Main Page
This web page is intended to be an extensive repository of three-dimensional electron microscopy (3DEM) methods. The advantages of having such a repository are
- You know which are the relevant articles in a particular topic, therefore, paper introductions, reviews, etc. are easier to write and you make sure you will cite all the related articles.
- You will be sure that your paper has more chances of being cited.
- You can add whatever information you find relevant to your method, external links, links to other papers, etc.
- You can link your method to a web page providing the corresponding software, so you know people can use your algorithms.
- You can use the Wiki search capabilities to locate relevant articles even if they are not at the topic you are looking at.
- As a community we will "reconstruct" our history.
- You can select the "watch" option above to receive notifications in case of further changes in the Main Page.
Developing image processing methods for 3DEM is not "well-paid" in terms of citations and impact factor. However, it is crucial for the advance of the field. Gathering methodological papers in a portal will help to increase the recognition of the field.
Please:
- Add your articles at the right place (you can add a single article in several topics if it is relevant to all of them). The easiest way to add an article is by editing the corresponding topic in the main page, adding your entry, then save the main page. Click on the red link that appears on your new entry, copy and paste the Wiki following code, add the information of your article
== Citation == == Abstract == == Keywords == == Links == == Related software == == Related methods == == Comments ==
- Maintain the information of each article as complete as possible.
- Sort articles by years and authors.
- Be respectful to other people's work.
How to subscribe to this page
You may subscribe to this page so that you will be notified every time someone adds a new method. To do so, you have to register in the page, and edit your preferences ("my preferences"). Be sure that you have activated the option "E-mail me when a page on my watchlist is changed". Finally, click on the "Watch" tab at the top of this page.
Electron microscopy images
Image formation
| Paper | 1971Glaeser_Damage | Radiation damage |
| Paper | 1971Thon_Model | CTF model |
| Paper | 1975Unwin_Imaging | Radiation dose |
| Paper | 1977Wade_Model | CTF model |
| Paper | 1978Wade_Model | CTF model |
| Paper | 1984Cohen_Validity | Validity of the CTF model at high frequencies |
| Paper | 1988Toyoshima_Model | Amplitud constrast |
| Paper | 1992Wade_Model | CTF model |
| Paper | 1993Toyoshima_Model | Amplitud constrast |
| Paper | 2002DeCarlo_Damage | Radiation damage in cryonegative staining |
| Paper | 2004Egerton_Damage | Radiation damage |
| Paper | 2004Sorzano_Normalization | Background noise is Gaussian |
| Paper | 2008Fanelli_ImageFormation | Review on the image formation model from the electron waves and open inverse-problems |
| Paper | 2009Baxter_NoiseCharacterization | Characterization of the different noise sources in cryo-EM |
| Paper | 2010Bammes_Damage | Radiation damage dependence on temperature |
| Paper | 2010Zewail_FourDimensional | Review on the use of ultrafast EM |
| Paper | 2011Bammes_CCD | Performance of CCD cameras |
| Paper | 2011Glaeser_Coma | Image formation model including coma |
| Paper | 2011Milazzo_DirectDetectors | Evaluation of Direct Detectors |
| Paper | 2011Zhang LimitingFactors | Limiting factor for atomic resolution in EM |
