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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)
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
SBGrid videos about the programs they offer
Madrid course on single particle analysis
NCCAT Single Particle short course 2020
Image formation
| Paper | 1971Erickson_CTF | CTF model |
| Paper | 1971Glaeser_Damage | Radiation damage |
| Chapter | 1971Hanszen_CTF | Image formation model |
| Paper | 1971Thon_Model | CTF model |
| Paper | 1974Taylor_Diffraction | Electron diffraction of crystals |
| Paper | 1975Unwin_Imaging | Radiation dose |
| Paper | 1977Wade_Model | CTF model |
| Paper | 1978Wade_Model | CTF model |
| Paper | 1979Hayward_Radiation | Radiation damage |
| Paper | 1984Cohen_Validity | Validity of the CTF model at high frequencies |
| Paper | 1988Toyoshima_Model | Amplitud constrast |
| Paper | 1992Wade_Model | CTF model |
| Paper | 1993Toyoshima_Model | Amplitud constrast |
| Paper | 2002DeCarlo_Damage | Radiation damage in cryonegative staining |
| Paper | 2004Egerton_Damage | Radiation damage |
| Paper | 2004Sorzano_Normalization | Background noise is Gaussian |
| Paper | 2008Fanelli_ImageFormation | Review on the image formation model from the electron waves and open inverse-problems |
| Paper | 2009Baxter_NoiseCharacterization | Characterization of the different noise sources in cryo-EM |
| Book | 2009Rose_Optics | Geometrical Charged-Particle Optics |
| Paper | 2010Baker_Damage | Radiation damage dependence on resolution |
| Paper | 2010Bammes_Damage | Radiation damage dependence on temperature |
| Paper | 2010Gomez_Multislice | Simulation of the multi slice model |
| Paper | 2010Zewail_FourDimensional | Review on the use of ultrafast EM |
| Paper | 2011Bammes_CCD | Performance of CCD cameras |
| Paper | 2011Glaeser_Coma | Image formation model including coma |
| Paper | 2011Milazzo_DirectDetectors | Evaluation of Direct Detectors |
| Paper | 2011Rullgard_ImageSimulation | Accurate simulation of EM images |
| Paper | 2011Zhang LimitingFactors | Limiting factor for atomic resolution in EM |
| Paper | 2012Bammes_DirectDetection | Performance of Direct detectors |
| Paper | 2012Campbell_MotionCorrection | Beam induced motion correction and direct detectors |
| Paper | 2012Shang_HydrationLayer | Simulation of PDB volumes explicitly considering the hydration layer |
| Paper | 2013Egerton_RadiationDamage | Review of TEM radiation damage and experimental ways of reducing it |
| Paper | 2013Bai_ElectronCounting | Electron counting and beam induced motion correction |
| Paper | 2013Li_ElectronCounting | Electron counting and beam induced motion correction |
| Paper | 2013Shigematsu H_Noisemodels | Noise models and cryo-EM drift correction with a direct-electron camera |
| Paper | 2013Li X K2 noisemodels | Influence of electron dose rate on electron counting images recorded with the K2 camera |
| Paper | 2013Vulovic_CTFApproximations | When to use the different approximations performed so that a projection with linear CTF is valid |
| Thesis | 2013Vulovic_ImageFormation | Ph.D. Thesis on the image formation in cryo-EM |
| Paper | 2014Danev_PhasePlate | Volta potential phase plate |
| Paper | 2015Chiu_K2 | Characterization of K2 |
| Paper | 2015Hawkes_AberrationCorrection | Historical account of the development of lens corrections |
| Paper | 2015Koeck_Quadratic | Limitations of the linear approximation and use of the quadratic terms |
| Paper | 2015Kuijper_FEI | Description of the FEI Falcons |
| Paper | 2015Lobato_MULTEM | Simulation of multislice diffraction |
| Paper | 2015McMullan_AmorphousIce | Beam induced movement is caused by Brownian motion |
| Paper | 2016Glaeser_Behaviour | Behaviour of the specimen under the electron beam |
| Paper | 2016Koeck_ADF | Simulations of Annular Dark Field TEM |
| Paper | 2017Fan_VPP | 3D Reconstruction with under-focus and over-focus Volta Phase Plate micrographs |
| Paper | 2017Koeck_ApertureDesign | Aperture design for singe side band imaging |
| Paper | 2017Mishyna_DNARadiation | Review of radiation damage on DNA |
| Paper | 2018Anoshina_Simulation | Simulation of 2D and 3D EM images |
| Paper | 2018Downing_DepthOfField | Effects of the Depth of Field |
| Paper | 2018DeJonge_SpatialResolution | Theory of spatial resolution in liquid water or ice layers |
| Paper | 2018Faruqi_DED | Review of Direct Detectors |
| Paper | 2018Hattne_RadiationDamage | Analysis of radiation damage in EM |
| Paper | 2018Hettler_Charging | Charging of carbon thin films |
| Paper | 2018Koeck_PhaseShift | Design of a phase shift device |
| Paper | 2018Koeck_PhaseShift | Design of a phase shift device |
| Paper | 2018Noble_ParticleDistribution | Particle distribution and ice thickness for Single Particles |
| Paper | 2018Russo_ChargeAccumulation | Charge accumulation in electron cryomicroscopy |
| Paper | 2018Russo_SingleBandEM | Ewald sphere correcion using single-side band image processing |
| Paper | 2019Peet_EnergyDependence | Energy dependence of radiation damage |
Collection geometry
| Chapter | 1980Hoppe_Wedge | Missing wedge |
| Paper | 1987Radermacher_RCT | Random Conical Tilt and Single axis tilt |
| Paper | 1988Radermacher_RCT | Random Conical Tilt and Single axis tilt |
| Paper | 1995Penczek_Dual | Dual axis tomography |
| Paper | 1997Mastronarde_Dual | Dual axis tomography |
| Paper | 2003Ludtke_FocusPairs | Focus pairs for single particles |
| Paper | 2005Lanzavecchia_Conical | Conical tomography |
| Paper | 2005Zampighi_Conical | Conical tomography |
| Paper | 2006Leschziner_OT | Orthogonal Tilt |
| Paper | 2006Messaoudi_Multiple | Multiple axis tomography |
| Paper | 2012Kudryashev_FocusPairs | Focus pairs tomography |
| Paper | 2014Hovden_TiltFocus | Combining tilt series with focus series |
| Paper | 2015Sorzano_RandomConicalTilt | General formulation of Random Conical Tilt |
| Paper | 2017Hagen_DoseTomography | Dose optimization for subtomogram averaging |
| Paper | 2017Tan_PreferredViews | Solving preferred views problems through tilting |
| Paper | 2017Donati_Compressed | Compressed sensing for STEM |
| Paper | 2018Oveisi_Stereo | Stereo-vision with EM |
| Paper | 2018Cheng_BeamShift | Fast image acquisition through beam-shift |
| Paper | 2019Wu_BeamShiftAndTilt | Fast image acquisition through beam-shift and beam tilt control |
Sample preparation
| Paper | 1982Dubochet_Sample | Vitreous ice |
| Paper | 1986Lepault_Sample | Fast freezing |
| Paper | 1995Dubochet_Sample | High-pressure freezing |
| Paper | 1995VanMarle_Sample | Sample damages in resin |
| Paper | 1998Adrian_Sample | Cryo negative staining |
| Paper | 2002DeCarlo_Damage | Radiation damage in cryonegative staining |
| Paper | 2002Hsieh_Sample | Cryofixation |
| Paper | 2004AlAmoudi_Sample | CEMOVIS |
| Paper | 2008Studer_Sample | Review on high pressure freezing |
| Paper | 2009Pierson_Sample | Review on sample preparation for electron tomography |
| Paper | 2010Zhang_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 | 2015Chari_ProteoPlex | Fast evaluation of the structural stability |
| Paper | 2016Passmore_Review | Tutorial chapter on sample preparation |
| Paper | 2016Razinkov_Vitrification | New vitrification method |
| Paper | 2016Takizawa_Sample | Review on sample preparation for EM |
| Paper | 2016Thompson_Sample | Review on sample preparation for EM |
| Paper | 2017Arnold_BlottingFree | Blotting-free preparation |
| Paper | 2017Earl_review | Review of sample preparation |
| Paper | 2017Feng_SprayingPlunging | Spraying plunging |
| Paper | 2017He_FIB | Cryo FIB lamella for TEM |
| Paper | 2017Peitsch_Sample | iMEM: Isolation of Plasma Membrane for Cryoelectron Microscopy |
| Paper | 2017Scapin_Storage | Cryo storage of samples |
| Paper | 2017Schaffer_FocusedIonBeam | Focused Ion Beam sample preparation for membrane proteins |
| Paper | 2017Scherr_HydrogelNanomembranes | Sample preparation for membrane proteins |
| Paper | 2018Anderson_CLEM | Correlated light and EM |
| Paper | 2018Arnold_Review | Review on sample preparation with special emphasis on microfluidic approaches |
| Paper | 2018Dandey_Spotiton | Spotiton, a device for vitrification |
| Paper | 2018Gewering_Detergents | Detergent background in negative stain |
| Paper | 2018Li_CLEM | Correlated light and EM |
| Paper | 2018Noble_Reducing | Reducing particle adsorption |
| Paper | 2018Rice_Ice | Routine determination of ice thickness |
