3DEM-Methods - User contributions [en]

2010Shatsky MultiVariate

2013-09-24T09:00:55Z

Javier: /* Keywords */

== Citation ==

Automated Multi-model Reconstruction from Single-Particle Electron Microscopy Data, 2010,
Maxim Shatsky, Richard J. Hall, Eva Nogales, Jitendra Malik, Steven E. Brenner,
J Struct Biol. 2010 April; 170(1): 98–108

== Abstract ==

Although three-dimensional electron microscopy (3D-EM) permits structural characterization of macromolecular assemblies in distinct functional states, the inability to classify projections from structurally heterogeneous samples has severely limited its application. We present a maximum likelihood-based classification method that does not depend on prior knowledge about the structural variability, and demonstrate its effectiveness for two macromolecular assemblies with different types of conformational variability: the Escherichia coli ribosome and Simian virus 40 (SV40) large T-antigen.

== Keywords ==

Heterogeneous reconstruction, heterogeneous data, multi-model reconstruction

== Links ==

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2841227/

2010Shatsky MultiVariate

2013-09-24T09:00:20Z

Javier: /* Abstract */

2010Shatsky MultiVariate

2013-09-24T08:58:17Z

Javier: /* Citation */

2010Shatsky MultiVariate

2013-09-24T08:51:38Z

Javier: Created page with "== Citation == Automated Multi-model Reconstruction from Single-Particle Electron Microscopy Data, 2010, Maxim Shatsky, Richard J. Hall, Eva Nogales, Jitendra Malik, Steven E..."

Main Page

2013-09-24T08:48:26Z

Javier: /* 3D Heterogeneity */

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

* You know which are the relevant articles in a particular topic, therefore, paper introductions, reviews, etc. are easier to write and you make sure you will cite all the related articles.
* You will be sure that your paper has more chances of being cited.
* You can add whatever information you find relevant to your method, external links, links to other papers, etc.
* You can link your method to a web page providing the corresponding software, so you know people can use your algorithms.
* You can use the Wiki search capabilities to locate relevant articles even if they are not at the topic you are looking at.
* As a community we will "reconstruct" our history.
* You can select the "watch" option above to receive notifications in case of further changes in the Main Page.

Developing image processing methods for 3DEM is not "[[well-paid]]" in terms of citations and impact factor. However, it is crucial for the advance of the field. Gathering methodological papers in a portal will help to increase the recognition of the field.

Please:

* Add your articles at the right place (you can add a single article in several topics if it is relevant to all of them). The easiest way to add an article is by editing the corresponding topic in the main page, adding your entry, then save the main page. Click on the red link that appears on your new entry, copy and paste the Wiki following code, add the information of your article

== Citation ==

== Abstract ==

== Keywords ==

== Links ==

== Related software ==

== Related methods ==

== Comments ==

* Maintain the information of each article as complete as possible.
* Sort articles by years and authors.
* Be respectful to other people's work.

== How to subscribe to this page ==

You may subscribe to this page so that you will be notified every time someone adds a new method. To do so, you have to register in the page, and edit your preferences ("my preferences"). Be sure that you have activated the option "E-mail me when a page on my watchlist is changed". Finally, click on the "Watch" tab at the top of this page.

== Electron microscopy images ==

=== Image formation ===

{|

| Paper
| [[1971Glaeser_Damage]]
| Radiation damage
|-

| Paper
| [[1971Thon_Model]]
| CTF model
|-

| Paper
| [[1975Unwin_Imaging]]
| Radiation dose
|-

| Paper
| [[1977Wade_Model]]
| CTF model
|-

| Paper
| [[1978Wade_Model]]
| CTF model
|-

| 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
| [[2010Bammes_Damage]]
| Radiation damage dependence on temperature
|-

| 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
| [[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
| [[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
|-
|}