| Paper | 2012Bammes_DirectDetection | Performance of Direct detectors |
| Paper | 2013Egerton_RadiationDamage | Review of TEM radiation damage and experimental ways of reducing it |
| Paper | 2013Bai_ElectronCounting | Electron counting and beam induced motion correction |
| Paper | 2013Li_ElectronCounting | Electron counting and beam induced motion correction |
Collection geometry
| Chapter | 1980Hoppe_Wedge | Missing wedge |
| Paper | 1987Radermacher_RCT | Random Conical Tilt and Single axis tilt |
| Paper | 1988Radermacher_RCT | Random Conical Tilt and Single axis tilt |
| Paper | 1995Penczek_Dual | Dual axis tomography |
| Paper | 1997Mastronarde_Dual | Dual axis tomography |
| Paper | 2005Lanzavecchia_Conical | Conical tomography |
| Paper | 2005Zampighi_Conical | Conical tomography |
| Paper | 2006Leschziner_OT | Orthogonal Tilt |
| Paper | 2006Messaoudi_Multiple | Multiple axis tomography |
Sample preparation
| Paper | 1982Dubochet_Sample | Vitreous ice |
| Paper | 1986Lepault_Sample | Fast freezing |
| Paper | 1995Dubochet_Sample | High-pressure freezing |
| Paper | 1995VanMarle_Sample | Sample damages in resin |
| Paper | 1998Adrian_Sample | Cryo negative staining |
| Paper | 2002DeCarlo_Damage | Radiation damage in cryonegative staining |
| Paper | 2002Hsieh_Sample | Cryofixation |
| Paper | 2004AlAmoudi_Sample | CEMOVIS |
| Paper | 2008Studer_Sample | Review on high pressure freezing |
| Paper | 2009Pierson_Sample | Review on sample preparation for electron tomography |
Automated data collection
| Paper | 1992Dierksen_Automatic | Automated data collection |
| Paper | 1992Koster_Automatic | Automated data collection |
| Paper | 2001Zhang_Automatic | Automated sample collection |
| Paper | 2003Ziese_Automatic | Automated autofocusing |
| Paper | 2004Potter_Automatic | Automated sample loading |
| Paper | 2004Zheng_Automatic | Automated data collection |
| Paper | 2005Lei_Automatic | Automated data collection: AutoEM |
| Paper | 2005Suloway_Automatic | Automated data collection: Leginon |
| Paper | 2007Yoshioka_RCT | Automated Random Conical Tilt |
Single particles
Automatic particle picking
| Paper | 1982VanHeel_Detection | Detection of particles in micrographs |
| Paper | 2001Nicholson_Review | Review on automatic particle picking |
| Paper | 2001Zhu_Filaments | Automatic identification of filaments in micrographs |
| Paper | 2004Sigworth_Detection | Classical detection theory and the cryo-EM particle selection problem |
| Paper | 2004Volkmann_ParticlePicking | An approach to automated particle picking from electron micrographs based on reduced representation templates |
| Paper | 2004Wong_ParticlePicking | Model-based particle picking for cryo-electron microscopy |
| Paper | 2004Zhu_Review | Review on automatic particle picking |
| Paper | 2007Chen_Signature | Automatic particle picking program: Signature |
| Paper | 2009Sorzano_MachineLearning | Automatic particle picking based on machine learning of rotational invariants |
| Paper | 2011Arbelaez_Comparison | Evaluation of the performance of software for automated particle-boxing |
2D Preprocessing
| Paper | 2003Rosenthal_DPR | Contrast enhancement through DPR |
| Paper | 2004Sorzano_Normalization | Normalization procedures and their statistical properties. |
| Paper | 2006Sorzano_Denoising | Strong denoising in wavelet space |
| Conference | 2009Sorzano_Downsampling | Differences between the different downsampling schemes |
| Paper | 2012Campbell_Movies | Alignment of beam induced motion in direct detectors |
