3DEM-Methods - User contributions [en]

2013Morin Sliz SBGrid

2013-09-12T06:41:35Z

Jose Maria Carazo: Created page with "== Citation == eLife 2013;2:e01456 == Abstract == SBGrid (www.sbgrid.org) is a collaboration established in 2000 to provide the structural biology community with support for ..."

== Citation ==
eLife 2013;2:e01456
== Abstract ==
SBGrid (www.sbgrid.org) is a collaboration
established in 2000 to provide the structural biology community with support for research computing. Such collaborations have traditionally
been supported by public funding agencies
(Finholt, 2003). However, SBGrid is unique in that
its ongoing operations are funded exclusively by
its members. By sharing the costs of research
computing support across many research
groups, SBGrid achieves efficiencies through
economies of scale, the sharing of expertise and
cooperation to promote common goals.
== Keywords ==
General presentation of SBGrid
== Links ==

== Related software ==

== Related methods ==

== Comments ==

Main Page

2013-09-12T06:39:44Z

Jose Maria Carazo: /* Relationship to other structural information sources */

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
| [[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]

Main Page

2013-09-11T15:03:09Z

Jose Maria Carazo: /* 3D reconstruction */

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
| [[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
|-

|}

== 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

2013-09-11T15:00:36Z

Jose Maria Carazo: /* 3D reconstruction */

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
| [[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
| [[2009 Sorzano Volumetric restrictions]]
| Volumetric restrictions in single particle 3DEM reconstruction

| 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
|-

|}

== 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]

2012Herman General Superiorization

2013-09-11T14:31:26Z

Jose Maria Carazo: Created page with "== Citation == Med Phys. 2012 Sep;39(9):5532-46 == Abstract == PURPOSE: To describe and mathematically validate the superiorization methodology, which is a recently developed ..."

== Citation ==
Med Phys. 2012 Sep;39(9):5532-46
== Abstract ==
PURPOSE:
To describe and mathematically validate the superiorization methodology, which is a recently developed heuristic approach to optimization, and to discuss its applicability to medical physics problem formulations that specify the desired solution (of physically given or otherwise obtained constraints) by an optimization criterion.

METHODS:
The superiorization methodology is presented as a heuristic solver for a large class of constrained optimization problems. The constraints come from the desire to produce a solution that is constraints-compatible, in the sense of meeting requirements provided by physically or otherwise obtained constraints. The underlying idea is that many iterative algorithms for finding such a solution are perturbation resilient in the sense that, even if certain kinds of changes are made at the end of each iterative step, the algorithm still produces a constraints-compatible solution. This property is exploited by using permitted changes to steer the algorithm to a solution that is not only constraints-compatible, but is also desirable according to a specified optimization criterion. The approach is very general, it is applicable to many iterative procedures and optimization criteria used in medical physics.

RESULTS:
The main practical contribution is a procedure for automatically producing from any given iterative algorithm its superiorized version, which will supply solutions that are superior according to a given optimization criterion. It is shown that if the original iterative algorithm satisfies certain mathematical conditions, then the output of its superiorized version is guaranteed to be as constraints-compatible as the output of the original algorithm, but it is superior to the latter according to the optimization criterion. This intuitive description is made precise in the paper and the stated claims are rigorously proved. Superiorization is illustrated on simulated computerized tomography data of a head cross section and, in spite of its generality, superiorization is shown to be competitive to an optimization algorithm that is specifically designed to minimize total variation.

CONCLUSIONS:
The range of applicability of superiorization to constrained optimization problems is very large. Its major utility is in the automatic nature of producing a superiorization algorithm from an algorithm aimed at only constraints-compatibility; while nonheuristic (exact) approaches need to be redesigned for a new optimization criterion. Thus superiorization provides a quick route to algorithms for the practical solution of constrained optimization problems.
== Keywords ==
General introduction to Superiorization
== Links ==

== Related software ==

== Related methods ==

== Comments ==

Main Page

2013-09-11T14:28:13Z

Jose Maria Carazo: /* 3D reconstruction */

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
| [[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
|-

|}

== 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]

2013Li X K2 noisemodels

2013-09-11T14:24:21Z

Jose Maria Carazo:

== Citation ==
J Struct Biol. 2013
== Abstract ==
A recent technological breakthrough in electron cryomicroscopy (cryoEM) is the development of direct electron detection cameras for data acquisition. By bypassing the traditional phosphor scintillator and fiber optic coupling, these cameras have greatly enhanced sensitivity and detective quantum efficiency (DQE). Of the three currently available commercial cameras, the Gatan K2 Summit was designed specifically for counting individual electron events. Counting further enhances the DQE, allows for practical doubling of detector resolution and eliminates noise arising from the variable deposition of energy by each primary electron. While counting has many advantages, undercounting of electrons happens when more than one electron strikes the same area of the detector within the analog readout period (coincidence loss), which influences image quality. In this work, we characterized the K2 Summit in electron counting mode, and studied the relationship of dose rate and coincidence loss and its influence on the quality of counted images. We found that coincidence loss reduces low frequency amplitudes but has no significant influence on the signal-to-noise ratio of the recorded image. It also has little influence on high frequency signals. Images of frozen hydrated archaeal 20S proteasome (∼700kDa, D7 symmetry) recorded at the optimal dose rate retained both high-resolution signal and low-resolution contrast and enabled calculating a 3.6Å three-dimensional reconstruction from only 10,000 particles.

== Keywords ==
Study of K2 rate dependent performance
== Links ==

== Related software ==

== Related methods ==

== Comments ==

2013Li X K2 noisemodels

2013-09-11T14:20:24Z

Jose Maria Carazo: Created page with "Influence of electron dose rate on electron counting images recorded with the K2 camera"

Influence of electron dose rate on electron counting images recorded with the K2 camera

Main Page

2013-09-11T14:19:31Z

Jose Maria Carazo: /* Image formation */

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
| [[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
|-

|}

=== 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]

2013Shigematsu H Noisemodels

2013-09-11T14:15:52Z

Jose Maria Carazo: /* Keywords */

== Citation ==

Shigematsu H, Sigworth FJ.Noise models and cryo-EM drift correction with a direct-electron camera.U ltramicroscopy. 2013 Aug;131:61-9.

== Abstract ==
Blurring due to specimen-holder drift is a common occurrence in cryo-EM images. Cameras employing active-pixel sensors are capable of high frame rates such that a single low-dose exposure can be acquired as a series of frames. In this paper we consider the possibility of tracking and compensating for overall drift in typical single-particle specimens through the analysis of frame sequences. A problem that arises in tracking through cross-correlation of frames obtained with the DE-12 camera from Direct Electron LLC is the presence of "hot-pixel noise". This random pattern of bright pixels is highly correlated among frames. We show how a model of this noise can be employed to greatly reduce its effects. A filter function is derived that optimizes the tracking of image shifts by cross-correlation, and we demonstrate the tracking of specimen drift in typical cryo-EM specimens.

== Keywords ==

"Hot pixel noise" in Direct Detectors (DE-12)

== Links ==

http://www.ncbi.nlm.nih.gov/pubmed/23748163

== Related software ==

== Related methods ==

== Comments ==

2013Shigematsu H Noisemodels

2013-09-11T14:13:32Z

Jose Maria Carazo: /* Abstract */

== Citation ==

Shigematsu H, Sigworth FJ.Noise models and cryo-EM drift correction with a direct-electron camera.U ltramicroscopy. 2013 Aug;131:61-9.

== Abstract ==
Blurring due to specimen-holder drift is a common occurrence in cryo-EM images. Cameras employing active-pixel sensors are capable of high frame rates such that a single low-dose exposure can be acquired as a series of frames. In this paper we consider the possibility of tracking and compensating for overall drift in typical single-particle specimens through the analysis of frame sequences. A problem that arises in tracking through cross-correlation of frames obtained with the DE-12 camera from Direct Electron LLC is the presence of "hot-pixel noise". This random pattern of bright pixels is highly correlated among frames. We show how a model of this noise can be employed to greatly reduce its effects. A filter function is derived that optimizes the tracking of image shifts by cross-correlation, and we demonstrate the tracking of specimen drift in typical cryo-EM specimens.

== Keywords ==

On the use of DNA origami gold particles as internal handedness starndar

== Links ==

http://www.ncbi.nlm.nih.gov/pubmed/23748163

== Related software ==

== Related methods ==

== Comments ==

Main Page

2013-09-11T14:11:10Z

Jose Maria Carazo: /* Image formation */

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
|-

|}

=== 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
| [[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
|-

|}

=== 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

2013-09-11T14:10:42Z

Jose Maria Carazo: /* 3D reconstruction */

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
|-

|}

=== 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
| [[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
|-

|}

=== 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]

2013Shigematsu H Noisemodels

2013-09-11T14:09:48Z

Jose Maria Carazo: /* Abstract */

== Citation ==

Shigematsu H, Sigworth FJ.Noise models and cryo-EM drift correction with a direct-electron camera.U ltramicroscopy. 2013 Aug;131:61-9.

== Abstract ==

== Keywords ==

On the use of DNA origami gold particles as internal handedness starndar

== Links ==

http://www.ncbi.nlm.nih.gov/pubmed/23748163

== Related software ==

== Related methods ==

== Comments ==

2009Baxter NoiseCharacterization

2013-01-17T18:42:11Z

Jose Maria Carazo: Created page with "== Citation == Determination of signal-to-noise ratios and spectral SNRs in cryo-EM low-dose imaging of molecules. Baxter WT, Grassucci RA, Gao H, Frank J. J Struct Biol. 200..."

== Citation ==

Determination of signal-to-noise ratios and spectral SNRs in cryo-EM low-dose imaging of molecules.
Baxter WT, Grassucci RA, Gao H, Frank J.
J Struct Biol. 2009 May;166(2):126-32

== Abstract ==

Attempts to develop efficient classification approaches to the problem of heterogeneity in single-particle reconstruction of macromolecules require phantom data with realistic noise models. We have estimated the signal-to-noise ratios and spectral signal-to-noise ratios for three steps in the electron microscopic image formation from data obtained experimentally. An important result is that structural noise, i.e., the irreproducible component of the object prior to image formation, is substantial, and of the same order of magnitude as the reproducible signal. Based on this result, the noise modeling for testing new classification techniques can be improved.

== Keywords ==

cryo Electron Microscopy, Noise Characterization

== Links ==

http://www.ncbi.nlm.nih.gov/pubmed/19269332

== Related software ==

== Related methods ==

== Comments ==

Main Page

2013-01-17T18:39:45Z

Jose Maria Carazo: /* Image formation */

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
| [[2009_Baxter_NoiseCharacterization]]
| Characterization of the different noise sources in cryo-EM
|-

| 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 ==

{|

| 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 

[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 

[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]

2012Oton ImageFormation

2013-01-16T17:08:18Z

Jose Maria Carazo: Created page with "== Citation == J Struct Biol. 2012 Apr;178(1):29-37. Image formation in cellular X-ray microscopy. Oton J, Sorzano CO, Pereiro E, Cuenca-Alba J, Navarro R, Carazo JM, Marabi..."

