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This web page is intended to be an extensive repository of three-dimensional electron microscopy (3DEM) methods. The advantages of having such a repository are
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Electron microscopy images
Online courses
CALTECH: http://cryo-em-course.caltech.edu/
MRC: ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/EM-course/
CNB-CSIC: http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/MadridJan2014EM
Image formation
| Paper | 1971Erickson_CTF | CTF model |
| Paper | 1971Glaeser_Damage | Radiation damage |
| Chapter | 1971Hanszen_CTF | Image formation model |
| Paper | 1971Thon_Model | CTF model |
| Paper | 1975Unwin_Imaging | Radiation dose |
| Paper | 1977Wade_Model | CTF model |
| Paper | 1978Wade_Model | CTF model |
| Paper | 1979Hayward_Radiation | Radiation damage |
| Paper | 1984Cohen_Validity | Validity of the CTF model at high frequencies |
| Paper | 1988Toyoshima_Model | Amplitud constrast |
| Paper | 1992Wade_Model | CTF model |
| Paper | 1993Toyoshima_Model | Amplitud constrast |
| Paper | 2002DeCarlo_Damage | Radiation damage in cryonegative staining |
| Paper | 2004Egerton_Damage | Radiation damage |
| Paper | 2004Sorzano_Normalization | Background noise is Gaussian |
| Paper | 2008Fanelli_ImageFormation | Review on the image formation model from the electron waves and open inverse-problems |
| Paper | 2009Baxter_NoiseCharacterization | Characterization of the different noise sources in cryo-EM |
| Paper | 2010Baker_Damage | Radiation damage dependence on resolution |
| Paper | 2010Bammes_Damage | Radiation damage dependence on temperature |
| Paper | 2010Gomez_Multislice | Simulation of the multi slice model |
| Paper | 2010Zewail_FourDimensional | Review on the use of ultrafast EM |
| Paper | 2011Bammes_CCD | Performance of CCD cameras |
| Paper | 2011Glaeser_Coma | Image formation model including coma |
| Paper | 2011Milazzo_DirectDetectors | Evaluation of Direct Detectors |
| Paper | 2011Rullgard_ImageSimulation | Accurate simulation of EM images |
| Paper | 2011Zhang LimitingFactors | Limiting factor for atomic resolution in EM |
| Paper | 2012Bammes_DirectDetection | Performance of Direct detectors |
| Paper | 2012Campbell_MotionCorrection | Beam induced motion correction and direct detectors |
| Paper | 2012Shang_HydrationLayer | Simulation of PDB volumes explicitly considering the hydration layer |
| Paper | 2013Egerton_RadiationDamage | Review of TEM radiation damage and experimental ways of reducing it |
| Paper | 2013Bai_ElectronCounting | Electron counting and beam induced motion correction |
| Paper | 2013Li_ElectronCounting | Electron counting and beam induced motion correction |
| Paper | 2013Shigematsu H_Noisemodels | Noise models and cryo-EM drift correction with a direct-electron camera |
| Paper | 2013Li X K2 noisemodels | Influence of electron dose rate on electron counting images recorded with the K2 camera |
| Paper | 2013Vulovic_CTFApproximations | When to use the different approximations performed so that a projection with linear CTF is valid |
| Thesis | 2013Vulovic_ImageFormation | Ph.D. Thesis on the image formation in cryo-EM |
| Paper | 2014Danev_PhasePlate | Volta potential phase plate |
| Paper | 2015Chiu_K2 | Characterization of K2 |
| Paper | 2015Hawkes_AberrationCorrection | Historical account of the development of lens corrections |
| Paper | 2015Koeck_Quadratic | Limitations of the linear approximation and use of the quadratic terms |
| Paper | 2015Kuijper_FEI | Description of the FEI Falcons |
| Paper | 2015Lobato_MULTEM | Simulation of multislice diffraction |
| Paper | 2015McMullan_AmorphousIce | Beam induced movement is caused by Brownian motion |
| Paper | 2016Koeck_ADF | Simulations of Annular Dark Field TEM |
Collection geometry
| Chapter | 1980Hoppe_Wedge | Missing wedge |
| Paper | 1987Radermacher_RCT | Random Conical Tilt and Single axis tilt |
| Paper | 1988Radermacher_RCT | Random Conical Tilt and Single axis tilt |
| Paper | 1995Penczek_Dual | Dual axis tomography |
| Paper | 1997Mastronarde_Dual | Dual axis tomography |
| Paper | 2003Ludtke_FocusPairs | Focus pairs for single particles |
| Paper | 2005Lanzavecchia_Conical | Conical tomography |
| Paper | 2005Zampighi_Conical | Conical tomography |
| Paper | 2006Leschziner_OT | Orthogonal Tilt |
| Paper | 2006Messaoudi_Multiple | Multiple axis tomography |
| Paper | 2012Kudryashev_FocusPairs | Focus pairs tomography |
| Paper | 2014Hovden_TiltFocus | Combining tilt series with focus series |
| Paper | 2015Sorzano_RandomConicalTilt | General formulation of Random Conical Tilt |
Sample preparation
| Paper | 1982Dubochet_Sample | Vitreous ice |
| Paper | 1986Lepault_Sample | Fast freezing |
| Paper | 1995Dubochet_Sample | High-pressure freezing |
| Paper | 1995VanMarle_Sample | Sample damages in resin |
| Paper | 1998Adrian_Sample | Cryo negative staining |
| Paper | 2002DeCarlo_Damage | Radiation damage in cryonegative staining |
| Paper | 2002Hsieh_Sample | Cryofixation |
| Paper | 2004AlAmoudi_Sample | CEMOVIS |
| Paper | 2008Studer_Sample | Review on high pressure freezing |
| Paper | 2009Pierson_Sample | Review on sample preparation for electron tomography |
| Paper | 2014Russo_GoldGrids | Gold grids for single particles |