| Paper | 2012Zhao_Denoising | Denoising using an invariant Fourier-Bessel eigenspace |
| Paper | 2013Norousi_Screening | Screening particles to identify outliers |
| Paper | 2013Bai_ElectronCounting | Electron counting and beam induced motion correction |
| Paper | 2013Li_ElectronCounting | Electron counting and beam induced motion correction |
2D Alignment
| Paper | 1981Frank_Averaging | 2D averaging and phase residual |
| Paper | 1982Saxton_Averaging | 2D averaging using correlation |
| Paper | 1998Sigworth_ML2D | Maximum likelihood alignment in 2D |
| Paper | 2005Scheres_ML2D | Multireference alignment and classification in 2D |
| Paper | 2010Sorzano_CL2D | Multireference alignment and classification in 2D |
2D Classification and clustering
| Paper | 1981VanHeel_MSA | Multivariate Statistical Analysis |
| Paper | 1984VanHeel_MSA | Multivariate Statistical Analysis |
| Paper | 2005Scheres_ML2D | Multireference alignment and classification in 2D |
| Paper | 2010Sorzano_CL2D | Multireference alignment and classification in 2D |
| Paper | 2012Yang_ISAC | Iterative Stable Alignment and clustering |
3D Alignment
| Paper | 1987VanHeel_CommonLines | Angular assignment using common lines (reference free) |
| Paper | 1988Provencher_Simultaneous | Simultaneaous alignment and reconstruction |
| Paper | 1988Radermacher_RCT | Random Conical Tilt and Single axis tilt |
| Paper | 1988Vogel_Simultaneous | Simultaneaous alignment and reconstruction |
| Paper | 1990Gelfand_Moments | Angular assignment using moments (reference free) |
| Paper | 1990Goncharov_Moments | Angular assignment using moments (reference free) |
| Paper | 1990Harauz_Quaternions | Use of quaternions to represent rotations |
| Paper | 1994Penczek_Real | Angular assignment using projection matching in real space |
| Paper | 1994Radermacher_Radon | Angular assignment in Radon space |
| Paper | 1996Penczek_CommonLines | Angular assignment using common lines (reference free) |
| Paper | 2003Rosenthal_DPR | Angular assignment using DPR |
| Paper | 2004Sorzano_Wavelet | Angular assignment in the wavelet space. |
| Paper | 2005Jonic_Splines | Angular assignment in Fourier space using spline interpolation. |
| Paper | 2005Yang_Simultaneous | Simultaneaous alignment and reconstruction |
| Paper | 2006Ogura_SimulatedAnnealing | Angular asignment by simulated annealing |
| Paper | 2007Grigorieff_Continuous | Continuous angular assignment in Fourier space |
| Paper | 2010Jaitly_Bayesian | Angular assignment by a Bayesian method and annealing |
| Paper | 2010Sanz_Random | Random model method |
| Paper | 2012Giannakis_Scattering | Construction of an initial volume, reference free, by graph analysis of the projections |
3D Reconstruction
| Paper | 1972Gilbert_SIRT | Simultaneous Iterative Reconstruction Technique (SIRT) |
| Paper | 1973Herman_ART | Algebraic Reconstruction Technique (ART) |
| Paper | 1984Andersen_SART | Simultaneous Algebraic Reconstruction Technique (SART) |
| Paper | 1986Harauz_FBP | Exact filters for Filtered Back Projection |
| Chapter | 1992Radermacher_WBP | Exact filters for Weighted Back Projection |
| Paper | 1997Zhu_RecCTF | 3D Reconstruction (SIRT like) and simultaneous CTF correction |
| Paper | 1998Boisset_Uneven | Artifacts in SIRT and WBP under uneven angular distributions |
| Paper | 1998Marabini_ART | Algebraic Reconstruction Technique with blobs (Xmipp) |
| Paper | 2001Sorzano_Uneven | Free parameter selection under uneven angular distributions |
