Software Tools For Molecular Microscopy

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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:

Contents

General packages[edit]

Packages that offer a comprehensive set of tools to permit the analysis of data in several classes of structural problems (in alphabetical order).


Appion[edit]

"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.


Bsoft[edit]

  • 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[edit]

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[edit]

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.; 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[edit]

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[edit]

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[edit]

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[edit]

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. 


MDPP[edit]

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:


MRC IMAGE PROCESSING PACKAGE[edit]

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:
  • 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[edit]

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:


SIMPLE[edit]

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[edit]

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:
  • Additional References:


SPIDER[edit]

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.


Suprim[edit]

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:


Xmipp[edit]

"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.

Specific packages[edit]

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[edit]

2dx[edit]

  • Website: http://2dx.org/
  • Current version: 3.1.0
  • Contact: Henning.Stahlberg@unibas.ch
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.
  • Support: Operating systems: Mac OS X, Linux Image format support: MRC, TIFF, CCP4
  • Cost: Free/Open Source, GPL
  • Primary Publication to Cite:
  • Additional References:

Icosahedral viruses[edit]

AUTO3DEM[edit]

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.

Helices[edit]

BBHP - Burnham-Brandeis Helical Package[edit]

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.
  • Support: Operating systems: Linux Image format support: MRC
  • Cost: Free
  • Primary Publication to Cite:
    • Owen CH, Morgan DG, DeRosier DJ (1996). "Image analysis of helical objects: the Brandeis Helical Package". J. Struct. Biol. 116: 167–175. PMID 8742740. 
  • Additional References:
    • Rost LE, Hanein D, DeRosier DJ (1998). "Reconstruction of symmetry deviations: a procedure to analyze partially decorated F-actin and other incomplete structures". Ultramicroscopy 72: 187–197. PMID 9639941. 


IHRSR[edit]

  • Website:
  • Contact: egelman@virginia.edu
The iterative helical real space reconstruction (IHRSR) algorithm can recontruct 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.
  • Support: Operating systems: Linux Image format support: SPIDER
  • Cost: Free
  • Primary Publication to Cite:
    • Egelman EH (January 2007). "The iterative helical real space reconstruction method: surmounting the problems posed by real polymers". J. Struct. Biol. 157 (1): 83–94. doi:10.1016/j.jsb.2006.05.015. PMID 16919474. 


Phoelix[edit]

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.
  • Support: Operating systems: Unix Image format support: MRC/suprim
  • Cost: Free/Open Source
  • Primary Publication to Cite:
    • Whittaker M, Carragher BO, Milligan RA (June 1995). "PHOELIX: a package for semi-automated helical reconstruction". Ultramicroscopy 58 (3-4): 245–59. PMID 7571117. 
  • Additional References:


Ruby-Helix[edit]

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.
  • Support: Operating systems: Fedora, Mac OS X Image format support: MRC
  • Cost: Free/Open Source, GPL
  • Primary Publication to Cite:
    • Metlagel Z, Kikkawa YS, Kikkawa M (January 2007). "Ruby-Helix: an implementation of helical image processing based on object-oriented scripting language". J. Struct. Biol. 157 (1): 95–105. doi:10.1016/j.jsb.2006.07.015. PMID 16996276. 
  • Additional References:


Spring[edit]

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.
  • Support: Operating systems: Unix (Mac OS X/Linux) Image format support: HDF5 from EMAN2
  • Cost: Free/Open Source, modified BSD
  • Written In: Python
  • Primary Publication to Cite:
    • Desfosses A, Ciuffa R, Gutsche I, Sachse C (2014). "SPRING - an image processing package for single-particle based helical reconstruction from electron cryomicrographs". J. Struct. Biol. 185 (1): 15–26. doi:10.1016/j.jsb.2013.11.003. PMID 24269218. 


Stokes Lab Procedures[edit]

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.
  • Support: Operating systems: Unix Image format support: MRC
  • Cost: Free/Open Source
  • Primary Publication to Cite:
    • Unpublished

Single particles[edit]

Frealign[edit]

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.
  • Support: Operating systems: Linux, IRIX, OSF, Mac OS X Image format support: MRC, Spider, IMAGIC
  • Cost: Free/Open Source, GPL
  • Primary Publication to Cite:


PFT3DR[edit]

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.