| Paper | 2015Cabra_Sample | Review on sample preparation for single particles with videos |
| Paper | 2016Passmore_Review | Tutorial chapter on sample preparation |
| Paper | 2016Razinkov_Vitrification | New vitrification method |
| Paper | 2016Thompson_Sample | Review on sample preparation for EM |
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 |
Single particles
Automatic particle picking
| Paper | 1982VanHeel_Detection | Detection of particles in micrographs |
| Paper | 2001Nicholson_Review | Review on automatic particle picking |
| Paper | 2001Zhu_Filaments | Automatic identification of filaments in micrographs |
| Paper | 2004Sigworth_Detection | Classical detection theory and the cryo-EM particle selection problem |
| Paper | 2004Volkmann_ParticlePicking | An approach to automated particle picking from electron micrographs based on reduced representation templates |
| Paper | 2004Wong_ParticlePicking | Model-based particle picking for cryo-electron microscopy |
| Paper | 2004Zhu_Review | Review on automatic particle picking |
| Paper | 2007Chen_Signature | Automatic particle picking program: Signature |
| Paper | 2007Woolford_SwarmPS | Automatic particle picking with several criteria, implemented in EMAN Boxer |
| Paper | 2009Sorzano_MachineLearning | Automatic particle picking based on machine learning of rotational invariants |
| Paper | 2011Arbelaez_Comparison | Evaluation of the performance of software for automated particle-boxing |
| Paper | 2013Abrishami_MachineLearning | A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs |
| Paper | 2013Hauer_2013 | Automatic tilt pair detection in Random Conical Tilt |
| Paper | 2013Shatsky_ParticlePicking | Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs |
| Paper | 2013Vargas_ParticleQuality | Automatic determination of particle quality |
| Paper | 2014Langlois_ParticlePicking | Automatic particle picking |
2D Preprocessing
| Paper | 2003Rosenthal_DPR | Contrast enhancement through DPR |
| Paper | 2004Sorzano_Normalization | Normalization procedures and their statistical properties. |
| Paper | 2006Sorzano_Denoising | Strong denoising in wavelet space |
| Conference | 2009Sorzano_Downsampling | Differences between the different downsampling schemes |
| Paper | 2012Brilot_Movies | Alignment of beam induced motion in direct detectors |
| Paper | 2012Campbell_Movies | Alignment of beam induced motion in direct detectors |
| Paper | 2012Zhao_Denoising | Denoising using an invariant Fourier-Bessel eigenspace |
| Paper | 2013Norousi_Screening | Screening particles to identify outliers |
| Paper | 2013Bai_ElectronCounting | Electron counting and beam induced motion correction |
| Paper | 2013Li_ElectronCounting | Electron counting and beam induced motion correction |
| Paper | 2013Shigematsu_Movies | Drift correction for movies considering dark field |
| Paper | 2013Vargas_ParticleQuality | Automatic determination of particle quality |
| Paper | 2014Scheres_Movies | Beam induced motion correction |
| Paper | 2015Abrishami_Movies | Alignment of direct detection device micrographs |
| Paper | 2015Grant_Anisotropic | Automatic estimation and correction of anisotropic magnification |
| Paper | 2015Grant_OptimalExposure | Filter movies according to the radiation damage |
| Paper | 2015Rubinstein_Alignment | Frame alignment at the level of particle |
| Paper | 2015Spear_DoseCompensation | Effect of dose compensation on resolution |
| Paper | 2015Zhao_AnisotropicMagnification | Correction of anisotropic magnification |
| Paper | 2016Jensen_RemovalVesicles | Removal of vesicles in membrane proteins |
2D Alignment
| Paper | 1981Frank_Averaging | 2D averaging and phase residual |
| Paper | 1982Saxton_Averaging | 2D averaging using correlation |
| Paper | 1998Sigworth_ML2D | Maximum likelihood alignment in 2D |
| Paper | 2003Cong_FRM2D | Fast Rotational Matching in 2D |
| Paper | 2005Cong_FRM2D | Fast Rotational Matching in 2D introduced in a 3D Alignment algorithm |
| Paper | 2005Scheres_ML2D | Multireference alignment and classification in 2D |
| Paper | 2010Sorzano_CL2D | Multireference alignment and classification in 2D |
2D Classification and clustering
| Paper | 1981VanHeel_MSA | Multivariate Statistical Analysis |
| Paper | 1984VanHeel_MSA | Multivariate Statistical Analysis |
| Paper | 2005Scheres_ML2D | Multireference alignment and classification in 2D |
| Paper | 2010Sorzano_CL2D | Multireference alignment and classification in 2D |
| Paper | 2011Singer_DiffusionMaps | Classification in 2D based on graph analysis of the projections |
| Paper | 2012Yang_ISAC | Iterative Stable Alignment and clustering |
| Paper | 2014Sorzano_Outlier | Outlier detection in 2D classifications. |
| Paper | 2014Zhao_Aspire | Fast classification based on rotational invariants and vector diffusion maps |
| Paper | 2015Huang_Robust | Robust w-estimators of 2D classes |
3D Alignment
| Paper | 1980Kam_AutoCorrelation | Reconstruction without angular assignment from autocorrelation function (reference free) |
| Paper | 1986Goncharov_CommonLines | Angular assignment using common lines (reference free) |
| Paper | 1987VanHeel_CommonLines | Angular assignment using common lines (reference free) |
| Paper | 1988Provencher_Simultaneous | Simultaneaous alignment and reconstruction |
| Paper | 1988Radermacher_RCT | Random Conical Tilt and Single axis tilt |
