• a package for data processing of 2DX crystals developed by the Stahlberg laboratory at the University of Basel.

Developers

Henning Stahlberg

Categories

Electron Microscopy

Versions

• Linux 32: 3.4.1
• Linux 64: 3.4.1
• OSX Intel: 3.4.1
• OSX PPC: 3.0.6

Citations

Gipson et al. 2dx--user-friendly image processing for 2D crystals. J Struct Biol (2007) vol. 157 (1) pp. 64-72

• an automated image reconstruction system that coordinates the execution of the parallel, numerically-intensive codes P3DR, PCUT, POR, PPFT, PSF and RobEM (a GUI driven program used both for image preprocessing and visualization).

Developers

Giovanni Cardone

Timothy Baker

Categories

Electron Microscopy

Versions

• Linux 32: 4.02
• Linux 64: 4.02
• OSX Intel: 4.02
• OSX PPC: 3.08

Citations

Yan X., R.S. Sinkovits, and T.S. Baker (2007) AUTO3DEM - an automated and high throughput program for image reconstruction of icosahedral particles. J. Struct. Bio. 157:73-82.

• a software package written for image processing of electron micrographs, interpretation of reconstructions, molecular modeling, and general image processing.

Developers

Bernard Heymann

Categories

Electron Microscopy

Versions

• Linux 32: 1.8.6
• Linux 64: 1.8.6
• OSX Intel: 1.8.6
• OSX PPC: 1.7.0
• SGI Irix: 0.8

Citations

Heymann and Belnap. Bsoft: image processing and molecular modeling for electron microscopy. J Struct Biol (2007) vol. 157 (1) pp. 3-18

• a suite of applications for the analysis of helical structures.

Developers

Niels Volkmann

Categories

Electron Microscopy

Versions

• Linux 32: 20.1
• Linux 64: 20.2
• OSX Intel: 20.1

Citations

Owen et al. Image analysis of helical objects: the Brandeis Helical Package. J Struct Biol (1996) vol. 116 (1) pp. 167-75

• allows sharpening of high resolution information in 3D maps obtained by electron cryomicroscopy according to the Rosenthal and Henderson approach (JMB 333:721-745, 2003). The program accepts 3D maps in any common EM format and also accepts FSC curves in the format of most common packages for single particles, cryoEM. As output, the program produces a sharpened map and the Guinier plot that allows assessment of the sharpening.

Developers

Jose-Jesus Fernandez

Categories

Electron Microscopy

Versions

• Linux 32: 200912
• Linux 64: 200912
• OSX Intel: 200912

Citations

Fernández et al. Sharpening high resolution information in single particle electron cryomicroscopy. Journal of structural biology (2008) vol. 164 (1) pp. 170-5

• a program to convert images from/to formats used in the "electron microscopical community" (3DEM)

Developers

Michael Schatz

Categories

Electron Microscopy

Versions

• Linux 32: 090720
• Linux 64: 090720
• OSX Intel: 090720

• a suite of scientific image processing tools for the transmission electron microscopy community, though it is beginning to be used in other fields as well. EMAN has a particular focus on single particle reconstruction. EMAN includes Foldhunter and Helixhunter.

Developers

Steven Ludtke

Categories

Electron Microscopy

Versions

• Linux 32: 1.9
• Linux 64: 1.9
• OSX Intel: 1.9
• OSX PPC: 1.9

Citations

Ludtke. 3-D structures of macromolecules using single-particle analysis in EMAN. Methods in molecular biology (Clifton, NJ) (2010) vol. 673 pp. 157-73

Technical Notes

there still seem to be some problems running under RH9 with Gnome. KDE has no problems Note: Under OS X, the main windows will get locked behind other "Aqua" windows. This is a bug in the way they programmed the forms with Qt.

• a scientific image processing suite with a particular focus on single particle reconstruction from cryoEM images. EMAN2 is a complete refactoring of the original EMAN1 library. The new system offers an easily extensible infrastructure, better documentation, easier customization, etc. However, it will be some time before the full capabilities of EMAN1 have been reimplemented in the new system. For this reason EMAN2 was designed to happily coexist with EMAN1 installations. It is strongly recommended that all EMAN2 installations be accompanied by an EMAN1 installation. The programs that DO exist in EMAN2 will generally be more capable and efficient than the EMAN1 counterparts.

Developers

Steven Ludtke

Categories

Electron Microscopy

Tomography

Versions

• Linux 32: 2.06
• Linux 64: 2.06
• OSX Intel: 2.06
• OSX PPC: 20090618

Citations

Tang et al. EMAN2: an extensible image processing suite for electron microscopy. Journal of structural biology (2007) vol. 157 (1) pp. 38-46

• (Fourier REconstruction and ALIGNment) a program for high-resolution refinement of 3D reconstructions from cryo-EM images of single particles. A GPU-enabled version is also available. Developed by Niko Grigorieff at Brandeis University.

