Paper
| [[2011Wisedchaisri_PhaseExtension]]
| Fragment-based phase extension
|-

| Paper
| [[2015Hattne_Processing]]
| Data Processing
|-

| Paper
| [[2016Hattne_Correction]]
| Image correction
|}

=== Software ===
{|

| Paper
| [[2014Iadanza_Processing]]
| Data Processing of still diffraction data
|}

=== Books and Reviews ===
{|
| Paper
| [[2014Nannenga_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Liu_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Rodriguez_Review ]]
| Review of MicroED
|-

|}

== Helical particles ==

=== Filament corrections ===

{|

| Paper
| [[1986Egelman_Curved]]
| Algorithm for correcting curved filaments
|-

| Paper
| [[1988Bluemke_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2006Wang_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2016Yang_Flexible]]
| Algorithm for correcting filaments with flexible subunits
|-

|}

=== Reconstruction ===

{|

| Paper
| [[1952Cochran_Fourier]]
| Fourier Bessel transform of filamentous structures
|-

| Paper
| [[1958Klug_Fourier]]
| Fourier Bessel decomposition of the projection images
|-

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2005Wang_Iterative]]
| Iterative Fourier-Bessel algorithm
|-

| Paper
| [[2007Egelman_Iterative]]
| Iterative real-space algorithm
|-

| Paper
| [[2013Desfosses_Spring]]
| Helical processing with Spring
|-

| Paper
| [[2015Zhang_seam]]
| Workflow for the detection of the lattice seam
|-

| Paper
| [[2016Rohou_Frealix]]
| Helical processing with Frealix
|-

|}

=== Validation ===

{|

| Paper
| [[2014Egelman_ambiguity]]
| How to detect incorrect models
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Carragher_Phoelix]]
| Phoelix
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Owen_Brandeis]]
| Brandeis
|-

|}

== Icosahedral particles ==

=== Reconstruction ===

{|

| Paper
| [[1970Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1971Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1996Fuller_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1997Thuman_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

|}

=== Classification ===

{|

| Paper
| [[2005Scheres_Virus]]
| Classification of virus capsids in real space
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1999Baker_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[1999Conway_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2000Thuman_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Lee_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Navaza_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2006Grunewald_Review]]
| Review of reconstruction of icosahedral viruses
|-

|}

=== Software ===

{|

| Paper
| [[1996Baker_EMPFT]]
| EMPFT
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2013Morin_Sliz SBGrid]]
| SBGrid presentation for eLife
|-

|}

== Databases ==

{|

| Paper
| [[2003Boutselakis_EMSD]]
| EMSD database
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2011Kim_CDDB]]
| Conformational Dynamics Data Bank
|-

| Paper
| [[2011Lawson_EMDB]]
| Electron Microscopy Data Bank
|-

| Paper
| [[2016Iudin_EMPIAR]]
| EMPIAR raw data database
|-

| Paper
| [[2016Patwhardan_EMDB]]
| EMDB, PDB, ...
|-

| Paper
| [[2017Shao_PDBQuality]]
| Quality metrics in PDB
|-

| Blog
| http://www.mybiosoftware.com
| Huge list of bioinformatics programs (many of them structural bioinformatics)
|-

|}

== Relationship to other structural information sources ==

{|

| Paper
| [[2000Engel_AFM]]
| Review of Atomic Force Microscopy
|-

| Paper
| [[2001Dimmeler_AFM]]
| Constraints from Atomic Force Microscopy
|-

| Paper
| [[2003Mobus_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_Review]]
| Review on correlative microscopy
|-

| Paper
| [[2005Boudier_EFTETJ]]
| Software for Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2005Vestergaard_SAXS]]
| Example of comparison of 3DEM and Small-angle X-ray scattering
|-

| Paper
| [[2007Hamada_SAXS]]
| Constraints from Small-angle X-ray scattering
|-

| Paper
| [[2013Xu_FRET]]
| EM+FRET
|-

|}

== X-ray tomography ==

{|

| Paper
| [[2012Oton_ImageFormation]]
| Image formation model in X-ray cell microscopy
|-

|}

== Mathematical tools necessary ==

== People developing methods ==
Please, add yourself to this list (due to privacy reasons, please, do not add anyone else to the list without his/her explicit consent). Sort by first name alphabetical order.

[http://biocomp.cnb.csic.es/~coss Carlos Oscar S. Sorzano]: CSIC, Madrid, Spain 

[http://www.curie.fr/recherche/themes/detail_equipe.cfm/lang/_fr/id_equipe/241.htm Cédric Messaoudi]: Institute Curie, Paris, France 

[http://scholar.google.es/citations?user=_jNYGScAAAAJ&hl=en Javier Vargas]:[mailto:jvargas@cnb.csic.es mail]: CSIC, Madrid, Spain 

[http://scholar.google.es/citations?hl=es&user=g2ZJPIYAAAAJ Joaquín Otón]: CSIC, Madrid, Spain 

[mailto:jrbcast@gmail.com José Román Bilbao-Castro]: UAL, Almería, Spain; CSIC, Madrid, Spain 

[José Miguel de la Rosa Trevín]: Biocomputing Unit CNB-CSIC, Madrid, Spain 

[http://cryoem.janelia.org Tamir Gonen]: [mailto:gonent@janelia.hhmi.org mail]: Howard Hughes Medical Institute, Ashburn, VA, USA 

[mailto:vabrishami@cnb.csic.es Vahid Abrishami]: CSIC, Madrid, Spain 

== 3DEM sites ==
* [http://3dem.ucsd.edu/ 3DEM web site]

* [http://en.wikibooks.org/wiki/Software_Tools_For_Molecular_Microscopy Software tools for molecular microscopy]

* [http://www.emdatabank.org/ The Electron Microscopy Data Bank (EMDB)]

* [http://ccdb.ucsd.edu The Cell Centered Database (CCDB)]

* [http://conventions.cnb.csic.es The geometrical software conventions web page ]

== Editing useful links ==

* [http://www.mediawiki.org/wiki/Help:Formatting Text formatting in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Links Adding links in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Images Adding images in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Tables Making tables in Mediawiki]

2017Hryc WeightedAtoms

2017-05-11T20:37:37Z

CoSS: Created page with "== Citation == Hryc, C. F.; Chen, D.-H.; Afonine, P. V.; Jakana, J.; Wang, Z.; Haase-Pettingell, C.; Jiang, W.; Adams, P. D.; King, J. A.; Schmid, M. F. & Chiu, W. Accurate m..."

== Citation ==

Hryc, C. F.; Chen, D.-H.; Afonine, P. V.; Jakana, J.; Wang, Z.; Haase-Pettingell, C.; Jiang, W.; Adams, P. D.; King, J. A.; Schmid, M. F. & Chiu, W. Accurate model annotation of a near-atomic resolution cryo-EM map. Proceedings of the National Academy of Sciences of the United States of America, 2017, 114, 3103-3108

== Abstract ==

Electron cryomicroscopy (cryo-EM) has been used to determine the atomic coordinates (models) from density maps of biological assemblies. These models can be assessed by their overall fit to the experimental data and stereochemical information. However, these models do not annotate the actual density values of the atoms nor their positional uncertainty. Here, we introduce a computational procedure to derive an atomic model from a cryo-EM map with annotated metadata. The accuracy of such a model is validated by a faithful replication of the experimental cryo-EM map computed using the coordinates and associated metadata. The functional interpretation of any structural features in the model and its utilization for future studies can be made in the context of its measure of uncertainty. We applied this protocol to the 3.3-?? map of the mature P22 bacteriophage capsid, a large and complex macromolecular assembly. With this protocol, we identify and annotate previously undescribed molecular interactions between capsid subunits that are crucial to maintain stability in the absence of cementing proteins or cross-linking, as occur in other bacteriophages.

== Keywords ==

== Links ==

https://www.ncbi.nlm.nih.gov/pubmed/28270620

== Related software ==

== Related methods ==

== Comments ==

Main Page

2017-05-11T20:30:44Z

CoSS: /* Fitting and docking */

== Presentation ==

This web page is intended to be an extensive repository of three-dimensional electron microscopy (3DEM) methods. The advantages of having such a repository are

* You know which are the relevant articles in a particular topic, therefore, paper introductions, reviews, etc. are easier to write and you make sure you will cite all the related articles.
* You will be sure that your paper has more chances of being cited.
* You can add whatever information you find relevant to your method, external links, links to other papers, etc.
* You can link your method to a web page providing the corresponding software, so you know people can use your algorithms.
* You can use the Wiki search capabilities to locate relevant articles even if they are not at the topic you are looking at.
* As a community we will "reconstruct" our history.
* You can select the "watch" option above to receive notifications in case of further changes in the Main Page.

Developing image processing methods for 3DEM is not "[[well-paid]]" in terms of citations and impact factor. However, it is crucial for the advance of the field. Gathering methodological papers in a portal will help to increase the recognition of the field.

Please:

* Add your articles at the right place (you can add a single article in several topics if it is relevant to all of them). The easiest way to add an article is by editing the corresponding topic in the main page, adding your entry, then save the main page. Click on the red link that appears on your new entry, copy and paste the Wiki following code, add the information of your article

== Citation ==

== Abstract ==

== Keywords ==

== Links ==

== Related software ==

== Related methods ==

== Comments ==

* Maintain the information of each article as complete as possible.
* Sort articles by years and authors.
* Be respectful to other people's work.

== How to subscribe to this page ==

You may subscribe to this page so that you will be notified every time someone adds a new method. To do so, you have to register in the page, and edit your preferences ("my preferences"). Be sure that you have activated the option "E-mail me when a page on my watchlist is changed". Finally, click on the "Watch" tab at the top of this page.

You may subscribe to changes on this page on the mailing list 3demmethods@cnb.csic.es. To send a new method to this mail list just send a mail to 3demmethods@cnb.csic.es

To subscribe to this list, visit the web page

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Alternatively, you may write a mail to sympa6@cnb.csic.es with the subject

<code>subscribe 3demmethods YourName YourFamilyName</code>

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To unsubscribe visit the page

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or write sympa6@cnb.csic.es with the subject

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and an empty mail body.

== Electron microscopy images ==

=== Online courses ===

CALTECH: http://cryo-em-course.caltech.edu/

MRC: ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/EM-course/

CNB-CSIC: http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/MadridJan2014EM

Workshop on Computational methods for CryoEM: https://www.youtube.com/watch?v=XdKO1iaPP8o

Workshop on Management of large CryoEM facilities: https://www.youtube.com/watch?v=as4seOPszL0

Icknield Course on Model Building and Refinement for High Resolution EM Maps: http://www.ccpem.ac.uk/training/icknield_2017/icknield_2017.php

=== Image formation ===

{|

| Paper
| [[1971Erickson_CTF]]
| CTF model
|-

| Paper
| [[1971Glaeser_Damage]]
| Radiation damage
|-

| Chapter
| [[1971Hanszen_CTF]]
| Image formation model
|-

| Paper
| [[1971Thon_Model]]
| CTF model
|-

| Paper
| [[1975Unwin_Imaging]]
| Radiation dose
|-

| Paper
| [[1977Wade_Model]]
| CTF model
|-

| Paper
| [[1978Wade_Model]]
| CTF model
|-

| Paper
| [[1979Hayward_Radiation]]
| Radiation damage
|-

| Paper
| [[1984Cohen_Validity]]
| Validity of the CTF model at high frequencies
|-

| Paper
| [[1988Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[1992Wade_Model]]
| CTF model
|-

| Paper
| [[1993Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2004Egerton_Damage]]
| Radiation damage
|-

| Paper
| [[2004Sorzano_Normalization]]
| Background noise is Gaussian
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2009Baxter_NoiseCharacterization]]
| Characterization of the different noise sources in cryo-EM
|-

| Paper
| [[2010Baker_Damage]]
| Radiation damage dependence on resolution
|-

| Paper
| [[2010Bammes_Damage]]
| Radiation damage dependence on temperature
|-

| Paper
| [[2010Gomez_Multislice]]
| Simulation of the multi slice model
|-

| Paper
| [[2010Zewail_FourDimensional]]
| Review on the use of ultrafast EM
|-

| Paper
| [[2011Bammes_CCD]]
| Performance of CCD cameras
|-

| Paper
| [[2011Glaeser_Coma]]
| Image formation model including coma
|-

| Paper
| [[2011Milazzo_DirectDetectors]]
| Evaluation of Direct Detectors
|-

| Paper
| [[2011Rullgard_ImageSimulation]]
| Accurate simulation of EM images
|-

| Paper
| [[2011Zhang LimitingFactors]]
| Limiting factor for atomic resolution in EM
|-

| Paper
| [[2012Bammes_DirectDetection]]
| Performance of Direct detectors
|-

| Paper
| [[2012Campbell_MotionCorrection]]
| Beam induced motion correction and direct detectors
|-

| Paper
| [[2012Shang_HydrationLayer]]
| Simulation of PDB volumes explicitly considering the hydration layer
|-

| Paper
| [[2013Egerton_RadiationDamage]]
| Review of TEM radiation damage and experimental ways of reducing it
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu H_Noisemodels]]
| Noise models and cryo-EM drift correction with a direct-electron camera
|-

| Paper
| [[2013Li X K2 noisemodels]]
| Influence of electron dose rate on electron counting images recorded with the K2 camera
|-

| Paper
| [[2013Vulovic_CTFApproximations]]
| When to use the different approximations performed so that a projection with linear CTF is valid
|-

| Thesis
| [[2013Vulovic_ImageFormation]]
| Ph.D. Thesis on the image formation in cryo-EM
|-

| Paper
| [[2014Danev_PhasePlate]]
| Volta potential phase plate
|-

| Paper
| [[2015Chiu_K2]]
| Characterization of K2
|-

| Paper
| [[2015Hawkes_AberrationCorrection]]
| Historical account of the development of lens corrections
|-

| Paper
| [[2015Koeck_Quadratic]]
| Limitations of the linear approximation and use of the quadratic terms
|-

| Paper
| [[2015Kuijper_FEI]]
| Description of the FEI Falcons
|-

| Paper
| [[2015Lobato_MULTEM]]
| Simulation of multislice diffraction
|-

| Paper
| [[2015McMullan_AmorphousIce]]
| Beam induced movement is caused by Brownian motion
|-

| Paper
| [[2016Koeck_ADF]]
| Simulations of Annular Dark Field TEM
|-

| Paper
| [[2017Mishyna_DNARadiation]]
| Review of radiation damage on DNA
|-

|}

=== Collection geometry ===

{|

| Chapter
| [[1980Hoppe_Wedge]]
| Missing wedge
|-

| Paper
| [[1987Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1995Penczek_Dual]]
| Dual axis tomography
|-