Search/Refine/Build[edit]

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.
  • Support: Operating systems: Linux Image format support: MRC
  • Cost: Free/Open Source, GPL
  • Primary Publication to Cite:
    • Lau, W.C.Y, Rubinstein, J.L. (2012). "Subnanometre-resolution structure of the intact Thermus thermophilus H+-driven ATP synthase". Nature 481: 214-218. PMID 22753497. 
  • Additional References:
    • Benlekbir S, Bueler SA, Rubinstein JL (2012). "Structure of the vacuolar-type ATPase from Saccharomyces cerevisiae at 11-Å resolution". Nature Structural and Molecular Biology 19 pages=1356-52. PMID 23142977. 

Tomography[edit]

EM3D[edit]

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.
  • Support: Operating systems: Windows, Mac OS X for PowerPC or Intel Image format support:
  • Cost: Free for academic use
  • Primary Publication to Cite:
    • Ress D, Harlow ML, Schwarz M, Marshall RM, McMahan UJ (1999). "Automatic acquisition of fiducial markers and alignment of images in tilt series for electron tomography". J Electron Microsc (Tokyo) 48 (3): 277–87. PMID 10425746EM3D's scheme for the automatic alignment of tilt-images is described. 
  • Additional References:
    • Ress DB, Harlow ML, Marshall RM, McMahan UJ (October 2004). "Methods for generating high-resolution structural models from electron microscope tomography data". Structure 12 (10): 1763–74. doi:10.1016/j.str.2004.07.022. PMID 15458626EM3D approach to model generation is detailed. 
    • Harlow ML, Ress D, Stoschek A, Marshall RM, McMahan UJ (January 2001). "The architecture of active zone material at the frog's neuromuscular junction". Nature 409 (6819): 479–84. doi:10.1038/35054000. PMID 11206537EM3D is first used for exposing cellular architecture at macromolecular resolution. 
    • Petersen JD, Chen X, Vinade L, Dosemeci A, Lisman JE, Reese TS (December 2003). "Distribution of postsynaptic density (PSD)-95 and Ca2+/calmodulin-dependent protein kinase II at the PSD". J. Neurosci. 23 (35): 11270–8. PMID 14657186EM3D 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. (2003). "Optimized Method for Isodensity Surface Models Obtained with Electron Microscope Tomography Data". Proceedings of the 25th Annual International Conference of IEEE. pp. 774-777EM3D's method for creating optimal isodensity surface models is described. 


IMOD[edit]

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.
  • Support: Operating systems: Linux, Windows, Mac OS X Image format support: MRC, TIFF
  • Cost: Free/Open Source, GPL
  • Primary Publication to Cite:
    • Kremer JR, Mastronarde DN, McIntosh JR (1996). "Computer visualization of three-dimensional image data using IMOD". J. Struct. Biol. 116 (1): 71–6. doi:10.1006/jsbi.1996.0013. PMID 8742726. 
  • Additional References:
    • Mastronarde DN (May 2008). "Correction for non-perpendicularity of beam and tilt axis in tomographic reconstructions with the IMOD package". J Microsc 230 (Pt 2): 212–7. doi:10.1111/j.1365-2818.2008.01977.x. PMID 18445149. 
    • Mastronarde DN (December 1997). "Dual-axis tomography: an approach with alignment methods that preserve resolution". J. Struct. Biol. 120 (3): 343–52. doi:10.1006/jsbi.1997.3919. PMID 9441937. 


protomo[edit]

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, and 3D reconstruction, besides some general image processing functionality.
  • Support: Operating systems: Linux Image format support: Most formats
  • Cost: Free
  • Primary Publication to Cite:
  • Additional References:
    • Winkler H, Taylor KA (February 2006). "Accurate marker-free alignment with simultaneous geometry determination and reconstruction of tilt series in electron tomography". Ultramicroscopy 106 (3): 240–54. doi:10.1016/j.ultramic.2005.07.007. PMID 16137829. 
    • Winkler H, Taylor KA (July 2003). "Focus gradient correction applied to tilt series image data used in electron tomography". J. Struct. Biol. 143 (1): 24–32. PMID 12892723. 
    • Taylor KA, Tang J, Cheng Y, Winkler H (December 1997). "The use of electron tomography for structural analysis of disordered protein arrays". J. Struct. Biol. 120 (3): 372–86. doi:10.1006/jsbi.1997.3932. PMID 9441940. 


