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Electron microscopy images

Online courses

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

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

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

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

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

Image formation

Paper	1971Erickson_CTF	CTF model
Paper	1971Glaeser_Damage	Radiation damage
Chapter	1971Hanszen_CTF	Image formation model
Paper	1971Thon_Model	CTF model
Paper	1975Unwin_Imaging	Radiation dose
Paper	1977Wade_Model	CTF model
Paper	1978Wade_Model	CTF model
Paper	1979Hayward_Radiation	Radiation damage
Paper	1984Cohen_Validity	Validity of the CTF model at high frequencies
Paper	1988Toyoshima_Model	Amplitud constrast
Paper	1992Wade_Model	CTF model
Paper	1993Toyoshima_Model	Amplitud constrast
Paper	2002DeCarlo_Damage	Radiation damage in cryonegative staining
Paper	2004Egerton_Damage	Radiation damage
Paper	2004Sorzano_Normalization	Background noise is Gaussian
Paper	2008Fanelli_ImageFormation	Review on the image formation model from the electron waves and open inverse-problems
Paper	2009Baxter_NoiseCharacterization	Characterization of the different noise sources in cryo-EM
Paper	2010Baker_Damage	Radiation damage dependence on resolution
Paper	2010Bammes_Damage	Radiation damage dependence on temperature
Paper	2010Gomez_Multislice	Simulation of the multi slice model
Paper	2010Zewail_FourDimensional	Review on the use of ultrafast EM
Paper	2011Bammes_CCD	Performance of CCD cameras
Paper	2011Glaeser_Coma	Image formation model including coma
Paper	2011Milazzo_DirectDetectors	Evaluation of Direct Detectors
Paper	2011Rullgard_ImageSimulation	Accurate simulation of EM images
Paper	2011Zhang LimitingFactors	Limiting factor for atomic resolution in EM
Paper	2012Bammes_DirectDetection	Performance of Direct detectors
Paper	2012Campbell_MotionCorrection	Beam induced motion correction and direct detectors
Paper	2012Shang_HydrationLayer	Simulation of PDB volumes explicitly considering the hydration layer
Paper	2013Egerton_RadiationDamage	Review of TEM radiation damage and experimental ways of reducing it
Paper	2013Bai_ElectronCounting	Electron counting and beam induced motion correction
Paper	2013Li_ElectronCounting	Electron counting and beam induced motion correction
Paper	2013Shigematsu H_Noisemodels	Noise models and cryo-EM drift correction with a direct-electron camera
Paper	2013Li X K2 noisemodels	Influence of electron dose rate on electron counting images recorded with the K2 camera
Paper	2013Vulovic_CTFApproximations	When to use the different approximations performed so that a projection with linear CTF is valid
Thesis	2013Vulovic_ImageFormation	Ph.D. Thesis on the image formation in cryo-EM
Paper	2014Danev_PhasePlate	Volta potential phase plate
Paper	2015Chiu_K2	Characterization of K2
Paper	2015Hawkes_AberrationCorrection	Historical account of the development of lens corrections
Paper	2015Koeck_Quadratic	Limitations of the linear approximation and use of the quadratic terms
Paper	2015Kuijper_FEI	Description of the FEI Falcons
Paper	2015Lobato_MULTEM	Simulation of multislice diffraction
Paper	2015McMullan_AmorphousIce	Beam induced movement is caused by Brownian motion
Paper	2016Koeck_ADF	Simulations of Annular Dark Field TEM
Paper	2017Mishyna_DNARadiation	Review of radiation damage on DNA

Collection geometry

Chapter	1980Hoppe_Wedge	Missing wedge
Paper	1987Radermacher_RCT	Random Conical Tilt and Single axis tilt
Paper	1988Radermacher_RCT	Random Conical Tilt and Single axis tilt
Paper	1995Penczek_Dual	Dual axis tomography
Paper	1997Mastronarde_Dual	Dual axis tomography
Paper	2003Ludtke_FocusPairs	Focus pairs for single particles
Paper	2005Lanzavecchia_Conical	Conical tomography
Paper	2005Zampighi_Conical	Conical tomography
Paper	2006Leschziner_OT	Orthogonal Tilt
Paper	2006Messaoudi_Multiple	Multiple axis tomography
Paper	2012Kudryashev_FocusPairs	Focus pairs tomography
Paper	2014Hovden_TiltFocus	Combining tilt series with focus series
Paper	2015Sorzano_RandomConicalTilt	General formulation of Random Conical Tilt

