Appion

Website: http://appion.org Current version: 2.0.0 Contact: nrammsoft@nysbc.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. Support: Operating systems: Linux, possibly other Unices may work as well. Image format support: CCP4, Imagic, JPEG, MRC, PNG, Spider, TIFF Cost: Free/Open Source, Apache License 2.0 Primary Publication to Cite: Lander GC, Stagg SM, Voss NR, et al. (April 2009). "Appion: an integrated, database-driven pipeline to facilitate EM image processing". J. Struct. Biol. 166 (1): 95–102. doi:10.1016/j.jsb.2009.01.002. PMID 19263523.  Additional References: Voss NR, Lyumkis D, Cheng A, et al. (March 2010). "A toolbox for ab initio 3-D reconstructions in single-particle electron microscopy". J. Struct. Biol. 169 (3): 389–98. doi:10.1016/j.jsb.2009.12.005. PMID 20018246.  Stagg SM, Lander GC, Quispe J, et al. (July 2008). "A test-bed for optimizing high-resolution single particle reconstructions". J. Struct. Biol. 163 (1): 29–39. doi:10.1016/j.jsb.2008.04.005. PMID 18534866.  Stagg SM, Lander GC, Pulokas J, et al. (September 2006). "Automated cryoEM data acquisition and analysis of 284742 particles of GroEL". J. Struct. Biol. 155 (3): 470–81. doi:10.1016/j.jsb.2006.04.005. PMID 16762565.

Bsoft

Website: http://bsoft.ws Current version: 1.8.8 Contact: Bernard_Heymann at nih.gov 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. Support: Operating systems: Unix (Mac OS X, IRIX, Linux, AIX, Solaris, Tru64), VMS Image format support: 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 Cost: Free/Open Source (Public domain) Written In: C++, Tcl/Tk Primary Publication to Cite: Heymann, J.B. (2001). "Bsoft: image and molecular processing in electron microscopy". Journal of Structural Biology 133 (2-3): 156-69.  Additional References: Heymann, J.B.; Belnap, D.M. (2007). "Bsoft: Image processing and molecular modeling for electron microscopy". Journal of Structural Biology 157: 3-18.  Heymann, J.B.; Cardone, G.; Winkler, D.C.; Steven, A.C. (2008). "Computational resources for cryo-electron tomography in Bsoft". Journal of Structural Biology 161: 232-242.

Cyclops

Website: http://www.bfsc.leidenuniv.nl/software/Cyclops Current version: 0.8rc1 Contact: plaisier @chem.leidenuniv.nl 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. Support: Operating systems: Windows XP Image format support: Imagic Cost: Free Primary Publication to Cite: Plaisier, J.R.; Jiang, L.; Abrahams, J.P. (2007). "Cyclops: New modular software suite for cryo-EM.". Journal of Structural Biology 157: 19-27.

EMAN2

Website: http://eman2.org Current version: 2.3 (April, 2019) Contact: sludtke@bcm.edu 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. Support: Operating systems: Linux (most variants), Mac OS X (versions from last ~5 years), Windows 10 Image format support: HDF5, SPIDER, MRC/CCP4, IMAGIC, PIF, ICOS, VTK, PGM, Amira, Xplor, Gatan DM2/DM3/DM4, TIFF, Scans-a-Lot, LST, PNG, V4L, JPEG Cost: Free/Open Source, GPL/BSD Written In: C++/Python Primary Publication to Cite: Tang, G.; Peng, L.; Baldwin, P.R.; 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

Website: http://blake.bcm.edu/eman Current version: 1.9 Contact: sludtke@bcm.edu 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. Support: Operating systems: Linux, Mac OS X, most Unix variants, Windows (GUI and utilities only) Image format support: HDF5, SPIDER, MRC/CCP4, IMAGIC, PIF, ICOS, VTK, PGM, Amira, Xplor, Gatan DM2/DM3, TIFF, Scans-a-Lot, LST, PNG, V4L, JPEG Cost: Free/Open Source, GPL/BSD Written In: C++ Primary Publication to Cite: Ludtke, S.J.; Baldwin, P.R.; Chiu, W. (1999). "EMAN: Semiautomated Software for High-Resolution Single-Particle Reconstructions". Journal of Structural Biology 128: 82-97.