PyTom[edit]

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.


RAPTOR[edit]

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.
  • Support: Operating systems: Linux Image format support: MRC
  • Cost: Free
  • Primary Publication to Cite:
    • Amat F, Moussavi F, Comolli LR, Elidan G, Downing KH, Horowitz M (March 2008). "Markov random field based automatic image alignment for electron tomography". J. Struct. Biol. 161 (3): 260–75. doi:10.1016/j.jsb.2007.07.007. PMID 17855124. 


SerialEM[edit]

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.
  • Support: Operating systems: Microsoft Windows Image format support: MRC
  • Cost: Free for academic use
  • Primary Publication to Cite:
    • Mastronarde DN (October 2005). "Automated electron microscope tomography using robust prediction of specimen movements". J. Struct. Biol. 152 (1): 36–51. doi:10.1016/j.jsb.2005.07.007. PMID 16182563. 


TOM Toolbox[edit]

The Tomography Toolbox is a collection of functions that extend the capability of the MATLAB (+ Image Procesing 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.
  • Support: Operating systems: Linux, Microsoft Windows Image format support: EM,MRC,Spider
  • Cost: Free
  • Primary Publication to Cite:
    • Nickell S, Förster F, Linaroudis A, et al. (March 2005). "TOM software toolbox: acquisition and analysis for electron tomography". J. Struct. Biol. 149 (3): 227–34. doi:10.1016/j.jsb.2004.10.006. PMID 15721576. 


TomoJ[edit]

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.


TxBR[edit]

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.
  • Support: Operating systems: Linux, Windows (≥ XP), Mac OS X (PowerPC and Intel) Image format support: MRC
  • Cost: Free
  • Primary Publication to Cite:
    • S. Phan, A. Lawrence (2008). "Tomography of Large Format Electron Microscope Tilt Series: Image Alignment and Volume Reconstruction". Congress on Image and Signal Processing, Vol. 2. pp. 176-182. 
  • Additional References:
    • Lawrence A, Bouwer JC, Perkins G, Ellisman MH (May 2006). "Transform-based backprojection for volume reconstruction of large format electron microscope tilt series". J. Struct. Biol. 154 (2): 144–67. doi:10.1016/j.jsb.2005.12.012. PMID 16542854. 


UCSF Tomography[edit]

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.


FEI Xplore3D™ Tomography Suite[edit]

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.
  • Support: Operating systems: Windows XP, Image format support: most image formats
  • Cost: Price available upon request, Perpetual right-to-use license
  • Primary Publication to Cite:
    • R.H.M. Schoenmakers, R.A. Perquin, T.F. Fliervoet, W. Voorhout, H. Schirmacher (July 2005). "New software for high resolution, high throughput electron tomography". Microscopy and Analysis 19 (4): 5-6. 
  • Additional References:
    • Li Peng, Sergey Ryazantsev, Ren Sun, Z. Hong Zhou (January 2010). "Three-Dimensional Visualization of Gammaherpesvirus Life Cycle in Host Cells by Electron Tomography". Structure 18 (1): 47-58. doi:10.1016/j.str.2009.10.017. PMID 20152152. 
    • Linda F. van Driel, Jack A. Valentijn, Karine M. Valentijn, Roman I. Koning, Abraham J. Koster (November 2009). "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. doi:10.1016/j.ejcb.2009.07.002. PMID 19726102. 
    • 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 (March 2008). "Combined structural and chemical analysis of the anammoxosome: A membrane-bounded intracytoplasmic compartment in anammox bacteria". Journal of Structural Biology 161 (3): 401-410. doi:10.1016/j.jsb.2007.05.005. PMID 17604181. 

