Software Tools For Molecular Microscopy

2 There are a large number of software tools or software applications that have been specifically developed for the field sometimes referred to as molecular microscopy or cryo-electron microscopy or cryoEM. Several special issues of the Journal of Structural Biology (see references below) have been specifically devoted to descriptions of these applications and several web sites provide partial lists of the software packages and where to obtain them. This article attempts to provide a complete list and up-to-date distribution information of all of the software of interest to the cryoEM community. Everyone in the community is encouraged to add content, correct errors, and make any other contributions that might be useful. The software tools described here have been loosely and somewhat arbitrarily organized into several categories as follows: General packages Packages that offer a comprehensive set of tools to permit the analysis of data in several classes of structural problems (in alphabetical order). Appion http://appion.org "Appion", is a comprehensive web interface and python scripting system for single-particle analysis, which allows performing the entire 3D-EM image processing work-flow, from micrograph preprocessing to 3D model refinement. The software is written entirely in python and designed in a highly modular way. Stand-alone programs may be invoked from the UNIX command line, or via standardized web interface. 3.5 nrammsoft@nysbc.org Linux, possibly other Unices may work as well. CCP4, Imagic, JPEG, MRC, PNG, Spider, TIFF Free/Open Source Apache License 2.0 Lander GC, Stagg SM, Voss NR, et al. Appion: an integrated, database-driven pipeline to facilitate EM image processing J. Struct. Biol. 166 1 95–102 2009 April 19263523 2775544 10.1016/j.jsb.2009.01.002 Voss NR, Lyumkis D, Cheng A, et al. A toolbox for ab initio 3-D reconstructions in single-particle electron microscopy J. Struct. Biol. 169 3 389–98 2010 March 20018246 10.1016/j.jsb.2009.12.005 Stagg SM, Lander GC, Quispe J, et al. A test-bed for optimizing high-resolution single particle reconstructions J. Struct. Biol. 163 1 29–39 2008 July 18534866 2505049 10.1016/j.jsb.2008.04.005 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 Bsoft http://bsoft.ws Bsoft is a collection of programs and a platform for development of software for image and molecular processing in structural biology. Problems in structural biology are approached with a highly modular design, allowing fast development of new algorithms without the burden of issues such as file I/O. It provides an easily accessible interface, a resource that can be and has been used in other packages. Several workflows such as for single particle analysis and tomography are supported with parameter exchange as well as the ability to do distributed processing across heterogeneous clusters of computers. Several tools are available for modeling structures as atomic coordinates or larger scale models for the interpretation of large molecular complexes such as viruses and sub-cellular organelles. 2.1.1 Bernard_Heymann at nih.gov Unix (Mac OS X, IRIX, Linux, AIX, Solaris, Tru64), VMS BioRad, Brix, CCP4, Digital Instruments, Digital Micrograph, DSN6, EM, Goodford, GRD, HKL, Imagic, IP, JPEG, MFF, Image Magick, MRC, PIC, PIF, PNG, PNM, SPE, Spider, Suprim, TIFF, XPLOR, RAW Free/Open Source (Public domain) C++, Tcl/Tk J.B. Heymann 2001 Bsoft: image and molecular processing in electron microscopy Journal of Structural Biology 133 2-3 156-69 J.B. Heymann D.M. Belnap 2007 Bsoft: Image processing and molecular modeling for electron microscopy Journal of Structural Biology 157 3-18 J.B. Heymann G. Cardone D.C. Winkler A.C. Steven 2008 Computational resources for cryo-electron tomography in Bsoft Journal of Structural Biology 161 232-242 Cyclops http://www.bfsc.leidenuniv.nl/software/Cyclops Cyclops is a new computer program designed as a graphical front-end that allows easy control and interaction with tasks and programs for 3D reconstruction of biological complexes using cryo-electron microscopy. It was designed for straightforward implementation in grid architectures. As a front-end to a collection of programs it provides a common interface to other programs, thus enhancing the usability of the suite and the productivity of the user. 0.8rc1 plaisier @chem.leidenuniv.nl Windows XP Imagic Free J.R. Plaisier L. Jiang J.P. Abrahams 2007 Cyclops: New modular software suite for cryo-EM. Journal of Structural Biology 157 19-27 EMAN2 http://eman2.org EMAN2 is a software suite for scientific image processing, with a particular focus on CryoEM single particle analysis, CryoET, Subtomogram Averaging and other TEM related image processing. EMAN2 is built on top of a robust image processing library in C++, wrapped in Python. All user programs including the GUIs are written in Python, so they may be customized or modified without even downloading the (freely available) source. The GUI includes widgets for 3-D display (isosurface, volume rendering and slices), single 2-D images, multiple 2-D images, 2-D plots and 3-D plots. The core library consists of several hundred image processing routines, as well as objects for conversion between orientation conventions and various data formats. It is a fully modular system, meaning newly added algorithms (for example a new filter, or a new 3-D reconstruction routine) automatically and immediately appear in all GUI's and command-line programs. 2.91 sludtke@bcm.edu Linux (most variants), Mac OS X (versions from last ~5 years), Windows 10 HDF5, SPIDER, MRC/CCP4, IMAGIC, PIF, ICOS, VTK, PGM, Amira, Xplor, Gatan DM2/DM3/DM4, TIFF, Scans-a-Lot, LST, PNG, V4L, JPEG Free/Open Source EMAN, SPIDER, IMAGIC, MRC, SGI, CHIMERA GPL/BSD C++/Python G. Tang L. Peng P.R. Baldwin Mann, D. S., Jiang, W., Rees, I., and Ludtke, S. J. EMAN2: An extensible image processing suite for electron microscopy Journal of Structural Biology 157 38-46 EMAN http://blake.bcm.edu/eman A suite of scientific image processing tools aimed primarily at single particle reconstruction. This is a technique for determining the 3-D structure of a molecule or macromolecular assembly from thousands to hundreds of thousands of noisy images of individual molecules, generally collected on a transmission electron microscope. EMAN's focus is on providing state of the art single particle reconstruction methods automated to the greatest extent possible. The goal is to permit even novice users to be able to reconstruct macromolecular structures with high veracity and at high resolution. It also has a variety of tools for more generic image processing, useful for electron tomography, 2-D crystallography and helical reconstructions. EMAN consists of a ~100,000 line C++ library with bindings to the popular Python programming language. It offers literally hundreds of different scientific image processing algorithms including Fourier processing, real-space filters, 3-D reconstruction, projection, etc. In EMAN2, all user-level programs, including GUI programs, are written in Python, permitting the advanced user to easily customize aspects of the package. EMAN is funded by the NIGMS through grant R01GM080139. 1.9 sludtke@bcm.edu Linux, Mac OS X, most Unix variants, Windows (GUI and utilities only) HDF5, SPIDER, MRC/CCP4, IMAGIC, PIF, ICOS, VTK, PGM, Amira, Xplor, Gatan DM2/DM3, TIFF, Scans-a-Lot, LST, PNG, V4L, JPEG Free/Open Source GPL/BSD C++ S.J. Ludtke P.R. Baldwin W. Chiu 1999 EMAN: Semiautomated Software for High-Resolution Single-Particle Reconstructions Journal of Structural Biology 128 82-97 Eos http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos An extensible and general image analysis system for electron microscopy. It supplies four supports. (1) 400-over small tools for image analysis including general image processing such as smoothing, labeling, binarization and EM-specific tools such as CTF correction, alignment, classification, 3D-reconstruction, map/PDB structural analysis and pseudo-atomic modeling. (2) Integrated tools for single particle analysis, helical reconstruction, electron tomography and so on. (3) Object-oriented libraries by C and (C) prototype-source codes for tool developers. 2.2 yasunaga@bio.kyutech.ac.jp Linux/Unix, Mac OS X(Intel), cygwin under MS Windows MRC, TIFF, DNS6(Map) etc. Free C, Tcl/Tk, Ruby/Tk, javascript Yasunaga T, Wakabayashi T Extensible and object-oriented system Eos supplies a new environment for image analysis of electron micrographs of macromolecules J. Struct. Biol. 116 1 155–60 1996 8742738 10.1006/jsbi.1996.0025 K Noda Nakamura M, Nishida R, Yoneda Y, Yamaguchi Y, TAMURA Y, Nakuamura, H. and Yasunaga T 2006 Atomic model construction of protein complexes from electron micrographs and visualization of their 3D structure using VR system J. Plasma Physics 72 06 1037-1040 long IMAGIC http://imagescience.de/imagic/ IMAGIC is an image analysis software package for electron microscopy, which is also used to process images from other devices, spectra and other multi-dimensional data-sets. Typical operations are: multi-dimensional mixed-radix Fourier transforms, correlation analysis, alignments, multivariate statistical classification, angular reconstitution to find the spatial orientation of EM projection images, three-dimensional reconstruction from EM projections, 2D image and 3D volume image processing. 