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Electron microscopy images

Online courses and Learning material

Caltech (same course in Coursera) (latest version of the course in EM-learning)

MRC

MRC training channel

CNB-CSIC

Workshop on Computational methods for CryoEM

Workshop on Management of large CryoEM facilities

Icknield Course on Model Building and Refinement for High Resolution EM Maps

Tutorial on how to prepare negative staining samples

Tutorial on how to prepare samples

Do's and don'ts on sample preparation

NRAMM Workshop 2017

SBGrid videos about the programs they offer

Madrid course on single particle analysis

CCP-EM Spring symposium 2019

NCCAT Single Particle short course 2020

Image formation

Paper	1971Erickson_CTF	CTF model
Paper	1971Glaeser_Damage	Radiation damage
Chapter	1971Hanszen_CTF	Image formation model
Paper	1971Thon_Model	CTF model
Paper	1974Taylor_Diffraction	Electron diffraction of crystals
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
Book	2009Rose_Optics	Geometrical Charged-Particle Optics
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	2016Glaeser_Behaviour	Behaviour of the specimen under the electron beam
Paper	2016Koeck_ADF	Simulations of Annular Dark Field TEM
Paper	2017Fan_VPP	3D Reconstruction with under-focus and over-focus Volta Phase Plate micrographs
Paper	2017Koeck_ApertureDesign	Aperture design for singe side band imaging
Paper	2017Mishyna_DNARadiation	Review of radiation damage on DNA
Paper	2018Anoshina_Simulation	Simulation of 2D and 3D EM images
Paper	2018Downing_DepthOfField	Effects of the Depth of Field
Paper	2018DeJonge_SpatialResolution	Theory of spatial resolution in liquid water or ice layers
Paper	2018Faruqi_DED	Review of Direct Detectors
Paper	2018Hattne_RadiationDamage	Analysis of radiation damage in EM
Paper	2018Hettler_Charging	Charging of carbon thin films
Paper	2018Koeck_PhaseShift	Design of a phase shift device
Paper	2018Koeck_PhaseShift	Design of a phase shift device
Paper	2018Noble_ParticleDistribution	Particle distribution and ice thickness for Single Particles
Paper	2018Russo_ChargeAccumulation	Charge accumulation in electron cryomicroscopy
Paper	2018Russo_SingleBandEM	Ewald sphere correcion using single-side band image processing
Paper	2019Peet_EnergyDependence	Energy dependence of radiation damage

Collection geometry

Chapter	1980Hoppe_Wedge	Missing wedge
Paper	1987Radermacher_RCT	Random Conical Tilt and Single axis tilt
Paper	1988Radermacher_RCT	Random Conical Tilt and Single axis tilt
Paper	1995Penczek_Dual	Dual axis tomography
Paper	1997Mastronarde_Dual	Dual axis tomography
Paper	2003Ludtke_FocusPairs	Focus pairs for single particles
Paper	2005Lanzavecchia_Conical	Conical tomography
Paper	2005Zampighi_Conical	Conical tomography
Paper	2006Leschziner_OT	Orthogonal Tilt
Paper	2006Messaoudi_Multiple	Multiple axis tomography
Paper	2012Kudryashev_FocusPairs	Focus pairs tomography
Paper	2014Hovden_TiltFocus	Combining tilt series with focus series
Paper	2015Sorzano_RandomConicalTilt	General formulation of Random Conical Tilt
Paper	2017Hagen_DoseTomography	Dose optimization for subtomogram averaging
Paper	2017Tan_PreferredViews	Solving preferred views problems through tilting
Paper	2017Donati_Compressed	Compressed sensing for STEM
Paper	2018Oveisi_Stereo	Stereo-vision with EM
Paper	2018Cheng_BeamShift	Fast image acquisition through beam-shift
Paper	2019Wu_BeamShiftAndTilt	Fast image acquisition through beam-shift and beam tilt control