| Paper | 2018Schmidli_Miniaturized | Protein isolation and sample preparation |
| Paper | 2018Wei_Grids | "Self-wicking" nanowire grids |
| Paper | 2019DImprima_Denaturation | Protein denaturation at the air-water interface and how to prevent it |
| Paper | 2019Song_FalconIII | Comparison of the modes of Falcon III |
| Paper | 2020Cianfrocco_Wrong | What could go wrong? |
Automated data collection
| Paper | 1992Dierksen_Automatic | Automated data collection |
| Paper | 1992Koster_Automatic | Automated data collection |
| Paper | 1996Fung_Automatic | Automated data collection for tomography |
| Paper | 2001Zhang_Automatic | Automated data collection: AutoEM |
| Paper | 2003Ziese_Automatic | Automated autofocusing |
| Paper | 2004Potter_Automatic | Automated sample loading |
| Paper | 2004Zheng_Automatic | Automated data collection |
| Paper | 2005Lei_Automatic | Automated data collection: AutoEM |
| Paper | 2005Suloway_Automatic | Automated data collection: Leginon |
| Paper | 2007Yoshioka_RCT | Automated Random Conical Tilt |
| Paper | 2011Korinek_TOM2 | Automated acquisition with TOM2 |
| Paper | 2015Li_UCSFImage | Automated acquisition with UCSFImage |
| Paper | 2016Gil_Fuzzy | Real time decisions during acquisition with neuro-fuzzy method |
| Paper | 2016Liu_TiltControl | Accurate control of the tilt angle for electron tomography |
| Paper | 2016Vargas_FoilHole | Determination of image quality at low magnification |
| Paper | 2017Alewijnse_Best | Best practices for managing large CryoEM facilities |
| Paper | 2017Biyani_Focus | Automatic processing of micrographs |
| Paper | 2018Gomez_Facilities | Use of Scipion at facilities |
| Paper | 2018Sorzano_Gain | Estimation of the DDD camera gain or residual gain |
| Paper | 2019Chreifi_TiltSeries | Rapid tilt-series acquisition for electron cryotomography |
| Paper | 2019Eng_ImageCompression | 3D Reconstruction from compressed images |
| Paper | 2019Hamaguchi_CryoARM | CryoARM data acquisition |
| Paper | 2019Maluenda_Scipion | Automated workflow processing for facilities |
| Paper | 2019Tegunov_Warp | Automatic micrograph processing with Warp |
| Paper | 2019Thompson_Protocol | Protocol for EM acquisition |
| Paper | 2020Baxa_Facility | Operational workflow in a facility |
Single particles
Automatic particle picking
| Paper | 1982VanHeel_Detection | Detection of particles in micrographs |
| Paper | 2001Nicholson_Review | Review on automatic particle picking |
| Paper | 2001Zhu_Filaments | Automatic identification of filaments in micrographs |
| Paper | 2004Sigworth_Detection | Classical detection theory and the cryo-EM particle selection problem |
| Paper | 2004Volkmann_ParticlePicking | An approach to automated particle picking from electron micrographs based on reduced representation templates |
| Paper | 2004Wong_ParticlePicking | Model-based particle picking for cryo-electron microscopy |
| Paper | 2004Zhu_Review | Review on automatic particle picking |
| Paper | 2007Chen_Signature | Automatic particle picking program: Signature |
| Paper | 2007Woolford_SwarmPS | Automatic particle picking with several criteria, implemented in EMAN Boxer |
| Paper | 2009Sorzano_MachineLearning | Automatic particle picking based on machine learning of rotational invariants |
| Paper | 2011Arbelaez_Comparison | Evaluation of the performance of software for automated particle-boxing |
| Paper | 2013Abrishami_MachineLearning | A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs |
| Paper | 2013Hauer_2013 | Automatic tilt pair detection in Random Conical Tilt |
| Paper | 2013Hoang_ParallelGPUPicking | Parallel GPU-accelerated particle picking |
| Paper | 2013Shatsky_ParticlePicking | Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs |
| Paper | 2013Vargas_ParticleQuality | Automatic determination of particle quality |
| Paper | 2014Langlois_ParticlePicking | Automatic particle picking |
| Paper | 2015Scheres_SemiAutoPicking | Semi-automated selection of cryo-EM particles |
| Paper | 2016Vilas_AutomaticTilt | Automatic identification of image pairs in untilted-tilted micrograph pairs |
| Paper | 2016Wang_DeepPicker | A deep learning approach for fully automated particle picking |
| Paper | 2017Zhu_DeepEM | Deep learning approach to picking |
| Paper | 2018Huber_Helices | Automated tracing of helices |
| Paper | 2018Heimowitz_ApplePicker | Automated particle picking |
| Paper | 2018Sanchez_DeepConsensus | Deep learning consensus of multiple automatic pickers |
| Paper | 2019Alazzawi_Clustering | Use of clustering algorithms to find particles in micrographs |
| Paper | 2019Bepler_Topaz | Deep learning for particle picking |
| Paper | 2019Carrasco_IP | Use of standard image processing for particle picking |
| Conference | 2019Li_Deep | Deep learning for particle picking without box size |
| Paper | 2019Wagner_Cryolo | Deep learning for particle picking |
| Paper | 2019Wang_Biobjective | Biobjective function for robust signal detection |
| Paper | 2019Zhang_Pixer | Deep learning for particle picking |
2D Preprocessing
| Paper | 1978Carrascosa_matching | Gray values matching by linear transformations |
| Paper | 2003Rosenthal_DPR | Contrast enhancement through DPR |
| Paper | 2004Sorzano_Normalization | Normalization procedures and their statistical properties. |
| Paper | 2006Sorzano_Denoising | Strong denoising in wavelet space |
| Conference | 2009Sorzano_Downsampling | Differences between the different downsampling schemes |
| Paper | 2012Brilot_Movies | Alignment of beam induced motion in direct detectors |
| Paper | 2012Campbell_Movies | Alignment of beam induced motion in direct detectors |
| Paper | 2012Zhao_Denoising | Denoising using an invariant Fourier-Bessel eigenspace |
| Paper | 2013Norousi_Screening | Screening particles to identify outliers |
| Paper | 2013Bai_ElectronCounting | Electron counting and beam induced motion correction |
| Paper | 2013Li_ElectronCounting | Electron counting and beam induced motion correction |
| Paper | 2013Shigematsu_Movies | Drift correction for movies considering dark field |
| Paper | 2013Vargas_ParticleQuality | Automatic determination of particle quality |
| Paper | 2014Scheres_Movies | Beam induced motion correction |
| Paper | 2015Abrishami_Movies | Alignment of direct detection device micrographs |
| Paper | 2015Grant_Anisotropic | Automatic estimation and correction of anisotropic magnification |
| Paper | 2015Grant_OptimalExposure | Filter movies according to the radiation damage |
| Paper | 2015Rubinstein_Alignment | Frame alignment at the level of particle |
| Paper | 2015Spear_DoseCompensation | Effect of dose compensation on resolution |
| Paper | 2015Zhao_AnisotropicMagnification | Correction of anisotropic magnification |
| Conference | 2016Bajic_Denoising | Denoising and deconvolution of micrographs |
| Paper | 2016Jensen_RemovalVesicles | Removal of vesicles in membrane proteins |
| Paper | 2016Bhamre_Denoising | Denoising by 2D covariance estimation |
| Paper | 2017Berndsen_EMPH | Automated hole masking algorithm |
| Paper | 2017McLeod_Zorro | Movie alignment by Zorro |
| Paper | 2017Zheng_MotionCorr2 | Movie alignment by MotionCorr2 |
| Paper | 2018Ouyang_Denoising | Denoising based on geodesic distance |
| Paper | 2018Wu_ContrastEnhancement | Contrast enhancement |
| Paper | 2019Zivanov_BayesianBIM | Bayesian correction of beam induced movement |
2D Alignment
| Paper | 1981Frank_Averaging | 2D averaging and phase residual |
| Paper | 1982Saxton_Averaging | 2D averaging using correlation |
| Paper | 1998Sigworth_ML2D | Maximum likelihood alignment in 2D |
| Paper | 2003Cong_FRM2D | Fast Rotational Matching in 2D |
| Paper | 2005Cong_FRM2D | Fast Rotational Matching in 2D introduced in a 3D Alignment algorithm |
| Paper | 2005Scheres_ML2D | Multireference alignment and classification in 2D |
| Paper | 2016Aguerrebere_Limits | Fundamental limits of 2D translational alignment |
| Paper | 2010Sorzano_CL2D | Multireference alignment and classification in 2D |
| Conference | 2017Anoshina_Correlation | New correlation measure for aligning images |
| Paper | 2019Radermacher_Correlation | On the properties of cross correlation for the alignment of images |
2D Classification and clustering
| Paper | 1981VanHeel_MSA | Multivariate Statistical Analysis |
| Paper | 1984VanHeel_MSA | Multivariate Statistical Analysis |
