Software Tools For Molecular Microscopy/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 http://2dx.org/ 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. It includes a single-particle Maximum Likelihood module, and 3D merging capability. 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. 3.1.0 Henning.Stahlberg@unibas.ch Mac OS X, Linux MRC, TIFF, CCP4 Free/Open Source GPL Gipson B, Zeng X, Zhang ZY, Stahlberg H 2dx--user-friendly image processing for 2D crystals J. Struct. Biol. 157 1 64–72 2007 January 17055742 10.1016/j.jsb.2006.07.020 Zeng X, Stahlberg H, Grigorieff N A maximum likelihood approach to two-dimensional crystals J. Struct. Biol. 160 3 362–74 2007 December 17964808 10.1016/j.jsb.2007.09.013 Icosahedral viruses AUTO3DEM http://cryoem.ucsd.edu/programs.shtm 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. 2.02 sinkovit@sdsc.edu Linux, UNIX PIF Free/Open Source BSD license Yan X, Sinkovits RS, Baker TS AUTO3DEM--an automated and high throughput program for image reconstruction of icosahedral particles J. Struct. Biol. 157 1 73–82 2007 January 17029842 1847775 10.1016/j.jsb.2006.08.007 Helices BBHP - Burnham-Brandeis Helical Package http://coan.burnham.org/other-projects/ The Brandeis Helical Package has been in use in one form or another for quite some time. Originally developed for VAX/VMS it has been modified, expanded, and ported several times. We first ported the package to Linux in 2006, using the Portland Group compilers. Subsequently we rewrote portions of the fortran code which were not supported by GNU fortran (g77) and now the package compiles and runs with gcc/g77. This has allowed us to support extra modern platforms. The re-christened Burnham-Brandeis Helical Package will now run on 32-bit Linux, 64-bit Linux, Mac OS X (Intel) and even Windows running Cygwin. At the same time, when porting to Linux, we took the opportunity to replace the main GUI portions of the package with updated programs. We had spent some time modifying the Tcl/Tk-based GUI programs Tkir (image viewer) and Tkll (layerline viewer) from SUPRIM to support a plugin architecture, where we could write new plugins to add functionality without further modifications to the core code-base. The first, tkinterp, provides an interface in Tkir for selecting layerlines, replacing the old interp program. The second, brandeisll, is a Tkll plugin to provide support for displaying the Burnham-Brandeis Helical Package "interp" layerline and bessel-function format. We've also included as part of the package, the AVID software for analyzing the variance within the helix. 20.0 coan@burnham.org Linux MRC Free Owen CH, Morgan DG, DeRosier DJ Image analysis of helical objects: the Brandeis Helical Package J. Struct. Biol. 116 167–175 1996 8742740 Rost LE, Hanein D, DeRosier DJ Reconstruction of symmetry deviations: a procedure to analyze partially decorated F-actin and other incomplete structures Ultramicroscopy 72 187–197 1998 9639941 IHRSR 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. egelman@virginia.edu Linux SPIDER Free Egelman EH The iterative helical real space reconstruction method: surmounting the problems posed by real polymers J. Struct. Biol. 157 1 83–94 2007 January 16919474 10.1016/j.jsb.2006.05.015 Phoelix http://ami.scripps.edu/redmine/projects/ami/wiki/Phoelix A set of procedures and algorithms for helical processing that we refer to as the PHOELIX package. The package was developed to provide a time-efficient and semiautomated method for determining a three-dimensional density map from a specimen with helical symmetry. The procedures which are part of PHOELIXn are drawn from the original MRC helical processing suite with extensions principally developed using the SUPRIM image processing package. The package in its current form has been optimized for the processing of actomyosin filaments but has been modified and applied to other helical structures. 