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_OpNS	Optimized negative staining for small protein and lipoprotein imaging
Paper	2012Zhang_Cryo-PS	Cryo-positive staining (cryo-PS)
Paper	2014Russo_GoldGrids	Gold grids for single particles
Paper	2015Cabra_Sample	Review on sample preparation for single particles with videos
Paper	2015Chari_ProteoPlex	Fast evaluation of the structural stability
Paper	2016Passmore_Review	Tutorial chapter on sample preparation
Paper	2016Razinkov_Vitrification	New vitrification method
Paper	2016Takizawa_Sample	Review on sample preparation for EM
Paper	2016Thompson_Sample	Review on sample preparation for EM
Paper	2017Arnold_BlottingFree	Blotting-free preparation
Paper	2017Earl_review	Review of sample preparation
Paper	2017Feng_SprayingPlunging	Spraying plunging
Paper	2017He_FIB	Cryo FIB lamella for TEM
Paper	2017Peitsch_Sample	iMEM: Isolation of Plasma Membrane for Cryoelectron Microscopy
Paper	2017Scapin_Storage	Cryo storage of samples
Paper	2017Schaffer_FocusedIonBeam	Focused Ion Beam sample preparation for membrane proteins
Paper	2017Scherr_HydrogelNanomembranes	Sample preparation for membrane proteins
Paper	2018Anderson_CLEM	Correlated light and EM
Paper	2018Arnold_Review	Review on sample preparation with special emphasis on microfluidic approaches
Paper	2018Dandey_Spotiton	Spotiton, a device for vitrification
Paper	2018Gewering_Detergents	Detergent background in negative stain
Paper	2018Li_CLEM	Correlated light and EM
Paper	2018Noble_Reducing	Reducing particle adsorption
Paper	2018Rice_Ice	Routine determination of ice thickness
Paper	2018Schmidli_Miniaturized	Protein isolation and sample preparation
Paper	2018Wei_Grids	"Self-wicking" nanowire grids
Paper	2019DImprima_Denaturation	Protein denaturation at the air-water interface and how to prevent it
Paper	2019Song_FalconIII	Comparison of the modes of Falcon III
Paper	2020Cianfrocco_Wrong	What could go wrong?

Automated data collection

Paper	1992Dierksen_Automatic	Automated data collection
Paper	1992Koster_Automatic	Automated data collection
Paper	1996Fung_Automatic	Automated data collection for tomography
Paper	2001Zhang_Automatic	Automated data collection: AutoEM
Paper	2003Ziese_Automatic	Automated autofocusing
Paper	2004Potter_Automatic	Automated sample loading
Paper	2004Zheng_Automatic	Automated data collection
Paper	2005Lei_Automatic	Automated data collection: AutoEM
Paper	2005Suloway_Automatic	Automated data collection: Leginon
Paper	2007Yoshioka_RCT	Automated Random Conical Tilt
Paper	2011Korinek_TOM2	Automated acquisition with TOM2
Paper	2015Li_UCSFImage	Automated acquisition with UCSFImage
Paper	2016Gil_Fuzzy	Real time decisions during acquisition with neuro-fuzzy method
Paper	2016Liu_TiltControl	Accurate control of the tilt angle for electron tomography
Paper	2016Vargas_FoilHole	Determination of image quality at low magnification
Paper	2017Alewijnse_Best	Best practices for managing large CryoEM facilities
Paper	2017Biyani_Focus	Automatic processing of micrographs
Paper	2018Gomez_Facilities	Use of Scipion at facilities
Paper	2018Sorzano_Gain	Estimation of the DDD camera gain or residual gain
Paper	2019Chreifi_TiltSeries	Rapid tilt-series acquisition for electron cryotomography
Paper	2019Eng_ImageCompression	3D Reconstruction from compressed images
Paper	2019Hamaguchi_CryoARM	CryoARM data acquisition
Paper	2019Maluenda_Scipion	Automated workflow processing for facilities
Paper	2019Tegunov_Warp	Automatic micrograph processing with Warp
Paper	2019Thompson_Protocol	Protocol for EM acquisition
Paper	2020Baxa_Facility	Operational workflow in a facility

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	2013Hoang_ParallelGPUPicking	Parallel GPU-accelerated particle picking
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	2015Scheres_SemiAutoPicking	Semi-automated selection of cryo-EM particles
Paper	2016Vilas_AutomaticTilt	Automatic identification of image pairs in untilted-tilted micrograph pairs
Paper	2016Wang_DeepPicker	A deep learning approach for fully automated particle picking
Paper	2017Zhu_DeepEM	Deep learning approach to picking
Paper	2018Huber_Helices	Automated tracing of helices
Paper	2018Heimowitz_ApplePicker	Automated particle picking
Paper	2018Sanchez_DeepConsensus	Deep learning consensus of multiple automatic pickers
Paper	2019Alazzawi_Clustering	Use of clustering algorithms to find particles in micrographs
Paper	2019Bepler_Topaz	Deep learning for particle picking
Paper	2019Carrasco_IP	Use of standard image processing for particle picking
Conference	2019Li_Deep	Deep learning for particle picking without box size
Paper	2019Wagner_Cryolo	Deep learning for particle picking
Paper	2019Wang_Biobjective	Biobjective function for robust signal detection
Paper	2019Zhang_Pixer	Deep learning for particle picking