| Paper
| [[1997Mastronarde_Dual]]
| Dual axis tomography
|-

| Paper
| [[2003Ludtke_FocusPairs]]
| Focus pairs for single particles
|-

| Paper
| [[2005Lanzavecchia_Conical]]
| Conical tomography
|-

| Paper
| [[2005Zampighi_Conical]]
| Conical tomography
|-

| Paper
| [[2006Leschziner_OT]]
| Orthogonal Tilt
|-

| Paper
| [[2006Messaoudi_Multiple]]
| Multiple axis tomography
|-

| Paper
| [[2012Kudryashev_FocusPairs]]
| Focus pairs tomography
|-

| Paper
| [[2014Hovden_TiltFocus]]
| Combining tilt series with focus series
|-

| Paper
| [[2015Sorzano_RandomConicalTilt]]
| General formulation of Random Conical Tilt
|-

| Paper
| [[2017Hagen_DoseTomography]]
| Dose optimization for subtomogram averaging
|-

|}

=== Sample preparation ===

{|

| Paper
| [[1982Dubochet_Sample]]
| Vitreous ice
|-

| Paper
| [[1986Lepault_Sample]]
| Fast freezing
|-

| Paper
| [[1995Dubochet_Sample]]
| High-pressure freezing
|-

| Paper
| [[1995VanMarle_Sample]]
| Sample damages in resin
|-

| Paper
| [[1998Adrian_Sample]]
| Cryo negative staining
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2002Hsieh_Sample]]
| Cryofixation
|-

| Paper
| [[2004AlAmoudi_Sample]]
| CEMOVIS
|-

| Paper
| [[2008Studer_Sample]]
| Review on high pressure freezing
|-

| Paper
| [[2009Pierson_Sample]]
| Review on sample preparation for electron tomography
|-

| Paper
| [[2010Zhang_NegativeStaining]]
| Negative staining for small protein imaging
|-

| Paper
| [[2012Zhang_PositiveStaining]]
| Positive staining
|-

| Paper
| [[2014Rames_NegativeStaining]]
| Optimized negative staining
|-

| Paper
| [[2014Russo_GoldGrids]]
| Gold grids for single particles
|-

| Paper
| [[2015Cabra_Sample]]
| Review on sample preparation for single particles with videos
|-

| Paper
| [[2016Passmore_Review]]
| Tutorial chapter on sample preparation
|-

| Paper
| [[2016Razinkov_Vitrification]]
| New vitrification method
|-

| Paper
| [[2016Takizawa_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2016Thompson_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2017Peitsch_Sample]]
| iMEM: Isolation of Plasma Membrane for Cryoelectron Microscopy
|-

|}

=== Automated data collection ===

{|

| Paper
| [[1992Dierksen_Automatic]]
| Automated data collection
|-

| Paper
| [[1992Koster_Automatic]]
| Automated data collection
|-

| Paper
| [[1996Fung_Automatic]]
| Automated data collection for tomography
|-

| Paper
| [[2001Zhang_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2003Ziese_Automatic]]
| Automated autofocusing
|-

| Paper
| [[2004Potter_Automatic]]
| Automated sample loading
|-

| Paper
| [[2004Zheng_Automatic]]
| Automated data collection
|-

| Paper
| [[2005Lei_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2005Suloway_Automatic]]
| Automated data collection: Leginon
|-

| Paper
| [[2007Yoshioka_RCT]]
| Automated Random Conical Tilt
|-

| Paper
| [[2011Korinek_TOM2]]
| Automated acquisition with TOM2
|-

| Paper
| [[2015Li_UCSFImage]]
| Automated acquisition with UCSFImage
|-

| Paper
| [[2016Gil_Fuzzy]]
| Real time decisions during acquisition with neuro-fuzzy method
|-

| Paper
| [[2016Liu_TiltControl]]
| Accurate control of the tilt angle for electron tomography
|-

| Paper
| [[2016Vargas_FoilHole]]
| Determination of image quality at low magnification
|-

|}

== Single particles ==

=== Automatic particle picking ===

{|

| Paper
| [[1982VanHeel_Detection]]
| Detection of particles in micrographs
|-

| Paper
| [[2001Nicholson_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2001Zhu_Filaments]]
| Automatic identification of filaments in micrographs
|-

| Paper
| [[2004Sigworth_Detection]]
| Classical detection theory and the cryo-EM particle selection problem
|-

| Paper
| [[2004Volkmann_ParticlePicking]]
| An approach to automated particle picking from electron micrographs based on reduced representation templates
|-

| Paper
| [[2004Wong_ParticlePicking]]
| Model-based particle picking for cryo-electron microscopy
|-

| Paper
| [[2004Zhu_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2007Chen_Signature]]
| Automatic particle picking program: Signature
|-

| Paper
| [[2007Woolford_SwarmPS]]
| Automatic particle picking with several criteria, implemented in EMAN Boxer
|-

| Paper
| [[2009Sorzano_MachineLearning]]
| Automatic particle picking based on machine learning of rotational invariants
|-

| Paper
| [[2011Arbelaez_Comparison]]
| Evaluation of the performance of software for automated particle-boxing
|-

| Paper
| [[2013Abrishami_MachineLearning]]
| A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs
|-

| Paper
| [[2013Hauer_2013]]
| Automatic tilt pair detection in Random Conical Tilt
|-

| Paper
| [[2013Shatsky_ParticlePicking]]
| Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Langlois_ParticlePicking]]
| Automatic particle picking
|-

| Paper
| [[2016Vilas_AutomaticTilt]]
| Automatic identification of image pairs in untilted-tilted micrograph pairs
|-

|}

=== 2D Preprocessing ===

{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast enhancement through DPR
|-

| Paper
| [[2004Sorzano_Normalization]]
| Normalization procedures and their statistical properties.
|-

| Paper
| [[2006Sorzano_Denoising]]
| Strong denoising in wavelet space
|-

| Conference
| [[2009Sorzano_Downsampling]]
| Differences between the different downsampling schemes
|-

| Paper
| [[2012Brilot_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Campbell_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Zhao_Denoising]]
| Denoising using an invariant Fourier-Bessel eigenspace
|-

| Paper
| [[2013Norousi_Screening]]
| Screening particles to identify outliers
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu_Movies]]
| Drift correction for movies considering dark field
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Scheres_Movies]]
| Beam induced motion correction
|-

| Paper
| [[2015Abrishami_Movies]]
| Alignment of direct detection device micrographs
|-

| Paper
| [[2015Grant_Anisotropic]]
| Automatic estimation and correction of anisotropic magnification
|-

| Paper
| [[2015Grant_OptimalExposure]]
| Filter movies according to the radiation damage
|-

| Paper
| [[2015Rubinstein_Alignment]]
| Frame alignment at the level of particle
|-

| Paper
| [[2015Spear_DoseCompensation]]
| Effect of dose compensation on resolution
|-

| Paper
| [[2015Zhao_AnisotropicMagnification]]
| Correction of anisotropic magnification
|-

| Conference
| [[2016Bajic_Denoising]]
| Denoising and deconvolution of micrographs
|-

| Paper
| [[2016Jensen_RemovalVesicles]]
| Removal of vesicles in membrane proteins
|-

| Paper
| [[2016Bhamre_Denoising]]
| Denoising by 2D covariance estimation
|-

| Paper
| [[2017McLeod_Zorro]]
| Movie alignment by Zorro
|-

|}

=== 2D Alignment ===

{|

| Paper
| [[1981Frank_Averaging]]
| 2D averaging and phase residual
|-

| Paper
| [[1982Saxton_Averaging]]
| 2D averaging using correlation
|-

| Paper
| [[1998Sigworth_ML2D]]
| Maximum likelihood alignment in 2D
|-

| Paper
| [[2003Cong_FRM2D]]
| Fast Rotational Matching in 2D
|-

| Paper
| [[2005Cong_FRM2D]]
| Fast Rotational Matching in 2D introduced in a 3D Alignment algorithm
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

|}

=== 2D Classification and clustering ===

{|

| Paper
| [[1981VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[1984VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2011Singer_DiffusionMaps]]
| Classification in 2D based on graph analysis of the projections
|-

| Paper
| [[2012Yang_ISAC]]
| Iterative Stable Alignment and clustering
|-

| Paper
| [[2014Sorzano_Outlier]]
| Outlier detection in 2D classifications.
|-

| Paper
| [[2014Zhao_Aspire]]
| Fast classification based on rotational invariants and vector diffusion maps
|-

| Paper
| [[2015Huang_Robust]]
| Robust w-estimators of 2D classes
|-

| Paper
| [[2016Reboul_Stochastic]]
| Stochastic Hill Climbing for calculating 2D classes
|-

| Conference
| [[2017Bhamre_Mahalanobis]]
| 2D classification using Mahalanobis distance
|-

|}

=== 3D Alignment ===

{|

| Paper
| [[1980Kam_AutoCorrelation]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[1986Goncharov_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1987VanHeel_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1988Provencher_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Vogel_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1990Gelfand_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Goncharov_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Harauz_Quaternions]]
| Use of quaternions to represent rotations
|-

| Paper
| [[1994Penczek_Real]]
| Angular assignment using projection matching in real space
|-

| Paper
| [[1994Radermacher_Radon]]
| Angular assignment in Radon space
|-

| Paper
| [[1996Penczek_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[2003Rosenthal_DPR]]
| Angular assignment using DPR
|-

| Paper
| [[2004Sorzano_Wavelet]]
| Angular assignment in the wavelet space.
|-

| Paper
| [[2005Jonic_Splines]]
| Angular assignment in Fourier space using spline interpolation.
|-

| Paper
| [[2005Yang_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[2006Ogura_SimulatedAnnealing]]
| Angular asignment by simulated annealing
|-

| Paper
| [[2007Grigorieff_Continuous]]
| Continuous angular assignment in Fourier space
|-

| Paper
| [[2010Jaitly_Bayesian]]
| Angular assignment by a Bayesian method and annealing
|-

| Paper
| [[2010Sanz_Random]]
| Random model method
|-

| Paper
| [[2010Singer_Voting]]
| Detecting consistent common lines by voting (reference free)
|-

| Paper
| [[2011Singer_SDP]]
| Angular assignment by semidefinite programming and eigenvectors (reference free)
|-

| Paper
| [[2012Giannakis_Scattering]]
| Construction of an initial volume, reference free, by graph analysis of the projections
|-

| Paper
| [[2012Shkolnisky_Sync]]
| Angular assignment by synchronization of rotations (reference free)
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Wang_LUD]]
| Angular assignment by least unsquared deviations (reference free)
|-

| Paper
| [[2014Vargas_RANSAC]]
| Initial model using RANSAC (reference free)
|-

| Paper
| [[2015Joubert_Pseudoatoms]]
| Initial model based on pseudo-atoms
|-

| Paper
| [[2015Singer_Kam]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[2015Sorzano_Significant]]
| Statistical approach to the initial volume estimation (reconstruct significant)
|-

| Conference
| [[2016Michels_Heterogeneous]]
| Initial volume in the presence of heterogeneity
|-

| Paper
| [[2016Cossio_BayesianGPU]]
| GPU implementation of the Bayesian 3D reconstruction approach
|-

|}

=== 3D Reconstruction ===
{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1986Harauz_FBP]]
| Exact filters for Filtered Back Projection
|-

| Chapter
| [[1992Radermacher_WBP]]
| Exact filters for Weighted Back Projection
|-

| Paper
| [[1997Zhu_RecCTF]]
| 3D Reconstruction (SIRT like) and simultaneous CTF correction
|-

| Paper
| [[1998Boisset_Uneven]]
| Artifacts in SIRT and WBP under uneven angular distributions
|-

| Paper
| [[1998Marabini_ART]]
| Algebraic Reconstruction Technique with blobs (Xmipp)
|-

| Paper
| [[2001Sorzano_Uneven]]
| Free parameter selection under uneven angular distributions
|-

| Paper
| [[2005Sorzano_Parameters]]
| Free parameter selection for optimizing multiple tasks
|-

| Paper
| [[2008Sorzano_Constraints]]
| Mass, surface, positivity and symmetry constraints for real-space algorithms
|-

| Paper
| [[2009Bilbao_ParallelART]]
| Efficient parallelization of ART
|-

| Paper
| [[2011Li_GradientFlow]]
| Regularized 3D Reconstruction by Gradient Flow
|-

| Paper
| [[2011Vonesch_Wavelets]]
| Fast wavelet-based 3D reconstruction
|-

| Paper
| [[2012Gopinath_ShapeRegularization]]
| Regularized 3D Reconstruction by Shape information
|-

| Paper
| [[2012Kucukelbir_adaptiveBasis]]
| 3D reconstruction in an adaptive basis promoting sparsity
|-

| Paper
| [[2012Sindelar_NoiseReduction]]
| Optimal noise reduction in 3D reconstructions
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Lyumkis_Optimod]]
| Construction of initial volumes with Optimod
|-

| Paper
| [[2013Wang FIRM]]
| Fast 3D reconstruction in Fourier domain
|-

| Paper
| [[2014Kunz_SART_OS]]
| Simultaneous ART with OS
|-

| Paper
| [[2015Abrishami_Fourier]]
| 3D Reconstruction in Fourier space
|-

| Paper
| [[2015Dvornek_SubspaceEM]]
| Fast Maximum a posteriori
|-

| Paper
| [[2015Moriya_Bayesian]]
| Bayesian approach to suppress limited angular artifacts
|-

| Paper
| [[2015Xu_GeometricFlow]]
| Multi-scale geometric flow
|-

| Arxiv
| [[2016Ye_Cohomology]]
| Cohomology properties of 3D reconstruction
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

|}

=== 3D Heterogeneity ===

{|

| Paper
| [[2004White_Size]]
| Heterogeneity classification of differently sized images
|-

| Paper
| [[2006Penczek_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Scheres_ML3D]]
| Maximum Likelihood alignment and classification in 3D
|-

| Paper
| [[2009Spahn_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2010Elmlund_AbInitio]]
| Solving the initial volume problem with multiple conformations
|-

| Paper
| [[2010Shatsky_MultiVariate]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2012Scheres_Bayesian]]
| A Bayesian view on cryo-EM structure determination
|-

| Paper
| [[2012Zheng_Covariance]]
| Estimation of the volume covariance
|-

| Paper
| [[2013Wang_MLVariance]]
| Maximum Likelihood estimate of the map variance
|-