1.3 amisoftware@scripps.edu Unix MRC/suprim Free/Open Source Whittaker M, Carragher BO, Milligan RA PHOELIX: a package for semi-automated helical reconstruction Ultramicroscopy 58 3-4 245–59 1995 June 7571117 Carragher B, Whittaker M, Milligan RA Helical processing using PHOELIX J. Struct. Biol. 116 1 107–12 1996 8742731 10.1006/jsbi.1996.0018 Ruby-Helix http://structure.m.u-tokyo.ac.jp/English/software/Ruby-Helix-Page/ruby-helix.html 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. 1.0 mkikkawa@m.u-tokyo.ac.jp Fedora, Mac OS X MRC Free/Open Source GPL Metlagel Z, Kikkawa YS, Kikkawa M Ruby-Helix: an implementation of helical image processing based on object-oriented scripting language J. Struct. Biol. 157 1 95–105 2007 January 16996276 10.1016/j.jsb.2006.07.015 Kikkawa M A new theory and algorithm for reconstructing helical structures with a seam J. Mol. Biol. 343 4 943–55 2004 October 15476812 10.1016/j.jmb.2004.08.051 Stokes Lab Procedures http://skirball.med.nyu.edu/research/sb/stokeslab/image-analysis.html Image Processing Software for Helical Crystals: outlines, procedures and hints for using the MRC helical processing software which has since been modified by several groups including Chikashi Toyoshima, Nigel Unwin, David DeRosier and David Stokes. stokes@saturn.med.nyu.edu Unix MRC Free/Open Source Unpublished Single particles Frealign http://emlab.rose2.brandeis.edu/ Frealign provides algorithms 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. 8.08 niko @brandeis.edu Linux, IRIX, OSF, Mac OS X MRC, Spider, IMAGIC Free/Open Source GPL Grigorieff N FREALIGN: high-resolution refinement of single particle structures J. Struct. Biol. 157 1 117–25 2007 January 16828314 10.1016/j.jsb.2006.05.004 PFT3DR http://www.chem.byu.edu/node/807 PFT3DR is package for determining orientations and origins of imaged particles and computing a three-dimensional reconstruction from the images and their assigned orientations and origins. The programs are enhanced versions of the PFT algorithm developed by Baker and Cheng (2000) and the Fourier Bessel reconstruction algorithm of Crowther et al. (1970). The original adaptations of the PFT3DR programs were specific to icosahedral viruses, but were enhanced to support nearly all symmetries found in biological particles. Other enhancements are described on the PFT3DR web site. 2 David_Belnap at byu.edu Unix (Linux, Mac OS X, etc.), VMS same as Bsoft Free/Open Source Baker TS, Cheng RH A model-based approach for determining orientations of biological macromolecules imaged by cryoelectron microscopy J. Struct. Biol. 116 1 120–30 1996 8742733 10.1006/jsbi.1996.0020 Crowther RA, Amos LA, Finch JT, De Rosier DJ, Klug A Three dimensional reconstructions of spherical viruses by fourier synthesis from electron micrographs Nature 226 5244 421–5 1970 May 4314822 Fuller SD, Butcher SJ, Cheng RH, Baker TS Three-dimensional reconstruction of icosahedral particles--the uncommon line J. Struct. Biol. 116 1 48–55 1996 8742722 10.1006/jsbi.1996.0009 Bubeck D, Filman DJ, Cheng N, Steven AC, Hogle JM, Belnap DM The structure of the poliovirus 135S cell entry intermediate at 10-angstrom resolution reveals the location of an externalized polypeptide that binds to membranes J. Virol. 79 12 7745–55 2005 June 15919927 1143686 10.1128/JVI.79.12.7745-7755.2005 Sanz-García, E, Stewart, AB, Belnap DM The random-model method enables ab initio three-dimensional reconstruction of asymmetric particles and determination of particle symmetry J. Struct. Biol. 171 2 216-222 2010 20353825 2885456 10.1016/j.jsb.2010.03.017 Search/Refine/Build https://sites.google.com/site/rubinsteingroup/ Search_Fspace, Refine_Fspace, and Build_Fspace, are relatively simple programs for calculating and refining 3D maps. Many of the approaches used are similar to approaches applied by Frealign. The website provided also has a number of other useful utilities for working on micrographs, stacks of MRC images, and parameter files. 