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| There are a large number of '''software tools''' or ] that have been specifically developed for the field sometimes referred to as '''molecular microscopy''' or ] 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: | |||
| {{Rwh}} | |||
| '''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 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:''''' | |||
| :#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. | |||
| (and now also) | |||
| :A suite of scientific image processing tools aimed primarily at ]. 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 ]. 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 ]. 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 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=== | |||
| : | |||
| :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:''''' | |||
| :#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 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:''''' | |||
| :#Grigorieff, N. FREALIGN: High-resolution refinement of single particle structures. Journal of Structural Biology In Press, Corrected Proof. | |||
| ===Tomography=== | |||
| : | |||
| :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:''''' | |||
| :#Winkler, H. (2006) 3D reconstruction and processing of volumetric data in cryo-electron tomography. Journal of Structural Biology In Press, Uncorrected Proof. | |||
| :#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. | |||
| :#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. | |||
| :#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: == | |||
| * ] | |||
| == 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, ]. ISBN 0195182189. | |||
| == External links: == | |||
| * The 3DEM list is a primary communication source among experts in the field of molecular and cellular electron microscopy. | |||
| * Basics of electron microscopy in single particle reconstruction, and it's applications to biology. | |||
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