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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 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:

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


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.


iplt

The Image Processing Library & Toolbox is an open-source project primarily aimed the 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.
Version: Unknown Contact: ansgar dot philippsen at unibas dot ch OS support: Unknown Image format support: Unknown Cost: Free/GPL
Publications:
  1. Philippsen, A., Schenk, A. D., Signorell, G. A., Mariani, V., Berneche, S., and Engel, A. Collaborative EM image processing with the IPLT image processing library and toolbox. Journal of Structural Biology In Press, Corrected Proof.
  2. Philippsen A, Schenk AD, Stahlberg H, Engel A. IPLT: image processing library and toolkit for the electron microscopy community. J Struct Biol. 2003 Oct-Nov;144(1-2):4-12.


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:

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

2dx
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.
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.
Version: 1.0.1 Contact: HStahlberg@ucdavis.edu OS support: Mac OSX (PPC and Intel), Linux (64bit and 32bit) Image format support: MRC, TIFF, CCP4 Cost: Free/GNU General Public License
Publications:
  1. 2dx – User-friendly image processing for 2D crystals. Journal of Structural Biology, In Press, Accepted Manuscript, Available online 1 September 2006, Bryant Gipson, Xiangyan Zeng, Zi Yan Zhang and Henning Stahlberg.

Icosahedral viruses

AUTO3DEM
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.
Version: 2.2 Contact: jhtang @ucsd.edu OS support: Linux Image format support: Unknown Cost: Free to academic users
Publications:
  1. AUTO3DEM – an automated and high throughput program for image reconstruction of icosahedral particles. Journal of Structural Biology, In Press, Accepted Manuscript, Available online 25 August 2006, Xiaodong Yan, Robert S. Sinkovits and Timothy S. Baker

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: Linux, IRIX, OSF Image format support: MRC, Spider 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.


UCSF Tomography
UCSF Tomography is used to collect single-axis tilt series on electron transimission microscopes. 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 data collection. A significant dose saving can thus be achieved and is critical in collecting cryo tilt series.
Version: v7.7.3c2 Contact: agard @nospam @msg.ucsf.edu OS support: Unknown Image format support: Unknown Cost: Free for academic use
Publications:
  1. Zheng, Q. S., Braunfeld, M. B., Sedat, J. W., and Agard, D. A. (2004). An improved strategy for automated electron microscopic tomography. Journal of Structural Biology 147, 91-101.
  2. Zheng, S. Q., Keszthelyi, B., Branlund, E., Lyle, J. M., Braunfeld, M. B., Sedat, J. W., and Agard, D. A. UCSF tomography: An integrated software suite for real-time electron microscopic tomographic data collection, alignment, and reconstruction. Journal of Structural Biology In Press, Corrected Proof.

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.

Particle Selection

Signature
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.
Version: Unknown Contact: james.z.chen @nospam @gmail.com OS support: Linux, Mac OS X, MS Windows Image format support: MRC, TIFF Cost: Free to academic community
Publications:
  1. Chen, J. Z., and Grigorieff, N. SIGNATURE: A single-particle selection system for molecular electron microscopy. Journal of Structural Biology In Press, Uncorrected Proof.


SwarmPS
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.
Version: Unknown Contact: d.woolford @imb.uq.edu.au OS support: Linux Image format support: Unknown Cost: Free for academic use under a software license agreement.
Publications:
  1. 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. SwarmPS: Rapid, semi-automated single particle selection software. Journal of Structural Biology In Press, Corrected Proof.

Visualization tools:

Chimera
Molecular modeling package enabling interactive segmentation, fitting, 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.
Version: 1.2255 Contact: chimera-users@cgl.ucsf.edu OS support: Windows, Macintosh, Linux, IRIX and Tru64 Image format support: MRC, CCP4, SPIDER, BRIX, SITUS, others Cost: Free for academic use
Publications:
  1. Goddard, T. D., Huang, C. C., and Ferrin, T. E. Visualizing density maps with UCSF Chimera. Journal of Structural Biology In Press, Corrected Proof.


Situs
Package for the modeling of atomic resolution structures into low-resolution density maps e.g. from electron microscopy, tomography, or small angle X-ray scattering..
Version: 2.2 Contact: situs@biomachina.org OS support: Unknown Image format support: Unknown Cost: Copyrighted
Publications:
  1. Wriggers, W., and Birmanns, S. (2001). Using Situs for Flexible and Rigid-Body Fitting of Multiresolution Single-Molecule Data. Journal of Structural Biology 133, 193-202.

See also:


References:

  • Advances in Computational Image Processing for Microscopy, JSB volume 116 1996
  • Chiu W, Baker ML, Jiang W, Dougherty M, Schmid MF. Electron cryomicroscopy of biological machines at subnanometer resolution. Structure. 2005 Mar;13(3):363-72.
  • 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.
  • MSD EM Databank. Archived EM maps at the Macromolecular Structure Database.
  • VIPERdb EM Database. Archive of icosahedral virus maps at the Virus Particle Explorer web site.
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