4D imagic@ImageScience.de Most platforms (Linux/Unix, Mac OS X (intel), MS Windows) IMAGIC-5 (Most formats can be imported/exported: Spider, CCP4, MRC, TIFF, etc.) Commercial and non-profit prices van Heel M, Harauz G, Orlova EV, Schmidt R, Schatz M A new generation of the IMAGIC image processing system J. Struct. Biol. 116 1 17–24 1996 8742718 10.1006/jsbi.1996.0004 M. Van Heel 1979 IMAGIC and its results Ultramicroscopy 4 117 Van Heel M. Portugal, R. Rohou, A., Linnemayr, C., Bebeacua, C., Schmidt, R., Grant, T., and Schatz, M. International Tables for Crystallography, Vol. F 2010 Four-Dimensional Cryo Electron Microscopy at Quasi Atomic Resolution: "IMAGIC 4D" IPLT http://www.iplt.org The Image Processing Library & Toolbox is an open-source project primarily aimed the electron microscopy community, with particular emphasis on 2D electron crystallography. It consists of several modular class libraries written in C++, each exposing a majority of their interface to Python, upon which the processing logic is build. Easy extendability has been a prime focus for the framework design, and we welcome any contribution from the community. andreas dot schenk at fmi dot ch Linux, Mac OS X, Windows (experimental) MRC, CCP4, TIFF, JPK, NANOSCOPE, SITUS, PNG, DM3, SPIDER Free/Open Source GPL C++/Python Philippsen A, Schenk AD, Signorell GA, Mariani V, Berneche S, Engel A Collaborative EM image processing with the IPLT image processing library and toolbox J. Struct. Biol. 157 1 28–37 2007 January 16919967 10.1016/j.jsb.2006.06.009 Philippsen A, Schenk AD, Stahlberg H, Engel A Iplt--image processing library and toolkit for the electron microscopy community J. Struct. Biol. 144 1-2 4–12 2003 14643205 10.1016/j.jsb.2003.09.032 Schenk AD, Philippsen A, Engel A, Walz T A pipeline for comprehensive and automated processing of electron diffraction data in IPLT J. Struct. Biol. 182 2 173-185 2013 23500887 10.1016/j.jsb.2013.02.017 MDPP http://sourceforge.net/projects/mdpp/ The Micrograph Data Processing Program (MDPP) is a fully-featured general purpose image processing package originally written to support research in structural biology requiring electron microscopy and image processing. The package includes software for 2D and 3D plane layer reconstruction and helical reconstruction v17.320 smithp01-at-nyumc.org macOS/Linux BMD, MRC, SPIDER, TIFF, JPEG, PNG Free GPLv3 FORTRAN and C Smith PR, Gottesman SM The micrograph data processing program J. Struct. Biol. 116 1 35–40 1996 8742720 10.1006/jsbi.1996.0007 MRC IMAGE PROCESSING PACKAGE http://www2.mrc-lmb.cam.ac.uk/image2000.html The MRC image processing package has been developed over many years, with contributions by many authors. It comprises software for image processing of 2D crystals, analysis of electron diffraction patterns, helical diffraction and single particle analysis, especially particles with icosahedral symmetry. It also includes visualization software for displaying and manipulating images in many ways. jms@mrc-lmb.cam.ac.uk DEC/Tru64, LINUX, UNIX, IRIX, Mac OS X MRC Free to academic users Crowther RA, Henderson R, Smith JM MRC image processing programs J. Struct. Biol. 116 1 9–16 1996 8742717 10.1006/jsbi.1996.0003 Smith JM Ximdisp--A visualization tool to aid structure determination from electron microscope images J. Struct. Biol. 125 2-3 223–8 1999 10222278 10.1006/jsbi.1998.4073 RELION https://relion.readthedocs.io At the heart of RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) lies a refinement program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM). It is developed in the group of Sjors Scheres at the MRC Laboratory of Molecular Biology. Briefly, the ill-posed problem of 3D-reconstruction is regularised by incorporating prior knowledge: the fact that macromolecular structures are smooth, i.e. they have limited power in the Fourier domain. In the corresponding Bayesian framework, many parameters of a statistical model are learned from the data, which leads to objective and high-quality results without the need for user expertise. Recent developments around this program have turned RELION into a general package, in which most of the single-particle analysis tasks may be performed. 4.0.0 scheres at mrc-lmb.cam.ac.uk Unix (Linux, Mac OS X, etc.) MRC, Spider Free/Open Source Scheres SHW A Bayesian View on Cryo-EM Structure Determination J. Mol. Biol. 415 2 406-418 2012 22100448 10.1016/j.jmb.2011.11.010 Scipion http://scipion.i2pc.es/ Scipion is an image processing framework for obtaining 3D models of macromolecular complexes using Electron Microscopy (3DEM). It integrates several software packages (such as Xmipp, Relion, Spider, Eman2, Bsoft, Frealign, Ctfind, etc) and presents a unified interface for both biologists and developers. Scipion allows to execute workflows combining different programs while taking care of formats and conversions. Additionally, all steps are tracked and can be reproduced later on. 3.0.10 scipion@cnb.csic.es UNIX HDF5, SPIDER, MRC/CCP4, IMAGIC, PIF, Gatan DM3, TIFF, JPEG, EM, SPE Free/Open Source GPL C++, Python, Java de la Rosa-Trevín, J.M., Quinana, A., del Cano, L. et al. Scipion: a software framework toward integration, reproducibility and validation in 3D Electron Microscopy submitted 2016 March SIMPLE http://simple.stanford.edu SIMPLE (Single-particle IMage Processing Linux Engine) implements an ab initio reconstruction algorithm tailored to flexible, asymmetrical single-particles. The SIMPLE front-end is developed according to the 'Unix toolkit philosophy'. The object-oriented back-end provides image clustering, ab inito 3D alignment, reconstruction, and refinement algorithms. 3.0 via the simple website Unix (Linux, Mac OS X) SPIDER Free/Open Source GPL modern Fortran Elmlund D, Elmlund H SIMPLE: software for ab initio reconstruction of flexible single-particles submitted 2012 Elmlund D, Davis R, Elmlund H Ab initio structure determination from electron microscopic images of single molecules coexisting in different functional states Structure 18 7 777–86 2010 July 20637414 10.1016/j.str.2010.06.001 SPARX http://sparx-em.org/sparxwiki SPARX (Single Particle Analysis for Resolution eXtension) is a new image processing environment with a particular emphasis on transmission electron microscopy (TEM) structure determination. It includes a user interface that provides a complete graphical programming environment with a novel data/process-flow infrastructure, an extensive library of python scripts that perform specific TEM-related computational tasks, and a core library of fundamental C++ image processing functions. In addition, SPARX relies on the EMAN2 library. 2.91 pawel.a.penczek@uth.tmc.edu Most platforms Most formats Free/Open Source BSD Hohn M, Tang G, Goodyear G, et al. SPARX, a new environment for Cryo-EM image processing J. Struct. Biol. 157 1 47–55 2007 January 16931051 10.1016/j.jsb.2006.07.003 Baldwin PR, Penczek PA The Transform Class in SPARX and EMAN2 J. Struct. Biol. 157 1 250–61 2007 January 16861004 10.1016/j.jsb.2006.06.002 SPIDER http://www.wadsworth.org/spider_doc/ SPIDER (System for Processing Image Data from Electron microscopy and Related fields) is an image processing system for electron microscopy. Contains numerous operations for: 3D reconstruction, averaging of single particle macromolecule specimens, multivariate statistical classification of images, and electron tomography. Computational modules are written in Fortran and the visualization GUI is written in C. Developed and maintained since 1978. 25.06 spider@wadsworth.org Unix (Linux) SPIDER, CCP4, Emispic, MRC, PDB, Raw Free/Open Source GPL Fortran, C Frank J, Radermacher M, Penczek P, Zhu J, Li Y, Ladjadj M, Leith A SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields J. Struct. Biol. 116 1 190–9 1996 8742743 10.1006/jsbi.1996.0030 Baxter WT, Leith A, Frank J SPIRE: the SPIDER reconstruction engine J. Struct. Biol. 157 1 56–63 2007 January 17055743 10.1016/j.jsb.2006.07.019 Yang C, Penczek PA, Leith A, et al. The parallelization of SPIDER on distributed-memory computers using MPI J. Struct. Biol. 157 1 240–9 2007 January 16859923 10.1016/j.jsb.2006.05.011 Shaikh TR, Gao H, Baxter WT, et al. SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs Nat Protoc 3 12 1941–74 2008 19180078 2737740 10.1038/nprot.2008.156 Suprim http://emg.nysbc.org/redmine/projects/suprim A flexible, modular software package intended for the processing of electron microscopy images. The system consists of a set of image processing tools or filters,written in the C programming language, and a command line style user interface based on the UNIX shell. The pipe and filter structure of UNIX and the availability of command files in the form of shell scripts eases the construction of complex image processing procedures from the simpler tools. 5.5 nrammsoft@nysbc.org Unix MRC/suprim Free/Open Source Schroeter JP, Bretaudiere JP SUPRIM: easily modified image processing software J. Struct. Biol. 116 1 131–7 1996 8742734 10.1006/jsbi.1996.0021 Xmipp http://xmipp.cnb.csic.es/ "X-Window-based Microscopy Image Processing Package", is a comprehensive package for single-particle analysis, which allows performing the entire 3D-EM image processing work-flow, from micrograph preprocessing to 3D model refinement. Among other tools, Xmipp contains programs for ART+blobs reconstruction, self-organizing maps and maximum-likelihood classification (in 2D and 3D). The software is written in C++ and designed in a highly modular way. Stand-alone programs may be invoked from the UNIX command line, or via standardized python scripts. A graphical user interface to the python scripts (written in python-tk) makes running Xmipp straightforward also for novice users. 3.20.07 xmipp@cnb.csic.es UNIX HDF5, SPIDER, MRC/CCP4, IMAGIC, PIF, Gatan DM3, TIFF, JPEG, EM, SPE Free/Open Source GPL C++, Python, Java de la Rosa-Trevín, J.M., Otón, J., Marabini, R. et al. Xmipp 3.0: An improved software suite for image processing in electron microscopy J. Struct. Biol. 184 2 321–328 2013 November 10.1016/j.jsb.2013.09.015 Sorzano CO, Marabini R, Velázquez-Muriel J, et al. XMIPP: a new generation of an open-source image processing package for electron microscopy J. Struct. Biol. 148 2 194–204 2004 November 15477099 10.1016/j.jsb.2004.06.006 Scheres SH, Núñez-Ramírez R, Sorzano CO, Carazo JM, Marabini R Image processing for electron microscopy single-particle analysis using XMIPP Nat Protoc 3 6 977–90 2008 18536645 2778070 10.1038/nprot.2008.62 Specific packages Packages that offer a comprehensive set of tools to permit the analysis of data in a single class of structural problem. For example packages specifically focused on objects with helical, icosahedral, crystalline symmetry, etc. Two-dimensional crystals 2dx http://2dx.org/ A software system designed as a user friendly, platform-independent software package for electron crystallography. 2dx assists in the management of an image-processing project, guides the user through the processing of 2D crystal images, and provides transparence for processing tasks and results. Algorithms are implemented in the form of script templates reminiscent of c-shell scripts. It includes a single-particle Maximum Likelihood module, and 3D merging capability. 2dx builds upon the MRC programs, which were extended by additional functions to interface with the GUI of 2dx, and to implement the optionally automatic processing. 