=== 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
|-

| Paper
| [[2007Yoshioka_RCT]]
| Automated Random Conical Tilt
|-

|}

== 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
| [[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
|-

|}

=== 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
|-

|}

=== 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
|-

| Paper
| [[2012Yang_ISAC]]
| Iterative Stable Alignment and clustering
|-

|}

=== 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
| [[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
| [[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
|-

| Paper
| [[2012Gopinath_ShapeRegularization]]
| Regularized 3D Reconstruction by Shape information
|-

| 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.
|-

|}

=== 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
| [[2010Shatsky_MultiVariate]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2013Wang_MLVariance]]
| Maximum Likelihood estimate of the map variance
|-

|}

=== Validation ===

{|

| Paper
| [[2011Henderson]]
| Tilt Validation
|-

|}
=== 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
| [[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
|-

|}

=== 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
|-

| Paper
| [[2013Chapman MS_Atomicmodeling]]
| Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters
|-

|}

=== 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
|-

| Paper
| [[2008Shaikh_SpiderProtocols]]
| Spider Protocols
|-

| Paper
| [[2012Wriggers_SitusConventions]]
| Conventions and workflows in Situs
|-

|}

== Electron tomography ==

=== Image alignment ===

{|

| Paper
| [[1996Owen_alignmentQuality]]
| Automatic alignment without fiducial markers and evaluation of alignment quality
|-

| 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
|-

|}

=== 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
| [[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
| [[2012Herman General Superiorization]]
| Superiorization: an optimization heuristic for medical physics
|-
|}

=== 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
|-

|}

== 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
|-

|}

== 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
| [[2013Morin_Sliz SBGrid]]
| SBGrid presentation for eLife
|-

|}

== 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.

[http://biocomp.cnb.csic.es/~coss Carlos Oscar S. Sorzano]: CSIC, Madrid, Spain 

[http://www.curie.fr/recherche/themes/detail_equipe.cfm/lang/_fr/id_equipe/241.htm Cédric Messaoudi]: Institute Curie, Paris, France 

[http://scholar.google.es/citations?user=_jNYGScAAAAJ&hl=en Javier Vargas]:[mailto:jvargas@cnb.csic.es mail]: CSIC, Madrid, Spain 

[http://scholar.google.es/citations?hl=es&user=g2ZJPIYAAAAJ Joaquín Otón]: CSIC, Madrid, Spain 

[mailto:jrbcast@gmail.com José Román Bilbao-Castro]: UAL, Almería, Spain; CSIC, Madrid, Spain 

[José Miguel de la Rosa Trevín]: Biocomputing Unit CNB-CSIC, Madrid, Spain 

== 3DEM sites ==
* [http://3dem.ucsd.edu/ 3DEM web site]

* [http://en.wikibooks.org/wiki/Software_Tools_For_Molecular_Microscopy Software tools for molecular microscopy]

* [http://www.emdatabank.org/ The Electron Microscopy Data Bank (EMDB)]

* [http://ccdb.ucsd.edu The Cell Centered Database (CCDB)]

* [http://conventions.cnb.csic.es The geometrical software conventions web page ]

== Editing useful links ==

* [http://www.mediawiki.org/wiki/Help:Formatting Text formatting in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Links Adding links in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Images Adding images in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Tables Making tables in Mediawiki]

2011Henderson

2013-07-26T10:57:05Z

Javier: Created page with "== Citation == Richard Henderson Shaoxia Chen, James Z. Chen, Nikolaus Grigorieff, Lori A. Passmore, Luciano Ciccarelli, John L. Rubinstein, R. Anthony Crowther, Phoebe L. St..."

== Citation ==

Richard Henderson Shaoxia Chen, James Z. Chen, Nikolaus Grigorieff, Lori A. Passmore, Luciano Ciccarelli, John L. Rubinstein, R. Anthony Crowther, Phoebe L. Stewart, and Peter . Rosenthal,
Tilt-Pair Analysis of Images from a Range of Different Specimens in Single-Particle Electron Cryomicroscopy. J Mol Biol. 2011 November 11; 413(5-3): 1028–1046.

== Abstract ==

The comparison of a pair of electron microscope images recorded at different specimen tilt angles provides a powerful approach for evaluating the quality of images, image-processing procedures, or three-dimensional structures. Here, we analyze tilt-pair images recorded from a range of specimens with different symmetries and molecular masses and show how the analysis can produce valuable information not easily obtained otherwise. We show that the accuracy of orientation determination of individual single particles depends on molecular mass, as expected theoretically since the information in each particle image increases with molecular mass. The angular uncertainty is less than 1° for particles of high molecular mass (~ 50 MDa), several degrees for particles in the range 1–5 MDa, and tens of degrees for particles below 1 MDa. Orientational uncertainty may be the major contributor to the effective temperature factor (B-factor) describing contrast loss and therefore the maximum resolution of a structure determination. We also made two unexpected observations. Single particles that are known to be flexible showed a wider spread in orientation accuracy, and the orientations of the largest particles examined changed by several degrees during typical low-dose exposures. Smaller particles presumably also reorient during the exposure; hence, specimen movement is a second major factor that limits resolution. Tilt pairs thus enable assessment of orientation accuracy, map quality, specimen motion, and conformational heterogeneity. A convincing tilt-pair parameter plot, where 60% of the particles show a single cluster around the expected tilt axis and tilt angle, provides confidence in a structure determined using electron cryomicroscopy.

