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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 (course slides)

SBGrid videos about the programs they offer

Madrid course on single particle analysis

CCP-EM Spring symposium 2019

CCP-EM Spring symposium 2020

NCCAT Single Particle short course 2020

Cell atlas book by Grant Jensen and Catherine Oikonomou

Purdue CryoEM Virtual Reality Augmented Training

NCCAT Short course on Tomography

Map with CryoEM Facilities

NCCAT Single Particle Analysis short course

One world CryoEM technical talks

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	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
Paper	2020Bromberg_Aberrations	Estimation of strong high-order aberrations
Paper	2020Gruza_Atomic	Detailed atomic models considering local charges and directional bonds
Paper	2020Naydenova_Buckling	Beam induced movement explained as ice buckling
Paper	2020Zhang_LimitsSimulated	Simulation of micrographs and 3D reconstruction for low weight proteins (14kDa)
Paper	2020Tichelaar_Thick	Effect of sample thickness on the CTF
Paper	2020Yip_Atomic	Atomic resolution by monochromator and a second-generation spherical aberration corrector
Paper	2020Zhang_LimitsSimulated	Simulation of micrographs and 3D reconstruction for low weight proteins (14kDa)
Paper	2021Egerton_Inelastic	PSF of inelastic scattering
Paper	2021Glaeser_Fading	Defocus-dependent Thon-ring fading
Paper	2021Wieferig_Devitrification	Devitrification reduces beam-induced movement in cryo-EM
Paper	2022Heymann_PSSNR	Progressive Spectral Signal-to-Noise Ratio to assess quality and radiation damage
Paper	2022Dickerson_Inelastic	The role of inelastic scattering in thick specimens
Paper	2022Kulik_TAAM	Theoretical 3D electron diffraction electrostatic potential maps of proteins
Paper	2022Ravikumar_SideChains	Comparison of side-chain dispersion in protein structures determined by cryo-EM and X-ray crystallography
Paper	2023Heymann_Ewald	The Ewald sphere/focus gradient does not limit the resolution of cryoEM reconstructions
Paper	2023Schreiber_charge	Time dynamics of charge buildup

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
Paper	2023Seifer_RevisedSaxton	Revised Saxton geometry for tilt series acquisition

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 (OpNS) 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	2018Ashtiani_femtolitre	Delivery of femtolitre droplets using surface acoustic wave based atomisation for cryo-EM grid preparation
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	2018Palovcak_Graphene	Preparation of graphene-oxide cryo-EM grids
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	2019Rubinstein_ultrasonic	Ultrasonic specimen preparation device
Paper	2019Song_FalconIII	Comparison of the modes of Falcon III
Paper	2020Cianfrocco_Wrong	What could go wrong?
Paper	2020Egelman_Ice	Problems with the ice
Paper	2020Fassler_Printing	3D printed cell culture grid holder
Paper	2020Klebl_Deposition	Sample deposition onto CryoEM grids: sprays and jets
Paper	2020Maeots_TimeResolved	Time resolved CryoEM by microfluidics
Paper	2020Tan_ThroughGrid	Through-grid wicking enables high-speed 1 cryoEM specimen preparation
Paper	2020Yoder_TimeResolved	Time resolved CryoEM by light estimulation
Paper	2020Zachs_FIB	Automation for FIB milling
Paper	2021Bieber_FIBET	Sample preparation for correlative FIB milling and CryoET
Paper	2021Budell_TimeResolved	Time resolved CryoEM with Spotiton
Paper	2021Casasanta_Microchip	Microchip-based structure determination of low-molecular weight proteins using cryo-electron microscopy
Paper	2021Frechard_Preparation	Optimization of Sample Preparation
Paper	2021Engstrom_Nitrogen	Samples vitrified in boiling nitrogen
Paper	2021Jagota_GoldNanoparticles	Gold nanoparticles to assess flexibility
Paper	2021Jiang_MoAu	Holey Gold Films on Molybdenum Grids
Paper	2021Jonaid_Liquid	Liquid phase EM
Paper	2021Ki_Conformational	Conformational Distribution of a Small Protein with Nanoparticle-Aided CryoEM
Paper	2021Li_detergents	The effect of detergents on preferential orientations
Paper	2021Voss_Melting	Rapid melting and revitrification as an approach to microsecond time-resolved cryoEM
Paper	2021Zhang_Pegylation	Improving particle quality in cryo-EM by PEGylation
Paper	2022Chen_Detergents	Role of detergents in the air-water interface
Paper	2022Levitz_Chameleon	Effects of dispense-to-plunge speed on particle concentration, complex formation, and final resolution
Paper	2022Naydenova_Grid	Integrated wafer-scale manufacturing of electron cryomicroscopy specimen supports
Paper	2022Russo_Review	Review of sample preparation issues
Paper	2022Scher_FIB	Sample preparation for FIB-SEM and Correlative microscopy
Paper	2023Liu_AirWater	Review on sample preparation techniques to deal with the air-water interface
Paper	2023Neselu_IceThickness	Effect of ice thickness on resolution
Paper	2023Zheng_Ultraflat	Uniform thin ice on ultraflat graphene grids

