3DEM-Methods - User contributions [en]

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2016-10-06T18:43:11Z

Gonenlab: /* 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 ==

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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

=== 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
|-

|}

=== 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
|-

|}

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

|}

=== 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
|-

|}

== 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
|-

|}

=== 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
|-

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

|}

=== 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
|-

|}

=== 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
|-

|}

=== 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 D_FREALIGN]]
| Likelihood-based classification of cryo-EM images using FREALIGN.
|-

| 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
|-

|}

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

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

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

| 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
|-

|}

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

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

|}

=== 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
|-

|}

=== 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
| [[2016Segura_3Diana]]
| Validation of hybrid 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
| [[2016Glaeser_HowGood]]
| How good can cryo-EM become?
|-

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

| 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
|-

|}

=== 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
| [[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
|-

|}

=== 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
|-

|}

=== 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
| [[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
|-

|}

=== 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.
|-
|}

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

|}

=== Single particle tomography ===

{|

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

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

|}

=== 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
|-

|}

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

|}

=== 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
|-

| 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]

2016Rodriguez Review

2016-10-06T18:42:37Z

Gonenlab: Created page with "== Citation == Rodriguez, J. A. & Gonen, T. High-Resolution Macromolecular Structure Determination by MicroED, a cryo-EM Method. Meth. Enzymol. (2016). == Abstract == Micro..."

== Citation ==

Rodriguez, J. A. & Gonen, T. High-Resolution Macromolecular Structure Determination by MicroED, a cryo-EM Method. Meth. Enzymol. (2016).

== Abstract ==

Microelectron diffraction (MicroED) is a new cryo-electron microscopy (cryo-EM) method capable of determining macromolecular structures at atomic resolution from vanishingly small 3D crystals. MicroED promises to solve atomic resolution structures from even the tiniest of crystals, less than a few hundred nanometers thick. MicroED complements frontier advances in crystallography and represents part of the rebirth of cryo-EM that is making macromolecular structure determination more accessible for all. Here we review the concept and practice of MicroED, for both the electron microscopist and crystallographer. Where other reviews have addressed specific details of the technique (Hattne et al., 2015; Shi et al., 2016; Shi, Nannenga, Iadanza, & Gonen, 2013), we aim to provide context and highlight important features that should be considered when performing a MicroED experiment.
== Keywords ==

== Links ==

Article http://www.sciencedirect.com/science/article/pii/S0076687916300350

== Related software ==

== Related methods ==

== Comments ==

Main Page

2016-10-06T18:39:30Z

Gonenlab: /* 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 subscribe to this list write a mail to sympa6@cnb.csic.es with the subject

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

and an empty mail body. To unsubscribe 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

=== 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
|-

|}

=== 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
|-

|}

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

|}

=== 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
|-

|}

== 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
|-

|}

=== 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
|-

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

|}

=== 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
|-

|}

=== 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
|-

|}

=== 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 D_FREALIGN]]
| Likelihood-based classification of cryo-EM images using FREALIGN.
|-

| 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
|-

|}

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

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

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

| 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
|-

|}

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

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

|}

=== 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
|-

|}

=== 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
| [[2016Segura_3Diana]]
| Validation of hybrid 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
| [[2016Glaeser_HowGood]]
| How good can cryo-EM become?
|-

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

| 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
|-

|}

=== 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
| [[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
|-

|}

=== 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
|-

|}

=== 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
| [[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
|-

|}

=== 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.
|-
|}

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

|}

=== Single particle tomography ===

{|

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

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

|}

=== 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
|-

|}

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

|}

=== 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
|-

| 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

2016-10-06T18:37:02Z

Gonenlab: /* 3D Crystals */

== 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 subscribe to this list write a mail to sympa6@cnb.csic.es with the subject

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

and an empty mail body. To unsubscribe 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

=== 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
|-

|}

=== 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
|-

|}

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

|}

=== 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
|-

|}

== 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
|-

|}

=== 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
|-

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

|}

=== 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
|-

|}

=== 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
|-

|}

=== 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 D_FREALIGN]]
| Likelihood-based classification of cryo-EM images using FREALIGN.
|-

| 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
|-

|}

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

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

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

| 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
|-

|}

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

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

|}

=== 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
|-

|}

=== 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
| [[2016Segura_3Diana]]
| Validation of hybrid 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
| [[2016Glaeser_HowGood]]
| How good can cryo-EM become?
|-

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

| 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
|-

|}

=== 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
| [[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
|-

|}

=== 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
|-

|}

=== 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
| [[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
|-

|}

=== 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.
|-
|}

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

|}

=== Single particle tomography ===

{|

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

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

|}

=== 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
|-

|}

=== 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
|-

|}

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

|}

=== 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
|-

| 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]

2016Liu Review

2016-10-06T17:19:58Z

Gonenlab: Created page with "== Citation == Liu, S. et al. Atomic resolution structure determination by the cryo-EM method MicroED. Protein Sci. (2016). == Abstract == The electron cryo-microscopy (cry..."