| Paper | 2005Scheres_ML2D | Multireference alignment and classification in 2D |
| Paper | 2010Sorzano_CL2D | Multireference alignment and classification in 2D |
| Paper | 2011Singer_DiffusionMaps | Classification in 2D based on graph analysis of the projections |
| Paper | 2012Yang_ISAC | Iterative Stable Alignment and clustering |
| Paper | 2014Sorzano_Outlier | Outlier detection in 2D classifications. |
| Paper | 2014Zhao_Aspire | Fast classification based on rotational invariants and vector diffusion maps |
| Paper | 2015Huang_Robust | Robust w-estimators of 2D classes |
| Paper | 2016Kimanius_Accelerated | GPU Accelerated image classification and high-resolution refinement |
| Paper | 2016Reboul_Stochastic | Stochastic Hill Climbing for calculating 2D classes |
| Conference | 2017Bhamre_Mahalanobis | 2D classification using Mahalanobis distance |
| Paper | 2017Wu_GTM | 2D classification using Generative Topographic Mapping |
| Conference | 2018Boumal_SinglePass | Single pass classification |
| Conference | 2018Shuo_Network | 2D Clustering by network metrics |
3D Alignment
| Paper | 1980Kam_AutoCorrelation | Reconstruction without angular assignment from autocorrelation function (reference free) |
| Paper | 1986Goncharov_CommonLines | Angular assignment using common lines (reference free) |
| Paper | 1987VanHeel_CommonLines | Angular assignment using common lines (reference free) |
| Paper | 1988Provencher_Simultaneous | Simultaneaous alignment and reconstruction |
| Paper | 1988Radermacher_RCT | Random Conical Tilt and Single axis tilt |
| Paper | 1988Vogel_Simultaneous | Simultaneaous alignment and reconstruction |
| Paper | 1990Gelfand_Moments | Angular assignment using moments (reference free) |
| Paper | 1990Goncharov_Moments | Angular assignment using moments (reference free) |
| Paper | 1990Harauz_Quaternions | Use of quaternions to represent rotations |
| Paper | 1994Penczek_Real | Angular assignment using projection matching in real space |
| Paper | 1994Radermacher_Radon | Angular assignment in Radon space |
| Paper | 1996Penczek_CommonLines | Angular assignment using common lines (reference free) |
| Paper | 2003Rosenthal_DPR | Angular assignment using DPR |
| Paper | 2004Sorzano_Wavelet | Angular assignment in the wavelet space. |
| Paper | 2005Jonic_Splines | Angular assignment in Fourier space using spline interpolation. |
| Paper | 2005Yang_Simultaneous | Simultaneaous alignment and reconstruction |
| Paper | 2006Ogura_SimulatedAnnealing | Angular asignment by simulated annealing |
| Paper | 2007Grigorieff_Continuous | Continuous angular assignment in Fourier space |
| Paper | 2010Jaitly_Bayesian | Angular assignment by a Bayesian method and annealing |
| Paper | 2010Sanz_Random | Random model method |
| Paper | 2010Singer_Voting | Detecting consistent common lines by voting (reference free) |
| Paper | 2011Singer_SDP | Angular assignment by semidefinite programming and eigenvectors (reference free) |
| Paper | 2012Giannakis_Scattering | Construction of an initial volume, reference free, by graph analysis of the projections |
| Paper | 2012Shkolnisky_Sync | Angular assignment by synchronization of rotations (reference free) |
| Paper | 2013Elmlund H_PRIME | PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy |
| Paper | 2013Wang_LUD | Angular assignment by least unsquared deviations (reference free) |
| Paper | 2014Vargas_RANSAC | Initial model using RANSAC (reference free) |
| Paper | 2015Joubert_Pseudoatoms | Initial model based on pseudo-atoms |
| Paper | 2015Singer_Kam | Reconstruction without angular assignment from autocorrelation function (reference free) |
| Paper | 2015Sorzano_Significant | Statistical approach to the initial volume estimation (reconstruct significant) |
| Paper | 2016Cossio_BayesianGPU | GPU implementation of the Bayesian 3D reconstruction approach |
| Conference | 2016Michels_Heterogeneous | Initial volume in the presence of heterogeneity |
| Paper | 2016Pragier_Graph | Graph partitioning approach to angular reconstitution |
| Paper | 2017Greenberg_CommonLines | Common lines for reference free ab-initio reconstruction |
| Paper | 2018Sorzano_Highres | New algorithm for 3D Reconstruction and alignment with emphasis on significance |
| Paper | 2018Sorzano_Swarm | Consensus of several initial volumes by swarm optimization |
| Paper | 2019Zehni_Joint | Continuous angular refinement and reconstruction |
| Paper | 2020Zehni_Joint | Continuous angular refinement and reconstruction |
3D Reconstruction
| Paper | 1972Gilbert_SIRT | Simultaneous Iterative Reconstruction Technique (SIRT) |
| Paper | 1973Herman_ART | Algebraic Reconstruction Technique (ART) |
| Paper | 1980Kam_SphericalHarmonics | 3D Reconstruction using spherical harmonics |
| Paper | 1984Andersen_SART | Simultaneous Algebraic Reconstruction Technique (SART) |
| Paper | 1986Harauz_FBP | Exact filters for Filtered Back Projection |
| Chapter | 1992Radermacher_WBP | Exact filters for Weighted Back Projection |
| Paper | 1997Zhu_RecCTF | 3D Reconstruction (SIRT like) and simultaneous CTF correction |
| Paper | 1998Boisset_Uneven | Artifacts in SIRT and WBP under uneven angular distributions |
| Paper | 1998Marabini_ART | Algebraic Reconstruction Technique with blobs (Xmipp) |
| Paper | 2001Sorzano_Uneven | Free parameter selection under uneven angular distributions |
| Paper | 2005Sorzano_Parameters | Free parameter selection for optimizing multiple tasks |
| Paper | 2008Sorzano_Constraints | Mass, surface, positivity and symmetry constraints for real-space algorithms |
| Paper | 2009Bilbao_ParallelART | Efficient parallelization of ART |
| Paper | 2011Li_GradientFlow | Regularized 3D Reconstruction by Gradient Flow |
| Paper | 2011Vonesch_Wavelets | Fast wavelet-based 3D reconstruction |
| Paper | 2012Gopinath_ShapeRegularization | Regularized 3D Reconstruction by Shape information |
| Paper | 2012Kucukelbir_adaptiveBasis | 3D reconstruction in an adaptive basis promoting sparsity |
| Paper | 2012Sindelar_NoiseReduction | Optimal noise reduction in 3D reconstructions |
| Paper | 2013Elmlund H_PRIME | PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy |
| Paper | 2013Lyumkis_Optimod | Construction of initial volumes with Optimod |
| Paper | 2013Wang FIRM | Fast 3D reconstruction in Fourier domain |
| Paper | 2014Kunz_SART_OS | Simultaneous ART with OS |
| Paper | 2015Abrishami_Fourier | 3D Reconstruction in Fourier space |
| Paper | 2015Dvornek_SubspaceEM | Fast Maximum a posteriori |
| Conference | 2018Michels_RBF | Ab-initio reconstruction with radial basis functions |
| Paper | 2015Moriya_Bayesian | Bayesian approach to suppress limited angular artifacts |
| Paper | 2015Xu_GeometricFlow | Multi-scale geometric flow |
| Arxiv | 2016Ye_Cohomology | Cohomology properties of 3D reconstruction |
| Paper | 2017Punjani_CryoSPARC | CryoSPARC |
| Paper | 2017Punjani_CryoSPARCTheory | Theory related to CryoSPARC |
| Paper | 2017Sorzano_SurveyIterative | Survey of iterative reconstruction methods for EM |
| Paper | 2018Bartesaghi_Refinement | Refinement of CTF, frame weight and alignment for high resolution reconstruction |
| Paper | 2018Hu_ParticleFilter | A particle filter framework for 3D reconstruction |
| Conference | 2018Levin_Kam | Ab initio reconstruction by autocorrelation analysis |
| Paper | 2018Reboul_Simple | Ab initio reconstruction with Simple |
| Paper | 2018Sorzano_Highres | New algorithm for 3D Reconstruction and alignment with emphasis on significance |
| Paper | 2018Sorzano_Swarm | Consensus of several initial volumes by swarm optimization |
| Paper | 2018Zhu_Ewald | 3D Reconstruction with Ewald sphere correction |
| Paper | 2019Gomez_Initial | Construction of initial models |
| Master | 2019Havelkova_Regularization | Regularization methods in 3D reconstruction |
| Paper | 2019Wilkinson_Scales | Combining data acquired at different scales |
3D Heterogeneity
| Paper | 2004White_Size | Heterogeneity classification of differently sized images |
| Paper | 2006Penczek_Bootstrap | 3D heterogeneity through bootstrap |
| Paper | 2007Leschziner_Review | Review of 3D heterogeneity handling algorithms |
| Paper | 2007Scheres_ML3D | Maximum Likelihood alignment and classification in 3D |
| Paper | 2008Herman_Graph | Classification by graph partitioning |
| Paper | 2009Spahn_Bootstrap | 3D heterogeneity through bootstrap |
| Paper | 2010Elmlund_AbInitio | Solving the initial volume problem with multiple conformations |