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	2019Eisenstein_FISE	Improved applicability and robustness of fast cryo-electron tomography data acquisition
Paper	2019Hamaguchi_CryoARM	CryoARM data acquisition
Paper	2019Maluenda_Scipion	Automated workflow processing for facilities
Paper	2019Schorb_ET	Automated acquisition in Electron Tomography
Paper	2019Tegunov_Warp	Automatic micrograph processing with Warp
Paper	2019Thompson_Protocol	Protocol for EM acquisition
Paper	2020Baxa_Facility	Operational workflow in a facility
Paper	2020Guo_EER	Electron event representation for acquisition
Paper	2020Li_Workflow	Workflow for automatic reconstruction
Paper	2020Sader_Facility	Microscope installation and operation in a facility
Paper	2020Schenk_CryoFlare	CryoFlare, automatic data acquisition
Paper	2020Stabrin_Transphire	TranSPHIRE: Automated and feedback-optimized on-the-fly processing for cryo-EM
Paper	2020Yokoyama_Good	Deep learning for determining good regions in a grid
Paper	2020Weis_Acquisition	Suggestions for high-quality and high-throughput acquisition
Paper	2021Feathers_Superresolution	Effects of superresolution and magnification on final resolution
Paper	2021Bouvette_Bisect	Beam image-shift accelerated data acquisition for near-atomic resolution single-particle cryo-electron tomography
Paper	2021Chreifi_FISE	Rapid tilt-series method for cryo-electron tomography: Characterizing stage behavior during FISE acquisition
Paper	2021Efremov_ComaCorrected	Coma-corrected rapid single-particle cryo-EM data collection on the CRYO ARM 300
Paper	2021Herzik_Setup	Setup for parallel illumination
Paper	2021Kayama_Multipurpose	Below 3 Å structure of apoferritin using a multipurpose TEM with a side entry cryoholder
Paper	2021Lane_NegativeBias	Negative potential bias for faster imaging
Paper	2021Rheinberger_IceThickness	Scripts to measure ice thickness
Paper	2021Yang_CRIM	Computer readable image markers (CRIM) for correlative microscopy
Paper	2021Weis_Strategies	Strategies for Optimization of Cryogenic Electron Tomography Data Acquisition
Paper	2021Wypych_gP2S	LIMS of microscope sessions
Paper	2021Yang_CLEM	Automated correlative microscopy
Paper	2021Yonekura_Hole	Automated hole detection using YOLO
Paper	2022Bepler_Smart	Smart data collection
Paper	2022Bouvette_SmartScope	SmartScope
Paper	2022Flutty_bits	Bit-precision for SPA and ET
Paper	2022Hagen_Screening	Screening of ice thickness using energy filter-based plasmon imaging
Paper	2022Hohle_Ice	Screening of ice thickness using interferometry
Paper	2022Peck_200	High-speed high-resolution data collection on a 200 keV cryo-TEM
Paper	2022Peck_Montage	Montage electron tomography
Paper	2022Zhu_ElectronCounting	New algorithm for electron counting at the microscope
Paper	2023Cheng_Leginon	Smart data collection with Leginon
Paper	2023Kim_Ptolemy	Smart data collection with Ptolemy

