Software Tools For Molecular Microscopy/Application tools

Packages that offer a tool or a set of tools to permit the analysis of data in one or more class of structural problems. These have generally been developed to manage one specific step in the structural analysis, for example CTF correction, particle picking etc. Data Acquisition Leginon http://leginon.scripps.edu Leginon is a system designed for automated collection of images from a transmission electron microscope. Instruments supported: FEI Tecnai series TEM, Tietz and Gatan CCD cameras. On August 1, 2007, Leginon 1.4 was released as open source. 2.0 amisoftware@scripps.edu Linux/Windows MRC Free/Open source Apache 2.0 Suloway C, Pulokas J, Fellmann D, et al. Automated molecular microscopy: the new Leginon system J. Struct. Biol. 151 1 41–60 2005 July 15890530 10.1016/j.jsb.2005.03.010 Suloway C, Shi J, Cheng A, et al. Fully automated, sequential tilt-series acquisition with Leginon J. Struct. Biol. 167 1 11–8 2009 July 19361558 2724967 10.1016/j.jsb.2009.03.019 Stagg SM, Lander GC, Pulokas J, et al. Automated cryoEM data acquisition and analysis of 284742 particles of GroEL J. Struct. Biol. 155 3 470–81 2006 September 16762565 10.1016/j.jsb.2006.04.005 Yoshioka C, Pulokas J, Fellmann D, Potter CS, Milligan RA, Carragher B Automation of random conical tilt and orthogonal tilt data collection using feature-based correlation J. Struct. Biol. 159 3 335–46 2007 September 17524663 2043090 10.1016/j.jsb.2007.03.005 Cheng A, Leung A, Fellmann D, et al. Towards automated screening of two-dimensional crystals J. Struct. Biol. 160 3 324–31 2007 December 17977016 2141647 10.1016/j.jsb.2007.09.012 SerialEM see Software_Tools_For_Molecular_Microscopy/Specific_packages#SerialEM UCSF Tomography see Software_Tools_For_Molecular_Microscopy/Specific_packages#UCSF_Tomography TOM Toolbox see Software_Tools_For_Molecular_Microscopy/Specific_packages#TOM_Toolbox Particle Selection DoG Picker http://ami.scripps.edu/redmine/projects/ami/wiki/DoGpicker DoG Picker is a simple particle picker that picks particles that resemble a blob using the Difference of Gaussians algorithm. It is intergrated into the TiltPicker program (below), 0.2 appion@scripps.edu Unix MRC Free/Open source Apache License v2.0 Python Voss NR, Yoshioka CK, Radermacher M, Potter CS, Carragher B DoG Picker and TiltPicker: software tools to facilitate particle selection in single particle electron microscopy J. Struct. Biol. 166 2 205–13 2009 May 19374019 2768396 10.1016/j.jsb.2009.01.004 FindEM http://ami.scripps.edu/redmine/projects/ami/wiki/FindEM The FindEM program is based on projection matching using local real-space correlation with a series of templates. Real-space algorithms are traditionally relatively slow, but a fast Fourier based implementation of the real-space local correlation function has been introduced which is approximately two orders of magnitude faster for the projection matching application. This algorithm is referred to as the “Fast Local Correlation Function” or FLCF. 2.0 appion@scripps.edu Unix MRC Free/Open source A.M. Roseman 2004 FindEM—a fast, efficient program for automatic selection of particles from electron micrographs Journal of Structural Biology 145 1-2 91-99 10.1016/j.jsb.2003.11.007 15065677 A.M. Roseman 2003 Particle finding in electron micrographs using a fast local correlation algorithm. Ultramicroscopy 94 225–236 3-4 12524193 Signature http://emlab.rose2.brandeis.edu A particle selection system for molecular electron microscopy. It applies a hierarchical screening procedure to identify molecular particles in EM micrographs. The user interface of the program