| Paper | 2005Sorzano_Parameters | Free parameter selection for optimizing multiple tasks |
| Paper | 2008Sorzano_Constraints | Mass, surface, positivity and symmetry constraints for real-space algorithms |
| Paper | 2009Bilbao_ParallelART | Efficient parallelization of ART |
| Paper | 2011Li_GradientFlow | Regularized 3D Reconstruction by Gradient Flow |
| Paper | 2012Gopinath_ShapeRegularization | Regularized 3D Reconstruction by Shape information |
3D Heterogeneity
| Paper | 2004White_Size | Heterogeneity classification of differently sized images |
| Paper | 2007Leschziner_Review | Review of 3D heterogeneity handling algorithms |
| Paper | 2007Scheres_ML3D | Maximum Likelihood alignment and classification in 3D |
| Paper | 2013Wang_MLVariance | Maximum Likelihood estimate of the map variance |
Resolution
| Paper | 1986Harauz_FBP | Fourier Shell Correlation |
| Paper | 1987Unser_SSNR | 2D Spectral Signal to Noise Ratio |
| Paper | 2002Penczek_SSNR | 3D Spectral Signal to Noise Ratio for Fourier based algorithms |
| Paper | 2003Rosenthal_DPR | Review of the FSC and establishment of a new threshold |
| Paper | 2005Unser_SSNR | 3D Spectral Signal to Noise Ratio for any kind of algorithms |
| Paper | 2005VanHeel_FSC | Establishment of a new threshold for FSC |
| Paper | 2007Sousa_AbInitio | Resolution measurement on neighbour Fourier voxels |
Sharpening of high resolution information
| Paper | 2003Rosenthal_DPR | Contrast restoration and map sharpening |
| Paper | 2008Fernandez_Bfactor | Bfactor determination and restoration |
CTF estimation and restoration
| Paper | 1982Schiske_Correction | CTF correction for tilted objects |
| Paper | 1988Toyoshima_Model | CTF estimation |
| Paper | 1995Frank_Wiener | CTF correction using Wiener filter |
| Paper | 1996Skoglund_MaxEnt | CTF correction with Maximum Entropy |
| Paper | 1996Zhou_Model | CTF model and user interface for manual fitting |
| Paper | 1997Fernandez_AR | PSD estimation using periodogram averaging and AR models |
| Paper | 1997Penczek_Wiener | CTF correction using Wiener filter |
| Paper | 1997Stark_Deconvolution | CTF correction using deconvolution |
| Paper | 1997Zhu_RecCTF | CTF correction and reconstruction |
| Paper | 2000DeRosier_EwaldCorrection | CTF correction considering the Ewald sphere |
| Paper | 2000Jensen_TiltedCorrection | CTF correction considering tilt in backprojection |
| Paper | 2001Saad_CTFEstimate | CTF estimation |
| Paper | 2003Huang_CTFEstimate | CTF estimation |
| Paper | 2003Mindell_CTFTILT | CTF estimation for tilted micrographs |
| Paper | 2003Sander_MSA | CTF estimation through MSA classification of PSDs |
| Paper | 2003Velazquez_ARMA | PSD and CTF estimation using ARMA models |
| Paper | 2004Sorzano_IDR | CTF restoration and reconstruction with Iterative Data Refinement |
| Conference | 2004Wan_CTF | Spatially variant CTF |
| Paper | 2004Zubelli_Chahine | CTF restoration and reconstruction with Chahine's multiplicative method |
| Conference | 2005Dubowy_SpaceVariant | CTF correction when this is space variant |
| Paper | 2005Mallick_ACE | CTF estimation |
| Paper | 2006Wolf_Ewald | CTF correction considering Ewald sphere |
| Paper | 2007Jonic_EnhancedPSD | PSD enhancement for better identification of Thon rings; Vitreous ice diffracts in Thon rings |
| Paper | 2007Philippsen_Model | CTF Model for tilted specimens |
| Paper | 2007Sorzano_CTF | CTF estimation using enhanced PSDs |
| Paper | 2009Sorzano_Sensitivity | Error sensitivity of the CTF models, non-uniqueness of the CTF parameters |
| Paper | 2010Jiang2010_CTFCorrection | Amplitude correction method |