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	2017Rickgauer_Detection	Picking by correlation
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
Paper	2020Sanchez_Cleaner	Deep learning for removing particles from the carbon edges, aggregations, contaminations, ...
Conference	2021Li_PickerOptimizers	Removal of badly picked particles with Deep Learning
Paper	2021Ohashi_GRIPS	Two-pass picking with GRIPS
Paper	2022Eldar_ASOCEM	Automatic segmentation of contaminations
Conference	2022Huang_DenoisingAndPicking	Simultaneous denoising and picking with deep learning
Paper	2022Olek_Icebreaker	Ice thickness detection and its use for particle picking
Paper	2022Zhang_EPicker	Particle picking based on continual learning

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
Paper	2020Bepler_TopazDenoise	Preprocessing of micrographs for better picking
Paper	2020Chung_2SDR	PCA to denoise particles
Paper	2020Chung_Prepro	Preprocessing of particles for better alignment
Conference	2020Huang_SuperResolution	Deep learning superresolution combination of frames
Paper	2020Palovcak_noise2noise	Noise2noise denoising of micrographs
Paper	2020Strelak_FlexAlign	Continuous deformation model for aligning movie frames
Conference	2021Fan_Denoising	Particle denoising using vector diffusion maps
Paper	2022Heymann_ProgressiveSSNR	Progressive SSNR to assess quality and radiation damage
Paper	2022Shi_Denoising	Contrast estimation and denoising in SPA
Paper	2023Huang_ZSSR	Multiple image super-resolution, upsampling with deep learning
Paper	2023Marshall_PCA	Fast PCA on single particle images
Paper	2023Sharon_Enhancement	Signal enhancement of SPA particles

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
Paper	2020Lederman_representation	A representation theory perspective of alignment and classification
Paper	2020Marshall_Invariants	Recovery of an image from its invariants
Paper	2021Chen_Fast	Fast alignment through Power Spectrum
Conference	2021Chung_CryoRALIB	Image alignment acceleration
Paper	2021Heimowitz_Centering	Centering noisy 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
Conference	2020Miolane_VAEGAN	2D Analysis by deep learning
Conference	2021Rao_Wasserstein	Wasserstein K-Means for Clustering Tomographic Projections
Paper	2022Wang_Spectral	2D classification with spectral clustering
Paper	2022Zhang_DRVAE	2D classification with deep learning and K-means++
Paper	2023Chen_Joint	2D classification with deep learning and joint unsupervised difference learning

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	2019Zehni_Joint	Continuous angular refinement and reconstruction
Paper	2020Sharon_NonUniformKam	Reconstruction and angular distribution estimation without angular assignment (reference free)
Paper	2020Xie_Network	Angular assignment considering a network of assignments
Paper	2021Jimenez_DeepAlign	Angular alignment using deep learning
Paper	2021Kojima_Preferred	Identification of preferred orientations
Conference	2021Nashed_CryoPoseNet	CryoPoseNet: Angular alignment with deep learning
Conference	2021Zhong_CryoDRGN2	CryoDRGN2: Angular alignment with deep learning
Paper	2022Lu_SphericalEmbeddings	Angular assignment through common lines and spherical embeddings
Paper	2022Wang_Thunder	Angular assignment implementation in GPU

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
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
Conference	2018Michels_RBF	Ab-initio reconstruction with radial basis functions
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
Paper	2020Alazzawi_Auto	Automatic full processing of micrographs to yield a 3D reconstruction
Paper	2020Pan_TV	3D Reconstruction with total variation regularization
Paper	2020Punjani_NonUniform	Non-uniform refinement
Paper	2020Ramlaul_Sidesplitter	Local filtering along the reconstruction iterations
Paper	2020Xie_Automatic	Automatic 3D reconstruction from projections
Conference	2020Venkatakrishnan_MBIR	Model based image reconstruction
Paper	2020Zhou_AutomaticSelection	Automatic selection of particles for 3D reconstruction
Paper	2021Abrishami_Localized	Localized reconstruction in scipion expedites the analysis of symmetry mismatches in Cryo-EM data
Paper	2021Gupta_CryoGAN	3D Reconstruction via Generative Adversarial Learning
Paper	2021Luo_Opus	3D Reconstruction with a sparse and smoothness constraint
Paper	2021Kimanius_PriorKnowledge	Incorporation of prior knowledge during 3D reconstruction
Paper	2021Sorzano_Uneven	Algorithmic robustness to uneven angular distributions
Paper	2022Havelkova_regularization	Regularization of iterative reconstruction algorithms
Paper	2023Bendory_Autocorrelation	Initial volume through autocorrelation analysis with sparsity constraints
Paper	2023Herreros_ZART	Correction of continuous heterogeneity during the 3D reconstruction

