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Revision as of 09:05, 25 January 2017

Presentation

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

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Electron microscopy images

Online courses

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

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

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

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

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 2010Zhang_NegativeStaining Negative staining for small protein imaging
Paper 2012Zhang_PositiveStaining Positive staining
Paper 2014Rames_NegativeStaining Optimized negative staining
Paper 2014Russo_GoldGrids Gold grids for single particles
Paper 2015Cabra_Sample Review on sample preparation for single particles with videos
Paper 2016Passmore_Review Tutorial chapter on sample preparation
Paper 2016Razinkov_Vitrification New vitrification method
Paper 2016Takizawa_Sample Review on sample preparation for EM
Paper 2016Thompson_Sample Review on sample preparation for EM
Paper 2017Peitsch_Sample iMEM: Isolation of Plasma Membrane for Cryoelectron Microscopy

Automated data collection

Paper 1992Dierksen_Automatic Automated data collection
Paper 1992Koster_Automatic Automated data collection
Paper 1996Fung_Automatic Automated data collection for tomography
Paper 2001Zhang_Automatic Automated data collection: AutoEM
Paper 2003Ziese_Automatic Automated autofocusing
Paper 2004Potter_Automatic Automated sample loading
Paper 2004Zheng_Automatic Automated data collection
Paper 2005Lei_Automatic Automated data collection: AutoEM
Paper 2005Suloway_Automatic Automated data collection: Leginon
Paper 2007Yoshioka_RCT Automated Random Conical Tilt
Paper 2011Korinek_TOM2 Automated acquisition with TOM2
Paper 2015Li_UCSFImage Automated acquisition with UCSFImage
Paper 2016Gil_Fuzzy Real time decisions during acquisition with neuro-fuzzy method
Paper 2016Liu_TiltControl Accurate control of the tilt angle for electron tomography
Paper 2016Vargas_FoilHole Determination of image quality at low magnification

Single particles

Automatic particle picking

Paper 1982VanHeel_Detection Detection of particles in micrographs
Paper 2001Nicholson_Review Review on automatic particle picking
Paper 2001Zhu_Filaments Automatic identification of filaments in micrographs
Paper 2004Sigworth_Detection Classical detection theory and the cryo-EM particle selection problem
Paper 2004Volkmann_ParticlePicking An approach to automated particle picking from electron micrographs based on reduced representation templates
Paper 2004Wong_ParticlePicking Model-based particle picking for cryo-electron microscopy
Paper 2004Zhu_Review Review on automatic particle picking
Paper 2007Chen_Signature Automatic particle picking program: Signature
Paper 2007Woolford_SwarmPS Automatic particle picking with several criteria, implemented in EMAN Boxer
Paper 2009Sorzano_MachineLearning Automatic particle picking based on machine learning of rotational invariants
Paper 2011Arbelaez_Comparison Evaluation of the performance of software for automated particle-boxing
Paper 2013Abrishami_MachineLearning A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs
Paper 2013Hauer_2013 Automatic tilt pair detection in Random Conical Tilt
Paper 2013Shatsky_ParticlePicking Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs
Paper 2013Vargas_ParticleQuality Automatic determination of particle quality
Paper 2014Langlois_ParticlePicking Automatic particle picking
Paper 2016Vilas_AutomaticTilt Automatic identification of image pairs in untilted-tilted micrograph pairs

2D Preprocessing

Paper 2003Rosenthal_DPR Contrast enhancement through DPR
Paper 2004Sorzano_Normalization Normalization procedures and their statistical properties.
Paper 2006Sorzano_Denoising Strong denoising in wavelet space
Conference 2009Sorzano_Downsampling Differences between the different downsampling schemes
Paper 2012Brilot_Movies Alignment of beam induced motion in direct detectors
Paper 2012Campbell_Movies Alignment of beam induced motion in direct detectors
Paper 2012Zhao_Denoising Denoising using an invariant Fourier-Bessel eigenspace
Paper 2013Norousi_Screening Screening particles to identify outliers
Paper 2013Bai_ElectronCounting Electron counting and beam induced motion correction
Paper 2013Li_ElectronCounting Electron counting and beam induced motion correction
Paper 2013Shigematsu_Movies Drift correction for movies considering dark field
Paper 2013Vargas_ParticleQuality Automatic determination of particle quality
Paper 2014Scheres_Movies Beam induced motion correction
Paper 2015Abrishami_Movies Alignment of direct detection device micrographs
Paper 2015Grant_Anisotropic Automatic estimation and correction of anisotropic magnification
Paper 2015Grant_OptimalExposure Filter movies according to the radiation damage
Paper 2015Rubinstein_Alignment Frame alignment at the level of particle
Paper 2015Spear_DoseCompensation Effect of dose compensation on resolution
Paper 2015Zhao_AnisotropicMagnification Correction of anisotropic magnification
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
Paper 2016Reboul_Stochastic Stochastic Hill Climbing for calculating 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
Paper 2016Cossio_BayesianGPU GPU implementation of the Bayesian 3D reconstruction approach

