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Software Tools for Macromolecular Microscopy: A Special Issue of the Journal of Structural Biology, Volume 157, Issue 1 - Softcover
Synopsis
This Special Issue of the Journal of Structural Biology focuses on the software tools used in electron microscopy. It provides a useful resource to newcomers to the field as well as an updated snapshot of software applications applicable to molecular microscopy.
Several of the papers in this Special Issue provide higher-level programming environments that will serve to integrate a number of software packages and, in one case, provide tools for converting parameters between packages.
The applications described represent a wide range and variety of software solutions. Along with half a dozen general software packages, there are a number of specific packages designed to address the analysis of one class of structural problems (e.g., helical, icosahedral or crystalline symmetry, or tomography), application tools to address one particular aspect of the analysis (e.g., CTF correction, particle selection, classification, initial model generation, resolution assessment), as well as tools for visualization and fitting of the final three-dimensional volumes.
About the Journal
The Journal of Structural Biology publishes papers dealing with the structural analysis of living material at every level of organization by all methods that lead to an understanding of biological function in terms of molecular and supermolecular structure.
Techniques covered include:
• Light microscopy including confocal microscopy
• All types of electron microscopy
• X-ray diffraction
• Nuclear magnetic resonance
• Scanning force microscopy, scanning probe microscopy, and tunneling microscopy
• Digital image processing
• Computational insights into structure
The field covered by the journal extends from the structural organization of cells and tissues, their membranes, compartments, organelles and supramolecular assemblies, to the structure and conformation of proteins and nucleic acids from the molecular to the atomic level.
Table of Contents
-Bridget Carragher, Clinton S. Potter, Fred J. Sigworth. Software tools for macromolecular microscopy
General Packages
-J. Bernard Heymann, David M. Belnap. Bsoft: Image processing and molecular modeling for electron microscopy
-J.R. Plaisier, L. Jiang, J.P. Abrahams. Cyclops: New modular software suite for cryo-EM
-Ansgar Philippsen, Andreas D. Schenk, Gian A. Signorell, Valerio Mariani, Simon Berneche, Andreas Engel. Collaborative EM image processing with the IPLT image processing library and toolbox
-Guang Tang, Liwei Peng, Philip R. Baldwin, Deepinder S. Mann, Wen Jiang, Ian Rees, Steven J. Ludtke. EMAN2: An extensible image processing suite for electron microscopy
-Michael Hohn, Grant Tang, Grant Goodyear, P.R. Baldwin, Zhong Huang, Pawel A. Penczek, Chao Yang, Robert M. Glaeser, Paul D. Adams, Steven J. Ludtke. SPARX, a new environment for Cryo-EM image processing
-William T. Baxter, ArDean Leith, Joachim Frank. SPIRE: The SPIDER Reconstruction Engine
Specific Packages
Two-dimensional Crystals, Icosahedral viruses, Helices, Single Particles, Tomography, Random conical tilt
-Bryant Gipson, Xiangyan Zeng, Zi Yan Zhang, Henning Stahlberg. 2dx - User-friendly image processing for 2D crystals
-Xiaodong Yan, Robert S. Sinkovits, Timothy S. Baker. AUTO3DEM - an automated and high throughput program for image reconstruction of icosahedral particles
-Edward H. Egelman. The iterative helical real space reconstruction method: Surmounting the problems posed by real polymers
-Zoltan Metlagel, Yayoi S. Kikkawa, Masahide Kikkawa. Ruby-Helix: An implementation of helical image processing based on object-oriented scripting language
-Andrew J. Pomfret, William J. Rice, David L. Stokes. Application of the iterative helical real-space reconstruction method to large membranous tubular crystals of P-type ATPases
-Nikolaus Grigorieff. FREALIGN: High-resolution refinement of single particle structures
-Hanspeter Winkler. 3D reconstruction and processing of volumetric data in cryo-electron tomography
-Shawn Q. Zheng, Bettina Keszthelyi, Eric Branlund, John M. Lyle, Michael B. Braunfeld, John W. Sedat, David A. Agard. UCSF tomography: An integrated software suite for real-time electron microscopic tomographic data collection, alignment, and reconstruction
-Shawn Q. Zheng, Justin M. Kollman, Michael B. Braunfeld, John W. Sedat, David A. Agard. Automated acquisition of electron microscopic random conical tilt sets
Application Tools
Image assessment, Particle selection, CTF correction, Resolution estimation, Initial model estimation, Classification, Reconstruction algorithms. Data format conversion
-S. Joni ć, C.O.S. Sorzano, M. Cottevieille, E. Larquet, N. Boisset. A novel method for improvement of visualization of power spectra for sorting cryo-electron micrographs and their local areas
-James Z. Chen, Nikolaus Grigorieff. SIGNATURE: A single-particle selection system for molecular electron microscopy
-David Woolford, Geoffery Ericksson, Rosalba Rothnagel, David Muller, Michael J. Landsberg, Radosav S. Pantelic, Alasdair McDowall, Bernard Pailthorpe, Paul R. Young, Ben Hankamer, Jasmine Banks. Swarm PS: Rapid, semi-automated single particle selection software
-K. Vince Fernando, Stephen D. Fuller. Determination of astigmatism in TEM images-Duncan Sousa, Nikolaus Grigorieff. Ab initio resolution measurement for single particle structures
-Xiaodong Yan, Kelly A. Dryden, Jinghua Tang, Timothy S. Baker. Ab initio random model method facilitates 3D reconstruction of icosahedral particles
-Jie Fu, Haixiao Gao, Joachim Frank. Unsupervised classification of single particles by cluster tracking in multi-dimensional space
-Chao Yang, Pawel A. Penczek, ArDean Leith, Francisco J. Asturias, Esmond G. Ng, Robert M. Glaeser, Joachim Frank. The parallelization of SPIDER on distributed-memory computers using MPI
-P.R. Baldwin, Pawel A. Penczek. The Transform Class in SPARX and EMAN2
Visualization and Fitting
-Jamie LeBarron, Kakoli Mitra, Joachim Frank. Displaying 3D data on RNA secondary structures: coloRNA
-Stefan Birmanns, Willy Wriggers. Multi-resolution anchor-point registration of biomolecular assemblies and their components
-Thomas D. Goddard, Conrad C. Huang, Thomas E. Ferrin. Visualizing density maps with UCSF Chimera
New Hardware
-Daniel Castaño Díez, Hannes Mueller, Achilleas S. Frangakis. Implementation and performance evaluation of reconstruction algorithms on graphics processors
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