3D Heterogeneity

Paper	2004White_Size	Heterogeneity classification of differently sized images
Paper	2006Penczek_Bootstrap	3D heterogeneity through bootstrap
Paper	2007Leschziner_Review	Review of 3D heterogeneity handling algorithms
Paper	2007Scheres_ML3D	Maximum Likelihood alignment and classification in 3D
Paper	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	2014Chen_Migration	Particle migration analysis in 3D classification
Paper	2014Dashti_Brownian	Continuous heterogeneity through Brownian trajectories
Paper	2014Schwander_manifold	Continuous heterogeneity through Manifold Analysis
Paper	2014Jin_NMA	HEMNMA: Continuous heterogeneity through Normal Mode Analysis
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	2020Dashti_Landscape	Retrieving functional pathways from single particle snapshots
Conference	2020Gupta_MultiCryoGAN	Reconstruction of continuously heterogeneous structures with adversarial networks
Paper	2020Harastani_NMA	HEMNMA in Scipion : Using HEMNMA for analyzing continuous heterogeneity with normal modes
Paper	2020Maji_Propagation	Propagation of conformational coordinates across angular space
Paper	2020Moscovich_DiffusionMaps	Heterogeneity analysis by diffusion maps and spectral volumes
Paper	2020Seitz_Polaris	Analysis of energy landscapes to find minimal action paths
Conference	2020Zhong_CryoDRGN	CryoDRGN to analyze the continuous heterogeneity by CryoEM
Paper	2020Verbeke_Separation	Heterogeneity analysis by comparing common lines
Paper	2021Chen_GM	Deep learning-based mixed-dimensional Gaussian mixture model for characterizing variability
Paper	2021Giraldo_cryoBIFE	A Bayesian approach to extracting free‑energy profiles
Conference	2021Hamitouche_NMADL	Continuous heterogeneity analysis through normal modes and deep learning
Paper	2021Herreros_Zernikes3D	Continuous heterogeneity analysis through Zernikes 3D
Paper	2021Kazemi_Enrich	ENRICH: A fast method to improve the quality of flexible macromolecular reconstructions
Paper	2021Matsumoto_DEFmap	Prediction of RMSF of Molecular Dynamics from a CryoEM map using deep learning
Chapter	2021Nakasako_Landscape	Estimation of free-energy landscape from images
Paper	2021Punjani_3DVA	3D Variability analysis from images
Paper	2021Sorzano_PCA	PCA is limited to low-resolution
Paper	2021Zhong_CryoDRGN	CryoDRGN to analyze the continuous heterogeneity by CryoEM
Paper	2022Ecoffet_MorphOT	More physically plausible morphing between two states
Paper	2022Gomez_Hierarchical	Hierarchical classification of particles
Paper	2022Hamitouche_DeepHEMNMA	DeepHEMNMA: Continuous heterogeneity analysis through normal modes and deep learning
Conference	2022Levy_CryoFire	CryoFire: heterogeneity and alignment through amortized inference
Paper	2022Rabuck_Quant	Workflow for discrete heterogeneity analysis
Paper	2022Skalidis_Endogenous	AI tools to recognize proteins in cellular fractions
Paper	2022Wu_Manifold	Continuous heterogeneity through manifold learning
Paper	2022Zhou_Data	Determination of the number of discrete 3D classes
Paper	2023Chen_GMM	Continuous heterogeneity analysis with GMMs and neural networks
Paper	2023Esteve_Spectral	Continuous heterogeneity analysis through the spectral decomposition of the atomic structure
Paper	2023Kinman_Analysis	Analysis of the continuous heterogeneity results of CryoDrgn
Paper	2023Seitz_Geometric	Geometric relationships between manifold embeddings of a continuum of 3D molecular structures and their 2D projections
Paper	2023Tang_Reweighting	Ensemble reweighting using Cryo-EM particles
Paper	2023Vuillemot_MDSPACE	MDSPACE: Continuous heterogeneity analysis through normal modes and MD simulation