== Citation ==

J Struct Biol. 2012 Apr;178(1):29-37.
Image formation in cellular X-ray microscopy.
Oton J, Sorzano CO, Pereiro E, Cuenca-Alba J, Navarro R, Carazo JM, Marabini R.

== Abstract ==

Soft X-ray Tomographic (TomoX) microscopy has become a reality in the last years. The resolution range of this technique nicely fits between confocal and electron microscopies and will play a key role in the elucidation of the organization between the molecular and the organelle levels. In fact, it offers the possibility of imaging three-dimensional structures of hydrated biological specimens near their native state without chemical pre-treatment. Ideally, TomoX reconstructs the specimen absorption coefficients from projections of this specimen, but, unfortunately, X-ray micrographs are only an approximation to projections of the specimen, resulting in inaccuracies if a tomographic reconstruction is performed without explicitly incorporating these approximations. In an attempt to mitigate some of these inaccuracies, we develop in this work an image formation model within the approximation of assuming incoherent illumination.

== Keywords ==

X-ray microscopy, image formation models

== Links ==

http://www.ncbi.nlm.nih.gov/pubmed/22343468

== Related software ==

== Related methods ==

== Comments ==

Main Page

2013-01-16T16:50:20Z

Jose Maria Carazo: /* X-ray tomography */

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 ==

{|

| 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 

[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 

[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]

2011Voortman Tilted

2013-01-15T11:00:39Z

Jose Maria Carazo: Created page with "== Citation == Ultramicroscopy. 2011 Jul;111(8):1029-36. A fast algorithm for computing and correcting the CTF for tilted, thick specimens in TEM. Voortman LM, Stallinga S, ..."

== Citation ==

Ultramicroscopy. 2011 Jul;111(8):1029-36.
A fast algorithm for computing and correcting the CTF for tilted, thick specimens in TEM.
Voortman LM, Stallinga S, Schoenmakers RH, van Vliet LJ, Rieger B.

== Abstract ==

Today, the resolution in phase-contrast cryo-electron tomography is for a significant part limited by the contrast transfer function (CTF) of the microscope. The CTF is a function of defocus and thus varies spatially as a result of the tilting of the specimen and the finite specimen thickness. Models that include spatial dependencies have not been adopted in daily practice because of their high computational complexity. Here we present an algorithm which reduces the processing time for computing the 'tilted' CTF by more than a factor 100. Our implementation of the full 3D CTF has a processing time on the order of a Radon transform of a full tilt-series. We derive and validate an expression for the damping envelope function describing the loss of resolution due to specimen thickness. Using simulations we quantify the effects of specimen thickness on the accuracy of various forward models. We study the influence of spatially varying CTF correction and subsequent tomographic reconstruction by simulation and present a new approach for space-variant phase-flipping. We show that our CTF correction strategies are successful in increasing the resolution after tomographic reconstruction.

== Keywords ==

CTF estimation, CTF correction, Tilted images

== Links ==

http://www.ncbi.nlm.nih.gov/pubmed/21740865

== Related software ==

== Related methods ==

== Comments ==

Main Page

2013-01-15T10:58:47Z

Jose Maria Carazo: /* 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.

== 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
| [[2011Zhang2011_LimitingFactors]]
| Limiting factor for atomic resolution in EM
|-

| Paper
| [[2011Glaeser_Coma]]
| Image formation model including coma
|-

|}

=== Collection geometry ===

{|

| Chapter
| [[1980Hoppe_Wedge]]
| Missing wedge
|-

| Paper
| [[1987Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1995Penczek_Dual]]
| Dual axis tomography
|-

| Paper
| [[1997Mastronarde_Dual]]
| Dual axis tomography
|-

| Paper
| [[2005Lanzavecchia_Conical]]
| Conical tomography
|-

| Paper
| [[2005Zampighi_Conical]]
| Conical tomography
|-

| Paper
| [[2006Leschziner_OT]]
| Orthogonal Tilt
|-

| Paper
| [[2006Messaoudi_Multiple]]
| Multiple axis tomography
|-

|}

=== Sample preparation ===

{|

| Paper
| [[1982Dubochet_Sample]]
| Vitreous ice
|-

| Paper
| [[1986Lepault_Sample]]
| Fast freezing
|-

| Paper
| [[1995Dubochet_Sample]]
| High-pressure freezing
|-

| Paper
| [[1995VanMarle_Sample]]
| Sample damages in resin
|-

| Paper
| [[1998Adrian_Sample]]
| Cryo negative staining
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2002Hsieh_Sample]]
| Cryofixation
|-

| Paper
| [[2004AlAmoudi_Sample]]
| CEMOVIS
|-

| Paper
| [[2008Studer_Sample]]
| Review on high pressure freezing
|-

| Paper
| [[2009Pierson_Sample]]
| Review on sample preparation for electron tomography
|-

|}

=== Automated data collection ===

{|

| Paper
| [[1992Dierksen_Automatic]]
| Automated data collection
|-

| Paper
| [[1992Koster_Automatic]]
| Automated data collection
|-

| Paper
| [[2001Zhang_Automatic]]
| Automated sample collection
|-

| Paper
| [[2003Ziese_Automatic]]
| Automated autofocusing
|-

| Paper
| [[2004Potter_Automatic]]
| Automated sample loading
|-

| Paper
| [[2004Zheng_Automatic]]
| Automated data collection
|-

| Paper
| [[2005Lei_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2005Suloway_Automatic]]
| Automated data collection: Leginon
|-

|}

== Single particles ==

=== Automatic particle picking ===

{|

| Paper
| [[1982VanHeel_Detection]]
| Detection of particles in micrographs
|-

| Paper
| [[2001Nicholson_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2001Zhu_Filaments]]
| Automatic identification of filaments in micrographs
|-

| Paper
| [[2004Zhu_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2009Sorzano_MachineLearning]]
| Automatic particle picking based on machine learning of rotational invariants
|-

|}

=== 2D Preprocessing ===

{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast enhancement through DPR
|-

| Paper
| [[2004Sorzano_Normalization]]
| Normalization procedures and their statistical properties.
|-

| Paper
| [[2006Sorzano_Denoising]]
| Strong denoising in wavelet space
|-

| Conference
| [[2009Sorzano_Downsampling]]
| Differences between the different downsampling schemes
|-

|}

=== 2D Alignment ===

{|

| Paper
| [[1981Frank_Averaging]]
| 2D averaging and phase residual
|-

| Paper
| [[1982Saxton_Averaging]]
| 2D averaging using correlation
|-

| Paper
| [[1998Sigworth_ML2D]]
| Maximum likelihood alignment in 2D
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

|}

=== 2D Classification and clustering ===

{|

| Paper
| [[1981VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[1984VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

|}

=== 3D Alignment ===

{|

| Paper
| [[1987VanHeel_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1988Provencher_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Vogel_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1990Gelfand_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Goncharov_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Harauz_Quaternions]]
| Use of quaternions to represent rotations
|-

| Paper
| [[1994Penczek_Real]]
| Angular assignment using projection matching in real space
|-

| Paper
| [[1994Radermacher_Radon]]
| Angular assignment in Radon space
|-

| Paper
| [[1996Penczek_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[2003Rosenthal_DPR]]
| Angular assignment using DPR
|-

| Paper
| [[2004Sorzano_Wavelet]]
| Angular assignment in the wavelet space.
|-

| Paper
| [[2005Jonic_Splines]]
| Angular assignment in Fourier space using spline interpolation.
|-

| Paper
| [[2005Yang_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

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

| Paper
| [[2012Giannakis_Scattering]]
| Construction of an initial volume, reference free, by graph analysis of the projections
|-

|}

=== 3D Reconstruction ===
{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1986Harauz_FBP]]
| Exact filters for Filtered Back Projection
|-

| Chapter
| [[1992Radermacher_WBP]]
| Exact filters for Weighted Back Projection
|-

| Paper
| [[1997Zhu_RecCTF]]
| 3D Reconstruction (SIRT like) and simultaneous CTF correction
|-

| Paper
| [[1998Boisset_Uneven]]
| Artifacts in SIRT and WBP under uneven angular distributions
|-

| Paper
| [[1998Marabini_ART]]
| Algebraic Reconstruction Technique with blobs (Xmipp)
|-

| Paper
| [[2001Sorzano_Uneven]]
| Free parameter selection under uneven angular distributions
|-

| Paper
| [[2005Sorzano_Parameters]]
| Free parameter selection for optimizing multiple tasks
|-

| Paper
| [[2008Sorzano_Constraints]]
| Mass, surface, positivity and symmetry constraints for real-space algorithms
|-

| Paper
| [[2009Bilbao_ParallelART]]
| Efficient parallelization of ART
|-

| Paper
| [[2011Li_GradientFlow]]
| Regularized 3D Reconstruction by Gradient Flow
|-

|}

=== 3D Heterogeneity ===

{|

| Paper
| [[2004White_Size]]
| Heterogeneity classification of differently sized images
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Scheres_ML3D]]
| Maximum Likelihood alignment and classification in 3D
|-

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

|}

=== Resolution ===

{|

| Paper
| [[1986Harauz_FBP]]
| Fourier Shell Correlation
|-

| Paper
| [[1987Unser_SSNR]]
| 2D Spectral Signal to Noise Ratio
|-

| Paper
| [[2002Penczek_SSNR]]
| 3D Spectral Signal to Noise Ratio for Fourier based algorithms
|-

| Paper
| [[2003Rosenthal_DPR]]
| Review of the FSC and establishment of a new threshold
|-

| Paper
| [[2005Unser_SSNR]]
| 3D Spectral Signal to Noise Ratio for any kind of algorithms
|-

| Paper
| [[2005VanHeel_FSC]]
| Establishment of a new threshold for FSC
|-

| Paper
| [[2007Sousa_AbInitio]]
| Resolution measurement on neighbour Fourier voxels
|-

|}

=== Sharpening of high resolution information ===
{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast restoration and map sharpening
|-

| Paper
| [[2008Fernandez_Bfactor]]
| Bfactor determination and restoration
|-

|}

=== CTF estimation and restoration ===

{|

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

| Paper
| [[1984Cohen_Validity]]
| Validity of the CTF model at high frequencies
|-

| Paper
| [[1988Toyoshima_Model]]
| CTF estimation
|-

| Paper
| [[1993Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[1995Frank_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1996Skoglund_MaxEnt]]
| CTF correction with Maximum Entropy
|-

| Paper
| [[1996Zhou_Model]]
| CTF model and user interface for manual fitting
|-

| Paper
| [[1997Fernandez_AR]]
| PSD estimation using periodogram averaging and AR models
|-

| Paper
| [[1997Penczek_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1997Stark_Deconvolution]]
| CTF correction using deconvolution
|-

| Paper
| [[1997Zhu_RecCTF]]
| CTF correction and reconstruction
|-

| Paper
| [[2000DeRosier_EwaldCorrection]]
| CTF correction considering the Ewald sphere
|-

| Paper
| [[2000Jensen_TiltedCorrection]]
| CTF correction considering tilt in backprojection
|-

| Paper
| [[2001Saad_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Huang_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Mindell_CTFTILT]]
| CTF estimation for tilted micrographs
|-

| Paper
| [[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
|-

|}

== 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 ]

== 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]

2010Kasantsev CTFCorrection

2013-01-15T10:54:29Z

Jose Maria Carazo: Created page with "== Citation == Ultramicroscopy. 2010 Aug;110(9):1128-42. Fully three-dimensional defocus-gradient corrected backprojection in cryoelectron microscopy. Kazantsev IG, Klukowsk..."