3.1.0 Henning.Stahlberg@unibas.ch Mac OS X, Linux MRC, TIFF, CCP4 Free/Open Source GPL Gipson B, Zeng X, Zhang ZY, Stahlberg H 2dx--user-friendly image processing for 2D crystals J. Struct. Biol. 157 1 64–72 2007 January 17055742 10.1016/j.jsb.2006.07.020 Zeng X, Stahlberg H, Grigorieff N A maximum likelihood approach to two-dimensional crystals J. Struct. Biol. 160 3 362–74 2007 December 17964808 10.1016/j.jsb.2007.09.013 Icosahedral viruses AUTO3DEM http://cryoem.ucsd.edu/programs.shtm An automation system designed to accelerate the computationally intensive process of three-dimensional structure determination from images of vitrified icosahedral virus particles. With minimal user input and intervention, AUTO3DEM manages the flow of data between the major image reconstruction programs, monitors the progress of the computations, and intelligently updates the input parameters as the resolution of the model is improved. 2.02 sinkovit@sdsc.edu Linux, UNIX PIF Free/Open Source BSD license Yan X, Sinkovits RS, Baker TS AUTO3DEM--an automated and high throughput program for image reconstruction of icosahedral particles J. Struct. Biol. 157 1 73–82 2007 January 17029842 1847775 10.1016/j.jsb.2006.08.007 Helices BBHP - Burnham-Brandeis Helical Package http://coan.burnham.org/other-projects/ The Brandeis Helical Package has been in use in one form or another for quite some time. Originally developed for VAX/VMS it has been modified, expanded, and ported several times. We first ported the package to Linux in 2006, using the Portland Group compilers. Subsequently we rewrote portions of the fortran code which were not supported by GNU fortran (g77) and now the package compiles and runs with gcc/g77. This has allowed us to support extra modern platforms. The re-christened Burnham-Brandeis Helical Package will now run on 32-bit Linux, 64-bit Linux, Mac OS X (Intel) and even Windows running Cygwin. At the same time, when porting to Linux, we took the opportunity to replace the main GUI portions of the package with updated programs. We had spent some time modifying the Tcl/Tk-based GUI programs Tkir (image viewer) and Tkll (layerline viewer) from SUPRIM to support a plugin architecture, where we could write new plugins to add functionality without further modifications to the core code-base. The first, tkinterp, provides an interface in Tkir for selecting layerlines, replacing the old interp program. The second, brandeisll, is a Tkll plugin to provide support for displaying the Burnham-Brandeis Helical Package "interp" layerline and bessel-function format. We've also included as part of the package, the AVID software for analyzing the variance within the helix. 20.0 coan@burnham.org Linux MRC Free Owen CH, Morgan DG, DeRosier DJ Image analysis of helical objects: the Brandeis Helical Package J. Struct. Biol. 116 167–175 1996 8742740 Rost LE, Hanein D, DeRosier DJ Reconstruction of symmetry deviations: a procedure to analyze partially decorated F-actin and other incomplete structures Ultramicroscopy 72 187–197 1998 9639941 Helixplorer http://rico.ibs.fr/helixplorer HELIXPLORER helps with the determination of helical symmetry parameters. The tool supposes you have at your disposal the diffraction pattern (Fourier transform) of an helical structure. Usually, we use the power-spectrum (PS) of a cryo-EM class average. HELIXPLORER draws the theoretically expected pattern calculated from an ideal helix on the top of your experimental diffraction pattern. It then calculates a score based on the average PS pixel value in the areas which should contain the maxima of the pattern. The obtained scores will then be plotted for all tested helical parameters as 1D or 2D graphs that you can click on (drag to zoom-in and right-click to zoom-out) to check the agreement between the experimental and theoretical patterns. Hopefully, the plots will show a (at least local) maximum score for the true helical symmetry parameters of your structure. Of course, there will be ambiguities and the maximum score will not always be unique but HELIXPLORER should help with selecting a manageable subset of possibilities. 1.0 leandro.estrozi@ibs.fr Requires web browser with Javascript. (Browser dependent) BMP,SVG,JPG,PNG and GIF. Free/Open Source CeCILL (http://www.cecill.info/index.en.html) Javascript Unpublished IHRSR The iterative helical real space reconstruction (IHRSR) algorithm can reconstruct helical filaments under conditions when traditional Fourier–Bessel approaches sometimes fail. For example when there is disorder or heterogeneity present, when the specimens diffract weakly, or when Bessel functions overlap. egelman@virginia.edu Linux SPIDER Free Egelman EH The iterative helical real space reconstruction method: surmounting the problems posed by real polymers J. Struct. Biol. 157 1 83–94 2007 January 16919474 10.1016/j.jsb.2006.05.015 Phoelix http://emg.nysbc.org/redmine/projects/phoelix A set of procedures and algorithms for helical processing that we refer to as the PHOELIX package. The package was developed to provide a time-efficient and semiautomated method for determining a three-dimensional density map from a specimen with helical symmetry. The procedures which are part of PHOELIXn are drawn from the original MRC helical processing suite with extensions principally developed using the SUPRIM image processing package. The package in its current form has been optimized for the processing of actomyosin filaments but has been modified and applied to other helical structures. 1.3 nrammsoft@nysbc.org Unix MRC/suprim Free/Open Source Whittaker M, Carragher BO, Milligan RA PHOELIX: a package for semi-automated helical reconstruction Ultramicroscopy 58 3-4 245–59 1995 June 7571117 Carragher B, Whittaker M, Milligan RA Helical processing using PHOELIX J. Struct. Biol. 116 1 107–12 1996 8742731 10.1006/jsbi.1996.0018 Ruby-Helix http://structure.m.u-tokyo.ac.jp/English/software/Ruby-Helix-Page/ruby-helix.html Set of programs for the analysis of “helical” objects with or without a seam. Ruby-Helix is built on top of the Ruby programming language and is the first implementation of asymmetric helical reconstruction for practical image analysis. It also allows easier and semi-automated analysis, performing iterative unbending and accurate determination of the repeat length. 1.0 mkikkawa@m.u-tokyo.ac.jp Fedora, Mac OS X MRC Free/Open Source GPL Metlagel Z, Kikkawa YS, Kikkawa M Ruby-Helix: an implementation of helical image processing based on object-oriented scripting language J. Struct. Biol. 157 1 95–105 2007 January 16996276 10.1016/j.jsb.2006.07.015 Kikkawa M A new theory and algorithm for reconstructing helical structures with a seam J. Mol. Biol. 343 4 943–55 2004 October 15476812 10.1016/j.jmb.2004.08.051 Spring http://www.sachse.embl.de/emspring Spring is a single-particle based helical reconstruction package and has been used to determine 3D structures of a variety of highly ordered and less ordered specimens from electron micrographs. Spring provides the entire single-particle based work-flow required for helical reconstruction from classification, symmetry determination to high-resolution refinement including multi-model refinement. 0.82 carsten.sachse at embl.de Unix (Mac OS X/Linux) HDF5 from EMAN2 Free/Open Source modified BSD Python Desfosses A, Ciuffa R, Gutsche I, Sachse C SPRING - an image processing package for single-particle based helical reconstruction from electron cryomicrographs J. Struct. Biol. 185 1 15–26 2014 24269218 10.1016/j.jsb.2013.11.003 Stokes Lab Procedures http://skirball.med.nyu.edu/research/sb/stokeslab/image-analysis.html Image Processing Software for Helical Crystals: outlines, procedures and hints for using the MRC helical processing software which has since been modified by several groups including Chikashi Toyoshima, Nigel Unwin, David DeRosier and David Stokes. stokes@saturn.med.nyu.edu Unix MRC Free/Open Source Unpublished Single particles Frealign http://emlab.rose2.brandeis.edu/ Frealign provides algorithms optimized for the efficient refinement of three-dimensional reconstructions and correction for the contrast transfer function of the microscope in the determination of macromolecular structures by single particle electron microscopy. 9.11 niko @brandeis.edu Linux, IRIX, OSF, Mac OS X MRC, Spider, IMAGIC Free/Open Source GPL Grigorieff N FREALIGN: high-resolution refinement of single particle structures J. Struct. Biol. 157 1 117–25 2007 January 16828314 10.1016/j.jsb.2006.05.004 JSPR http://jiang.bio.purdue.edu/jspr software for single particle cryo-EM image processing and 3-D reconstruction. Major features include automated CTF fitting, de novo initial model, Gold-standard independent refinements, grid-less optimization, refinement of defocus, astigmatism, and magnification, multiple model competition refinement, symmetry mismatch refinement, parallel processing using Pub/Sub model and HTCondor, and merging of multiple data sets imaged at different mags, etc. Based on EMAN/EMAN2 libraries. 1 jiang12 @purdue.edu Linux MRC, HDF, LST and all image formats supported by EMAN2 Free C++/Python Jiang, Wen Single Particle Cryo-electron Microscopy and 3-D Reconstruction of Viruses Methods in Molecular Biology 1117 401-43 2013 December 24357374 10.1007/978-1-62703-776-1_19 http://link.springer.com/protocol/10.1007%2F978-1-62703-776-1_19 PFT3DR http://www.chem.byu.edu/node/807 PFT3DR is package for determining orientations and origins of imaged particles and computing a three-dimensional reconstruction from the images and their assigned orientations and origins. The programs are enhanced versions of the PFT algorithm developed by Baker and Cheng (2000) and the Fourier Bessel reconstruction algorithm of Crowther et al. (1970). The original adaptations of the PFT3DR programs were specific to icosahedral viruses, but were enhanced to support nearly all symmetries found in biological particles. Other enhancements are described on the PFT3DR web site. 2 David_Belnap at byu.edu Unix (Linux, Mac OS X, etc.), VMS same as Bsoft Free/Open Source Baker TS, Cheng RH A model-based approach for determining orientations of biological macromolecules imaged by cryoelectron microscopy J. Struct. Biol. 116 1 120–30 1996 8742733 10.1006/jsbi.1996.0020 Crowther RA, Amos LA, Finch JT, De Rosier DJ, Klug A Three dimensional reconstructions of spherical viruses by fourier synthesis from electron micrographs Nature 226 5244 421–5 1970 May 4314822 Fuller SD, Butcher SJ, Cheng RH, Baker TS Three-dimensional reconstruction of icosahedral particles--the uncommon line J. Struct. Biol. 116 1 48–55 1996 8742722 10.1006/jsbi.1996.0009 Bubeck D, Filman DJ, Cheng N, Steven AC, Hogle JM, Belnap DM The structure of the poliovirus 135S cell entry intermediate at 10-angstrom resolution reveals the location of an externalized polypeptide that binds to membranes J. Virol. 