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	2020Chen_Atomic	Validation of the atomic models derived from CryoEM
Paper	2020Cossio_CrossValidation	Need for cross validation
Paper	2020Ortiz_CrossValidation	Cross validation for SPA
Paper	2020Sazzed_helices	Validation of helix quality
Paper	2020Stojkovic_PTM	Validation of post-translational modifications
Paper	2020Tiwari_PixelSize	Fine determination of the pixel size
Paper	2021Mendez_Graph	Identification of incorrectly oriented particles
Paper	2021Pintilie_Validation	Review of map validation approaches
Paper	2021Olek_FDR	Cryo-EM Map–Based Model Validation Using the False Discovery Rate Approach
Paper	2022Garcia_DeepHand	Checking the correct handedness with a neural network
Paper	2022Sorzano_Bias	Bias, variance, gold-standard and overfitting in SPA
Paper	2022Sorzano_Validation	Validation scheme and server for SPA
Paper	2022Terashi_DAQ	Validation of models fitted into CryoEM maps
Paper	2022Waarshamanage_EMDA	Validation of models fitted into CryoEM maps

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
Conference	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	2019Heymann_Statistics	SNR, FSC, and related statistics
Paper	2019Ramirez_DeepRes	Resolution determination by deep learning
Paper	2020Baldwin_Lyumkis_SCF	Resolution attenuation through non-uniform Fourier sampling
Paper	2020Beckers_Permutation	Permutation tests for the FSC
Paper	2020Penczek_mFSC	Modified FSC to avoid mask induced artifacts
Paper	2020Vilas_MonoDir	Local and directional resolution
Paper	2023Dai_CryoRes	Local resolution through deep learning

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)
Conference	2020Mullick_SuperResolution	Superresolution from a map
Paper	2020Ramirez_LocalDeblur	Local deblur (local Wiener filter)
Paper	2020Terwilliger_density	Density modification of CryoEM maps
Paper	2020Vilas_Bfactor	Global B-factor correction does not represent macromolecules
Paper	2021Beckers_Interpretation	Improvements from the raw reconstruction to a structure to model
Paper	2021Kaur_LocSpiral	LocSpiral, LocBsharpen, LocBfactor
Paper	2021Fernandez_Adjustment	Map adjustment for subtraction, consensus and sharpening
Paper	2021Sanchez_DeepEMhancer	Deep learning algorithm for volume restoration
Paper	2022Gilles_Wilson	A molecular prior distribution for Bayesian inference based on Wilson statistics
Paper	2022Vargas_tubular	Map enhancement by multiscale tubular filter

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	2014Penczek_CTER	Estimation of the CTF errors
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
Paper	2020Heimowitz_Aspire	CTF determination in Aspire
Paper	2020Zivanov_HighOrder	Estimation of high order aberrations

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	2019Beckers_FDR	Segmentation of the protein using False Discovery Rate
Paper	2020Beckers_FDR	Segmentation of the protein using False Discovery Rate (GUI)
Paper	2020Farkas_MemBlob	Segmentation of membrane in membrane embedded proteins
Paper	2020Terashi_MainMastSeg	Segmentation of proteins into domains
Paper	2021He_EMNUSS	EMNUSS: Identification of secondary structure in CryoEM maps with deep learning