| Paper | 2010Shatsky_MultiVariate | Multivariate Statistical Analysis |
| Paper | 2012Scheres_Bayesian | A Bayesian view on cryo-EM structure determination |
| Paper | 2012Zheng_Covariance | Estimation of the volume covariance |
| Paper | 2013Wang_MLVariance | Maximum Likelihood estimate of the map variance |
| Paper | 2013Lyumkis D_FREALIGN | Likelihood-based classification of cryo-EM images using FREALIGN. |
| Paper | 2014Jin_NMA | Continuous heterogeneity through Normal Mode Analysis |
| Paper | 2014Dashti_Brownian | Continuous heterogeneity through Brownian trajectories |
| Paper | 2014Chen_Migration | Particle migration analysis in 3D classification |
| Paper | 2015Anden_Covariance | 3D Covariance matrix estimation for heterogeneity |
| Paper | 2015Bai_Focused | Focused classification |
| Paper | 2015Katsevich_Covariance | 3D Covariance matrix estimation for heterogeneity |
| Paper | 2015Klaholz_MRA | Multivariate Statistical Analysis of Jackknife and Bootstrapping on random subsets |
| Paper | 2015Liao_Covariance | Estimation of the 3D covariance from 2D projections |
| Paper | 2015Tagare_Direct | Direct reconstruction of PCA components |
| Paper | 2016Gong_Mechanical | Mechanical model for macromolecules |
| Paper | 2016Rawson_Movement | Movement and flexibility |
| Paper | 2016Shan_Multibody | Multibody refinement |
| Paper | 2016Sorzano_StructMap | Sorting a discrete set of conformational states |
| Paper | 2016Sorzano_Strain | Calculate local stretches, strains and rotations from two conformational states |
| Paper | 2017Punjani_CryoSPARC | CryoSPARC |
| Paper | 2017Schillbach_Warpcraft | Warpcraft: 3D Reconstruction in the presence of continuous heterogeneity |
| Paper | 2018Anden_Covariance | Structural Variability from Noisy Tomographic Projections |
| Paper | 2018Haselbach_FreeEnergy | Analysis of the free energy landscape through PCA |
| Paper | 2018Nakane_MultiBody | Structural Variability through multi-body refinement |
| Paper | 2019Serna_Review | Review of classification tools |
| Paper | 2018Solernou_FFEA | Fluctuating Finite Element Analysis, continuum approach to Molecular Dynamics |
| Paper | 2019Sorzano_Review | Review of continuous heterogeneity biophysics |
| Paper | 2019Zhang_Local | Local variability and covariance |
| Paper | 2020Harastani_NMA | Using Scipion for analyzing local heterogeneity with normal modes |
Validation
| Paper | 2008Stagg_TestBed | Effect of voltage, dosis, number of particles and Euler jumps on resolution |
| Paper | 2011Henderson | Tilt Validation |
| Paper | 2011Read | Validation of PDBs |
| Paper | 2012Henderson | EM Map Validation |
| Paper | 2013Cossio_Bayesian | EM Map Validation in a probabilistic setting |
| Paper | 2013Chen_NoiseSubstitution | Noise substitution at high resolution for measuring overfitting |
| Paper | 2013Ludtke_Validation | Structural validation, example of the Calcium release channel |
| Paper | 2013Murray_Validation | Validation of a 3DEM structure through a particular example |
| Paper | 2014Russo_StatisticalSignificance | EM Map Validation through the statistical significance of the tilt-pair angular assignment |
| Paper | 2014Stagg_Reslog | EM Map Validation through the resolution evolution with the number of particles |
| Paper | 2014Wasilewski_Tilt | Web implementation of the tilt pair validation |
| Paper | 2015Heymann_Alignability | EM Map Validation through the resolution of reconstructions from particles and noise |
| Paper | 2015Oliveira_FreqLimited | Comparison of gold standard and frequency limited optimization |
| Paper | 2015Rosenthal_Review | Review of validation methods |
| Paper | 2015Wriggers_Secondary | Validation by secondary structure |
| Paper | 2016Degiacomi_IM | Comparison of Ion Mobility data and EM volumes |
| Paper | 2016Kim_SAXS | Comparison of SAXS data and EM projections |
| Paper | 2016Rosenthal_Review | Review of validation methods |
| Paper | 2016Vargas_Alignability | Validation by studying the tendency of an angular assignment to cluster in the projection space |
| Paper | 2017Monroe_PDBRefinement | Validation by comparison to a refined PDB |
| Paper | 2018Afonine_Phenix | Tools in Phenix for the validation of EM maps |
| Paper | 2018Heymann_Bsoft | Map validation using Bsoft |
| Paper | 2018Heymann_Challenge | A summary of the assessments of the 3D Map Challenge |
| Paper | 2018Jonic_Gaussian | Assessment of sets of volumes by pseudoatomic structures |
| Paper | 2018Naydenova_AngularDistribution | Evaluating the angular distribution of a 3D reconstruction |
| Paper | 2018Pages_Symmetry | Looking for a symmetry axis in a PDB |
| Paper | 2018Pintilie_SSE | Evaluating the quality of SSE and side chains |
| Paper | 2019Herzik_Multimodel | Local and global quality by multi-model fitting |
| Paper | 2020Stojkovic_PTM | Validation of post-translational modifications |
Resolution
| Paper | 1986Harauz_FBP | Fourier Shell Correlation |
| Paper | 1987Unser_SSNR | 2D Spectral Signal to Noise Ratio |
| Paper | 2002Penczek_SSNR | 3D Spectral Signal to Noise Ratio for Fourier based algorithms |
| Paper | 2003Rosenthal_DPR | Review of the FSC and establishment of a new threshold |
| Paper | 2005Unser_SSNR | 3D Spectral Signal to Noise Ratio for any kind of algorithms |
| Paper | 2005VanHeel_FSC | Establishment of a new threshold for FSC |
| Paper | 2007Sousa_AbInitio | Resolution measurement on neighbour Fourier voxels |
| Paper | 2014Kucukelbir_Local | Quantifying the local resolution of cryo-EM density maps |
| Paper | 2016Pintilie_Probabilistic | Probabilistic models and resolution |
| Paper | 2017Sorzano_FourierProperties | Statistical properties of resolution measures defined in Fourier space |
| Conference | 2018Avramov_DeepLearning | Deep learning classification of volumes into low, medium and high resolution |
| Paper | 2018Carugo_BFactors | How large can B-factors be in protein crystals |
| Paper | 2018Kim_FourierError | Comparison between a gold standard and a reconstruction |
| Paper | 2018Rupp_Problems | Problems of resolution as a proxy number for map quality |
| Paper | 2018Vilas_MonoRes | Local resolution by monogenic signals |
| Paper | 2018Yang_Multiscale | Resolution from a multiscale spectral analysis |
| Paper | 2019Avramov_DeepLearning | Deep learning classification of volumes into low, medium and high resolution |
| Paper | 2019Ramirez_DeepRes | Resolution determination by deep learning |
| Paper | 2020Baldwin_Lyumkis_SCF | Resolution attenuation through non-uniform Fourier sampling |
| Paper | 2020Vilas_MonoDir | Local and directional resolution |
Sharpening of high resolution information
| Paper | 2003Rosenthal_DPR | Contrast restoration and map sharpening |
| Paper | 2008Fernandez_Bfactor | Bfactor determination and restoration |
| Paper | 2013Fiddy_SaxtonAlgorithm | Phase retrieval or extension |
| Paper | 2014Kishchenko_SphericalDeconvolution | Spherical deconvolution |
| Paper | 2015Spiegel_VISDEM | Visualization improvement by the use of pseudoatomic profiles |
| Paper | 2016Jonic_Pseudoatoms | Approximation with pseudoatoms |
| Paper | 2016Jonic_Denoising | Denoising and high-frequency boosting by pseudoatom approximation |
| Paper | 2017Jakobi_LocScale | Sharpening based on an atomic model |
| Paper | 2019Ramlaul_Filtering | Local agreement filtering (denoising) |
| Paper | 2020Vilas_Bfactor | Global B-factor correction does not represent macromolecules |
CTF estimation and restoration
| Paper | 1982Schiske_Correction | CTF correction for tilted objects |
| Paper | 1988Toyoshima_Model | CTF estimation |
| Paper | 1995Frank_Wiener | CTF correction using Wiener filter |
| Paper | 1996Skoglund_MaxEnt | CTF correction with Maximum Entropy |
| Paper | 1996Zhou_Model | CTF model and user interface for manual fitting |
| Paper | 1997Fernandez_AR | PSD estimation using periodogram averaging and AR models |
| Paper | 1997Penczek_Wiener | CTF correction using Wiener filter |
| Paper | 1997Stark_Deconvolution | CTF correction using deconvolution |
| Paper | 1997Zhu_RecCTF | CTF correction and reconstruction |
| Paper | 2000DeRosier_EwaldCorrection | CTF correction considering the Ewald sphere |
| Paper | 2000Jensen_TiltedCorrection | CTF correction considering tilt in backprojection |
| Paper | 2001Saad_CTFEstimate | CTF estimation |
| Paper | 2003Huang_CTFEstimate | CTF estimation |