79 12 7745–55 2005 June 15919927 1143686 10.1128/JVI.79.12.7745-7755.2005 Sanz-García, E, Stewart, AB, Belnap DM The random-model method enables ab initio three-dimensional reconstruction of asymmetric particles and determination of particle symmetry J. Struct. Biol. 171 2 216-222 2010 20353825 2885456 10.1016/j.jsb.2010.03.017 Search/Refine/Build https://sites.google.com/site/rubinsteingroup/ Search_Fspace, Refine_Fspace, and Build_Fspace, are relatively simple programs for calculating and refining 3D maps. Many of the approaches used are similar to approaches applied by Frealign. The website provided also has a number of other useful utilities for working on micrographs, stacks of MRC images, and parameter files. 1.01 john.rubinstein at utoronto.ca Linux MRC Free/Open Source GPL Lau, W.C.Y, Rubinstein, J.L. Subnanometre-resolution structure of the intact Thermus thermophilus H+-driven ATP synthase Nature 481 214-218 2012 22753497 Benlekbir S, Bueler SA, Rubinstein JL Structure of the vacuolar-type ATPase from Saccharomyces cerevisiae at 11-Å resolution Nature Structural and Molecular Biology 19 pages=1356-52 2012 23142977 Tomography EM3D http://em3d.stanford.edu/index.html EM3D is a software application designed to analyze and visualize electron microscope (EM) tomography data. It is especially for cellular and molecular biologists. From a tilt series of 2D electron micrographs taken at many tilt angles with respect to the electron beam, this program can then perform auto-align and quickly render those data into a lucid 3D model, which allows you to perform object rotating for viewing. In addition, EM3D also provides analysis tools for quantify structural information from the models, including their moments, proximity relationships, and spatial reliability. And all of these functions can be executed with a very intuited graphic user interface. EM3D is available free-of-charge Mac OS X for PowerPC or Intel, and Windows. EM3D was developed in the laboratory of Dr. U. J. McMahan, Professor of Neurobiology and of Structural Biology at Stanford University School of Medicine and continues to be developed at the Dept. of Biology, Texas A&M University. 2.0 grantser@bio.tamu.edu Windows, Mac OS X for PowerPC or Intel Free for academic use Ress D, Harlow ML, Schwarz M, Marshall RM, McMahan UJ Automatic acquisition of fiducial markers and alignment of images in tilt series for electron tomography J Electron Microsc (Tokyo) 48 3 277–87 1999 10425746 EM3D's scheme for the automatic alignment of tilt-images is described. Ress DB, Harlow ML, Marshall RM, McMahan UJ Methods for generating high-resolution structural models from electron microscope tomography data Structure 12 10 1763–74 2004 October 15458626 10.1016/j.str.2004.07.022 EM3D approach to model generation is detailed. Harlow ML, Ress D, Stoschek A, Marshall RM, McMahan UJ The architecture of active zone material at the frog's neuromuscular junction Nature 409 6819 479–84 2001 January 11206537 10.1038/35054000 EM3D is first used for exposing cellular architecture at macromolecular resolution. Petersen JD, Chen X, Vinade L, Dosemeci A, Lisman JE, Reese TS Distribution of postsynaptic density (PSD)-95 and Ca2+/calmodulin-dependent protein kinase II at the PSD J. Neurosci. 23 35 11270–8 2003 December 14657186 EM3D is used to examine the architecture of the postsynaptic density at brain synapses. Ress, D., Harlow, M.L., Marshall, R.A., and McMahan, U.J. Proceedings of the 25th Annual International Conference of IEEE 2003 774-777 Optimized Method for Isodensity Surface Models Obtained with Electron Microscope Tomography Data EM3D's method for creating optimal isodensity surface models is described. SNARK14 http://turing.iimas.unam.mx/SNARK14M/ SNARK14 is a programming system for the reconstruction of 2D images from 1D projections. It is designed to help researchers interested in developing and evaluating reconstruction algorithms. In the area of image reconstruction, researchers often desire to compare two or more reconstruction techniques and assess their relative merits. SNARK14 provides a uniform framework in which to implement algorithms and evaluate their performance. SNARK14 has been designed to treat both parallel and divergent projection geometries and can create test data for use by reconstruction algorithms. A number of frequently used reconstruction algorithms are incorporated. snark14.unam@gmail.com VirtualBox (for most OS an appropriate VirtualBox platform package is available from: https://www.virtualbox.org/wiki/Downloads) Free/Open Source Klukowska J., Davidi R., Herman GT SNARK09 - A software package for the reconstruction of 2D images from 1D projections Computer Methods and Programs in Biomedicine. 110 424–440 2013 Herman, Gabor Fundamentals of Computerized Tomography: Image Reconstruction from Projections Springer London 2009 2 IMOD http://bio3d.colorado.edu/imod/ IMOD is a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3-D data from any orientation, and modeling and display of the image files. It includes a complete graphical user interface for generating tomograms, combining tomograms from tilt series taken around two axes, and stacking tomograms from serial sections. 4.11 mast at colorado dot edu Linux, Windows, Mac OS X MRC, TIFF Free/Open Source GPL Kremer JR, Mastronarde DN, McIntosh JR Computer visualization of three-dimensional image data using IMOD J. Struct. Biol. 116 1 71–6 1996 8742726 10.1006/jsbi.1996.0013 Mastronarde DN Correction for non-perpendicularity of beam and tilt axis in tomographic reconstructions with the IMOD package J Microsc 230 Pt 2 212–7 2008 May 18445149 10.1111/j.1365-2818.2008.01977.x Mastronarde DN Dual-axis tomography: an approach with alignment methods that preserve resolution J. Struct. Biol. 120 3 343–52 1997 December 9441937 10.1006/jsbi.1997.3919 protomo http://www.electrontomography.org Protomo is a suite of programs and shell scripts primarily developed for electron tomography. It offers routines for preprocessing micrographs, CTF-correction of images of untilted and tilted specimens, marker-free alignment of tilt series, 3D reconstruction, and processing of volumetric data from tomograms with multivariate statistical analysis and classification. 3.1 contact@electrontomography.org Linux CCP4, EM, FFF, IMAGIC, MRC, SPIDER, SUPRIM, TIFF Free C Winkler H 3D reconstruction and processing of volumetric data in cryo-electron tomography J. Struct. Biol. 157 1 126–37 2007 January 16973379 10.1016/j.jsb.2006.07.014 Winkler H, Taylor KA Accurate marker-free alignment with simultaneous geometry determination and reconstruction of tilt series in electron tomography Ultramicroscopy 106 3 240–54 2006 February 16137829 10.1016/j.ultramic.2005.07.007 Winkler H, Taylor KA Focus gradient correction applied to tilt series image data used in electron tomography J. Struct. Biol. 143 1 24–32 2003 July 12892723 Taylor KA, Tang J, Cheng Y, Winkler H The use of electron tomography for structural analysis of disordered protein arrays J. Struct. Biol. 120 3 372–86 1997 December 9441940 10.1006/jsbi.1997.3932 PyTom http://www.pytom.org, http://www.biochem.mpg.de/309018/PyTom PyTom is a python-based package for tomogram analysis. It supports tasks such as particle localization and identification by template matching, subtomogram averaging, and subtomogram classification. The package is open source, does not rely on any commercial software, and is platform-independent. The implementation in python should allow easy scripting for specific tasks. 1.0.1 foerster@biochem.mpg.de, hrabe@biochem.mpg.de, ychen@biochem.mpg.de Linux, Mac OS, Windows .em, .spi, .mrc Free GPL / BSD Python Hrabe T, Chen Y, Pfeffer S, Cuellar LK, Mangold AV, Förster F PyTom: a python-based toolbox for localization of macromolecules in cryo-electron tomograms and subtomogram analysis. J Struct Biol 178 2 178-88 2012 10.1016/j.jsb.2011.12.003 http://dx.doi.org/10.1016/j.jsb.2011.12.003 Chen Y, Förster F Iterative reconstruction of cryo-electron tomograms using nonuniform fast Fourier transforms. J Struct Biol 185 309-316 2014 24326216 10.1016/j.jsb.2013.12.001 http://dx.doi.org/10.1016/j.jsb.2013.12.001 Chen Y, Pfeffer S, Hrabe T, Schuller JM, Förster F Fast and accurate reference-free alignment of subtomograms. J Struct Biol 182 235-45 2013 23523719 10.1016/j.jsb.2013.03.002 http://dx.doi.org/10.1016/j.jsb.2013.03.002 RAPTOR http://www-vlsi.stanford.edu/TEM/software.htm Robust Alignment and Projection Estimation for Tomographic Reconstruction (RAPTOR) is a free available software to align raw stacks obtained from electron microscopes for tomographic purposes. It is intended to automatically obtain a full-precision alignment comparable to the one obtained with extended manual intervention. Fiducial particles are needed in the image for the alignment. It has been designed to be compatible with IMOD software, so results can be checked with the usual IMOD tools for alignment and reconstruction. 2.1 famat at stanford dot edu Linux MRC Free Amat F, Moussavi F, Comolli LR, Elidan G, Downing KH, Horowitz M Markov random field based automatic image alignment for electron tomography J. Struct. Biol. 161 3 260–75 2008 March 17855124 10.1016/j.jsb.2007.07.007 SerialEM http://bio3d.colorado.edu/SerialEM/ SerialEM is a program to acquire tilt series for electron tomography on Tecnai and newer JEOL microscopes. It uses an approach based on prediction of specimen position during the tilt series from the position at previous tilts. With this method, it achieves both the robustness of the older approach to tilt series acquisition (track and focus at every tilt) and the speed of the newer precalibration approach. It provides a complete interface for camera control and image acquisition, viewing, and saving. It includes a low dose mode for tracking and focusing away from the area of interest, energy filter control, acquisition of tilt series using a montage of overlapping frames, and a navigator module for mapping the grid and returning to selected locations. It supports Gatan, Tietz, FEI, AMT, and some Direct Electron CCD cameras. 