3D Reconstruction

Paper 1972Gilbert_SIRT Simultaneous Iterative Reconstruction Technique (SIRT)
Paper 1973Herman_ART Algebraic Reconstruction Technique (ART)
Paper 1984Andersen_SART Simultaneous Algebraic Reconstruction Technique (SART)
Paper 1986Harauz_FBP Exact filters for Filtered Back Projection
Chapter 1992Radermacher_WBP Exact filters for Weighted Back Projection
Paper 1997Zhu_RecCTF 3D Reconstruction (SIRT like) and simultaneous CTF correction
Paper 1998Boisset_Uneven Artifacts in SIRT and WBP under uneven angular distributions
Paper 1998Marabini_ART Algebraic Reconstruction Technique with blobs (Xmipp)
Paper 2001Sorzano_Uneven Free parameter selection under uneven angular distributions
Paper 2005Sorzano_Parameters Free parameter selection for optimizing multiple tasks
Paper 2008Sorzano_Constraints Mass, surface, positivity and symmetry constraints for real-space algorithms
Paper 2009Bilbao_ParallelART Efficient parallelization of ART
Paper 2011Li_GradientFlow Regularized 3D Reconstruction by Gradient Flow
Paper 2011Vonesch_Wavelets Fast wavelet-based 3D reconstruction
Paper 2012Gopinath_ShapeRegularization Regularized 3D Reconstruction by Shape information
Paper 2012Kucukelbir_adaptiveBasis 3D reconstruction in an adaptive basis promoting sparsity
Paper 2012Sindelar_NoiseReduction Optimal noise reduction in 3D reconstructions
Paper 2013Elmlund H_PRIME PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
Paper 2013Lyumkis_Optimod Construction of initial volumes with Optimod
Paper 2013Wang FIRM Fast 3D reconstruction in Fourier domain
Paper 2014Kunz_SART_OS Simultaneous ART with OS
Paper 2015Abrishami_Fourier 3D Reconstruction in Fourier space
Paper 2015Dvornek_SubspaceEM Fast Maximum a posteriori
Paper 2015Moriya_Bayesian Bayesian approach to suppress limited angular artifacts
Paper 2015Xu_GeometricFlow Multi-scale geometric flow
Arxiv 2016Ye_Cohomology Cohomology properties of 3D reconstruction

3D Heterogeneity

Paper 2004White_Size Heterogeneity classification of differently sized images
Paper 2006Penczek_Bootstrap 3D heterogeneity through bootstrap
Paper 2007Leschziner_Review Review of 3D heterogeneity handling algorithms
Paper 2007Scheres_ML3D Maximum Likelihood alignment and classification in 3D
Paper 2009Spahn_Bootstrap 3D heterogeneity through bootstrap
Paper 2010Elmlund_AbInitio Solving the initial volume problem with multiple conformations
Paper 2010Shatsky_MultiVariate Multivariate Statistical Analysis
Paper 2012Scheres_Bayesian A Bayesian view on cryo-EM structure determination
Paper 2012Zheng_Covariance Estimation of the volume covariance
Paper 2013Wang_MLVariance Maximum Likelihood estimate of the map variance
Paper 2013Lyumkis D_FREALIGN Likelihood-based classification of cryo-EM images using FREALIGN.
Paper 2014Jin_NMA Continuous heterogeneity through Normal Mode Analysis
Paper 2014Dashti_Brownian Continuous heterogeneity through Brownian trajectories
Paper 2014Chen_Migration Particle migration analysis in 3D classification
Paper 2015Anden_Covariance 3D Covariance matrix estimation for heterogeneity
Paper 2015Bai_Focused Focused classification
Paper 2015Katsevich_Covariance 3D Covariance matrix estimation for heterogeneity
Paper 2015Klaholz_MRA Multivariate Statistical Analysis of Jackknife and Bootstrapping on random subsets
Paper 2015Liao_Covariance Estimation of the 3D covariance from 2D projections
Paper 2015Tagare_Direct Direct reconstruction of PCA components
Paper 2016Gong_Mechanical Mechanical model for macromolecules
Paper 2016Rawson_Movement Movement and flexibility
Paper 2016Sorzano_StructMap Sorting a discrete set of conformational states
Paper 2016Sorzano_Strain Calculate local stretches, strains and rotations from two conformational states