== Keywords ==

electron microscopy, structure validation, particle orientation, beam-induced specimen motion, radiation damage

== Links ==

doi = "http://dx.doi.org/10.1016/j.jmb.2011.09.008",

== Related software ==

== Related methods ==

== Comments ==

Main Page

2013-07-26T10:52:18Z

Javier:

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

* You know which are the relevant articles in a particular topic, therefore, paper introductions, reviews, etc. are easier to write and you make sure you will cite all the related articles.
* You will be sure that your paper has more chances of being cited.
* You can add whatever information you find relevant to your method, external links, links to other papers, etc.
* You can link your method to a web page providing the corresponding software, so you know people can use your algorithms.
* You can use the Wiki search capabilities to locate relevant articles even if they are not at the topic you are looking at.
* As a community we will "reconstruct" our history.
* You can select the "watch" option above to receive notifications in case of further changes in the Main Page.

Developing image processing methods for 3DEM is not "[[well-paid]]" in terms of citations and impact factor. However, it is crucial for the advance of the field. Gathering methodological papers in a portal will help to increase the recognition of the field.

Please:

* Add your articles at the right place (you can add a single article in several topics if it is relevant to all of them). The easiest way to add an article is by editing the corresponding topic in the main page, adding your entry, then save the main page. Click on the red link that appears on your new entry, copy and paste the Wiki following code, add the information of your article

== Citation ==

== Abstract ==

== Keywords ==

== Links ==

== Related software ==

== Related methods ==

== Comments ==

* Maintain the information of each article as complete as possible.
* Sort articles by years and authors.
* Be respectful to other people's work.

== How to subscribe to this page ==

You may subscribe to this page so that you will be notified every time someone adds a new method. To do so, you have to register in the page, and edit your preferences ("my preferences"). Be sure that you have activated the option "E-mail me when a page on my watchlist is changed". Finally, click on the "Watch" tab at the top of this page.

== Electron microscopy images ==

=== Image formation ===

{|

| Paper
| [[1971Glaeser_Damage]]
| Radiation damage
|-

| Paper
| [[1971Thon_Model]]
| CTF model
|-

| Paper
| [[1975Unwin_Imaging]]
| Radiation dose
|-

| Paper
| [[1977Wade_Model]]
| CTF model
|-

| Paper
| [[1978Wade_Model]]
| CTF model
|-

| 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
| [[2010Bammes_Damage]]
| Radiation damage dependence on temperature
|-

| 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
| [[2011Zhang LimitingFactors]]
| Limiting factor for atomic resolution in EM
|-

| Paper
| [[2012Bammes_DirectDetection]]
| Performance of Direct detectors
|-

| 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
|-

|}

=== 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
|-

| Paper
| [[2007Yoshioka_RCT]]
| Automated Random Conical Tilt
|-

|}

== 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
| [[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
|-

|}

=== 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
| [[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
|-

|}

=== 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
|-

| Paper
| [[2012Yang_ISAC]]
| Iterative Stable Alignment and clustering
|-

|}

=== 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
| [[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
| [[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
|-

| Paper
| [[2012Gopinath_ShapeRegularization]]
| Regularized 3D Reconstruction by Shape information
|-

|}

=== 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
|-

|}
=== Validation ===

{|

| Paper
| [[2011Henderson]]
| Tilt Validation
|-

|}
=== 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
| [[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
|-

|}

=== 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
|-

| Paper
| [[2008Shaikh_SpiderProtocols]]
| Spider Protocols
|-

|}

== Electron tomography ==

=== Image alignment ===

{|

| Paper
| [[1996Owen_alignmentQuality]]
| Automatic alignment without fiducial markers and evaluation of alignment quality
|-

| 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
|-

|}

=== 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
| [[2013Goris_SIRT_TV_DART]]
| Combination of SIRT, Total Variation and Discrete ART to reconstruct and segment at the same time
|-
|}

=== 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
|-

|}

== 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
|-

|}

== 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
|-

|}

== 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.