== Citation ==

Liu, S. et al. Atomic resolution structure determination by the cryo-EM method MicroED. Protein Sci. (2016).

== Abstract ==

The electron cryo-microscopy (cryoEM) method MicroED has been rapidly developing. In this review we highlight some of the key steps in MicroED from crystal analysis to structure determination. We compare and contrast MicroED and the latest X-ray based diffraction method the X-ray free-electron laser (XFEL). Strengths and shortcomings of both MicroED and XFEL are discussed. Finally, all current MicroED structures are tabulated with a view to the future.
== Keywords ==

== Links ==

Article http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=27452773&retmode=ref&cmd=prlinks

== Related software ==

== Related methods ==

== Comments ==

2014Nannenga Review

2016-10-06T17:19:10Z

Gonenlab: Created page with "== Citation == Nannenga, B. L. & Gonen, T. Protein structure determination by MicroED. Curr. Opin. Struct. Biol. 27C, 24–31 (2014). == Abstract == In this review we disc..."

== Citation ==

Nannenga, B. L. & Gonen, T. Protein structure determination by MicroED. Curr. Opin. Struct. Biol. 27C, 24–31 (2014).

== Abstract ==

In this review we discuss the current advances relating to structure determination from protein microcrystals with special emphasis on the newly developed method called MicroED. This method uses a transmission electron cryo-microscope to collect electron diffraction data from extremely small 3-dimensional (3D) crystals. MicroED has been used to solve the 3D structure of the model protein lysozyme to 2.9Å resolution. As the method further matures, MicroED promises to offer a unique and widely applicable approach to protein crystallography using nanocrystals.

== Keywords ==

== Links ==

Article http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=24709395&retmode=ref&cmd=prlinks
== Related software ==

== Related methods ==

== Comments ==

2014Iadanza Processing

2016-10-06T17:18:22Z

Gonenlab: Created page with "== Citation == Iadanza, M. G. & Gonen, T. A suite of software for processing MicroED data of extremely small protein crystals. J Appl Crystallogr 47, 1140–1145 (2014). ==..."

== Citation ==

Iadanza, M. G. & Gonen, T. A suite of software for processing MicroED data of extremely small protein crystals. J Appl Crystallogr 47, 1140–1145 (2014).

== Abstract ==
We demonstrate that it is feasible to determine high-resolution protein structures by electron crystallography of three-dimensional crystals in an electron cryo-microscope (CryoEM). Lysozyme microcrystals were frozen on an electron microscopy grid, and electron diffraction data collected to 1.7 Å resolution. We developed a data collection protocol to collect a full-tilt series in electron diffraction to atomic resolution. A single tilt series contains up to 90 individual diffraction patterns collected from a single crystal with tilt angle increment of 0.1-1° and a total accumulated electron dose less than 10 electrons per angstrom squared. We indexed the data from three crystals and used them for structure determination of lysozyme by molecular replacement followed by crystallographic refinement to 2.9 Å resolution. This proof of principle paves the way for the implementation of a new technique, which we name 'MicroED', that may have wide applicability in structural biology. DOI: http://dx.doi.org/10.7554/eLife.01345.001.
== Keywords ==

== Links ==

Article http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=24252878&retmode=ref&cmd=prlinks

== Related software ==

== Related methods ==

== Comments ==

2016Hattne Correction

2016-10-06T17:17:40Z

Gonenlab: Created page with "== Citation == Hattne, J., Shi, D., la Cruz, de, M. J., Reyes, F. E. & Gonen, T. Modeling truncated pixel values of faint reflections in MicroED images. J Appl Crystallogr 49..."

== Citation ==

Hattne, J., Shi, D., la Cruz, de, M. J., Reyes, F. E. & Gonen, T. Modeling truncated pixel values of faint reflections in MicroED images. J Appl Crystallogr 49, 1029–1034 (2016).