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
Paper	2016Bhamre_Denoising	Denoising by 2D covariance estimation

2D Alignment

Paper	1981Frank_Averaging	2D averaging and phase residual
Paper	1982Saxton_Averaging	2D averaging using correlation
Paper	1998Sigworth_ML2D	Maximum likelihood alignment in 2D
Paper	2003Cong_FRM2D	Fast Rotational Matching in 2D
Paper	2005Cong_FRM2D	Fast Rotational Matching in 2D introduced in a 3D Alignment algorithm
Paper	2005Scheres_ML2D	Multireference alignment and classification in 2D
Paper	2010Sorzano_CL2D	Multireference alignment and classification in 2D

2D Classification and clustering

Paper	1981VanHeel_MSA	Multivariate Statistical Analysis
Paper	1984VanHeel_MSA	Multivariate Statistical Analysis
Paper	2005Scheres_ML2D	Multireference alignment and classification in 2D
Paper	2010Sorzano_CL2D	Multireference alignment and classification in 2D
Paper	2011Singer_DiffusionMaps	Classification in 2D based on graph analysis of the projections
Paper	2012Yang_ISAC	Iterative Stable Alignment and clustering
Paper	2014Sorzano_Outlier	Outlier detection in 2D classifications.
Paper	2014Zhao_Aspire	Fast classification based on rotational invariants and vector diffusion maps
Paper	2015Huang_Robust	Robust w-estimators of 2D classes
Paper	2016Reboul_Stochastic	Stochastic Hill Climbing for calculating 2D classes
Conference	2017Bhamre_Mahalanobis	2D classification using Mahalanobis distance

3D Alignment

Paper	1980Kam_AutoCorrelation	Reconstruction without angular assignment from autocorrelation function (reference free)
Paper	1986Goncharov_CommonLines	Angular assignment using common lines (reference free)
Paper	1987VanHeel_CommonLines	Angular assignment using common lines (reference free)
Paper	1988Provencher_Simultaneous	Simultaneaous alignment and reconstruction
Paper	1988Radermacher_RCT	Random Conical Tilt and Single axis tilt
Paper	1988Vogel_Simultaneous	Simultaneaous alignment and reconstruction
Paper	1990Gelfand_Moments	Angular assignment using moments (reference free)
Paper	1990Goncharov_Moments	Angular assignment using moments (reference free)
Paper	1990Harauz_Quaternions	Use of quaternions to represent rotations
Paper	1994Penczek_Real	Angular assignment using projection matching in real space
Paper	1994Radermacher_Radon	Angular assignment in Radon space
Paper	1996Penczek_CommonLines	Angular assignment using common lines (reference free)
Paper	2003Rosenthal_DPR	Angular assignment using DPR
Paper	2004Sorzano_Wavelet	Angular assignment in the wavelet space.
Paper	2005Jonic_Splines	Angular assignment in Fourier space using spline interpolation.
Paper	2005Yang_Simultaneous	Simultaneaous alignment and reconstruction
Paper	2006Ogura_SimulatedAnnealing	Angular asignment by simulated annealing
Paper	2007Grigorieff_Continuous	Continuous angular assignment in Fourier space
Paper	2010Jaitly_Bayesian	Angular assignment by a Bayesian method and annealing
Paper	2010Sanz_Random	Random model method
Paper	2010Singer_Voting	Detecting consistent common lines by voting (reference free)
Paper	2011Singer_SDP	Angular assignment by semidefinite programming and eigenvectors (reference free)
Paper	2012Giannakis_Scattering	Construction of an initial volume, reference free, by graph analysis of the projections
Paper	2012Shkolnisky_Sync	Angular assignment by synchronization of rotations (reference free)
Paper	2013Elmlund H_PRIME	PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
Paper	2013Wang_LUD	Angular assignment by least unsquared deviations (reference free)
Paper	2014Vargas_RANSAC	Initial model using RANSAC (reference free)
Paper	2015Joubert_Pseudoatoms	Initial model based on pseudo-atoms
Paper	2015Singer_Kam	Reconstruction without angular assignment from autocorrelation function (reference free)
Paper	2015Sorzano_Significant	Statistical approach to the initial volume estimation (reconstruct significant)
Conference	2016Michels_Heterogeneous	Initial volume in the presence of heterogeneity
Paper	2016Cossio_BayesianGPU	GPU implementation of the Bayesian 3D reconstruction approach