| Paper
| [[2013Lyumkis D_FREALIGN]]
| Likelihood-based classification of cryo-EM images using FREALIGN.
|-

| Paper
| [[2014Jin_NMA]]
| Continuous heterogeneity through Normal Mode Analysis
|-

| Paper
| [[2014Dashti_Brownian]]
| Continuous heterogeneity through Brownian trajectories
|-

| Paper
| [[2014Chen_Migration]]
| Particle migration analysis in 3D classification
|-

| Paper
| [[2015Anden_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Bai_Focused]]
| Focused classification
|-

| Paper
| [[2015Katsevich_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Klaholz_MRA]]
| Multivariate Statistical Analysis of Jackknife and Bootstrapping on random subsets
|-

| Paper
| [[2015Liao_Covariance]]
| Estimation of the 3D covariance from 2D projections
|-

| Paper
| [[2015Tagare_Direct]]
| Direct reconstruction of PCA components
|-

| Paper
| [[2016Gong_Mechanical]]
| Mechanical model for macromolecules
|-

| Paper
| [[2016Rawson_Movement]]
| Movement and flexibility
|-

| Paper
| [[2016Sorzano_StructMap]]
| Sorting a discrete set of conformational states
|-

| Paper
| [[2016Sorzano_Strain]]
| Calculate local stretches, strains and rotations from two conformational states
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

|}

=== Validation ===

{|

| Paper
| [[2008Stagg_TestBed]]
| Effect of voltage, dosis, number of particles and Euler jumps on resolution
|-

| Paper
| [[2011Henderson]]
| Tilt Validation
|-

| Paper
| [[2011Read]]
| Validation of PDBs
|-

| Paper
| [[2012Henderson]]
| EM Map Validation
|-

| Paper
| [[2013Cossio_Bayesian]]
| EM Map Validation in a probabilistic setting
|-

| Paper
| [[2013Chen_NoiseSubstitution]]
| Noise substitution at high resolution for measuring overfitting
|-

| Paper
| [[2014Russo_StatisticalSignificance]]
| EM Map Validation through the statistical significance of the tilt-pair angular assignment
|-

| Paper
| [[2014Stagg_Reslog]]
| EM Map Validation through the resolution evolution with the number of particles
|-

| Paper
| [[2014Wasilewski_Tilt]]
| Web implementation of the tilt pair validation
|-

| Paper
| [[2015Heymann_Alignability]]
| EM Map Validation through the resolution of reconstructions from particles and noise
|-

| Paper
| [[2015Oliveira_FreqLimited]]
| Comparison of gold standard and frequency limited optimization
|-

| Paper
| [[2015Wriggers_Secondary]]
| Validation by secondary structure
|-

| Paper
| [[2016Kim_SAXS]]
| Comparison of SAXS data and EM projections
|-

| Paper
| [[2016Rosenthal_Review]]
| Review of validation methods
|-

| Paper
| [[2016Vargas_Alignability]]
| Validation by studying the tendency of an angular assignment to cluster in the projection space
|-

| Paper
| [[2017Monroe_PDBRefinement]]
| Validation by comparison to a refined PDB
|-

|}

=== Resolution ===

{|

| Paper
| [[1986Harauz_FBP]]
| Fourier Shell Correlation
|-

| Paper
| [[1987Unser_SSNR]]
| 2D Spectral Signal to Noise Ratio
|-

| Paper
| [[2002Penczek_SSNR]]
| 3D Spectral Signal to Noise Ratio for Fourier based algorithms
|-

| Paper
| [[2003Rosenthal_DPR]]
| Review of the FSC and establishment of a new threshold
|-

| Paper
| [[2005Unser_SSNR]]
| 3D Spectral Signal to Noise Ratio for any kind of algorithms
|-

| Paper
| [[2005VanHeel_FSC]]
| Establishment of a new threshold for FSC
|-

| Paper
| [[2007Sousa_AbInitio]]
| Resolution measurement on neighbour Fourier voxels
|-

| Paper
| [[2014Kucukelbir_Local]]
| Quantifying the local resolution of cryo-EM density maps
|-

| Paper
| [[2016Pintilie_Probabilistic]]
| Probabilistic models and resolution
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Statistical properties of resolution measures defined in Fourier space
|-

|}

=== Sharpening of high resolution information ===
{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast restoration and map sharpening
|-

| Paper
| [[2008Fernandez_Bfactor]]
| Bfactor determination and restoration
|-

| Paper
| [[2013Fiddy_SaxtonAlgorithm]]
| Phase retrieval or extension
|-

| Paper
| [[2014Kishchenko_SphericalDeconvolution]]
| Spherical deconvolution
|-

| Paper
| [[2015Spiegel_VISDEM]]
| Visualization improvement by the use of pseudoatomic profiles
|-

| Paper
| [[2016Jonic_Pseudoatoms]]
| Approximation with pseudoatoms
|-

| Paper
| [[2016Jonic_Denoising]]
| Denoising and high-frequency boosting by pseudoatom approximation
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[1982Schiske_Correction]]
| CTF correction for tilted objects
|-

| Paper
| [[1988Toyoshima_Model]]
| CTF estimation
|-

| Paper
| [[1995Frank_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1996Skoglund_MaxEnt]]
| CTF correction with Maximum Entropy
|-

| Paper
| [[1996Zhou_Model]]
| CTF model and user interface for manual fitting
|-

| Paper
| [[1997Fernandez_AR]]
| PSD estimation using periodogram averaging and AR models
|-

| Paper
| [[1997Penczek_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1997Stark_Deconvolution]]
| CTF correction using deconvolution
|-

| Paper
| [[1997Zhu_RecCTF]]
| CTF correction and reconstruction
|-

| Paper
| [[2000DeRosier_EwaldCorrection]]
| CTF correction considering the Ewald sphere
|-

| Paper
| [[2000Jensen_TiltedCorrection]]
| CTF correction considering tilt in backprojection
|-

| Paper
| [[2001Saad_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Huang_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Mindell_CTFTILT]]
| CTF estimation for tilted micrographs
|-

| Paper
| [[2003Sander_MSA]]
| CTF estimation through MSA classification of PSDs
|-

| Paper
| [[2003Velazquez_ARMA]]
| PSD and CTF estimation using ARMA models
|-

| Paper
| [[2004Sorzano_IDR]]
| CTF restoration and reconstruction with Iterative Data Refinement
|-

| Conference
| [[2004Wan_CTF]]
| Spatially variant CTF
|-

| Paper
| [[2004Zubelli_Chahine]]
| CTF restoration and reconstruction with Chahine's multiplicative method
|-

| Conference
| [[2005Dubowy_SpaceVariant]]
| CTF correction when this is space variant
|-

| Paper
| [[2005Mallick_ACE]]
| CTF estimation
|-

| Paper
| [[2006Wolf_Ewald]]
| CTF correction considering Ewald sphere
|-

| Paper
| [[2007Jonic_EnhancedPSD]]
| PSD enhancement for better identification of Thon rings; Vitreous ice diffracts in Thon rings
|-

| Paper
| [[2007Philippsen_Model]]
| CTF Model for tilted specimens
|-

| Paper
| [[2007Sorzano_CTF]]
| CTF estimation using enhanced PSDs
|-

| Paper
| [[2009Sorzano_Sensitivity]]
| Error sensitivity of the CTF models, non-uniqueness of the CTF parameters
|-

| Paper
| [[2010Jiang2010_CTFCorrection]]
| Amplitude correction method
|-

| Paper
| [[2010Kasantsev_CTFCorrection]]
| Mathematical foundations of Kornberg and Jensen method
|-

| Paper
| [[2010Leong_CTFCorrection]]
| Correction for spatially variant CTF
|-

| Paper
| [[2011Glaeser_Coma]]
| The effect of coma at high-resolution
|-

| Paper
| [[2011Mariani_Tilted]]
| CTF simulation and correction of tilted specimens
|-

| Paper
| [[2011Sindelar_Wiener]]
| CTF correction using a modified version of Wiener filter
|-

| Paper
| [[2011Voortman_Tilted]]
| CTF correction for tilted specimen
|-

| Paper
| [[2012Voortman_VaryingCTF]]
| Correcting a spatially varying CTF
|-

| Paper
| [[2013Vargas_FastDef]]
| Fast defocus
|-

| Paper
| [[2015Rohou_CTFFind4]]
| CTF Find 4
|-

| Paper
| [[2015Sheth_CTFquality]]
| Visualization and quality assessment of CTF
|-

| Paper
| [[2016Zhang_GCTF]]
| gCTF
|-

|}

=== Segmentation ===

{|

| Paper
| [[2006Baker_segmentation]]
| Segmentation of molecular subunits
|-

|}

=== Fitting and docking ===

{|

| Paper
| [[1999Volkmann_Fitting]]
| Fitting in real space
|-

| Paper
| [[2001Baker_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2001Jones_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2003Kovacs_FRM3D]]
| Fast Rotational Alignment of two EM maps
|-

| Paper
| [[2004Tama_NMA1]]
| Flexible fitting with Normal Modes (I)
|-

| Paper
| [[2004Tama_NMA2]]
| Flexible fitting with Normal Modes (II)
|-

| Paper
| [[2005Velazquez_Superfamilies]]
| Recognition of the superfamily folding in medium-high resolution volumes
|-

| Paper
| [[2007DeVries_Haddock]]
| Docking with Haddock 2.0
|-

| Paper
| [[2007Kleywegt_QualityControl]]
| Quality control and validation of fitting
|-

| Paper
| [[2012Biswas_Secondary]]
| Secondary structure determination in EM volumes
|-

| Paper
| [[2012Velazquez_Constraints]]
| Multicomponent fitting by using constraints from other information sources
|-

| Paper
| [[2013Chapman MS_Atomicmodeling]]
| Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters
|-

| Paper
| [[2013Esquivel_Modelling]]
| Review on modelling (secondary structure, fitting, ...)
|-

| Paper
| [[2013Lopez_Imodfit]]
| Fitting based on vibrational analysis
|-

| Paper
| [[2013Nogales_3DEMLoupe]]
| Normal Mode Analysis of reconstructed volumes
|-

| Paper
| [[2014AlNasr_Secondary]]
| Identification of secondary structure elements in EM volumes
|-

| Paper
| [[2014Politis_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Rey_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Villa_Review]]
| Review of atomic fitting into EM volumes
|-

| Paper
| [[2015Barad_EMRinger]]
| Validation of hybrid models
|-

| Paper
| [[2015Bettadapura_PF2Fit]]
| Fast rigid fitting of PDBs into EM maps
|-

| Paper
| [[2015Carrillo_CapsidMaps]]
| Analysis of virus capsids using Google Maps
|-

| Paper
| [[2015Schroeder_Hybrid]]
| Review on model building
|-

| Paper
| [[2015Tamo_Dynamics]]
| Dynamics in integrative modeling
|-

| Paper
| [[2015Sorzano_AtomsToVoxels]]
| Accurate conversion of an atomic model into a voxel density volume
|-

| Paper
| [[2016Joseph_Evolution]]
| Evolutionary constraints for the fitting of atomic models into density maps
|-

| Paper
| [[2016Segura_3Diana]]
| Validation of hybrid models
|-

| Paper
| [[2016Singharoy_MDFF]]
| Construction of hybrid models driven by EM density and molecular dynamics
|-

| Paper
| [[2016Wang_Rosetta]]
| Construction of hybrid models driven by EM density using Rosetta
|-

| Paper
| [[2017Hryc_WeightedAtoms]]
| Construction of hybrid models by locally weighting the different atoms
|-

|}

=== Books and reviews ===

{|

| Book
| [[1980Herman_Tomography]]
| General book on tomography
|-

| Book
| [[1988Kak_Tomography]]
| General book on tomography
|-

| Paper
| [[2000Tao_Review]]
| Review of single particles
|-

| Paper
| [[2000VanHeel_Review]]
| Review of single particles
|-

| Paper
| [[2002Frank_Review]]
| Review of single particles
|-

| Paper
| [[2002Schmid_Review]]
| Review of single particles
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2004Subramaniam_Review]]
| Review of single particles
|-

| Paper
| [[2005Steven_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_book]]
| Book covering all aspects of electron microscopy of single particles
|-

| Paper
| [[2006Sorzano_Review]]
| Review of optimization problems in electron microscopy
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems in Electron Tomography
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2008Mueller_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2008Taylor_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2010DeRosier_Review]]
| Personal account of how 3DEM developed in the early days
|-

| Chapter
| [[2012Sorzano_Review]]
| Review of single particle analysis using Xmipp
|-

| Chapter
| [[2012Devaux_Protocol]]
| Protocols for performing single particle analysis
|-

| Paper
| [[2014Bai_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Carazo_Review]]
| Review of the reconstruction process
|-

| Paper
| [[2015Cheng_Review]]
| A primer to Single Particle Cryo-EM
|-

| Paper
| [[2015Cheng_Reviewb]]
| Single Particle Cryo-EM at crystallographic resolution
|-

| Paper
| [[2015Elmlund_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Henderson_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Nogales_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Schroeder_Review]]
| Review of advances in the electron microscope
|-

| Paper
| [[2015Wu_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Carroni_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Egelman_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Eisenstein_CryoEM]]
| News feature on the Method of the Year
|-

| Paper
| [[2016FernandezLeiro_Review]]
| Review of EM
|-

| Paper
| [[2016Glaeser_HowGood]]
| How good can cryo-EM become?
|-

| Paper
| [[2016Jonic_PseudoAtoms]]
| Review of the applications of the use of pseudoatoms in EM
|-

| Chapter
| [[2016Mio_Review]]
| Overview of the process to obtain EM reconstructions
|-

| Paper
| [[2016Jonic_Review]]
| A review of computational ways to handle heterogeneity
|-

| Paper
| [[2016Nogales_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Subramaniam_Review]]
| Why cryo-EM is now suitable for crystallographic journals
|-

| Paper
| [[2016Vinothkumar_Review]]
| Historical review and current limitations
|-

| Paper
| [[2017Frank_Review]]
| Historical review of EM
|-

| Paper
| [[2017Jonic_Review]]
| Review of computational methods to analyze conformational variability
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Review of statistical properties of resolution measures defined in Fourier space
|-
|}