== Abstract ==

The weak pixel counts surrounding the Bragg spots in a diffraction image are important for establishing a model of the background underneath the peak and estimating the reliability of the integrated intensities. Under certain circumstances, particularly with equipment not optimized for low-intensity measurements, these pixel values may be corrupted by corrections applied to the raw image. This can lead to truncation of low pixel counts, resulting in anomalies in the integrated Bragg intensities, such as systematically higher signal-to-noise ratios. A correction for this effect can be approximated by a three-parameter lognormal distribution fitted to the weakly positive-valued pixels at similar scattering angles. The procedure is validated by the improved refinement of an atomic model against structure factor amplitudes derived from corrected micro-electron diffraction (MicroED) images.

== Keywords ==

== Links ==

Article http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=27275145&retmode=ref&cmd=prlinks

== Related software ==

== Related methods ==

== Comments ==

2015Hattne Processing

2016-10-06T17:16:56Z

Gonenlab: Created page with "== Citation == Hattne, J. et al. MicroED data collection and processing. Acta Crystallogr A Found Adv 71, 353–360 (2015). == Abstract == MicroED, a method at the intersec..."

== Citation ==

Hattne, J. et al. MicroED data collection and processing. Acta Crystallogr A Found Adv 71, 353–360 (2015).

== Abstract ==

MicroED, a method at the intersection of X-ray crystallography and electron cryo-microscopy, has rapidly progressed by exploiting advances in both fields and has already been successfully employed to determine the atomic structures of several proteins from sub-micron-sized, three-dimensional crystals. A major limiting factor in X-ray crystallography is the requirement for large and well ordered crystals. By permitting electron diffraction patterns to be collected from much smaller crystals, or even single well ordered domains of large crystals composed of several small mosaic blocks, MicroED has the potential to overcome the limiting size requirement and enable structural studies on difficult-to-crystallize samples. This communication details the steps for sample preparation, data collection and reduction necessary to obtain refined, high-resolution, three-dimensional models by MicroED, and presents some of its unique challenges.

== Keywords ==

== Links ==

Article http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=26131894&retmode=ref&cmd=prlinks

== Related software ==

== Related methods ==

== Comments ==

2011Wisedchaisri PhaseExtension

2016-10-06T17:16:14Z

Gonenlab: Created page with "== Citation == Wisedchaisri, G. & Gonen, T. Fragment-based phase extension for three-dimensional structure determination of membrane proteins by electron crystallography. Str..."

== Citation ==

Wisedchaisri, G. & Gonen, T. Fragment-based phase extension for three-dimensional structure determination of membrane proteins by electron crystallography. Structure 19, 976–987 (2011)

== Abstract ==

In electron crystallography, membrane protein structure is determined from two-dimensional crystals where the protein is embedded in a membrane. Once large and well-ordered 2D crystals are grown, one of the bottlenecks in electron crystallography is the collection of image data to directly provide experimental phases to high resolution. Here, we describe an approach to bypass this bottleneck, eliminating the need for high-resolution imaging. We use the strengths of electron crystallography in rapidly obtaining accurate experimental phase information from low-resolution images and accurate high-resolution amplitude information from electron diffraction. The low-resolution experimental phases were used for the placement of α helix fragments and extended to high resolution using phases from the fragments. Phases were further improved by density modifications followed by fragment expansion and structure refinement against the high-resolution diffraction data. Using this approach, structures of three membrane proteins were determined rapidly and accurately to atomic resolution without high-resolution image data.

== Keywords ==

== Links ==

Article http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=21742264&retmode=ref&cmd=prlinks

== Related software ==

== Related methods ==

== Comments ==

2016Shi Preparation

2016-10-06T17:15:26Z

Gonenlab: /* Links */

== Citation ==

Shi, D. et al. The collection of MicroED data for macromolecular crystallography. Nat Protoc 11, 895–904 (2016)

== Abstract ==

The formation of large, well-ordered crystals for crystallographic experiments remains a crucial bottleneck to the structural understanding of many important biological systems. To help alleviate this problem in crystallography, we have developed the MicroED method for the collection of electron diffraction data from 3D microcrystals and nanocrystals of radiation-sensitive biological material. In this approach, liquid solutions containing protein microcrystals are deposited on carbon-coated electron microscopy grids and are vitrified by plunging them into liquid ethane. MicroED data are collected for each selected crystal using cryo-electron microscopy, in which the crystal is diffracted using very few electrons as the stage is continuously rotated. This protocol gives advice on how to identify microcrystals by light microscopy or by negative-stain electron microscopy in samples obtained from standard protein crystallization experiments. The protocol also includes information about custom-designed equipment for controlling crystal rotation and software for recording experimental parameters in diffraction image metadata. Identifying microcrystals, preparing samples and setting up the microscope for diffraction data collection take approximately half an hour for each step. Screening microcrystals for quality diffraction takes roughly an hour, and the collection of a single data set is ∼10 min in duration. Complete data sets and resulting high-resolution structures can be obtained from a single crystal or by merging data from multiple crystals.