2D Preprocessing

Paper	1978Carrascosa_matching	Gray values matching by linear transformations
Paper	2003Rosenthal_DPR	Contrast enhancement through DPR
Paper	2004Sorzano_Normalization	Normalization procedures and their statistical properties.
Paper	2006Sorzano_Denoising	Strong denoising in wavelet space
Conference	2009Sorzano_Downsampling	Differences between the different downsampling schemes
Paper	2012Brilot_Movies	Alignment of beam induced motion in direct detectors
Paper	2012Campbell_Movies	Alignment of beam induced motion in direct detectors
Paper	2012Zhao_Denoising	Denoising using an invariant Fourier-Bessel eigenspace
Paper	2013Norousi_Screening	Screening particles to identify outliers
Paper	2013Bai_ElectronCounting	Electron counting and beam induced motion correction
Paper	2013Li_ElectronCounting	Electron counting and beam induced motion correction
Paper	2013Shigematsu_Movies	Drift correction for movies considering dark field
Paper	2013Vargas_ParticleQuality	Automatic determination of particle quality
Paper	2014Scheres_Movies	Beam induced motion correction
Paper	2015Abrishami_Movies	Alignment of direct detection device micrographs
Paper	2015Grant_Anisotropic	Automatic estimation and correction of anisotropic magnification
Paper	2015Grant_OptimalExposure	Filter movies according to the radiation damage
Paper	2015Rubinstein_Alignment	Frame alignment at the level of particle
Paper	2015Spear_DoseCompensation	Effect of dose compensation on resolution
Paper	2015Zhao_AnisotropicMagnification	Correction of anisotropic magnification
Conference	2016Bajic_Denoising	Denoising and deconvolution of micrographs
Paper	2016Jensen_RemovalVesicles	Removal of vesicles in membrane proteins
Paper	2016Bhamre_Denoising	Denoising by 2D covariance estimation
Paper	2017Berndsen_EMPH	Automated hole masking algorithm
Paper	2017McLeod_Zorro	Movie alignment by Zorro
Paper	2017Zheng_MotionCorr2	Movie alignment by MotionCorr2
Paper	2018Ouyang_Denoising	Denoising based on geodesic distance
Paper	2018Wu_ContrastEnhancement	Contrast enhancement
Paper	2019Zivanov_BayesianBIM	Bayesian correction of beam induced movement

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	2016Aguerrebere_Limits	Fundamental limits of 2D translational alignment
Paper	2010Sorzano_CL2D	Multireference alignment and classification in 2D
Conference	2017Anoshina_Correlation	New correlation measure for aligning images
Paper	2019Radermacher_Correlation	On the properties of cross correlation for the alignment of images

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	2016Kimanius_Accelerated	GPU Accelerated image classification and high-resolution refinement
Paper	2016Reboul_Stochastic	Stochastic Hill Climbing for calculating 2D classes
Conference	2017Bhamre_Mahalanobis	2D classification using Mahalanobis distance
Paper	2017Wu_GTM	2D classification using Generative Topographic Mapping
Conference	2018Boumal_SinglePass	Single pass classification
Conference	2018Shuo_Network	2D Clustering by network metrics

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)
Paper	2016Cossio_BayesianGPU	GPU implementation of the Bayesian 3D reconstruction approach
Conference	2016Michels_Heterogeneous	Initial volume in the presence of heterogeneity
Paper	2016Pragier_Graph	Graph partitioning approach to angular reconstitution
Paper	2017Greenberg_CommonLines	Common lines for reference free ab-initio reconstruction
Paper	2018Sorzano_Highres	New algorithm for 3D Reconstruction and alignment with emphasis on significance
Paper	2018Sorzano_Swarm	Consensus of several initial volumes by swarm optimization
Paper	2019Zehni_Joint	Continuous angular refinement and reconstruction
Paper	2020Zehni_Joint	Continuous angular refinement and reconstruction

3D Reconstruction

Paper	1972Gilbert_SIRT	Simultaneous Iterative Reconstruction Technique (SIRT)
Paper	1973Herman_ART	Algebraic Reconstruction Technique (ART)
Paper	1980Kam_SphericalHarmonics	3D Reconstruction using spherical harmonics
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
Conference	2018Michels_RBF	Ab-initio reconstruction with radial basis functions
Paper	2015Moriya_Bayesian	Bayesian approach to suppress limited angular artifacts
Paper	2015Xu_GeometricFlow	Multi-scale geometric flow
Arxiv	2016Ye_Cohomology	Cohomology properties of 3D reconstruction
Paper	2017Punjani_CryoSPARC	CryoSPARC
Paper	2017Punjani_CryoSPARCTheory	Theory related to CryoSPARC
Paper	2017Sorzano_SurveyIterative	Survey of iterative reconstruction methods for EM
Paper	2018Bartesaghi_Refinement	Refinement of CTF, frame weight and alignment for high resolution reconstruction
Paper	2018Hu_ParticleFilter	A particle filter framework for 3D reconstruction
Conference	2018Levin_Kam	Ab initio reconstruction by autocorrelation analysis
Paper	2018Reboul_Simple	Ab initio reconstruction with Simple
Paper	2018Sorzano_Highres	New algorithm for 3D Reconstruction and alignment with emphasis on significance
Paper	2018Sorzano_Swarm	Consensus of several initial volumes by swarm optimization
Paper	2018Zhu_Ewald	3D Reconstruction with Ewald sphere correction
Paper	2019Gomez_Initial	Construction of initial models
Master	2019Havelkova_Regularization	Regularization methods in 3D reconstruction
Paper	2019Wilkinson_Scales	Combining data acquired at different scales