[http://biocomp.cnb.csic.es/~coss Carlos Oscar S. Sorzano]: CSIC, Madrid, Spain 

[http://www.curie.fr/recherche/themes/detail_equipe.cfm/lang/_fr/id_equipe/241.htm Cédric Messaoudi]: Institute Curie, Paris, France 

[http://scholar.google.es/citations?user=_jNYGScAAAAJ&hl=en Javier Vargas]:[mailto:jvargas@cnb.csic.es mail]: CSIC, Madrid, Spain 

[http://scholar.google.es/citations?hl=es&user=g2ZJPIYAAAAJ Joaquín Otón]: CSIC, Madrid, Spain 

[mailto:jrbcast@gmail.com José Román Bilbao-Castro]: UAL, Almería, Spain; CSIC, Madrid, Spain 

[José Miguel de la Rosa Trevín]: Biocomputing Unit CNB-CSIC, Madrid, Spain 

== 3DEM sites ==
* [http://3dem.ucsd.edu/ 3DEM web site]

* [http://en.wikibooks.org/wiki/Software_Tools_For_Molecular_Microscopy Software tools for molecular microscopy]

* [http://www.emdatabank.org/ The Electron Microscopy Data Bank (EMDB)]

* [http://ccdb.ucsd.edu The Cell Centered Database (CCDB)]

* [http://conventions.cnb.csic.es The geometrical software conventions web page ]

== Editing useful links ==

* [http://www.mediawiki.org/wiki/Help:Formatting Text formatting in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Links Adding links in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Images Adding images in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Tables Making tables in Mediawiki]

2010Sanz Random

2013-05-29T07:18:29Z

Javier: Created page with "== Citation == Sanz-García E, Stewart AB, Belnap DM. The random-model method enables ab initio 3D reconstruction of asymmetric particles and determination of particle symmet..."

== Citation ==

Sanz-García E, Stewart AB, Belnap DM. The random-model method enables ab initio 3D reconstruction of asymmetric particles and determination of particle symmetry. J Struct Biol. 2010 Aug;171(2):216-22. doi: 10.1016/j.jsb.2010.03.017. Epub 2010 Mar 28.

== Abstract ==

Model-based, 3D reconstruction techniques depend on reliable starting models. We present an extension of the random-model method (RMM) that allows the ab initio generation of suitable starting models directly from un-averaged, experimental images of asymmetric or symmetric particles. Therefore, the asymmetric RMM can also be used to determine point-group symmetry. The procedure is facilitated by the use of (a) variable angular step-sizes during iterative origin and orientation searches, (b) high numbers of particle images, and (c) highly defocused images. The method is inhibited by mixed-handedness orientation assignments and by particles with inconspicuous features. For symmetric particles, symmetric RMMs can overcome these deficiencies.

== Keywords ==

== Links ==

http://www.ncbi.nlm.nih.gov/pubmed/20353825

== Related software ==

== Related methods ==

== Comments ==

Main Page

2013-05-29T07:16:49Z

Javier: /* 3D Alignment */

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

* You know which are the relevant articles in a particular topic, therefore, paper introductions, reviews, etc. are easier to write and you make sure you will cite all the related articles.
* You will be sure that your paper has more chances of being cited.
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== Citation ==

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== Electron microscopy images ==

=== Image formation ===

{|

| Paper
| [[1971Glaeser_Damage]]
| Radiation damage
|-

| Paper
| [[1971Thon_Model]]
| CTF model
|-

| Paper
| [[1975Unwin_Imaging]]
| Radiation dose
|-

| Paper
| [[1977Wade_Model]]
| CTF model
|-

| Paper
| [[1978Wade_Model]]
| CTF model
|-

| 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
| [[2010Bammes_Damage]]
| Radiation damage dependence on temperature
|-

| 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
| [[2011Zhang LimitingFactors]]
| Limiting factor for atomic resolution in EM
|-

| Paper
| [[2012Bammes_DirectDetection]]
| Performance of Direct detectors
|-

| 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
|-

|}

=== 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
|-

| Paper
| [[2007Yoshioka_RCT]]
| Automated Random Conical Tilt
|-

|}

== 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
| [[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
|-

|}

=== 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
| [[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
|-