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	2008Rusu_Interpolation	Biomolecular pleiomorphism probed by spatial interpolation of coarse models
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	2019Kidmose_Namdinator	Namdinator: Flexible fitting with NAMD
Paper	2019Klaholz_Review	Review of Phenix tools to modelling
Paper	2019Subramaniya_DeepSSE	Secondary structure prediction from maps using deep learning
Paper	2019Zhang_CoarseGrained	Coarse-graining of EM maps
Paper	2020Costa_MDeNM	Flexible fitting with molecular dynamics and normal modes
Paper	2020Cragnolini_Tempy2	TEMpy2 library for density-fitting and validation
Paper	2020Dodd_ModelBuilding	Model building possibilities, with special emphasis on flexible fitting
Paper	2020Ho_CryoID	Identification of proteins in structural proteomics from cryoEM volumes
Paper	2020Hoh_Buccaneer	Structure modelling with Buccaneer
Paper	2020Joseph_comparison	Comparison of map and model, or two maps
Paper	2020Kim_Review	Review of the options for atomic modelling
Paper	2020Leelananda_Constraints	NMR Chemical Shifts and Cryo-EM Density Restraints in Iterative Rosetta-MD structure refinement
Paper	2020Liebschner_Ceres	CERES: Web server of refined atomic maps of CryoEM deposited maps by Phenix
Paper	2020Oroguchi	Assessment of Force Field Accuracy Using Cryogenic Electron Microscopy Data
Paper	2020Vant_Flexible	Flexible fitting with molecular dynamics and neural network potentials
Paper	2021Behkamal_Secondary	Secondary structure from medium resolution maps
Paper	2021Chojnowski_quality	Quality of models automatically fitted with ARP/wARP
Paper	2021Han_Vesper	VESPER: global and local cryo-EM map alignment using local density vectors
Paper	2021Lawson_Challenge	Validation recommendations based on outcomes of the 2019 EMDataResource challenge
Paper	2021Mori_Flexible	Efficient Flexible Fitting Refinement with Automatic Error Fixing
Paper	2021Pfab_DeepTracer	DeepTracer for fast de novo cryo-EM protein structure modeling
Paper	2021Saltzberg_IMP	Using the Integrative Modeling Platform to model a cryoEM map
Paper	2021Terwilliger_CryoID	Identification of sequence in a CryoEM map from a set of candidates
Paper	2021Titarenko_LocalCorr	Performance improvement of local correlation for docking
Conference	2021Vuillemot_NMA	Flexible fitting using a combined Bayesian and Normal Mode approach with Hamiltonian Monte Carlo sampling
Paper	2022Antanasijevic_ab	Sequence determination of antibodies bound to a map
Paper	2022Behkamal_LPTD	LPTD: Topology determination of CryoEM maps
Paper	2022Chojnowski_findMySeq	Identify sequence in CryoEM map using Deep Learning
Paper	2022Hryc_Pathwalking	Atomic modelling with Pathwalking
Paper	2022He_EMBuild	Atomic modelling for complexes with EMbuild
Paper	2022Krieger_Prody2	Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0
Paper	2022Neijenhuis_Haddock	Protein-protein interface refinement in complex maps with Haddock2.4
Paper	2022Urzhumtsev_Direct	Calculation of the EM map from an atomic model
Paper	2022Urzhumtsev_XrayEM	Effect of the local resolution on the atomic modeling
Paper	2022Vuillemot_NMMD	NMMD: Flexible fitting with simultaneous Normal Mode and Molecular Dynamics displacements
Paper	2022Zhang_CRITASSER	Atomic models of assemble protein structures with deep learning
Paper	2023Millan_LL	Likelihood-based docking of models into cryo-EM maps
Paper	2023Read_LL	Likelihood-based signal and noise analysis for docking of models into cryo-EM maps
Paper	2023Terashi_DAQrefine	Atomic model refinement using AlphaFold2 and DAQ