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	2008Herman_Graph	Classification by graph partitioning
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	2016Shan_Multibody	Multibody refinement
Paper	2016Sorzano_StructMap	Sorting a discrete set of conformational states
Paper	2016Sorzano_Strain	Calculate local stretches, strains and rotations from two conformational states
Paper	2017Punjani_CryoSPARC	CryoSPARC
Paper	2017Schillbach_Warpcraft	Warpcraft: 3D Reconstruction in the presence of continuous heterogeneity
Paper	2018Anden_Covariance	Structural Variability from Noisy Tomographic Projections
Paper	2018Haselbach_FreeEnergy	Analysis of the free energy landscape through PCA
Paper	2018Nakane_MultiBody	Structural Variability through multi-body refinement
Paper	2019Serna_Review	Review of classification tools
Paper	2018Solernou_FFEA	Fluctuating Finite Element Analysis, continuum approach to Molecular Dynamics
Paper	2019Sorzano_Review	Review of continuous heterogeneity biophysics
Paper	2019Zhang_Local	Local variability and covariance
Paper	2020Harastani_NMA	Using Scipion for analyzing local heterogeneity with normal modes

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	2013Ludtke_Validation	Structural validation, example of the Calcium release channel
Paper	2013Murray_Validation	Validation of a 3DEM structure through a particular example
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	2015Rosenthal_Review	Review of validation methods
Paper	2015Wriggers_Secondary	Validation by secondary structure
Paper	2016Degiacomi_IM	Comparison of Ion Mobility data and EM volumes
Paper	2016Kim_SAXS	Comparison of SAXS data and EM projections
Paper	2016Rosenthal_Review	Review of validation methods
Paper	2016Vargas_Alignability	Validation by studying the tendency of an angular assignment to cluster in the projection space
Paper	2017Monroe_PDBRefinement	Validation by comparison to a refined PDB
Paper	2018Afonine_Phenix	Tools in Phenix for the validation of EM maps
Paper	2018Heymann_Bsoft	Map validation using Bsoft
Paper	2018Heymann_Challenge	A summary of the assessments of the 3D Map Challenge
Paper	2018Jonic_Gaussian	Assessment of sets of volumes by pseudoatomic structures
Paper	2018Naydenova_AngularDistribution	Evaluating the angular distribution of a 3D reconstruction
Paper	2018Pages_Symmetry	Looking for a symmetry axis in a PDB
Paper	2018Pintilie_SSE	Evaluating the quality of SSE and side chains
Paper	2019Herzik_Multimodel	Local and global quality by multi-model fitting
Paper	2020Stojkovic_PTM	Validation of post-translational modifications

Resolution

Paper	1986Harauz_FBP	Fourier Shell Correlation
Paper	1987Unser_SSNR	2D Spectral Signal to Noise Ratio
Paper	2002Penczek_SSNR	3D Spectral Signal to Noise Ratio for Fourier based algorithms
Paper	2003Rosenthal_DPR	Review of the FSC and establishment of a new threshold
Paper	2005Unser_SSNR	3D Spectral Signal to Noise Ratio for any kind of algorithms
Paper	2005VanHeel_FSC	Establishment of a new threshold for FSC
Paper	2007Sousa_AbInitio	Resolution measurement on neighbour Fourier voxels
Paper	2014Kucukelbir_Local	Quantifying the local resolution of cryo-EM density maps
Paper	2016Pintilie_Probabilistic	Probabilistic models and resolution
Paper	2017Sorzano_FourierProperties	Statistical properties of resolution measures defined in Fourier space
Conference	2018Avramov_DeepLearning	Deep learning classification of volumes into low, medium and high resolution
Paper	2018Carugo_BFactors	How large can B-factors be in protein crystals
Paper	2018Kim_FourierError	Comparison between a gold standard and a reconstruction
Paper	2018Rupp_Problems	Problems of resolution as a proxy number for map quality
Paper	2018Vilas_MonoRes	Local resolution by monogenic signals
Paper	2018Yang_Multiscale	Resolution from a multiscale spectral analysis
Paper	2019Avramov_DeepLearning	Deep learning classification of volumes into low, medium and high resolution
Paper	2019Ramirez_DeepRes	Resolution determination by deep learning
Paper	2020Baldwin_Lyumkis_SCF	Resolution attenuation through non-uniform Fourier sampling
Paper	2020Vilas_MonoDir	Local and directional 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
Paper	2017Jakobi_LocScale	Sharpening based on an atomic model
Paper	2019Ramlaul_Filtering	Local agreement filtering (denoising)
Paper	2020Vilas_Bfactor	Global B-factor correction does not represent macromolecules