| Paper | 1988Vogel_Simultaneous | Simultaneaous alignment and reconstruction |
| Paper | 1990Gelfand_Moments | Angular assignment using moments (reference free) |
| Paper | 1990Goncharov_Moments | Angular assignment using moments (reference free) |
| Paper | 1990Harauz_Quaternions | Use of quaternions to represent rotations |
| Paper | 1994Penczek_Real | Angular assignment using projection matching in real space |
| Paper | 1994Radermacher_Radon | Angular assignment in Radon space |
| Paper | 1996Penczek_CommonLines | Angular assignment using common lines (reference free) |
| Paper | 2003Rosenthal_DPR | Angular assignment using DPR |
| Paper | 2004Sorzano_Wavelet | Angular assignment in the wavelet space. |
| Paper | 2005Jonic_Splines | Angular assignment in Fourier space using spline interpolation. |
| Paper | 2005Yang_Simultaneous | Simultaneaous alignment and reconstruction |
| Paper | 2006Ogura_SimulatedAnnealing | Angular asignment by simulated annealing |
| Paper | 2007Grigorieff_Continuous | Continuous angular assignment in Fourier space |
| Paper | 2010Jaitly_Bayesian | Angular assignment by a Bayesian method and annealing |
| Paper | 2010Sanz_Random | Random model method |
| Paper | 2010Singer_Voting | Detecting consistent common lines by voting (reference free) |
| Paper | 2011Singer_SDP | Angular assignment by semidefinite programming and eigenvectors (reference free) |
| Paper | 2012Giannakis_Scattering | Construction of an initial volume, reference free, by graph analysis of the projections |
| Paper | 2012Shkolnisky_Sync | Angular assignment by synchronization of rotations (reference free) |
| Paper | 2013Elmlund H_PRIME | PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy |
| Paper | 2013Wang_LUD | Angular assignment by least unsquared deviations (reference free) |
| Paper | 2014Vargas_RANSAC | Initial model using RANSAC (reference free) |
| Paper | 2015Joubert_Pseudoatoms | Initial model based on pseudo-atoms |
| Paper | 2015Singer_Kam | Reconstruction without angular assignment from autocorrelation function (reference free) |
| Paper | 2015Sorzano_Significant | Statistical approach to the initial volume estimation (reconstruct significant) |
| Conference | 2016Michels_Heterogeneous | Initial volume in the presence of heterogeneity |
3D Reconstruction
| Paper | 1972Gilbert_SIRT | Simultaneous Iterative Reconstruction Technique (SIRT) |
| Paper | 1973Herman_ART | Algebraic Reconstruction Technique (ART) |
| Paper | 1984Andersen_SART | Simultaneous Algebraic Reconstruction Technique (SART) |
| Paper | 1986Harauz_FBP | Exact filters for Filtered Back Projection |
| Chapter | 1992Radermacher_WBP | Exact filters for Weighted Back Projection |
| Paper | 1997Zhu_RecCTF | 3D Reconstruction (SIRT like) and simultaneous CTF correction |
| Paper | 1998Boisset_Uneven | Artifacts in SIRT and WBP under uneven angular distributions |
| Paper | 1998Marabini_ART | Algebraic Reconstruction Technique with blobs (Xmipp) |
| Paper | 2001Sorzano_Uneven | Free parameter selection under uneven angular distributions |
| Paper | 2005Sorzano_Parameters | Free parameter selection for optimizing multiple tasks |
| Paper | 2008Sorzano_Constraints | Mass, surface, positivity and symmetry constraints for real-space algorithms |
| Paper | 2009Bilbao_ParallelART | Efficient parallelization of ART |
| Paper | 2011Li_GradientFlow | Regularized 3D Reconstruction by Gradient Flow |
| Paper | 2011Vonesch_Wavelets | Fast wavelet-based 3D reconstruction |
| Paper | 2012Gopinath_ShapeRegularization | Regularized 3D Reconstruction by Shape information |
| Paper | 2012Kucukelbir_adaptiveBasis | 3D reconstruction in an adaptive basis promoting sparsity |
| Paper | 2012Sindelar_NoiseReduction | Optimal noise reduction in 3D reconstructions |
| Paper | 2013Elmlund H_PRIME | PRIME: Probabilistic Initial 3D Model Generation for Single-Particle Cryo-Electron Microscopy |
| Paper | 2013Lyumkis D_FREALIGN | Likelihood-based classification of cryo-EM images using FREALIGN. |
| Paper | 2013Lyumkis_Optimod | Construction of initial volumes with Optimod |
| Paper | 2013Wang FIRM | Fast 3D reconstruction in Fourier domain |
| Paper | 2014Kunz_SART_OS | Simultaneous ART with OS |
| Paper | 2015Abrishami_Fourier | 3D Reconstruction in Fourier space |
| Paper | 2015Dvornek_SubspaceEM | Fast Maximum a posteriori |
| Paper | 2015Moriya_Bayesian | Bayesian approach to suppress limited angular artifacts |
| Paper | 2015Xu_GeometricFlow | Multi-scale geometric flow |
| Arxiv | 2016Ye_Cohomology | Cohomology properties of 3D reconstruction |
3D Heterogeneity
| Paper | 2004White_Size | Heterogeneity classification of differently sized images |
| Paper | 2006Penczek_Bootstrap | 3D heterogeneity through bootstrap |
| Paper | 2007Leschziner_Review | Review of 3D heterogeneity handling algorithms |
| Paper | 2007Scheres_ML3D | Maximum Likelihood alignment and classification in 3D |
| Paper | 2009Spahn_Bootstrap | 3D heterogeneity through bootstrap |
| Paper | 2010Shatsky_MultiVariate | Multivariate Statistical Analysis |
| Paper | 2012Scheres_Bayesian | A Bayesian view on cryo-EM structure determination |
| Paper | 2013Wang_MLVariance | Maximum Likelihood estimate of the map variance |
| Paper | 2014Jin_NMA | Continuous heterogeneity through Normal Mode Analysis |