| Paper | 2010Kasantsev_CTFCorrection | Mathematical foundations of Kornberg and Jensen method |
| Paper | 2010Leong_CTFCorrection | Correction for spatially variant CTF |
| Paper | 2011Glaeser_Coma | The effect of coma at high-resolution |
| Paper | 2011Mariani_Tilted | CTF simulation and correction of tilted specimens |
| Paper | 2011Sindelar_Wiener | CTF correction using a modified version of Wiener filter |
| Paper | 2011Voortman_Tilted | CTF correction for tilted specimen |
| Paper | 2012Voortman_VaryingCTF | Correcting a spatially varying CTF |
| Paper | 2013Vargas_FastDef | Fast defocus |
Segmentation
| Paper | 2006Baker_segmentation | Segmentation of molecular subunits |
Fitting and docking
| Paper | 1999Volkmann_Fitting | Fitting in real space |
| Paper | 2001Baker_Review | Review of protein structure prediction |
| Paper | 2001Jones_Review | Review of protein structure prediction |
| Paper | 2004Tama_NMA1 | Flexible fitting with Normal Modes (I) |
| Paper | 2004Tama_NMA2 | Flexible fitting with Normal Modes (II) |
| Paper | 2005Velazquez_Superfamilies | Recognition of the superfamily folding in medium-high resolution volumes |
| Paper | 2007Kleywegt_QualityControl | Quality control and validation of fitting |
| Paper | 2012Velazquez_Constraints | Multicomponent fitting by using constraints from other information sources |
Books and reviews
| Book | 1980Herman_Tomography | General book on tomography |
| Book | 1988Kak_Tomography | General book on tomography |
| Paper | 2000Tao_Review | Review of single particles |
| Paper | 2000VanHeel_Review | Review of single particles |
| Paper | 2002Frank_Review | Review of single particles |
| Paper | 2002Schmid_Review | Review of single particles |
| Paper | 2004Henderson_Review | Review of electron microscopy |
| Paper | 2004Subramaniam_Review | Review of single particles |
| Paper | 2006Fernandez_Review | Review of electron microscopy |
| Book | 2006Frank_book | Book covering all aspects of electron microscopy of single particles |
| Paper | 2006Sorzano_Review | Review of optimization problems in electron microscopy |
| Paper | 2007Leschziner_Review | Review of 3D heterogeneity handling algorithms |
| Paper | 2007Sorzano_Review | Review of the image processing steps |
| Paper | 2008Fanelli_ImageFormation | Review on the image formation model from the electron waves and open inverse-problems in Electron Tomography |
| Paper | 2008Fernandez_HPCReview | High performance computing in electron cryomicroscopy |
| Paper | 2008Jonic_Review | Comparison between electron tomography and single particles |
| Paper | 2010DeRosier_Review | Personal account of how 3DEM developed in the early days |
| Chapter | 2012Sorzano_Review | Review of single particle analysis using Xmipp |
| Chapter | 2012Devaux_Protocol | Protocols for performing single particle analysis |
Software
| Paper | 1996Frank_Spider | Spider |
| Paper | 1996VanHeel_Imagic | Imagic |
| Paper | 1999Lutdke_Eman | Eman |
| Paper | 2004Sorzano_Xmipp | Xmipp |
| Paper | 2007Baldwin_AngularTransformations | The Transform Class in SPARX and EMAN2 |
| Paper | 2007Heymann_Bsoft | Bsoft |
| Paper | 2008Scheres_XmippProtocols | Xmipp Protocols |
| Paper | 2008Shaikh_SpiderProtocols | Spider Protocols |
Electron tomography
Image alignment
| Paper | 1996Owen_alignmentQuality | Automatic alignment without fiducial markers and evaluation of alignment quality |
| Paper | 2001Brandt_Automatic1 | Automatic alignment without fiducial markers |