| Paper | 2003Mindell_CTFTILT | CTF estimation for tilted micrographs |
| Paper | 2003Sander_MSA | CTF estimation through MSA classification of PSDs |
| Paper | 2003Velazquez_ARMA | PSD and CTF estimation using ARMA models |
| Paper | 2004Sorzano_IDR | CTF restoration and reconstruction with Iterative Data Refinement |
| Conference | 2004Wan_CTF | Spatially variant CTF |
| Paper | 2004Zubelli_Chahine | CTF restoration and reconstruction with Chahine's multiplicative method |
| Conference | 2005Dubowy_SpaceVariant | CTF correction when this is space variant |
| Paper | 2005Mallick_ACE | CTF estimation |
| Paper | 2006Wolf_Ewald | CTF correction considering Ewald sphere |
| Paper | 2007Jonic_EnhancedPSD | PSD enhancement for better identification of Thon rings; Vitreous ice diffracts in Thon rings |
| Paper | 2007Philippsen_Model | CTF Model for tilted specimens |
| Paper | 2007Sorzano_CTF | CTF estimation using enhanced PSDs |
| Paper | 2009Sorzano_Sensitivity | Error sensitivity of the CTF models, non-uniqueness of the CTF parameters |
| Paper | 2010Jiang2010_CTFCorrection | Amplitude correction method |
| Paper | 2010Kasantsev_CTFCorrection | Mathematical foundations of Kornberg and Jensen method |
| Paper | 2010Leong_CTFCorrection | Correction for spatially variant CTF |
| Paper | 2011Glaeser_Coma | The effect of coma at high-resolution |
| Paper | 2011Mariani_Tilted | CTF simulation and correction of tilted specimens |
| Paper | 2011Sindelar_Wiener | CTF correction using a modified version of Wiener filter |
| Paper | 2011Voortman_Tilted | CTF correction for tilted specimen |
| Paper | 2012Voortman_VaryingCTF | Correcting a spatially varying CTF |
| Paper | 2013Vargas_FastDef | Fast defocus |
| Paper | 2015Rohou_CTFFind4 | CTF Find 4 |
| Paper | 2015Sheth_CTFquality | Visualization and quality assessment of CTF |
| Paper | 2016Zhang_GCTF | gCTF |
| Paper | 2018Su_GoCTF | goCTF, CTF for tilted specimens |
Segmentation
| Paper | 2006Baker_segmentation | Segmentation of molecular subunits |
| Paper | 2010Pintilie_segger | Segmentation of molecular subunits |
| Conference | 2017Nissenson_VolumeCut | Segmentation of an EM volume using an atomic model |
| Paper | 2020Farkas_MemBlob | Segmentation of membrane in membrane embedded proteins |
Fitting and docking
| Paper | 1999Volkmann_Fitting | Fitting in real space |
| Paper | 2001Baker_Review | Review of protein structure prediction |
| Paper | 2001Jones_Review | Review of protein structure prediction |
| Paper | 2003Kovacs_FRM3D | Fast Rotational Alignment of two EM maps |
| Paper | 2004Tama_NMA1 | Flexible fitting with Normal Modes (I) |
| Paper | 2004Tama_NMA2 | Flexible fitting with Normal Modes (II) |
| Paper | 2005Velazquez_Superfamilies | Recognition of the superfamily folding in medium-high resolution volumes |
| Paper | 2007DeVries_Haddock | Docking with Haddock 2.0 |
| Paper | 2007Kleywegt_QualityControl | Quality control and validation of fitting |
| Paper | 2012Biswas_Secondary | Secondary structure determination in EM volumes |
| Paper | 2012Velazquez_Constraints | Multicomponent fitting by using constraints from other information sources |
| Paper | 2013Chapman MS_Atomicmodeling | Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters |
| Paper | 2013Esquivel_Modelling | Review on modelling (secondary structure, fitting, ...) |
| Paper | 2013Lopez_Imodfit | Fitting based on vibrational analysis |
| Paper | 2013Nogales_3DEMLoupe | Normal Mode Analysis of reconstructed volumes |
| Paper | 2014AlNasr_Secondary | Identification of secondary structure elements in EM volumes |
| Paper | 2014Politis_MassSpect | Integration of mass spectroscopy information |
| Paper | 2014Rey_MassSpect | Integration of mass spectroscopy information |
| Paper | 2014Villa_Review | Review of atomic fitting into EM volumes |
| Paper | 2015Barad_EMRinger | Validation of hybrid models |
| Paper | 2015Bettadapura_PF2Fit | Fast rigid fitting of PDBs into EM maps |
| Paper | 2015Carrillo_CapsidMaps | Analysis of virus capsids using Google Maps |
| Paper | 2015Hanson_Continuum | Modelling assemblies with continuum mechanics |
| Paper | 2015Lopez_Review | Review of structural modelling from EM data |
| Paper | 2015Schroeder_Hybrid | Review on model building |
| Paper | 2015Tamo_Dynamics | Dynamics in integrative modeling |
| Paper | 2015Sorzano_AtomsToVoxels | Accurate conversion of an atomic model into a voxel density volume |
| Paper | 2016Joseph_Evolution | Evolutionary constraints for the fitting of atomic models into density maps |
| Paper | 2016Joseph_Refinement | Refinement of atomic models in high-resolution EM reconstructions using Flex-EM |
| Paper | 2016Murshudov_Refinement | Refinement of atomic models in high-resolution EM reconstructions |
| Paper | 2016Segura_3Diana | Validation of hybrid models |
| Paper | 2016Singharoy_MDFF | Construction of hybrid models driven by EM density and molecular dynamics |
| Paper | 2016Wang_Rosetta | Construction of hybrid models driven by EM density using Rosetta |
| Paper | 2017Chen_CoarseGraining | Coarse graining of EM volumes |
| Paper | 2017Joseph_Metrics | Metrics analysis for the comparison of structures |
| Paper | 2017Hryc_WeightedAtoms | Construction of hybrid models by locally weighting the different atoms |
| Paper | 2017Matsumoto_Distribution | Estimating the distribution of conformations of atomic models |
| Paper | 2017Michel_ContactPrediction | Structure prediction by contact prediction |
| Paper | 2017Miyashita_EnsembleFitting | Ensemble fitting using Molecular Dynamics |
| Paper | 2017Turk_ModelBuilding | Tutorial on model building and protein visualization |
| Paper | 2017Wang_PartialCharges | Appearance of partial charges in EM maps |
| Paper | 2017Wlodawer | Comparison of X-ray and EM high resolution structures |
| Paper | 2018Cassidy_review | Review of methods for hybrid modeling |
| Paper | 2018Chen_SudeChains | A comparison of side chains between X-ray and EM maps |
| Paper | 2018Kawabata_Pseudoatoms | Modelling the EM map with Gaussian pseudoatoms |
| Paper | 2018Kovacs_Medium | Modelling of medium resolution EM maps |
| Paper | 2018Neumann_validation | Validation of fitting, resolution assessment and quality of fit |
| Paper | 2018Terwilliger_map_to_model | Phenix map_to_model, automatic modelling of EM volumes |
| Paper | 2018Wang_MD | Constructing atomic models using molecular dynamics |
| Paper | 2018Xia_MVPENM | Multiscale Normal Mode Analysis |
| Paper | 2018Yu_Atomic | Constructing atomic models using existing tools |
| Paper | 2019Bonomi_Multiscale | Bayesian multi-scale modelling |
| Paper | 2019Klaholz_Review | Review of Phenix tools to modelling |
| Paper | 2019Zhang_CoarseGrained | Coarse-graining of EM maps |
| Paper | 2020Ho_CryoID | Identification of proteins in structural proteomics from cryoEM volumes |
| Paper | 2020Joseph_comparison | Comparison of map and model, or two maps |
Books and reviews
| Book | 1980Herman_Tomography | General book on tomography |
| Book | 1988Kak_Tomography | General book on tomography |
| Paper | 2000Tao_Review | Review of single particles |
| Paper | 2000VanHeel_Review | Review of single particles |
| Paper | 2002Frank_Review | Review of single particles |
| Paper | 2002Schmid_Review | Review of single particles |
| Paper | 2004Henderson_Review | Review of electron microscopy |
| Paper | 2004Subramaniam_Review | Review of single particles |
| Paper | 2005Steven_Review | Review of electron microscopy |
| Paper | 2006Fernandez_Review | Review of electron microscopy |
| Book | 2006Frank_book | Book covering all aspects of electron microscopy of single particles |
| Paper | 2006Sorzano_Review | Review of optimization problems in electron microscopy |
| Paper | 2007Leschziner_Review | Review of 3D heterogeneity handling algorithms |
| Paper | 2007Sorzano_Review | Review of the image processing steps |
| Paper | 2008Fanelli_ImageFormation | Review on the image formation model from the electron waves and open inverse-problems in Electron Tomography |
| Paper | 2008Fernandez_HPCReview | High performance computing in electron cryomicroscopy |
| Paper | 2008Jonic_Review | Comparison between electron tomography and single particles |
| Paper | 2008Mueller_Review | Review of Electron microscopy |
| Paper | 2008Taylor_Review | Review of Electron microscopy |
| Paper | 2010DeRosier_Review | Personal account of how 3DEM developed in the early days |
