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Revision as of 21:09, 13 September 2006 by Bcarr (talk | contribs) (→Specific packages:: Adding content)(diff) ← Previous revision | Latest revision (diff) | Newer revision → (diff)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:
- 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:
- 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.
- 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 (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:
- Baxter, W. T., Leith, A., and Frank, J. SPIRE: The SPIDER reconstruction engine. Journal of Structural Biology In Press, Accepted Manuscript.
- 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.
- 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:
- JSB article.
Icosahedral viruses
- Description.
- Version: #.# Contact: email adress OS support: Platforms Image format support: Formats Cost: Free/Open Source
- Publications:
- JSB article.
Helices
- Description.
- Version: #.# Contact: email adress OS support: Platforms Image format support: Formats Cost: Free/Open Source
- Publications:
- JSB article.
Single particles
- Description.
- Version: #.# Contact: email adress OS support: Platforms Image format support: Formats Cost: Free/Open Source
- Publications:
- JSB article.
Tomography
Application tools:
- Content to be added shortly
Visualization tools:
- Content to be added shortly
See also:
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.