=== Software ===

{|

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[1999Lutdke_Eman]]
| Eman
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Baldwin_AngularTransformations]]
| The Transform Class in SPARX and EMAN2
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Grigorieff_Frealign]]
| Frealign
|-

| Paper
| [[2008Scheres_XmippProtocols]]
| Xmipp Protocols
|-

| Paper
| [[2008Shaikh_SpiderProtocols]]
| Spider Protocols
|-

| Paper
| [[2012Wriggers_SitusConventions]]
| Conventions and workflows in Situs
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2015Cianfrocco_Cloud]]
| Software execution in the cloud
|-

| Paper
| [[2015Cheng_MRC2014]]
| Extensions to MRC file format
|-

| Paper
| [[2013DeLaRosa_Scipion]]
| Scipion
|-

| Paper
| [[2016Scheres_Relion]]
| Tutorial on the use of Relion
|-

| Paper
| [[2016Grigorieff_Frealign]]
| Tutorial on the use of Frealign
|-

|}

== Electron tomography ==

=== Image preprocessing ===

{|

| Paper
| [[2015Yan_thickness]]
| Determination of thickness, tilt and electron mean free path
|-

|}

=== Image alignment ===

{|

| Paper
| [[1982Guckenberger_commonOrigin]]
| Determination of a common origin in the micrographs of titl series in three-dimensional electron microscopy
|-

| Paper
| [[1992Lawrence_leastSquares]]
| Least squares solution of the alignment problem
|-

| Paper
| [[1995Penczek_dual]]
| Dual tilt alignment
|-

| Paper
| [[1996Owen_alignmentQuality]]
| Automatic alignment without fiducial markers and evaluation of alignment quality
|-

| Paper
| [[1998Grimm_normalization]]
| Discussion of several gray level normalization methods for electron tomography
|-

| Paper
| [[2001Brandt_Automatic1]]
| Automatic alignment without fiducial markers
|-

| Paper
| [[2001Brandt_Automatic2]]
| Automatic alignment with fiducial markers
|-

| Paper
| [[2006Winkler_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2006Castano_alignment]]
| Alignment with non-perpendicularity
|-

| Paper
| [[2007Castano_alignment]]
| Fiducial-less alignment of cryo-sections
|-

| Paper
| [[2009Sorzano_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2010Cantele_dualAlignment]]
| Alignment of dual series
|-

| Paper
| [[2014Tomonaga_Automatic]]
| Automatic alignment of tilt series using the projection themselves
|-

| Paper
| [[2014Han_Automatic]]
| Automatic alignment of tilt series using SIFT features
|-

| Paper
| [[2015Han_Automatic]]
| Automatic alignment of tilt series using fiducials
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[2003Winkler_CTF]]
| Focus gradient correction in electron tomography
|-

| Paper
| [[2006Fernandez_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Zanetti_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Xiong_CTF]]
| CTF determination and correction for low dose tomographic tilt series
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2017Kunz_3DCTF]]
| 3D CTF Correction
|-

|}

=== 3D reconstruction ===

{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1992Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[1997Marabini_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2002Fernandez_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2007Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[2008Fernandez_CARP]]
| Component Averaged Row Projections (CARP)
|-

| Paper
| [[2012Herman General Superiorization]]
| Superiorization: an optimization heuristic for medical physics
|-

| Paper
| [[2012Zhang_IPET_FETR]]
| IPET and FETR, a reconstruction algorithm for single molecule tomography
|-

| Paper
| [[2013Goris_SIRT_TV_DART]]
| Combination of SIRT, Total Variation and Discrete ART to reconstruct and segment at the same time
|-

| Paper
| [[2013Briegel A_Challenge]]
| The challenge of determining handedness in electron tomography and the use of DNA origami gold nanoparticle helices as molecular standards
|-

| Paper
| [[2013Messaoudi_EnergyFiltered]]
| 3D Reconstruction of Energy-Filtered TEM
|-

| Paper
| [[2016Deng_ICON]]
| 3D Reconstruction with missing information restoration
|-

| Paper
| [[2016Guay_Compressed]]
| 3D Reconstruction using compressed sensing
|-

|}

=== Noise reduction ===
{|

| Paper
| [[2001Frangakis_NAD]]
| Noise reduction with Nonlinear Anisotropic Diffusion
|-

| Paper
| [[2003Fernandez_AND]]
| Anisotropic nonlinear diffusion for electron tomography
|-

| Paper
| [[2003Jiang_Bilateral]]
| Bilateral denoising filter in electron microscopy
|-

| Paper
| [[2005Fernandez_AND]]
| Anisotropic nonlinear denoising in electron tomography
|-

| Paper
| [[2007Heide_median]]
| Iterative median filtering in electron tomography
|-

| Paper
| [[2007Fernandez_autAND]]
| Anisotropic nonlinear diffusion with automated parameter tuning
|-

| Paper
| [[2009Fernandez_Beltrami]]
| Nonlinear filtering based on Beltrami flow
|-

| Paper
| [[2010Bilbao_MeanShift]]
| Mean Shift Filtering
|-

| Paper
| [[2014Kovacik_wedgeArtefacts]]
| Removal of wedge artefacts
|-

| Paper
| [[2014Maiorca_beadArtefacts]]
| Removal of gold bead artefacts
|-

|}

=== Segmentation ===

{|

| Paper
| [[2002Frangakis_Eigenanalysis]]
| Segmentation using eigenvector analysis.
|-

| Paper
| [[2002Volkmann_Watershed]]
| Segmentation using watershed transform.
|-

| Paper
| [[2003Bajaj_BoundarySegmentation]]
| Segmentation based on fast marching.
|-

| Paper
| [[2005Cyrklaff_Thresholding]]
| Segmentation using optimal thresholding.
|-

| Paper
| [[2007Lebbink_TemplateMatching]]
| Segmentation using template matching.
|-

| Paper
| [[2007Sandberg_OrientationFields]]
| Segmentation using orientation fields.
|-

| Paper
| [[2007Sandberg_SegmentationReview]]
| Review on segmentation in electron tomography.
|-

| Paper
| [[2008Garduno_FuzzySegmentation]]
| Segmentation using fuzzy set theory principles.
|-

| Paper
| [[2009Lebbink_TemplateMatching2]]
| Segmentation using template matching.
|-

| Paper
| [[2012RubbiyaAli_EdgeDetection]]
| Parameter-Free Segmentation of Macromolecular Structures.
|-

| Conference
| [[2015Xu_TemplateMatching]]
| Detection of macromolecular complexes with a reduced representation of the templates.
|-

|}

=== Resolution ===
{|

| Paper
| [[2005Cardone_Resolution]]
| Resolution criterion for electron tomography
|-

| Chapter
| [[2007Penczek_Resolution]]
| Review of resolution criteria for electron tomography
|-

| Paper
| [[2015Diebolder_ConicalFSC]]
| Conical Fourier Shell Correlation
|-

|}

=== Subtomogram analysis ===

{|

| Paper
| [[2000Bohm_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2002Frangakis_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2006Nickell_Review]]
| Review of macromolecule finding by template matching (Visual Proteomics)
|-

| Paper
| [[2007Best_Review]]
| Review of Localization of Protein Complexes by Pattern Recognition
|-

| Paper
| [[2007Forster_Review]]
| Review of structure determination by subtomogram averaging
|-

| Paper
| [[2008Forster_Classification]]
| Classification of subtomograms using constrained correlation
|-

| Paper
| [[2008Bartesaghi_Classification]]
| Classification and averaging of subtomograms
|-

| Paper
| [[2008Schmid_Averaging]]
| Alignment and averaging of subtomograms
|-

| Paper
| [[2010Amat_Averaging]]
| Alignment and averaging of subtomograms exploiting thresholding in Fourier space
|-

| Paper
| [[2013Chen_Averaging]]
| Fast alignment of subtomograms using spherical harmonics
|-

| Paper
| [[2013Kuybeda_Averaging]]
| Alignment and averaging of subtomograms using the nuclear norm of the cluster
|-

| Paper
| [[2013Shatsky_Averaging]]
| Alignment and averaging of subtomograms with constrained cross-correlation
|-

| Paper
| [[2014Chen_Autofocus]]
| Subtomogram averaging and classification with special attention to differences
|-

| Paper
| [[2014Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2014Voortman_LimitingFactors]]
| Limiting factors of subtomogram averaging
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2015Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2016Bharat_Relion]]
| Subtomogram averaging with Relion
|-

| Paper
| [[2016Song_MatrixNorm]]
| Matrix norm minimization for tomographic reconstruction and alignment
|-

| Paper
| [[2017Castano_ParticlePicking]]
| Particle picking in tomograms for subtomogram averaging
|-

|}

=== Single particle tomography ===

{|

| Paper
| [[2012Bartesaghi_Constrained]]
| 3D reconstruction by imposing geometrical constraints
|-

| Paper
| [[2015Galaz_SingleParticleTomography]]
| Set of tools for Single Particle Tomography in EMAN2
|-

| Paper
| [[2016Galaz_SingleParticleTomography]]
| Alignment algorithms and CTF correction
|-

|}

=== Books and reviews ===

{|

| Paper
| [[2000Baumeister_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Koster_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Sali_Review]]
| Review of electron tomography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2005Lucic_Review]]
| Review of electron tomography
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_TomoBook]]
| Electron Tomography
|-

| Book
| [[2007McIntosh_Book]]
| Cellular Electron Microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2012Kudryashev_Review]]
| Review of subtomogram averaging
|-

| Paper
| [[2016Beck_Review]]
| Review of molecular sociology
|-

|}

=== Software ===

{|

| Paper
| [[1996Kremer_IMOD]]
| IMOD
|-

| Paper
| [[1996Chen_Priism/IVE]]
| Priism/IVE
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2005Nickell_TOM]]
| TOM Toolbox
|-

| Paper
| [[2007Messaoudi_TomoJ]]
| TomoJ
|-

| Paper
| [[2008Heymann_BsoftTomo]]
| Bsoft
|-

| Paper
| [[2015Ding_CaltechTomography]]
| Caltech tomography database
|-

| Paper
| [[2015Noble_AppionProtomo]]
| Batch fiducial-less tilt-series alignment in Appion using Protomo
|-

| Paper
| [[2015vanAarle_Astra]]
| ASTRA Toolbox
|-

|}

== 2D Crystals ==

=== 2D Preprocessing ===

{|

| Paper
| [[1986Henderson_Processing]]
| General 2D processing
|-

| Paper
| [[2000He_PhaseAlignment]]
| Phase consistency and Alignment
|-

| Paper
| [[2006Gil_Unbending]]
| Crystal unbending
|-

|}

=== Classification ===
{|

| Paper
| [[1988Frank_Classification]]
| MSA and classification in electron crystallography
|-

| Paper
| [[1996Fernandez_SOM]]
| Classification based on self organizing maps
|-

| Paper
| [[1998Sherman_MSA]]
| Classification based on MSA
|-

|}
=== 3D Reconstruction ===

{|

| Paper
| [[1985Wang_Solvent]]
| Solvent flattening
|-

| Paper
| [[1990Henderson_Processing]]
| General 3D processing
|-

| Paper
| [[2004Marabini_ART]]
| Algebraic Reconstruction Technique with blobs for crystals (Xmipp)
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1998Walz_Review]]
| Review of 2D crystallography
|-

| Paper
| [[1999Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Ellis_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of single particles, electron tomography and crystallography
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Gipson_2dx]]
| 2dx
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Philippsen_IPLT]]
| IPLT
|-

|}

== 3D Crystals - MicroED ==

=== Sample Preparation ===
{|
| Paper
| [[2016Shi_Preparation]]
| Sample Preparation
|}
=== Data Collection ===
{|
| Paper
| [[2014Nannenga_CR]]
| Continuous rotation

|}
=== Data Processing ===
{|

| Paper
| [[2011Wisedchaisri_PhaseExtension]]
| Fragment-based phase extension
|-

| Paper
| [[2015Hattne_Processing]]
| Data Processing
|-

| Paper
| [[2016Hattne_Correction]]
| Image correction
|}

=== Software ===
{|

| Paper
| [[2014Iadanza_Processing]]
| Data Processing of still diffraction data
|}

=== Books and Reviews ===
{|
| Paper
| [[2014Nannenga_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Liu_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Rodriguez_Review ]]
| Review of MicroED
|-

|}

== Helical particles ==

=== Filament corrections ===

{|

| Paper
| [[1986Egelman_Curved]]
| Algorithm for correcting curved filaments
|-

| Paper
| [[1988Bluemke_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2006Wang_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2016Yang_Flexible]]
| Algorithm for correcting filaments with flexible subunits
|-

|}

=== Reconstruction ===

{|

| Paper
| [[1952Cochran_Fourier]]
| Fourier Bessel transform of filamentous structures
|-

| Paper
| [[1958Klug_Fourier]]
| Fourier Bessel decomposition of the projection images
|-

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2005Wang_Iterative]]
| Iterative Fourier-Bessel algorithm
|-

| Paper
| [[2007Egelman_Iterative]]
| Iterative real-space algorithm
|-

| Paper
| [[2013Desfosses_Spring]]
| Helical processing with Spring
|-

| Paper
| [[2015Zhang_seam]]
| Workflow for the detection of the lattice seam
|-

| Paper
| [[2016Rohou_Frealix]]
| Helical processing with Frealix
|-

|}

=== Validation ===

{|

| Paper
| [[2014Egelman_ambiguity]]
| How to detect incorrect models
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Carragher_Phoelix]]
| Phoelix
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Owen_Brandeis]]
| Brandeis
|-

|}

== Icosahedral particles ==

=== Reconstruction ===

{|

| Paper
| [[1970Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1971Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1996Fuller_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1997Thuman_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

|}

=== Classification ===

{|

| Paper
| [[2005Scheres_Virus]]
| Classification of virus capsids in real space
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1999Baker_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[1999Conway_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2000Thuman_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Lee_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Navaza_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2006Grunewald_Review]]
| Review of reconstruction of icosahedral viruses
|-

|}

=== Software ===

{|

| Paper
| [[1996Baker_EMPFT]]
| EMPFT
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2013Morin_Sliz SBGrid]]
| SBGrid presentation for eLife
|-

|}

== Databases ==

{|

| Paper
| [[2003Boutselakis_EMSD]]
| EMSD database
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2011Kim_CDDB]]
| Conformational Dynamics Data Bank
|-

| Paper
| [[2011Lawson_EMDB]]
| Electron Microscopy Data Bank
|-

| Paper
| [[2016Iudin_EMPIAR]]
| EMPIAR raw data database
|-

| Paper
| [[2016Patwhardan_EMDB]]
| EMDB, PDB, ...
|-

| Paper
| [[2017Shao_PDBQuality]]
| Quality metrics in PDB
|-

| Blog
| http://www.mybiosoftware.com
| Huge list of bioinformatics programs (many of them structural bioinformatics)
|-

|}

== Relationship to other structural information sources ==

{|

| Paper
| [[2000Engel_AFM]]
| Review of Atomic Force Microscopy
|-

| Paper
| [[2001Dimmeler_AFM]]
| Constraints from Atomic Force Microscopy
|-

| Paper
| [[2003Mobus_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_Review]]
| Review on correlative microscopy
|-

| Paper
| [[2005Boudier_EFTETJ]]
| Software for Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2005Vestergaard_SAXS]]
| Example of comparison of 3DEM and Small-angle X-ray scattering
|-

| Paper
| [[2007Hamada_SAXS]]
| Constraints from Small-angle X-ray scattering
|-

| Paper
| [[2013Xu_FRET]]
| EM+FRET
|-

|}

== X-ray tomography ==

{|

| Paper
| [[2012Oton_ImageFormation]]
| Image formation model in X-ray cell microscopy
|-

|}

== Mathematical tools necessary ==

== People developing methods ==
Please, add yourself to this list (due to privacy reasons, please, do not add anyone else to the list without his/her explicit consent). Sort by first name alphabetical order.