Eos

Website: http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos Current version: 2.2 Contact: yasunaga@bio.kyutech.ac.jp 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. Support: Operating systems: Linux/Unix, Mac OS X(Intel), cygwin under MS Windows Image format support: MRC, TIFF, DNS6(Map) etc. Cost: Free Written In: C, Tcl/Tk, Ruby/Tk, javascript Primary Publication to Cite: Yasunaga T, Wakabayashi T (1996). "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. doi:10.1006/jsbi.1996.0025. PMID 8742738.  Additional References: Noda, K; 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.

IMAGIC

Website: http://imagescience.de/imagic/ Current version: 4D Contact: imagic@ImageScience.de 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. Support: Operating systems: Most platforms (Linux/Unix, Mac OS X (intel), MS Windows) Image format support: IMAGIC-5 (Most formats can be imported/exported: Spider, CCP4, MRC, TIFF, etc.) Cost: Commercial and non-profit prices Primary Publication to Cite: van Heel M, Harauz G, Orlova EV, Schmidt R, Schatz M (1996). "A new generation of the IMAGIC image processing system". J. Struct. Biol. 116 (1): 17–24. doi:10.1006/jsbi.1996.0004. PMID 8742718.  Additional References: Van Heel, M. (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. (2010). "Four-Dimensional Cryo Electron Microscopy at Quasi Atomic Resolution: "IMAGIC 4D"". International Tables for Crystallography, Vol. F.

IPLT

Website: http://www.iplt.org Contact: andreas dot schenk at fmi dot ch 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. Support: Operating systems: Linux, Mac OS X, Windows (experimental) Image format support: MRC, CCP4, TIFF, JPK, NANOSCOPE, SITUS, PNG, DM3, SPIDER Cost: Free/Open Source, GPL Written In: C++/Python Primary Publication to Cite: Philippsen A, Schenk AD, Signorell GA, Mariani V, Berneche S, Engel A (January 2007). "Collaborative EM image processing with the IPLT image processing library and toolbox". J. Struct. Biol. 157 (1): 28–37. doi:10.1016/j.jsb.2006.06.009. PMID 16919967.  Additional References: Philippsen A, Schenk AD, Stahlberg H, Engel A (2003). "Iplt--image processing library and toolkit for the electron microscopy community". J. Struct. Biol. 144 (1-2): 4–12. doi:10.1016/j.jsb.2003.09.032. PMID 14643205.  Schenk AD, Philippsen A, Engel A, Walz T (2013). "A pipeline for comprehensive and automated processing of electron diffraction data in IPLT". J. Struct. Biol. 182 (2): 173-185. doi:10.1016/j.jsb.2013.02.017. PMID 23500887.

MDPP

Website: http://sourceforge.net/projects/mdpp/ Current version: v17.320 Contact: smithp01-at-nyumc.org 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 Support: Operating systems: macOS/Linux Image format support: BMD, MRC, SPIDER, TIFF, JPEG, PNG Cost: Free, GPLv3 Written In: FORTRAN and C Primary Publication to Cite: Smith PR, Gottesman SM (1996). "The micrograph data processing program". J. Struct. Biol. 116 (1): 35–40. doi:10.1006/jsbi.1996.0007. PMID 8742720.