3D Reconstruction

Paper	1972Gilbert_SIRT	Simultaneous Iterative Reconstruction Technique (SIRT)
Paper	1973Herman_ART	Algebraic Reconstruction Technique (ART)
Paper	1984Andersen_SART	Simultaneous Algebraic Reconstruction Technique (SART)
Paper	1986Harauz_FBP	Exact filters for Filtered Back Projection
Chapter	1992Radermacher_WBP	Exact filters for Weighted Back Projection
Paper	1997Zhu_RecCTF	3D Reconstruction (SIRT like) and simultaneous CTF correction
Paper	1998Boisset_Uneven	Artifacts in SIRT and WBP under uneven angular distributions
Paper	1998Marabini_ART	Algebraic Reconstruction Technique with blobs (Xmipp)
Paper	2001Sorzano_Uneven	Free parameter selection under uneven angular distributions
Paper	2005Sorzano_Parameters	Free parameter selection for optimizing multiple tasks
Paper	2008Sorzano_Constraints	Mass, surface, positivity and symmetry constraints for real-space algorithms
Paper	2009Bilbao_ParallelART	Efficient parallelization of ART
Paper	2011Li_GradientFlow	Regularized 3D Reconstruction by Gradient Flow
Paper	2011Vonesch_Wavelets	Fast wavelet-based 3D reconstruction
Paper	2012Gopinath_ShapeRegularization	Regularized 3D Reconstruction by Shape information
Paper	2012Kucukelbir_adaptiveBasis	3D reconstruction in an adaptive basis promoting sparsity
Paper	2012Sindelar_NoiseReduction	Optimal noise reduction in 3D reconstructions
Paper	2013Elmlund H_PRIME	PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy
Paper	2013Lyumkis_Optimod	Construction of initial volumes with Optimod
Paper	2013Wang FIRM	Fast 3D reconstruction in Fourier domain
Paper	2014Kunz_SART_OS	Simultaneous ART with OS
Paper	2015Abrishami_Fourier	3D Reconstruction in Fourier space
Paper	2015Dvornek_SubspaceEM	Fast Maximum a posteriori
Paper	2015Moriya_Bayesian	Bayesian approach to suppress limited angular artifacts
Paper	2015Xu_GeometricFlow	Multi-scale geometric flow
Arxiv	2016Ye_Cohomology	Cohomology properties of 3D reconstruction
Paper	2017Punjani_CryoSPARC	CryoSPARC