1.01 john.rubinstein at utoronto.ca Linux MRC Free/Open Source GPL Lau, W.C.Y, Rubinstein, J.L. Subnanometre-resolution structure of the intact Thermus thermophilus H+-driven ATP synthase Nature 481 214-218 2012 22753497 Benlekbir S, Bueler SA, Rubinstein JL Structure of the vacuolar-type ATPase from Saccharomyces cerevisiae at 11-Å resolution Nature Structural and Molecular Biology 19 pages=1356-52 2012 23142977 Tomography ASTRA Toolbox http://www.visielab.ua.ac.be/software The ASTRA Toolbox is an open platform for 3D image reconstruction in tomography. The ASTRA Toolbox provides an extensive set of fast (GPU accelerated) and flexible building blocks that can be used in advanced reconstruction algorithms. astra@ua.ac.be Linux, Microsoft Windows EM,MRC,Matlab Free Palenstijn WJ, Batenburg KJ, Sijbers J Performance improvements for iterative electron tomography reconstruction using graphics processing units (GPUs) J. Struct. Biol. 176 2 250-253 2011 November 21840398 10.1016/j.jsb.2011.07.017 Palenstijn WJ, Batenburg KJ, Sijbers J The ASTRA Tomography Toolbox) 13th International Conference on Computational and Mathematical Methods in Science and Engineering 2013 http://www.visielab.ua.ac.be/sites/default/files/cmmse2013.pdf EM3D http://em3d.stanford.edu/index.html EM3D is a software application designed to analyze and visualize electron microscope (EM) tomography data. It is especially for cellular and molecular biologists. From a tilt series of 2D electron micrographs taken at many tilt angles with respect to the electron beam, this program can then perform auto-align and quickly render those data into a lucid 3D model, which allows you to perform object rotating for viewing. In addition, EM3D also provides analysis tools for quantify structural information from the models, including their moments, proximity relationships, and spatial reliability. And all of these functions can be executed with a very intuited graphic user interface. EM3D is available free-of-charge Mac OS X for PowerPC or Intel, and Windows. EM3D was developed in the laboratory of Dr. U. J. McMahan, Professor of Neurobiology and of Structural Biology at Stanford University School of Medicine and continues to be developed at the Dept. of Biology, Texas A&M University. 2.0 grantser@bio.tamu.edu Windows, Mac OS X for PowerPC or Intel Free for academic use Ress D, Harlow ML, Schwarz M, Marshall RM, McMahan UJ Automatic acquisition of fiducial markers and alignment of images in tilt series for electron tomography J Electron Microsc (Tokyo) 48 3 277–87 1999 10425746 EM3D's scheme for the automatic alignment of tilt-images is described. Ress DB, Harlow ML, Marshall RM, McMahan UJ Methods for generating high-resolution structural models from electron microscope tomography data Structure 12 10 1763–74 2004 October 15458626 10.1016/j.str.2004.07.022 EM3D approach to model generation is detailed. Harlow ML, Ress D, Stoschek A, Marshall RM, McMahan UJ The architecture of active zone material at the frog's neuromuscular junction Nature 409 6819 479–84 2001 January 11206537 10.1038/35054000 EM3D is first used for exposing cellular architecture at macromolecular resolution. Petersen JD, Chen X, Vinade L, Dosemeci A, Lisman JE, Reese TS Distribution of postsynaptic density (PSD)-95 and Ca2+/calmodulin-dependent protein kinase II at the PSD J. Neurosci. 23 35 11270–8 2003 December 14657186 EM3D is used to examine the architecture of the postsynaptic density at brain synapses. Ress, D., Harlow, M.L., Marshall, R.A., and McMahan, U.J. Proceedings of the 25th Annual International Conference of IEEE 2003 774-777 Optimized Method for Isodensity Surface Models Obtained with Electron Microscope Tomography Data EM3D's method for creating optimal isodensity surface models is described. IMOD http://bio3d.colorado.edu/imod/ IMOD is a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3-D data from any orientation, and modeling and display of the image files. It includes a complete graphical user interface for generating tomograms, combining tomograms from tilt series taken around two axes, and stacking tomograms from serial sections. 4.1 mast at colorado dot edu Linux, Windows, Mac OS X MRC, TIFF Free/Open Source GPL Kremer JR, Mastronarde DN, McIntosh JR Computer visualization of three-dimensional image data using IMOD J. Struct. Biol. 116 1 71–6 1996 8742726 10.1006/jsbi.1996.0013 Mastronarde DN Correction for non-perpendicularity of beam and tilt axis in tomographic reconstructions with the IMOD package J Microsc 230 Pt 2 212–7 2008 May 18445149 10.1111/j.1365-2818.2008.01977.x Mastronarde DN Dual-axis tomography: an approach with alignment methods that preserve resolution J. Struct. Biol. 120 3 343–52 1997 December 9441937 10.1006/jsbi.1997.3919 protomo http://www.electrontomography.org 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. 