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	2020Abriata_Review	Considerations of structure prediction and CryoEM
Paper	2020Akbar_Review	Review of membrane protein reconstructions
Paper	2020Bendory_Review	Review of image processing problems
Paper	2020Dubach_Review	Review of resolution in X-ray crystallography and CryoEM
TechReport	2020Lai_Statistics	Review of statistical properties of image alignment
Paper	2020Hu_Quaternions	Review of the use of quaternions to describe rotations
Paper	2020McCafferty_Review	Review of SPA and Mass Spectroscopy
Paper	2020Seffernick_Hybrid	Review of hybrid (computational and experimental) methods to get protein structure
Paper	2020Nakane_Atomic	Single-particle cryo-EM at atomic resolution
Paper	2020Vilas_Review	Review of local resolution
Paper	2020Wu_Review	Review of current limitations, with special emphasis on protein size
Paper	2020Singer_Sigworth_Review	Review of single particle analysis
Paper	2021Bai_Review	Review of breakthroughs leading to atomic resolution
Paper	2021DImprima_Review	Review of sample preparation for single particle analysis
Paper	2021Lander_Review	Review of focused analysis in SPA
Paper	2021Raimondi_Review	General review of SPA
Paper	2022Beton_Fitting	Review of fitting in SPA
Paper	2022Burley_PDB	Review of cryoEM derived structures at PDB
Paper	2022Caldraft_Tilt	Review of applications of tilt pairs in SPA
Paper	2022Donnat_GAN	Review of Generative modelling with neural networks
Paper	2022Guaita_Review	Recent advances and current trends in cryo-electron microscopy
Paper	2022Jones_Comment	Comment on the impact of AlphaFold and next challenges ahead
Paper	2022Namba_Review	Review of the current state of SPA
Paper	2022Ourmazd_Comment	Comment on the impact of AlphaFold and next challenges ahead
Paper	2022Palmer_Local	Review of local methods in CryoEM
Paper	2022Sorzano_1000	CryoEM is the field of 1000+ methods
Paper	2022Subramaniam_Comment	Comment on the impact of AlphaFold and next challenges ahead
Paper	2022Treder_DL	Review of Deep Learning applications in CryoEM
Paper	2022Vant_MD	Review of Molecular Dynamics analysis of CryoEM maps
Paper	2023Amann_TimeResolved	Review of time-resolved cryoEM
Paper	2023Liu_AWI	Review of the Air-Water Interface
Paper	2023Si_DeNovo	Review of the de-novo atomic modelling
Paper	2023Toader_Heterogeneity	Review of continuous heterogeneity

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
Paper	2020Caesar_Simple3	Simple 3
Paper	2021Baldwin_SCF	Visualizer of the Sampling Compensation Factor
Paper	2021Jimenez_Scipion	Scipion workflow example for image processing
Paper	2021Kimanius_Relion4	Changes in Relion 4.0
Paper	2021Maji_BlackBox	Exploration of image processing concepts
Paper	2021Sharov_Relion	Use of Relion within Scipion
Paper	2021Sorzano_Scipion	Use of Scipion as a way to compare the results of multiple methods
Paper	2021Strelak_Xmipp	Advances in Xmipp
Paper	2022DiIorio_Multiple	A Robust Single-Particle Cryo-Electron Microscopy (cryo-EM) Processing Workflow with cryoSPARC, RELION, and Scipion.
Paper	2022Fluty_Precision	Precision requirements and data compression
Paper	2022Harastani_ContinuousFlex	ContinuousFlex: Software for continuous heterogeneity analysis in cryo-EM and cryo-ET

Electron tomography

Image preprocessing

Paper	2015Yan_thickness	Determination of thickness, tilt and electron mean free path
Paper	2018Wu_contrast	Contrast enhancement to improve alignability

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
Paper	2020Sorzano_automatic	Automatic alignment considering several geometrical distortions
Paper	2021Han_LocalConstraints	Automatic alignment considering local constraints
Paper	2022Zheng_Aretomo	Automatic alignment based on projection matching

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	2014Paavolainen_Missing	Compensation of the missing wedge
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	2020Sanchez_Hybrid	3D reconstruction with a special acquisition and alignment scheme
Paper	2020Song_Tygress	3D reconstruction with a special acquisition and alignment scheme
Paper	2021Fernandez_TomoAlign	3D reconstruction with sample motion and CTF correction
Paper	2021Geng_Nudim	Non-uniform FFT reconstruction and total variation to fill the missing wedge

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
Paper	2022Liu_Isonet	Isotropic reconstructions using deep learning

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 Tomography by deep learning
Paper	2020Salfer_PyCurv	Curvature analysis of segmented tomograms
Paper	2021Dimchev_filaments	Segmentation of filaments in tomograms
Paper	2022Frangakis_Curvature	Use of mean curvature for segmentation and visualization of tomograms
Paper	2022Lamm_MemBrain	Membrane segmentation using deep learning
Paper	2023Zeng_AITOM	Structural pattern mining by unsupervised deep iterative subtomogram clustering