|}

=== 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
|-

| Paper
| [[2012Yang_ISAC]]
| Iterative Stable Alignment and clustering
|-

|}

=== 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
| [[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
| [[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
|-

| Paper
| [[2012Gopinath_ShapeRegularization]]
| Regularized 3D Reconstruction by Shape information
|-

|}

=== 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
| [[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
|-

|}

=== 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
|-

| Paper
| [[2008Shaikh_SpiderProtocols]]
| Spider Protocols
|-

|}

== Electron tomography ==

=== Image alignment ===

{|

| Paper
| [[1996Owen_alignmentQuality]]
| Automatic alignment without fiducial markers and evaluation of alignment quality
|-

| 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
|-

|}

=== 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
| [[2013Goris_SIRT_TV_DART]]
| Combination of SIRT, Total Variation and Discrete ART to reconstruct and segment at the same time
|-
|}

=== 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
|-

|}

== 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
|-

|}

== 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
|-

|}

== 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.

[http://biocomp.cnb.csic.es/~coss Carlos Oscar S. Sorzano]: CSIC, Madrid, Spain 

[http://www.curie.fr/recherche/themes/detail_equipe.cfm/lang/_fr/id_equipe/241.htm Cédric Messaoudi]: Institute Curie, Paris, France 

[http://scholar.google.es/citations?user=_jNYGScAAAAJ&hl=en Javier Vargas]:[mailto:jvargas@cnb.csic.es mail]: CSIC, Madrid, Spain 

[http://scholar.google.es/citations?hl=es&user=g2ZJPIYAAAAJ Joaquín Otón]: CSIC, Madrid, Spain 

[mailto:jrbcast@gmail.com José Román Bilbao-Castro]: UAL, Almería, Spain; CSIC, Madrid, Spain 

[José Miguel de la Rosa Trevín]: Biocomputing Unit CNB-CSIC, Madrid, Spain 

== 3DEM sites ==
* [http://3dem.ucsd.edu/ 3DEM web site]

* [http://en.wikibooks.org/wiki/Software_Tools_For_Molecular_Microscopy Software tools for molecular microscopy]

* [http://www.emdatabank.org/ The Electron Microscopy Data Bank (EMDB)]

* [http://ccdb.ucsd.edu The Cell Centered Database (CCDB)]

* [http://conventions.cnb.csic.es The geometrical software conventions web page ]

== Editing useful links ==

* [http://www.mediawiki.org/wiki/Help:Formatting Text formatting in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Links Adding links in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Images Adding images in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Tables Making tables in Mediawiki]

2010Jaitly Bayesian

2013-05-28T09:47:14Z

Javier: /* Keywords */

== Citation ==

Navdeep Jaitly, Marcus A. Brubaker, John L. Rubinstein and Ryan H. Lilien, A Bayesian method for 3D macromolecular structure inference using class average images from single particle electron microscopy. Bioinformatics (2010) 26 (19): 2406-2415. doi: 10.1093/bioinformatics/btq456 First published online: August 11, 2010

== Abstract ==

Motivation: Electron cryo-microscopy can be used to infer 3D structures of large macromolecules with high resolution, but the large amounts of data captured necessitate the development of appropriate statistical models to describe the data generation process, and to perform structure inference. We present a new method for performing ab initio inference of the 3D structures of macromolecules from single particle electron cryo-microscopy experiments using class average images.

Results: We demonstrate this algorithm on one phantom, one synthetic dataset and three real (experimental) datasets (ATP synthase, V-type ATPase and GroEL). Structures consistent with the known structures were inferred for all datasets.

Availability: The software and source code for this method is available for download from our website: http://compbio.cs.toronto.edu/cryoem/

== Keywords ==

Initial volume

== Links ==

http://bioinformatics.oxfordjournals.org/content/26/19/2406.short

2010Jaitly Bayesian

2013-05-28T09:46:44Z

Javier: /* Keywords */

2010Jaitly Bayesian

2013-05-28T09:46:34Z

Javier: /* Abstract */

2010Jaitly Bayesian

2013-05-28T09:45:50Z

Javier: /* Citation */

2010Jaitly Bayesian

2013-05-28T09:45:10Z

Javier: Created page with "== Citation == Navdeep Jaitly, Marcus A. Brubaker, John L. Rubinstein and Ryan H. Lilien, A Bayesian method for 3D macromolecular structure inference using class average ima..."