3D Heterogeneity

Paper	2004White_Size	Heterogeneity classification of differently sized images
Paper	2006Penczek_Bootstrap	3D heterogeneity through bootstrap
Paper	2007Leschziner_Review	Review of 3D heterogeneity handling algorithms
Paper	2007Scheres_ML3D	Maximum Likelihood alignment and classification in 3D
Paper	2009Spahn_Bootstrap	3D heterogeneity through bootstrap
Paper	2010Elmlund_AbInitio	Solving the initial volume problem with multiple conformations
Paper	2010Shatsky_MultiVariate	Multivariate Statistical Analysis
Paper	2012Scheres_Bayesian	A Bayesian view on cryo-EM structure determination
Paper	2012Zheng_Covariance	Estimation of the volume covariance
Paper	2013Wang_MLVariance	Maximum Likelihood estimate of the map variance
Paper	2013Lyumkis D_FREALIGN	Likelihood-based classification of cryo-EM images using FREALIGN.
Paper	2014Jin_NMA	Continuous heterogeneity through Normal Mode Analysis
Paper	2014Dashti_Brownian	Continuous heterogeneity through Brownian trajectories
Paper	2014Chen_Migration	Particle migration analysis in 3D classification
Paper	2015Anden_Covariance	3D Covariance matrix estimation for heterogeneity
Paper	2015Bai_Focused	Focused classification
Paper	2015Katsevich_Covariance	3D Covariance matrix estimation for heterogeneity
Paper	2015Klaholz_MRA	Multivariate Statistical Analysis of Jackknife and Bootstrapping on random subsets
Paper	2015Liao_Covariance	Estimation of the 3D covariance from 2D projections
Paper	2015Tagare_Direct	Direct reconstruction of PCA components
Paper	2016Gong_Mechanical	Mechanical model for macromolecules
Paper	2016Rawson_Movement	Movement and flexibility
Paper	2016Sorzano_StructMap	Sorting a discrete set of conformational states
Paper	2016Sorzano_Strain	Calculate local stretches, strains and rotations from two conformational states
Paper	2017Punjani_CryoSPARC	CryoSPARC

Validation

Paper	2008Stagg_TestBed	Effect of voltage, dosis, number of particles and Euler jumps on resolution
Paper	2011Henderson	Tilt Validation
Paper	2011Read	Validation of PDBs
Paper	2012Henderson	EM Map Validation
Paper	2013Cossio_Bayesian	EM Map Validation in a probabilistic setting
Paper	2013Chen_NoiseSubstitution	Noise substitution at high resolution for measuring overfitting
Paper	2014Russo_StatisticalSignificance	EM Map Validation through the statistical significance of the tilt-pair angular assignment
Paper	2014Stagg_Reslog	EM Map Validation through the resolution evolution with the number of particles
Paper	2014Wasilewski_Tilt	Web implementation of the tilt pair validation
Paper	2015Heymann_Alignability	EM Map Validation through the resolution of reconstructions from particles and noise
Paper	2015Oliveira_FreqLimited	Comparison of gold standard and frequency limited optimization
Paper	2015Wriggers_Secondary	Validation by secondary structure
Paper	2016Kim_SAXS	Comparison of SAXS data and EM projections
Paper	2016Rosenthal_Review	Review of validation methods
Paper	2016Vargas_Alignability	Validation by studying the tendency of an angular assignment to cluster in the projection space
Paper	2017Monroe_PDBRefinement	Validation by comparison to a refined PDB

Resolution

Paper	1986Harauz_FBP	Fourier Shell Correlation
Paper	1987Unser_SSNR	2D Spectral Signal to Noise Ratio
Paper	2002Penczek_SSNR	3D Spectral Signal to Noise Ratio for Fourier based algorithms
Paper	2003Rosenthal_DPR	Review of the FSC and establishment of a new threshold
Paper	2005Unser_SSNR	3D Spectral Signal to Noise Ratio for any kind of algorithms
Paper	2005VanHeel_FSC	Establishment of a new threshold for FSC
Paper	2007Sousa_AbInitio	Resolution measurement on neighbour Fourier voxels
Paper	2014Kucukelbir_Local	Quantifying the local resolution of cryo-EM density maps
Paper	2016Pintilie_Probabilistic	Probabilistic models and resolution
Paper	2017Sorzano_FourierProperties	Statistical properties of resolution measures defined in Fourier space

Sharpening of high resolution information

Paper	2003Rosenthal_DPR	Contrast restoration and map sharpening
Paper	2008Fernandez_Bfactor	Bfactor determination and restoration
Paper	2013Fiddy_SaxtonAlgorithm	Phase retrieval or extension
Paper	2014Kishchenko_SphericalDeconvolution	Spherical deconvolution
Paper	2015Spiegel_VISDEM	Visualization improvement by the use of pseudoatomic profiles
Paper	2016Jonic_Pseudoatoms	Approximation with pseudoatoms
Paper	2016Jonic_Denoising	Denoising and high-frequency boosting by pseudoatom approximation