3.8 mast at colorado dot edu Microsoft Windows MRC Free for academic use Mastronarde DN Automated electron microscope tomography using robust prediction of specimen movements J. Struct. Biol. 152 1 36–51 2005 October 16182563 10.1016/j.jsb.2005.07.007 TOM Toolbox http://www.biochem.mpg.de/tom/ The Tomography Toolbox is a collection of functions that extend the capability of the MATLAB (+ Image Processing Toolbox) numeric computing environment. The toolbox supports a wide range of functions for tomography. Automated data acquisition procedures have changed the perspectives of electron tomography (ET) in a profound manner. Elaborate data acquisition schemes with autotuning functions minimize exposure of the specimen to the electron beam and sophisticated image analysis routines retrieve a maximum of information from noisy data sets. ‘TOM software toolbox’ integrates established algorithms and new concepts tailored to the special needs of low dose ET. It provides a user-friendly unified platform for all processing steps: acquisition, alignment, reconstruction, and analysis. Designed as a collection of computational procedures it is a complete software solution within a highly flexible framework. TOM represents a new way of working with the electron microscope and can serve as the basis for future high-throughput applications. tom@biochem.mpg.de Linux, Microsoft Windows EM,MRC,Spider Free Nickell S, Förster F, Linaroudis A, et al. TOM software toolbox: acquisition and analysis for electron tomography J. Struct. Biol. 149 3 227–34 2005 March 15721576 10.1016/j.jsb.2004.10.006 TomoJ https://sourceforge.net/projects/tomoj/ TomoJ is a Java plug-in for ImageJ to perform tomographic reconstruction using ART, SIRT and WBP algorithms. It includes free reference alignment procedures in addition to standard cross-correlation methods in a friendly user interface. 2.7 tomoj@curie.fr All, same as ImageJ program Free/Open Source CeCILL Licence Java Messaoudii C, Boudier T, Sanchez Sorzano CO, Marco S TomoJ: tomography software for three-dimensional reconstruction in transmission electron microscopy BMC Bioinformatics 8 288 2007 17683598 1976622 10.1186/1471-2105-8-288 Sorzano CO, Messaoudi C, Eibauer M, et al. Marker-free image registration of electron tomography tilt-series BMC Bioinformatics 10 124 2009 19397789 2694187 10.1186/1471-2105-10-124 Ettention http://www.ettention.org Ettention is a software package for electron tomography. The software combines a modular design that allows algorithmic experimentation with modular GPU code and the possibility to reconstruct high resolution volumes. Ettention is fully integrated in the eTomo GUI of IMOD. 1.1 contact@ettention.org Windows, Linux NVidia, Xeon Phi, AMD Free/Open Source w:LPGL C++/OpenCL Dahmen T., Marsalek L., Marniok N., Turoňová B., Bogachev S., Trampert P., Nickels S. and Slusallek P. Ettention: building blocks for iterative reconstruction algorithms Proceedings of Microscopy & Microanalysis 2015 TxBR https://confluence.crbs.ucsd.edu/display/ncmir/TxBR Tomographic reconstruction from large-format electron microscope data requires special procedures to handle geometric distortions arising from electron optics as opposed to light-ray optics. In particular, electrons travel in curvilinear paths through the sample, and defocus and other aberrations can have significant effects. TxBR handles geometric nonlinearities associated with charged-particle optics, distortion due to sample warping, and transform sets associated with non-standard modes of data collection. In addition, TxBR makes provision for marker-free alignment and specialized montaging for tomography of serial sections. 3.0 sph at ncmir dot ucsd dot edu Linux, Windows (≥ XP), Mac OS X (PowerPC and Intel) MRC Free S. Phan, A. Lawrence Congress on Image and Signal Processing, Vol. 2 2008 176-182 Tomography of Large Format Electron Microscope Tilt Series: Image Alignment and Volume Reconstruction Lawrence A, Bouwer JC, Perkins G, Ellisman MH Transform-based backprojection for volume reconstruction of large format electron microscope tilt series J. Struct. Biol. 154 2 144–67 2006 May 16542854 10.1016/j.jsb.2005.12.012 UCSF Tomography http://www.msg.ucsf.edu/em/EMNEW2/tomography_page.html UCSF Tomography is an integrated software suite that provides full automation from target finding, sequential tomographic data collection, to real-time reconstruction for both single and dual axes as well as automated acquisition of random conical data sets. This software was implemented based upon a novel approach in which the compustage tilting is modeled as geometric rotation. The spatial movement of the sample as a result of stage tilting can be predicted based upon previously collected tomographic images. Therefore, there is no need to collect tracking and focusing images during the entire tomographic data collection. A significant dose saving can thus be achieved and is critical in collecting cryo tilt series. Real-time reconstruction is achieved by calculating a weighted back-projection on a small Linux cluster (five dual-processor computer nodes) concurrently with the UCSF tomography data collection running on the microscope’s computer, and using the fiducial-marker free alignment data generated during the data collection process. The real-time reconstructed 3D volume provides users with immediate feedback to fully asses all aspects of the experiment ranging from sample choice, ice thickness, experimental parameters to the quality of specimen preparation. To facilitate dual-axis tomographic data collection, a hierarchical scheme for target finding and relocation after specimen rotation was developed and integrated with the predictive data collection and real-time reconstruction, allowing full automation from target finding to data collection and to reconstruction of 3D volumes with little user intervention. An on-site scheme was developed for random conical data collection where tracking and focusing are performed at the same location as the final conical tilt images. Lower magnifications combined with short exposure are used to substantially reduce dose and to allow larger tilt steps. The system also includes a feature for montaging untilted images to ensure that all of the particles in the tilted image may be used in the reconstruction. v7.7.4E4 agard@msg.ucsf.edu Windows 2000, XP MRC Free for academic use Zheng SQ, Keszthelyi B, Branlund E, et al. UCSF tomography: an integrated software suite for real-time electron microscopic tomographic data collection, alignment, and reconstruction J. Struct. Biol. 157 1 138–47 2007 January 16904341 10.1016/j.jsb.2006.06.005 Zheng QS, Braunfeld MB, Sedat JW, Agard DA An improved strategy for automated electron microscopic tomography J. Struct. Biol. 147 2 91–101 2004 August 15193638 10.1016/j.jsb.2004.02.005 Zheng SQ, Kollman JM, Braunfeld MB, Sedat JW, Agard DA Automated acquisition of electron microscopic random conical tilt sets J. Struct. Biol. 157 1 148–55 2007 January 17169745 2556511 10.1016/j.jsb.2006.10.026 Zheng SQ, Matsuda A, Braunfeld MB, Sedat JW, Agard DA Dual-axis target mapping and automated sequential acquisition of dual-axis EM tomographic data J. Struct. Biol. 168 2 323–31 2009 November 19545637 2776717 10.1016/j.jsb.2009.06.010 FEI Xplore3D™ Tomography Suite http://www.fei.com/LifeSciences/ Xplore3D provides a complete solution for 3D tomographic acquisition, reconstruction, and visualization into one integrated package. The advanced capabilities include batch acquisition, dual-axis tomography, low-dose imaging, STEM tomography, energy filtering, and hardware acceleration for reconstruction. Batch scheduling permits unattended overnight data acquisition from multiple grid positions. Accurate, interactive alignment routines can use cross-correlation (no markers needed), bead tracking, or general feature tracking. Advanced reconstruction techniques include weighted back-projection, ART, and SIRT. Xplore3D includes a post-alignment and reconstruction module, Inspect3D. robert dot snyder at fei dot com Windows XP, most image formats Price available upon request Perpetual right-to-use license R.H.M. Schoenmakers, R.A. Perquin, T.F. Fliervoet, W. Voorhout, H. Schirmacher New software for high resolution, high throughput electron tomography Microscopy and Analysis 19 4 5-6 2005 July Li Peng, Sergey Ryazantsev, Ren Sun, Z. Hong Zhou Three-Dimensional Visualization of Gammaherpesvirus Life Cycle in Host Cells by Electron Tomography Structure 18 1 47-58 2010 January 20152152 10.1016/j.str.2009.10.017 Linda F. van Driel, Jack A. Valentijn, Karine M. Valentijn, Roman I. Koning, Abraham J. Koster Tools for correlative cryo-fluorescence microscopy and cryo-electron tomography applied to whole mitochondria in human endothelial cells European Journal of Cell Biology 88 11 669-684 2009 November 19726102 10.1016/j.ejcb.2009.07.002 Laura van Niftrik, Willie J.C. Geerts, Elly G. van Donselaar, Bruno M. Humbel, Alevtyna Yakushevska, Arie J. Verkleij, Mike S.M. Jetten, Marc Strous Combined structural and chemical analysis of the anammoxosome: A membrane-bounded intracytoplasmic compartment in anammox bacteria Journal of Structural Biology 161 3 401-410 2008 March 17604181 10.1016/j.jsb.2007.05.005 AuTom http://ear.ict.ac.cn/downloads/ Automatic Tomography (Au-Tom) is for automatic reconstruction of electron tomography (ET), which covered the pre-processing, alignment and reconstruction of electron tomography. In our package, fiducial marker-based datasets and maker-free datasets are done with totally different subprocess. The presented package has the following characteristics: accurate alignment modules for datasets that contain substantial biological structures but free of fiducial markers; fully automatic alignment modules for datasets that have fiducial markers embedded in; a wide coverage of reconstruction methods with a new iterative reconstruction method that recovers “missing wedge” based on compressed-sensing theory; multi-platform acceleration solutions that support faster iterative algebraic reconstruction. Currently, the marker-basd alignment and reconstruction of AuTom is the mostly well challenged module, while the marker-free alignment still has the limitations of data features. Autom has been built under Red Hat Enterprise 6.4, Cenots 6.5,Ubuntu 14.04 and Ubuntu 16.04. Other systems may not be supported well. beta1.0.1 zhangfa@ict.ac.cn wanxiaohua@ict.ac.cn Linux MRC Free Han R, Wan X, Wang Z, et al AuTom: A novel automatic platform for electron tomography reconstruction J. Struct. Biol. 199 3 196-208 2017 Sep 28756247 10.1016/j.jsb.2017.07.008 Deng Y, Chen Y, Zhang Y, Wang S, Zhang