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
Paper	2020Vilas_Monotomo	Resolution determination in tomograms

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
Paper	2020Basanta_workflow	Workflow for subtomogram averaging
Paper	2021Du_Active	Active learning to reduce the need of annotated samples
Paper	2021Harastani_HEMNMA3D	HEMNMA-3D: Continuous flexibility analysis of subtomograms using normal modes
Paper	2021Lucas_Cistem	Identification of particles in tomograms using Cistem
Paper	2021Scaramuzza_Dynamo	Subtomogram averaging workflow using Dynamo
Paper	2021Singla_Measures	Analysis of different measures to analyze subtomogram clusters
Paper	2021Tegunov_M	Image processing workflow for tilt-series (introduction of M)
Conference	2021Zeng_OpenSet	Unsupervised open set classification using deep learning
Paper	2022Boehning_CompressedSensing	Compressed sensing for subtomogram averaging
Paper	2022Hao_Picking	Detection of molecules in tomograms
Paper	2022Harastani_TomoFlow	TomoFlow: Continuous flexibility analysis of subtomograms using 3D dense optical flow
Paper	2022Metskas_STA	Tricks for a better Subtomogram Averaging
Paper	2022Moebel_unsupervised	Unsupervised classification of subtomograms using neural networks
Paper	2022Peters_Feature	Feature guided, focused 3D signal permutation for STA

Single particle tomography

Paper	2012Bartesaghi_Constrained	3D reconstruction by imposing geometrical constraints
Paper	2012Zhang_IPET_FETR	FETR: a focused reconstruction algorithm for a single molecule 3D structure without averaging
Paper	2015Galaz_SingleParticleTomography	Set of tools for Single Particle Tomography in EMAN2
Paper	2016Galaz_SingleParticleTomography	Alignment algorithms and CTF correction

Missing-wedge correction

Paper	2020Kovacs_Filaments	Removal of missing wedge artifacts in filamentous tomograms
Paper	2020Moebel_MCMC	Missing wedge correction with Monte Carlo Markov Chains
Paper	2020Zhai_LoTTor	Missing-wedge correction by LoTTor (Low-Tilt Tomographic 3D Reconstruction for a single molecule structure)

Molecular 3D dynamics

Paper

2015Zhang_IPET

3D structural fluctuation of macromoles)

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	2016Ercius_Review	Electron tomography for hard and soft materials research
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
Paper	2021Frangakis_Review	Review of tomogram denoising in electron tomography
Paper	2022Forster_Review	Review of subtomogram averaging
Paper	2022Liedtke_Review	Review of electron tomography in bacterial cell biology
Paper	2022Liu_Review	Review of beam image shift and subtomogram averaging
Paper	2023Kim_Review	Review of particle picking and volume segmentation

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	2012Zhang IPET FETR	IPET
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	2016Liu_FullMechTomo	Fully mechanically controlled automated electron microscopic tomography
Paper	2017Han_AuTom	Software platform for Electron Tomography
Paper	2017Wan_Simulator	Electron Tomography Simulator
Paper	2021Burt_RWD	Interoperability between Relion, Warp M, and Dynamo
Paper	2022Jimenez_ScipionTomo	Electron tomography within Scipion
Paper	2022Martinez_PyOrg	Point pattern analysis for coordinates in tomograms
Paper	2022Ni_EmClarity	Processing protocols with EmClarity

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 picking

Paper

2021Thurber_Automated

Automated picking of filaments

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
Paper	2021Egelman_Review	Review of reconstruction problems in helical structures
Paper	2022Wang_Review	Review of reconstruction problems in helical structures

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

Liquid-cell TEM / in-situ TEM

Paper

2020Ren_LTEM

Real-time dynamic imaging of sample in liquid phase

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
Paper	2022Wang_EMDB	Validation analysis of EMDB entries
Paper	2022Westbrook_mmCIF	PDBx/mmCIF ecosystem
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
Paper	2022Graziadei_CrossLinking	Review on the use of crosslinking mass spectrometry in CryoEM
Paper	2022Klumpe_FIB	A modular platform for automated cryo-FIB workflows

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

Gang (Gary) Ren: The Molecular Foundry, LBNL, USA

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