CTF estimation and restoration

Paper	1982Schiske_Correction	CTF correction for tilted objects
Paper	1988Toyoshima_Model	CTF estimation
Paper	1995Frank_Wiener	CTF correction using Wiener filter
Paper	1996Skoglund_MaxEnt	CTF correction with Maximum Entropy
Paper	1996Zhou_Model	CTF model and user interface for manual fitting
Paper	1997Fernandez_AR	PSD estimation using periodogram averaging and AR models
Paper	1997Penczek_Wiener	CTF correction using Wiener filter
Paper	1997Stark_Deconvolution	CTF correction using deconvolution
Paper	1997Zhu_RecCTF	CTF correction and reconstruction
Paper	2000DeRosier_EwaldCorrection	CTF correction considering the Ewald sphere
Paper	2000Jensen_TiltedCorrection	CTF correction considering tilt in backprojection
Paper	2001Saad_CTFEstimate	CTF estimation
Paper	2003Huang_CTFEstimate	CTF estimation
Paper	2003Mindell_CTFTILT	CTF estimation for tilted micrographs
Paper	2003Sander_MSA	CTF estimation through MSA classification of PSDs
Paper	2003Velazquez_ARMA	PSD and CTF estimation using ARMA models
Paper	2004Sorzano_IDR	CTF restoration and reconstruction with Iterative Data Refinement
Conference	2004Wan_CTF	Spatially variant CTF
Paper	2004Zubelli_Chahine	CTF restoration and reconstruction with Chahine's multiplicative method
Conference	2005Dubowy_SpaceVariant	CTF correction when this is space variant
Paper	2005Mallick_ACE	CTF estimation
Paper	2006Wolf_Ewald	CTF correction considering Ewald sphere
Paper	2007Jonic_EnhancedPSD	PSD enhancement for better identification of Thon rings; Vitreous ice diffracts in Thon rings
Paper	2007Philippsen_Model	CTF Model for tilted specimens
Paper	2007Sorzano_CTF	CTF estimation using enhanced PSDs
Paper	2009Sorzano_Sensitivity	Error sensitivity of the CTF models, non-uniqueness of the CTF parameters
Paper	2010Jiang2010_CTFCorrection	Amplitude correction method
Paper	2010Kasantsev_CTFCorrection	Mathematical foundations of Kornberg and Jensen method
Paper	2010Leong_CTFCorrection	Correction for spatially variant CTF
Paper	2011Glaeser_Coma	The effect of coma at high-resolution
Paper	2011Mariani_Tilted	CTF simulation and correction of tilted specimens
Paper	2011Sindelar_Wiener	CTF correction using a modified version of Wiener filter
Paper	2011Voortman_Tilted	CTF correction for tilted specimen
Paper	2012Voortman_VaryingCTF	Correcting a spatially varying CTF
Paper	2013Vargas_FastDef	Fast defocus
Paper	2015Rohou_CTFFind4	CTF Find 4
Paper	2015Sheth_CTFquality	Visualization and quality assessment of CTF
Paper	2016Zhang_GCTF	gCTF