| Paper | 2014Dashti_Brownian | Continuous heterogeneity through Brownian trajectories |
| Paper | 2014Chen_Migration | Particle migration analysis in 3D classification |
| Paper | 2015Anden_Covariance | 3D Covariance matrix estimation for heterogeneity |
| Paper | 2015Bai_Focused | Focused classification |
| Paper | 2015Katsevich_Covariance | 3D Covariance matrix estimation for heterogeneity |
| Paper | 2015Klaholz_MRA | Multivariate Statistical Analysis of Jackknife and Bootstrapping on random subsets |
| Paper | 2015Liao_Covariance | Estimation of the 3D covariance from 2D projections |
| Paper | 2015Tagare_Direct | Direct reconstruction of PCA components |
| Paper | 2016Gong_Mechanical | Mechanical model for macromolecules |
| Paper | 2016Rawson_Movement | Movement and flexibility |
| Paper | 2016Sorzano_StructMap | Sorting a discrete set of conformational states |
| Paper | 2016Sorzano_Strain | Calculate local stretches, strains and rotations from two conformational states |
Validation
| Paper | 2008Stagg_TestBed | Effect of voltage, dosis, number of particles and Euler jumps on resolution |
| Paper | 2011Henderson | Tilt Validation |
| Paper | 2011Read | Validation of PDBs |
| Paper | 2012Henderson | EM Map Validation |
| Paper | 2013Cossio_Bayesian | EM Map Validation in a probabilistic setting |
| Paper | 2013Chen_NoiseSubstitution | Noise substitution at high resolution for measuring overfitting |
| Paper | 2014Russo_StatisticalSignificance | EM Map Validation through the statistical significance of the tilt-pair angular assignment |
| Paper | 2014Stagg_Reslog | EM Map Validation through the resolution evolution with the number of particles |
| Paper | 2014Wasilewski_Tilt | Web implementation of the tilt pair validation |
| Paper | 2015Heymann_Alignability | EM Map Validation through the resolution of reconstructions from particles and noise |
| Paper | 2015Oliveira_FreqLimited | Comparison of gold standard and frequency limited optimization |
| Paper | 2015Wriggers_Secondary | Validation by secondary structure |
| Paper | 2016Rosenthal_Review | Review of validation methods |
| Paper | 2016Vargas_Alignability | Validation by studying the tendency of an angular assignment to cluster in the projection space |
Resolution
| Paper | 1986Harauz_FBP | Fourier Shell Correlation |
| Paper | 1987Unser_SSNR | 2D Spectral Signal to Noise Ratio |
| Paper | 2002Penczek_SSNR | 3D Spectral Signal to Noise Ratio for Fourier based algorithms |
| Paper | 2003Rosenthal_DPR | Review of the FSC and establishment of a new threshold |
| Paper | 2005Unser_SSNR | 3D Spectral Signal to Noise Ratio for any kind of algorithms |
| Paper | 2005VanHeel_FSC | Establishment of a new threshold for FSC |
| Paper | 2007Sousa_AbInitio | Resolution measurement on neighbour Fourier voxels |
| Paper | 2014Kucukelbir_Local | Quantifying the local resolution of cryo-EM density maps |
| Paper | 2016Pintilie_Probabilistic | Probabilistic models and resolution |
Sharpening of high resolution information
| Paper | 2003Rosenthal_DPR | Contrast restoration and map sharpening |
| Paper | 2008Fernandez_Bfactor | Bfactor determination and restoration |
| Paper | 2013Fiddy_SaxtonAlgorithm | Phase retrieval or extension |
| Paper | 2014Kishchenko_SphericalDeconvolution | Spherical deconvolution |
| Paper | 2015Spiegel_VISDEM | Visualization improvement by the use of pseudoatomic profiles |
| Paper | 2016Jonic_Pseudoatoms | Approximation with pseudoatoms |
| Paper | 2016Jonic_Denoising | Denoising and high-frequency boosting by pseudoatom approximation |
CTF estimation and restoration
| Paper | 1982Schiske_Correction | CTF correction for tilted objects |
| Paper | 1988Toyoshima_Model | CTF estimation |
| Paper | 1995Frank_Wiener | CTF correction using Wiener filter |
| Paper | 1996Skoglund_MaxEnt | CTF correction with Maximum Entropy |
| Paper | 1996Zhou_Model | CTF model and user interface for manual fitting |
| Paper | 1997Fernandez_AR | PSD estimation using periodogram averaging and AR models |
| Paper | 1997Penczek_Wiener | CTF correction using Wiener filter |
| Paper | 1997Stark_Deconvolution | CTF correction using deconvolution |
| Paper | 1997Zhu_RecCTF | CTF correction and reconstruction |
| Paper | 2000DeRosier_EwaldCorrection | CTF correction considering the Ewald sphere |
| Paper | 2000Jensen_TiltedCorrection | CTF correction considering tilt in backprojection |
| Paper | 2001Saad_CTFEstimate | CTF estimation |
| Paper | 2003Huang_CTFEstimate | CTF estimation |
| Paper | 2003Mindell_CTFTILT | CTF estimation for tilted micrographs |
| Paper | 2003Sander_MSA | CTF estimation through MSA classification of PSDs |
| Paper | 2003Velazquez_ARMA | PSD and CTF estimation using ARMA models |
| Paper | 2004Sorzano_IDR | CTF restoration and reconstruction with Iterative Data Refinement |
| Conference | 2004Wan_CTF | Spatially variant CTF |
| Paper | 2004Zubelli_Chahine | CTF restoration and reconstruction with Chahine's multiplicative method |
| Conference | 2005Dubowy_SpaceVariant | CTF correction when this is space variant |
| Paper | 2005Mallick_ACE | CTF estimation |
| Paper | 2006Wolf_Ewald | CTF correction considering Ewald sphere |
| Paper | 2007Jonic_EnhancedPSD | PSD enhancement for better identification of Thon rings; Vitreous ice diffracts in Thon rings |
| Paper | 2007Philippsen_Model | CTF Model for tilted specimens |