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
Paper	2018Su_GoCTF	goCTF, CTF for tilted specimens

Segmentation

Paper	2006Baker_segmentation	Segmentation of molecular subunits
Paper	2010Pintilie_segger	Segmentation of molecular subunits
Conference	2017Nissenson_VolumeCut	Segmentation of an EM volume using an atomic model
Paper	2020Farkas_MemBlob	Segmentation of membrane in membrane embedded proteins

Fitting and docking

Paper	1999Volkmann_Fitting	Fitting in real space
Paper	2001Baker_Review	Review of protein structure prediction
Paper	2001Jones_Review	Review of protein structure prediction
Paper	2003Kovacs_FRM3D	Fast Rotational Alignment of two EM maps
Paper	2004Tama_NMA1	Flexible fitting with Normal Modes (I)
Paper	2004Tama_NMA2	Flexible fitting with Normal Modes (II)
Paper	2005Velazquez_Superfamilies	Recognition of the superfamily folding in medium-high resolution volumes
Paper	2007DeVries_Haddock	Docking with Haddock 2.0
Paper	2007Kleywegt_QualityControl	Quality control and validation of fitting
Paper	2012Biswas_Secondary	Secondary structure determination in EM volumes
Paper	2012Velazquez_Constraints	Multicomponent fitting by using constraints from other information sources
Paper	2013Chapman MS_Atomicmodeling	Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters
Paper	2013Esquivel_Modelling	Review on modelling (secondary structure, fitting, ...)
Paper	2013Lopez_Imodfit	Fitting based on vibrational analysis
Paper	2013Nogales_3DEMLoupe	Normal Mode Analysis of reconstructed volumes
Paper	2014AlNasr_Secondary	Identification of secondary structure elements in EM volumes
Paper	2014Politis_MassSpect	Integration of mass spectroscopy information
Paper	2014Rey_MassSpect	Integration of mass spectroscopy information
Paper	2014Villa_Review	Review of atomic fitting into EM volumes
Paper	2015Barad_EMRinger	Validation of hybrid models
Paper	2015Bettadapura_PF2Fit	Fast rigid fitting of PDBs into EM maps
Paper	2015Carrillo_CapsidMaps	Analysis of virus capsids using Google Maps
Paper	2015Hanson_Continuum	Modelling assemblies with continuum mechanics
Paper	2015Lopez_Review	Review of structural modelling from EM data
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	2016Joseph_Refinement	Refinement of atomic models in high-resolution EM reconstructions using Flex-EM
Paper	2016Murshudov_Refinement	Refinement of atomic models in high-resolution EM reconstructions
Paper	2016Segura_3Diana	Validation of hybrid models
Paper	2016Singharoy_MDFF	Construction of hybrid models driven by EM density and molecular dynamics
Paper	2016Wang_Rosetta	Construction of hybrid models driven by EM density using Rosetta
Paper	2017Chen_CoarseGraining	Coarse graining of EM volumes
Paper	2017Joseph_Metrics	Metrics analysis for the comparison of structures
Paper	2017Hryc_WeightedAtoms	Construction of hybrid models by locally weighting the different atoms
Paper	2017Matsumoto_Distribution	Estimating the distribution of conformations of atomic models
Paper	2017Michel_ContactPrediction	Structure prediction by contact prediction
Paper	2017Miyashita_EnsembleFitting	Ensemble fitting using Molecular Dynamics
Paper	2017Turk_ModelBuilding	Tutorial on model building and protein visualization
Paper	2017Wang_PartialCharges	Appearance of partial charges in EM maps
Paper	2017Wlodawer	Comparison of X-ray and EM high resolution structures
Paper	2018Cassidy_review	Review of methods for hybrid modeling
Paper	2018Chen_SudeChains	A comparison of side chains between X-ray and EM maps
Paper	2018Kawabata_Pseudoatoms	Modelling the EM map with Gaussian pseudoatoms
Paper	2018Kovacs_Medium	Modelling of medium resolution EM maps
Paper	2018Neumann_validation	Validation of fitting, resolution assessment and quality of fit
Paper	2018Terwilliger_map_to_model	Phenix map_to_model, automatic modelling of EM volumes
Paper	2018Wang_MD	Constructing atomic models using molecular dynamics
Paper	2018Xia_MVPENM	Multiscale Normal Mode Analysis
Paper	2018Yu_Atomic	Constructing atomic models using existing tools
Paper	2019Bonomi_Multiscale	Bayesian multi-scale modelling
Paper	2019Klaholz_Review	Review of Phenix tools to modelling
Paper	2019Zhang_CoarseGrained	Coarse-graining of EM maps
Paper	2020Ho_CryoID	Identification of proteins in structural proteomics from cryoEM volumes
Paper	2020Joseph_comparison	Comparison of map and model, or two maps

