# Software Tools For Molecular Microscopy/General packages
## 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

    Website: http://appion.org Current version: 2.0.0 Contact: appion@scripps.edu "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. (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. PMC 2775544. PMID 19263523. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link) Additional References: Voss NR, Lyumkis D, Cheng A; et al. (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. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link) Stagg SM, Lander GC, Quispe J; et al. (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. PMC 2505049. PMID 18534866. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link) Stagg SM, Lander GC, Pulokas J; et al. (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. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)

#### 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://blake.bcm.edu/emanwiki/EMAN2 Current version: 2.0.7 & 2.1alpha1 (June 2013) Contact: sludtke@bcm.edu EMAN2 is a software suite for scientific image processing, with a particular focus on TEM and single particle analysis. New tools are being added to support other specialties such as IHRSR (helical processing in real-space), RCT (random conical tilt) and single particle cryoET. It is a complete refactoring of the original EMAN suite. EMAN2 has a tiered strucutre with an easy to use workflow interface at the top, followed by high-level command line programs, low level command line programs, Python scripting support and core C++ libraries. 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 (10.6+, 10.7+ recommended), Windows XP/Vista/7/8 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. "EMAN2: An extensible image processing suite for electron microscopy". Journal of Structural Biology. 157: 38–46. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)

#### 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 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 (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. {{cite journal}}: Cite has empty unknown parameter: |pmcid= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)

#### 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.{{cite journal}}: CS1 maint: multiple names: authors list (link) Additional References: Van Heel, M. (1979). "IMAGIC and its results". Ultramicroscopy. 4: 117. {{cite journal}}: Cite has empty unknown parameters: |pmcid= and |coauthors= (help) Van Heel, M. (2010). "Four-Dimensional Cryo Electron Microscopy at Quasi Atomic Resolution: "IMAGIC 4D"". International Tables for Crystallography, Vol. F. {{cite book}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)

#### IPLT

    Website: http://www.iplt.org Contact: andreas underscore schenk at hms dot harvard dot edu 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 (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. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link) 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.{{cite journal}}: CS1 maint: multiple names: authors list (link)

#### MDPP

    Website: http://sourceforge.net/projects/mdpp/ Current version: v12.320 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: Mac OS X/Linux Image format support: BMD, MRC, SPIDER, TIFF, JPEG 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.{{cite journal}}: CS1 maint: multiple names: authors list (link) 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: 1.3 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.

#### 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 (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. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)

#### 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. (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. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link) Additional References: Baldwin PR, Penczek PA (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. {{cite journal}}: Unknown parameter |month= ignored (help)

#### SPIDER

    Website: http://www.wadsworth.org/spider_doc/spider/docs/spider.html Current version: 18.10+ 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, Mac OS X) 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.{{cite journal}}: CS1 maint: multiple names: authors list (link) Additional References: Baxter WT, Leith A, Frank J (2007). "SPIRE: the SPIDER reconstruction engine". J. Struct. Biol. 157 (1): 56–63. doi:10.1016/j.jsb.2006.07.019. PMID 17055743. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link) Yang C, Penczek PA, Leith A; et al. (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. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link) 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. PMC 2737740. PMID 19180078. {{cite journal}}: Explicit use of et al. in: |author= (help)CS1 maint: multiple names: authors list (link)

#### Suprim

    Website: http://ami.scripps.edu/redmine/projects/ami/wiki/Suprim Current version: 5.5 Contact: amisoftware@scripps.edu 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: J.M. de la Rosa-Trevín, J. Otón, R. Marabini, A. Zaldívar, J. Vargas, J.M. Carazo, C.O.S. Sorzano (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. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link) Additional References: Sorzano CO, Marabini R, Velázquez-Muriel J; et al. (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. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link) 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. PMC 2778070. PMID 18536645.{{cite journal}}: CS1 maint: multiple names: authors list (link)