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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 is being created to provide a starting point for a more complete list and up-to-date distribution information of all of the software of interest to the cryoEM community.

The software tools described here have been loosely and somewhat arbitrarily organized into several categories as follows:

General packages: Packages that offer a comprehensive set of tools to permit the analysis of data in several classes of structural problems.

Specific packages: Packages that offer a comprehensive set of tools to permit the analysis of data in a single class of structural problem. For example packages specifically focused on objects with helical, icosahedral, crystalline symmetry, etc.

Application tools: Packages that offer a tool or a set of tools to permit the analysis of data in one or more class of structural problems. These have generally been developed to manage one specific step in the structural analysis, for example CTF correction, particle picking etc.

Visualization tools: Packages that facilitate the analysis or presentation of the results.

General packages:

Cyclops

Cyclops is a new computer program designed as a graphical front-end that allows easy control and interaction with tasks and programs for 3D reconstruction of biological complexes using cryo-electron microscopy. It was designed for straightforward implementation in grid architectures. As a front-end to a collection of programs it provides a common interface to other programs, thus enhancing the usability of the suite and the productivity of the user.

Version: Unknown Contact: plaisier @chem.leidenuniv.nl OS support: Unknown Image format support: Unknown Cost: Free/GPL license

Publications:

1. Plaisier, J. R., Jiang, L., and Abrahams, J. P. Cyclops: New modular software suite for cryo-EM. Journal of Structural Biology In Press, Corrected Proof.

EMAN (and now alsoEMAN2)

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.

Version: 1.7 Contact: sludtke@bcm.tmc.edu OS support: Most platforms Image format support: Most formats Cost: Free/Open Source

Publications to Cite:

1. Ludtke, S. J., Baldwin, P. R., and Chiu, W. (1999). EMAN: Semiautomated Software for High-Resolution Single-Particle Reconstructions. Journal of Structural Biology 128, 82-97.
2. 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 In Press, Corrected Proof.

Spider

SPIDER (System for Processing Image Data from Electron microscopy and Related fields) is an image processing system for electron microscopy.

Version: 14.11+ Contact: spider@wadsworth.org OS support: Most platforms Image format support: Most formats Cost: Free (GNU General Public License)

Publications:

1. Baxter, W. T., Leith, A., and Frank, J. SPIRE: The SPIDER reconstruction engine. Journal of Structural Biology In Press, Accepted Manuscript.
2. Frank, J., Radermacher, M., Penczek, P., Zhu, J., Li, Y., Ladjadj, M., and Leith, A. (1996). SPIDER and WEB: Processing and Visualization of Images in 3D Electron Microscopy and Related Fields. Journal of Structural Biology 116, 190-199.
3. Yang, C., Penczek, P. A., Leith, A., Asturias, F. J., Ng, E. G., Glaeser, R. M., and Frank, J. The parallelization of SPIDER on distributed-memory computers using MPI. Journal of Structural Biology In Press, Corrected Proof.

Specific packages:

Content to be added soon

Two-dimensional crystals

Description.

Version: #.# Contact: email adress OS support: Platforms Image format support: Formats Cost: Free/Open Source

Publications:

1. JSB article.

Icosahedral viruses

Description.

Version: #.# Contact: email adress OS support: Platforms Image format support: Formats Cost: Free/Open Source

Publications:

1. JSB article.

Helices

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.

Version: Unknown Contact: Unknown OS support: Unknown Image format support: Unknown Cost: Free

Publications:

1. Egelman, E. H. The iterative helical real space reconstruction method: Surmounting the problems posed by real polymers. Journal of Structural Biology In Press, Corrected Proof.

Ruby-Helix

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..

Version: Unknown Contact: Masahide.Kikkawa @nospam@ UTsouthwestern.edu OS support: Fedora, Mac OS X Image format support: MRC Cost: Free/Open Source

Publications:

1. Kikkawa, M. A new theory and algorithm for reconstructing helical structures with a seam. J Mol Biol. 2004 Oct 29;343(4):943-55
2. Metlagel, Z., Kikkawa, Y. S., and Kikkawa, M. Ruby-Helix: An implementation of helical image processing based on object-oriented scripting language. Journal of Structural Biology In Press, Uncorrected Proof.

Single particles

Frealign

Frealign provides algoritms 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.

Version: 7 Contact: niko @brandeis.edu OS support: Unkown Image format support: Unknown Cost: Free

Publications:

1. Grigorieff, N. FREALIGN: High-resolution refinement of single particle structures. Journal of Structural Biology In Press, Corrected Proof.

Tomography

protomo

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.

Version: 1.1 Contact: protomo@electrontomography.org OS support: Linux Image format support: Most formats Cost: Free

Publications:

1. Winkler, H. (2006) 3D reconstruction and processing of volumetric data in cryo-electron tomography. Journal of Structural Biology In Press, Uncorrected Proof.
2. Winkler, H. and Taylor, K. A. (2006) Accurate marker-free alignment with simultaneous geometry determination and reconstruction of tilt series in electron tomography. Ultramicroscopy 106, 240-254.
3. Winkler, H. and Taylor, K. A. (2003) Focus gradient correction applied to tilt series image data used in electron tomography. Journal of Structural Biology 143, 24-32.
4. Taylor, K. A., Tang, J., Cheng, Y., and Winkler, H. (1997) The use of electron tomography for structural analysis of disordered protein arrays. Journal of Structural Biology 120, 372-386.

Application tools:

Content to be added shortly

Visualization tools:

Content to be added shortly

See also:

• Cryo-electron microscopy

References:

• Advances in Computational Image Processing for Microscopy, JSB volume 116 1996
• Frank, Joachim (2006). Three-Dimensional Electron Microscopy of Macromolecular Assemblies: Visualization of Biological Molecules in Their Native State, 2nd edition, Oxford University Press. ISBN 0195182189.

External links:

• 3DEM mailing listThe 3DEM list is a primary communication source among experts in the field of molecular and cellular electron microscopy.
• EM for Dummies. Basics of electron microscopy in single particle reconstruction, and it's applications to biology.