F, Sun F ICON: 3D reconstruction with ‘missing-information’ restoration in biological electron tomography J. Struct. Biol. 195 1 100-112 2016 Jul 27079261 10.1016/j.jsb.2016.04.004 Han R, Wang L, Liu Z, Sun F, Zhang F A novel fully automatic scheme for fiducial marker-based alignment in electron tomography J. Struct. Biol. 192 3 403-417 2015 Dec 26433028 10.1016/j.jsb.2015.09.022 Han R, Zhang F, Wan X, Fernández JJ, Sun F, Liu Z A novel fully automatic scheme for fiducial marker-based alignment in electron tomography J. Struct. Biol. 186 1 167-180 2014 Apr 24582712 10.1016/j.jsb.2014.02.011 Han R, Zhang F, Gao X A fast fiducial marker tracking model for fully automatic alignment in electron tomography Bioinformatics 34 5 853-863 2018 Mar 29069299 10.1093/bioinformatics/btx653 Han R, Wan X, Li L, Lawrence A, Yang P, Li Y, Wang S, Sun F, Liu Z, Gao X, Zhang F AuTom-dualx: a toolkit for fully automatic fiducial marker-based alignment of dual-axis tilt series with simultaneous reconstruction Bioinformatic 35 2 319-328 2019 Jan 30010792 10.1093/bioinformatics/bty620 Application tools Subvolume averaging Dynamo http://www.dynamo-em.org Dynamo is a software package for subtomogram averaging of Cryo-EM data. It is intended to provide users with big flexibility when adding new algorithms into standard procedures and adapting them for different computing environments as desktops, multicore machines, (multi)GPUs or clusters of CPUs. 1.1.514 daniel.castano@unibas.ch Linux, Mac OS, Windows .em, .spi, .mrc Free for academic use GPL / BSD Castaño-Díez D, Kudryashev M, Arheit M, Stahlberg H Dynamo: A flexible, user-friendly development tool for subtomogram averaging of cryo-EM data in high-performance computing environments. J Struct Biology 3 2012 http://dx.doi.org/10.1016/j.jsb.2011.12.017 Jsubtomo http://www.opic.ox.ac.uk/jsubtomo Jsubtomo is an open source software package based on Bsoft for averaging of tomographic sub-volumes. It includes tools for locating sub-volumes in tomograms using constrained cross-correlation, missing wedge-weighted averaging and refinement. Initial estimate of particle orientation can be easily included to constrain refinement. Python scripts are available for parallel processing and iterative refinement. 1.2 juha at strubi dot ox dot ac dot uk Linux, Mac OS, Windows Most, including .map, .mrc, .em, .spi, .img, .pif Free C Huiskonen JT, Hepojoki J, Laurinmäki P, Vaheri A, Lankinen H, Butcher SJ, Grünewald K. Electron cryotomography of Tula hantavirus suggests a unique assembly paradigm for enveloped viruses. J Virology 84 10 4889-97 2010 10.1128/JVI.00057-10 PEET http://bio3d.colorado.edu/PEET PEET is an open-source package for subvolume alignment, averaging, and classification. PEET is most easily used in conjunction with IMOD. 1.8.0 john.heumann@colorado.edu Linux, Mac OS-X, Windows .mrc Free GPL Matlab, C, C++ Nicastro D, Schwartz C, Pierson J, Gaudette R, Porter M, McIntosh J.R. The molecular architecture of axonemes revealed by cryoelectron tomography. Science 313 5789 944-948 2006 10.1126/science.1128618 Mass measurements MASDET http://campus.uni-muenster.de/masdet.html A fast and user-friendly multiplatform software for mass determination by dark-field electron microscopy. MASDET offers several subroutines for the main mass analysis steps, namely image display and selection of regions of interest (ROI), mass evaluation and data analysis. Two program-modes constitute the core procedures for mass determination: (i) the program-mode AREA determines the mass-per-area of sheet-like structures (e.g., protein S-layers, thin organic and inorganic films) and the mass-per-box for globular structures (e.g., single macromolecules, globular assemblies, organic/inorganic nanoparticles), and (ii) the program-mode FILAMENT determines the mass-per-length for filamentous structures (e.g., intermediate filaments, DNA-protein complexes, tobacco mosaic virus, nanowires) in individual ROIs. The statistical analysis of the mass data in individual ROIs contains graphical data display (histograms and XY-plots) and allows up to 10 Gaussian curves to be fitted. The dark-field micrographs can also be recalculated to a mass-thickness profile and/or mass-thickness map using data from Monte Carlo simulations. 1.13 krzyzane at uni-muenster dot de Windows (both standalone program and p-files run from MATLAB); Mac OS X, Linux (p-files to be run from MATLAB) Basel IMAG, Muenster TIFF (other formats will be implemented by us on request) Free for academic use Krzyzanek V, Müller SA, Engel A, Reichelt R MASDET--A fast and user-friendly multiplatform software for mass determination by dark-field electron microscopy J. Struct. Biol. 165 2 78–87 2009 February 19041401 10.1016/j.jsb.2008.10.006 Krzyzanek V, Reichelt R MONCA: A New MATLAB Package for Monte Carlo Simulation of Electron Scattering in Thin Specimens in the Energy Range 10 - 200 keV Microsc. Microanal. 9 Suppl. 3 110-111 2003 10.1017/S1431927603014065 http://journals.cambridge.org/action/displayAbstract?aid=173725 Reichelt R, Engel A Monte Carlo calculations of elastic and inelastic electron scattering in biological and plastic materials Ultramicrosc. 13 3 279-293 1984 10.1016/0304-3991(84)90206-7 Data Acquisition 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. Leginon http://emg.nysbc.org/redmine/projects/leginon 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. 3.5 nrammsoft@nysbc.org 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 Particle Selection DoG Picker http://emg.nysbc.org/redmine/projects/software/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 nvoss [at] roosevelt.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://emg.nysbc.org/redmine/projects/software/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 nvoss [at] roosevelt.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://emg.nysbc.org/redmine/projects/software/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 nvoss [at] roosevelt.edu 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 Gautomatch http://www.mrc-lmb.cam.ac.uk/kzhang/Gautomatch A GPU-accelerated automatic particle selection program. Ice contanmination, carbon edge, aggregation etc. are automatically detected and rejected before real particle picking. Typical speed: 1~2s per 4096X4096 micrograph using 15 templates on GTX 980; Flexible usage; With or without templates; .box/.star as default output and particle stacks optional; Diagnostic micrographs as options to easily optimize the parameters; Single command for batch processing on whole datasets; 0.56 kzhang@mrc-lmb.cam.ac.uk Linux MRC Free for Research CUDA Kai Zhang Gautomatch: Accurate Real-time Picking To be published CTF Estimation and Correction ACE http://emg.nysbc.org/redmine/projects/software/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 nrammsoft@nysbc.org 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://emg.nysbc.org/redmine/projects/software/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 nvoss [at] roosevelt.edu Unix (specifically, Mac OS X and Linux) MRC Free/Open source Apache License v2.0 Objective-C Unpublished ctfEval https://github.com/vossman/ctfeval Program to visualize and assess the quality of CTF estimation parameters 0.1 nvoss [at] roosevelt.edu Linux, Mac OS X MRC Free/Open Source Apache License v2.0 Python submitted 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 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 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 Gctf http://www.mrc-lmb.cam.ac.uk/kzhang/Gctf/ A GPU-accelerated Real-time CTF determination and Correction Program; Fully automatic, batch processing, local CTF for particles, CTF refinement for single frames, self-consistency verification, Equiphase Average(EPA) diagnostic power spectra; Fully compatible with Relion, Frealgin etc. 1.18 kzhang@mrc-lmb.cam.ac.uk Linux MRC Free for research CUDA Kai Zhang 2015 Gctf: real-time CTF determination and correction Journal of Structural Biology 26592709 10.1016/j.jsb.2015.11.003 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++ SuRVoS Workbench https://diamondlightsource.github.io/SuRVoS/ SuRVoS Workbench is a program for the segmentation of 3D image datasets. SuRVoS combines high-level algorithms for feature detection, and super-region building for smarter, semi-automatic segmentation and analysis. This software guides users through the process of partitioning 3D volumes into hierarchical segmentation layers (super-regions) and then interactively segmenting the data with the user's knowledge as input training annotations for semi-automatic segmentation and refinement. After segmentation, SuRVoS provides a suite of tools for classifying data objects and producing information about their characteristics (size, intensity, volume, location, etc). 1.0 michele.darrow@diamond.ac.uk imanol.luengo@diamond.ac.uk mark.basham@diamond.ac.uk scientificsoftware@diamond.ac.uk Linux MRC, Tiff Stacks, HDF5 Free Apache V2 Python, C++, CUDA Imanol Luengo Darrow, MC., Spink MC., Sun Y., Dai W., He CY., Chiu W., Pridmore T., Ashton AW., Duke EMH., Basham M., French AP. 2017 SuRVoS: Super-Region Volume Segmentation Workbench J Struct Biol 198 1 43-53 28246039 10.1016/j.jsb.2017.02.007 PMC5405849 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 Visualization and Modeling ADP_EM http://chaconlab.org/adpem/index.html ADP_EM is an ultra fast multiresolution fitting tool of atomic structures into low/medium resolution EM maps which has been specially designed to support high throughput coverage. The method uses spherical harmonics to effectively speed up the rotational scan. It can be considered as a practical step-down of the Fast Rotational Matching (FRM) described elsewhere in Kovacs et al. 2003. Please, download the program and test by yourself the efficiency and robustness reached with this new approach. 1.03 pablo@chaconlab.org Windows, Linux CCP4, SITUS Free C/C++ J.I. Garzón Julio A. Kovacs; Ruben Abagyan; and P. Chacón. 