Validation

Paper 2008Stagg_TestBed Effect of voltage, dosis, number of particles and Euler jumps on resolution
Paper 2011Henderson Tilt Validation
Paper 2011Read Validation of PDBs
Paper 2012Henderson EM Map Validation
Paper 2013Cossio_Bayesian EM Map Validation in a probabilistic setting
Paper 2013Chen_NoiseSubstitution Noise substitution at high resolution for measuring overfitting
Paper 2014Russo_StatisticalSignificance EM Map Validation through the statistical significance of the tilt-pair angular assignment
Paper 2014Stagg_Reslog EM Map Validation through the resolution evolution with the number of particles
Paper 2014Wasilewski_Tilt Web implementation of the tilt pair validation
Paper 2015Heymann_Alignability EM Map Validation through the resolution of reconstructions from particles and noise
Paper 2015Oliveira_FreqLimited Comparison of gold standard and frequency limited optimization
Paper 2015Wriggers_Secondary Validation by secondary structure
Paper 2016Kim_SAXS Comparison of SAXS data and EM projections
Paper 2016Rosenthal_Review Review of validation methods
Paper 2016Vargas_Alignability Validation by studying the tendency of an angular assignment to cluster in the projection space

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 2016Joseph_Evolution Evolutionary constraints for the fitting of atomic models into density maps
Paper 2016Segura_3Diana Validation of hybrid models
Paper 2016Singharoy_MDFF Construction of hybrid models driven by EM density and molecular dynamics
Paper 2016Wang_Rosetta Construction of hybrid models driven by EM density using Rosetta

Books and reviews

Book 1980Herman_Tomography General book on tomography
Book 1988Kak_Tomography General book on tomography
Paper 2000Tao_Review Review of single particles
Paper 2000VanHeel_Review Review of single particles
Paper 2002Frank_Review Review of single particles
Paper 2002Schmid_Review Review of single particles
Paper 2004Henderson_Review Review of electron microscopy
Paper 2004Subramaniam_Review Review of single particles
Paper 2005Steven_Review Review of electron microscopy
Paper 2006Fernandez_Review Review of electron microscopy
Book 2006Frank_book Book covering all aspects of electron microscopy of single particles
Paper 2006Sorzano_Review Review of optimization problems in electron microscopy
Paper 2007Leschziner_Review Review of 3D heterogeneity handling algorithms
Paper 2007Sorzano_Review Review of the image processing steps
Paper 2008Fanelli_ImageFormation Review on the image formation model from the electron waves and open inverse-problems in Electron Tomography
Paper 2008Fernandez_HPCReview High performance computing in electron cryomicroscopy
Paper 2008Jonic_Review Comparison between electron tomography and single particles
Paper 2008Mueller_Review Review of Electron microscopy
Paper 2008Taylor_Review Review of Electron microscopy
Paper 2010DeRosier_Review Personal account of how 3DEM developed in the early days
Chapter 2012Sorzano_Review Review of single particle analysis using Xmipp
Chapter 2012Devaux_Protocol Protocols for performing single particle analysis
Paper 2014Bai_Review Recent advances in cryo-EM
Paper 2015Carazo_Review Review of the reconstruction process
Paper 2015Cheng_Review A primer to Single Particle Cryo-EM
Paper 2015Cheng_Reviewb Single Particle Cryo-EM at crystallographic resolution
Paper 2015Elmlund_Review Recent advances in cryo-EM
Paper 2015Henderson_Review Recent advances in cryo-EM
Paper 2015Nogales_Review Recent advances in cryo-EM
Paper 2015Schroeder_Review Review of advances in the electron microscope
Paper 2015Wu_Review Review of advances in cryo-EM
Paper 2016Carroni_CryoEM Review of advances in Cryo-EM
Paper 2016Egelman_CryoEM Review of advances in Cryo-EM
Paper 2016Eisenstein_CryoEM News feature on the Method of the Year
Paper 2016FernandezLeiro_Review Review of EM
Paper 2016Glaeser_HowGood How good can cryo-EM become?
Paper 2016Jonic_PseudoAtoms Review of the applications of the use of pseudoatoms in EM
Chapter 2016Mio_Review Overview of the process to obtain EM reconstructions
Paper 2016Jonic_Review A review of computational ways to handle heterogeneity
Paper 2016Nogales_Review Review of advances in cryo-EM
Paper 2016Subramaniam_Review Why cryo-EM is now suitable for crystallographic journals
Paper 2016Vinothkumar_Review Historical review and current limitations
Paper 2017Frank_Review Historical review of EM
Paper 2017Jonic_Review Review of computational methods to analyze conformational variability