Main Page

2013-05-28T09:42:54Z

Javier: /* 3D Alignment */

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

* You know which are the relevant articles in a particular topic, therefore, paper introductions, reviews, etc. are easier to write and you make sure you will cite all the related articles.
* You will be sure that your paper has more chances of being cited.
* You can add whatever information you find relevant to your method, external links, links to other papers, etc.
* You can link your method to a web page providing the corresponding software, so you know people can use your algorithms.
* You can use the Wiki search capabilities to locate relevant articles even if they are not at the topic you are looking at.
* As a community we will "reconstruct" our history.
* You can select the "watch" option above to receive notifications in case of further changes in the Main Page.

Developing image processing methods for 3DEM is not "[[well-paid]]" in terms of citations and impact factor. However, it is crucial for the advance of the field. Gathering methodological papers in a portal will help to increase the recognition of the field.

Please:

* Add your articles at the right place (you can add a single article in several topics if it is relevant to all of them). The easiest way to add an article is by editing the corresponding topic in the main page, adding your entry, then save the main page. Click on the red link that appears on your new entry, copy and paste the Wiki following code, add the information of your article

== Citation ==

== Abstract ==

== Keywords ==

== Links ==

== Related software ==

== Related methods ==

== Comments ==

* Maintain the information of each article as complete as possible.
* Sort articles by years and authors.
* Be respectful to other people's work.

== How to subscribe to this page ==

You may subscribe to this page so that you will be notified every time someone adds a new method. To do so, you have to register in the page, and edit your preferences ("my preferences"). Be sure that you have activated the option "E-mail me when a page on my watchlist is changed". Finally, click on the "Watch" tab at the top of this page.

== Electron microscopy images ==

=== Image formation ===

{|

| Paper
| [[1971Glaeser_Damage]]
| Radiation damage
|-

| Paper
| [[1971Thon_Model]]
| CTF model
|-

| Paper
| [[1975Unwin_Imaging]]
| Radiation dose
|-

| Paper
| [[1977Wade_Model]]
| CTF model
|-

| Paper
| [[1978Wade_Model]]
| CTF model
|-

| 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
| [[2010Bammes_Damage]]
| Radiation damage dependence on temperature
|-

| 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
| [[2011Zhang LimitingFactors]]
| Limiting factor for atomic resolution in EM
|-

| Paper
| [[2012Bammes_DirectDetection]]
| Performance of Direct detectors
|-

| 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
|-

|}

=== 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
|-

| Paper
| [[2007Yoshioka_RCT]]
| Automated Random Conical Tilt
|-

|}

== 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
| [[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
|-

|}

=== 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
| [[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
|-

|}

=== 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
|-

| Paper
| [[2012Yang_ISAC]]
| Iterative Stable Alignment and clustering
|-

|}

=== 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
| [[2006Ogura_SimulatedAnnealing]]
| Angular asignment by simulated annealing
|-

| Paper
| [[2007Grigorieff_Continuous]]
| Continuous angular assignment in Fourier space
|-

| Paper
| [[2010Jaitly_Bayesian]]
| Angular asignment by a Bayesian method and annealing
|-

| 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
|-

| Paper
| [[2012Gopinath_ShapeRegularization]]
| Regularized 3D Reconstruction by Shape information
|-

|}

=== 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
| [[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
|-

|}

=== 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
|-

| Paper
| [[2008Shaikh_SpiderProtocols]]
| Spider Protocols
|-

|}

== Electron tomography ==

=== Image alignment ===

{|

| Paper
| [[1996Owen_alignmentQuality]]
| Automatic alignment without fiducial markers and evaluation of alignment quality
|-

| 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
|-

|}

=== 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
| [[2013Goris_SIRT_TV_DART]]
| Combination of SIRT, Total Variation and Discrete ART to reconstruct and segment at the same time
|-
|}

=== 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
|-

|}

== 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
|-

|}

== 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
|-

|}

== 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.