2007 ADP_EM: Fast exhaustive multi-resolution docking for high-throughput coverage. Bioinformatics 23 4 427-33 Julio A. Kovacs, Pablo Chacón, Yao Cong, Essam Metwally, and Willy Wriggers Fast Rotational Matching of Rigid Bodies by Fast Fourier Transform Acceleration of Five Degrees of Freedom. Acta Cryst. D. 59 1371-1376 2003 Amira http://www.amira.com Amira is a software solution that satisfies your demanding needs to work with clinical or preclinical image data, nuclear data, optical or electron microscopy imagery, molecular models, vector and flow data, simulation data on finite element models, and all types of multidimensional image, vector, tensor, and geometry data. 5.4.3. info@vsg3d.com Win/Linux/Mac TIFF, BMP, JPEG, PNG, SGI, Leica, Zeiss, BioRad, Olympus, MRC, DICOM, Analyze 3D, Fidap, I-DEAS, Fluent, DXF, STL, VRML, Inventor, CATIA 4/5, IGES Depends on license Stalling Detlev Malte Westerhoff, Hans-Christian Hege Charles D. Hansen Christopher R. Johnson The Visualization Handbook Elsevier 2005 749-767 Chapter 38, Amira: A Highly Interactive System for Visual Data Analysis http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.129.6785&rep=rep1&type=pdf Automated Segmentation of Actin Networks (Software Package for Amira) http://www.zib.de/en/visual/software/cryoem.html This software package brings an automated procedure for the segmentation of actin filaments from cryo-electron tomograms. It is based on a combination of template matching with a new tracing algorithm and allows a statistically sound assessment of the properties of filamentous actin networks. The whole analysis workflow, from denoising to segmentation, can be performed within the visualization framework Amira 5.4.5 Our segmentation package enables the user to obtain geometric data on individual actin filaments and to use this data for statistical analysis. The software has been developed in collaboration between the Zuse Institute Berlin (ZIB) and the Max Planck Institute of Biochemistry. 1.4 baum at zib dot de / rigort at biochem dot mpg dot de 64-bit versions for Linux and Windows, 32-bit version for MacX. 3D tomographic data, EM, MRC, others package: free for academic use; Amira trial license (valid for 3 weeks) available, otherwise: licensed version of Amira 5.4.5 required Rigort A., Guenther D., Hegerl R., Baum D., Weber B., Prohaska S., Medalia O., Baumeister W., Hege H.C Automated segmentation of electron tomograms for a quantitative description of actin filament networks http://www.ncbi.nlm.nih.gov/pubmed/21907807 J. Struct. Biol. 21907807 10.1016/j.jsb.2011.08.012 CoAn/CoFi http://coan.burnham.org Software for statistics-based fitting of atomic models into density maps of lower resolution such as those obtained by electron microscopy and image reconstruction. coan@burnham.org Linux MRC Free for academic users Volkmann N, Hanein D 1999 Quantitative fitting of atomic models into observed densities derived by electron microscopy J. Struct. Biol. 125 176-184 10222273 Volkmann N, Hanein D 2003 Docking of atomic models into reconstructions from electron microscopy Methods Enzymol. 374 204-225 14696375 Volkmann N 2009 Confidence intervals for fitting of atomic models into low-resolution densities Acta Crystallogr D Biol Crystallogr. 65 679-689 19564688 UCSF Chimera http://www.cgl.ucsf.edu/chimera Molecular modeling package with many density map capabilities. Supports fitting atomic models in maps, interactive segmentation, coarse modeling, measuring and coloring of density maps for elucidating structures of large molecular assemblies. The map capabilities were designed for analyzing electron microscope single particle reconstructions and tomography. Includes many methods for analysis of atomic resolution molecular models and multiple sequence alignments. 1.15 chimera-users@cgl.ucsf.edu Windows, Macintosh, Linux MRC, CCP4, SPIDER, BRIX, SITUS, PIF, HDF5, others Free for academic use TD Goddard Huang CC, Ferrin TE 2007 Visualizing density maps with UCSF Chimera Journal of Structural Biology 157 1 281-7 16963278 coloRNA http://franklab.cpmc.columbia.edu/franklab/colorna The purpose of coloRNA is the following: if we have two versions of an RNA structure (given as pdb files), differing as a consequence of conformational changes, and given the secondary structure, then the program is able to determine the distances between corresponding residues and heat-map them onto the secondary structure. That is, very mobile/flexible residues show up in red, moderate ones in yellow and green, very stable ones in blue. So it is possible, with the aid of the program, to determine which parts of the secondary structure are responsible for the mobility of the 3D structure. 1.1 hl2485@columbia.edu Linux pdb files, others file formats (see readme.txt) Free Python 2.3.3 with Tkinter 8.4 J. LeBarron Mitra, K., and Frank, J. 2007 Displaying 3D data on RNA secondary structures: coloRNA. J Struct Biol 157 1 262-270 17070699 10.1016/j.jsb.2006.08.018 EMDataBank http://www.emdatabank.org EMDataBank.org, a resource for deposition and retrieval of 3DEM map, model and associated metadata, unifies public access to the two major EM Structural Data archives: EM Data Bank (EMDB) and Protein Data Bank (PDB), and facilitates use of EM structural data by the wider scientific community. The resource offers Java-based 3D viewers which can be accessed from EMDataBank atlas pages. Atlas pages of interest can be found using EMSEARCH (http://www.emdatabank.org/search.html). AstexViewer, a molecular graphics program originally developed to display crystallographic data was recently re-released under an open source license and has been adapted for display of EM maps and associated PDB coordinate models. A compact map format is used to improve web download speed and minimize memory requirements (very large maps are down-sampled). Current capabilities include ability to control map contour level, opacity, color, solid vs. mesh surface rendering, and concurrent display of one or more PDB coordinate entries. help@emdatabank.org requires web browser with Java (1.5 or higher preferred), viewing large maps may require increasing the Java Runtime memory Free C. Lawson et al. 2011 EMDataBank.org: Unified Data Resource for Cryo EM Nucleic Acids Research 39(Database issue) D456 20935055 10.1093/nar/gkq880 PMC3013769 M. Tagari et al. 2002 New electron microscopy database and deposition system Trends Biochem. Sci. 27 589 12417136 K. Henrick et al. 2003 EMDep: a web-based system for the deposition and validation of high-resolution electron microscopy macromolecular structural information J. Struct. Biol. 144 228 14643225 EMfit http://bilbo.bio.purdue.edu/~viruswww/Rossmann_home/softwares/emfit.php Program for fitting atomic models into electron microscopy maps. Fitting criteria includes the sum of densities at atomic sites, the lack of atoms in negative or low density, the absence of atomic clashes between symmetry-related positions of the atomic structure, and the distances between identifiable features in the map and their positions on the fitted atomic structure, etc. 5.0 mr@indiana.bio.purdue.edu Linux, AIX TSB ASCII EM, XPLOR ASCII Free/Open Source M.G. Rossmann R. Bernal, S. V. Pletnev 2001 Combining electron microscopic with X ray crystallographic structures Journal of Structural Biology 136 190-200 M.G. Rossmann 2000 Fitting atomic models into electron microscopy maps Acta Crystallogr D56 1341-1349 EMPackage (Electron Tomography Toolbox for Amira) http://www.biophys.uni-frankfurt.de/frangakis/Amiratools.htm The EMPackage is a powerful toolbox for three-dimensional electron microscopy in Amira. The main aim of the toolbox is to decrease the amount of different programs needed to analyse EM data, by enabling denoising and segmentation tasks directly in Amira. Amira has to be installed and a license is needed for Amira. 1.0.0 frangakis.group@googlemail.com Win/Linux/Mac File formats supported in Amira plus additionally CCP4, EM, IMAGIC, SPIDER Free for academic use, but requires Amira S. Pruggnaller M. Mayr, A.S. Frangakis 2008 A visualization and segmentation toolbox for electron microscopy Journal of Structural Biology Gorgon http://gorgon.wustl.edu An interactive molecular modeling system specifically geared towards cryo-EM and other low resolution structures of macromolecular complexes. The long term goal of the gorgon project is to be able to address to every part of the molecular modeling pipeline starting from the initial volumetric reconstruction of the complex all the way to the final placement of each individual atom. Gorgon is being developed as a collaboration between Washington University in St. Louis and Baylor College of Medicine. Gorgon currently provides the following feature categories: Visualization: A comprehensive visualization framework for volumetric data (iso-contours, cross-sections and solid rendering), geometric skeletons, secondary structure elements and atomic models (PDB). Geometric operations: Many geometric operations such as skeletonization (binary / grayscale and interactive), smoothing, resampling, cropping, etc. are provided. Protein structure prediction: We provide tools which allow users to find the correspondence between predicted secondary structure elements in the sequence and the observed secondary structure elements in the volume Protein backbone tracing: The c-alpha backbone of a protein can be easily traced manually or semi-automatically using the many supporting elements offered by Gorgon. 2.0.0 sasakthi.abeysinghe@wustl.edu Windows 2000/XP/Vista, MacOS X, Linux MRC, CCP4, RAW, OFF, PDB, SEQ, SSE, WRL/VRML Free S.S. Abeysinghe Baker, M., Chiu, W., and Ju, T. 2008 Segmentation-free skeletonization of grayscale volumes for shape understanding Shape Modeling and Applications 63-71 S.S. Abeysinghe Ju, T., Baker, M., and Chiu, W. 2008 Shape modeling and matching in identifying 3D protein structures Computer-Aided Design 40 6 708-720 M. Baker Ju, T., and Chiu, W. 2007 Identification of Secondary Structure Elements in Intermediate Resolution Density Maps Structure 15 1 7-19 T. Ju Baker, M., and Chiu, W. 2007 Computing a family of skeletons of volumetric models for shape description Computer-Aided Design 39 5 352-360 iMODFIT http://chaconlab.org/imodfit/index.html iMODFIT is an efficient tool for fast flexible fitting of atomic structures into low/medium resolution EM maps based on Normal Mode Analysis in internal Coordinates. It is able to deal with protein and nucleic acid structures with small ligands at several coarse-graining levels. Please, download the program and test by yourself the efficiency and robustness reached with this new approach. 