Application tools[edit]

Subvolume averaging[edit]

Dynamo[edit]

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.
  • Support: Operating systems: Linux, Mac OS, Windows Image format support: .em, .spi, .mrc
  • Cost: Free for academic use, GPL / BSD
  • Primary Publication to Cite:
    • Castaño-Díez D, Kudryashev M, Arheit M, Stahlberg H (2012). "Dynamo: A flexible, user-friendly development tool for subtomogram averaging of cryo-EM data in high-performance computing environments.". J Struct Biology (3). doi:http://dx.doi.org/10.1016/j.jsb.2011.12.017 


Jsubtomo[edit]

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.
  • Support: Operating systems: Linux, Mac OS, Windows Image format support: Most, including .map, .mrc, .em, .spi, .img, .pif
  • Cost: Free
  • Written In: C
  • Primary Publication to Cite:
    • Huiskonen JT, Hepojoki J, Laurinmäki P, Vaheri A, Lankinen H, Butcher SJ, Grünewald K. (2010). "Electron cryotomography of Tula hantavirus suggests a unique assembly paradigm for enveloped viruses.". J Virology 84 (10): 4889-97. doi:10.1128/JVI.00057-10 


PEET[edit]

PEET is an open-source package for subvolume alignment, averaging, and classification. PEET is most easily used in conjunction with IMOD.
  • Support: Operating systems: Linux, Mac OS-X, Windows Image format support: .mrc
  • Cost: Free, GPL
  • Written In: Matlab, C, C++
  • Primary Publication to Cite:
    • Nicastro D, Schwartz C, Pierson J, Gaudette R, Porter M, McIntosh J.R. (2006). "The molecular architecture of axonemes revealed by cryoelectron tomography.". Science 313 (5789): 944-948. doi:10.1126/science.1128618 

Mass measurements[edit]

MASDET[edit]

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.


Data Acquisition[edit]

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[edit]

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.

Particle Selection[edit]

DoG Picker[edit]

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),


FindEM[edit]

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.
  • Support: Operating systems: Unix Image format support: MRC
  • Cost: Free/Open source
  • Primary Publication to Cite:
    • Roseman, A.M. (2004). "FindEM—a fast, efficient program for automatic selection of particles from electron micrographs". Journal of Structural Biology 145 (1-2): 91-99. doi:10.1016/j.jsb.2003.11.007. PMID 15065677. 
  • Additional References:
    • Roseman, A.M. (2003). "Particle finding in electron micrographs using a fast local correlation algorithm.". Ultramicroscopy 94 (3-4): 225–236. PMID 12524193. 


Signature[edit]

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.
  • Support: Operating systems: Linux, Mac OS X, MS Windows Image format support: MRC, TIFF
  • Cost: Free/Open Source, GPL
  • Primary Publication to Cite:
    • Chen, J. Z.; Grigorieff, N. (2007). "SIGNATURE: A single-particle selection system for molecular electron microscopy". Journal of Structural Biology 157: 168-173. 


SwarmPS[edit]

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.
  • Support: Operating systems: Linux Image format support: Most image formats
  • Cost: Free for academic use under a software license agreement
  • Primary Publication to Cite:
    • Woolford, D.; 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[edit]

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.


TMaCS[edit]

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.
  • Support: Operating systems: Linux Image format support: MRC
  • Cost: Free/Open Source
  • Primary Publication to Cite:
    • Zhao J, Brubaker MA, Rubinstein JL (2013). "TMaCS: A hybrid template matching and classification system for automated particle selection". J. Struct. Biol. In Press. 

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CTF Estimation and Correction[edit]

ACE[edit]

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
  • Support: Operating systems: MATLAB Image format support: MRC
  • Cost: Free/Open Source, Apache License v2.0
  • Written In: MATLAB
  • Primary Publication to Cite:
    • Mallick, S.P.; B Carragher, CS Potter, DJ Kriegman (2005). "ACE: Automated CTF Estimation". Ultramicroscopy 104 (1): 8-29. 