provides versatile functions to facilitate image data visualization, particle annotation and particle quality inspection. The system design emphasizes both functionality and usability. niko @brandeis.edu Linux, Mac OS X, MS Windows MRC, TIFF Free/Open Source GPL J. Z. Chen Grigorieff, N. 2007 SIGNATURE: A single-particle selection system for molecular electron microscopy Journal of Structural Biology 157 168-173 SwarmPS http://www.imb.uq.edu.au/swarmps A specialised graphical user interface designed to streamline the process of particle selection from electron micrograph data sets. It provides implementations of both template matching and edge detection algorithms, has an intuitive and easy to use interface, and can be used to obtain useful results on most data sets that are generated in electron microscopy. Currently users can expect to select about 1000-4000 particles per hour of interaction. 0.9.2 d.woolford @imb.uq.edu.au Linux Most image formats Free for academic use under a software license agreement D. Woolford Ericksson, G., Rothnagel, R., Muller, D., Landsberg, M. J., Pantelic, R. S., McDowall, A., Pailthorpe, B., Young, P. R., Hankamer, B., and Banks, J. 2007 SwarmPS: Rapid, semi-automated single particle selection software Journal of Structural Biology 157 174-188 TiltPicker http://ami.scripps.edu/redmine/projects/ami/wiki/TiltPicker A graphical user interface for picking particles from image tilt pairs for such applications as random conical tilt (RCT) and orthogonal tilt reconstruction (OTR). TiltPicker borrows its interface from Leginon and re-implements many of the tilt picking features of SPIDER WEB that can be run on modern computers. 2.0 vossman77@yahoo.com Linux, Mac OS X, Windows, other Unices Free/Open Source Apache v2.0 Voss NR, Yoshioka CK, Radermacher M, Potter CS, Carragher B DoG Picker and TiltPicker: software tools to facilitate particle selection in single particle electron microscopy J. Struct. Biol. 166 2 205–13 2009 May 19374019 2768396 10.1016/j.jsb.2009.01.004 TMaCS https://sites.google.com/site/rubinsteingroup/particle-selection Template Matching and Classification System. Template matching identifies candidate particle images while a Support Vector Machine algorithm is interactively trained to distinguish particles from non-particles. 1.0 john.rubinstein@utoronto.ca, jianhua.zhao@utoronto.ca Linux MRC Free/Open Source Zhao J, Brubaker MA, Rubinstein JL TMaCS: A hybrid template matching and classification system for automated particle selection J. Struct. Biol. In Press 2013 }} CTF Estimation and Correction ACE http://ami.scripps.edu/redmine/projects/ami/wiki/ACE A completely automated algorithm for estimating the parameters of the contrast transfer function (CTF) of a transmission electron microscope. A MATLAB implementation of the algorithm, called ACE, is freely available. See also author's website: http://graphics.ucsd.edu/~spmallick/research/ace/index.html 2.3.1 amisoftware@scripps.edu MATLAB MRC Free/Open Source Apache License v2.0 MATLAB S.P. Mallick B Carragher, CS Potter, DJ Kriegman 2005 ACE: Automated CTF Estimation Ultramicroscopy 104 1 8-29 ACE2 http://ami.scripps.edu/redmine/projects/ami/wiki/ACE2 ACE2 is CTF estimation and correction program using the algorithms developed by Satya et al. (see ACE) rewritten in Objective-C programming language and does not require MATLAB. 