| Paper | 2001Brandt_Automatic2 | Automatic alignment with fiducial markers |
| Paper | 2006Winkler_alignment | Marker-free alignment and refinement |
| Paper | 2006Castano_alignment | Alignment with non-perpendicularity |
| Paper | 2007Castano_alignment | Fiducial-less alignment of cryo-sections |
| Paper | 2009Sorzano_alignment | Marker-free alignment and refinement |
| Paper | 2010Cantele_dualAlignment | Alignment of dual series |
CTF estimation and restoration
| Paper | 2003Winkler_CTF | Focus gradient correction in electron tomography |
| Paper | 2006Fernandez_CTF | CTF determination and correction in electron tomography |
| Paper | 2009Zanetti_CTF | CTF determination and correction in electron tomography |
| Paper | 2009Xiong_CTF | CTF determination and correction for low dose tomographic tilt series |
3D reconstruction
| Paper | 1972Gilbert_SIRT | Simultaneous Iterative Reconstruction Technique (SIRT) |
| Paper | 1973Herman_ART | Algebraic Reconstruction Technique (ART) |
| Paper | 1984Andersen_SART | Simultaneous Algebraic Reconstruction Technique (SART) |
| Paper | 1992Radermacher_WBP | Weighted Backprojection in electron tomography |
| Paper | 1997Marabini_reconstruction | Iterative reconstruction in electron tomography |
| Paper | 2002Fernandez_reconstruction | Iterative reconstruction in electron tomography |
| Paper | 2007Radermacher_WBP | Weighted Backprojection in electron tomography |
| Paper | 2008Fernandez_CARP | Component Averaged Row Projections (CARP) |
| Paper | 2013Goris_SIRT_TV_DART | Combination of SIRT, Total Variation and Discrete ART to reconstruct and segment at the same time |
Noise reduction
| Paper | 2001Frangakis_NAD | Noise reduction with Nonlinear Anisotropic Diffusion |
| Paper | 2003Fernandez_AND | Anisotropic nonlinear diffusion for electron tomography |
| Paper | 2003Jiang_Bilateral | Bilateral denoising filter in electron microscopy |
| Paper | 2005Fernandez_AND | Anisotropic nonlinear denoising in electron tomography |
| Paper | 2007Heide_median | Iterative median filtering in electron tomography |
| Paper | 2007Fernandez_autAND | Anisotropic nonlinear diffusion with automated parameter tuning |
| Paper | 2009Fernandez_Beltrami | Nonlinear filtering based on Beltrami flow |
| Paper | 2010Bilbao_MeanShift | Mean Shift Filtering |
Segmentation
| Paper | 2002Frangakis_Eigenanalysis | Segmentation using eigenvector analysis. |
| Paper | 2002Volkmann_Watershed | Segmentation using watershed transform. |
| Paper | 2003Bajaj_BoundarySegmentation | Segmentation based on fast marching. |
| Paper | 2005Cyrklaff_Thresholding | Segmentation using optimal thresholding. |
| Paper | 2007Lebbink_TemplateMatching | Segmentation using template matching. |
| Paper | 2007Sandberg_OrientationFields | Segmentation using orientation fields. |
| Paper | 2007Sandberg_SegmentationReview | Review on segmentation in electron tomography. |
| Paper | 2008Garduno_FuzzySegmentation | Segmentation using fuzzy set theory principles. |
| Paper | 2009Lebbink_TemplateMatching2 | Segmentation using template matching. |
Resolution
| Paper | 2005Cardone_Resolution | Resolution criterion for electron tomography |
Subtomogram analysis
| Paper | 2000Bohm_Template | Macromolecule finding by template matching |
| Paper | 2002Frangakis_Template | Macromolecule finding by template matching |
| Paper | 2006Nickell_Review | Review of macromolecule finding by template matching (Visual Proteomics) |
| Paper | 2007Best_Review | Review of Localization of Protein Complexes by Pattern Recognition |