MRC IMAGE PROCESSING PACKAGE

Website: http://www2.mrc-lmb.cam.ac.uk/image2000.html Contact: jms@mrc-lmb.cam.ac.uk 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. Support: Operating systems: DEC/Tru64, LINUX, UNIX, IRIX, Mac OS X Image format support: MRC Cost: Free to academic users Primary Publication to Cite: Crowther RA, Henderson R, Smith JM (1996). "MRC image processing programs". J. Struct. Biol. 116 (1): 9–16. doi:10.1006/jsbi.1996.0003. PMID 8742717.  Additional References: Smith JM (1999). "Ximdisp--A visualization tool to aid structure determination from electron microscope images". J. Struct. Biol. 125 (2-3): 223–8. doi:10.1006/jsbi.1998.4073. PMID 10222278.

RELION

Website: http://www2.mrc-lmb.cam.ac.uk/relion Current version: 1.4 Contact: scheres at mrc-lmb.cam.ac.uk 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. Support: Operating systems: Unix (Linux, Mac OS X, etc.) Image format support: MRC, Spider Cost: Free/Open Source Primary Publication to Cite: Scheres SHW (2012). "A Bayesian View on Cryo-EM Structure Determination". J. Mol. Biol. 415 (2): 406-418. doi:10.1016/j.jmb.2011.11.010. PMID 22100448.

Scipion

Website: http://scipion.i2pc.es/ Current version: 1.2.0 Contact: scipion@cnb.csic.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. Support: Operating systems: UNIX Image format support: HDF5, SPIDER, MRC/CCP4, IMAGIC, PIF, Gatan DM3, TIFF, JPEG, EM, SPE Cost: Free/Open Source, GPL Written In: C++, Python, Java Primary Publication to Cite: de la Rosa-Trevín, J.M., Quinana, A., del Cano, L. et al. (March 2016). "Scipion: a software framework toward integration, reproducibility and validation in 3D Electron Microscopy". submitted.

SIMPLE

Website: http://simple.stanford.edu Current version: 1.0.0 Contact: via the simple website 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. Support: Operating systems: Unix (Linux, Mac OS X) Image format support: SPIDER Cost: Free/Open Source, GPL Written In: modern Fortran Primary Publication to Cite: Elmlund D, Elmlund H (2012). "SIMPLE: software for ab initio reconstruction of flexible single-particles". submitted.  Additional References: Elmlund D, Davis R, Elmlund H (July 2010). "Ab initio structure determination from electron microscopic images of single molecules coexisting in different functional states". Structure 18 (7): 777–86. doi:10.1016/j.str.2010.06.001. PMID 20637414.

SPARX

Website: http://sparx-em.org/sparxwiki Current version: 2.0 Contact: pawel.a.penczek@uth.tmc.edu 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. Support: Operating systems: Most platforms Image format support: Most formats Cost: Free/Open Source, BSD Primary Publication to Cite: Hohn M, Tang G, Goodyear G, et al. (January 2007). "SPARX, a new environment for Cryo-EM image processing". J. Struct. Biol. 157 (1): 47–55. doi:10.1016/j.jsb.2006.07.003. PMID 16931051.  Additional References: Baldwin PR, Penczek PA (January 2007). "The Transform Class in SPARX and EMAN2". J. Struct. Biol. 157 (1): 250–61. doi:10.1016/j.jsb.2006.06.002. PMID 16861004.

SPIDER

Website: http://www.wadsworth.org/spider_doc/ Current version: 23.02 Contact: spider@wadsworth.org 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. Support: Operating systems: Unix (Linux) Image format support: SPIDER, CCP4, Emispic, MRC, PDB, Raw Cost: Free/Open Source, GPL Written In: Fortran, C Primary Publication to Cite: Frank J, Radermacher M, Penczek P, Zhu J, Li Y, Ladjadj M, Leith A (1996). "SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields". J. Struct. Biol. 116 (1): 190–9. doi:10.1006/jsbi.1996.0030. PMID 8742743.  Additional References: Baxter WT, Leith A, Frank J (January 2007). "SPIRE: the SPIDER reconstruction engine". J. Struct. Biol. 157 (1): 56–63. doi:10.1016/j.jsb.2006.07.019. PMID 17055743.  Yang C, Penczek PA, Leith A, et al. (January 2007). "The parallelization of SPIDER on distributed-memory computers using MPI". J. Struct. Biol. 157 (1): 240–9. doi:10.1016/j.jsb.2006.05.011. PMID 16859923.  Shaikh TR, Gao H, Baxter WT, et al. (2008). "SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs". Nat Protoc 3 (12): 1941–74. doi:10.1038/nprot.2008.156. PMID 19180078.