[http://biocomp.cnb.csic.es/~coss Carlos Oscar S. Sorzano]: CSIC, Madrid, Spain 

[http://www.curie.fr/recherche/themes/detail_equipe.cfm/lang/_fr/id_equipe/241.htm Cédric Messaoudi]: Institute Curie, Paris, France 

[http://scholar.google.es/citations?user=_jNYGScAAAAJ&hl=en Javier Vargas]:[mailto:jvargas@cnb.csic.es mail]: CSIC, Madrid, Spain 

[http://scholar.google.es/citations?hl=es&user=g2ZJPIYAAAAJ Joaquín Otón]: CSIC, Madrid, Spain 

[mailto:jrbcast@gmail.com José Román Bilbao-Castro]: UAL, Almería, Spain; CSIC, Madrid, Spain 

[José Miguel de la Rosa Trevín]: Biocomputing Unit CNB-CSIC, Madrid, Spain 

== 3DEM sites ==
* [http://3dem.ucsd.edu/ 3DEM web site]

* [http://en.wikibooks.org/wiki/Software_Tools_For_Molecular_Microscopy Software tools for molecular microscopy]

* [http://www.emdatabank.org/ The Electron Microscopy Data Bank (EMDB)]

* [http://ccdb.ucsd.edu The Cell Centered Database (CCDB)]

* [http://conventions.cnb.csic.es The geometrical software conventions web page ]

== Editing useful links ==

* [http://www.mediawiki.org/wiki/Help:Formatting Text formatting in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Links Adding links in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Images Adding images in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Tables Making tables in Mediawiki]

Main Page

2013-01-16T09:18:59Z

Javier: /* People developing methods */

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

* You know which are the relevant articles in a particular topic, therefore, paper introductions, reviews, etc. are easier to write and you make sure you will cite all the related articles.
* You will be sure that your paper has more chances of being cited.
* You can add whatever information you find relevant to your method, external links, links to other papers, etc.
* You can link your method to a web page providing the corresponding software, so you know people can use your algorithms.
* You can use the Wiki search capabilities to locate relevant articles even if they are not at the topic you are looking at.
* As a community we will "reconstruct" our history.
* You can select the "watch" option above to receive notifications in case of further changes in the Main Page.

Developing image processing methods for 3DEM is not "[[well-paid]]" in terms of citations and impact factor. However, it is crucial for the advance of the field. Gathering methodological papers in a portal will help to increase the recognition of the field.

Please:

* Add your articles at the right place (you can add a single article in several topics if it is relevant to all of them). The easiest way to add an article is by editing the corresponding topic in the main page, adding your entry, then save the main page. Click on the red link that appears on your new entry, copy and paste the Wiki following code, add the information of your article

== Citation ==

== Abstract ==

== Keywords ==

== Links ==

== Related software ==

== Related methods ==

== Comments ==

* Maintain the information of each article as complete as possible.
* Sort articles by years and authors.
* Be respectful to other people's work.

== How to subscribe to this page ==

You may subscribe to this page so that you will be notified every time someone adds a new method. To do so, you have to register in the page, and edit your preferences ("my preferences"). Be sure that you have activated the option "E-mail me when a page on my watchlist is changed". Finally, click on the "Watch" tab at the top of this page.

== 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
| [[2011Zhang 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
| [[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
| [[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
|-

|}

=== 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
|-

|}

== X-ray tomography ==

{|

|}

== 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.

[http://biocomp.cnb.csic.es/~coss Carlos Oscar S. Sorzano]: CSIC, Madrid, Spain 

[http://www.curie.fr/recherche/themes/detail_equipe.cfm/lang/_fr/id_equipe/241.htm Cédric Messaoudi]: Institute Curie, Paris, France 

[mailto:jrbcast@gmail.com José Román Bilbao-Castro]: UAL, Almería, Spain; CSIC, Madrid, Spain 

[http://scholar.google.es/citations?user=_jNYGScAAAAJ&hl=en Javier Vargas]:[mailto:jvargas@cnb.csic.es mail]: CSIC, Madrid, Spain 

== 3DEM sites ==
* [http://3dem.ucsd.edu/ 3DEM web site]

* [http://en.wikibooks.org/wiki/Software_Tools_For_Molecular_Microscopy Software tools for molecular microscopy]

* [http://www.emdatabank.org/ The Electron Microscopy Data Bank (EMDB)]

* [http://ccdb.ucsd.edu The Cell Centered Database (CCDB)]

* [http://conventions.cnb.csic.es The geometrical software conventions web page ]

== Editing useful links ==

* [http://www.mediawiki.org/wiki/Help:Formatting Text formatting in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Links Adding links in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Images Adding images in Mediawiki]
* [http://www.mediawiki.org/wiki/Help:Tables Making tables in Mediawiki]

2011Glaeser Coma

2012-11-21T10:27:53Z

Javier: Created page with "== Citation == Glaeser R. M., Typke D., Tiemeijer P. C., Pulokas J., Chang A. Review: Precise Beam-Tilt Alignment And Collimation Are Required To Minimize The Phase Error Ass..."