Segmentation

Paper

2006Baker_segmentation

Segmentation of molecular subunits

Fitting and docking

Paper	1999Volkmann_Fitting	Fitting in real space
Paper	2001Baker_Review	Review of protein structure prediction
Paper	2001Jones_Review	Review of protein structure prediction
Paper	2003Kovacs_FRM3D	Fast Rotational Alignment of two EM maps
Paper	2004Tama_NMA1	Flexible fitting with Normal Modes (I)
Paper	2004Tama_NMA2	Flexible fitting with Normal Modes (II)
Paper	2005Velazquez_Superfamilies	Recognition of the superfamily folding in medium-high resolution volumes
Paper	2007DeVries_Haddock	Docking with Haddock 2.0
Paper	2007Kleywegt_QualityControl	Quality control and validation of fitting
Paper	2012Biswas_Secondary	Secondary structure determination in EM volumes
Paper	2012Velazquez_Constraints	Multicomponent fitting by using constraints from other information sources
Paper	2013Chapman MS_Atomicmodeling	Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters
Paper	2013Esquivel_Modelling	Review on modelling (secondary structure, fitting, ...)
Paper	2013Lopez_Imodfit	Fitting based on vibrational analysis
Paper	2013Nogales_3DEMLoupe	Normal Mode Analysis of reconstructed volumes
Paper	2014AlNasr_Secondary	Identification of secondary structure elements in EM volumes
Paper	2014Politis_MassSpect	Integration of mass spectroscopy information
Paper	2014Rey_MassSpect	Integration of mass spectroscopy information
Paper	2014Villa_Review	Review of atomic fitting into EM volumes
Paper	2015Barad_EMRinger	Validation of hybrid models
Paper	2015Bettadapura_PF2Fit	Fast rigid fitting of PDBs into EM maps
Paper	2015Carrillo_CapsidMaps	Analysis of virus capsids using Google Maps
Paper	2015Schroeder_Hybrid	Review on model building
Paper	2015Tamo_Dynamics	Dynamics in integrative modeling
Paper	2015Sorzano_AtomsToVoxels	Accurate conversion of an atomic model into a voxel density volume
Paper	2016Joseph_Evolution	Evolutionary constraints for the fitting of atomic models into density maps
Paper	2016Segura_3Diana	Validation of hybrid models
Paper	2016Singharoy_MDFF	Construction of hybrid models driven by EM density and molecular dynamics
Paper	2016Wang_Rosetta	Construction of hybrid models driven by EM density using Rosetta

Books and reviews

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

Software

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

Electron tomography

Image preprocessing

Paper

2015Yan_thickness

Determination of thickness, tilt and electron mean free path

Image alignment

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

CTF estimation and restoration

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

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
Paper	2016Galaz_SingleParticleTomography	Alignment algorithms and CTF correction

Books and reviews

Paper	2000Baumeister_Review	Review of electron tomography
Paper	2003Koster_Review	Review of electron tomography
Paper	2003Sali_Review	Review of electron tomography
Paper	2004Henderson_Review	Review of electron microscopy
Paper	2005Lucic_Review	Review of electron tomography
Paper	2006Fernandez_Review	Review of electron microscopy
Book	2006Frank_TomoBook	Electron Tomography
Book	2007McIntosh_Book	Cellular Electron Microscopy
Paper	2007Sorzano_Review	Review of the image processing steps
Paper	2008Fanelli_ImageFormation	Review on the image formation model from the electron waves and open inverse-problems
Paper	2008Fernandez_HPCReview	High performance computing in electron cryomicroscopy
Paper	2008Jonic_Review	Comparison between electron tomography and single particles
Paper	2012Kudryashev_Review	Review of subtomogram averaging
Paper	2016Beck_Review	Review of molecular sociology

Software

Paper	1996Kremer_IMOD	IMOD
Paper	1996Chen_Priism/IVE	Priism/IVE
Paper	1996Frank_Spider	Spider
Paper	2004Sorzano_Xmipp	Xmipp
Paper	2005Nickell_TOM	TOM Toolbox
Paper	2007Messaoudi_TomoJ	TomoJ
Paper	2008Heymann_BsoftTomo	Bsoft
Paper	2015Ding_CaltechTomography	Caltech tomography database
Paper	2015Noble_AppionProtomo	Batch fiducial-less tilt-series alignment in Appion using Protomo
Paper	2015vanAarle_Astra	ASTRA Toolbox

2D Crystals

2D Preprocessing

Paper	1986Henderson_Processing	General 2D processing
Paper	2000He_PhaseAlignment	Phase consistency and Alignment
Paper	2006Gil_Unbending	Crystal unbending

Classification

Paper	1988Frank_Classification	MSA and classification in electron crystallography
Paper	1996Fernandez_SOM	Classification based on self organizing maps
Paper	1998Sherman_MSA	Classification based on MSA

3D Reconstruction

Paper	1985Wang_Solvent	Solvent flattening
Paper	1990Henderson_Processing	General 3D processing
Paper	2004Marabini_ART	Algebraic Reconstruction Technique with blobs for crystals (Xmipp)

Books and reviews

Paper	1998Walz_Review	Review of 2D crystallography
Paper	1999Glaeser_Review	Review of 2D crystallography
Paper	2001Ellis_Review	Review of 2D crystallography
Paper	2001Glaeser_Review	Review of 2D crystallography
Paper	2004Henderson_Review	Review of electron microscopy
Paper	2006Fernandez_Review	Review of single particles, electron tomography and crystallography
Paper	2007Sorzano_Review	Review of the image processing steps