| Chapter | 2012Sorzano_Review | Review of single particle analysis using Xmipp |
| Chapter | 2012Devaux_Protocol | Protocols for performing single particle analysis |
| Paper | 2014Bai_Review | Recent advances in cryo-EM |
| Paper | 2015Carazo_Review | Review of the reconstruction process |
| Paper | 2015Cheng_Review | A primer to Single Particle Cryo-EM |
| Paper | 2015Cheng_Reviewb | Single Particle Cryo-EM at crystallographic resolution |
| Paper | 2015Elmlund_Review | Recent advances in cryo-EM |
| Paper | 2015Henderson_Review | Recent advances in cryo-EM |
| Paper | 2015Nogales_Review | Recent advances in cryo-EM |
| Paper | 2015Schroeder_Review | Review of advances in the electron microscope |
| Paper | 2015VanDenBedem_Integrative | Review of integrative structural biology |
| Paper | 2015Wu_Review | Review of advances in cryo-EM |
| Paper | 2016Carroni_CryoEM | Review of advances in Cryo-EM |
| Paper | 2016Egelman_CryoEM | Review of advances in Cryo-EM |
| Paper | 2016Eisenstein_CryoEM | News feature on the Method of the Year |
| Paper | 2016FernandezLeiro_Review | Review of EM |
| Paper | 2016Glaeser_HowGood | How good can cryo-EM become? |
| Paper | 2016Jonic_PseudoAtoms | Review of the applications of the use of pseudoatoms in EM |
| Chapter | 2016Mio_Review | Overview of the process to obtain EM reconstructions |
| Paper | 2016Jonic_Review | A review of computational ways to handle heterogeneity |
| Paper | 2016Nogales_Review | Review of advances in cryo-EM |
| Paper | 2016Subramaniam_Review | Why cryo-EM is now suitable for crystallographic journals |
| Paper | 2016Vinothkumar_Review | Historical review and current limitations |
| Report | 2017Brezinski_Nobel | Scientific background on the Nobel Prize in Chemistry 2017 |
| Paper | 2017Cheng_review | Why CryoEM became so hot |
| Paper | 2017Danev_Review | Review of the use of phase plates in EM |
| Paper | 2017Elmlund_Review | Review of the main current difficulties of EM |
| Paper | 2017Frank_Review | Historical review of EM |
| Paper | 2017Frank_TimeResolved | Review of time-resolved of EM |
| Paper | 2017Jonic_Review | Review of computational methods to analyze conformational variability |
| Paper | 2017Merino_DrugEM | Applications of EM for drug design |
| Paper | 2017Rawson_Limitations | Limitations of EM for drug design |
| Paper | 2017Sorzano_FourierProperties | Review of statistical properties of resolution measures defined in Fourier space |
| Paper | 2017Sorzano_SurveyIterative | Survey of iterative reconstruction methods for EM |
| Paper | 2018Bruggeman_Crowdsourcing | Exploring crowdsourcing for EM image processing |
| Paper | 2018Cheng_Review | Review of EM and future ahead |
| Paper | 2018Cossio_ML | Review of Maximum Likelihood methods |
| Paper | 2018Grimes_Crystallography | Review of X-ray crystallography and its relationship to EM |
| Paper | 2018Murata_Review | Review of EM for structure dynamics |
| Paper | 2018Quentin_Biomedical | Review of EM as a tool for biomedical research |
| Paper | 2018Scapin_DrugDiscovery | Review of EM as a tool for drug discovery |
| Paper | 2018Vilas_ImageProcessing | Review of the recent developments in image processing for single particle analysis |
| Paper | 2018vonLoeffelholz_VPP | Comparison of Volta Phase Plate reconstructions close to focus and with defocus |
| Paper | 2018Eisenstein_DrugDesigners | Drug designers embrace cryo-EM |
| Paper | 2019Benjin_Review | Review of SPA |
| Paper | 2019Danev_Review | Review of future directions |
| Paper | 2019Lyumkis_Review | Challenges and reviews |
| Paper | 2019Sorzano_Review | Review of continuous heterogeneity biophysics |
| Paper | 2020Bendory_Review | Review of image processing problems |
Software
| Paper | 1996Frank_Spider | Spider |
| Paper | 1996VanHeel_Imagic | Imagic |
| Paper | 1999Lutdke_Eman | Eman |
| Paper | 2004Sorzano_Xmipp | Xmipp |
| Paper | 2007Baldwin_AngularTransformations | The Transform Class in SPARX and EMAN2 |
| Paper | 2007Heymann_Bsoft | Bsoft |
| Paper | 2007Grigorieff_Frealign | Frealign |
| Paper | 2008Scheres_XmippProtocols | Xmipp Protocols |
| Paper | 2008Shaikh_SpiderProtocols | Spider Protocols |
| Paper | 2012Wriggers_SitusConventions | Conventions and workflows in Situs |
| Paper | 2013DeLaRosa_Xmipp30 | Xmipp 3.0 |
| Paper | 2015Cianfrocco_Cloud | Software execution in the cloud |
| Paper | 2015Cheng_MRC2014 | Extensions to MRC file format |
| Paper | 2013DeLaRosa_Scipion | Scipion |
| Paper | 2016Scheres_Relion | Tutorial on the use of Relion |
| Paper | 2016Grigorieff_Frealign | Tutorial on the use of Frealign |
| Paper | 2017Moriya_Sphire | Tutorial on the use of Sphire |
| Paper | 2018Bell_EMAN2 | New tools in EMAN2 |
| Paper | 2018Cianfrocco_cloud | CryoEM Cloud Tools |
| Paper | 2018Grant_cisTEM | cisTEM |
| Paper | 2018McLeod_MRCZ | MRC Compression format |
| Paper | 2018Zivanov_Relion3 | Relion 3 |
Electron tomography
Image preprocessing
| Paper | 2015Yan_thickness | Determination of thickness, tilt and electron mean free path |
Image alignment
| Paper | 1982Guckenberger_commonOrigin | Determination of a common origin in the micrographs of titl series in three-dimensional electron microscopy |
| Paper | 1992Lawrence_leastSquares | Least squares solution of the alignment problem |
| Paper | 1995Penczek_dual | Dual tilt alignment |
| Paper | 1996Owen_alignmentQuality | Automatic alignment without fiducial markers and evaluation of alignment quality |
| Paper | 1998Grimm_normalization | Discussion of several gray level normalization methods for electron tomography |
| Paper | 2001Brandt_Automatic1 | Automatic alignment without fiducial markers |
| Paper | 2001Brandt_Automatic2 | Automatic alignment with fiducial markers |
| Paper | 2006Winkler_alignment | Marker-free alignment and refinement |
| Paper | 2006Castano_alignment | Alignment with non-perpendicularity |
| Paper | 2007Castano_alignment | Fiducial-less alignment of cryo-sections |
| Paper | 2009Sorzano_alignment | Marker-free alignment and refinement |
| Paper | 2010Cantele_dualAlignment | Alignment of dual series |
| Paper | 2014Tomonaga_Automatic | Automatic alignment of tilt series using the projection themselves |
| Paper | 2014Han_Automatic | Automatic alignment of tilt series using SIFT features |
| Paper | 2015Han_Automatic | Automatic alignment of tilt series using fiducials |
| Paper | 2017Mastronarde_Automatic | Automatic alignment and reconstruction of tilt series in IMOD |
| Paper | 2018Fernadez_Beam | Image alignment considering beam induced motion |
| Paper | 2018Han_Fast | Automatic alignment using fiducial markers |
| Paper | 2019Fernandez_residual | Alignment of tilt series using residual interpolation |
| Paper | 2019Han_Dual | Automatic alignment using fiducial markers in dual tilt series |
CTF estimation and restoration
| Paper | 2003Winkler_CTF | Focus gradient correction in electron tomography |
| Paper | 2006Fernandez_CTF | CTF determination and correction in electron tomography |
| Paper | 2009Zanetti_CTF | CTF determination and correction in electron tomography |
| Paper | 2009Xiong_CTF | CTF determination and correction for low dose tomographic tilt series |
| Paper | 2012Eibauer_CTF | CTF determination and correction |
| Paper | 2015Bharat_CTFCorrectedSubtomogramAveraging | Subtomogram averaging with CTF correction using a Bayesian prior |
| Paper | 2017Turonova_3DCTF | 3D CTF Correction |
| Paper | 2017Kunz_3DCTF | 3D CTF Correction |
3D reconstruction
| Paper | 1972Gilbert_SIRT | Simultaneous Iterative Reconstruction Technique (SIRT) |
| Paper | 1973Herman_ART | Algebraic Reconstruction Technique (ART) |
| Paper | 1984Andersen_SART | Simultaneous Algebraic Reconstruction Technique (SART) |
| Paper | 1992Radermacher_WBP | Weighted Backprojection in electron tomography |
| Paper | 1997Marabini_reconstruction | Iterative reconstruction in electron tomography |
| Paper | 2002Fernandez_reconstruction | Iterative reconstruction in electron tomography |
| Paper | 2007Radermacher_WBP | Weighted Backprojection in electron tomography |
| Paper | 2008Fernandez_CARP | Component Averaged Row Projections (CARP) |
| Paper | 2010Xu_Long | Iterative reconstructions with long object correction and GPU implementation |
| Paper | 2012Herman General Superiorization | Superiorization: an optimization heuristic for medical physics |