Suprim

Website: http://emg.nysbc.org/redmine/projects/suprim Current version: 5.5 Contact: nrammsoft@nysbc.org 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. Support: Operating systems: Unix Image format support: MRC/suprim Cost: Free/Open Source Primary Publication to Cite: Schroeter JP, Bretaudiere JP (1996). "SUPRIM: easily modified image processing software". J. Struct. Biol. 116 (1): 131–7. doi:10.1006/jsbi.1996.0021. PMID 8742734.

Xmipp

Website: http://xmipp.cnb.csic.es/ Current version: 3.1 Contact: 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. Support: Operating systems: UNIX Image format support: HDF5, SPIDER, MRC/CCP4, IMAGIC, PIF, Gatan DM3, TIFF, JPEG, EM, SPE Cost: Free/Open Source, GPL Written In: C++, Python, Java Primary Publication to Cite: de la Rosa-Trevín, J.M., Otón, J., Marabini, R. et al. (November 2013). "Xmipp 3.0: An improved software suite for image processing in electron microscopy". J. Struct. Biol. 184 (2): 321–328. doi:10.1016/j.jsb.2013.09.015.  Additional References: Sorzano CO, Marabini R, Velázquez-Muriel J, et al. (November 2004). "XMIPP: a new generation of an open-source image processing package for electron microscopy". J. Struct. Biol. 148 (2): 194–204. doi:10.1016/j.jsb.2004.06.006. PMID 15477099.  Scheres SH, Núñez-Ramírez R, Sorzano CO, Carazo JM, Marabini R (2008). "Image processing for electron microscopy single-particle analysis using XMIPP". Nat Protoc 3 (6): 977–90. doi:10.1038/nprot.2008.62. PMID 18536645.

Two-dimensional crystals

Icosahedral viruses

Helices

Single particles

Tomography

Subvolume averaging

Mass measurements

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.

Particle Selection

CTF Estimation and Correction

3D Reconstruction

Resolution Estimation

Denoising

Segmentation

B-Factor Estimation and Correction

Initial Model Construction

ADP_EM

Website: http://chaconlab.org/adpem/index.html Current version: 1.03 Contact: pablo@chaconlab.org 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. Support: Operating systems: Windows, Linux Image format support: CCP4, SITUS Cost: Free Written In: C/C++ Primary Publication to Cite: Garzón, J.I.; 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.  Additional References: Julio A. Kovacs, Pablo Chacón, Yao Cong, Essam Metwally, and Willy Wriggers (2003). "Fast Rotational Matching of Rigid Bodies by Fast Fourier Transform Acceleration of Five Degrees of Freedom.". Acta Cryst. D. 59: 1371-1376.

Amira

Website: http://www.amira.com Current version: 5.4.3. Contact: info@vsg3d.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. Support: Operating systems: Win/Linux/Mac Image format support: 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 Cost: Depends on license Primary Publication to Cite: Stalling, Detlev; Malte Westerhoff, Hans-Christian Hege (2005). "Chapter 38, Amira: A Highly Interactive System for Visual Data Analysis". in Hansen, Charles D.; Johnson, Christopher R.. The Visualization Handbook. Elsevier. pp. 749-767. 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)

Website: http://www.zib.de/en/visual/software/cryoem.html Current version: 1.4 Contact: baum at zib dot de / rigort at biochem dot mpg dot de 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. Support: Operating systems: 64-bit versions for Linux and Windows, 32-bit version for MacX. Image format support: 3D tomographic data, EM, MRC, others Cost: package: free for academic use; Amira trial license (valid for 3 weeks) available, otherwise: licensed version of Amira 5.4.5 required Primary Publication to Cite: 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. . J. Struct. Biol.. doi:10.1016/j.jsb.2011.08.012. PMID 21907807. http://www.ncbi.nlm.nih.gov/pubmed/21907807.