[http://biocomp.cnb.csic.es/~coss Carlos Oscar S. Sorzano]: CSIC, Madrid, Spain 

[http://www.curie.fr/recherche/themes/detail_equipe.cfm/lang/_fr/id_equipe/241.htm Cédric Messaoudi]: Institute Curie, Paris, France 

[http://scholar.google.es/citations?user=_jNYGScAAAAJ&hl=en Javier Vargas]:[mailto:jvargas@cnb.csic.es mail]: CSIC, Madrid, Spain 

[http://scholar.google.es/citations?hl=es&user=g2ZJPIYAAAAJ Joaquín Otón]: CSIC, Madrid, Spain 

[mailto:jrbcast@gmail.com José Román Bilbao-Castro]: UAL, Almería, Spain; CSIC, Madrid, Spain 

[José Miguel de la Rosa Trevín]: Biocomputing Unit CNB-CSIC, Madrid, Spain 

[http://cryoem.janelia.org Tamir Gonen]: [mailto:gonent@janelia.hhmi.org mail]: Howard Hughes Medical Institute, Ashburn, VA, USA 

[mailto:vabrishami@cnb.csic.es Vahid Abrishami]: CSIC, Madrid, Spain 

== 3DEM sites ==
* [http://3dem.ucsd.edu/ 3DEM web site]

* [http://en.wikibooks.org/wiki/Software_Tools_For_Molecular_Microscopy Software tools for molecular microscopy]

* [http://www.emdatabank.org/ The Electron Microscopy Data Bank (EMDB)]

* [http://ccdb.ucsd.edu The Cell Centered Database (CCDB)]

* [http://conventions.cnb.csic.es The geometrical software conventions web page ]

== Editing useful links ==

* [http://www.mediawiki.org/wiki/Help:Formatting Text formatting in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Links Adding links in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Images Adding images in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Tables Making tables in Mediawiki]

Main Page

2017-05-11T20:24:08Z

CoSS: /* 2D Preprocessing */

== Presentation ==

This web page is intended to be an extensive repository of three-dimensional electron microscopy (3DEM) methods. The advantages of having such a repository are

* You know which are the relevant articles in a particular topic, therefore, paper introductions, reviews, etc. are easier to write and you make sure you will cite all the related articles.
* You will be sure that your paper has more chances of being cited.
* You can add whatever information you find relevant to your method, external links, links to other papers, etc.
* You can link your method to a web page providing the corresponding software, so you know people can use your algorithms.
* You can use the Wiki search capabilities to locate relevant articles even if they are not at the topic you are looking at.
* As a community we will "reconstruct" our history.
* You can select the "watch" option above to receive notifications in case of further changes in the Main Page.

Developing image processing methods for 3DEM is not "[[well-paid]]" in terms of citations and impact factor. However, it is crucial for the advance of the field. Gathering methodological papers in a portal will help to increase the recognition of the field.

Please:

* Add your articles at the right place (you can add a single article in several topics if it is relevant to all of them). The easiest way to add an article is by editing the corresponding topic in the main page, adding your entry, then save the main page. Click on the red link that appears on your new entry, copy and paste the Wiki following code, add the information of your article

== Citation ==

== Abstract ==

== Keywords ==

== Links ==

== Related software ==

== Related methods ==

== Comments ==

* Maintain the information of each article as complete as possible.
* Sort articles by years and authors.
* Be respectful to other people's work.

== How to subscribe to this page ==

You may subscribe to this page so that you will be notified every time someone adds a new method. To do so, you have to register in the page, and edit your preferences ("my preferences"). Be sure that you have activated the option "E-mail me when a page on my watchlist is changed". Finally, click on the "Watch" tab at the top of this page.

You may subscribe to changes on this page on the mailing list 3demmethods@cnb.csic.es. To send a new method to this mail list just send a mail to 3demmethods@cnb.csic.es

To subscribe to this list, visit the web page

https://listas.csic.es/cnb/wws/subscribe/3demmethods

Alternatively, you may write a mail to sympa6@cnb.csic.es with the subject

<code>subscribe 3demmethods YourName YourFamilyName</code>

and an empty mail body.

To unsubscribe visit the page

https://listas.csic.es/cnb/wws/sigrequest/3demmethods

or write sympa6@cnb.csic.es with the subject

<code>unsubscribe 3demmethods</code>

and an empty mail body.

== Electron microscopy images ==

=== Online courses ===

CALTECH: http://cryo-em-course.caltech.edu/

MRC: ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/EM-course/

CNB-CSIC: http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/MadridJan2014EM

Workshop on Computational methods for CryoEM: https://www.youtube.com/watch?v=XdKO1iaPP8o

Workshop on Management of large CryoEM facilities: https://www.youtube.com/watch?v=as4seOPszL0

Icknield Course on Model Building and Refinement for High Resolution EM Maps: http://www.ccpem.ac.uk/training/icknield_2017/icknield_2017.php

=== Image formation ===

{|

| Paper
| [[1971Erickson_CTF]]
| CTF model
|-

| Paper
| [[1971Glaeser_Damage]]
| Radiation damage
|-

| Chapter
| [[1971Hanszen_CTF]]
| Image formation model
|-

| Paper
| [[1971Thon_Model]]
| CTF model
|-

| Paper
| [[1975Unwin_Imaging]]
| Radiation dose
|-

| Paper
| [[1977Wade_Model]]
| CTF model
|-

| Paper
| [[1978Wade_Model]]
| CTF model
|-

| Paper
| [[1979Hayward_Radiation]]
| Radiation damage
|-

| Paper
| [[1984Cohen_Validity]]
| Validity of the CTF model at high frequencies
|-

| Paper
| [[1988Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[1992Wade_Model]]
| CTF model
|-

| Paper
| [[1993Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2004Egerton_Damage]]
| Radiation damage
|-

| Paper
| [[2004Sorzano_Normalization]]
| Background noise is Gaussian
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2009Baxter_NoiseCharacterization]]
| Characterization of the different noise sources in cryo-EM
|-

| Paper
| [[2010Baker_Damage]]
| Radiation damage dependence on resolution
|-

| Paper
| [[2010Bammes_Damage]]
| Radiation damage dependence on temperature
|-

| Paper
| [[2010Gomez_Multislice]]
| Simulation of the multi slice model
|-

| Paper
| [[2010Zewail_FourDimensional]]
| Review on the use of ultrafast EM
|-

| Paper
| [[2011Bammes_CCD]]
| Performance of CCD cameras
|-

| Paper
| [[2011Glaeser_Coma]]
| Image formation model including coma
|-

| Paper
| [[2011Milazzo_DirectDetectors]]
| Evaluation of Direct Detectors
|-

| Paper
| [[2011Rullgard_ImageSimulation]]
| Accurate simulation of EM images
|-

| Paper
| [[2011Zhang LimitingFactors]]
| Limiting factor for atomic resolution in EM
|-

| Paper
| [[2012Bammes_DirectDetection]]
| Performance of Direct detectors
|-

| Paper
| [[2012Campbell_MotionCorrection]]
| Beam induced motion correction and direct detectors
|-

| Paper
| [[2012Shang_HydrationLayer]]
| Simulation of PDB volumes explicitly considering the hydration layer
|-

| Paper
| [[2013Egerton_RadiationDamage]]
| Review of TEM radiation damage and experimental ways of reducing it
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu H_Noisemodels]]
| Noise models and cryo-EM drift correction with a direct-electron camera
|-

| Paper
| [[2013Li X K2 noisemodels]]
| Influence of electron dose rate on electron counting images recorded with the K2 camera
|-

| Paper
| [[2013Vulovic_CTFApproximations]]
| When to use the different approximations performed so that a projection with linear CTF is valid
|-

| Thesis
| [[2013Vulovic_ImageFormation]]
| Ph.D. Thesis on the image formation in cryo-EM
|-

| Paper
| [[2014Danev_PhasePlate]]
| Volta potential phase plate
|-

| Paper
| [[2015Chiu_K2]]
| Characterization of K2
|-

| Paper
| [[2015Hawkes_AberrationCorrection]]
| Historical account of the development of lens corrections
|-

| Paper
| [[2015Koeck_Quadratic]]
| Limitations of the linear approximation and use of the quadratic terms
|-

| Paper
| [[2015Kuijper_FEI]]
| Description of the FEI Falcons
|-

| Paper
| [[2015Lobato_MULTEM]]
| Simulation of multislice diffraction
|-

| Paper
| [[2015McMullan_AmorphousIce]]
| Beam induced movement is caused by Brownian motion
|-

| Paper
| [[2016Koeck_ADF]]
| Simulations of Annular Dark Field TEM
|-

| Paper
| [[2017Mishyna_DNARadiation]]
| Review of radiation damage on DNA
|-

|}

=== Collection geometry ===

{|

| Chapter
| [[1980Hoppe_Wedge]]
| Missing wedge
|-

| Paper
| [[1987Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1995Penczek_Dual]]
| Dual axis tomography
|-

| Paper
| [[1997Mastronarde_Dual]]
| Dual axis tomography
|-

| Paper
| [[2003Ludtke_FocusPairs]]
| Focus pairs for single particles
|-

| Paper
| [[2005Lanzavecchia_Conical]]
| Conical tomography
|-

| Paper
| [[2005Zampighi_Conical]]
| Conical tomography
|-

| Paper
| [[2006Leschziner_OT]]
| Orthogonal Tilt
|-

| Paper
| [[2006Messaoudi_Multiple]]
| Multiple axis tomography
|-

| Paper
| [[2012Kudryashev_FocusPairs]]
| Focus pairs tomography
|-

| Paper
| [[2014Hovden_TiltFocus]]
| Combining tilt series with focus series
|-

| Paper
| [[2015Sorzano_RandomConicalTilt]]
| General formulation of Random Conical Tilt
|-

| Paper
| [[2017Hagen_DoseTomography]]
| Dose optimization for subtomogram averaging
|-

|}

=== Sample preparation ===

{|

| Paper
| [[1982Dubochet_Sample]]
| Vitreous ice
|-

| Paper
| [[1986Lepault_Sample]]
| Fast freezing
|-

| Paper
| [[1995Dubochet_Sample]]
| High-pressure freezing
|-

| Paper
| [[1995VanMarle_Sample]]
| Sample damages in resin
|-

| Paper
| [[1998Adrian_Sample]]
| Cryo negative staining
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2002Hsieh_Sample]]
| Cryofixation
|-

| Paper
| [[2004AlAmoudi_Sample]]
| CEMOVIS
|-

| Paper
| [[2008Studer_Sample]]
| Review on high pressure freezing
|-

| Paper
| [[2009Pierson_Sample]]
| Review on sample preparation for electron tomography
|-

| Paper
| [[2010Zhang_NegativeStaining]]
| Negative staining for small protein imaging
|-

| Paper
| [[2012Zhang_PositiveStaining]]
| Positive staining
|-

| Paper
| [[2014Rames_NegativeStaining]]
| Optimized negative staining
|-

| Paper
| [[2014Russo_GoldGrids]]
| Gold grids for single particles
|-

| Paper
| [[2015Cabra_Sample]]
| Review on sample preparation for single particles with videos
|-

| Paper
| [[2016Passmore_Review]]
| Tutorial chapter on sample preparation
|-

| Paper
| [[2016Razinkov_Vitrification]]
| New vitrification method
|-

| Paper
| [[2016Takizawa_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2016Thompson_Sample]]
| Review on sample preparation for EM
|-

| Paper
| [[2017Peitsch_Sample]]
| iMEM: Isolation of Plasma Membrane for Cryoelectron Microscopy
|-

|}

=== Automated data collection ===

{|

| Paper
| [[1992Dierksen_Automatic]]
| Automated data collection
|-

| Paper
| [[1992Koster_Automatic]]
| Automated data collection
|-

| Paper
| [[1996Fung_Automatic]]
| Automated data collection for tomography
|-

| Paper
| [[2001Zhang_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2003Ziese_Automatic]]
| Automated autofocusing
|-

| Paper
| [[2004Potter_Automatic]]
| Automated sample loading
|-

| Paper
| [[2004Zheng_Automatic]]
| Automated data collection
|-

| Paper
| [[2005Lei_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2005Suloway_Automatic]]
| Automated data collection: Leginon
|-

| Paper
| [[2007Yoshioka_RCT]]
| Automated Random Conical Tilt
|-

| Paper
| [[2011Korinek_TOM2]]
| Automated acquisition with TOM2
|-

| Paper
| [[2015Li_UCSFImage]]
| Automated acquisition with UCSFImage
|-

| Paper
| [[2016Gil_Fuzzy]]
| Real time decisions during acquisition with neuro-fuzzy method
|-

| Paper
| [[2016Liu_TiltControl]]
| Accurate control of the tilt angle for electron tomography
|-

| Paper
| [[2016Vargas_FoilHole]]
| Determination of image quality at low magnification
|-

|}

== Single particles ==

=== Automatic particle picking ===

{|

| Paper
| [[1982VanHeel_Detection]]
| Detection of particles in micrographs
|-

| Paper
| [[2001Nicholson_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2001Zhu_Filaments]]
| Automatic identification of filaments in micrographs
|-

| Paper
| [[2004Sigworth_Detection]]
| Classical detection theory and the cryo-EM particle selection problem
|-

| Paper
| [[2004Volkmann_ParticlePicking]]
| An approach to automated particle picking from electron micrographs based on reduced representation templates
|-