| Paper | 2007Sorzano_CTF | CTF estimation using enhanced PSDs |
| Paper | 2009Sorzano_Sensitivity | Error sensitivity of the CTF models, non-uniqueness of the CTF parameters |
| Paper | 2010Jiang2010_CTFCorrection | Amplitude correction method |
| Paper | 2010Kasantsev_CTFCorrection | Mathematical foundations of Kornberg and Jensen method |
| Paper | 2010Leong_CTFCorrection | Correction for spatially variant CTF |
| Paper | 2011Glaeser_Coma | The effect of coma at high-resolution |
| Paper | 2011Mariani_Tilted | CTF simulation and correction of tilted specimens |
| Paper | 2011Sindelar_Wiener | CTF correction using a modified version of Wiener filter |
| Paper | 2011Voortman_Tilted | CTF correction for tilted specimen |
| Paper | 2012Voortman_VaryingCTF | Correcting a spatially varying CTF |
| Paper | 2013Vargas_FastDef | Fast defocus |
| Paper | 2015Rohou_CTFFind4 | CTF Find 4 |
| Paper | 2015Sheth_CTFquality | Visualization and quality assessment of CTF |
| Paper | 2016Zhang_GCTF | gCTF |
Segmentation
| Paper | 2006Baker_segmentation | Segmentation of molecular subunits |
Fitting and docking
| Paper | 1999Volkmann_Fitting | Fitting in real space |
| Paper | 2001Baker_Review | Review of protein structure prediction |
| Paper | 2001Jones_Review | Review of protein structure prediction |
| Paper | 2003Kovacs_FRM3D | Fast Rotational Alignment of two EM maps |
| Paper | 2004Tama_NMA1 | Flexible fitting with Normal Modes (I) |
| Paper | 2004Tama_NMA2 | Flexible fitting with Normal Modes (II) |
| Paper | 2005Velazquez_Superfamilies | Recognition of the superfamily folding in medium-high resolution volumes |
| Paper | 2007DeVries_Haddock | Docking with Haddock 2.0 |
| Paper | 2007Kleywegt_QualityControl | Quality control and validation of fitting |
| Paper | 2012Biswas_Secondary | Secondary structure determination in EM volumes |
| Paper | 2012Velazquez_Constraints | Multicomponent fitting by using constraints from other information sources |
| Paper | 2013Chapman MS_Atomicmodeling | Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters |
| Paper | 2013Esquivel_Modelling | Review on modelling (secondary structure, fitting, ...) |
| Paper | 2013Lopez_Imodfit | Fitting based on vibrational analysis |
| Paper | 2013Nogales_3DEMLoupe | Normal Mode Analysis of reconstructed volumes |
| Paper | 2014AlNasr_Secondary | Identification of secondary structure elements in EM volumes |
| Paper | 2014Politis_MassSpect | Integration of mass spectroscopy information |
| Paper | 2014Rey_MassSpect | Integration of mass spectroscopy information |
| Paper | 2014Villa_Review | Review of atomic fitting into EM volumes |
| Paper | 2015Barad_EMRinger | Validation of hybrid models |
| Paper | 2015Bettadapura_PF2Fit | Fast rigid fitting of PDBs into EM maps |
| Paper | 2015Carrillo_CapsidMaps | Analysis of virus capsids using Google Maps |
| Paper | 2015Schroeder_Hybrid | Review on model building |
| Paper | 2015Tamo_Dynamics | Dynamics in integrative modeling |
| Paper | 2015Sorzano_AtomsToVoxels | Accurate conversion of an atomic model into a voxel density volume |
| Paper | 2016Segura_3Diana | Validation of hybrid models |
Books and reviews
| Book | 1980Herman_Tomography | General book on tomography |
| Book | 1988Kak_Tomography | General book on tomography |
| Paper | 2000Tao_Review | Review of single particles |
| Paper | 2000VanHeel_Review | Review of single particles |
| Paper | 2002Frank_Review | Review of single particles |
| Paper | 2002Schmid_Review | Review of single particles |
| Paper | 2004Henderson_Review | Review of electron microscopy |
| Paper | 2004Subramaniam_Review | Review of single particles |
| Paper | 2005Steven_Review | Review of electron microscopy |
| Paper | 2006Fernandez_Review | Review of electron microscopy |
| Book | 2006Frank_book | Book covering all aspects of electron microscopy of single particles |
| Paper | 2006Sorzano_Review | Review of optimization problems in electron microscopy |
| Paper | 2007Leschziner_Review | Review of 3D heterogeneity handling algorithms |
| Paper | 2007Sorzano_Review | Review of the image processing steps |
| Paper | 2008Fanelli_ImageFormation | Review on the image formation model from the electron waves and open inverse-problems in Electron Tomography |
| Paper | 2008Fernandez_HPCReview | High performance computing in electron cryomicroscopy |
| Paper | 2008Jonic_Review | Comparison between electron tomography and single particles |
| Paper | 2008Mueller_Review | Review of Electron microscopy |
| Paper | 2008Taylor_Review | Review of Electron microscopy |
| Paper | 2010DeRosier_Review | Personal account of how 3DEM developed in the early days |
| Chapter | 2012Sorzano_Review | Review of single particle analysis using Xmipp |
| Chapter | 2012Devaux_Protocol | Protocols for performing single particle analysis |
| Paper | 2014Bai_Review | Recent advances in cryo-EM |
| Paper | 2015Carazo_Review | Review of the reconstruction process |
| Paper | 2015Cheng_Review | A primer to Single Particle Cryo-EM |
| Paper | 2015Cheng_Reviewb | Single Particle Cryo-EM at crystallographic resolution |
| Paper | 2015Elmlund_Review | Recent advances in cryo-EM |
| Paper | 2015Henderson_Review | Recent advances in cryo-EM |
| Paper | 2015Nogales_Review | Recent advances in cryo-EM |
| Paper | 2015Schroeder_Review | Review of advances in the electron microscope |