| Paper | 2012Zhang_IPET_FETR | IPET and FETR, a reconstruction algorithm for single molecule tomography |
| Paper | 2013Goris_SIRT_TV_DART | Combination of SIRT, Total Variation and Discrete ART to reconstruct and segment at the same time |
| Paper | 2013Briegel A_Challenge | The challenge of determining handedness in electron tomography and the use of DNA origami gold nanoparticle helices as molecular standards |
| Paper | 2013Messaoudi_EnergyFiltered | 3D Reconstruction of Energy-Filtered TEM |
| Paper | 2015Venkatakrishnan_MBIR | 3D Reconstruction with priors |
| Paper | 2016Deng_ICON | 3D Reconstruction with missing information restoration |
| Paper | 2016Guay_Compressed | 3D Reconstruction using compressed sensing |
| Paper | 2016Turonova_Artifacts | Artifacts observed during 3D reconstruction |
| Paper | 2019Yan_MBIR | 3D Reconstruction with priors and demonstration of its use in biological samples |
| Paper | 2020Song_Tygress | 3D reconstruction with a special acquisition and alignment scheme |
Noise reduction
| Paper | 2001Frangakis_NAD | Noise reduction with Nonlinear Anisotropic Diffusion |
| Paper | 2003Fernandez_AND | Anisotropic nonlinear diffusion for electron tomography |
| Paper | 2003Jiang_Bilateral | Bilateral denoising filter in electron microscopy |
| Paper | 2005Fernandez_AND | Anisotropic nonlinear denoising in electron tomography |
| Paper | 2007Heide_median | Iterative median filtering in electron tomography |
| Paper | 2007Fernandez_autAND | Anisotropic nonlinear diffusion with automated parameter tuning |
| Paper | 2009Fernandez_Beltrami | Nonlinear filtering based on Beltrami flow |
| Paper | 2010Bilbao_MeanShift | Mean Shift Filtering |
| Paper | 2014Kovacik_wedgeArtefacts | Removal of wedge artefacts |
| Paper | 2014Maiorca_beadArtefacts | Removal of gold bead artefacts |
| Paper | 2018Trampert_Inpainting | Removal of the missing wedge by inpainting |
| Paper | 2018Moreno_TomoEED | Fast Anisotropic Diffusion |
| Paper | 2018Wu_Enhacing | Enhancing the image contrast of electron tomography |
Segmentation
| Paper | 2002Frangakis_Eigenanalysis | Segmentation using eigenvector analysis. |
| Paper | 2002Volkmann_Watershed | Segmentation using watershed transform. |
| Paper | 2003Bajaj_BoundarySegmentation | Segmentation based on fast marching. |
| Paper | 2005Cyrklaff_Thresholding | Segmentation using optimal thresholding. |
| Paper | 2007Lebbink_TemplateMatching | Segmentation using template matching. |
| Paper | 2007Sandberg_OrientationFields | Segmentation using orientation fields. |
| Paper | 2007Sandberg_SegmentationReview | Review on segmentation in electron tomography. |
| Paper | 2008Garduno_FuzzySegmentation | Segmentation using fuzzy set theory principles. |
| Paper | 2009Lebbink_TemplateMatching2 | Segmentation using template matching. |
| Paper | 2012RubbiyaAli_EdgeDetection | Parameter-Free Segmentation of Macromolecular Structures. |
| Conference | 2015Xu_TemplateMatching | Detection of macromolecular complexes with a reduced representation of the templates. |
| Paper | 2017Ali_RAZA | Automated segmentation of tomograms |
| Paper | 2017Chen_Annotation | Automated annotation of tomograms |
| Paper | 2017Tasel_ActiveContours | Segmentation with active contours |
| Paper | 2017Xu_DeepLearning | Finding proteins in tomograms using deep learning |
| Paper | 2018Zeng_DeepLearning | Mining features in Electron Tomographt by deep learning |
Resolution
| Paper | 2005Cardone_Resolution | Resolution criterion for electron tomography |
| Chapter | 2007Penczek_Resolution | Review of resolution criteria for electron tomography |
| Paper | 2015Diebolder_ConicalFSC | Conical Fourier Shell Correlation |
Subtomogram analysis
| Paper | 2000Bohm_Template | Macromolecule finding by template matching |
| Paper | 2002Frangakis_Template | Macromolecule finding by template matching |
| Paper | 2006Nickell_Review | Review of macromolecule finding by template matching (Visual Proteomics) |
| Paper | 2007Best_Review | Review of Localization of Protein Complexes by Pattern Recognition |
| Paper | 2007Forster_Review | Review of structure determination by subtomogram averaging |
| Paper | 2008Forster_Classification | Classification of subtomograms using constrained correlation |
| Paper | 2008Bartesaghi_Classification | Classification and averaging of subtomograms |
| Paper | 2008Schmid_Averaging | Alignment and averaging of subtomograms |
| Paper | 2010Amat_Averaging | Alignment and averaging of subtomograms exploiting thresholding in Fourier space |
| Paper | 2010Yu_PPCA | Probabilistic PCA for volume classification |
| Paper | 2013Chen_Averaging | Fast alignment of subtomograms using spherical harmonics |
| Paper | 2013Kuybeda_Averaging | Alignment and averaging of subtomograms using the nuclear norm of the cluster |
| Paper | 2013Shatsky_Averaging | Alignment and averaging of subtomograms with constrained cross-correlation |
| Paper | 2013Yu_Projection | Subtomogram averaging by aligning their projections |
| Paper | 2014Chen_Autofocus | Subtomogram averaging and classification with special attention to differences |
| Paper | 2014Yu_ReferenceBias | Scoring the reference bias |
| Paper | 2014Voortman_LimitingFactors | Limiting factors of subtomogram averaging |
| Paper | 2015Bharat_CTFCorrectedSubtomogramAveraging | Subtomogram averaging with CTF correction using a Bayesian prior |
| Paper | 2015Yu_ReferenceBias | Scoring the reference bias |
| Paper | 2016Bharat_Relion | Subtomogram averaging with Relion |
| Paper | 2016Song_MatrixNorm | Matrix norm minimization for tomographic reconstruction and alignment |
| Paper | 2017Castano_ParticlePicking | Particle picking in tomograms for subtomogram averaging |
| Paper | 2017Frazier_Tomominer | TomoMiner a software platform for large-scale subtomogram analysis |
| Paper | 2018Himes_emClarity | emClarity for subtomogram averaging |
| Paper | 2018Zhao_Fast | Fast alignment and maximum likelihod for subtomogram averaging |
| Paper | 2019Fokine_Enhancement | Subtomogram enhancement through the locked self-rotation |
| Paper | 2019Han_Constrained | Constrained reconstruction to enhance resolution |
Single particle tomography
| Paper | 2012Bartesaghi_Constrained | 3D reconstruction by imposing geometrical constraints |
| Paper | 2015Galaz_SingleParticleTomography | Set of tools for Single Particle Tomography in EMAN2 |
| Paper | 2016Galaz_SingleParticleTomography | Alignment algorithms and CTF correction |
Individual particle electron tomography
| Paper | 2012Zhang_IPET_FETR | FETR, a focused 3D reconstruction algorithm for a single molecule |
Missing-Wedge Correction
| Paper | 20120Zhai_LoTTor | Missing-wedge correction by LoTTor (Low-Tilt Tomographic 3D Reconstruction) |
Books and reviews
| Paper | 2000Baumeister_Review | Review of electron tomography |
| Paper | 2003Koster_Review | Review of electron tomography |
| Paper | 2003Sali_Review | Review of electron tomography |
| Paper | 2004Henderson_Review | Review of electron microscopy |
| Paper | 2005Lucic_Review | Review of electron tomography |
| Paper | 2006Fernandez_Review | Review of electron microscopy |
| Book | 2006Frank_TomoBook | Electron Tomography |
| Book | 2007McIntosh_Book | Cellular Electron Microscopy |
| Paper | 2007Sorzano_Review | Review of the image processing steps |
| Paper | 2008Fanelli_ImageFormation | Review on the image formation model from the electron waves and open inverse-problems |
| Paper | 2008Fernandez_HPCReview | High performance computing in electron cryomicroscopy |
| Paper | 2008Jonic_Review | Comparison between electron tomography and single particles |
| Paper | 2012Kudryashev_Review | Review of subtomogram averaging |
| Paper | 2013Briggs_Review | Review of subtomogram averaging |
| Paper | 2016Beck_Review | Review of molecular sociology |
| Paper | 2017Galaz_Review | Review of single particle tomography |
| Paper | 2017Plitzko_Review | Review of electron tomography, FRET and FIB milling |
| Paper | 2019Schur_Review | Review of electron tomography and subtomogram averaging |
Software
| Paper | 1996Kremer_IMOD | IMOD |
| Paper | 1996Chen_Priism/IVE | Priism/IVE |
| Paper | 1996Frank_Spider | Spider |
| Paper | 2004Sorzano_Xmipp | Xmipp |
| Paper | 2005Nickell_TOM | TOM Toolbox |
| Paper | 2007Messaoudi_TomoJ | TomoJ |
| Paper | 2008Heymann_BsoftTomo | Bsoft |
| Paper | 2015Ding_CaltechTomography | Caltech tomography database |