1.1 protomo@electrontomography.org Linux Most formats Free Winkler H 3D reconstruction and processing of volumetric data in cryo-electron tomography J. Struct. Biol. 157 1 126–37 2007 January 16973379 10.1016/j.jsb.2006.07.014 Winkler H, Taylor KA Accurate marker-free alignment with simultaneous geometry determination and reconstruction of tilt series in electron tomography Ultramicroscopy 106 3 240–54 2006 February 16137829 10.1016/j.ultramic.2005.07.007 Winkler H, Taylor KA Focus gradient correction applied to tilt series image data used in electron tomography J. Struct. Biol. 143 1 24–32 2003 July 12892723 Taylor KA, Tang J, Cheng Y, Winkler H The use of electron tomography for structural analysis of disordered protein arrays J. Struct. Biol. 120 3 372–86 1997 December 9441940 10.1006/jsbi.1997.3932 PyTom http://www.biochem.mpg.de/en/rg/foerster/Content_Software/PyTom/index.html PyTom is a python-based package for tomogram analysis. It supports tasks such as particle localization and identification by template matching, subtomogram averaging, and subtomogram classification. The package is open source, does not rely on any commercial software, and is platform-independent. The implementation in python should allow easy scripting for specific tasks. 1.0.1 foerster@biochem.mpg.de, hrabe@biochem.mpg.de, ychen@biochem.mpg.de Linux, Mac OS, Windows .em, .spi, .mrc Free GPL / BSD Python Hrabe T, Chen Y, Pfeffer S, Cuellar LK, Mangold AV, Förster F PyTom: a python-based toolbox for localization of macromolecules in cryo-electron tomograms and subtomogram analysis. J Struct Biology 178 2 178-88 2012 10.1016/j.jsb.2011.12.003 http://dx.doi.org/10.1016/j.jsb.2011.12.003 Chen Y, Hrabe T, Pfeffer S, Pauly O, Mateus D, Navab N, Förster F Detection and identification of macromolecular complexes in cryo-electron tomograms using support vector machines. Biomedical Imaging (ISBI), 2012 9th IEEE International Symposium on 1373-76 2012 10.1109/ISBI.2012.6235823 http://dx.doi.org/10.1109/ISBI.2012.6235823 RAPTOR http://www-vlsi.stanford.edu/TEM/software.htm Robust Alignment and Projection Estimation for Tomographic Reconstruction (RAPTOR) is a free available software to align raw stacks obtained from electron microscopes for tomographic purposes. It is intended to automatically obtain a full-precision alignment comparable to the one obtained with extended manual intervention. Fiducial particles are needed in the image for the alignment. It has been designed to be compatible with IMOD software, so results can be checked with the usual IMOD tools for alignment and reconstruction. 2.1 famat at stanford dot edu Linux MRC Free Amat F, Moussavi F, Comolli LR, Elidan G, Downing KH, Horowitz M Markov random field based automatic image alignment for electron tomography J. Struct. Biol. 161 3 260–75 2008 March 17855124 10.1016/j.jsb.2007.07.007 SerialEM http://bio3d.colorado.edu/SerialEM/ SerialEM is a program to acquire tilt series for electron tomography on Tecnai and newer JEOL microscopes. It uses an approach based on prediction of specimen position during the tilt series from the position at previous tilts. With this method, it achieves both the robustness of the older approach to tilt series acquisition (track and focus at every tilt) and the speed of the newer precalibration approach. It provides a complete interface for camera control and image acquisition, viewing, and saving. It includes a low dose mode for tracking and focusing away from the area of interest, energy filter control, acquisition of tilt series using a montage of overlapping frames, and a navigator module for mapping the grid and returning to selected locations. It supports Gatan, Tietz, FEI, AMT, and some Direct Electron CCD cameras. 