| Paper | 2015Wu_Review | Review of advances in cryo-EM |
| Paper | 2016Carroni_CryoEM | Review of advances in Cryo-EM |
| Paper | 2016Egelman_CryoEM | Review of advances in Cryo-EM |
| Paper | 2016Eisenstein_CryoEM | News feature on the Method of the Year |
| Paper | 2016Glaeser_HowGood | How good can cryo-EM become? |
| Chapter | 2016Mio_Review | Overview of the process to obtain EM reconstructions |
| 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 |
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 | 2008Scheres_XmippProtocols | Xmipp Protocols |
| Paper | 2008Shaikh_SpiderProtocols | Spider Protocols |
| Paper | 2012Wriggers_SitusConventions | Conventions and workflows in Situs |
| Paper | 2013DeLaRosa_Xmipp30 | Xmipp 3.0 |
| Paper | 2015Cianfrocco_Cloud | Software execution in the cloud |
| Paper | 2015Cheng_MRC2014 | Extensions to MRC file format |
| Paper | 2013DeLaRosa_Scipion | Scipion |
| Paper | 2016Scheres_Relion | Tutorial on the use of Relion |
| Paper | 2016Grigorieff_Frealign | Tutorial on the use of Frealign |
Electron tomography
Image preprocessing
| Paper | 2015Yan_thickness | Determination of thickness, tilt and electron mean free path |
Image alignment
| Paper | 1982Guckenberger_commonOrigin | Determination of a common origin in the micrographs of titl series in three-dimensional electron microscopy |
| Paper | 1992Lawrence_leastSquares | Least squares solution of the alignment problem |
| Paper | 1995Penczek_dual | Dual tilt alignment |
| Paper | 1996Owen_alignmentQuality | Automatic alignment without fiducial markers and evaluation of alignment quality |
| Paper | 1998Grimm_normalization | Discussion of several gray level normalization methods for electron tomography |
| Paper | 2001Brandt_Automatic1 | Automatic alignment without fiducial markers |
| Paper | 2001Brandt_Automatic2 | Automatic alignment with fiducial markers |
| Paper | 2006Winkler_alignment | Marker-free alignment and refinement |
| Paper | 2006Castano_alignment | Alignment with non-perpendicularity |
| Paper | 2007Castano_alignment | Fiducial-less alignment of cryo-sections |
| Paper | 2009Sorzano_alignment | Marker-free alignment and refinement |
| Paper | 2010Cantele_dualAlignment | Alignment of dual series |
CTF estimation and restoration
| Paper | 2003Winkler_CTF | Focus gradient correction in electron tomography |
| Paper | 2006Fernandez_CTF | CTF determination and correction in electron tomography |
| Paper | 2009Zanetti_CTF | CTF determination and correction in electron tomography |
| Paper | 2009Xiong_CTF | CTF determination and correction for low dose tomographic tilt series |
| Paper | 2015Bharat_CTFCorrectedSubtomogramAveraging | Subtomogram averaging with CTF correction using a Bayesian prior |
3D reconstruction
| Paper | 1972Gilbert_SIRT | Simultaneous Iterative Reconstruction Technique (SIRT) |
| Paper | 1973Herman_ART | Algebraic Reconstruction Technique (ART) |
| Paper | 1984Andersen_SART | Simultaneous Algebraic Reconstruction Technique (SART) |
| Paper | 1992Radermacher_WBP | Weighted Backprojection in electron tomography |
| Paper | 1997Marabini_reconstruction | Iterative reconstruction in electron tomography |
| Paper | 2002Fernandez_reconstruction | Iterative reconstruction in electron tomography |
| Paper | 2007Radermacher_WBP | Weighted Backprojection in electron tomography |
| Paper | 2008Fernandez_CARP | Component Averaged Row Projections (CARP) |
| Paper | 2012Herman General Superiorization | Superiorization: an optimization heuristic for medical physics |
| Paper | 2013Goris_SIRT_TV_DART | Combination of SIRT, Total Variation and Discrete ART to reconstruct and segment at the same time |
| Paper | 2013Briegel A_Challenge | The challenge of determining handedness in electron tomography and the use of DNA origami gold nanoparticle helices as molecular standards |
| Paper | 2013Messaoudi_EnergyFiltered | 3D Reconstruction of Energy-Filtered TEM |
| Paper | 2016Deng_ICON | 3D Reconstruction with missing information restoration |
Noise reduction
| Paper | 2001Frangakis_NAD | Noise reduction with Nonlinear Anisotropic Diffusion |
| Paper | 2003Fernandez_AND | Anisotropic nonlinear diffusion for electron tomography |
| Paper | 2003Jiang_Bilateral | Bilateral denoising filter in electron microscopy |
| Paper | 2005Fernandez_AND | Anisotropic nonlinear denoising in electron tomography |
| Paper | 2007Heide_median | Iterative median filtering in electron tomography |
| Paper | 2007Fernandez_autAND | Anisotropic nonlinear diffusion with automated parameter tuning |
| Paper | 2009Fernandez_Beltrami | Nonlinear filtering based on Beltrami flow |
| Paper | 2010Bilbao_MeanShift | Mean Shift Filtering |
| Paper | 2014Kovacik_wedgeArtefacts | Removal of wedge artefacts |
| Paper | 2014Maiorca_beadArtefacts | Removal of gold bead artefacts |
Segmentation
| Paper | 2002Frangakis_Eigenanalysis | Segmentation using eigenvector analysis. |
| Paper | 2002Volkmann_Watershed | Segmentation using watershed transform. |
| Paper | 2003Bajaj_BoundarySegmentation | Segmentation based on fast marching. |
| Paper | 2005Cyrklaff_Thresholding | Segmentation using optimal thresholding. |
| Paper | 2007Lebbink_TemplateMatching | Segmentation using template matching. |
| Paper | 2007Sandberg_OrientationFields | Segmentation using orientation fields. |