| Paper
| [[2004Wong_ParticlePicking]]
| Model-based particle picking for cryo-electron microscopy
|-

| Paper
| [[2004Zhu_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2007Chen_Signature]]
| Automatic particle picking program: Signature
|-

| Paper
| [[2007Woolford_SwarmPS]]
| Automatic particle picking with several criteria, implemented in EMAN Boxer
|-

| Paper
| [[2009Sorzano_MachineLearning]]
| Automatic particle picking based on machine learning of rotational invariants
|-

| Paper
| [[2011Arbelaez_Comparison]]
| Evaluation of the performance of software for automated particle-boxing
|-

| Paper
| [[2013Abrishami_MachineLearning]]
| A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs
|-

| Paper
| [[2013Hauer_2013]]
| Automatic tilt pair detection in Random Conical Tilt
|-

| Paper
| [[2013Shatsky_ParticlePicking]]
| Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Langlois_ParticlePicking]]
| Automatic particle picking
|-

| Paper
| [[2016Vilas_AutomaticTilt]]
| Automatic identification of image pairs in untilted-tilted micrograph pairs
|-

|}

=== 2D Preprocessing ===

{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast enhancement through DPR
|-

| Paper
| [[2004Sorzano_Normalization]]
| Normalization procedures and their statistical properties.
|-

| Paper
| [[2006Sorzano_Denoising]]
| Strong denoising in wavelet space
|-

| Conference
| [[2009Sorzano_Downsampling]]
| Differences between the different downsampling schemes
|-

| Paper
| [[2012Brilot_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Campbell_Movies]]
| Alignment of beam induced motion in direct detectors
|-

| Paper
| [[2012Zhao_Denoising]]
| Denoising using an invariant Fourier-Bessel eigenspace
|-

| Paper
| [[2013Norousi_Screening]]
| Screening particles to identify outliers
|-

| Paper
| [[2013Bai_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Li_ElectronCounting]]
| Electron counting and beam induced motion correction
|-

| Paper
| [[2013Shigematsu_Movies]]
| Drift correction for movies considering dark field
|-

| Paper
| [[2013Vargas_ParticleQuality]]
| Automatic determination of particle quality
|-

| Paper
| [[2014Scheres_Movies]]
| Beam induced motion correction
|-

| Paper
| [[2015Abrishami_Movies]]
| Alignment of direct detection device micrographs
|-

| Paper
| [[2015Grant_Anisotropic]]
| Automatic estimation and correction of anisotropic magnification
|-

| Paper
| [[2015Grant_OptimalExposure]]
| Filter movies according to the radiation damage
|-

| Paper
| [[2015Rubinstein_Alignment]]
| Frame alignment at the level of particle
|-

| Paper
| [[2015Spear_DoseCompensation]]
| Effect of dose compensation on resolution
|-

| Paper
| [[2015Zhao_AnisotropicMagnification]]
| Correction of anisotropic magnification
|-

| Conference
| [[2016Bajic_Denoising]]
| Denoising and deconvolution of micrographs
|-

| Paper
| [[2016Jensen_RemovalVesicles]]
| Removal of vesicles in membrane proteins
|-

| Paper
| [[2016Bhamre_Denoising]]
| Denoising by 2D covariance estimation
|-

| Paper
| [[2017McLeod_Zorro]]
| Movie alignment by Zorro
|-

|}

=== 2D Alignment ===

{|

| Paper
| [[1981Frank_Averaging]]
| 2D averaging and phase residual
|-

| Paper
| [[1982Saxton_Averaging]]
| 2D averaging using correlation
|-

| Paper
| [[1998Sigworth_ML2D]]
| Maximum likelihood alignment in 2D
|-

| Paper
| [[2003Cong_FRM2D]]
| Fast Rotational Matching in 2D
|-

| Paper
| [[2005Cong_FRM2D]]
| Fast Rotational Matching in 2D introduced in a 3D Alignment algorithm
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

|}

=== 2D Classification and clustering ===

{|

| Paper
| [[1981VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[1984VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2011Singer_DiffusionMaps]]
| Classification in 2D based on graph analysis of the projections
|-

| Paper
| [[2012Yang_ISAC]]
| Iterative Stable Alignment and clustering
|-

| Paper
| [[2014Sorzano_Outlier]]
| Outlier detection in 2D classifications.
|-

| Paper
| [[2014Zhao_Aspire]]
| Fast classification based on rotational invariants and vector diffusion maps
|-

| Paper
| [[2015Huang_Robust]]
| Robust w-estimators of 2D classes
|-

| Paper
| [[2016Reboul_Stochastic]]
| Stochastic Hill Climbing for calculating 2D classes
|-

| Conference
| [[2017Bhamre_Mahalanobis]]
| 2D classification using Mahalanobis distance
|-

|}

=== 3D Alignment ===

{|

| Paper
| [[1980Kam_AutoCorrelation]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[1986Goncharov_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1987VanHeel_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1988Provencher_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Vogel_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1990Gelfand_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Goncharov_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Harauz_Quaternions]]
| Use of quaternions to represent rotations
|-

| Paper
| [[1994Penczek_Real]]
| Angular assignment using projection matching in real space
|-

| Paper
| [[1994Radermacher_Radon]]
| Angular assignment in Radon space
|-

| Paper
| [[1996Penczek_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[2003Rosenthal_DPR]]
| Angular assignment using DPR
|-

| Paper
| [[2004Sorzano_Wavelet]]
| Angular assignment in the wavelet space.
|-

| Paper
| [[2005Jonic_Splines]]
| Angular assignment in Fourier space using spline interpolation.
|-

| Paper
| [[2005Yang_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[2006Ogura_SimulatedAnnealing]]
| Angular asignment by simulated annealing
|-

| Paper
| [[2007Grigorieff_Continuous]]
| Continuous angular assignment in Fourier space
|-

| Paper
| [[2010Jaitly_Bayesian]]
| Angular assignment by a Bayesian method and annealing
|-

| Paper
| [[2010Sanz_Random]]
| Random model method
|-

| Paper
| [[2010Singer_Voting]]
| Detecting consistent common lines by voting (reference free)
|-

| Paper
| [[2011Singer_SDP]]
| Angular assignment by semidefinite programming and eigenvectors (reference free)
|-

| Paper
| [[2012Giannakis_Scattering]]
| Construction of an initial volume, reference free, by graph analysis of the projections
|-

| Paper
| [[2012Shkolnisky_Sync]]
| Angular assignment by synchronization of rotations (reference free)
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Wang_LUD]]
| Angular assignment by least unsquared deviations (reference free)
|-

| Paper
| [[2014Vargas_RANSAC]]
| Initial model using RANSAC (reference free)
|-

| Paper
| [[2015Joubert_Pseudoatoms]]
| Initial model based on pseudo-atoms
|-

| Paper
| [[2015Singer_Kam]]
| Reconstruction without angular assignment from autocorrelation function (reference free)
|-

| Paper
| [[2015Sorzano_Significant]]
| Statistical approach to the initial volume estimation (reconstruct significant)
|-

| Conference
| [[2016Michels_Heterogeneous]]
| Initial volume in the presence of heterogeneity
|-

| Paper
| [[2016Cossio_BayesianGPU]]
| GPU implementation of the Bayesian 3D reconstruction approach
|-

|}

=== 3D Reconstruction ===
{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1986Harauz_FBP]]
| Exact filters for Filtered Back Projection
|-

| Chapter
| [[1992Radermacher_WBP]]
| Exact filters for Weighted Back Projection
|-

| Paper
| [[1997Zhu_RecCTF]]
| 3D Reconstruction (SIRT like) and simultaneous CTF correction
|-

| Paper
| [[1998Boisset_Uneven]]
| Artifacts in SIRT and WBP under uneven angular distributions
|-

| Paper
| [[1998Marabini_ART]]
| Algebraic Reconstruction Technique with blobs (Xmipp)
|-

| Paper
| [[2001Sorzano_Uneven]]
| Free parameter selection under uneven angular distributions
|-

| Paper
| [[2005Sorzano_Parameters]]
| Free parameter selection for optimizing multiple tasks
|-

| Paper
| [[2008Sorzano_Constraints]]
| Mass, surface, positivity and symmetry constraints for real-space algorithms
|-

| Paper
| [[2009Bilbao_ParallelART]]
| Efficient parallelization of ART
|-

| Paper
| [[2011Li_GradientFlow]]
| Regularized 3D Reconstruction by Gradient Flow
|-

| Paper
| [[2011Vonesch_Wavelets]]
| Fast wavelet-based 3D reconstruction
|-

| Paper
| [[2012Gopinath_ShapeRegularization]]
| Regularized 3D Reconstruction by Shape information
|-

| Paper
| [[2012Kucukelbir_adaptiveBasis]]
| 3D reconstruction in an adaptive basis promoting sparsity
|-

| Paper
| [[2012Sindelar_NoiseReduction]]
| Optimal noise reduction in 3D reconstructions
|-

| Paper
| [[2013Elmlund H_PRIME]]
| PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
|-

| Paper
| [[2013Lyumkis_Optimod]]
| Construction of initial volumes with Optimod
|-

| Paper
| [[2013Wang FIRM]]
| Fast 3D reconstruction in Fourier domain
|-

| Paper
| [[2014Kunz_SART_OS]]
| Simultaneous ART with OS
|-

| Paper
| [[2015Abrishami_Fourier]]
| 3D Reconstruction in Fourier space
|-

| Paper
| [[2015Dvornek_SubspaceEM]]
| Fast Maximum a posteriori
|-

| Paper
| [[2015Moriya_Bayesian]]
| Bayesian approach to suppress limited angular artifacts
|-

| Paper
| [[2015Xu_GeometricFlow]]
| Multi-scale geometric flow
|-

| Arxiv
| [[2016Ye_Cohomology]]
| Cohomology properties of 3D reconstruction
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

|}

=== 3D Heterogeneity ===

{|

| Paper
| [[2004White_Size]]
| Heterogeneity classification of differently sized images
|-

| Paper
| [[2006Penczek_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Scheres_ML3D]]
| Maximum Likelihood alignment and classification in 3D
|-

| Paper
| [[2009Spahn_Bootstrap]]
| 3D heterogeneity through bootstrap
|-

| Paper
| [[2010Elmlund_AbInitio]]
| Solving the initial volume problem with multiple conformations
|-

| Paper
| [[2010Shatsky_MultiVariate]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2012Scheres_Bayesian]]
| A Bayesian view on cryo-EM structure determination
|-

| Paper
| [[2012Zheng_Covariance]]
| Estimation of the volume covariance
|-

| Paper
| [[2013Wang_MLVariance]]
| Maximum Likelihood estimate of the map variance
|-

| Paper
| [[2013Lyumkis D_FREALIGN]]
| Likelihood-based classification of cryo-EM images using FREALIGN.
|-

| Paper
| [[2014Jin_NMA]]
| Continuous heterogeneity through Normal Mode Analysis
|-

| Paper
| [[2014Dashti_Brownian]]
| Continuous heterogeneity through Brownian trajectories
|-

| Paper
| [[2014Chen_Migration]]
| Particle migration analysis in 3D classification
|-

| Paper
| [[2015Anden_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Bai_Focused]]
| Focused classification
|-

| Paper
| [[2015Katsevich_Covariance]]
| 3D Covariance matrix estimation for heterogeneity
|-

| Paper
| [[2015Klaholz_MRA]]
| Multivariate Statistical Analysis of Jackknife and Bootstrapping on random subsets
|-

| Paper
| [[2015Liao_Covariance]]
| Estimation of the 3D covariance from 2D projections
|-

| Paper
| [[2015Tagare_Direct]]
| Direct reconstruction of PCA components
|-

| Paper
| [[2016Gong_Mechanical]]
| Mechanical model for macromolecules
|-

| Paper
| [[2016Rawson_Movement]]
| Movement and flexibility
|-

| Paper
| [[2016Sorzano_StructMap]]
| Sorting a discrete set of conformational states
|-

| Paper
| [[2016Sorzano_Strain]]
| Calculate local stretches, strains and rotations from two conformational states
|-

| Paper
| [[2017Punjani_CryoSPARC]]
| CryoSPARC
|-

|}

=== Validation ===

{|

| Paper
| [[2008Stagg_TestBed]]
| Effect of voltage, dosis, number of particles and Euler jumps on resolution
|-

| Paper
| [[2011Henderson]]
| Tilt Validation
|-

| Paper
| [[2011Read]]
| Validation of PDBs
|-

| Paper
| [[2012Henderson]]
| EM Map Validation
|-

| Paper
| [[2013Cossio_Bayesian]]
| EM Map Validation in a probabilistic setting
|-

| Paper
| [[2013Chen_NoiseSubstitution]]
| Noise substitution at high resolution for measuring overfitting
|-

| Paper
| [[2014Russo_StatisticalSignificance]]
| EM Map Validation through the statistical significance of the tilt-pair angular assignment
|-

| Paper
| [[2014Stagg_Reslog]]
| EM Map Validation through the resolution evolution with the number of particles
|-

| Paper
| [[2014Wasilewski_Tilt]]
| Web implementation of the tilt pair validation
|-

| Paper
| [[2015Heymann_Alignability]]
| EM Map Validation through the resolution of reconstructions from particles and noise
|-

| Paper
| [[2015Oliveira_FreqLimited]]
| Comparison of gold standard and frequency limited optimization
|-

| Paper
| [[2015Wriggers_Secondary]]
| Validation by secondary structure
|-

| Paper
| [[2016Kim_SAXS]]
| Comparison of SAXS data and EM projections
|-

| Paper
| [[2016Rosenthal_Review]]
| Review of validation methods
|-

| Paper
| [[2016Vargas_Alignability]]
| Validation by studying the tendency of an angular assignment to cluster in the projection space
|-

| Paper
| [[2017Monroe_PDBRefinement]]
| Validation by comparison to a refined PDB
|-

|}

=== Resolution ===

{|

| Paper
| [[1986Harauz_FBP]]
| Fourier Shell Correlation
|-

| Paper
| [[1987Unser_SSNR]]
| 2D Spectral Signal to Noise Ratio
|-

| Paper
| [[2002Penczek_SSNR]]
| 3D Spectral Signal to Noise Ratio for Fourier based algorithms
|-

| Paper
| [[2003Rosenthal_DPR]]
| Review of the FSC and establishment of a new threshold
|-

| Paper
| [[2005Unser_SSNR]]
| 3D Spectral Signal to Noise Ratio for any kind of algorithms
|-