== Keywords ==

== Links ==
Article http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=27077331&retmode=ref&cmd=prlinks

== Related software ==

== Related methods ==

== Comments ==

2014Nannenga CR

2016-10-06T17:15:12Z

Gonenlab: Created page with "== Citation == Nannenga, B. L., Shi, D., Leslie, A. G. W. & Gonen, T. High-resolution structure determination by continuous-rotation data collection in MicroED. Nat. Methods..."

== Citation ==

Nannenga, B. L., Shi, D., Leslie, A. G. W. & Gonen, T. High-resolution structure determination by continuous-rotation data collection in MicroED. Nat. Methods 11, 927–930 (2014).

== Abstract ==

MicroED uses very small three-dimensional protein crystals and electron diffraction for structure determination. We present an improved data collection protocol for MicroED called 'continuous rotation'. Microcrystals are continuously rotated during data collection, yielding more accurate data. The method enables data processing with the crystallographic software tool MOSFLM, which resulted in improved resolution for the model protein lysozyme. These improvements are paving the way for the broad implementation and application of MicroED in structural biology.
== Keywords ==

== Links ==

Article http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=25086503&retmode=ref&cmd=prlinks

== Related software ==

== Related methods ==

== Comments ==

2016Shi Preparation

2016-10-06T17:13:41Z

Gonenlab: Created page with "== Citation == Shi, D. et al. The collection of MicroED data for macromolecular crystallography. Nat Protoc 11, 895–904 (2016) == Abstract == The formation of large, well..."

== Citation ==

Shi, D. et al. The collection of MicroED data for macromolecular crystallography. Nat Protoc 11, 895–904 (2016)

== Abstract ==

The formation of large, well-ordered crystals for crystallographic experiments remains a crucial bottleneck to the structural understanding of many important biological systems. To help alleviate this problem in crystallography, we have developed the MicroED method for the collection of electron diffraction data from 3D microcrystals and nanocrystals of radiation-sensitive biological material. In this approach, liquid solutions containing protein microcrystals are deposited on carbon-coated electron microscopy grids and are vitrified by plunging them into liquid ethane. MicroED data are collected for each selected crystal using cryo-electron microscopy, in which the crystal is diffracted using very few electrons as the stage is continuously rotated. This protocol gives advice on how to identify microcrystals by light microscopy or by negative-stain electron microscopy in samples obtained from standard protein crystallization experiments. The protocol also includes information about custom-designed equipment for controlling crystal rotation and software for recording experimental parameters in diffraction image metadata. Identifying microcrystals, preparing samples and setting up the microscope for diffraction data collection take approximately half an hour for each step. Screening microcrystals for quality diffraction takes roughly an hour, and the collection of a single data set is ∼10 min in duration. Complete data sets and resulting high-resolution structures can be obtained from a single crystal or by merging data from multiple crystals.

== Keywords ==

== Links ==
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=27077331&retmode=ref&cmd=prlinks

== Related software ==

== Related methods ==

== Comments ==

Main Page

2016-10-06T17:12:24Z

Gonenlab: /* 3D Crystals */

== 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 subscribe to this list write a mail to sympa6@cnb.csic.es with the subject

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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

=== 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
|-

|}

=== 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
|-

|}

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

|}

=== 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
|-

|}

== 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
|-

|}

=== 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
|-

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

|}

=== 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
|-

|}

=== 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
|-

|}

=== 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 D_FREALIGN]]
| Likelihood-based classification of cryo-EM images using FREALIGN.
|-

| 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
|-

|}

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

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

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

| 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
|-

|}

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

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

|}

=== 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
|-

|}

=== 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
| [[2016Segura_3Diana]]
| Validation of hybrid 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
| [[2016Glaeser_HowGood]]
| How good can cryo-EM become?
|-