2.0 appion@scripps.edu Unix (specifically, Mac OS X and Linux) MRC Free/Open source Apache License v2.0 Objective-C Unpublished CTFfind3 and CTFtilt http://emlab.rose2.brandeis.edu/ Programs for finding CTFs of electron micrographs 3.3 and 1.4 niko [at] brandeis.edu Linux, IRIX, OSF MRC Free/Open Source GPL Fortran J.A. Mindell Grigorieff, N. 2003 Accurate determination of local defocus and specimen tilt in electron microscopy Journal of Structural Biology 142 334-347 ctf Explorer http://www.maxsidorov.com/ctfexplorer/index.htm allows to calculate the Phase Contrast Transfer Function (CTF): a useful characteristics in Electron Microscopy 0.999a Maxim V. Sidorov, mathebuilder [at] gmail.com Windows 95/98/NT4/2000/XP w:Postcardware, freeware Max V. Sidorov 2002 ctfExplorer: Interactive Software for 1d and 2d Calculation and Visualization Of TEM Phase Contrast Transfer Function 8 S02 1572CD-1573CD 10.1017.S1431927602104442 EMCTF http://sites.google.com/site/3demimageprocessing/emctf CTF determination of non-astigmatic images in electron cryomicroscopy 1.1 jjfernandez.software at gmail.com Linux, Mac OS X MRC Free for academic users J.J. Fernandez Li, S. and Crowther, R. A. 2006 CTF determination and correction in electron cryotomography Ultramicroscopy 106 587-596 10.1016/j.ultramic.2006.02.004 J.J. Fernandez Sanjurjo, J.R. and Carazo, J. M. 1997 A spectral estimation approach to contrast transfer function detection in electron microscopy Ultramicroscopy 68 267-295 10.1016/S0304-3991(97)00032-6 TOMOCTF http://sites.google.com/site/3demimageprocessing/tomoctf CTF determination and correction in electron tomography 1.1 (October 2012) jjfernandez.software at gmail.com Linux, Mac OS X MRC Free for academic users J.J. Fernandez Li, S. and Crowther, R. A. 2006 CTF determination and correction in electron cryotomography Ultramicroscopy 106 587-596 10.1016/j.ultramic.2006.02.004 fitctf http://ncmi.bcm.edu/software/fitctf Estimating contrast transfer function and associated parameters by constrained non-linear optimization CYang@lbl.gov Linux, Windows, and Mac OS X MRC free C Yang Jiang, W., Chen, D-H., Adiga, U., Ng, E G., and Chiu, W. 2009 Estimating contrast transfer function and associated parameters by constrained non-linear optimization Journal of Microscopy 233 3 391-403 19250460 10.1111/j.1365-2818.2009.03137.x FitCTF2 http://jiang.bio.purdue.edu/software.php A graph theory method for determination of cryo-EM image focuses jiang12@purdue.edu Linux MRC Free for academic users Python Wen Jiang Guo, F., and Liu, Z. 2012 A graph theory method for determination of cryo-EM image focuses Journal of Structural Biology 180 2 343-351 10.1016/j.jsb.2012.07.005 3D Reconstruction TOMO3D http://sites.google.com/site/3demimageprocessing/tomo3d Fast tomographic reconstruction on standard multicore computers with WBP and SIRT. 1.3.4 (April 2012) jjfernandez.software at gmail.com Linux, Mac OS X, Windows MRC Free for academic users J.I. Agulleiro Fernandez J.J. 2011 Fast tomographic reconstruction on multicore computers Bioinformatics 27 582-583 10.1093/bioinformatics/btq692 http://dx.doi.org/10.1093/bioinformatics/btq692 J.I. Agulleiro Garzon E.M., Garcia I., Fernandez J.J. 2010 Vectorization with SIMD extensions speeds up reconstruction in electron tomography Journal of Structural Biology 170 570-575 10.1016/j.jsb.2010.01.008 http://dx.doi.org/10.1016/j.jsb.2010.01.008 J.I. Agulleiro Fernandez J.J. 2012 Evaluation of a multicore-optimized implementation for tomographic reconstruction PLoS ONE 7 11 e48261 23139768 10.1371/journal.pone.0048261 http://dx.doi.org/10.1371/journal.pone.0048261 TOMO3Dhybrid http://sites.google.com/site/3demimageprocessing/tomo3dhybrid Fast tomographic reconstruction (WBP,SIRT) with CPU+GPU co-processing 1.0 (February 2012) jjfernandez.software at gmail.com Linux MRC Free for academic users J.I. Agulleiro Vazquez F., Garzon E.M., Fernandez J.J. 2012 Hybrid computing: CPU+GPU