Software

Paper 1996Frank_Spider Spider
Paper 1996VanHeel_Imagic Imagic
Paper 1999Lutdke_Eman Eman
Paper 2004Sorzano_Xmipp Xmipp
Paper 2007Baldwin_AngularTransformations The Transform Class in SPARX and EMAN2
Paper 2007Heymann_Bsoft Bsoft
Paper 2007Grigorieff_Frealign Frealign
Paper 2008Scheres_XmippProtocols Xmipp Protocols
Paper 2008Shaikh_SpiderProtocols Spider Protocols
Paper 2012Wriggers_SitusConventions Conventions and workflows in Situs
Paper 2013DeLaRosa_Xmipp30 Xmipp 3.0
Paper 2015Cianfrocco_Cloud Software execution in the cloud
Paper 2015Cheng_MRC2014 Extensions to MRC file format
Paper 2013DeLaRosa_Scipion Scipion
Paper 2016Scheres_Relion Tutorial on the use of Relion
Paper 2016Grigorieff_Frealign Tutorial on the use of Frealign

Electron tomography

Image preprocessing

Paper 2015Yan_thickness Determination of thickness, tilt and electron mean free path

Image alignment

Paper 1982Guckenberger_commonOrigin Determination of a common origin in the micrographs of titl series in three-dimensional electron microscopy
Paper 1992Lawrence_leastSquares Least squares solution of the alignment problem
Paper 1995Penczek_dual Dual tilt alignment
Paper 1996Owen_alignmentQuality Automatic alignment without fiducial markers and evaluation of alignment quality
Paper 1998Grimm_normalization Discussion of several gray level normalization methods for electron tomography
Paper 2001Brandt_Automatic1 Automatic alignment without fiducial markers
Paper 2001Brandt_Automatic2 Automatic alignment with fiducial markers
Paper 2006Winkler_alignment Marker-free alignment and refinement
Paper 2006Castano_alignment Alignment with non-perpendicularity
Paper 2007Castano_alignment Fiducial-less alignment of cryo-sections
Paper 2009Sorzano_alignment Marker-free alignment and refinement
Paper 2010Cantele_dualAlignment Alignment of dual series
Paper 2014Tomonaga_Automatic Automatic alignment of tilt series using the projection themselves
Paper 2014Han_Automatic Automatic alignment of tilt series using SIFT features
Paper 2015Han_Automatic Automatic alignment of tilt series using fiducials

CTF estimation and restoration

Paper 2003Winkler_CTF Focus gradient correction in electron tomography
Paper 2006Fernandez_CTF CTF determination and correction in electron tomography
Paper 2009Zanetti_CTF CTF determination and correction in electron tomography
Paper 2009Xiong_CTF CTF determination and correction for low dose tomographic tilt series
Paper 2015Bharat_CTFCorrectedSubtomogramAveraging Subtomogram averaging with CTF correction using a Bayesian prior