CoAn/CoFi

Website: http://coan.burnham.org Contact: 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. Support: Operating systems: Linux Image format support: MRC Cost: Free for academic users Primary Publication to Cite: Volkmann N, Hanein D (1999). "Quantitative fitting of atomic models into observed densities derived by electron microscopy". J. Struct. Biol. 125: 176-184. PMID 10222273.  Additional References: Volkmann N, Hanein D (2003). "Docking of atomic models into reconstructions from electron microscopy". Methods Enzymol. 374: 204-225. PMID 14696375.  Volkmann N (2009). "Confidence intervals for fitting of atomic models into low-resolution densities". Acta Crystallogr D Biol Crystallogr. 65: 679-689. PMID 19564688.

UCSF Chimera

Website: http://www.cgl.ucsf.edu/chimera Current version: 1.4.1 Contact: chimera-users@cgl.ucsf.edu 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. Support: Operating systems: Windows, Macintosh, Linux Image format support: MRC, CCP4, SPIDER, BRIX, SITUS, PIF, HDF5, others Cost: Free for academic use Primary Publication to Cite: Goddard, TD; Huang CC, Ferrin TE (2007). "Visualizing density maps with UCSF Chimera". Journal of Structural Biology 157 (1): 281-7. PMID 16963278.

coloRNA

Website: http://franklab.cpmc.columbia.edu/franklab/colorna Current version: 1.1 Contact: hl2485@columbia.edu 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. Support: Operating systems: Linux Image format support: pdb files, others file formats (see readme.txt) Cost: Free Written In: Python 2.3.3 with Tkinter 8.4 Primary Publication to Cite: LeBarron, J.; Mitra, K., and Frank, J. (2007). "Displaying 3D data on RNA secondary structures: coloRNA.". J Struct Biol 157 (1): 262-270. doi:10.1016/j.jsb.2006.08.018. PMID 17070699.

EMDataBank

Website: http://www.emdatabank.org Contact: help@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. Support: Operating systems: requires web browser with Java (1.5 or higher preferred), viewing large maps may require increasing the Java Runtime memory Image format support: Cost: Free Primary Publication to Cite: Lawson, C.; et al. (2011). "EMDataBank.org: Unified Data Resource for Cryo EM". Nucleic Acids Research 39(Database issue): D456. doi:10.1093/nar/gkq880. PMID 20935055.  Additional References: Tagari, M.; et al. (2002). "New electron microscopy database and deposition system". Trends Biochem. Sci. 27: 589. PMID 12417136.  Henrick, K.; 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. PMID 14643225.

EMfit

Website: http://bilbo.bio.purdue.edu/~viruswww/Rossmann_home/softwares/emfit.php Current version: 5.0 Contact: mr@indiana.bio.purdue.edu 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. Support: Operating systems: Linux, AIX Image format support: TSB ASCII EM, XPLOR ASCII Cost: Free/Open Source Primary Publication to Cite: Rossmann, M.G. (2000). "Fitting atomic models into electron microscopy maps". Acta Crystallogr D56: 1341-1349.

EMPackage (Electron Tomography Toolbox for Amira)

Website: http://www.biophys.uni-frankfurt.de/frangakis/Amiratools.htm Current version: 1.0.0 Contact: frangakis.group@googlemail.com 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. Support: Operating systems: Win/Linux/Mac Image format support: File formats supported in Amira plus additionally CCP4, EM, IMAGIC, SPIDER Cost: Free for academic use, but requires Amira Primary Publication to Cite: Pruggnaller, S.; M. Mayr, A.S. Frangakis (2008). "A visualization and segmentation toolbox for electron microscopy". Journal of Structural Biology.