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	2015VanDenBedem_Integrative	Review of integrative structural biology
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
Report	2017Brezinski_Nobel	Scientific background on the Nobel Prize in Chemistry 2017
Paper	2017Cheng_review	Why CryoEM became so hot
Paper	2017Danev_Review	Review of the use of phase plates in EM
Paper	2017Elmlund_Review	Review of the main current difficulties of EM
Paper	2017Frank_Review	Historical review of EM
Paper	2017Frank_TimeResolved	Review of time-resolved of EM
Paper	2017Jonic_Review	Review of computational methods to analyze conformational variability
Paper	2017Merino_DrugEM	Applications of EM for drug design
Paper	2017Rawson_Limitations	Limitations of EM for drug design
Paper	2017Sorzano_FourierProperties	Review of statistical properties of resolution measures defined in Fourier space
Paper	2017Sorzano_SurveyIterative	Survey of iterative reconstruction methods for EM
Paper	2018Bruggeman_Crowdsourcing	Exploring crowdsourcing for EM image processing
Paper	2018Cheng_Review	Review of EM and future ahead
Paper	2018Cossio_ML	Review of Maximum Likelihood methods
Paper	2018Grimes_Crystallography	Review of X-ray crystallography and its relationship to EM
Paper	2018Murata_Review	Review of EM for structure dynamics
Paper	2018Quentin_Biomedical	Review of EM as a tool for biomedical research
Paper	2018Scapin_DrugDiscovery	Review of EM as a tool for drug discovery
Paper	2018Vilas_ImageProcessing	Review of the recent developments in image processing for single particle analysis
Paper	2018vonLoeffelholz_VPP	Comparison of Volta Phase Plate reconstructions close to focus and with defocus
Paper	2018Eisenstein_DrugDesigners	Drug designers embrace cryo-EM
Paper	2019Benjin_Review	Review of SPA
Paper	2019Danev_Review	Review of future directions
Paper	2019Lyumkis_Review	Challenges and reviews
Paper	2019Sorzano_Review	Review of continuous heterogeneity biophysics
Paper	2020Bendory_Review	Review of image processing problems

Software

Paper	1996Frank_Spider	Spider
Paper	1996VanHeel_Imagic	Imagic
Paper	1999Lutdke_Eman	Eman
Paper	2004Sorzano_Xmipp	Xmipp
Paper	2007Baldwin_AngularTransformations	The Transform Class in SPARX and EMAN2
Paper	2007Heymann_Bsoft	Bsoft
Paper	2007Grigorieff_Frealign	Frealign
Paper	2008Scheres_XmippProtocols	Xmipp Protocols
Paper	2008Shaikh_SpiderProtocols	Spider Protocols
Paper	2012Wriggers_SitusConventions	Conventions and workflows in Situs
Paper	2013DeLaRosa_Xmipp30	Xmipp 3.0
Paper	2015Cianfrocco_Cloud	Software execution in the cloud
Paper	2015Cheng_MRC2014	Extensions to MRC file format
Paper	2013DeLaRosa_Scipion	Scipion
Paper	2016Scheres_Relion	Tutorial on the use of Relion
Paper	2016Grigorieff_Frealign	Tutorial on the use of Frealign
Paper	2017Moriya_Sphire	Tutorial on the use of Sphire
Paper	2018Bell_EMAN2	New tools in EMAN2
Paper	2018Cianfrocco_cloud	CryoEM Cloud Tools
Paper	2018Grant_cisTEM	cisTEM
Paper	2018McLeod_MRCZ	MRC Compression format
Paper	2018Zivanov_Relion3	Relion 3