2.8 mast at colorado dot edu Microsoft Windows MRC Free for academic use Mastronarde DN Automated electron microscope tomography using robust prediction of specimen movements J. Struct. Biol. 152 1 36–51 2005 October 16182563 10.1016/j.jsb.2005.07.007 TOM Toolbox http://www.biochem.mpg.de/tom/ The Tomography Toolbox is a collection of functions that extend the capability of the MATLAB (+ Image Procesing Toolbox) numeric computing environment. The toolbox supports a wide range of functions for tomography. Automated data acquisition procedures have changed the perspectives of electron tomography (ET) in a profound manner. Elaborate data acquisition schemes with autotuning functions minimize exposure of the specimen to the electron beam and sophisticated image analysis routines retrieve a maximum of information from noisy data sets. ‘TOM software toolbox’ integrates established algorithms and new concepts tailored to the special needs of low dose ET. It provides a user-friendly unified platform for all processing steps: acquisition, alignment, reconstruction, and analysis. Designed as a collection of computational procedures it is a complete software solution within a highly flexible framework. TOM represents a new way of working with the electron microscope and can serve as the basis for future high-throughput applications. tom@biochem.mpg.de Linux, Microsoft Windows EM,MRC,Spider Free Nickell S, Förster F, Linaroudis A, et al. TOM software toolbox: acquisition and analysis for electron tomography J. Struct. Biol. 149 3 227–34 2005 March 15721576 10.1016/j.jsb.2004.10.006 TomoJ http://u759.curie.fr/en/download/softwares/TomoJ TomoJ is a Java plug-in for ImageJ to perform tomographic reconstruction using ART, SIRT and WBP algorithms. It includes free reference alignment procedures in addition to standard cross-correlation methods in a friendly user interface. 2.15 tomoj@curie.fr All, same as ImageJ program Free/Open Source CeCILL Licence Java Messaoudii C, Boudier T, Sanchez Sorzano CO, Marco S TomoJ: tomography software for three-dimensional reconstruction in transmission electron microscopy BMC Bioinformatics 8 288 2007 17683598 1976622 10.1186/1471-2105-8-288 Sorzano CO, Messaoudi C, Eibauer M, et al. Marker-free image registration of electron tomography tilt-series BMC Bioinformatics 10 124 2009 19397789 2694187 10.1186/1471-2105-10-124 TxBR https://confluence.crbs.ucsd.edu/display/ncmir/TxBR Tomographic reconstruction from large-format electron microscope data requires special procedures to handle geometric distortions arising from electron optics as opposed to light-ray optics. In particular, electrons travel in curvilinear paths through the sample, and defocus and other aberrations can have significant effects. TxBR handles geometric nonlinearities associated with charged-particle optics, distortion due to sample warping, and transform sets associated with non-standard modes of data collection. In addition, TxBR makes provision for marker-free alignment and specialized montaging for tomography of serial sections. 3.0 sph at ncmir dot ucsd dot edu Linux, Windows (≥ XP), Mac OS X (PowerPC and Intel) MRC Free S. Phan, A. Lawrence Congress on Image and Signal Processing, Vol. 2 2008 176-182 Tomography of Large Format Electron Microscope Tilt Series: Image Alignment and Volume Reconstruction Lawrence A, Bouwer JC, Perkins G, Ellisman MH Transform-based backprojection for volume reconstruction of large format electron microscope tilt series J. Struct. Biol. 154 2 144–67 2006 May 16542854 10.1016/j.jsb.2005.12.012 UCSF Tomography http://www.msg.ucsf.edu/em/EMNEW2/tomography_page.html UCSF Tomography is an integrated software suite that provides full automation from target finding, sequential tomographic data collection, to real-time reconstruction for both single and dual axes as well as automated acquisition of random conical data sets. 