| Paper | 2015Noble_AppionProtomo | Batch fiducial-less tilt-series alignment in Appion using Protomo |
| Paper | 2015vanAarle_Astra | ASTRA Toolbox |
| Paper | 2017Han_AuTom | Software platform for Electron Tomography |
| Paper | 2017Wan_Simulator | Electron Tomography Simulator |
2D Crystals
2D Preprocessing
| Paper | 1982Saxton_Averaging | Radial Correlation Function |
| Paper | 1984Saxton_Distortions | 3D Reconstruction of distorted crystals |
| Paper | 1986Henderson_Processing | General 2D processing |
| Paper | 2000He_PhaseAlignment | Phase consistency and Alignment |
| Paper | 2006Gil_Unbending | Crystal unbending |
Classification
| Paper | 1988Frank_Classification | MSA and classification in electron crystallography |
| Paper | 1996Fernandez_SOM | Classification based on self organizing maps |
| Paper | 1998Sherman_MSA | Classification based on MSA |
3D Reconstruction
| Paper | 1985Wang_Solvent | Solvent flattening |
| Paper | 1990Henderson_Processing | General 3D processing |
| Paper | 2004Marabini_ART | Algebraic Reconstruction Technique with blobs for crystals (Xmipp) |
| Paper | 2018Biyani_Badlu | Image processing for badly ordered crystals |
Books and reviews
| Paper | 1998Walz_Review | Review of 2D crystallography |
| Paper | 1999Glaeser_Review | Review of 2D crystallography |
| Paper | 2001Ellis_Review | Review of 2D crystallography |
| Paper | 2001Glaeser_Review | Review of 2D crystallography |
| Paper | 2004Henderson_Review | Review of electron microscopy |
| Paper | 2006Fernandez_Review | Review of single particles, electron tomography and crystallography |
| Paper | 2007Sorzano_Review | Review of the image processing steps |
Software
| Paper | 1996Crowther_MRC | MRC |
| Paper | 2004Sorzano_Xmipp | Xmipp |
| Paper | 2007Gipson_2dx | 2dx |
| Paper | 2007Heymann_Bsoft | Bsoft |
| Paper | 2007Philippsen_IPLT | IPLT |
3D Crystals - MicroED
Sample Preparation
| Paper | 2016Shi_Preparation | Sample Preparation |
Data Collection
| Paper | 2014Nannenga_CR | Continuous rotation |
Data Processing
| Paper | 2011Wisedchaisri_PhaseExtension | Fragment-based phase extension |
| Paper | 2015Hattne_Processing | Data Processing |
| Paper | 2016Hattne_Correction | Image correction |
Software
| Paper | 2014Iadanza_Processing | Data Processing of still diffraction data |
Books and Reviews
| Paper | 2014Nannenga_Review | Review of MicroED |
| Paper | 2016Liu_Review | Review of MicroED |
| Paper | 2016Rodriguez_Review | Review of MicroED |
Helical particles
Filament corrections
| Paper | 1986Egelman_Curved | Algorithm for correcting curved filaments |
| Paper | 1988Bluemke_Pitch | Algorithm for correcting filaments with different helical pitches |
| Paper | 2006Wang_Pitch | Algorithm for correcting filaments with different helical pitches |
| Paper | 2016Yang_Flexible | Algorithm for correcting filaments with flexible subunits |
| Paper | 2019Ohashi_SoftBody | Algorithm for correcting filaments with flexible helices |
Reconstruction
| Paper | 1952Cochran_Fourier | Fourier Bessel transform of filamentous structures |
| Paper | 1958Klug_Fourier | Fourier Bessel decomposition of the projection images |
| Paper | 1970DeRosier_Rec | Image processing steps towards 3D reconstruction |
| Paper | 1988Stewart_Rec | Image processing steps towards 3D reconstruction |
| Paper | 1992Morgan_Rec | Image processing steps towards 3D reconstruction |
| Paper | 2005Wang_Iterative | Iterative Fourier-Bessel algorithm |
| Paper | 2007Egelman_Iterative | Iterative real-space algorithm |
| Paper | 2010Egelman_Pitfalls | Pitfalls in helical reconstruction |
| Paper | 2013Desfosses_Spring | Helical processing with Spring |
| Paper | 2015Zhang_seam | Workflow for the detection of the lattice seam |
| Paper | 2016Rohou_Frealix | Helical processing with Frealix |
| Paper | 2017_He | Helical processing with Relion |
| Paper | 2019_Pothula | 3D Classification through 2D analysis |
Validation
| Paper | 2014Egelman_ambiguity | How to detect incorrect models |
Books and reviews
| Paper | 1970DeRosier_Rec | Image processing steps towards 3D reconstruction |
| Paper | 1992Morgan_Rec | Image processing steps towards 3D reconstruction |
| Paper | 2004Henderson_Review | Review of electron microscopy |
| Paper | 2015Sachse_Review | Review of the image processing steps in helical particles |
Software
| Paper | 1996Carragher_Phoelix | Phoelix |
| Paper | 1996Crowther_MRC | MRC |
| Paper | 1996Owen_Brandeis | Brandeis |
Icosahedral particles
Reconstruction
| Paper | 1970Crowther_Rec | Reconstruction of icosahedral viruses in Fourier space |
| Paper | 1971Crowther_Rec | Reconstruction of icosahedral viruses in Fourier space |
| Paper | 1996Fuller_Rec | Reconstruction of icosahedral viruses in Fourier space |
| Paper | 1997Thuman_Rec | Reconstruction of icosahedral viruses in Fourier space |
| Paper | 2019Goetschius_Asymmetric | Approaches to reconstruct asymmetric features in viruses |
Classification
| Paper | 2005Scheres_Virus | Classification of virus capsids in real space |
Books and reviews
| Paper | 1999Baker_Review | Review of reconstruction of icosahedral viruses |
| Paper | 1999Conway_Review | Review of reconstruction of icosahedral viruses |
| Paper | 2000Thuman_Review | Review of reconstruction of icosahedral viruses |
| Paper | 2003Lee_Review | Review of reconstruction of icosahedral viruses |
| Paper | 2003Navaza_Review | Review of reconstruction of icosahedral viruses |
| Paper | 2006Grunewald_Review | Review of reconstruction of icosahedral viruses |
Software
| Paper | 1996Baker_EMPFT | EMPFT |
| Paper | 1996Crowther_MRC | MRC |
| Paper | 1996Frank_Spider | Spider |
| Paper | 1996VanHeel_Imagic | Imagic |
| Paper | 2004Sorzano_Xmipp | Xmipp |
| Paper | 2013DeLaRosa_Xmipp30 | Xmipp 3.0 |
| Paper | 2013Morin_Sliz SBGrid | SBGrid presentation for eLife |
Databases
| Paper | 2003Boutselakis_EMSD | EMSD database |
| Paper | 2005Heymann_Conventions | Conventions for software interoperability |
| Paper | 2005Heymann_Conventions | Conventions for software interoperability |
| Paper | 2011Kim_CDDB | Conformational Dynamics Data Bank |
| Paper | 2011Lawson_EMDB | Electron Microscopy Data Bank |
| Paper | 2013Ison_EDAM | EDAM, an ontology of bioinformatics operations |
| Paper | 2016Iudin_EMPIAR | EMPIAR raw data database |
| Paper | 2016Patwhardan_EMDB | EMDB, PDB, ... |
| Paper | 2017Gore_Validation | Validations of PDB submissions |
| Paper | 2017Patwhardan_Trends | Trends at EMDB |
| Paper | 2017Shao_PDBQuality | Quality metrics in PDB |
| Paper | 2018Tawari_search | Search of 3D structures in a database using 2D experimental images |
| Paper | 2018wwwPDB_PDB | Review of PDB advances |
| Blog | http://www.mybiosoftware.com | Huge list of bioinformatics programs (many of them structural bioinformatics) |
Relationship to other structural information sources
| Paper | 2000Engel_AFM | Review of Atomic Force Microscopy |
| Paper | 2001Dimmeler_AFM | Constraints from Atomic Force Microscopy |
| Paper | 2003Mobus_EnergyLoss | Chemical mapping by energy loss electron tomography |
| Paper | 2004Leapman_EnergyLoss | Chemical mapping by energy loss electron tomography |
| Paper | 2004Leapman_Review | Review on correlative microscopy |
| Paper | 2005Boudier_EFTETJ | Software for Chemical mapping by energy loss electron tomography |
| Paper | 2005Vestergaard_SAXS | Example of comparison of 3DEM and Small-angle X-ray scattering |
| Paper | 2007Hamada_SAXS | Constraints from Small-angle X-ray scattering |
| Paper | 2013Xu_FRET | EM+FRET |
| Paper | 2017Kim_SAXS | Compatibility of EM experimental images and SAXS curves |
| Paper | 2018Ando_Correlative | Review of correlative microscopy techniques |
| Paper | 2018Sieben_Multicolor | Correlative microscopy with superresolution optical images |
| Paper | 2019Huber_EDXS_HAADF | Combined reconstruction using EDXS and HAADF data |
| Paper | 2019Jimenez_SAXS | Selection of EM initial volumes by SAXS curves |
X-ray tomography
| Paper | 2012Oton_ImageFormation | Image formation model in X-ray cell microscopy |
Mathematical tools necessary
People developing methods
Please, add yourself to this list (due to privacy reasons, please, do not add anyone else to the list without his/her explicit consent). Sort by first name alphabetical order.
Carlos Oscar S. Sorzano: CSIC, Madrid, Spain
Cédric Messaoudi: Institute Curie, Paris, France
Javier Vargas:: 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