== Citation ==

Glaeser R. M., Typke D., Tiemeijer P. C., Pulokas J., Chang A. Review: Precise Beam-Tilt Alignment And Collimation Are Required To Minimize The Phase Error Associated With Coma In High-Resolution Cryo-EM

. J Struct Biol. 2011 April;174(1):1-10.

== Abstract ==

Electron microscopy at a resolution of 0.4 nm or better requires more careful adjustment of the
illumination than is the case at a resolution of 0.8 nm. The use of current-axis alignment is not
always sufficient, for example, to avoid the introduction of large phase errors, at higher resolution,
due to axial coma. In addition, one must also ensure that off-axis coma does not corrupt the data
quality at the higher resolution. We particularly emphasize that the standard CTF correction does
not account for the phase error associated with coma. We explain the cause of both axial coma and
the typically most troublesome component of off-axis coma in terms of the well-known shift of the
electron diffraction pattern relative to the optical axis that occurs when the illumination is not
parallel to the axis. We review the experimental conditions under which coma causes unacceptably
large phase errors, and we discuss steps that can be taken when setting up the conditions of
illumination, so as to ensure that neither axial nor off-axis coma is a problem.

== Keywords ==

Beam alignment; coma; phase error

== Links ==

http://www.sciencedirect.com/science/article/pii/S1047847710003825

== Related software ==

== Related methods ==

== Comments ==

Main Page

2012-11-21T10:20:48Z

Javier: /* CTF estimation and restoration */

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

* You know which are the relevant articles in a particular topic, therefore, paper introductions, reviews, etc. are easier to write and you make sure you will cite all the related articles.
* You will be sure that your paper has more chances of being cited.
* You can add whatever information you find relevant to your method, external links, links to other papers, etc.
* You can link your method to a web page providing the corresponding software, so you know people can use your algorithms.
* You can use the Wiki search capabilities to locate relevant articles even if they are not at the topic you are looking at.
* As a community we will "reconstruct" our history.
* You can select the "watch" option above to receive notifications in case of further changes in the Main Page.

Developing image processing methods for 3DEM is not "[[well-paid]]" in terms of citations and impact factor. However, it is crucial for the advance of the field. Gathering methodological papers in a portal will help to increase the recognition of the field.

Please:

* Add your articles at the right place (you can add a single article in several topics if it is relevant to all of them). The easiest way to add an article is by editing the corresponding topic in the main page, adding your entry, then save the main page. Click on the red link that appears on your new entry, copy and paste the Wiki following code, add the information of your article

== Citation ==

== Abstract ==

== Keywords ==

== Links ==

== Related software ==

== Related methods ==

== Comments ==

* Maintain the information of each article as complete as possible.
* Sort articles by years and authors.
* Be respectful to other people's work.

== 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
|-

|}

=== 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
|-

|}

=== 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
|-

|}

=== 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]]
| Review : Precise Beam-Tilt Alignment Ana Collimation Are Required To Minimize The Phase Error Associated with Coma In High-Resolution Cryo-EM
|-

|}

=== 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
|-

|}

=== 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
|-

|}

=== 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
|-

|}

=== 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
|-

|}

== 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.

[http://biocomp.cnb.csic.es/~coss Carlos Oscar S. Sorzano]: CSIC, Madrid, Spain 

[http://www.curie.fr/recherche/themes/detail_equipe.cfm/lang/_fr/id_equipe/241.htm Cédric Messaoudi]: Institute Curie, Paris, France 

[mailto:jrbcast@gmail.com José Román Bilbao-Castro]: UAL, Almería, Spain; CSIC, Madrid, Spain 

== 3DEM sites ==
* [http://3dem.ucsd.edu/ 3DEM web site]

* [http://en.wikibooks.org/wiki/Software_Tools_For_Molecular_Microscopy Software tools for molecular microscopy]

* [http://www.emdatabank.org/ The Electron Microscopy Data Bank (EMDB)]

* [http://ccdb.ucsd.edu The Cell Centered Database (CCDB)]

* [http://conventions.cnb.csic.es The geometrical software conventions web page ]

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