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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

Image formation

Paper	1971Glaeser_Damage	Radiation damage
Paper	1975Unwin_Imaging	Radiation dose
Paper	1988Toyoshima_Model	Amplitud constrast
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	2010Zewail_FourDimensional	Review on the use of ultrafast EM
Paper	2011Zhang2011_LimitingFactors	Limiting factor for atomic resolution in EM
Paper	2011Glaeser_Coma	Image formation model including coma

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	2005Lanzavecchia_Conical	Conical tomography
Paper	2005Zampighi_Conical	Conical tomography
Paper	2006Leschziner_OT	Orthogonal Tilt
Paper	2006Messaoudi_Multiple	Multiple axis tomography

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

Automated data collection

Paper	1992Dierksen_Automatic	Automated data collection
Paper	1992Koster_Automatic	Automated data collection
Paper	2001Zhang_Automatic	Automated sample collection
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

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	2004Zhu_Review	Review on automatic particle picking
Paper	2009Sorzano_MachineLearning	Automatic particle picking based on machine learning of rotational invariants

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

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	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

3D Alignment

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	2007Grigorieff_Continuous	Continuous angular assignment in Fourier space
Paper	2012Giannakis_Scattering	Construction of an initial volume, reference free, by graph analysis of the projections

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

3D Heterogeneity

Paper	2004White_Size	Heterogeneity classification of differently sized images
Paper	2007Leschziner_Review	Review of 3D heterogeneity handling algorithms
Paper	2007Scheres_ML3D	Maximum Likelihood alignment and classification in 3D
Paper	2013Wang_MLVariance	Maximum Likelihood estimate of the map variance

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

Sharpening of high resolution information

Paper	2003Rosenthal_DPR	Contrast restoration and map sharpening
Paper	2008Fernandez_Bfactor	Bfactor determination and restoration

CTF estimation and restoration

Paper	1971Thon_Model	CTF model
Paper	1984Cohen_Validity	Validity of the CTF model at high frequencies
Paper	1988Toyoshima_Model	CTF estimation
Paper	1993Toyoshima_Model	Amplitud constrast
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	2003Velazquez_ARMA	PSD and CTF estimation using ARMA models
Paper	2004Sorzano_IDR	CTF restoration and reconstruction with Iterative Data Refinement
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	2011Sindelar_Wiener	CTF correction using a modified version of Wiener filter
Paper	2011Glaeser_Coma	The effect of coma at high-resolution
Paper	2012Voortman_VaryingCTF	Correcting a spatially varying CTF

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	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	2007Kleywegt_QualityControl	Quality control and validation of fitting
Paper	2012Velazquez_Constraints	Multicomponent fitting by using constraints from other information sources

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	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	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

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

Electron tomography

Image alignment

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

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

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)

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

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.

Resolution

Paper

2005Cardone_Resolution

Resolution criterion for electron tomography

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

Single particle tomography

Paper

2012Bartesaghi_Constrained

3D reconstruction by imposing geometrical constraints

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

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

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

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

Reconstruction

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

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

Data bases

Paper	2003Boutselakis_EMSD	EMSD database
Paper	2005Heymann_Conventions	Conventions for software interoperability

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

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

José Román Bilbao-Castro: UAL, Almería, Spain; CSIC, Madrid, Spain

3DEM sites

• 3DEM web site

• Software tools for molecular microscopy

• The Electron Microscopy Data Bank (EMDB)

• The Cell Centered Database (CCDB)

• The geometrical software conventions web page

Editing useful links

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