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 tomographic data collection. A significant dose saving can thus be achieved and is critical in collecting cryo tilt series. Real-time reconstruction is achieved by calculating a weighted back-projection on a small Linux cluster (five dual-processor computer nodes) concurrently with the UCSF tomography data collection running on the microscope’s computer, and using the fiducial-marker free alignment data generated during the data collection process. The real-time reconstructed 3D volume provides users with immediate feedback to fully asses all aspects of the experiment ranging from sample choice, ice thickness, experimental parameters to the quality of specimen preparation. To facilitate dual-axis tomographic data collection, a hierarchical scheme for target finding and relocation after specimen rotation was developed and integrated with the predictive data collection and real-time reconstruction, allowing full automation from target finding to data collection and to reconstruction of 3D volumes with little user intervention. An on-site scheme was developed for random conical data collection where tracking and focusing are performed at the same location as the final conical tilt images. Lower magnifications combined with short exposure are used to substantially reduce dose and to allow larger tilt steps. The system also includes a feature for montaging untilted images to ensure that all of the particles in the tilted image may be used in the reconstruction. v7.7.4E4 agard@msg.ucsf.edu Windows 2000, XP MRC Free for academic use Zheng SQ, Keszthelyi B, Branlund E, et al. UCSF tomography: an integrated software suite for real-time electron microscopic tomographic data collection, alignment, and reconstruction J. Struct. Biol. 157 1 138–47 2007 January 16904341 10.1016/j.jsb.2006.06.005 Zheng QS, Braunfeld MB, Sedat JW, Agard DA An improved strategy for automated electron microscopic tomography J. Struct. Biol. 147 2 91–101 2004 August 15193638 10.1016/j.jsb.2004.02.005 Zheng SQ, Kollman JM, Braunfeld MB, Sedat JW, Agard DA Automated acquisition of electron microscopic random conical tilt sets J. Struct. Biol. 157 1 148–55 2007 January 17169745 2556511 10.1016/j.jsb.2006.10.026 Zheng SQ, Matsuda A, Braunfeld MB, Sedat JW, Agard DA Dual-axis target mapping and automated sequential acquisition of dual-axis EM tomographic data J. Struct. Biol. 168 2 323–31 2009 November 19545637 2776717 10.1016/j.jsb.2009.06.010 FEI Xplore3D™ Tomography Suite http://www.fei.com/LifeSciences/ Xplore3D provides a complete solution for 3D tomographic acquisition, reconstruction, and visualization into one integrated package. The advanced capabilities include batch acquisition, dual-axis tomography, low-dose imaging, STEM tomography, energy filtering, and hardware acceleration for reconstruction. Batch scheduling permits unattended overnight data acquisition from multiple grid positions. Accurate, interactive alignment routines can use cross-correlation (no markers needed), bead tracking, or general feature tracking. Advanced reconstruction techniques include weighted back-projection, ART, and SIRT. Xplore3D includes a post-alignment and reconstruction module, Inspect3D. robert dot snyder at fei dot com Windows XP, most image formats Price available upon request Perpetual right-to-use license R.H.M. Schoenmakers, R.A. Perquin, T.F. Fliervoet, W. Voorhout, H. Schirmacher New software for high resolution, high throughput electron tomography Microscopy and Analysis 19 4 5-6 2005 July Li Peng, Sergey Ryazantsev, Ren Sun, Z. Hong Zhou Three-Dimensional Visualization of Gammaherpesvirus Life Cycle in Host Cells by Electron Tomography Structure 18 1 47-58 2010 January 20152152 10.1016/j.str.2009.10.017 Linda F. van Driel, Jack A. Valentijn, Karine M. Valentijn, Roman I. Koning, Abraham J. Koster Tools for correlative cryo-fluorescence microscopy and cryo-electron tomography applied to whole mitochondria in human endothelial cells European Journal of Cell Biology 88 11 669-684 2009 November 19726102 10.1016/j.ejcb.2009.07.002 Laura van Niftrik, Willie J.C. Geerts, Elly G. van Donselaar, Bruno M. Humbel, Alevtyna Yakushevska, Arie J. Verkleij, Mike S.M. Jetten, Marc Strous Combined structural and chemical analysis of the anammoxosome: A membrane-bounded intracytoplasmic compartment in anammox bacteria Journal of Structural Biology 161 3 401-410 2008 March 17604181 10.1016/j.jsb.2007.05.005 Subvolume averaging Dynamo http://www.dynamo-em.org Dynamo is a software package for subtomogram averaging and