Gorgon

Website: http://gorgon.wustl.edu Current version: 2.0.0 Contact: sasakthi.abeysinghe@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. Support: Operating systems: Windows 2000/XP/Vista, MacOS X, Linux Image format support: MRC, CCP4, RAW, OFF, PDB, SEQ, SSE, WRL/VRML Cost: Free Primary Publication to Cite: Abeysinghe, S.S.; Baker, M., Chiu, W., and Ju, T. (2008). "Segmentation-free skeletonization of grayscale volumes for shape understanding". Shape Modeling and Applications: 63-71.  Additional References: Abeysinghe, S.S.; Ju, T., Baker, M., and Chiu, W. (2008). "Shape modeling and matching in identifying 3D protein structures". Computer-Aided Design 40 (6): 708-720.  Baker, M.; Ju, T., and Chiu, W. (2007). "Identification of Secondary Structure Elements in Intermediate Resolution Density Maps". Structure 15 (1): 7-19.  Ju, T.; 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

Website: http://chaconlab.org/imodfit/index.html Current version: 1.02 Contact: pablo@chaconlab.org 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. Support: Operating systems: Linux Image format support: CCP4, SITUS Cost: Free Written In: C/C++ Primary Publication to Cite: López-Blanco, J.R.; Garzón, J.I. ; Chacón, P. (2011). (in preparation).

NORMA

Website: http://www.elnemo.org/NORMA Current version: 1.0 Contact: Karsten Suhre 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 is 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). Support: Operating systems: Linux Image format support: EZD, CCP4, MRC, PIF Cost: Free Primary Publication to Cite: Suhre, K.; 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

Website: http://www.openstructure.org Current version: 1.0.0 Contact: Torsten Schwede 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. Support: Operating systems: Win/Linux/MacOS X Image format support: CCP4, DAT, TIFF, MRC, SPIDER, Nanoscope, PNG, SITUS, JPK, PDB, SDF, CRD, CHARMM trajectory files, maestro, many sequence and alignment formats Cost: Free, LGPL Written In: C++/Python Primary Publication to Cite: Biasini, M.; 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. doi:10.1093/bioinformatics/btq481. PMID 20733063.

PyMOL

Website: http://pymol.org Current version: 1.2 Contact: licensing@Schrödinger.com Support: Operating systems: Linux, Unix, Mac OS X, and Windows Image format support: CCP4, MRC, PDB, many more Cost: Subscription/Open Source Written In: Python Primary Publication to Cite: Unpublished

RIVEM

Website: http://bilbo.bio.purdue.edu/~viruswww/Rossmann_home/softwares/river_programs/rivem.php Current version: 3.2 Contact: xc@purdue.edu 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 Support: Operating systems: Linux, AIX Image format support: XPLOR ASCII Cost: Free Primary Publication to Cite: Xiao, C.; Rossmann, M. G. (2007). "Interpretation of electron density with stereographic roadmap projections". Journal of Structural Biology 158: 182-187.

Sculptor

Website: http://sculptor.biomachina.org/ Current version: 2.1 Contact: 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. Support: Operating systems: Windows, Macintosh, Linux Image format support: MRC, CCP4, SITUS, SPIDER Cost: Free/Open Source, LGPL Written In: C++ Primary Publication to Cite: Wahle, M.; Wriggers W (2015). "Multi-scale Visualization of Molecular Architecture Using Real-Time Ambient Occlusion in Sculptor". PLoS Comput. Biol 11 (10): e1004516. doi:10.1371/journal.pcbi.1004516.  Additional References: Birmanns, S.; Rusu M, Wriggers W (2011). "Using Sculptor and Situs for Simultaneous Assembly of Atomic Components into Low-Resolution Shapes". J. Struct. Biol.. doi:10.1016/j.jsb.2010.11.002.