| Paper
| [[2005VanHeel_FSC]]
| Establishment of a new threshold for FSC
|-

| Paper
| [[2007Sousa_AbInitio]]
| Resolution measurement on neighbour Fourier voxels
|-

| Paper
| [[2014Kucukelbir_Local]]
| Quantifying the local resolution of cryo-EM density maps
|-

| Paper
| [[2016Pintilie_Probabilistic]]
| Probabilistic models and resolution
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Statistical properties of resolution measures defined in Fourier space
|-

|}

=== Sharpening of high resolution information ===
{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast restoration and map sharpening
|-

| Paper
| [[2008Fernandez_Bfactor]]
| Bfactor determination and restoration
|-

| Paper
| [[2013Fiddy_SaxtonAlgorithm]]
| Phase retrieval or extension
|-

| Paper
| [[2014Kishchenko_SphericalDeconvolution]]
| Spherical deconvolution
|-

| Paper
| [[2015Spiegel_VISDEM]]
| Visualization improvement by the use of pseudoatomic profiles
|-

| Paper
| [[2016Jonic_Pseudoatoms]]
| Approximation with pseudoatoms
|-

| Paper
| [[2016Jonic_Denoising]]
| Denoising and high-frequency boosting by pseudoatom approximation
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[1982Schiske_Correction]]
| CTF correction for tilted objects
|-

| Paper
| [[1988Toyoshima_Model]]
| CTF estimation
|-

| Paper
| [[1995Frank_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1996Skoglund_MaxEnt]]
| CTF correction with Maximum Entropy
|-

| Paper
| [[1996Zhou_Model]]
| CTF model and user interface for manual fitting
|-

| Paper
| [[1997Fernandez_AR]]
| PSD estimation using periodogram averaging and AR models
|-

| Paper
| [[1997Penczek_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1997Stark_Deconvolution]]
| CTF correction using deconvolution
|-

| Paper
| [[1997Zhu_RecCTF]]
| CTF correction and reconstruction
|-

| Paper
| [[2000DeRosier_EwaldCorrection]]
| CTF correction considering the Ewald sphere
|-

| Paper
| [[2000Jensen_TiltedCorrection]]
| CTF correction considering tilt in backprojection
|-

| Paper
| [[2001Saad_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Huang_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Mindell_CTFTILT]]
| CTF estimation for tilted micrographs
|-

| Paper
| [[2003Sander_MSA]]
| CTF estimation through MSA classification of PSDs
|-

| Paper
| [[2003Velazquez_ARMA]]
| PSD and CTF estimation using ARMA models
|-

| Paper
| [[2004Sorzano_IDR]]
| CTF restoration and reconstruction with Iterative Data Refinement
|-

| Conference
| [[2004Wan_CTF]]
| Spatially variant CTF
|-

| Paper
| [[2004Zubelli_Chahine]]
| CTF restoration and reconstruction with Chahine's multiplicative method
|-

| Conference
| [[2005Dubowy_SpaceVariant]]
| CTF correction when this is space variant
|-

| Paper
| [[2005Mallick_ACE]]
| CTF estimation
|-

| Paper
| [[2006Wolf_Ewald]]
| CTF correction considering Ewald sphere
|-

| Paper
| [[2007Jonic_EnhancedPSD]]
| PSD enhancement for better identification of Thon rings; Vitreous ice diffracts in Thon rings
|-

| Paper
| [[2007Philippsen_Model]]
| CTF Model for tilted specimens
|-

| Paper
| [[2007Sorzano_CTF]]
| CTF estimation using enhanced PSDs
|-

| Paper
| [[2009Sorzano_Sensitivity]]
| Error sensitivity of the CTF models, non-uniqueness of the CTF parameters
|-

| Paper
| [[2010Jiang2010_CTFCorrection]]
| Amplitude correction method
|-

| Paper
| [[2010Kasantsev_CTFCorrection]]
| Mathematical foundations of Kornberg and Jensen method
|-

| Paper
| [[2010Leong_CTFCorrection]]
| Correction for spatially variant CTF
|-

| Paper
| [[2011Glaeser_Coma]]
| The effect of coma at high-resolution
|-

| Paper
| [[2011Mariani_Tilted]]
| CTF simulation and correction of tilted specimens
|-

| Paper
| [[2011Sindelar_Wiener]]
| CTF correction using a modified version of Wiener filter
|-

| Paper
| [[2011Voortman_Tilted]]
| CTF correction for tilted specimen
|-

| Paper
| [[2012Voortman_VaryingCTF]]
| Correcting a spatially varying CTF
|-

| Paper
| [[2013Vargas_FastDef]]
| Fast defocus
|-

| Paper
| [[2015Rohou_CTFFind4]]
| CTF Find 4
|-

| Paper
| [[2015Sheth_CTFquality]]
| Visualization and quality assessment of CTF
|-

| Paper
| [[2016Zhang_GCTF]]
| gCTF
|-

|}

=== Segmentation ===

{|

| Paper
| [[2006Baker_segmentation]]
| Segmentation of molecular subunits
|-

|}

=== Fitting and docking ===

{|

| Paper
| [[1999Volkmann_Fitting]]
| Fitting in real space
|-

| Paper
| [[2001Baker_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2001Jones_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2003Kovacs_FRM3D]]
| Fast Rotational Alignment of two EM maps
|-

| Paper
| [[2004Tama_NMA1]]
| Flexible fitting with Normal Modes (I)
|-

| Paper
| [[2004Tama_NMA2]]
| Flexible fitting with Normal Modes (II)
|-

| Paper
| [[2005Velazquez_Superfamilies]]
| Recognition of the superfamily folding in medium-high resolution volumes
|-

| Paper
| [[2007DeVries_Haddock]]
| Docking with Haddock 2.0
|-

| Paper
| [[2007Kleywegt_QualityControl]]
| Quality control and validation of fitting
|-

| Paper
| [[2012Biswas_Secondary]]
| Secondary structure determination in EM volumes
|-

| Paper
| [[2012Velazquez_Constraints]]
| Multicomponent fitting by using constraints from other information sources
|-

| Paper
| [[2013Chapman MS_Atomicmodeling]]
| Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters
|-

| Paper
| [[2013Esquivel_Modelling]]
| Review on modelling (secondary structure, fitting, ...)
|-

| Paper
| [[2013Lopez_Imodfit]]
| Fitting based on vibrational analysis
|-

| Paper
| [[2013Nogales_3DEMLoupe]]
| Normal Mode Analysis of reconstructed volumes
|-

| Paper
| [[2014AlNasr_Secondary]]
| Identification of secondary structure elements in EM volumes
|-

| Paper
| [[2014Politis_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Rey_MassSpect]]
| Integration of mass spectroscopy information
|-

| Paper
| [[2014Villa_Review]]
| Review of atomic fitting into EM volumes
|-

| Paper
| [[2015Barad_EMRinger]]
| Validation of hybrid models
|-

| Paper
| [[2015Bettadapura_PF2Fit]]
| Fast rigid fitting of PDBs into EM maps
|-

| Paper
| [[2015Carrillo_CapsidMaps]]
| Analysis of virus capsids using Google Maps
|-

| Paper
| [[2015Schroeder_Hybrid]]
| Review on model building
|-

| Paper
| [[2015Tamo_Dynamics]]
| Dynamics in integrative modeling
|-

| Paper
| [[2015Sorzano_AtomsToVoxels]]
| Accurate conversion of an atomic model into a voxel density volume
|-

| Paper
| [[2016Joseph_Evolution]]
| Evolutionary constraints for the fitting of atomic models into density maps
|-

| Paper
| [[2016Segura_3Diana]]
| Validation of hybrid models
|-

| Paper
| [[2016Singharoy_MDFF]]
| Construction of hybrid models driven by EM density and molecular dynamics
|-

| Paper
| [[2016Wang_Rosetta]]
| Construction of hybrid models driven by EM density using Rosetta
|-

|}

=== Books and reviews ===

{|

| Book
| [[1980Herman_Tomography]]
| General book on tomography
|-

| Book
| [[1988Kak_Tomography]]
| General book on tomography
|-

| Paper
| [[2000Tao_Review]]
| Review of single particles
|-

| Paper
| [[2000VanHeel_Review]]
| Review of single particles
|-

| Paper
| [[2002Frank_Review]]
| Review of single particles
|-

| Paper
| [[2002Schmid_Review]]
| Review of single particles
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2004Subramaniam_Review]]
| Review of single particles
|-

| Paper
| [[2005Steven_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_book]]
| Book covering all aspects of electron microscopy of single particles
|-

| Paper
| [[2006Sorzano_Review]]
| Review of optimization problems in electron microscopy
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems in Electron Tomography
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2008Mueller_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2008Taylor_Review]]
| Review of Electron microscopy
|-

| Paper
| [[2010DeRosier_Review]]
| Personal account of how 3DEM developed in the early days
|-

| Chapter
| [[2012Sorzano_Review]]
| Review of single particle analysis using Xmipp
|-

| Chapter
| [[2012Devaux_Protocol]]
| Protocols for performing single particle analysis
|-

| Paper
| [[2014Bai_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Carazo_Review]]
| Review of the reconstruction process
|-

| Paper
| [[2015Cheng_Review]]
| A primer to Single Particle Cryo-EM
|-

| Paper
| [[2015Cheng_Reviewb]]
| Single Particle Cryo-EM at crystallographic resolution
|-

| Paper
| [[2015Elmlund_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Henderson_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Nogales_Review]]
| Recent advances in cryo-EM
|-

| Paper
| [[2015Schroeder_Review]]
| Review of advances in the electron microscope
|-

| Paper
| [[2015Wu_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Carroni_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Egelman_CryoEM]]
| Review of advances in Cryo-EM
|-

| Paper
| [[2016Eisenstein_CryoEM]]
| News feature on the Method of the Year
|-

| Paper
| [[2016FernandezLeiro_Review]]
| Review of EM
|-

| Paper
| [[2016Glaeser_HowGood]]
| How good can cryo-EM become?
|-

| Paper
| [[2016Jonic_PseudoAtoms]]
| Review of the applications of the use of pseudoatoms in EM
|-

| Chapter
| [[2016Mio_Review]]
| Overview of the process to obtain EM reconstructions
|-

| Paper
| [[2016Jonic_Review]]
| A review of computational ways to handle heterogeneity
|-

| Paper
| [[2016Nogales_Review]]
| Review of advances in cryo-EM
|-

| Paper
| [[2016Subramaniam_Review]]
| Why cryo-EM is now suitable for crystallographic journals
|-

| Paper
| [[2016Vinothkumar_Review]]
| Historical review and current limitations
|-

| Paper
| [[2017Frank_Review]]
| Historical review of EM
|-

| Paper
| [[2017Jonic_Review]]
| Review of computational methods to analyze conformational variability
|-

| Paper
| [[2017Sorzano_FourierProperties]]
| Review of statistical properties of resolution measures defined in Fourier space
|-
|}

=== Software ===

{|

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[1999Lutdke_Eman]]
| Eman
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Baldwin_AngularTransformations]]
| The Transform Class in SPARX and EMAN2
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Grigorieff_Frealign]]
| Frealign
|-

| Paper
| [[2008Scheres_XmippProtocols]]
| Xmipp Protocols
|-

| Paper
| [[2008Shaikh_SpiderProtocols]]
| Spider Protocols
|-

| Paper
| [[2012Wriggers_SitusConventions]]
| Conventions and workflows in Situs
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2015Cianfrocco_Cloud]]
| Software execution in the cloud
|-

| Paper
| [[2015Cheng_MRC2014]]
| Extensions to MRC file format
|-

| Paper
| [[2013DeLaRosa_Scipion]]
| Scipion
|-

| Paper
| [[2016Scheres_Relion]]
| Tutorial on the use of Relion
|-

| Paper
| [[2016Grigorieff_Frealign]]
| Tutorial on the use of Frealign
|-

|}

== Electron tomography ==

=== Image preprocessing ===

{|

| Paper
| [[2015Yan_thickness]]
| Determination of thickness, tilt and electron mean free path
|-

|}

=== Image alignment ===

{|

| Paper
| [[1982Guckenberger_commonOrigin]]
| Determination of a common origin in the micrographs of titl series in three-dimensional electron microscopy
|-

| Paper
| [[1992Lawrence_leastSquares]]
| Least squares solution of the alignment problem
|-

| Paper
| [[1995Penczek_dual]]
| Dual tilt alignment
|-

| Paper
| [[1996Owen_alignmentQuality]]
| Automatic alignment without fiducial markers and evaluation of alignment quality
|-

| Paper
| [[1998Grimm_normalization]]
| Discussion of several gray level normalization methods for electron tomography
|-

| Paper
| [[2001Brandt_Automatic1]]
| Automatic alignment without fiducial markers
|-

| Paper
| [[2001Brandt_Automatic2]]
| Automatic alignment with fiducial markers
|-

| Paper
| [[2006Winkler_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2006Castano_alignment]]
| Alignment with non-perpendicularity
|-

| Paper
| [[2007Castano_alignment]]
| Fiducial-less alignment of cryo-sections
|-

| Paper
| [[2009Sorzano_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2010Cantele_dualAlignment]]
| Alignment of dual series
|-

| Paper
| [[2014Tomonaga_Automatic]]
| Automatic alignment of tilt series using the projection themselves
|-

| Paper
| [[2014Han_Automatic]]
| Automatic alignment of tilt series using SIFT features
|-

| Paper
| [[2015Han_Automatic]]
| Automatic alignment of tilt series using fiducials
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[2003Winkler_CTF]]
| Focus gradient correction in electron tomography
|-

| Paper
| [[2006Fernandez_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Zanetti_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Xiong_CTF]]
| CTF determination and correction for low dose tomographic tilt series
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2017Kunz_3DCTF]]
| 3D CTF Correction
|-

|}

=== 3D reconstruction ===

{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1992Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[1997Marabini_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2002Fernandez_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2007Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[2008Fernandez_CARP]]
| Component Averaged Row Projections (CARP)
|-

| Paper
| [[2012Herman General Superiorization]]
| Superiorization: an optimization heuristic for medical physics
|-

| Paper
| [[2012Zhang_IPET_FETR]]
| IPET and FETR, a reconstruction algorithm for single molecule tomography
|-

| Paper
| [[2013Goris_SIRT_TV_DART]]
| Combination of SIRT, Total Variation and Discrete ART to reconstruct and segment at the same time
|-

| Paper
| [[2013Briegel A_Challenge]]
| The challenge of determining handedness in electron tomography and the use of DNA origami gold nanoparticle helices as molecular standards
|-