1.02 pablo@chaconlab.org Linux CCP4, SITUS Free C/C++ J.R. López-Blanco Garzón, J.I. ; Chacón, P. 2011 (in preparation) NORMA http://www.elnemo.org/NORMA NORMA is a freely available software suite that allows the modelling of large conformational changes of high-resolution three-dimensional protein structures under the constraint of a low-resolution electron-density map. Typical applications are the interpretation of electron-microscopy data using atomic scale X-ray structural models. The software package provided should enable the interested user to perform flexible fitting on new cases without encountering major technical difficulties. The NORMA software suite includes three fully executable reference cases and extensive user instructions. It comes with a Linux version of the URO fitting package (by J. Navaza) and the elNemo elastic network model normal mode analysis code (by Y.H. Sanejouand). 1.0 Karsten Suhre Linux EZD, CCP4, MRC, PIF Free K. Suhre Navaza, J., and Sanejouand, Y.H. 2006 NORMA: a tool for flexible fitting of high resolution protein structures into low resolution electron microscopy derived density maps Acta Cryst D62 1098-1100 OpenStructure http://www.openstructure.org OpenStructure is a software development platform tailored to the implementation of novel computational structural biology and molecular modeling methods. OpenStructure has been designed to handle and manipulate a wide range of data types as required in the field of integrative modeling, where data originating from a variety of experimental techniques are used to guide the model building process. The toolkit allows the development of sophisticated stand-alone applications, but also offers interfaces to flexibly incorporate external software, where appropriate, without the need to re-implement existing functionalities. At the top level, OpenStructure features a graphical user interface with components for rendering of biological macromolecules, density maps, image stacks, widgets for sequence analysis and graphical scene setup, and an integrated Python shell. While the graphical interface is conveniently used without prior knowledge of the underlying layers, the GUI maintains a tight integration with the scripting functionality. Any object that is visualized on the screen can be accessed at the Python level. Likewise, it is possible to create and manipulate graphical objects from within a script. This setup allows the combination of human-based and automatic data analysis, and freely customizing the graphical interface itself. 1.0.0 Torsten Schwede Win/Linux/MacOS X CCP4, DAT, TIFF, MRC, SPIDER, Nanoscope, PNG, SITUS, JPK, PDB, SDF, CRD, CHARMM trajectory files, maestro, many sequence and alignment formats Free LGPL C++/Python M. Biasini Mariani V., Haas J., Scheuber S., Schenk A.D., Schwede T., and Philippsen A. 2010 OpenStructure: a flexible software framework for computational structural biology Bioinformatics 26 20 2626–2628 20733063 10.1093/bioinformatics/btq481 PMC2951092 PyMOL http://pymol.org 1.2 licensing@Schrödinger.com Linux, Unix, Mac OS X, and Windows CCP4, MRC, PDB, many more Subscription/Open Source Python Unpublished RIVEM http://bilbo.bio.purdue.edu/~viruswww/Rossmann_home/softwares/river_programs/rivem.php Program developed to project electron density of virus radially onto a sphere that is then presented as a stereographic diagram. Features that constitute the viral surface can be simultaneously represented in terms of atoms, amino acid residues, potential charge distribution, and surface topology 3.2 xc@purdue.edu Linux, AIX XPLOR ASCII Free C. Xiao Rossmann, M. G. 2007 Interpretation of electron density with stereographic roadmap projections Journal of Structural Biology 158 182-187 Sculptor http://sculptor.biomachina.org/ Sculptor is an interactive multi-resolution docking and visualization program for low-resolution density maps and atomic structures. We are developing Sculptor as a GUI-based extension of the Situs docking programs, to allow an interactive exploration and analysis of volumetric maps. Sculptor combines 3D rendering with advanced mathematical concepts like clustering techniques and pattern matching algorithms to permit an almost instantaneous fitting of the high-resolution structures and to facilitate typical post-processing work like map editing or resolution adjustment. 2.1 sculptor@biomachina.org Windows, Macintosh, Linux MRC, CCP4, SITUS, SPIDER Free/Open Source LGPL C++ M. Wahle Wriggers W 2015 Multi-scale Visualization of Molecular Architecture Using Real-Time Ambient Occlusion in Sculptor PLoS Comput. Biol 11 10 e1004516 10.1371/journal.pcbi.1004516 PMC4623981 S. Birmanns Rusu M, Wriggers W 2011 Using Sculptor and Situs for Simultaneous Assembly of Atomic Components into Low-Resolution Shapes J. Struct. Biol. 10.1016/j.jsb.2010.11.002 PMC3352678 Situs http://situs.biomachina.org/ Situs is a modular software package for the integration of biophysical data across the spatial resolution scales. It has been developed over the last decade with a focus on bridging the resolution gap between atomic structures, coarse-grained models, and volumetric data from low-resolution biophysical origins, such as electron microscopy, tomography, or small-angle scattering. Structural models can be created and refined with various flexible and rigid body docking strategies. The software consists of multiple, stand-alone programs for the format conversion, analysis, visualization, manipulation, and assembly of 3D data sets. 2.8 situs@biomachina.org Windows, Macintosh, Linux MRC, CCP4, SITUS, SPIDER, XPLOR, ASCII Free/Open Source GPL C/C++ W. Wriggers 2012 Conventions and Workflows for Using Situs Acta Cryst. D 68 344-351 10.1107/S0907444911049791 PMC3322594 W. Wriggers 2010 Using Situs for the Integration of Multi-Resolution Structures Biophysical Reviews 2 21-27 10.1007/s12551-009-0026-3 PMC2821521 UROX http://sites.google.com/site/xsiebert/urox An interactive tool for fitting atomic models into electron microscopy reconstructions (or into envelopes derived from small-angle X-ray or neutron scattering). The correlation between the electron density of the atomic models and the map is calculated and updated as a model is moved on the graphical display with the help of the mouse. Calculations are performed in reciprocal-space and the symmetry of the reconstruction is taken into account. The computations are fast and an entire EM reconstruction can be used. Versions above 2.0 include Normal-Modes flexible fitting and "map on map" fitting (in addition to "model in map" fitting). 2.0.2 xsiebert@gmail.com Linux EZD, CCP4, MRC, PIF Free Siebert X, Navaza J UROX 2.0: an interactive tool for fitting atomic models into electron-microscopy reconstructions Acta Crystallogr. D Biol. Crystallogr. 65 Pt 7 651–8 2009 July 19564685 2703571 10.1107/S0907444909008671 Navaza J, Lepault J, Rey FA, Alvarez-Rúa C, Borge J On the fitting of model electron densities into EM reconstructions: a reciprocal-space formulation Acta Crystallogr. D Biol. Crystallogr. 58 Pt 10 Pt 2 1820–5 2002 October 12351826 V3D http://penglab.janelia.org/proj/v3d V3D is a general tool for 3D microscopy image visualization and analysis, as well as display and analysis of the extracted surface models. It features fast 3D rendering of large data sets. It comes with a flexible plugin interface which allows developing additional toolkits easily. V3D is cross-platform and runs on Mac, Linux and Windows. It has a number of easy to use features specially designed for multicolor 3D microscopic data. 2.687 pengh@janelia.hhmi.org Mac, Linux, and Windows tif, LSM, RAW, MRC Free H. Peng et al. 2010 V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets Nature Biotechnology 28 4 348-353 10.1038/nbt.1612 Utilities BBHP/Suprim add-ons http://coan.burnham.org/other-projects Two plugins for the Burnham-Brandeis Helical Package and/or Suprim, tkfilter for tomogram symmetry filtering and tkstraighten for boxing and straightening helical filaments. coan@burnham.org MRC Free for academic users unpublished crop http://emlab.rose2.brandeis.edu/software Program for cutting sections out of 2D and 3D density maps. 1.0 niko @brandeis.edu Linux/Mac MRC Free/Open Source GPL unpublished diffmap http://emlab.rose2.brandeis.edu/software Program to calculate difference maps between two density maps. 1.12 niko @brandeis.edu Linux/Mac MRC Free/Open Source GPL unpublished em2em http://www.imagescience.de/em2em.html Program to convert images (2D images and 3D volumes) from/to formats typically used in the EM community. em2em@ImageScience.de Most platforms (Linux/Unix, Mac OS X (intel), MS Windows) Most formats (IMAGIC, Spider, CCP4, MRC, CCP4, TIFF, etc.) Free unpublished Matlab functions for 3dEM file formats http://www.mathworks.com/matlabcentral/fileexchange/27021 Fred Sigworth MATLAB-supported systems Imagic, MRC and DM3 Free/Open Source BSD license MATLAB Unpublished Nexperion Sentinel http://www.nexperion.net/sentinel An integrated monitoring and logging tool for TEMs (different manufacturers) aiming to improve uptime. Sentinel's scope includes critical subsystems of the microscope, its peripherals, and the environment. Guenter Resch <guenter.resch@nexperion.net> Windows n/a Commercial Unpublished References Carragher B, Smith PR Advances in computational image processing for microscopy J. Struct. Biol. 116 1 2–8 1996 8742716 10.1006/jsbi.1996.0002 Smith R, Carragher B Software tools for molecular microscopy J. Struct. Biol. 163 3 224–8 2008 September 18406627 2572711 10.1016/j.jsb.2008.03.002 Chiu W, Baker ML, Jiang W, Dougherty M, Schmid MF Electron cryomicroscopy of biological machines at subnanometer resolution Structure 13 3 363–72 2005 March 15766537 10.1016/j.str.2004.12.016 Frank, Joachim Three-dimensional electron microscopy of macromolecular assemblies: visualization of biological molecules in their native state Oxford University Press Oxford [Oxfordshire] 2006 0-19-518218-9 2 External links A special issue of The Journal of Structural Biology that focuses specifically on Software Tools for Macromolecular Microscopy 3DEM mailing listThe 3DEM list is a primary communication source among experts in the field of molecular and cellular electron microscopy. EM for Dummies. Basics of electron microscopy in single particle reconstruction, and its applications to biology. EM Data Bank (EMDB) Archive of experimentally determined 3D maps and associated data. VIPERdb EM Database. Archive of icosahedral virus maps at the Virus Particle Explorer web site. 3DEM Conventions Common conventions for interchange and archiving of three-dimensional electron microscopy information in structural biology. Journal of Structural Biology main page Voss et al. (2010) Software tools for molecular microscopy: an open-text Wikibook. Methods Enzymol 482, 381-392. Scientific software S 25%