co-processing and its application to tomographic reconstruction Ultramicroscopy 115 109-114 10.1016/j.ultramic.2012.02.003 http://dx.doi.org/10.1016/j.ultramic.2012.02.003 Resolution Estimation FSC http://imagescience.de/fsc/ Program to calculate the Fourier Shell Correlation of two 3D volumes. The three-dimensional Fourier Shell Correlation (FSC) measures the normalised cross correlation coefficient between two 3D volumes over corresponding shells in Fourier space, i.e., as a function of spatial frequency. The (modified) 3-sigma criterion indicates where the FSC systematically emerges above the expected random correlations of the background noise. The 1/2-bit information threshold criteria express where we have already collected a sufficient amount of data in the final 3D reconstruction to allow a direct structural interpretation at that resolution level. The 1/2-bit curve is calibrated to approximately yield resolution values comparable to resolution values in use in X-ray crystallography (FOM). michael @ImageScience.de Linux/Unix, Mac OS X (Intel), MS Windows IMAGIC, Spider, CCP4, MRC, TIFF, etc. Free G. Harauz M. van Heel 1986 Exact filters for general geometry three dimensional reconstruction Optik 78 146–156 M. van Heel M. Schatz 2005 Fourier shell correlation threshold criteria Journal of Structural Biology 151 250-262 RMEASURE http://emlab.rose2.brandeis.edu/ A computational method that allows the measurement of the signal-to-noise ratio and resolution of a three-dimensional structure obtained by single particle electron microscopy and reconstruction. The method does not rely on the availability of the original image data or the calculation of several structures from different parts of the data that are needed for the commonly used Fourier Shell Correlation criterion. Instead, the correlation between neighboring Fourier pixels is calculated and used to distinguish signal from noise. 1.05 niko @brandeis.edu Linux, IRIX, OSF, Mac OS X MRC, Spider Free/Open Source GPL D. Sousa N. Grigorieff 2007 Ab initio resolution measurement for single particle structures Journal of Structural Biology 157 201-210 Denoising iMed http://coan.burnham.org Software for automatic noise reduction using iterative median filtering. coan@burnham.org Linux MRC Free for academic users van der Heide P, Xu XP, Marsh BJ, Hanein D, Volkmann N 2007 Efficient automatic noise reduction of electron tomographic reconstructions based on iterative median filtering J. Struct. Biol. 158 196-204 17224280 TOMOAND http://sites.google.com/site/3demimageprocessing/tomoand Package for noise reduction in electron cryotomography with Anisotropic Nonlinear Diffusion. 2.0 (September 2011) jjfernandez.software at gmail.com Linux, Mac OS X MRC Free for academic users J.J. Fernandez Li, S. 2003 An improved algorithm for anisotropic nonlinear diffusion for denoising cryotomograms Journal of Structural Biology 144 152-161 10.1016/j.jsb.2003.09.010 J.J. Fernandez Li, S. and Lucic, V. 2007 Three-dimensional anisotropic noise reduction with automated parameter tuning. Application to electron cryotomography Lecture Notes in Computer Science 4788 60-69 10.1007/978-3-540-75271-4_7 TOMOBFLOW http://sites.google.com/site/3demimageprocessing/tomobflow Package for noise reduction in electron tomography with Beltrami flow. 1.3 (July 2011) jjfernandez.software at gmail.com Linux, Mac OS X MRC Free for academic users J.J. Fernandez 2009 TOMOBFLOW: Feature-preserving noise filtering for electron tomography BMC Bioinformatics 10 178 10.1186/1471-2105-10-178 http://www.biomedcentral.com/1471-2105/10/178 XMSF http://sites.google.com/site/xmsfilter/ Package for noise reduction and pre-segmentation in electron tomography based on Mean-Shift. 