classification of Cryo-EM data. It is intended to provide users with big flexibility when adding new algorithms into standard procedures and adapting them for different computing environments as desktops, multicore machines, (multi)GPUs or clusters of CPUs. It includes several tools for tomogram visualization and particle picking in several geometries (as filamentes, vesicles, membranes) 1.1.136 daniel.castano@unibas.ch Linux, Mac OS, Windows .em, .spi, .mrc Free for academic use GPL / BSD Castaño-Díez D, Kudryashev M, Arheit M, Stahlberg H Dynamo: A flexible, user-friendly development tool for subtomogram averaging of cryo-EM data in high-performance computing environments. J Struct Biology 3 2012 http://dx.doi.org/10.1016/j.jsb.2011.12.017 Jsubtomo http://www.opic.ox.ac.uk/jsubtomo Jsubtomo is an open source software package based on Bsoft for averaging of tomographic sub-volumes. It includes tools for locating sub-volumes in tomograms using constrained cross-correlation, missing wedge-weighted averaging and refinement. Initial estimate of particle orientation can be easily included to constrain refinement. Python scripts are available for parallel processing and iterative refinement. 1.2 juha at strubi dot ox dot ac dot uk Linux, Mac OS, Windows Most, including .map, .mrc, .em, .spi, .img, .pif Free C Huiskonen JT, Hepojoki J, Laurinmäki P, Vaheri A, Lankinen H, Butcher SJ, Grünewald K. Electron cryotomography of Tula hantavirus suggests a unique assembly paradigm for enveloped viruses. J Virology 84 10 4889-97 2010 10.1128/JVI.00057-10 PEET http://bio3d.colorado.edu/PEET PEET is an open-source package for subvolume alignment, averaging, and classification. PEET is most easily used in conjunction with IMOD. 1.8.0 john.heumann@colorado.edu Linux, Mac OS-X, Windows .mrc Free GPL Matlab, C, C++ Nicastro D, Schwartz C, Pierson J, Gaudette R, Porter M, McIntosh J.R. The molecular architecture of axonemes revealed by cryoelectron tomography. Science 313 5789 944-948 2006 10.1126/science.1128618 Mass measurements MASDET http://campus.uni-muenster.de/masdet.html A fast and user-friendly multiplatform software for mass determination by dark-field electron microscopy. MASDET offers several subroutines for the main mass analysis steps, namely image display and selection of regions of interest (ROI), mass evaluation and data analysis. Two program-modes constitute the core procedures for mass determination: (i) the program-mode AREA determines the mass-per-area of sheet-like structures (e.g., protein S-layers, thin organic and inorganic films) and the mass-per-box for globular structures (e.g., single macromolecules, globular assemblies, organic/inorganic nanoparticles), and (ii) the program-mode FILAMENT determines the mass-per-length for filamentous structures (e.g., intermediate filaments, DNA-protein complexes, tobacco mosaic virus, nanowires) in individual ROIs. The statistical analysis of the mass data in individual ROIs contains graphical data display (histograms and XY-plots) and allows up to 10 Gaussian curves to be fitted. The dark-field micrographs can also be recalculated to a mass-thickness profile and/or mass-thickness map using data from Monte Carlo simulations. 1.13 krzyzane at uni-muenster dot de Windows (both standalone program and p-files run from MATLAB); Mac OS X, Linux (p-files to be run from MATLAB) Basel IMAG, Muenster TIFF (other formats will be implemented by us on request) Free for academic use Krzyzanek V, Müller SA, Engel A, Reichelt R MASDET--A fast and user-friendly multiplatform software for mass determination by dark-field electron microscopy J. Struct. Biol. 165 2 78–87 2009 February 19041401 10.1016/j.jsb.2008.10.006 Krzyzanek V, Reichelt R MONCA: A New MATLAB Package for Monte Carlo Simulation of Electron Scattering in Thin Specimens in the Energy Range 10 - 200 keV Microsc. Microanal. 9 Suppl. 3 110-111 2003 10.1017/S1431927603014065 http://journals.cambridge.org/action/displayAbstract?aid=173725 Reichelt R, Engel A Monte Carlo calculations of elastic and inelastic electron scattering in biological and plastic materials Ultramicrosc. 13 3 279-293 1984 10.1016/0304-3991(84)90206-7