Electron tomography

Image preprocessing

Paper

2015Yan_thickness

Determination of thickness, tilt and electron mean free path

Image alignment

Paper	1982Guckenberger_commonOrigin	Determination of a common origin in the micrographs of titl series in three-dimensional electron microscopy
Paper	1992Lawrence_leastSquares	Least squares solution of the alignment problem
Paper	1995Penczek_dual	Dual tilt alignment
Paper	1996Owen_alignmentQuality	Automatic alignment without fiducial markers and evaluation of alignment quality
Paper	1998Grimm_normalization	Discussion of several gray level normalization methods for electron tomography
Paper	2001Brandt_Automatic1	Automatic alignment without fiducial markers
Paper	2001Brandt_Automatic2	Automatic alignment with fiducial markers
Paper	2006Winkler_alignment	Marker-free alignment and refinement
Paper	2006Castano_alignment	Alignment with non-perpendicularity
Paper	2007Castano_alignment	Fiducial-less alignment of cryo-sections
Paper	2009Sorzano_alignment	Marker-free alignment and refinement
Paper	2010Cantele_dualAlignment	Alignment of dual series
Paper	2014Tomonaga_Automatic	Automatic alignment of tilt series using the projection themselves
Paper	2014Han_Automatic	Automatic alignment of tilt series using SIFT features
Paper	2015Han_Automatic	Automatic alignment of tilt series using fiducials
Paper	2017Mastronarde_Automatic	Automatic alignment and reconstruction of tilt series in IMOD
Paper	2018Fernadez_Beam	Image alignment considering beam induced motion
Paper	2018Han_Fast	Automatic alignment using fiducial markers
Paper	2019Fernandez_residual	Alignment of tilt series using residual interpolation
Paper	2019Han_Dual	Automatic alignment using fiducial markers in dual tilt 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	2012Eibauer_CTF	CTF determination and correction
Paper	2015Bharat_CTFCorrectedSubtomogramAveraging	Subtomogram averaging with CTF correction using a Bayesian prior
Paper	2017Turonova_3DCTF	3D CTF Correction
Paper	2017Kunz_3DCTF	3D CTF Correction

3D reconstruction

Paper	1972Gilbert_SIRT	Simultaneous Iterative Reconstruction Technique (SIRT)
Paper	1973Herman_ART	Algebraic Reconstruction Technique (ART)
Paper	1984Andersen_SART	Simultaneous Algebraic Reconstruction Technique (SART)
Paper	1992Radermacher_WBP	Weighted Backprojection in electron tomography
Paper	1997Marabini_reconstruction	Iterative reconstruction in electron tomography
Paper	2002Fernandez_reconstruction	Iterative reconstruction in electron tomography
Paper	2007Radermacher_WBP	Weighted Backprojection in electron tomography
Paper	2008Fernandez_CARP	Component Averaged Row Projections (CARP)
Paper	2010Xu_Long	Iterative reconstructions with long object correction and GPU implementation
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	2015Venkatakrishnan_MBIR	3D Reconstruction with priors
Paper	2016Deng_ICON	3D Reconstruction with missing information restoration
Paper	2016Guay_Compressed	3D Reconstruction using compressed sensing
Paper	2016Turonova_Artifacts	Artifacts observed during 3D reconstruction
Paper	2019Yan_MBIR	3D Reconstruction with priors and demonstration of its use in biological samples
Paper	2020Song_Tygress	3D reconstruction with a special acquisition and alignment scheme

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
Paper	2018Trampert_Inpainting	Removal of the missing wedge by inpainting
Paper	2018Moreno_TomoEED	Fast Anisotropic Diffusion
Paper	2018Wu_Enhancement	Enhancing the image contrast of electron tomography

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.
Paper	2017Ali_RAZA	Automated segmentation of tomograms
Paper	2017Chen_Annotation	Automated annotation of tomograms
Paper	2017Tasel_ActiveContours	Segmentation with active contours
Paper	2017Xu_DeepLearning	Finding proteins in tomograms using deep learning
Paper	2018Zeng_DeepLearning	Mining features in Electron Tomographt by deep learning

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	2010Yu_PPCA	Probabilistic PCA for volume classification
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	2013Yu_Projection	Subtomogram averaging by aligning their projections
Paper	2014Chen_Autofocus	Subtomogram averaging and classification with special attention to differences
Paper	2014Yu_ReferenceBias	Scoring the reference bias
Paper	2014Voortman_LimitingFactors	Limiting factors of subtomogram averaging
Paper	2015Bharat_CTFCorrectedSubtomogramAveraging	Subtomogram averaging with CTF correction using a Bayesian prior
Paper	2015Yu_ReferenceBias	Scoring the reference bias
Paper	2016Bharat_Relion	Subtomogram averaging with Relion
Paper	2016Song_MatrixNorm	Matrix norm minimization for tomographic reconstruction and alignment
Paper	2017Castano_ParticlePicking	Particle picking in tomograms for subtomogram averaging
Paper	2017Frazier_Tomominer	TomoMiner a software platform for large-scale subtomogram analysis
Paper	2018Himes_emClarity	emClarity for subtomogram averaging
Paper	2018Zhao_Fast	Fast alignment and maximum likelihod for subtomogram averaging
Paper	2019Fokine_Enhancement	Subtomogram enhancement through the locked self-rotation
Paper	2019Han_Constrained	Constrained reconstruction to enhance resolution

Single particle tomography

Paper	2012Bartesaghi_Constrained	3D reconstruction by imposing geometrical constraints
Paper	2015Galaz_SingleParticleTomography	Set of tools for Single Particle Tomography in EMAN2
Paper	2016Galaz_SingleParticleTomography	Alignment algorithms and CTF correction