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

| 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
|-

|}

=== 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
| [[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
|-

|}

=== 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
|-

|}

=== 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
| [[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
|-

|}

=== 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.
|-
|}

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

|}

=== Single particle tomography ===

{|

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

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

|}

=== 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
|-

|}

=== 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 ==

=== 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
|-

|}

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

|}

=== 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
|-

| 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

2016-10-06T17:09:48Z

Gonenlab: /* 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 subscribe to this list write a mail to sympa6@cnb.csic.es with the subject

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

and an empty mail body. To unsubscribe 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

=== 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
|-

|}

=== 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
|-

|}

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

|}

=== 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
|-

|}

== 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
|-

|}

=== 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
|-

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

|}

=== 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
|-

|}

=== 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
|-

|}

=== 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 D_FREALIGN]]
| Likelihood-based classification of cryo-EM images using FREALIGN.
|-

| 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
|-

|}

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

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

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

| 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
|-

|}

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

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

|}

=== 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
|-

|}

=== 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
| [[2016Segura_3Diana]]
| Validation of hybrid 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
| [[2016Glaeser_HowGood]]
| How good can cryo-EM become?
|-

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

| 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
|-

|}

=== 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
| [[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
|-

|}

=== 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
|-

|}

=== 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
| [[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
|-

|}

=== 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.
|-
|}

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

|}

=== Single particle tomography ===

{|

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

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

|}

=== 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
|-

|}

=== 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 ==

=== 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 Lysozyme still diffraction data
|}

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

|}

=== 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
|-

| 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

2016-10-06T17:09:32Z

Gonenlab: /* Data Processing */

== 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 subscribe to this list write a mail to sympa6@cnb.csic.es with the subject

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

and an empty mail body. To unsubscribe 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

=== 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
|-

|}

=== 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
|-

|}

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

|}

=== 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
|-

|}

== 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
|-

|}

=== 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
|-

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

|}

=== 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
|-

|}

=== 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
|-

|}

=== 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 D_FREALIGN]]
| Likelihood-based classification of cryo-EM images using FREALIGN.
|-

| 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
|-

|}

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

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

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

| 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
|-

|}

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

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

|}

=== 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
|-

|}

=== 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
| [[2016Segura_3Diana]]
| Validation of hybrid 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
| [[2016Glaeser_HowGood]]
| How good can cryo-EM become?
|-

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

| 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
|-

|}

=== 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
| [[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
|-

|}

=== 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
|-

|}

=== 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
| [[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
|-

|}

=== 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.
|-
|}

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

|}

=== Single particle tomography ===

{|

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

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

|}

=== 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
|-

|}

=== 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 ==

=== 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
| [[2014_Iadanza_LysozymeProcessing]]
| Data Processing of Lysozyme still diffraction data
|}

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

|}

=== 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
|-

| 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

2016-10-06T17:09:18Z

Gonenlab: /* Data Processing */

== 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 subscribe to this list write a mail to sympa6@cnb.csic.es with the subject

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

and an empty mail body. To unsubscribe 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

=== 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
|-

|}

=== 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
|-

|}

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

|}

=== 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
|-

|}

== 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
|-

|}

=== 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
|-

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

|}

=== 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
|-

|}

=== 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
|-

|}

=== 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 D_FREALIGN]]
| Likelihood-based classification of cryo-EM images using FREALIGN.
|-

| 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
|-

|}

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

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

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

| 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
|-

|}

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

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

|}

=== 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
|-

|}

=== 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
| [[2016Segura_3Diana]]
| Validation of hybrid 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
| [[2016Glaeser_HowGood]]
| How good can cryo-EM become?
|-

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

| 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
|-

|}

=== 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
| [[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
|-

|}

=== 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
|-

|}

=== 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
| [[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
|-

|}

=== 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.
|-
|}

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

|}

=== Single particle tomography ===

{|

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

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

|}

=== 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
|-

|}

=== 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 ==

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

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

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

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

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

=== Software ===
{|

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

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

|}

=== 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
|-

| 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

2016-10-06T17:08:52Z

Gonenlab: /* 3D Crystals */

== 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.
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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