Software

Paper	1996Crowther_MRC	MRC
Paper	2004Sorzano_Xmipp	Xmipp
Paper	2007Gipson_2dx	2dx
Paper	2007Heymann_Bsoft	Bsoft
Paper	2007Philippsen_IPLT	IPLT

3D Crystals - MicroED

Sample Preparation

Paper

2016Shi_Preparation

Sample Preparation

Data Collection

Paper

2014Nannenga_CR

Continuous rotation

Data Processing

Paper	2011Wisedchaisri_PhaseExtension	Fragment-based phase extension
Paper	2015Hattne_Processing	Data Processing
Paper	2016Hattne_Correction	Image correction

Software

Paper

2014Iadanza_Processing

Data Processing of still diffraction data

Books and Reviews

Paper	2014Nannenga_Review	Review of MicroED
Paper	2016Liu_Review	Review of MicroED
Paper	2016Rodriguez_Review	Review of MicroED

Helical particles

Filament corrections

Paper	1986Egelman_Curved	Algorithm for correcting curved filaments
Paper	1988Bluemke_Pitch	Algorithm for correcting filaments with different helical pitches
Paper	2006Wang_Pitch	Algorithm for correcting filaments with different helical pitches
Paper	2016Yang_Flexible	Algorithm for correcting filaments with flexible subunits

Reconstruction

Paper	1952Cochran_Fourier	Fourier Bessel transform of filamentous structures
Paper	1958Klug_Fourier	Fourier Bessel decomposition of the projection images
Paper	1970DeRosier_Rec	Image processing steps towards 3D reconstruction
Paper	1992Morgan_Rec	Image processing steps towards 3D reconstruction
Paper	2005Wang_Iterative	Iterative Fourier-Bessel algorithm
Paper	2007Egelman_Iterative	Iterative real-space algorithm
Paper	2013Desfosses_Spring	Helical processing with Spring
Paper	2015Zhang_seam	Workflow for the detection of the lattice seam
Paper	2016Rohou_Frealix	Helical processing with Frealix

Validation

Paper

2014Egelman_ambiguity

How to detect incorrect models

Books and reviews

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

Software

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

Icosahedral particles

Reconstruction

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

Classification

Paper

2005Scheres_Virus

Classification of virus capsids in real space

Books and reviews

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

Software

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

Databases

Paper	2003Boutselakis_EMSD	EMSD database
Paper	2005Heymann_Conventions	Conventions for software interoperability
Paper	2005Heymann_Conventions	Conventions for software interoperability
Paper	2011Kim_CDDB	Conformational Dynamics Data Bank
Paper	2011Lawson_EMDB	Electron Microscopy Data Bank
Paper	2016Iudin_EMPIAR	EMPIAR raw data database
Paper	2016Patwhardan_EMDB	EMDB, PDB, ...
Paper	2017Shao_PDBQuality	Quality metrics in PDB
Blog	http://www.mybiosoftware.com	Huge list of bioinformatics programs (many of them structural bioinformatics)

Relationship to other structural information sources

Paper	2000Engel_AFM	Review of Atomic Force Microscopy
Paper	2001Dimmeler_AFM	Constraints from Atomic Force Microscopy
Paper	2003Mobus_EnergyLoss	Chemical mapping by energy loss electron tomography
Paper	2004Leapman_EnergyLoss	Chemical mapping by energy loss electron tomography
Paper	2004Leapman_Review	Review on correlative microscopy
Paper	2005Boudier_EFTETJ	Software for Chemical mapping by energy loss electron tomography
Paper	2005Vestergaard_SAXS	Example of comparison of 3DEM and Small-angle X-ray scattering
Paper	2007Hamada_SAXS	Constraints from Small-angle X-ray scattering
Paper	2013Xu_FRET	EM+FRET

X-ray tomography

Paper

2012Oton_ImageFormation

Image formation model in X-ray cell microscopy

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

• 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