Individual particle electron tomography

Paper

2012Zhang_IPET_FETR

FETR: a focused 3D reconstruction algorithm for a single molecule structure

Missing-Wedge Correction

Paper

2020Zhai_LoTTor

Missing-wedge correction by LoTTor (Low-tilt Tomographic 3D Reconstruction for a single molecule structure)

Books and reviews

Paper	2000Baumeister_Review	Review of electron tomography
Paper	2003Koster_Review	Review of electron tomography
Paper	2003Sali_Review	Review of electron tomography
Paper	2004Henderson_Review	Review of electron microscopy
Paper	2005Lucic_Review	Review of electron tomography
Paper	2006Fernandez_Review	Review of electron microscopy
Book	2006Frank_TomoBook	Electron Tomography
Book	2007McIntosh_Book	Cellular Electron Microscopy
Paper	2007Sorzano_Review	Review of the image processing steps
Paper	2008Fanelli_ImageFormation	Review on the image formation model from the electron waves and open inverse-problems
Paper	2008Fernandez_HPCReview	High performance computing in electron cryomicroscopy
Paper	2008Jonic_Review	Comparison between electron tomography and single particles
Paper	2012Kudryashev_Review	Review of subtomogram averaging
Paper	2013Briggs_Review	Review of subtomogram averaging
Paper	2016Beck_Review	Review of molecular sociology
Paper	2017Galaz_Review	Review of single particle tomography
Paper	2017Plitzko_Review	Review of electron tomography, FRET and FIB milling
Paper	2019Schur_Review	Review of electron tomography and 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
Paper	2015Liu_FullMechTomo	Fully Mechanically Controlled Automated Electron Microscopic Tomography
Paper	2017Han_AuTom	Software platform for Electron Tomography
Paper	2017Wan_Simulator	Electron Tomography Simulator

2D Crystals

2D Preprocessing

Paper	1982Saxton_Averaging	Radial Correlation Function
Paper	1984Saxton_Distortions	3D Reconstruction of distorted crystals
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)
Paper	2018Biyani_Badlu	Image processing for badly ordered crystals

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
Paper	2019Ohashi_SoftBody	Algorithm for correcting filaments with flexible helices

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	1988Stewart_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	2010Egelman_Pitfalls	Pitfalls in helical reconstruction
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
Paper	2017_He	Helical processing with Relion
Paper	2019_Pothula	3D Classification through 2D analysis

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	2015Sachse_Review	Review of the image processing steps in helical particles

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
Paper	2019Goetschius_Asymmetric	Approaches to reconstruct asymmetric features in viruses

Classification

Paper

2005Scheres_Virus

Classification of virus capsids in real space

Books and reviews

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

Software

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

Databases

Paper	2003Boutselakis_EMSD	EMSD database
Paper	2005Heymann_Conventions	Conventions for software interoperability
Paper	2005Heymann_Conventions	Conventions for software interoperability
Paper	2011Kim_CDDB	Conformational Dynamics Data Bank
Paper	2011Lawson_EMDB	Electron Microscopy Data Bank
Paper	2013Ison_EDAM	EDAM, an ontology of bioinformatics operations
Paper	2016Iudin_EMPIAR	EMPIAR raw data database
Paper	2016Patwhardan_EMDB	EMDB, PDB, ...
Paper	2017Gore_Validation	Validations of PDB submissions
Paper	2017Patwhardan_Trends	Trends at EMDB
Paper	2017Shao_PDBQuality	Quality metrics in PDB
Paper	2018Tawari_search	Search of 3D structures in a database using 2D experimental images
Paper	2018wwwPDB_PDB	Review of PDB advances
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
Paper	2017Kim_SAXS	Compatibility of EM experimental images and SAXS curves
Paper	2018Ando_Correlative	Review of correlative microscopy techniques
Paper	2018Sieben_Multicolor	Correlative microscopy with superresolution optical images
Paper	2019Huber_EDXS_HAADF	Combined reconstruction using EDXS and HAADF data
Paper	2019Jimenez_SAXS	Selection of EM initial volumes by SAXS curves

X-ray tomography

Paper

2012Oton_ImageFormation

Image formation model in X-ray cell microscopy

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:: 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: Howard Hughes Medical Institute, Ashburn, VA, USA

Tomas Majtner: Biocomputing Unit CNB-CSIC, Madrid, Spain

[Vahid Abrishami]: CSIC, Madrid, Spain

3DEM sites

• 3DEM web site

• Software tools for molecular microscopy

• The Electron Microscopy Data Bank (EMDB)

• The Cell Centered Database (CCDB)

• The geometrical software conventions web page

Editing useful links

• Text formatting in Mediawiki
• Adding links in Mediawiki
• Adding images in Mediawiki
• Making tables in Mediawiki