| Paper | 2007Sandberg_SegmentationReview | Review on segmentation in electron tomography. |
| Paper | 2008Garduno_FuzzySegmentation | Segmentation using fuzzy set theory principles. |
| Paper | 2009Lebbink_TemplateMatching2 | Segmentation using template matching. |
| Paper | 2012RubbiyaAli_EdgeDetection | Parameter-Free Segmentation of Macromolecular Structures. |
Resolution
| Paper | 2005Cardone_Resolution | Resolution criterion for electron tomography |
| Chapter | 2007Penczek_Resolution | Review of resolution criteria for electron tomography |
| Paper | 2015Diebolder_ConicalFSC | Conical Fourier Shell Correlation |
Subtomogram analysis
| Paper | 2000Bohm_Template | Macromolecule finding by template matching |
| Paper | 2002Frangakis_Template | Macromolecule finding by template matching |
| Paper | 2006Nickell_Review | Review of macromolecule finding by template matching (Visual Proteomics) |
| Paper | 2007Best_Review | Review of Localization of Protein Complexes by Pattern Recognition |
| Paper | 2007Forster_Review | Review of structure determination by subtomogram averaging |
| Paper | 2008Forster_Classification | Classification of subtomograms using constrained correlation |
| Paper | 2008Bartesaghi_Classification | Classification and averaging of subtomograms |
| Paper | 2008Schmid_Averaging | Alignment and averaging of subtomograms |
| Paper | 2010Amat_Averaging | Alignment and averaging of subtomograms exploiting thresholding in Fourier space |
| Paper | 2013Chen_Averaging | Fast alignment of subtomograms using spherical harmonics |
| Paper | 2013Kuybeda_Averaging | Alignment and averaging of subtomograms using the nuclear norm of the cluster |
| Paper | 2013Shatsky_Averaging | Alignment and averaging of subtomograms with constrained cross-correlation |
| Paper | 2014Chen_Autofocus | Subtomogram averaging and classification with special attention to differences |
| Paper | 2014Yu_ReferenceBias | Scoring the reference bias |
| Paper | 2014Voortman_LimitingFactors | Limiting factors of subtomogram averaging |
| Paper | 2015Bharat_CTFCorrectedSubtomogramAveraging | Subtomogram averaging with CTF correction using a Bayesian prior |
| Paper | 2015Yu_ReferenceBias | Scoring the reference bias |
| Paper | 2016Song_MatrixNorm | Matrix norm minimization for tomographic reconstruction and alignment |
Single particle tomography
| Paper | 2012Bartesaghi_Constrained | 3D reconstruction by imposing geometrical constraints |
| Paper | 2015Galaz_SingleParticleTomography | Set of tools for Single Particle Tomography in EMAN2 |
Books and reviews
| Paper | 2000Baumeister_Review | Review of electron tomography |
| Paper | 2003Koster_Review | Review of electron tomography |
| Paper | 2003Sali_Review | Review of electron tomography |
| Paper | 2004Henderson_Review | Review of electron microscopy |
| Paper | 2005Lucic_Review | Review of electron tomography |
| Paper | 2006Fernandez_Review | Review of electron microscopy |
| Book | 2006Frank_TomoBook | Electron Tomography |
| Book | 2007McIntosh_Book | Cellular Electron Microscopy |
| Paper | 2007Sorzano_Review | Review of the image processing steps |
| Paper | 2008Fanelli_ImageFormation | Review on the image formation model from the electron waves and open inverse-problems |
| Paper | 2008Fernandez_HPCReview | High performance computing in electron cryomicroscopy |
| Paper | 2008Jonic_Review | Comparison between electron tomography and single particles |
| Paper | 2012Kudryashev_Review | Review of subtomogram averaging |
Software
| Paper | 1996Kremer_IMOD | IMOD |
| Paper | 1996Chen_Priism/IVE | Priism/IVE |
| Paper | 1996Frank_Spider | Spider |
| Paper | 2004Sorzano_Xmipp | Xmipp |
| Paper | 2005Nickell_TOM | TOM Toolbox |
| Paper | 2007Messaoudi_TomoJ | TomoJ |
| Paper | 2008Heymann_BsoftTomo | Bsoft |
| Paper | 2015Ding_CaltechTomography | Caltech tomography database |
| Paper | 2015Noble_AppionProtomo | Batch fiducial-less tilt-series alignment in Appion using Protomo |
| Paper | 2015vanAarle_Astra | ASTRA Toolbox |
2D Crystals
2D Preprocessing
| Paper | 1986Henderson_Processing | General 2D processing |
| Paper | 2000He_PhaseAlignment | Phase consistency and Alignment |
| Paper | 2006Gil_Unbending | Crystal unbending |
Classification
| Paper | 1988Frank_Classification | MSA and classification in electron crystallography |
| Paper | 1996Fernandez_SOM | Classification based on self organizing maps |
| Paper | 1998Sherman_MSA | Classification based on MSA |
3D Reconstruction
| Paper | 1985Wang_Solvent | Solvent flattening |
| Paper | 1990Henderson_Processing | General 3D processing |
| Paper | 2004Marabini_ART | Algebraic Reconstruction Technique with blobs for crystals (Xmipp) |
Books and reviews
| Paper | 1998Walz_Review | Review of 2D crystallography |
| Paper | 1999Glaeser_Review | Review of 2D crystallography |
| Paper | 2001Ellis_Review | Review of 2D crystallography |
| Paper | 2001Glaeser_Review | Review of 2D crystallography |
| Paper | 2004Henderson_Review | Review of electron microscopy |
| Paper | 2006Fernandez_Review | Review of single particles, electron tomography and crystallography |
| Paper | 2007Sorzano_Review | Review of the image processing steps |
Software
| Paper | 1996Crowther_MRC | MRC |
| Paper | 2004Sorzano_Xmipp | Xmipp |
| Paper | 2007Gipson_2dx | 2dx |
| Paper | 2007Heymann_Bsoft | Bsoft |