3D reconstruction

Paper 1972Gilbert_SIRT Simultaneous Iterative Reconstruction Technique (SIRT)
Paper 1973Herman_ART Algebraic Reconstruction Technique (ART)
Paper 1984Andersen_SART Simultaneous Algebraic Reconstruction Technique (SART)
Paper 1992Radermacher_WBP Weighted Backprojection in electron tomography
Paper 1997Marabini_reconstruction Iterative reconstruction in electron tomography
Paper 2002Fernandez_reconstruction Iterative reconstruction in electron tomography
Paper 2007Radermacher_WBP Weighted Backprojection in electron tomography
Paper 2008Fernandez_CARP Component Averaged Row Projections (CARP)
Paper 2012Herman General Superiorization Superiorization: an optimization heuristic for medical physics
Paper 2012Zhang_IPET_FETR IPET and FETR, a reconstruction algorithm for single molecule tomography
Paper 2013Goris_SIRT_TV_DART Combination of SIRT, Total Variation and Discrete ART to reconstruct and segment at the same time
Paper 2013Briegel A_Challenge The challenge of determining handedness in electron tomography and the use of DNA origami gold nanoparticle helices as molecular standards
Paper 2013Messaoudi_EnergyFiltered 3D Reconstruction of Energy-Filtered TEM
Paper 2016Deng_ICON 3D Reconstruction with missing information restoration
Paper 2016Guay_Compressed 3D Reconstruction using compressed sensing

Noise reduction

Paper 2001Frangakis_NAD Noise reduction with Nonlinear Anisotropic Diffusion
Paper 2003Fernandez_AND Anisotropic nonlinear diffusion for electron tomography
Paper 2003Jiang_Bilateral Bilateral denoising filter in electron microscopy
Paper 2005Fernandez_AND Anisotropic nonlinear denoising in electron tomography
Paper 2007Heide_median Iterative median filtering in electron tomography
Paper 2007Fernandez_autAND Anisotropic nonlinear diffusion with automated parameter tuning
Paper 2009Fernandez_Beltrami Nonlinear filtering based on Beltrami flow
Paper 2010Bilbao_MeanShift Mean Shift Filtering
Paper 2014Kovacik_wedgeArtefacts Removal of wedge artefacts
Paper 2014Maiorca_beadArtefacts Removal of gold bead artefacts

Segmentation

Paper 2002Frangakis_Eigenanalysis Segmentation using eigenvector analysis.
Paper 2002Volkmann_Watershed Segmentation using watershed transform.
Paper 2003Bajaj_BoundarySegmentation Segmentation based on fast marching.
Paper 2005Cyrklaff_Thresholding Segmentation using optimal thresholding.
Paper 2007Lebbink_TemplateMatching Segmentation using template matching.
Paper 2007Sandberg_OrientationFields Segmentation using orientation fields.
Paper 2007Sandberg_SegmentationReview Review on segmentation in electron tomography.
Paper 2008Garduno_FuzzySegmentation Segmentation using fuzzy set theory principles.
Paper 2009Lebbink_TemplateMatching2 Segmentation using template matching.
Paper 2012RubbiyaAli_EdgeDetection Parameter-Free Segmentation of Macromolecular Structures.
Conference 2015Xu_TemplateMatching Detection of macromolecular complexes with a reduced representation of the templates.

Resolution

Paper 2005Cardone_Resolution Resolution criterion for electron tomography
Chapter 2007Penczek_Resolution Review of resolution criteria for electron tomography
Paper 2015Diebolder_ConicalFSC Conical Fourier Shell Correlation