ACE2[edit]

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.
  • Support: Operating systems: Unix (specifically, Mac OS X and Linux) Image format support: MRC
  • Cost: Free/Open source, Apache License v2.0
  • Written In: Objective-C
  • Primary Publication to Cite:
    • Unpublished


ctfEval[edit]

Program to visualize and assess the quality of CTF estimation parameters


ctf Explorer[edit]

allows to calculate the Phase Contrast Transfer Function (CTF): a useful characteristics in Electron Microscopy
  • Support: Operating systems: Windows 95/98/NT4/2000/XP Image format support:
  • Cost: , w:Postcardware, freeware
  • Primary Publication to Cite:
    • Sidorov, Max V. (2002). ctfExplorer: Interactive Software for 1d and 2d Calculation and Visualization Of TEM Phase Contrast Transfer Function. 8. pp. 1572CD-1573CD. doi:10.1017.S1431927602104442. 


CTFfind3 and CTFtilt[edit]

Programs for finding CTFs of electron micrographs
  • Support: Operating systems: Linux, IRIX, OSF Image format support: MRC
  • Cost: Free/Open Source, GPL
  • Written In: Fortran
  • Primary Publication to Cite:
    • Mindell, J.A.; Grigorieff, N. (2003). "Accurate determination of local defocus and specimen tilt in electron microscopy". Journal of Structural Biology 142: 334-347. 


EMCTF[edit]

CTF determination of non-astigmatic images in electron cryomicroscopy
  • Support: Operating systems: Linux, Mac OS X Image format support: MRC
  • Cost: Free for academic users
  • Primary Publication to Cite:
    • Fernandez, J.J.; Li, S. and Crowther, R. A. (2006). "CTF determination and correction in electron cryotomography". Ultramicroscopy 106: 587-596. doi:10.1016/j.ultramic.2006.02.004. 
  • Additional References:
    • Fernandez, J.J.; Sanjurjo, J.R. and Carazo, J. M. (1997). "A spectral estimation approach to contrast transfer function detection in electron microscopy". Ultramicroscopy 68: 267-295. doi:10.1016/S0304-3991(97)00032-6. 


TOMOCTF[edit]

CTF determination and correction in electron tomography
  • Support: Operating systems: Linux, Mac OS X Image format support: MRC
  • Cost: Free for academic users
  • Primary Publication to Cite:
    • Fernandez, J.J.; Li, S. and Crowther, R. A. (2006). "CTF determination and correction in electron cryotomography". Ultramicroscopy 106: 587-596. doi:10.1016/j.ultramic.2006.02.004. 


fitctf[edit]

Estimating contrast transfer function and associated parameters by constrained non-linear optimization
  • Support: Operating systems: Linux, Windows, and Mac OS X Image format support: MRC
  • Cost: free
  • Primary Publication to Cite:
    • Yang, C; 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. doi:10.1111/j.1365-2818.2009.03137.x. PMID 19250460. 


FitCTF2[edit]

A graph theory method for determination of cryo-EM image focuses
  • Support: Operating systems: Linux Image format support: MRC
  • Cost: Free for academic users
  • Written In: Python
  • Primary Publication to Cite:
    • Jiang, Wen; 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. doi:10.1016/j.jsb.2012.07.005. 

3D Reconstruction[edit]

TOMO3D[edit]

Fast tomographic reconstruction on standard multicore computers with WBP and SIRT.


TOMO3Dhybrid[edit]

Fast tomographic reconstruction (WBP,SIRT) with CPU+GPU co-processing

Resolution Estimation[edit]

FSC[edit]

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).
  • Support: Operating systems: Linux/Unix, Mac OS X (Intel), MS Windows Image format support: IMAGIC, Spider, CCP4, MRC, TIFF, etc.
  • Cost: Free
  • Primary Publication to Cite:
    • Harauz, G.; M. van Heel (1986). "Exact filters for general geometry three dimensional reconstruction". Optik 78: 146–156. 
  • Additional References:
    • van Heel, M.; M. Schatz (2005). "Fourier shell correlation threshold criteria". Journal of Structural Biology 151: 250-262. 


RMEASURE[edit]

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.
  • Support: Operating systems: Linux, IRIX, OSF, Mac OS X Image format support: MRC, Spider
  • Cost: Free/Open Source, GPL
  • Primary Publication to Cite:
    • Sousa, D.; N. Grigorieff (2007). "Ab initio resolution measurement for single particle structures". Journal of Structural Biology 157: 201-210. 