| Paper | 2007Philippsen_IPLT | IPLT |
3D Crystals - MicroED
Sample Preparation
| Paper | 2016Shi_Preparation | Sample Preparation |
Data Collection
| Paper | 2014Nannenga_CR | Continuous rotation |
Data Processing
| Paper | 2011Wisedchaisri_PhaseExtension | Fragment-based phase extension |
| Paper | 2015Hattne_Processing | Data Processing |
| Paper | 2016Hattne_Correction | Image correction |
Software
| Paper | 2014Iadanza_Processing | Data Processing of still diffraction data |
Books and Reviews
| Paper | 2014Nannenga_Review | Review of MicroED |
| Paper | 2016Liu_Review | Review of MicroED |
| Paper | 2016Rodriguez_Review | Review of MicroED |
Helical particles
Filament corrections
| Paper | 1986Egelman_Curved | Algorithm for correcting curved filaments |
| Paper | 1988Bluemke_Pitch | Algorithm for correcting filaments with different helical pitches |
| Paper | 2006Wang_Pitch | Algorithm for correcting filaments with different helical pitches |
| Paper | 2016Yang_Flexible | Algorithm for correcting filaments with flexible subunits |
Reconstruction
| Paper | 1952Cochran_Fourier | Fourier Bessel transform of filamentous structures |
| Paper | 1958Klug_Fourier | Fourier Bessel decomposition of the projection images |
| Paper | 1970DeRosier_Rec | Image processing steps towards 3D reconstruction |
| Paper | 1992Morgan_Rec | Image processing steps towards 3D reconstruction |
| Paper | 2005Wang_Iterative | Iterative Fourier-Bessel algorithm |
| Paper | 2007Egelman_Iterative | Iterative real-space algorithm |
| Paper | 2015Zhang_seam | Workflow for the detection of the lattice seam |
Validation
| Paper | 2014Egelman_ambiguity | How to detect incorrect models |
Books and reviews
| Paper | 1970DeRosier_Rec | Image processing steps towards 3D reconstruction |
| Paper | 1992Morgan_Rec | Image processing steps towards 3D reconstruction |
| Paper | 2004Henderson_Review | Review of electron microscopy |
| Paper | 2007Sorzano_Review | Review of the image processing steps |
Software
| Paper | 1996Carragher_Phoelix | Phoelix |
| Paper | 1996Crowther_MRC | MRC |
| Paper | 1996Owen_Brandeis | Brandeis |
Icosahedral particles
Reconstruction
| Paper | 1970Crowther_Rec | Reconstruction of icosahedral viruses in Fourier space |
| Paper | 1971Crowther_Rec | Reconstruction of icosahedral viruses in Fourier space |
| Paper | 1996Fuller_Rec | Reconstruction of icosahedral viruses in Fourier space |
| Paper | 1997Thuman_Rec | Reconstruction of icosahedral viruses in Fourier space |
Classification
| Paper | 2005Scheres_Virus | Classification of virus capsids in real space |
Books and reviews
| Paper | 1999Baker_Review | Review of reconstruction of icosahedral viruses |
| Paper | 1999Conway_Review | Review of reconstruction of icosahedral viruses |
| Paper | 2000Thuman_Review | Review of reconstruction of icosahedral viruses |
| Paper | 2003Lee_Review | Review of reconstruction of icosahedral viruses |
| Paper | 2003Navaza_Review | Review of reconstruction of icosahedral viruses |
| Paper | 2006Grunewald_Review | Review of reconstruction of icosahedral viruses |
Software
| Paper | 1996Baker_EMPFT | EMPFT |
| Paper | 1996Crowther_MRC | MRC |
| Paper | 1996Frank_Spider | Spider |
| Paper | 1996VanHeel_Imagic | Imagic |
| Paper | 2004Sorzano_Xmipp | Xmipp |
| Paper | 2013DeLaRosa_Xmipp30 | Xmipp 3.0 |
| Paper | 2013Morin_Sliz SBGrid | SBGrid presentation for eLife |
Databases
| Paper | 2003Boutselakis_EMSD | EMSD database |
| Paper | 2005Heymann_Conventions | Conventions for software interoperability |
| Paper | 2005Heymann_Conventions | Conventions for software interoperability |
| Paper | 2011Kim_CDDB | Conformational Dynamics Data Bank |
| Paper | 2011Lawson_EMDB | Electron Microscopy Data Bank |
| Blog | http://www.mybiosoftware.com | Huge list of bioinformatics programs (many of them structural bioinformatics) |
Relationship to other structural information sources
| Paper | 2000Engel_AFM | Review of Atomic Force Microscopy |
| Paper | 2001Dimmeler_AFM | Constraints from Atomic Force Microscopy |
| Paper | 2003Mobus_EnergyLoss | Chemical mapping by energy loss electron tomography |
| Paper | 2004Leapman_EnergyLoss | Chemical mapping by energy loss electron tomography |
| Paper | 2004Leapman_Review | Review on correlative microscopy |
| Paper | 2005Boudier_EFTETJ | Software for Chemical mapping by energy loss electron tomography |
| Paper | 2005Vestergaard_SAXS | Example of comparison of 3DEM and Small-angle X-ray scattering |
| Paper | 2007Hamada_SAXS | Constraints from Small-angle X-ray scattering |
| Paper | 2013Xu_FRET | EM+FRET |
X-ray tomography
| Paper | 2012Oton_ImageFormation | Image formation model in X-ray cell microscopy |
Mathematical tools necessary
People developing methods
Please, add yourself to this list (due to privacy reasons, please, do not add anyone else to the list without his/her explicit consent). Sort by first name alphabetical order.
Carlos Oscar S. Sorzano: CSIC, Madrid, Spain
Cédric Messaoudi: Institute Curie, Paris, France
Javier Vargas:mail: CSIC, Madrid, Spain
Joaquín Otón: CSIC, Madrid, Spain
José Román Bilbao-Castro: UAL, Almería, Spain; CSIC, Madrid, Spain
[José Miguel de la Rosa Trevín]: Biocomputing Unit CNB-CSIC, Madrid, Spain
Tamir Gonen: mail: Howard Hughes Medical Institute, Ashburn, VA, USA
Vahid Abrishami: CSIC, Madrid, Spain