Developers

Nikolaus Grigorieff

Categories

Electron Microscopy

Versions

• Linux 32: 8.11
• Linux 64: 8.11
• OSX Intel: 8.11
• OSX PPC: 8.09

Citations

Grigorieff. FREALIGN: high-resolution refinement of single particle structures. Journal of structural biology (2007) vol. 157 (1) pp. 117-25

Li et al. GPU-enabled FREALIGN: accelerating single particle 3D reconstruction and refinement in Fourier space on graphics processors. Journal of structural biology (2010) vol. 172 (3) pp. 407-12

• EM utilities from the lab of Niko Grigorieff that include ctffind, ctftilt, bfactor, crop, diffmap and rmeasure.

Developers

Nikolaus Grigorieff

Categories

Electron Microscopy

Versions

• Linux 32: 20110914
• Linux 64: 20110914
• OSX Intel: 20110914
• OSX PPC: 20100726

Citations

ctffind and ctftilt: Mindell and Grigorieff. Accurate determination of local defocus and specimen tilt in electron microscopy. J Struct Biol. 2003. 142:334-47.

rmeasure: Sousa and Grigorieff. Ab initio resolution measurement for single particle structures. J Struct Biol. 2007. 157:201-10.

ImageJ is a public domain Java image processing program inspired by NIH Image for the Macintosh. It can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw". It supports "stacks", a series of images that share a single window. It is multithreaded, so time-consuming operations such as image file reading can be performed in parallel with other operations.

This installation includes the LOCI BioFormats plugin for reading and editing EM image stacks.

Categories

Electron Microscopy

Utilities

Versions

• Linux 32: fiji
• Linux 64: fiji
• OSX Intel: fiji

• a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial- 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 displaying the image files. IMOD was developed primarily by David Mastronarde, Rick Gaudette, Sue Held, Jim Kremer, and Quanren Xiong at the Boulder Laboratory for 3-D Electron Microscopy of Cells.

Developers

David Mastronarde

Categories

Electron Microscopy

Tomography

Versions

• Linux 32: 4.5.2
• Linux 64: 4.5.2
• OSX Intel: 4.5.2
• OSX PPC: 4.1.9

Citations

Kremer et al. Computer visualization of three-dimensional image data using IMOD. J Struct Biol (1996) vol. 116 (1) pp. 71-6

Mastronarde. Dual-axis tomography: an approach with alignment methods that preserve resolution. J Struct Biol (1997) vol. 120 (3) pp. 343-52

• determines the structure of macromolecular assemblies. The approach has been to study specimens with some form of symmetry, such as crystals or helical and icosahedral particles, using programs suitable for many kinds of 2-D and 3-D analysis.

Developers

Jude Short

Categories

2D Crystallography

Electron Microscopy

Versions

• Linux 32: 05.05.2011
• Linux 64: 05.05.2011
• OSX Intel: 05.05.2011
• OSX PPC: 27.06.2007
• SGI Irix: 13.08.2002

Citations

Smith. Ximdisp--A visualization tool to aid structure determination from electron microscope images. Journal of structural biology (1999) vol. 125 (2-3) pp. 223-8

Crowther et al. MRC image processing programs. Journal of structural biology (1996) vol. 116 (1) pp. 9-16

• a software suite for the modelling of large conformational changes of 3-D protein structures under the constraint of a low resolution electron density map. A typical application for this software is the interpretation of electron microscopy data using atomic scale resolution structural models. The software package provided here should enable the interested user to perform flexible fitting on new cases without encountering major technical difficulties.

Developers

Karsten Suhre

Categories

Electron Microscopy

Versions

• Linux 32: 1.0
• Linux 64: 1.0

Citations

Suhre et al. NORMA: a tool for flexible fitting of high-resolution protein structures into low-resolution electron-microscopy-derived density maps. Acta crystallographica Section D, Biological crystallography (2006) vol. 62 (Pt 9) pp. 1098-100

PARTICLE is a software package for single-particle EM image processing. It provides an integrated computing environment with comprehensive data analysis functions for particle selection, particle classification, 3D reconstruction and model evaluation. In addition, PARTICLE emphasizes on data visualization that enables the user to "see" the data throughout the process.

Developers

James Chen

Categories

Electron Microscopy

Versions

• Linux 64: 1.0
• OSX Intel: 1.0

Technical Notes

Chen, Z et al (2012). PARTICLE (Version 1.0) [Software]. Available from http://www.image-analysis.net/EM

• performs orientation searches and positional refinement of icosahedral viruses.

Developers

David Belnap

Categories

Electron Microscopy

Versions

• Linux 32: 20110124
• Linux 64: 20110124
• OSX Intel: 20110124
• OSX PPC: 20110124

Citations

PFT2: Baker and Cheng. A model-based approach for determining orientations of biological macromolecules imaged by cryoelectron microscopy. J Struct Biol. 1996. 116(1):120-30. Sanz-García et al. The random-model method enables ab initio 3D reconstruction of asymmetric particles and determination of particle symmetry. J Struct Biol. 2010. 171(2):216-22.