| Paper | 2007Forster_Review | Review of structure determination by subtomogram averaging |
| Paper | 2008Forster_Classification | Classification of subtomograms using constrained correlation |
| Paper | 2008Bartesaghi_Classification | Classification and averaging of subtomograms |
| Paper | 2008Schmid_Averaging | Alignment and averaging of subtomograms |
| Paper | 2010Amat_Averaging | Alignment and averaging of subtomograms exploiting thresholding in Fourier space |
Single particle tomography
| Paper | 2012Bartesaghi_Constrained | 3D reconstruction by imposing geometrical constraints |
Books and reviews
| Paper | 2000Baumeister_Review | Review of electron tomography |
| Paper | 2003Koster_Review | Review of electron tomography |
| Paper | 2003Sali_Review | Review of electron tomography |
| Paper | 2004Henderson_Review | Review of electron microscopy |
| Paper | 2005Lucic_Review | Review of electron tomography |
| Paper | 2006Fernandez_Review | Review of electron microscopy |
| Book | 2006Frank_TomoBook | Electron Tomography |
| Book | 2007McIntosh_Book | Cellular Electron Microscopy |
| Paper | 2007Sorzano_Review | Review of the image processing steps |
| Paper | 2008Fanelli_ImageFormation | Review on the image formation model from the electron waves and open inverse-problems |
| Paper | 2008Fernandez_HPCReview | High performance computing in electron cryomicroscopy |
| Paper | 2008Jonic_Review | Comparison between electron tomography and single particles |
Software
| Paper | 1996Kremer_IMOD | IMOD |
| Paper | 1996Chen_Priism/IVE | Priism/IVE |
| Paper | 1996Frank_Spider | Spider |
| Paper | 2004Sorzano_Xmipp | Xmipp |
| Paper | 2005Nickell_TOM | TOM Toolbox |
| Paper | 2007Messaoudi_TomoJ | TomoJ |
| Paper | 2008Heymann_BsoftTomo | Bsoft |
2D Crystals
2D Preprocessing
| Paper | 1986Henderson_Processing | General 2D processing |
| Paper | 2000He_PhaseAlignment | Phase consistency and Alignment |
| Paper | 2006Gil_Unbending | Crystal unbending |
Classification
| Paper | 1988Frank_Classification | MSA and classification in electron crystallography |
| Paper | 1996Fernandez_SOM | Classification based on self organizing maps |
| Paper | 1998Sherman_MSA | Classification based on MSA |
3D Reconstruction
| Paper | 1985Wang_Solvent | Solvent flattening |
| Paper | 1990Henderson_Processing | General 3D processing |
| Paper | 2004Marabini_ART | Algebraic Reconstruction Technique with blobs for crystals (Xmipp) |
Books and reviews
| Paper | 1998Walz_Review | Review of 2D crystallography |
| Paper | 1999Glaeser_Review | Review of 2D crystallography |
| Paper | 2001Ellis_Review | Review of 2D crystallography |
| Paper | 2001Glaeser_Review | Review of 2D crystallography |
| Paper | 2004Henderson_Review | Review of electron microscopy |
| Paper | 2006Fernandez_Review | Review of single particles, electron tomography and crystallography |
| Paper | 2007Sorzano_Review | Review of the image processing steps |
Software
| Paper | 1996Crowther_MRC | MRC |
| Paper | 2004Sorzano_Xmipp | Xmipp |
| Paper | 2007Gipson_2dx | 2dx |
| Paper | 2007Heymann_Bsoft | Bsoft |
| Paper | 2007Philippsen_IPLT | IPLT |
Helical particles
Filament corrections
| Paper | 1986Egelman_Curved | Algorithm for correcting curved filaments |
| Paper | 1988Bluemke_Pitch | Algorithm for correcting filaments with different helical pitches |
| Paper | 2006Wang_Pitch | Algorithm for correcting filaments with different helical pitches |
Reconstruction
| Paper | 1958Klug_Fourier | Fourier Bessel decomposition of the projection images |