== Citation ==

Ultramicroscopy. 2010 Aug;110(9):1128-42.
Fully three-dimensional defocus-gradient corrected backprojection in cryoelectron microscopy.
Kazantsev IG, Klukowska J, Herman GT, Cernetic L.

== Abstract ==

Recognizing that the microscope depth of field is a significant resolution-limiting factor in 3D cryoelectron microscopy, Jensen and Kornberg proposed a concept they called defocus-gradient corrected backprojection (DGCBP) and illustrated by computer simulations that DGCBP can effectively eliminate the depth of field limitation. They did not provide a mathematical justification for their concept. Our paper provides this, by showing (in the idealized case of noiseless data being available for all projection directions) that the reconstructions obtained based on DGCBP from data produced with distance-dependent blurring are essentially the same as what is obtained by a classical method of reconstruction of a 3D object from its line integrals. The approach is general enough to be applicable for correcting for any distance-dependent blurring during projection data collection. We present a new implementation of the DGCBP concept, one that closely follows the mathematics of its justifications, and illustrate it using mathematically described phantoms and their reconstructions from finitely many distance-dependently blurred projections.

== Keywords ==

CTF correction, backprojection

== Links ==

http://www.ncbi.nlm.nih.gov/pubmed/20462697

== Related software ==

== Related methods ==

== Comments ==

Main Page

2013-01-15T10:51:38Z

Jose Maria Carazo: /* 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.

== 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
| [[2011Zhang2011_LimitingFactors]]
| Limiting factor for atomic resolution in EM
|-

| Paper
| [[2011Glaeser_Coma]]
| Image formation model including coma
|-

|}

=== Collection geometry ===

{|

| Chapter
| [[1980Hoppe_Wedge]]
| Missing wedge
|-

| Paper
| [[1987Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1995Penczek_Dual]]
| Dual axis tomography
|-

| Paper
| [[1997Mastronarde_Dual]]
| Dual axis tomography
|-

| Paper
| [[2005Lanzavecchia_Conical]]
| Conical tomography
|-

| Paper
| [[2005Zampighi_Conical]]
| Conical tomography
|-

| Paper
| [[2006Leschziner_OT]]
| Orthogonal Tilt
|-

| Paper
| [[2006Messaoudi_Multiple]]
| Multiple axis tomography
|-

|}

=== Sample preparation ===

{|

| Paper
| [[1982Dubochet_Sample]]
| Vitreous ice
|-

| Paper
| [[1986Lepault_Sample]]
| Fast freezing
|-

| Paper
| [[1995Dubochet_Sample]]
| High-pressure freezing
|-

| Paper
| [[1995VanMarle_Sample]]
| Sample damages in resin
|-

| Paper
| [[1998Adrian_Sample]]
| Cryo negative staining
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2002Hsieh_Sample]]
| Cryofixation
|-

| Paper
| [[2004AlAmoudi_Sample]]
| CEMOVIS
|-

| Paper
| [[2008Studer_Sample]]
| Review on high pressure freezing
|-

| Paper
| [[2009Pierson_Sample]]
| Review on sample preparation for electron tomography
|-

|}

=== Automated data collection ===

{|

| Paper
| [[1992Dierksen_Automatic]]
| Automated data collection
|-

| Paper
| [[1992Koster_Automatic]]
| Automated data collection
|-

| Paper
| [[2001Zhang_Automatic]]
| Automated sample collection
|-

| Paper
| [[2003Ziese_Automatic]]
| Automated autofocusing
|-

| Paper
| [[2004Potter_Automatic]]
| Automated sample loading
|-

| Paper
| [[2004Zheng_Automatic]]
| Automated data collection
|-

| Paper
| [[2005Lei_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2005Suloway_Automatic]]
| Automated data collection: Leginon
|-

|}

== Single particles ==

=== Automatic particle picking ===

{|

| Paper
| [[1982VanHeel_Detection]]
| Detection of particles in micrographs
|-

| Paper
| [[2001Nicholson_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2001Zhu_Filaments]]
| Automatic identification of filaments in micrographs
|-

| Paper
| [[2004Zhu_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2009Sorzano_MachineLearning]]
| Automatic particle picking based on machine learning of rotational invariants
|-

|}

=== 2D Preprocessing ===

{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast enhancement through DPR
|-

| Paper
| [[2004Sorzano_Normalization]]
| Normalization procedures and their statistical properties.
|-

| Paper
| [[2006Sorzano_Denoising]]
| Strong denoising in wavelet space
|-

| Conference
| [[2009Sorzano_Downsampling]]
| Differences between the different downsampling schemes
|-

|}

=== 2D Alignment ===

{|

| Paper
| [[1981Frank_Averaging]]
| 2D averaging and phase residual
|-

| Paper
| [[1982Saxton_Averaging]]
| 2D averaging using correlation
|-

| Paper
| [[1998Sigworth_ML2D]]
| Maximum likelihood alignment in 2D
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

|}

=== 2D Classification and clustering ===

{|

| Paper
| [[1981VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[1984VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

|}

=== 3D Alignment ===

{|

| Paper
| [[1987VanHeel_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1988Provencher_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Vogel_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1990Gelfand_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Goncharov_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Harauz_Quaternions]]
| Use of quaternions to represent rotations
|-

| Paper
| [[1994Penczek_Real]]
| Angular assignment using projection matching in real space
|-

| Paper
| [[1994Radermacher_Radon]]
| Angular assignment in Radon space
|-

| Paper
| [[1996Penczek_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[2003Rosenthal_DPR]]
| Angular assignment using DPR
|-

| Paper
| [[2004Sorzano_Wavelet]]
| Angular assignment in the wavelet space.
|-

| Paper
| [[2005Jonic_Splines]]
| Angular assignment in Fourier space using spline interpolation.
|-

| Paper
| [[2005Yang_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

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

| Paper
| [[2012Giannakis_Scattering]]
| Construction of an initial volume, reference free, by graph analysis of the projections
|-

|}

=== 3D Reconstruction ===
{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1986Harauz_FBP]]
| Exact filters for Filtered Back Projection
|-

| Chapter
| [[1992Radermacher_WBP]]
| Exact filters for Weighted Back Projection
|-

| Paper
| [[1997Zhu_RecCTF]]
| 3D Reconstruction (SIRT like) and simultaneous CTF correction
|-

| Paper
| [[1998Boisset_Uneven]]
| Artifacts in SIRT and WBP under uneven angular distributions
|-

| Paper
| [[1998Marabini_ART]]
| Algebraic Reconstruction Technique with blobs (Xmipp)
|-

| Paper
| [[2001Sorzano_Uneven]]
| Free parameter selection under uneven angular distributions
|-

| Paper
| [[2005Sorzano_Parameters]]
| Free parameter selection for optimizing multiple tasks
|-

| Paper
| [[2008Sorzano_Constraints]]
| Mass, surface, positivity and symmetry constraints for real-space algorithms
|-

| Paper
| [[2009Bilbao_ParallelART]]
| Efficient parallelization of ART
|-

| Paper
| [[2011Li_GradientFlow]]
| Regularized 3D Reconstruction by Gradient Flow
|-

|}

=== 3D Heterogeneity ===

{|

| Paper
| [[2004White_Size]]
| Heterogeneity classification of differently sized images
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Scheres_ML3D]]
| Maximum Likelihood alignment and classification in 3D
|-

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

|}

=== Resolution ===

{|

| Paper
| [[1986Harauz_FBP]]
| Fourier Shell Correlation
|-

| Paper
| [[1987Unser_SSNR]]
| 2D Spectral Signal to Noise Ratio
|-

| Paper
| [[2002Penczek_SSNR]]
| 3D Spectral Signal to Noise Ratio for Fourier based algorithms
|-

| Paper
| [[2003Rosenthal_DPR]]
| Review of the FSC and establishment of a new threshold
|-

| Paper
| [[2005Unser_SSNR]]
| 3D Spectral Signal to Noise Ratio for any kind of algorithms
|-

| Paper
| [[2005VanHeel_FSC]]
| Establishment of a new threshold for FSC
|-

| Paper
| [[2007Sousa_AbInitio]]
| Resolution measurement on neighbour Fourier voxels
|-

|}

=== Sharpening of high resolution information ===
{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast restoration and map sharpening
|-

| Paper
| [[2008Fernandez_Bfactor]]
| Bfactor determination and restoration
|-

|}

=== CTF estimation and restoration ===

{|

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

| Paper
| [[1984Cohen_Validity]]
| Validity of the CTF model at high frequencies
|-

| Paper
| [[1988Toyoshima_Model]]
| CTF estimation
|-

| Paper
| [[1993Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[1995Frank_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1996Skoglund_MaxEnt]]
| CTF correction with Maximum Entropy
|-

| Paper
| [[1996Zhou_Model]]
| CTF model and user interface for manual fitting
|-

| Paper
| [[1997Fernandez_AR]]
| PSD estimation using periodogram averaging and AR models
|-

| Paper
| [[1997Penczek_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1997Stark_Deconvolution]]
| CTF correction using deconvolution
|-

| Paper
| [[1997Zhu_RecCTF]]
| CTF correction and reconstruction
|-

| Paper
| [[2000DeRosier_EwaldCorrection]]
| CTF correction considering the Ewald sphere
|-

| Paper
| [[2000Jensen_TiltedCorrection]]
| CTF correction considering tilt in backprojection
|-

| Paper
| [[2001Saad_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Huang_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Mindell_CTFTILT]]
| CTF estimation for tilted micrographs
|-

| Paper
| [[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
| [[2011Sindelar_Wiener]]
| CTF correction using a modified version of Wiener filter
|-

| Paper
| [[2011Glaeser_Coma]]
| The effect of coma at high-resolution
|-

| Paper
| [[2012Voortman_VaryingCTF]]
| Correcting a spatially varying CTF
|-

|}

=== Segmentation ===

{|

| Paper
| [[2006Baker_segmentation]]
| Segmentation of molecular subunits
|-

|}

=== Fitting and docking ===

{|

| Paper
| [[1999Volkmann_Fitting]]
| Fitting in real space
|-

| Paper
| [[2001Baker_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2001Jones_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2004Tama_NMA1]]
| Flexible fitting with Normal Modes (I)
|-