Subtomogram analysis

Paper 2000Bohm_Template Macromolecule finding by template matching
Paper 2002Frangakis_Template Macromolecule finding by template matching
Paper 2006Nickell_Review Review of macromolecule finding by template matching (Visual Proteomics)
Paper 2007Best_Review Review of Localization of Protein Complexes by Pattern Recognition
Paper 2007Forster_Review Review of structure determination by subtomogram averaging
Paper 2008Forster_Classification Classification of subtomograms using constrained correlation
Paper 2008Bartesaghi_Classification Classification and averaging of subtomograms
Paper 2008Schmid_Averaging Alignment and averaging of subtomograms
Paper 2010Amat_Averaging Alignment and averaging of subtomograms exploiting thresholding in Fourier space
Paper 2013Chen_Averaging Fast alignment of subtomograms using spherical harmonics
Paper 2013Kuybeda_Averaging Alignment and averaging of subtomograms using the nuclear norm of the cluster
Paper 2013Shatsky_Averaging Alignment and averaging of subtomograms with constrained cross-correlation
Paper 2014Chen_Autofocus Subtomogram averaging and classification with special attention to differences
Paper 2014Yu_ReferenceBias Scoring the reference bias
Paper 2014Voortman_LimitingFactors Limiting factors of subtomogram averaging
Paper 2015Bharat_CTFCorrectedSubtomogramAveraging Subtomogram averaging with CTF correction using a Bayesian prior
Paper 2015Yu_ReferenceBias Scoring the reference bias
Paper 2016Bharat_Relion Subtomogram averaging with Relion
Paper 2016Song_MatrixNorm Matrix norm minimization for tomographic reconstruction and alignment

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 2013Desfosses_Spring Helical processing with Spring
Paper 2015Zhang_seam Workflow for the detection of the lattice seam
Paper 2016Rohou_Frealix Helical processing with Frealix

Validation

Paper 2014Egelman_ambiguity How to detect incorrect models

Books and reviews

Paper 1970DeRosier_Rec Image processing steps towards 3D reconstruction
Paper 1992Morgan_Rec Image processing steps towards 3D reconstruction
Paper 2004Henderson_Review Review of electron microscopy
Paper 2007Sorzano_Review Review of the image processing steps

Software

Paper 1996Carragher_Phoelix Phoelix
Paper 1996Crowther_MRC MRC
Paper 1996Owen_Brandeis Brandeis

Icosahedral particles

Reconstruction

Paper 1970Crowther_Rec Reconstruction of icosahedral viruses in Fourier space
Paper 1971Crowther_Rec Reconstruction of icosahedral viruses in Fourier space
Paper 1996Fuller_Rec Reconstruction of icosahedral viruses in Fourier space
Paper 1997Thuman_Rec Reconstruction of icosahedral viruses in Fourier space

Classification

Paper 2005Scheres_Virus Classification of virus capsids in real space

Books and reviews

Paper 1999Baker_Review Review of reconstruction of icosahedral viruses
Paper 1999Conway_Review Review of reconstruction of icosahedral viruses
Paper 2000Thuman_Review Review of reconstruction of icosahedral viruses
Paper 2003Lee_Review Review of reconstruction of icosahedral viruses
Paper 2003Navaza_Review Review of reconstruction of icosahedral viruses
Paper 2006Grunewald_Review Review of reconstruction of icosahedral viruses

Software

Paper 1996Baker_EMPFT EMPFT
Paper 1996Crowther_MRC MRC
Paper 1996Frank_Spider Spider
Paper 1996VanHeel_Imagic Imagic
Paper 2004Sorzano_Xmipp Xmipp
Paper 2013DeLaRosa_Xmipp30 Xmipp 3.0
Paper 2013Morin_Sliz SBGrid SBGrid presentation for eLife

Databases

Paper 2003Boutselakis_EMSD EMSD database
Paper 2005Heymann_Conventions Conventions for software interoperability
Paper 2005Heymann_Conventions Conventions for software interoperability
Paper 2011Kim_CDDB Conformational Dynamics Data Bank
Paper 2011Lawson_EMDB Electron Microscopy Data Bank
Paper 2016Iudin_EMPIAR EMPIAR raw data database
Paper 2016Patwhardan_EMDB EMDB, PDB, ...
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.

Carlos Oscar S. Sorzano: CSIC, Madrid, Spain

Cédric Messaoudi: Institute Curie, Paris, France

Javier Vargas:mail: CSIC, Madrid, Spain

Joaquín Otón: CSIC, Madrid, Spain

José Román Bilbao-Castro: UAL, Almería, Spain; CSIC, Madrid, Spain

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

Tamir Gonen: mail: Howard Hughes Medical Institute, Ashburn, VA, USA

Vahid Abrishami: CSIC, Madrid, Spain

3DEM sites

Editing useful links

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