| Paper
| [[2013Messaoudi_EnergyFiltered]]
| 3D Reconstruction of Energy-Filtered TEM
|-

| Paper
| [[2016Deng_ICON]]
| 3D Reconstruction with missing information restoration
|-

| Paper
| [[2016Guay_Compressed]]
| 3D Reconstruction using compressed sensing
|-

|}

=== Noise reduction ===
{|

| Paper
| [[2001Frangakis_NAD]]
| Noise reduction with Nonlinear Anisotropic Diffusion
|-

| Paper
| [[2003Fernandez_AND]]
| Anisotropic nonlinear diffusion for electron tomography
|-

| Paper
| [[2003Jiang_Bilateral]]
| Bilateral denoising filter in electron microscopy
|-

| Paper
| [[2005Fernandez_AND]]
| Anisotropic nonlinear denoising in electron tomography
|-

| Paper
| [[2007Heide_median]]
| Iterative median filtering in electron tomography
|-

| Paper
| [[2007Fernandez_autAND]]
| Anisotropic nonlinear diffusion with automated parameter tuning
|-

| Paper
| [[2009Fernandez_Beltrami]]
| Nonlinear filtering based on Beltrami flow
|-

| Paper
| [[2010Bilbao_MeanShift]]
| Mean Shift Filtering
|-

| Paper
| [[2014Kovacik_wedgeArtefacts]]
| Removal of wedge artefacts
|-

| Paper
| [[2014Maiorca_beadArtefacts]]
| Removal of gold bead artefacts
|-

|}

=== Segmentation ===

{|

| Paper
| [[2002Frangakis_Eigenanalysis]]
| Segmentation using eigenvector analysis.
|-

| Paper
| [[2002Volkmann_Watershed]]
| Segmentation using watershed transform.
|-

| Paper
| [[2003Bajaj_BoundarySegmentation]]
| Segmentation based on fast marching.
|-

| Paper
| [[2005Cyrklaff_Thresholding]]
| Segmentation using optimal thresholding.
|-

| Paper
| [[2007Lebbink_TemplateMatching]]
| Segmentation using template matching.
|-

| Paper
| [[2007Sandberg_OrientationFields]]
| Segmentation using orientation fields.
|-

| Paper
| [[2007Sandberg_SegmentationReview]]
| Review on segmentation in electron tomography.
|-

| Paper
| [[2008Garduno_FuzzySegmentation]]
| Segmentation using fuzzy set theory principles.
|-

| Paper
| [[2009Lebbink_TemplateMatching2]]
| Segmentation using template matching.
|-

| Paper
| [[2012RubbiyaAli_EdgeDetection]]
| Parameter-Free Segmentation of Macromolecular Structures.
|-

| Conference
| [[2015Xu_TemplateMatching]]
| Detection of macromolecular complexes with a reduced representation of the templates.
|-

|}

=== Resolution ===
{|

| Paper
| [[2005Cardone_Resolution]]
| Resolution criterion for electron tomography
|-

| Chapter
| [[2007Penczek_Resolution]]
| Review of resolution criteria for electron tomography
|-

| Paper
| [[2015Diebolder_ConicalFSC]]
| Conical Fourier Shell Correlation
|-

|}

=== Subtomogram analysis ===

{|

| Paper
| [[2000Bohm_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2002Frangakis_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2006Nickell_Review]]
| Review of macromolecule finding by template matching (Visual Proteomics)
|-

| Paper
| [[2007Best_Review]]
| Review of Localization of Protein Complexes by Pattern Recognition
|-

| Paper
| [[2007Forster_Review]]
| Review of structure determination by subtomogram averaging
|-

| Paper
| [[2008Forster_Classification]]
| Classification of subtomograms using constrained correlation
|-

| Paper
| [[2008Bartesaghi_Classification]]
| Classification and averaging of subtomograms
|-

| Paper
| [[2008Schmid_Averaging]]
| Alignment and averaging of subtomograms
|-

| Paper
| [[2010Amat_Averaging]]
| Alignment and averaging of subtomograms exploiting thresholding in Fourier space
|-

| Paper
| [[2013Chen_Averaging]]
| Fast alignment of subtomograms using spherical harmonics
|-

| Paper
| [[2013Kuybeda_Averaging]]
| Alignment and averaging of subtomograms using the nuclear norm of the cluster
|-

| Paper
| [[2013Shatsky_Averaging]]
| Alignment and averaging of subtomograms with constrained cross-correlation
|-

| Paper
| [[2014Chen_Autofocus]]
| Subtomogram averaging and classification with special attention to differences
|-

| Paper
| [[2014Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2014Voortman_LimitingFactors]]
| Limiting factors of subtomogram averaging
|-

| Paper
| [[2015Bharat_CTFCorrectedSubtomogramAveraging]]
| Subtomogram averaging with CTF correction using a Bayesian prior
|-

| Paper
| [[2015Yu_ReferenceBias]]
| Scoring the reference bias
|-

| Paper
| [[2016Bharat_Relion]]
| Subtomogram averaging with Relion
|-

| Paper
| [[2016Song_MatrixNorm]]
| Matrix norm minimization for tomographic reconstruction and alignment
|-

| Paper
| [[2017Castano_ParticlePicking]]
| Particle picking in tomograms for subtomogram averaging
|-

|}

=== Single particle tomography ===

{|

| Paper
| [[2012Bartesaghi_Constrained]]
| 3D reconstruction by imposing geometrical constraints
|-

| Paper
| [[2015Galaz_SingleParticleTomography]]
| Set of tools for Single Particle Tomography in EMAN2
|-

| Paper
| [[2016Galaz_SingleParticleTomography]]
| Alignment algorithms and CTF correction
|-

|}

=== Books and reviews ===

{|

| Paper
| [[2000Baumeister_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Koster_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Sali_Review]]
| Review of electron tomography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2005Lucic_Review]]
| Review of electron tomography
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_TomoBook]]
| Electron Tomography
|-

| Book
| [[2007McIntosh_Book]]
| Cellular Electron Microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2012Kudryashev_Review]]
| Review of subtomogram averaging
|-

| Paper
| [[2016Beck_Review]]
| Review of molecular sociology
|-

|}

=== Software ===

{|

| Paper
| [[1996Kremer_IMOD]]
| IMOD
|-

| Paper
| [[1996Chen_Priism/IVE]]
| Priism/IVE
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2005Nickell_TOM]]
| TOM Toolbox
|-

| Paper
| [[2007Messaoudi_TomoJ]]
| TomoJ
|-

| Paper
| [[2008Heymann_BsoftTomo]]
| Bsoft
|-

| Paper
| [[2015Ding_CaltechTomography]]
| Caltech tomography database
|-

| Paper
| [[2015Noble_AppionProtomo]]
| Batch fiducial-less tilt-series alignment in Appion using Protomo
|-

| Paper
| [[2015vanAarle_Astra]]
| ASTRA Toolbox
|-

|}

== 2D Crystals ==

=== 2D Preprocessing ===

{|

| Paper
| [[1986Henderson_Processing]]
| General 2D processing
|-

| Paper
| [[2000He_PhaseAlignment]]
| Phase consistency and Alignment
|-

| Paper
| [[2006Gil_Unbending]]
| Crystal unbending
|-

|}

=== Classification ===
{|

| Paper
| [[1988Frank_Classification]]
| MSA and classification in electron crystallography
|-

| Paper
| [[1996Fernandez_SOM]]
| Classification based on self organizing maps
|-

| Paper
| [[1998Sherman_MSA]]
| Classification based on MSA
|-

|}
=== 3D Reconstruction ===

{|

| Paper
| [[1985Wang_Solvent]]
| Solvent flattening
|-

| Paper
| [[1990Henderson_Processing]]
| General 3D processing
|-

| Paper
| [[2004Marabini_ART]]
| Algebraic Reconstruction Technique with blobs for crystals (Xmipp)
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1998Walz_Review]]
| Review of 2D crystallography
|-

| Paper
| [[1999Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Ellis_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of single particles, electron tomography and crystallography
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Gipson_2dx]]
| 2dx
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Philippsen_IPLT]]
| IPLT
|-

|}

== 3D Crystals - MicroED ==

=== Sample Preparation ===
{|
| Paper
| [[2016Shi_Preparation]]
| Sample Preparation
|}
=== Data Collection ===
{|
| Paper
| [[2014Nannenga_CR]]
| Continuous rotation

|}
=== Data Processing ===
{|

| Paper
| [[2011Wisedchaisri_PhaseExtension]]
| Fragment-based phase extension
|-

| Paper
| [[2015Hattne_Processing]]
| Data Processing
|-

| Paper
| [[2016Hattne_Correction]]
| Image correction
|}

=== Software ===
{|

| Paper
| [[2014Iadanza_Processing]]
| Data Processing of still diffraction data
|}

=== Books and Reviews ===
{|
| Paper
| [[2014Nannenga_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Liu_Review ]]
| Review of MicroED
|-

| Paper
| [[2016Rodriguez_Review ]]
| Review of MicroED
|-

|}

== Helical particles ==

=== Filament corrections ===

{|

| Paper
| [[1986Egelman_Curved]]
| Algorithm for correcting curved filaments
|-

| Paper
| [[1988Bluemke_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2006Wang_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2016Yang_Flexible]]
| Algorithm for correcting filaments with flexible subunits
|-

|}

=== Reconstruction ===

{|

| Paper
| [[1952Cochran_Fourier]]
| Fourier Bessel transform of filamentous structures
|-

| Paper
| [[1958Klug_Fourier]]
| Fourier Bessel decomposition of the projection images
|-

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2005Wang_Iterative]]
| Iterative Fourier-Bessel algorithm
|-

| Paper
| [[2007Egelman_Iterative]]
| Iterative real-space algorithm
|-

| Paper
| [[2013Desfosses_Spring]]
| Helical processing with Spring
|-

| Paper
| [[2015Zhang_seam]]
| Workflow for the detection of the lattice seam
|-

| Paper
| [[2016Rohou_Frealix]]
| Helical processing with Frealix
|-

|}

=== Validation ===

{|

| Paper
| [[2014Egelman_ambiguity]]
| How to detect incorrect models
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Carragher_Phoelix]]
| Phoelix
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Owen_Brandeis]]
| Brandeis
|-

|}

== Icosahedral particles ==

=== Reconstruction ===

{|

| Paper
| [[1970Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1971Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1996Fuller_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1997Thuman_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

|}

=== Classification ===

{|

| Paper
| [[2005Scheres_Virus]]
| Classification of virus capsids in real space
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1999Baker_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[1999Conway_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2000Thuman_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Lee_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Navaza_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2006Grunewald_Review]]
| Review of reconstruction of icosahedral viruses
|-

|}

=== Software ===

{|

| Paper
| [[1996Baker_EMPFT]]
| EMPFT
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2013DeLaRosa_Xmipp30]]
| Xmipp 3.0
|-

| Paper
| [[2013Morin_Sliz SBGrid]]
| SBGrid presentation for eLife
|-

|}

== Databases ==

{|

| Paper
| [[2003Boutselakis_EMSD]]
| EMSD database
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

| Paper
| [[2011Kim_CDDB]]
| Conformational Dynamics Data Bank
|-

| Paper
| [[2011Lawson_EMDB]]
| Electron Microscopy Data Bank
|-

| Paper
| [[2016Iudin_EMPIAR]]
| EMPIAR raw data database
|-

| Paper
| [[2016Patwhardan_EMDB]]
| EMDB, PDB, ...
|-

| Paper
| [[2017Shao_PDBQuality]]
| Quality metrics in PDB
|-

| Blog
| http://www.mybiosoftware.com
| Huge list of bioinformatics programs (many of them structural bioinformatics)
|-

|}

== Relationship to other structural information sources ==

{|

| Paper
| [[2000Engel_AFM]]
| Review of Atomic Force Microscopy
|-

| Paper
| [[2001Dimmeler_AFM]]
| Constraints from Atomic Force Microscopy
|-

| Paper
| [[2003Mobus_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_Review]]
| Review on correlative microscopy
|-

| Paper
| [[2005Boudier_EFTETJ]]
| Software for Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2005Vestergaard_SAXS]]
| Example of comparison of 3DEM and Small-angle X-ray scattering
|-

| Paper
| [[2007Hamada_SAXS]]
| Constraints from Small-angle X-ray scattering
|-

| Paper
| [[2013Xu_FRET]]
| EM+FRET
|-

|}

== X-ray tomography ==

{|

| Paper
| [[2012Oton_ImageFormation]]
| Image formation model in X-ray cell microscopy
|-

|}

== Mathematical tools necessary ==

== People developing methods ==
Please, add yourself to this list (due to privacy reasons, please, do not add anyone else to the list without his/her explicit consent). Sort by first name alphabetical order.

[http://biocomp.cnb.csic.es/~coss Carlos Oscar S. Sorzano]: CSIC, Madrid, Spain 

[http://www.curie.fr/recherche/themes/detail_equipe.cfm/lang/_fr/id_equipe/241.htm Cédric Messaoudi]: Institute Curie, Paris, France 

[http://scholar.google.es/citations?user=_jNYGScAAAAJ&hl=en Javier Vargas]:[mailto:jvargas@cnb.csic.es mail]: CSIC, Madrid, Spain 

[http://scholar.google.es/citations?hl=es&user=g2ZJPIYAAAAJ Joaquín Otón]: CSIC, Madrid, Spain 

[mailto:jrbcast@gmail.com José Román Bilbao-Castro]: UAL, Almería, Spain; CSIC, Madrid, Spain 

[José Miguel de la Rosa Trevín]: Biocomputing Unit CNB-CSIC, Madrid, Spain 

[http://cryoem.janelia.org Tamir Gonen]: [mailto:gonent@janelia.hhmi.org mail]: Howard Hughes Medical Institute, Ashburn, VA, USA 

[mailto:vabrishami@cnb.csic.es Vahid Abrishami]: CSIC, Madrid, Spain 

== 3DEM sites ==
* [http://3dem.ucsd.edu/ 3DEM web site]

* [http://en.wikibooks.org/wiki/Software_Tools_For_Molecular_Microscopy Software tools for molecular microscopy]

* [http://www.emdatabank.org/ The Electron Microscopy Data Bank (EMDB)]

* [http://ccdb.ucsd.edu The Cell Centered Database (CCDB)]

* [http://conventions.cnb.csic.es The geometrical software conventions web page ]

== Editing useful links ==

* [http://www.mediawiki.org/wiki/Help:Formatting Text formatting in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Links Adding links in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Images Adding images in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Tables Making tables in Mediawiki]