| Paper
| [[2004Tama_NMA2]]
| Flexible fitting with Normal Modes (II)
|-

| Paper
| [[2005Velazquez_Superfamilies]]
| Recognition of the superfamily folding in medium-high resolution volumes
|-

| Paper
| [[2007Kleywegt_QualityControl]]
| Quality control and validation of fitting
|-

| Paper
| [[2012Velazquez_Constraints]]
| Multicomponent fitting by using constraints from other information sources
|-

|}

=== Books and reviews ===

{|

| Book
| [[1980Herman_Tomography]]
| General book on tomography
|-

| Book
| [[1988Kak_Tomography]]
| General book on tomography
|-

| Paper
| [[2000Tao_Review]]
| Review of single particles
|-

| Paper
| [[2000VanHeel_Review]]
| Review of single particles
|-

| Paper
| [[2002Frank_Review]]
| Review of single particles
|-

| Paper
| [[2002Schmid_Review]]
| Review of single particles
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2004Subramaniam_Review]]
| Review of single particles
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_book]]
| Book covering all aspects of electron microscopy of single particles
|-

| Paper
| [[2006Sorzano_Review]]
| Review of optimization problems in electron microscopy
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems in Electron Tomography
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2010DeRosier_Review]]
| Personal account of how 3DEM developed in the early days
|-

| Chapter
| [[2012Sorzano_Review]]
| Review of single particle analysis using Xmipp
|-

| Chapter
| [[2012Devaux_Protocol]]
| Protocols for performing single particle analysis
|-

|}

=== Software ===

{|

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[1999Lutdke_Eman]]
| Eman
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Baldwin_AngularTransformations]]
| The Transform Class in SPARX and EMAN2
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2008Scheres_XmippProtocols]]
| Xmipp Protocols
|-

|}

== Electron tomography ==

=== Image alignment ===

{|

| Paper
| [[2001Brandt_Automatic1]]
| Automatic alignment without fiducial markers
|-

| Paper
| [[2001Brandt_Automatic2]]
| Automatic alignment with fiducial markers
|-

| Paper
| [[2006Winkler_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2006Castano_alignment]]
| Alignment with non-perpendicularity
|-

| Paper
| [[2007Castano_alignment]]
| Fiducial-less alignment of cryo-sections
|-

| Paper
| [[2009Sorzano_alignment]]
| Marker-free alignment and refinement
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[2003Winkler_CTF]]
| Focus gradient correction in electron tomography
|-

| Paper
| [[2006Fernandez_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Zanetti_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Xiong_CTF]]
| CTF determination and correction for low dose tomographic tilt series
|-

|}

=== 3D reconstruction ===

{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1992Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[1997Marabini_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2002Fernandez_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2007Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[2008Fernandez_CARP]]
| Component Averaged Row Projections (CARP)
|-
|}

=== Noise reduction ===
{|

| Paper
| [[2001Frangakis_NAD]]
| Noise reduction with Nonlinear Anisotropic Diffusion
|-

| Paper
| [[2003Fernandez_AND]]
| Anisotropic nonlinear diffusion for electron tomography
|-

| Paper
| [[2003Jiang_Bilateral]]
| Bilateral denoising filter in electron microscopy
|-

| Paper
| [[2005Fernandez_AND]]
| Anisotropic nonlinear denoising in electron tomography
|-

| Paper
| [[2007Heide_median]]
| Iterative median filtering in electron tomography
|-

| Paper
| [[2007Fernandez_autAND]]
| Anisotropic nonlinear diffusion with automated parameter tuning
|-

| Paper
| [[2009Fernandez_Beltrami]]
| Nonlinear filtering based on Beltrami flow
|-

| Paper
| [[2010Bilbao_MeanShift]]
| Mean Shift Filtering
|-

|}

=== Segmentation ===

{|

| Paper
| [[2002Frangakis_Eigenanalysis]]
| Segmentation using eigenvector analysis.
|-

| Paper
| [[2002Volkmann_Watershed]]
| Segmentation using watershed transform.
|-

| Paper
| [[2003Bajaj_BoundarySegmentation]]
| Segmentation based on fast marching.
|-

| Paper
| [[2005Cyrklaff_Thresholding]]
| Segmentation using optimal thresholding.
|-

| Paper
| [[2007Lebbink_TemplateMatching]]
| Segmentation using template matching.
|-

| Paper
| [[2007Sandberg_OrientationFields]]
| Segmentation using orientation fields.
|-

| Paper
| [[2007Sandberg_SegmentationReview]]
| Review on segmentation in electron tomography.
|-

| Paper
| [[2008Garduno_FuzzySegmentation]]
| Segmentation using fuzzy set theory principles.
|-

| Paper
| [[2009Lebbink_TemplateMatching2]]
| Segmentation using template matching.
|-

|}

=== Resolution ===
{|

| Paper
| [[2005Cardone_Resolution]]
| Resolution criterion for electron tomography
|-

|}

=== Subtomogram analysis ===

{|

| Paper
| [[2000Bohm_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2002Frangakis_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2006Nickell_Review]]
| Review of macromolecule finding by template matching (Visual Proteomics)
|-

| Paper
| [[2007Best_Review]]
| Review of Localization of Protein Complexes by Pattern Recognition
|-

| Paper
| [[2007Forster_Review]]
| Review of structure determination by subtomogram averaging
|-

| Paper
| [[2008Forster_Classification]]
| Classification of subtomograms using constrained correlation
|-

| Paper
| [[2008Bartesaghi_Classification]]
| Classification and averaging of subtomograms
|-

| Paper
| [[2008Schmid_Averaging]]
| Alignment and averaging of subtomograms
|-

| Paper
| [[2010Amat_Averaging]]
| Alignment and averaging of subtomograms exploiting thresholding in Fourier space
|-

|}

=== Single particle tomography ===

{|

| Paper
| [[2012Bartesaghi_Constrained]]
| 3D reconstruction by imposing geometrical constraints
|-

|}

=== Books and reviews ===

{|

| Paper
| [[2000Baumeister_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Koster_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Sali_Review]]
| Review of electron tomography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2005Lucic_Review]]
| Review of electron tomography
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_TomoBook]]
| Electron Tomography
|-

| Book
| [[2007McIntosh_Book]]
| Cellular Electron Microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

|}

=== Software ===

{|

| Paper
| [[1996Kremer_IMOD]]
| IMOD
|-

| Paper
| [[1996Chen_Priism/IVE]]
| Priism/IVE
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2005Nickell_TOM]]
| TOM Toolbox
|-

| Paper
| [[2007Messaoudi_TomoJ]]
| TomoJ
|-

| Paper
| [[2008Heymann_BsoftTomo]]
| Bsoft
|-

|}

== 2D Crystals ==

=== 2D Preprocessing ===

{|

| Paper
| [[1986Henderson_Processing]]
| General 2D processing
|-

| Paper
| [[2000He_PhaseAlignment]]
| Phase consistency and Alignment
|-

| Paper
| [[2006Gil_Unbending]]
| Crystal unbending
|-

|}

=== Classification ===
{|

| Paper
| [[1988Frank_Classification]]
| MSA and classification in electron crystallography
|-

| Paper
| [[1996Fernandez_SOM]]
| Classification based on self organizing maps
|-

| Paper
| [[1998Sherman_MSA]]
| Classification based on MSA
|-

|}
=== 3D Reconstruction ===

{|

| Paper
| [[1985Wang_Solvent]]
| Solvent flattening
|-

| Paper
| [[1990Henderson_Processing]]
| General 3D processing
|-

| Paper
| [[2004Marabini_ART]]
| Algebraic Reconstruction Technique with blobs for crystals (Xmipp)
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1998Walz_Review]]
| Review of 2D crystallography
|-

| Paper
| [[1999Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Ellis_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of single particles, electron tomography and crystallography
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Gipson_2dx]]
| 2dx
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Philippsen_IPLT]]
| IPLT
|-

|}

== Helical particles ==

=== Filament corrections ===

{|

| Paper
| [[1986Egelman_Curved]]
| Algorithm for correcting curved filaments
|-

| Paper
| [[1988Bluemke_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2006Wang_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

|}

=== Reconstruction ===

{|

| Paper
| [[1958Klug_Fourier]]
| Fourier Bessel decomposition of the projection images
|-

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2005Wang_Iterative]]
| Iterative Fourier-Bessel algorithm
|-

| Paper
| [[2007Egelman_Iterative]]
| Iterative real-space algorithm
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Carragher_Phoelix]]
| Phoelix
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Owen_Brandeis]]
| Brandeis
|-

|}

== Icosahedral particles ==

=== Reconstruction ===

{|

| Paper
| [[1970Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1971Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1996Fuller_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1997Thuman_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

|}

=== Classification ===

{|

| Paper
| [[2005Scheres_Virus]]
| Classification of virus capsids in real space
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1999Baker_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[1999Conway_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2000Thuman_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Lee_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Navaza_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2006Grunewald_Review]]
| Review of reconstruction of icosahedral viruses
|-

|}

=== Software ===

{|

| Paper
| [[1996Baker_EMPFT]]
| EMPFT
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

|}

== Data bases ==

{|

| Paper
| [[2003Boutselakis_EMSD]]
| EMSD database
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

|}

== Relationship to other structural information sources ==

{|

| Paper
| [[2000Engel_AFM]]
| Review of Atomic Force Microscopy
|-

| Paper
| [[2001Dimmeler_AFM]]
| Constraints from Atomic Force Microscopy
|-

| Paper
| [[2003Mobus_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_Review]]
| Review on correlative microscopy
|-

| Paper
| [[2005Boudier_EFTETJ]]
| Software for Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2005Vestergaard_SAXS]]
| Example of comparison of 3DEM and Small-angle X-ray scattering
|-

| Paper
| [[2007Hamada_SAXS]]
| Constraints from Small-angle X-ray scattering
|-

|}

== 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 ]

== 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]

2010Leong CTFCorrection

2013-01-15T10:45:07Z

Jose Maria Carazo: Created page with "== Citation == Methods Enzymol. 2010;482:369-80. Correcting for the ewald sphere in high-resolution single-particle reconstructions. Leong PA, Yu X, Zhou ZH, Jensen GJ. == ..."

== Citation ==

Methods Enzymol. 2010;482:369-80.
Correcting for the ewald sphere in high-resolution single-particle reconstructions.
Leong PA, Yu X, Zhou ZH, Jensen GJ.

== Abstract ==

To avoid the challenges of crystallization and the size limitations of NMR, it has long been hoped that single-particle cryo-electron microscopy (cryo-EM) would eventually yield atomically interpretable reconstructions. For the most favorable class of specimens (large icosahedral viruses), one of the key obstacles is curvature of the Ewald sphere, which leads to a breakdown of the Projection Theorem used by conventional three-dimensional (3D) reconstruction programs. Here, we review the basic problem and our implementation of the "paraboloid" reconstruction method, which overcomes the limitation by averaging information from images recorded from different points of view.