Denoising[edit]

iMed[edit]

Software for automatic noise reduction using iterative median filtering.
  • Support: Operating systems: Linux Image format support: MRC
  • Cost: Free for academic users
  • Primary Publication to Cite:
    • 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. PMID 17224280. 


TOMOAND[edit]

Package for noise reduction in electron cryotomography with Anisotropic Nonlinear Diffusion.
  • Support: Operating systems: Linux, Mac OS X Image format support: MRC
  • Cost: Free for academic users
  • Primary Publication to Cite:
    • Fernandez, J.J.; Li, S. (2003). "An improved algorithm for anisotropic nonlinear diffusion for denoising cryotomograms". Journal of Structural Biology 144: 152-161. doi:10.1016/j.jsb.2003.09.010. 
  • Additional References:
    • Fernandez, J.J.; 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. doi:10.1007/978-3-540-75271-4_7. 


TOMOBFLOW[edit]

Package for noise reduction in electron tomography with Beltrami flow.


XMSF[edit]

Package for noise reduction and pre-segmentation in electron tomography based on Mean-Shift.

Segmentation[edit]

CoDiv[edit]

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.
  • Support: Operating systems: Linux Image format support: MRC
  • Cost: Free for academic users
  • Primary Publication to Cite:
    • Volkmann N (2002). "A novel three-dimensional variant of the watershed transform for segmentation of electron density maps". J. Struct. Biol. 138: 123-129. PMID 12160708. 


Population[edit]

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.
  • Support: Operating systems: Linux/Windows Image format support: RAW/BMP/JPEG/PNG/PGM
  • Cost: Free for academic/industrial users, MIT
  • Written In: C++
  • Primary Publication to Cite:


TOMOSEGMEM[edit]

Package for segmentation of membranes in tomograms.


TomoSegMemTV[edit]

Package for robust membrane segmentation based on Tensor Voting for tomograms.

B-Factor Estimation and Correction[edit]

bfactor[edit]

Program for filtering 3D maps and applying B-factors.
  • Support: Operating systems: Linux/Mac Image format support: MRC
  • Cost: Free/Open Source, GPL
  • Primary Publication to Cite:
    • Unpublished


EM-BFACTOR[edit]

Package for sharpening high resolution information in single particle electron cryomicroscopy
  • Support: Operating systems: Linux, Mac OS X Image format support: Most common formats used in 3DEM
  • Cost: Free for academic users
  • Primary Publication to Cite:
    • Fernandez, J.J.; 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. doi:10.1016/j.jsb.2008.05.010. 
  • Additional References:
    • Rosenthal, P.B.; 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. doi:10.1016/j.jmb.2003.07.013. 

Initial Model Construction[edit]

ROTAN[edit]

Program for estimating the relative angular orientation of single particles that present side views
  • Support: Operating systems: Linux Image format support: MRC
  • Cost: Free for academic users
  • Primary Publication to Cite:
    • Baker, L.A.; Rubinstein, R. (2008). "Angle determination for side views in single particle electron microscopy". Journal of Structural Biology 162: 260-270. 
  • Additional References:
    • Rubinstein, J.L.; Walker, J.E. and Henderson, R. (2003). "Structure of the mitochondrial ATP synthase by electron cryomicroscopy". EMBO Journal 22: 6182-6192. 

Visualization and Modeling[edit]

ADP_EM[edit]

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[edit]

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.


Automated Segmentation of Actin Networks (Software Package for Amira)[edit]

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.


CoAn/CoFi[edit]

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[edit]

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[edit]

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:


EMDataBank[edit]

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[edit]

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)[edit]

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[edit]

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[edit]

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[edit]

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[edit]

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[edit]

  • Website: http://pymol.org
  • Current version: 1.2
  • Contact: licensing@schrodinger.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[edit]

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[edit]

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:
    • 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. 
  • Additional References:



Situs[edit]

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.


UROX[edit]

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).


V3D[edit]

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. 

Utilities[edit]

BBHP/Suprim add-ons[edit]

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[edit]

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[edit]

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[edit]

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[edit]

  • 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[edit]

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

References[edit]

External links[edit]