=== 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
|-

|}

=== 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
|-

|}

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

|}

=== 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
|-

|}

== 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
|-

|}

=== 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
|-

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

|}

=== 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
|-

|}

=== 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
|-

|}

=== 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 D_FREALIGN]]
| Likelihood-based classification of cryo-EM images using FREALIGN.
|-

| 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
|-

|}

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

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

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

| 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
|-

|}

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

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

|}

=== 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
|-

|}

=== 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
| [[2016Segura_3Diana]]
| Validation of hybrid 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
| [[2016Glaeser_HowGood]]
| How good can cryo-EM become?
|-

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

| 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
|-

|}

=== 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
| [[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
|-

|}

=== 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
|-

|}

=== 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
| [[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
|-

|}

=== 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.
|-
|}

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

|}

=== Single particle tomography ===

{|

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

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

|}

=== 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
|-

|}

=== 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 ==

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

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

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

| Paper
| [[2015_Hattne_Processing]]
| Data Processing
|

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

=== Software ===
{|

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

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

|}

=== 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
|-

| 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

2016-10-06T17:07:37Z

Gonenlab:

== 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 subscribe to this list write a mail to sympa6@cnb.csic.es with the subject

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

and an empty mail body. To unsubscribe 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

=== 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
|-

|}

=== 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
|-

|}

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

|}

=== 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
|-

|}

== 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
|-

|}

=== 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
|-

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

|}

=== 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
|-

|}

=== 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
|-

|}

=== 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 D_FREALIGN]]
| Likelihood-based classification of cryo-EM images using FREALIGN.
|-

| 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
|-

|}

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

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

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

| 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
|-

|}

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

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

|}

=== 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
|-

|}

=== 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
| [[2016Segura_3Diana]]
| Validation of hybrid 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
| [[2016Glaeser_HowGood]]
| How good can cryo-EM become?
|-

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

| 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
|-

|}

=== 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
| [[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
|-

|}

=== 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
|-

|}

=== 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
| [[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
|-

|}

=== 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.
|-
|}

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

|}

=== Single particle tomography ===

{|

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

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

|}

=== 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
|-

|}

=== 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 ==

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

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

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

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

| Paper
| [[2016_Hattne_Correction]]
| Image correction
| -

|}

=== Software ===
{|

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

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

|}

=== 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
|-

| 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

2016-10-06T13:54:36Z

Gonenlab:

== 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 subscribe to this list write a mail to sympa6@cnb.csic.es with the subject

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

and an empty mail body. To unsubscribe 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

=== 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
|-

|}

=== 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
|-

|}

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

|}

=== 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
|-

|}

== 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
|-

|}

=== 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
|-

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

|}

=== 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
|-

|}

=== 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
|-

|}

=== 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 D_FREALIGN]]
| Likelihood-based classification of cryo-EM images using FREALIGN.
|-

| 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
|-

|}

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

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

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

| 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
|-

|}

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

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

|}

=== 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
|-

|}

=== 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
| [[2016Segura_3Diana]]
| Validation of hybrid 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
| [[2016Glaeser_HowGood]]
| How good can cryo-EM become?
|-

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

| 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
|-

|}

=== 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
| [[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
|-

|}

=== 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
|-

|}

=== 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
| [[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
|-

|}

=== 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.
|-
|}

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

|}

=== Single particle tomography ===

{|

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

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

|}

=== 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
|-

|}

=== 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 ==

=== Sample Preparation ===

=== Data Collection ===

=== Data Analysis ===

=== Software ===

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

|}

=== 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
|-

| 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

2016-10-06T13:39:45Z

Gonenlab: /* People developing methods */

== 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 subscribe to this list write a mail to sympa6@cnb.csic.es with the subject

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

and an empty mail body. To unsubscribe 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

=== 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
|-

|}

=== 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
|-

|}

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

|}

=== 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
|-

|}

== 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
|-

|}

=== 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
|-

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

|}

=== 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
|-

|}

=== 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
|-

|}

=== 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 D_FREALIGN]]
| Likelihood-based classification of cryo-EM images using FREALIGN.
|-

| 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
|-

|}

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

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

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

| 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
|-

|}

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

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

|}

=== 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
|-

|}

=== 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
| [[2016Segura_3Diana]]
| Validation of hybrid 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
| [[2016Glaeser_HowGood]]
| How good can cryo-EM become?
|-

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

| 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
|-

|}

=== 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
| [[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
|-

|}

=== 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
|-

|}

=== 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
| [[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
|-

|}

=== 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.
|-
|}

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

|}

=== Single particle tomography ===

{|

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

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

|}

=== 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
|-

|}

=== 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
|-

|}

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

|}

=== 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
|-

| 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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