== Keywords ==

Spatially variant CTF, correction

== Links ==

http://www.ncbi.nlm.nih.gov/pubmed/20888969

== Related software ==

== Related methods ==

== Comments ==

Main Page

2013-01-15T10:38:21Z

Jose Maria Carazo: /* 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.

== 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
| [[2011Zhang2011_LimitingFactors]]
| Limiting factor for atomic resolution in EM
|-

| Paper
| [[2011Glaeser_Coma]]
| Image formation model including coma
|-

|}

=== Collection geometry ===

{|

| Chapter
| [[1980Hoppe_Wedge]]
| Missing wedge
|-

| Paper
| [[1987Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1995Penczek_Dual]]
| Dual axis tomography
|-

| Paper
| [[1997Mastronarde_Dual]]
| Dual axis tomography
|-

| Paper
| [[2005Lanzavecchia_Conical]]
| Conical tomography
|-

| Paper
| [[2005Zampighi_Conical]]
| Conical tomography
|-

| Paper
| [[2006Leschziner_OT]]
| Orthogonal Tilt
|-

| Paper
| [[2006Messaoudi_Multiple]]
| Multiple axis tomography
|-

|}

=== Sample preparation ===

{|

| Paper
| [[1982Dubochet_Sample]]
| Vitreous ice
|-

| Paper
| [[1986Lepault_Sample]]
| Fast freezing
|-

| Paper
| [[1995Dubochet_Sample]]
| High-pressure freezing
|-

| Paper
| [[1995VanMarle_Sample]]
| Sample damages in resin
|-

| Paper
| [[1998Adrian_Sample]]
| Cryo negative staining
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2002Hsieh_Sample]]
| Cryofixation
|-

| Paper
| [[2004AlAmoudi_Sample]]
| CEMOVIS
|-

| Paper
| [[2008Studer_Sample]]
| Review on high pressure freezing
|-

| Paper
| [[2009Pierson_Sample]]
| Review on sample preparation for electron tomography
|-

|}

=== Automated data collection ===

{|

| Paper
| [[1992Dierksen_Automatic]]
| Automated data collection
|-

| Paper
| [[1992Koster_Automatic]]
| Automated data collection
|-

| Paper
| [[2001Zhang_Automatic]]
| Automated sample collection
|-

| Paper
| [[2003Ziese_Automatic]]
| Automated autofocusing
|-

| Paper
| [[2004Potter_Automatic]]
| Automated sample loading
|-

| Paper
| [[2004Zheng_Automatic]]
| Automated data collection
|-

| Paper
| [[2005Lei_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2005Suloway_Automatic]]
| Automated data collection: Leginon
|-

|}

== Single particles ==

=== Automatic particle picking ===

{|

| Paper
| [[1982VanHeel_Detection]]
| Detection of particles in micrographs
|-

| Paper
| [[2001Nicholson_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2001Zhu_Filaments]]
| Automatic identification of filaments in micrographs
|-

| Paper
| [[2004Zhu_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2009Sorzano_MachineLearning]]
| Automatic particle picking based on machine learning of rotational invariants
|-

|}

=== 2D Preprocessing ===

{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast enhancement through DPR
|-

| Paper
| [[2004Sorzano_Normalization]]
| Normalization procedures and their statistical properties.
|-

| Paper
| [[2006Sorzano_Denoising]]
| Strong denoising in wavelet space
|-

| Conference
| [[2009Sorzano_Downsampling]]
| Differences between the different downsampling schemes
|-

|}

=== 2D Alignment ===

{|

| Paper
| [[1981Frank_Averaging]]
| 2D averaging and phase residual
|-

| Paper
| [[1982Saxton_Averaging]]
| 2D averaging using correlation
|-

| Paper
| [[1998Sigworth_ML2D]]
| Maximum likelihood alignment in 2D
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

|}

=== 2D Classification and clustering ===

{|

| Paper
| [[1981VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[1984VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

|}

=== 3D Alignment ===

{|

| Paper
| [[1987VanHeel_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1988Provencher_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Vogel_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1990Gelfand_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Goncharov_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Harauz_Quaternions]]
| Use of quaternions to represent rotations
|-

| Paper
| [[1994Penczek_Real]]
| Angular assignment using projection matching in real space
|-

| Paper
| [[1994Radermacher_Radon]]
| Angular assignment in Radon space
|-

| Paper
| [[1996Penczek_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[2003Rosenthal_DPR]]
| Angular assignment using DPR
|-

| Paper
| [[2004Sorzano_Wavelet]]
| Angular assignment in the wavelet space.
|-

| Paper
| [[2005Jonic_Splines]]
| Angular assignment in Fourier space using spline interpolation.
|-

| Paper
| [[2005Yang_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

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

| Paper
| [[2012Giannakis_Scattering]]
| Construction of an initial volume, reference free, by graph analysis of the projections
|-

|}

=== 3D Reconstruction ===
{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1986Harauz_FBP]]
| Exact filters for Filtered Back Projection
|-

| Chapter
| [[1992Radermacher_WBP]]
| Exact filters for Weighted Back Projection
|-

| Paper
| [[1997Zhu_RecCTF]]
| 3D Reconstruction (SIRT like) and simultaneous CTF correction
|-

| Paper
| [[1998Boisset_Uneven]]
| Artifacts in SIRT and WBP under uneven angular distributions
|-

| Paper
| [[1998Marabini_ART]]
| Algebraic Reconstruction Technique with blobs (Xmipp)
|-

| Paper
| [[2001Sorzano_Uneven]]
| Free parameter selection under uneven angular distributions
|-

| Paper
| [[2005Sorzano_Parameters]]
| Free parameter selection for optimizing multiple tasks
|-

| Paper
| [[2008Sorzano_Constraints]]
| Mass, surface, positivity and symmetry constraints for real-space algorithms
|-

| Paper
| [[2009Bilbao_ParallelART]]
| Efficient parallelization of ART
|-

| Paper
| [[2011Li_GradientFlow]]
| Regularized 3D Reconstruction by Gradient Flow
|-

|}

=== 3D Heterogeneity ===

{|

| Paper
| [[2004White_Size]]
| Heterogeneity classification of differently sized images
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Scheres_ML3D]]
| Maximum Likelihood alignment and classification in 3D
|-

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

|}

=== Resolution ===

{|

| Paper
| [[1986Harauz_FBP]]
| Fourier Shell Correlation
|-

| Paper
| [[1987Unser_SSNR]]
| 2D Spectral Signal to Noise Ratio
|-

| Paper
| [[2002Penczek_SSNR]]
| 3D Spectral Signal to Noise Ratio for Fourier based algorithms
|-

| Paper
| [[2003Rosenthal_DPR]]
| Review of the FSC and establishment of a new threshold
|-

| Paper
| [[2005Unser_SSNR]]
| 3D Spectral Signal to Noise Ratio for any kind of algorithms
|-

| Paper
| [[2005VanHeel_FSC]]
| Establishment of a new threshold for FSC
|-

| Paper
| [[2007Sousa_AbInitio]]
| Resolution measurement on neighbour Fourier voxels
|-

|}

=== Sharpening of high resolution information ===
{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast restoration and map sharpening
|-

| Paper
| [[2008Fernandez_Bfactor]]
| Bfactor determination and restoration
|-

|}

=== CTF estimation and restoration ===

{|

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

| Paper
| [[1984Cohen_Validity]]
| Validity of the CTF model at high frequencies
|-

| Paper
| [[1988Toyoshima_Model]]
| CTF estimation
|-

| Paper
| [[1993Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[1995Frank_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1996Skoglund_MaxEnt]]
| CTF correction with Maximum Entropy
|-

| Paper
| [[1996Zhou_Model]]
| CTF model and user interface for manual fitting
|-

| Paper
| [[1997Fernandez_AR]]
| PSD estimation using periodogram averaging and AR models
|-

| Paper
| [[1997Penczek_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1997Stark_Deconvolution]]
| CTF correction using deconvolution
|-

| Paper
| [[1997Zhu_RecCTF]]
| CTF correction and reconstruction
|-

| Paper
| [[2000DeRosier_EwaldCorrection]]
| CTF correction considering the Ewald sphere
|-

| Paper
| [[2000Jensen_TiltedCorrection]]
| CTF correction considering tilt in backprojection
|-

| Paper
| [[2001Saad_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Huang_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Mindell_CTFTILT]]
| CTF estimation for tilted micrographs
|-

| Paper
| [[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
| [[2010Leong_CTFCorrection]]
| Correction for spatially variant CTF
|-

| Paper
| [[2011Sindelar_Wiener]]
| CTF correction using a modified version of Wiener filter
|-

| Paper
| [[2011Glaeser_Coma]]
| The effect of coma at high-resolution
|-

| Paper
| [[2012Voortman_VaryingCTF]]
| Correcting a spatially varying CTF
|-

|}

=== Segmentation ===

{|

| Paper
| [[2006Baker_segmentation]]
| Segmentation of molecular subunits
|-

|}

=== Fitting and docking ===

{|

| Paper
| [[1999Volkmann_Fitting]]
| Fitting in real space
|-

| Paper
| [[2001Baker_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2001Jones_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2004Tama_NMA1]]
| Flexible fitting with Normal Modes (I)
|-

| Paper
| [[2004Tama_NMA2]]
| Flexible fitting with Normal Modes (II)
|-

| Paper
| [[2005Velazquez_Superfamilies]]
| Recognition of the superfamily folding in medium-high resolution volumes
|-

| Paper
| [[2007Kleywegt_QualityControl]]
| Quality control and validation of fitting
|-

| Paper
| [[2012Velazquez_Constraints]]
| Multicomponent fitting by using constraints from other information sources
|-

|}

=== Books and reviews ===

{|

| Book
| [[1980Herman_Tomography]]
| General book on tomography
|-

| Book
| [[1988Kak_Tomography]]
| General book on tomography
|-

| Paper
| [[2000Tao_Review]]
| Review of single particles
|-

| Paper
| [[2000VanHeel_Review]]
| Review of single particles
|-

| Paper
| [[2002Frank_Review]]
| Review of single particles
|-

| Paper
| [[2002Schmid_Review]]
| Review of single particles
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2004Subramaniam_Review]]
| Review of single particles
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_book]]
| Book covering all aspects of electron microscopy of single particles
|-

| Paper
| [[2006Sorzano_Review]]
| Review of optimization problems in electron microscopy
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems in Electron Tomography
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2010DeRosier_Review]]
| Personal account of how 3DEM developed in the early days
|-

| Chapter
| [[2012Sorzano_Review]]
| Review of single particle analysis using Xmipp
|-

| Chapter
| [[2012Devaux_Protocol]]
| Protocols for performing single particle analysis
|-

|}

=== Software ===

{|

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[1999Lutdke_Eman]]
| Eman
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Baldwin_AngularTransformations]]
| The Transform Class in SPARX and EMAN2
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2008Scheres_XmippProtocols]]
| Xmipp Protocols
|-

|}

== Electron tomography ==

=== Image alignment ===

{|

| Paper
| [[2001Brandt_Automatic1]]
| Automatic alignment without fiducial markers
|-

| Paper
| [[2001Brandt_Automatic2]]
| Automatic alignment with fiducial markers
|-

| Paper
| [[2006Winkler_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2006Castano_alignment]]
| Alignment with non-perpendicularity
|-

| Paper
| [[2007Castano_alignment]]
| Fiducial-less alignment of cryo-sections
|-

| Paper
| [[2009Sorzano_alignment]]
| Marker-free alignment and refinement
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[2003Winkler_CTF]]
| Focus gradient correction in electron tomography
|-

| Paper
| [[2006Fernandez_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Zanetti_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Xiong_CTF]]
| CTF determination and correction for low dose tomographic tilt series
|-

|}

=== 3D reconstruction ===

{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1992Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[1997Marabini_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2002Fernandez_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2007Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[2008Fernandez_CARP]]
| Component Averaged Row Projections (CARP)
|-
|}