| Paper | 1970DeRosier_Rec | Image processing steps towards 3D reconstruction |
| Paper | 1992Morgan_Rec | Image processing steps towards 3D reconstruction |
| Paper | 2005Wang_Iterative | Iterative Fourier-Bessel algorithm |
| Paper | 2007Egelman_Iterative | Iterative real-space algorithm |
Books and reviews
| Paper | 1970DeRosier_Rec | Image processing steps towards 3D reconstruction |
| Paper | 1992Morgan_Rec | Image processing steps towards 3D reconstruction |
| Paper | 2004Henderson_Review | Review of electron microscopy |
| Paper | 2007Sorzano_Review | Review of the image processing steps |
Software
| Paper | 1996Carragher_Phoelix | Phoelix |
| Paper | 1996Crowther_MRC | MRC |
| Paper | 1996Owen_Brandeis | Brandeis |
Icosahedral particles
Reconstruction
| Paper | 1970Crowther_Rec | Reconstruction of icosahedral viruses in Fourier space |
| Paper | 1971Crowther_Rec | Reconstruction of icosahedral viruses in Fourier space |
| Paper | 1996Fuller_Rec | Reconstruction of icosahedral viruses in Fourier space |
| Paper | 1997Thuman_Rec | Reconstruction of icosahedral viruses in Fourier space |
Classification
| Paper | 2005Scheres_Virus | Classification of virus capsids in real space |
Books and reviews
| Paper | 1999Baker_Review | Review of reconstruction of icosahedral viruses |
| Paper | 1999Conway_Review | Review of reconstruction of icosahedral viruses |
| Paper | 2000Thuman_Review | Review of reconstruction of icosahedral viruses |
| Paper | 2003Lee_Review | Review of reconstruction of icosahedral viruses |
| Paper | 2003Navaza_Review | Review of reconstruction of icosahedral viruses |
| Paper | 2006Grunewald_Review | Review of reconstruction of icosahedral viruses |
Software
| Paper | 1996Baker_EMPFT | EMPFT |
| Paper | 1996Crowther_MRC | MRC |
| Paper | 1996Frank_Spider | Spider |
| Paper | 1996VanHeel_Imagic | Imagic |
| Paper | 2004Sorzano_Xmipp | Xmipp |
Databases
| Paper | 2003Boutselakis_EMSD | EMSD database |
| Paper | 2005Heymann_Conventions | Conventions for software interoperability |
| Paper | 2005Heymann_Conventions | Conventions for software interoperability |
| Paper | 2011Kim_CDDB | Conformational Dynamics Data Bank |
| Paper | 2011Lawson_EMDB | Electron Microscopy Data Bank |
Relationship to other structural information sources
| Paper | 2000Engel_AFM | Review of Atomic Force Microscopy |
| Paper | 2001Dimmeler_AFM | Constraints from Atomic Force Microscopy |
| Paper | 2003Mobus_EnergyLoss | Chemical mapping by energy loss electron tomography |
| Paper | 2004Leapman_EnergyLoss | Chemical mapping by energy loss electron tomography |
| Paper | 2004Leapman_Review | Review on correlative microscopy |
| Paper | 2005Boudier_EFTETJ | Software for Chemical mapping by energy loss electron tomography |
| Paper | 2005Vestergaard_SAXS | Example of comparison of 3DEM and Small-angle X-ray scattering |
| Paper | 2007Hamada_SAXS | Constraints from Small-angle X-ray scattering |
X-ray tomography
| Paper | 2012Oton_ImageFormation | Image formation model in X-ray cell microscopy |
Mathematical tools necessary
People developing methods
Please, add yourself to this list (due to privacy reasons, please, do not add anyone else to the list without his/her explicit consent). Sort by first name alphabetical order.
Carlos Oscar S. Sorzano: CSIC, Madrid, Spain
Cédric Messaoudi: Institute Curie, Paris, France
Javier Vargas:mail: CSIC, Madrid, Spain
Joaquín Otón: CSIC, Madrid, Spain
José Román Bilbao-Castro: UAL, Almería, Spain; CSIC, Madrid, Spain
[José Miguel de la Rosa Trevín]: Biocomputing Unit CNB-CSIC, Madrid, Spain