Situs

Website: http://situs.biomachina.org/ Current version: 2.8 Contact: 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. Support: Operating systems: Windows, Macintosh, Linux Image format support: MRC, CCP4, SITUS, SPIDER, XPLOR, ASCII Cost: Free/Open Source, GPL Written In: C/C++ Primary Publication to Cite: Wriggers, W. (2012). "Conventions and Workflows for Using Situs". Acta Cryst. D 68: 344-351. doi:10.1107/S0907444911049791.  Additional References: Wriggers, W. (2010). "Using Situs for the Integration of Multi-Resolution Structures". Biophysical Reviews 2: 21-27. doi:10.1007/s12551-009-0026-3.

UROX

Website: http://sites.google.com/site/xsiebert/urox Current version: 2.0.2 Contact: xsiebert@gmail.com 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). Support: Operating systems: Linux Image format support: EZD, CCP4, MRC, PIF Cost: Free Primary Publication to Cite: Siebert X, Navaza J (July 2009). "UROX 2.0: an interactive tool for fitting atomic models into electron-microscopy reconstructions". Acta Crystallogr. D Biol. Crystallogr. 65 (Pt 7): 651–8. doi:10.1107/S0907444909008671. PMID 19564685.  Additional References: Navaza J, Lepault J, Rey FA, Alvarez-Rúa C, Borge J (October 2002). "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. PMID 12351826.

V3D

Website: http://penglab.janelia.org/proj/v3d Current version: 2.687 Contact: pengh@janelia.hhmi.org 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. Support: Operating systems: Mac, Linux, and Windows Image format support: tif, LSM, RAW, MRC Cost: Free Primary Publication to Cite: Peng, H.; 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. doi:10.1038/nbt.1612.

BBHP/Suprim add-ons

Website: http://coan.burnham.org/other-projects Contact: coan@burnham.org Two plugins for the Burnham-Brandeis Helical Package and/or Suprim, tkfilter for tomogram symmetry filtering and tkstraighten for boxing and straightening helical filaments. Support: Operating systems: Image format support: MRC Cost: Free for academic users Primary Publication to Cite: unpublished

crop

Website: http://emlab.rose2.brandeis.edu/software Current version: 1.0 Contact: niko @brandeis.edu Program for cutting sections out of 2D and 3D density maps. Support: Operating systems: Linux/Mac Image format support: MRC Cost: Free/Open Source, GPL Primary Publication to Cite: unpublished

diffmap

Website: http://emlab.rose2.brandeis.edu/software Current version: 1.12 Contact: niko @brandeis.edu Program to calculate difference maps between two density maps. Support: Operating systems: Linux/Mac Image format support: MRC Cost: Free/Open Source, GPL Primary Publication to Cite: unpublished

em2em

Website: http://www.imagescience.de/em2em.html Contact: em2em@ImageScience.de Program to convert images (2D images and 3D volumes) from/to formats typically used in the EM community. Support: Operating systems: Most platforms (Linux/Unix, Mac OS X (intel), MS Windows) Image format support: Most formats (IMAGIC, Spider, CCP4, MRC, CCP4, TIFF, etc.) Cost: Free Primary Publication to Cite: unpublished

Matlab functions for 3dEM file formats

Website: http://www.mathworks.com/matlabcentral/fileexchange/27021 Contact: Fred Sigworth Support: Operating systems: MATLAB-supported systems Image format support: Imagic, MRC and DM3 Cost: Free/Open Source, BSD license Written In: MATLAB Primary Publication to Cite: Unpublished

Nexperion Sentinel

Website: http://www.nexperion.net/sentinel Contact: Guenter Resch <guenter.resch@nexperion.net> 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. Support: Operating systems: Windows Image format support: n/a Cost: Commercial Primary Publication to Cite: Unpublished