=== Noise reduction ===
{|

| Paper
| [[2001Frangakis_NAD]]
| Noise reduction with Nonlinear Anisotropic Diffusion
|-

| Paper
| [[2003Fernandez_AND]]
| Anisotropic nonlinear diffusion for electron tomography
|-

| Paper
| [[2003Jiang_Bilateral]]
| Bilateral denoising filter in electron microscopy
|-

| Paper
| [[2005Fernandez_AND]]
| Anisotropic nonlinear denoising in electron tomography
|-

| Paper
| [[2007Heide_median]]
| Iterative median filtering in electron tomography
|-

| Paper
| [[2007Fernandez_autAND]]
| Anisotropic nonlinear diffusion with automated parameter tuning
|-

| Paper
| [[2009Fernandez_Beltrami]]
| Nonlinear filtering based on Beltrami flow
|-

| Paper
| [[2010Bilbao_MeanShift]]
| Mean Shift Filtering
|-

|}

=== Segmentation ===

{|

| Paper
| [[2002Frangakis_Eigenanalysis]]
| Segmentation using eigenvector analysis.
|-

| Paper
| [[2002Volkmann_Watershed]]
| Segmentation using watershed transform.
|-

| Paper
| [[2003Bajaj_BoundarySegmentation]]
| Segmentation based on fast marching.
|-

| Paper
| [[2005Cyrklaff_Thresholding]]
| Segmentation using optimal thresholding.
|-

| Paper
| [[2007Lebbink_TemplateMatching]]
| Segmentation using template matching.
|-

| Paper
| [[2007Sandberg_OrientationFields]]
| Segmentation using orientation fields.
|-

| Paper
| [[2007Sandberg_SegmentationReview]]
| Review on segmentation in electron tomography.
|-

| Paper
| [[2008Garduno_FuzzySegmentation]]
| Segmentation using fuzzy set theory principles.
|-

| Paper
| [[2009Lebbink_TemplateMatching2]]
| Segmentation using template matching.
|-

|}

=== Resolution ===
{|

| Paper
| [[2005Cardone_Resolution]]
| Resolution criterion for electron tomography
|-

|}

=== Subtomogram analysis ===

{|

| Paper
| [[2000Bohm_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2002Frangakis_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2006Nickell_Review]]
| Review of macromolecule finding by template matching (Visual Proteomics)
|-

| Paper
| [[2007Best_Review]]
| Review of Localization of Protein Complexes by Pattern Recognition
|-

| Paper
| [[2007Forster_Review]]
| Review of structure determination by subtomogram averaging
|-

| Paper
| [[2008Forster_Classification]]
| Classification of subtomograms using constrained correlation
|-

| Paper
| [[2008Bartesaghi_Classification]]
| Classification and averaging of subtomograms
|-

| Paper
| [[2008Schmid_Averaging]]
| Alignment and averaging of subtomograms
|-

| Paper
| [[2010Amat_Averaging]]
| Alignment and averaging of subtomograms exploiting thresholding in Fourier space
|-

|}

=== Single particle tomography ===

{|

| Paper
| [[2012Bartesaghi_Constrained]]
| 3D reconstruction by imposing geometrical constraints
|-

|}

=== Books and reviews ===

{|

| Paper
| [[2000Baumeister_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Koster_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Sali_Review]]
| Review of electron tomography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2005Lucic_Review]]
| Review of electron tomography
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_TomoBook]]
| Electron Tomography
|-

| Book
| [[2007McIntosh_Book]]
| Cellular Electron Microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

|}

=== Software ===

{|

| Paper
| [[1996Kremer_IMOD]]
| IMOD
|-

| Paper
| [[1996Chen_Priism/IVE]]
| Priism/IVE
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2005Nickell_TOM]]
| TOM Toolbox
|-

| Paper
| [[2007Messaoudi_TomoJ]]
| TomoJ
|-

| Paper
| [[2008Heymann_BsoftTomo]]
| Bsoft
|-

|}

== 2D Crystals ==

=== 2D Preprocessing ===

{|

| Paper
| [[1986Henderson_Processing]]
| General 2D processing
|-

| Paper
| [[2000He_PhaseAlignment]]
| Phase consistency and Alignment
|-

| Paper
| [[2006Gil_Unbending]]
| Crystal unbending
|-

|}

=== Classification ===
{|

| Paper
| [[1988Frank_Classification]]
| MSA and classification in electron crystallography
|-

| Paper
| [[1996Fernandez_SOM]]
| Classification based on self organizing maps
|-

| Paper
| [[1998Sherman_MSA]]
| Classification based on MSA
|-

|}
=== 3D Reconstruction ===

{|

| Paper
| [[1985Wang_Solvent]]
| Solvent flattening
|-

| Paper
| [[1990Henderson_Processing]]
| General 3D processing
|-

| Paper
| [[2004Marabini_ART]]
| Algebraic Reconstruction Technique with blobs for crystals (Xmipp)
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1998Walz_Review]]
| Review of 2D crystallography
|-

| Paper
| [[1999Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Ellis_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of single particles, electron tomography and crystallography
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Gipson_2dx]]
| 2dx
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Philippsen_IPLT]]
| IPLT
|-

|}

== Helical particles ==

=== Filament corrections ===

{|

| Paper
| [[1986Egelman_Curved]]
| Algorithm for correcting curved filaments
|-

| Paper
| [[1988Bluemke_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2006Wang_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

|}

=== Reconstruction ===

{|

| Paper
| [[1958Klug_Fourier]]
| Fourier Bessel decomposition of the projection images
|-

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2005Wang_Iterative]]
| Iterative Fourier-Bessel algorithm
|-

| Paper
| [[2007Egelman_Iterative]]
| Iterative real-space algorithm
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Carragher_Phoelix]]
| Phoelix
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Owen_Brandeis]]
| Brandeis
|-

|}

== Icosahedral particles ==

=== Reconstruction ===

{|

| Paper
| [[1970Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1971Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1996Fuller_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1997Thuman_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

|}

=== Classification ===

{|

| Paper
| [[2005Scheres_Virus]]
| Classification of virus capsids in real space
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1999Baker_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[1999Conway_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2000Thuman_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Lee_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Navaza_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2006Grunewald_Review]]
| Review of reconstruction of icosahedral viruses
|-

|}

=== Software ===

{|

| Paper
| [[1996Baker_EMPFT]]
| EMPFT
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

|}

== Data bases ==

{|

| Paper
| [[2003Boutselakis_EMSD]]
| EMSD database
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

|}

== Relationship to other structural information sources ==

{|

| Paper
| [[2000Engel_AFM]]
| Review of Atomic Force Microscopy
|-

| Paper
| [[2001Dimmeler_AFM]]
| Constraints from Atomic Force Microscopy
|-

| Paper
| [[2003Mobus_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_Review]]
| Review on correlative microscopy
|-

| Paper
| [[2005Boudier_EFTETJ]]
| Software for Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2005Vestergaard_SAXS]]
| Example of comparison of 3DEM and Small-angle X-ray scattering
|-

| Paper
| [[2007Hamada_SAXS]]
| Constraints from Small-angle X-ray scattering
|-

|}

== 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 ]

== 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]

2004Wan CTF

2013-01-15T10:32:56Z

Jose Maria Carazo: Created page with "== Citation == Yi Wan and Wah Chiu, International Conference on Communications, Circuits and Systems, 2004. ICCCAS 2004. 2: 960.964 == Abstract == Over the past years electr..."

== Citation ==
Yi Wan and Wah Chiu,
International Conference on Communications, Circuits and Systems, 2004. ICCCAS 2004. 2: 960.964

== Abstract ==

Over the past years electron cryo-microscopy (cryo-EM) has established itself as an important tool in studying the three dimensional structure of biological molecules up to the resolution of 6-9 Å. However, as we pursue even higher resolution (i.e., 3-4 Å), the depth-of-field problem inherent in the contrast transfer function emerges as a limiting factor. This problem has been previously addressed in the research community (Jensen, G.J., 2000; DeRosier, D.J., 2000; Zhou, Z.H. and Chiu, W., 2003; Cohen, H.A. et al., 1984). We develop a full theoretical solution to this problem. We show that the projected image from the electron microscope corresponds to neither a slice, nor an Ewald sphere, in the Fourier space, but a pair of quadratic surfaces in that space. The general solutions to this problem for both single and double defocus exposures are developed. Simulations show the correctness of the theory.

== Keywords ==

CTF, full contrast transfer function correction

== Links ==

http://ieeexplore.ieee.org/xpl/login.jsp?tp=&arnumber=1346339&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D1346339

== Related software ==

== Related methods ==

== Comments ==

Main Page

2013-01-15T10:00:15Z

Jose Maria Carazo: /* 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.