1.0 jbc747 at ual.es Linux Several, including SPIDER, MRC, IMAGIC, etc. Free for academic users J.R. Bilbao-Castro Sorzano C.O.S., Garcia I., Fernandez J.J. 2010 XMSF: Structure-preserving noise reduction and pre-segmentation in microscope tomography Bioinformatics 26 2786-2787 10.1093/bioinformatics/btq496 http://bioinformatics.oxfordjournals.org/content/26/21/2786 Segmentation CoDiv http://coan.burnham.org CoDiv - Continental Divide Watershed Segmentation. Software for semi-automatic segmentation of density maps such as those obtained by electron microscopy and image reconstruction or electron tomography. coan@burnham.org Linux MRC Free for academic users Volkmann N 2002 A novel three-dimensional variant of the watershed transform for segmentation of electron density maps J. Struct. Biol. 138 123-129 12160708 Population http://www.population-image.fr CoDiv - Population is dedicated to the quantitative/qualitative analysis of images coming from 2D/3D microscopy with filtering, segmentation, geometrical/physical characterization, visualization and modeling. 2.0 ocds@shinoe.org Linux/Windows RAW/BMP/JPEG/PNG/PGM Free for academic/industrial users MIT C++ TOMOSEGMEM http://sites.google.com/site/3demimageprocessing/tomosegmem Package for segmentation of membranes in tomograms. 1.0 (December 2011) jjfernandez.software at gmail.com Linux, Mac OS X MRC Free for academic users Martinez-Sanchez A, Garcia I, Fernandez JJ 2011 A differential structure approach to membrane segmentation in electron tomography J. Struct. Biol. 175 372-383 10.1016/j.jsb.2011.05.010 http://dx.doi.org/10.1016/j.jsb.2011.05.010 TomoSegMemTV http://sites.google.com/site/3demimageprocessing/tomosegmemtv Package for robust membrane segmentation based on Tensor Voting for tomograms. 1.0 (April 2014) an.martinez.s.sw at gmail.com Linux, Mac OS X, Windows MRC Free for academic users Martinez-Sanchez A, Garcia I, Asano S, Lucic V, Fernandez JJ 2014 Robust membrane detection based on tensor voting for electron tomography J. Struct. Biol. 186 49-61 10.1016/j.jsb.2014.02.015 http://dx.doi.org/10.1016/j.jsb.2014.02.015 B-Factor Estimation and Correction bfactor http://emlab.rose2.brandeis.edu/software Program for filtering 3D maps and applying B-factors. 1.03 niko @brandeis.edu Linux/Mac MRC Free/Open Source GPL Unpublished EM-BFACTOR http://sites.google.com/site/3demimageprocessing/embfactor Package for sharpening high resolution information in single particle electron cryomicroscopy 1.1 jjfernandez.software at gmail.com Linux, Mac OS X Most common formats used in 3DEM Free for academic users J.J. Fernandez Luque, D., Caston, J.R., Carrascosa, J.L. 2008 Sharpening high resolution information in single particle electron cryomicroscopy Journal of Structural Biology 164 170-175 10.1016/j.jsb.2008.05.010 P.B. Rosenthal Henderson, R. 2003 Optimal Determination of Particle Orientation, Absolute Hand, and Contrast Loss in Single-particle Electron Cryomicroscopy Journal of Molecular Biology 333 721-745 10.1016/j.jmb.2003.07.013 Initial Model Construction ROTAN http://www.sickkids.ca/research/rubinstein/software/index.html Program for estimating the relative angular orientation of single particles that present side views john.rubinstein at utoronto.ca Linux MRC Free for academic users L.A. Baker Rubinstein, R. 2008 Angle determination for side views in single particle electron microscopy Journal of Structural Biology 162 260-270 J.L. Rubinstein Walker, J.E. and Henderson, R. 2003 Structure of the mitochondrial ATP synthase by electron cryomicroscopy EMBO Journal 22 6182-6192