== 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
| [[2011Zhang2011_LimitingFactors]]
| Limiting factor for atomic resolution in EM
|-

| Paper
| [[2011Glaeser_Coma]]
| Image formation model including coma
|-

|}

=== Collection geometry ===

{|

| Chapter
| [[1980Hoppe_Wedge]]
| Missing wedge
|-

| Paper
| [[1987Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1995Penczek_Dual]]
| Dual axis tomography
|-

| Paper
| [[1997Mastronarde_Dual]]
| Dual axis tomography
|-

| Paper
| [[2005Lanzavecchia_Conical]]
| Conical tomography
|-

| Paper
| [[2005Zampighi_Conical]]
| Conical tomography
|-

| Paper
| [[2006Leschziner_OT]]
| Orthogonal Tilt
|-

| Paper
| [[2006Messaoudi_Multiple]]
| Multiple axis tomography
|-

|}

=== Sample preparation ===

{|

| Paper
| [[1982Dubochet_Sample]]
| Vitreous ice
|-

| Paper
| [[1986Lepault_Sample]]
| Fast freezing
|-

| Paper
| [[1995Dubochet_Sample]]
| High-pressure freezing
|-

| Paper
| [[1995VanMarle_Sample]]
| Sample damages in resin
|-

| Paper
| [[1998Adrian_Sample]]
| Cryo negative staining
|-

| Paper
| [[2002DeCarlo_Damage]]
| Radiation damage in cryonegative staining
|-

| Paper
| [[2002Hsieh_Sample]]
| Cryofixation
|-

| Paper
| [[2004AlAmoudi_Sample]]
| CEMOVIS
|-

| Paper
| [[2008Studer_Sample]]
| Review on high pressure freezing
|-

| Paper
| [[2009Pierson_Sample]]
| Review on sample preparation for electron tomography
|-

|}

=== Automated data collection ===

{|

| Paper
| [[1992Dierksen_Automatic]]
| Automated data collection
|-

| Paper
| [[1992Koster_Automatic]]
| Automated data collection
|-

| Paper
| [[2001Zhang_Automatic]]
| Automated sample collection
|-

| Paper
| [[2003Ziese_Automatic]]
| Automated autofocusing
|-

| Paper
| [[2004Potter_Automatic]]
| Automated sample loading
|-

| Paper
| [[2004Zheng_Automatic]]
| Automated data collection
|-

| Paper
| [[2005Lei_Automatic]]
| Automated data collection: AutoEM
|-

| Paper
| [[2005Suloway_Automatic]]
| Automated data collection: Leginon
|-

|}

== Single particles ==

=== Automatic particle picking ===

{|

| Paper
| [[1982VanHeel_Detection]]
| Detection of particles in micrographs
|-

| Paper
| [[2001Nicholson_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2001Zhu_Filaments]]
| Automatic identification of filaments in micrographs
|-

| Paper
| [[2004Zhu_Review]]
| Review on automatic particle picking
|-

| Paper
| [[2009Sorzano_MachineLearning]]
| Automatic particle picking based on machine learning of rotational invariants
|-

|}

=== 2D Preprocessing ===

{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast enhancement through DPR
|-

| Paper
| [[2004Sorzano_Normalization]]
| Normalization procedures and their statistical properties.
|-

| Paper
| [[2006Sorzano_Denoising]]
| Strong denoising in wavelet space
|-

| Conference
| [[2009Sorzano_Downsampling]]
| Differences between the different downsampling schemes
|-

|}

=== 2D Alignment ===

{|

| Paper
| [[1981Frank_Averaging]]
| 2D averaging and phase residual
|-

| Paper
| [[1982Saxton_Averaging]]
| 2D averaging using correlation
|-

| Paper
| [[1998Sigworth_ML2D]]
| Maximum likelihood alignment in 2D
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

|}

=== 2D Classification and clustering ===

{|

| Paper
| [[1981VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[1984VanHeel_MSA]]
| Multivariate Statistical Analysis
|-

| Paper
| [[2005Scheres_ML2D]]
| Multireference alignment and classification in 2D
|-

| Paper
| [[2010Sorzano_CL2D]]
| Multireference alignment and classification in 2D
|-

|}

=== 3D Alignment ===

{|

| Paper
| [[1987VanHeel_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[1988Provencher_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1988Radermacher_RCT]]
| Random Conical Tilt and Single axis tilt
|-

| Paper
| [[1988Vogel_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

| Paper
| [[1990Gelfand_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Goncharov_Moments]]
| Angular assignment using moments (reference free)
|-

| Paper
| [[1990Harauz_Quaternions]]
| Use of quaternions to represent rotations
|-

| Paper
| [[1994Penczek_Real]]
| Angular assignment using projection matching in real space
|-

| Paper
| [[1994Radermacher_Radon]]
| Angular assignment in Radon space
|-

| Paper
| [[1996Penczek_CommonLines]]
| Angular assignment using common lines (reference free)
|-

| Paper
| [[2003Rosenthal_DPR]]
| Angular assignment using DPR
|-

| Paper
| [[2004Sorzano_Wavelet]]
| Angular assignment in the wavelet space.
|-

| Paper
| [[2005Jonic_Splines]]
| Angular assignment in Fourier space using spline interpolation.
|-

| Paper
| [[2005Yang_Simultaneous]]
| Simultaneaous alignment and reconstruction
|-

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

| Paper
| [[2012Giannakis_Scattering]]
| Construction of an initial volume, reference free, by graph analysis of the projections
|-

|}

=== 3D Reconstruction ===
{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1986Harauz_FBP]]
| Exact filters for Filtered Back Projection
|-

| Chapter
| [[1992Radermacher_WBP]]
| Exact filters for Weighted Back Projection
|-

| Paper
| [[1997Zhu_RecCTF]]
| 3D Reconstruction (SIRT like) and simultaneous CTF correction
|-

| Paper
| [[1998Boisset_Uneven]]
| Artifacts in SIRT and WBP under uneven angular distributions
|-

| Paper
| [[1998Marabini_ART]]
| Algebraic Reconstruction Technique with blobs (Xmipp)
|-

| Paper
| [[2001Sorzano_Uneven]]
| Free parameter selection under uneven angular distributions
|-

| Paper
| [[2005Sorzano_Parameters]]
| Free parameter selection for optimizing multiple tasks
|-

| Paper
| [[2008Sorzano_Constraints]]
| Mass, surface, positivity and symmetry constraints for real-space algorithms
|-

| Paper
| [[2009Bilbao_ParallelART]]
| Efficient parallelization of ART
|-

| Paper
| [[2011Li_GradientFlow]]
| Regularized 3D Reconstruction by Gradient Flow
|-

|}

=== 3D Heterogeneity ===

{|

| Paper
| [[2004White_Size]]
| Heterogeneity classification of differently sized images
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Scheres_ML3D]]
| Maximum Likelihood alignment and classification in 3D
|-

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

|}

=== Resolution ===

{|

| Paper
| [[1986Harauz_FBP]]
| Fourier Shell Correlation
|-

| Paper
| [[1987Unser_SSNR]]
| 2D Spectral Signal to Noise Ratio
|-

| Paper
| [[2002Penczek_SSNR]]
| 3D Spectral Signal to Noise Ratio for Fourier based algorithms
|-

| Paper
| [[2003Rosenthal_DPR]]
| Review of the FSC and establishment of a new threshold
|-

| Paper
| [[2005Unser_SSNR]]
| 3D Spectral Signal to Noise Ratio for any kind of algorithms
|-

| Paper
| [[2005VanHeel_FSC]]
| Establishment of a new threshold for FSC
|-

| Paper
| [[2007Sousa_AbInitio]]
| Resolution measurement on neighbour Fourier voxels
|-

|}

=== Sharpening of high resolution information ===
{|

| Paper
| [[2003Rosenthal_DPR]]
| Contrast restoration and map sharpening
|-

| Paper
| [[2008Fernandez_Bfactor]]
| Bfactor determination and restoration
|-

|}

=== CTF estimation and restoration ===

{|

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

| Paper
| [[1984Cohen_Validity]]
| Validity of the CTF model at high frequencies
|-

| Paper
| [[1988Toyoshima_Model]]
| CTF estimation
|-

| Paper
| [[1993Toyoshima_Model]]
| Amplitud constrast
|-

| Paper
| [[1995Frank_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1996Skoglund_MaxEnt]]
| CTF correction with Maximum Entropy
|-

| Paper
| [[1996Zhou_Model]]
| CTF model and user interface for manual fitting
|-

| Paper
| [[1997Fernandez_AR]]
| PSD estimation using periodogram averaging and AR models
|-

| Paper
| [[1997Penczek_Wiener]]
| CTF correction using Wiener filter
|-

| Paper
| [[1997Stark_Deconvolution]]
| CTF correction using deconvolution
|-

| Paper
| [[1997Zhu_RecCTF]]
| CTF correction and reconstruction
|-

| Paper
| [[2000DeRosier_EwaldCorrection]]
| CTF correction considering the Ewald sphere
|-

| Paper
| [[2000Jensen_TiltedCorrection]]
| CTF correction considering tilt in backprojection
|-

| Paper
| [[2001Saad_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Huang_CTFEstimate]]
| CTF estimation
|-

| Paper
| [[2003Mindell_CTFTILT]]
| CTF estimation for tilted micrographs
|-

| Paper
| [[2003Velazquez_ARMA]]
| PSD and CTF estimation using ARMA models
|-

| Paper
| [[2004Sorzano_IDR]]
| CTF restoration and reconstruction with Iterative Data Refinement
|-

| 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
| [[2011Sindelar_Wiener]]
| CTF correction using a modified version of Wiener filter
|-

| Paper
| [[2011Glaeser_Coma]]
| The effect of coma at high-resolution
|-

| Paper
| [[2012Voortman_VaryingCTF]]
| Correcting a spatially varying CTF
|-

|}

=== Segmentation ===

{|

| Paper
| [[2006Baker_segmentation]]
| Segmentation of molecular subunits
|-

|}

=== Fitting and docking ===

{|

| Paper
| [[1999Volkmann_Fitting]]
| Fitting in real space
|-

| Paper
| [[2001Baker_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2001Jones_Review]]
| Review of protein structure prediction
|-

| Paper
| [[2004Tama_NMA1]]
| Flexible fitting with Normal Modes (I)
|-

| Paper
| [[2004Tama_NMA2]]
| Flexible fitting with Normal Modes (II)
|-

| Paper
| [[2005Velazquez_Superfamilies]]
| Recognition of the superfamily folding in medium-high resolution volumes
|-

| Paper
| [[2007Kleywegt_QualityControl]]
| Quality control and validation of fitting
|-

| Paper
| [[2012Velazquez_Constraints]]
| Multicomponent fitting by using constraints from other information sources
|-

|}

=== Books and reviews ===

{|

| Book
| [[1980Herman_Tomography]]
| General book on tomography
|-

| Book
| [[1988Kak_Tomography]]
| General book on tomography
|-

| Paper
| [[2000Tao_Review]]
| Review of single particles
|-

| Paper
| [[2000VanHeel_Review]]
| Review of single particles
|-

| Paper
| [[2002Frank_Review]]
| Review of single particles
|-

| Paper
| [[2002Schmid_Review]]
| Review of single particles
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2004Subramaniam_Review]]
| Review of single particles
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_book]]
| Book covering all aspects of electron microscopy of single particles
|-

| Paper
| [[2006Sorzano_Review]]
| Review of optimization problems in electron microscopy
|-

| Paper
| [[2007Leschziner_Review]]
| Review of 3D heterogeneity handling algorithms
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems in Electron Tomography
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

| Paper
| [[2010DeRosier_Review]]
| Personal account of how 3DEM developed in the early days
|-

| Chapter
| [[2012Sorzano_Review]]
| Review of single particle analysis using Xmipp
|-

| Chapter
| [[2012Devaux_Protocol]]
| Protocols for performing single particle analysis
|-

|}

=== Software ===

{|

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[1999Lutdke_Eman]]
| Eman
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Baldwin_AngularTransformations]]
| The Transform Class in SPARX and EMAN2
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2008Scheres_XmippProtocols]]
| Xmipp Protocols
|-

|}

== Electron tomography ==

=== Image alignment ===

{|

| Paper
| [[2001Brandt_Automatic1]]
| Automatic alignment without fiducial markers
|-

| Paper
| [[2001Brandt_Automatic2]]
| Automatic alignment with fiducial markers
|-

| Paper
| [[2006Winkler_alignment]]
| Marker-free alignment and refinement
|-

| Paper
| [[2006Castano_alignment]]
| Alignment with non-perpendicularity
|-

| Paper
| [[2007Castano_alignment]]
| Fiducial-less alignment of cryo-sections
|-

| Paper
| [[2009Sorzano_alignment]]
| Marker-free alignment and refinement
|-

|}

=== CTF estimation and restoration ===

{|

| Paper
| [[2003Winkler_CTF]]
| Focus gradient correction in electron tomography
|-

| Paper
| [[2006Fernandez_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Zanetti_CTF]]
| CTF determination and correction in electron tomography
|-

| Paper
| [[2009Xiong_CTF]]
| CTF determination and correction for low dose tomographic tilt series
|-

|}

=== 3D reconstruction ===

{|

| Paper
| [[1972Gilbert_SIRT]]
| Simultaneous Iterative Reconstruction Technique (SIRT)
|-

| Paper
| [[1973Herman_ART]]
| Algebraic Reconstruction Technique (ART)
|-

| Paper
| [[1984Andersen_SART]]
| Simultaneous Algebraic Reconstruction Technique (SART)
|-

| Paper
| [[1992Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[1997Marabini_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2002Fernandez_reconstruction]]
| Iterative reconstruction in electron tomography
|-

| Paper
| [[2007Radermacher_WBP]]
| Weighted Backprojection in electron tomography
|-

| Paper
| [[2008Fernandez_CARP]]
| Component Averaged Row Projections (CARP)
|-
|}

=== Noise reduction ===
{|

| Paper
| [[2001Frangakis_NAD]]
| Noise reduction with Nonlinear Anisotropic Diffusion
|-

| Paper
| [[2003Fernandez_AND]]
| Anisotropic nonlinear diffusion for electron tomography
|-

| Paper
| [[2003Jiang_Bilateral]]
| Bilateral denoising filter in electron microscopy
|-

| Paper
| [[2005Fernandez_AND]]
| Anisotropic nonlinear denoising in electron tomography
|-

| Paper
| [[2007Heide_median]]
| Iterative median filtering in electron tomography
|-

| Paper
| [[2007Fernandez_autAND]]
| Anisotropic nonlinear diffusion with automated parameter tuning
|-

| Paper
| [[2009Fernandez_Beltrami]]
| Nonlinear filtering based on Beltrami flow
|-

| Paper
| [[2010Bilbao_MeanShift]]
| Mean Shift Filtering
|-

|}

=== Segmentation ===

{|

| Paper
| [[2002Frangakis_Eigenanalysis]]
| Segmentation using eigenvector analysis.
|-

| Paper
| [[2002Volkmann_Watershed]]
| Segmentation using watershed transform.
|-

| Paper
| [[2003Bajaj_BoundarySegmentation]]
| Segmentation based on fast marching.
|-

| Paper
| [[2005Cyrklaff_Thresholding]]
| Segmentation using optimal thresholding.
|-

| Paper
| [[2007Lebbink_TemplateMatching]]
| Segmentation using template matching.
|-

| Paper
| [[2007Sandberg_OrientationFields]]
| Segmentation using orientation fields.
|-

| Paper
| [[2007Sandberg_SegmentationReview]]
| Review on segmentation in electron tomography.
|-

| Paper
| [[2008Garduno_FuzzySegmentation]]
| Segmentation using fuzzy set theory principles.
|-

| Paper
| [[2009Lebbink_TemplateMatching2]]
| Segmentation using template matching.
|-

|}

=== Resolution ===
{|

| Paper
| [[2005Cardone_Resolution]]
| Resolution criterion for electron tomography
|-

|}

=== Subtomogram analysis ===

{|

| Paper
| [[2000Bohm_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2002Frangakis_Template]]
| Macromolecule finding by template matching
|-

| Paper
| [[2006Nickell_Review]]
| Review of macromolecule finding by template matching (Visual Proteomics)
|-

| Paper
| [[2007Best_Review]]
| Review of Localization of Protein Complexes by Pattern Recognition
|-

| Paper
| [[2007Forster_Review]]
| Review of structure determination by subtomogram averaging
|-

| Paper
| [[2008Forster_Classification]]
| Classification of subtomograms using constrained correlation
|-

| Paper
| [[2008Bartesaghi_Classification]]
| Classification and averaging of subtomograms
|-

| Paper
| [[2008Schmid_Averaging]]
| Alignment and averaging of subtomograms
|-

| Paper
| [[2010Amat_Averaging]]
| Alignment and averaging of subtomograms exploiting thresholding in Fourier space
|-

|}

=== Single particle tomography ===

{|

| Paper
| [[2012Bartesaghi_Constrained]]
| 3D reconstruction by imposing geometrical constraints
|-

|}

=== Books and reviews ===

{|

| Paper
| [[2000Baumeister_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Koster_Review]]
| Review of electron tomography
|-

| Paper
| [[2003Sali_Review]]
| Review of electron tomography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2005Lucic_Review]]
| Review of electron tomography
|-

| Paper
| [[2006Fernandez_Review]]
| Review of electron microscopy
|-

| Book
| [[2006Frank_TomoBook]]
| Electron Tomography
|-

| Book
| [[2007McIntosh_Book]]
| Cellular Electron Microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

| Paper
| [[2008Fanelli_ImageFormation]]
| Review on the image formation model from the electron waves and open inverse-problems
|-

| Paper
| [[2008Fernandez_HPCReview]]
| High performance computing in electron cryomicroscopy
|-

| Paper
| [[2008Jonic_Review]]
| Comparison between electron tomography and single particles
|-

|}

=== Software ===

{|

| Paper
| [[1996Kremer_IMOD]]
| IMOD
|-

| Paper
| [[1996Chen_Priism/IVE]]
| Priism/IVE
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2005Nickell_TOM]]
| TOM Toolbox
|-

| Paper
| [[2007Messaoudi_TomoJ]]
| TomoJ
|-

| Paper
| [[2008Heymann_BsoftTomo]]
| Bsoft
|-

|}

== 2D Crystals ==

=== 2D Preprocessing ===

{|

| Paper
| [[1986Henderson_Processing]]
| General 2D processing
|-

| Paper
| [[2000He_PhaseAlignment]]
| Phase consistency and Alignment
|-

| Paper
| [[2006Gil_Unbending]]
| Crystal unbending
|-

|}

=== Classification ===
{|

| Paper
| [[1988Frank_Classification]]
| MSA and classification in electron crystallography
|-

| Paper
| [[1996Fernandez_SOM]]
| Classification based on self organizing maps
|-

| Paper
| [[1998Sherman_MSA]]
| Classification based on MSA
|-

|}
=== 3D Reconstruction ===

{|

| Paper
| [[1985Wang_Solvent]]
| Solvent flattening
|-

| Paper
| [[1990Henderson_Processing]]
| General 3D processing
|-

| Paper
| [[2004Marabini_ART]]
| Algebraic Reconstruction Technique with blobs for crystals (Xmipp)
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1998Walz_Review]]
| Review of 2D crystallography
|-

| Paper
| [[1999Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Ellis_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2001Glaeser_Review]]
| Review of 2D crystallography
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2006Fernandez_Review]]
| Review of single particles, electron tomography and crystallography
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

| Paper
| [[2007Gipson_2dx]]
| 2dx
|-

| Paper
| [[2007Heymann_Bsoft]]
| Bsoft
|-

| Paper
| [[2007Philippsen_IPLT]]
| IPLT
|-

|}

== Helical particles ==

=== Filament corrections ===

{|

| Paper
| [[1986Egelman_Curved]]
| Algorithm for correcting curved filaments
|-

| Paper
| [[1988Bluemke_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

| Paper
| [[2006Wang_Pitch]]
| Algorithm for correcting filaments with different helical pitches
|-

|}

=== Reconstruction ===

{|

| Paper
| [[1958Klug_Fourier]]
| Fourier Bessel decomposition of the projection images
|-

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2005Wang_Iterative]]
| Iterative Fourier-Bessel algorithm
|-

| Paper
| [[2007Egelman_Iterative]]
| Iterative real-space algorithm
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1970DeRosier_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[1992Morgan_Rec]]
| Image processing steps towards 3D reconstruction
|-

| Paper
| [[2004Henderson_Review]]
| Review of electron microscopy
|-

| Paper
| [[2007Sorzano_Review]]
| Review of the image processing steps
|-

|}

=== Software ===

{|

| Paper
| [[1996Carragher_Phoelix]]
| Phoelix
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Owen_Brandeis]]
| Brandeis
|-

|}

== Icosahedral particles ==

=== Reconstruction ===

{|

| Paper
| [[1970Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1971Crowther_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1996Fuller_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

| Paper
| [[1997Thuman_Rec]]
| Reconstruction of icosahedral viruses in Fourier space
|-

|}

=== Classification ===

{|

| Paper
| [[2005Scheres_Virus]]
| Classification of virus capsids in real space
|-

|}

=== Books and reviews ===

{|

| Paper
| [[1999Baker_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[1999Conway_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2000Thuman_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Lee_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2003Navaza_Review]]
| Review of reconstruction of icosahedral viruses
|-

| Paper
| [[2006Grunewald_Review]]
| Review of reconstruction of icosahedral viruses
|-

|}

=== Software ===

{|

| Paper
| [[1996Baker_EMPFT]]
| EMPFT
|-

| Paper
| [[1996Crowther_MRC]]
| MRC
|-

| Paper
| [[1996Frank_Spider]]
| Spider
|-

| Paper
| [[1996VanHeel_Imagic]]
| Imagic
|-

| Paper
| [[2004Sorzano_Xmipp]]
| Xmipp
|-

|}

== Data bases ==

{|

| Paper
| [[2003Boutselakis_EMSD]]
| EMSD database
|-

| Paper
| [[2005Heymann_Conventions]]
| Conventions for software interoperability
|-

|}

== Relationship to other structural information sources ==

{|

| Paper
| [[2000Engel_AFM]]
| Review of Atomic Force Microscopy
|-

| Paper
| [[2001Dimmeler_AFM]]
| Constraints from Atomic Force Microscopy
|-

| Paper
| [[2003Mobus_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_EnergyLoss]]
| Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2004Leapman_Review]]
| Review on correlative microscopy
|-

| Paper
| [[2005Boudier_EFTETJ]]
| Software for Chemical mapping by energy loss electron tomography
|-

| Paper
| [[2005Vestergaard_SAXS]]
| Example of comparison of 3DEM and Small-angle X-ray scattering
|-

| Paper
| [[2007Hamada_SAXS]]
| Constraints from Small-angle X-ray scattering
|-

|}

== 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 ]

== 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]
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