EM3DR2: Crowther et al. Three dimensional reconstructions of spherical viruses by fourier synthesis from electron micrographs. Nature. 1970. 226(5244):421-5.

• the graphical interface to a collection of applications for the analysis and visualization of multidimensional data, with a focus on data from 3D optical microscopy and electron tomography. IVE (Image Visualization environment) is the core set of software libraries that are the foundation for the tools in Priism.

Developers

IVE Developer Group

Categories

Electron Microscopy

Tomography

Versions

• Linux 32: 4.2.7
• Linux 64: 4.2.7
• OSX Intel: 4.2.7
• OSX PPC: 4.2.7

Citations

Chen et al. IVE (Image Visualization Environment): a software platform for all three-dimensional microscopy applications. Journal of structural biology (1996) vol. 116 (1) pp. 56-60

Chen, H., Clyborne, W., Sedat, J.W., and Agard, D. A. (1992) PRIISM: an integrated system for display and analysis of three-dimensional microscope images. Proceedings of SPIE - the International Society for Optical Engineering. 1660: 784-790.

• an automated particle selection system for electron microscopy. The application was written by James Chen in Niko Grigorieff laboratory at Brandeis.

Developers

James Chen

Categories

Electron Microscopy

Versions

• Linux 32: 1.0
• Linux 64: 1.0
• OSX Intel: 1.0-1
• OSX PPC: 1.0

Citations

Chen & Grigorieff. SIGNATURE: a single-particle selection system for molecular electron microscopy. J Struct Biol. 2007. 157:168-73.

• a program package for modeling of atomic resolution structures into low-resolution density maps. The software supports both rigid-body and flexible docking using a variety of fitting strategies.

Developers

Situs Developer Team

Willy Wriggers

Categories

Electron Microscopy

SAXS

Versions

• Linux 32: 2.6.3
• Linux 64: 2.6.3
• OSX Intel: 2.6.3
• OSX PPC: 2.6.1
• SGI Irix: 2.1a3

Citations

Wriggers. Using Situs for the Integration of Multi-Resolution Structures. Biophysical Reviews. 2010. 2: 21-27.

• (single particle analysis for resolution extension) is an image processing environment with a particular emphasis on transmission electron microscopy (TEM) structure determination. It includes a graphical user interface that provides a complete graphical programming environment.

Developers

Pawel Penczek

Categories

Electron Microscopy

Versions

• Linux 32: 2.06
• Linux 64: 2.06
• OSX Intel: 2.06
• OSX PPC: 20090618

Citations

Hohn et al. SPARX, a new environment for Cryo-EM image processing. J. Struct. Biol. 2007. 157: 47-55.

Tang et al. EMAN2: An extensible image processing suite for electron microscopy. J. Struct. Biol. 2007. 157: 38-46.

Baldwin and Penczek. The Transform Class in SPARX and EMAN2. J. Struct. Biol. 2007. 157: 250-261.

• (System for Processing Image Data from Electron microscopy and Related fields) is a large image processing suite for electron microscopy, developed over the last 23 years by Joachim Frank and his laboratory.

Developers

ArDean Leith

Joachim Frank

Categories

Electron Microscopy

Versions

• Linux 32: 20.12
• Linux 64: 20.12
• OSX Intel: 20.12
• OSX PPC: 13.0
• SGI Irix: 8.02

Citations

Frank et al. SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. J Struct Biol. 1996. 116(1):190-9.

Technical Notes

Start the vncserver & vncviewer

vncserver :5 -cc 3 -depth 8 -localhost -geometry 1252x934
vncviewer :5

When the viewer window closes, the vncserver will be killed

vncserver -kill :5
to reset password remove .vnc directory from your HOME

The OSX build is a test build of the port. If there are any problems please
let us know so that we can correct them immediately.

• a graphical user interface for executing SPIDER batch files and other programs. It also offers a way to manage and organize the many output files created by SPIDER during reconstruction projects.

Spire is designed to simplify running projects that consist of numerous SPIDER batch files. Users who are new to SPIDER can quickly start processing electron micrographs. Spire provides a convenient environment for testing and debugging batch files. However, Spire does not deal with program correctness per se; it simply runs your SPIDER procedure files, and saves a list of output files to a project file.

Developers

ArDean Leith

Categories

Electron Microscopy

Versions

• Linux 32: 1.5.4
• Linux 64: 1.5.4
• OSX Intel: 1.5.4

Citations

Baxter et al. SPIRE: The SPIDER Reconstruction Engine. Journal of Structural Biology. 2007. 157: 56–63.

• a software package intended primarily for the processing of transmission electron micrographs. One of several applications developed by Automated Molecular Imaging Group at The Scripps Research Institute.

Developers

Automated Molecular Imaging Group

Bridget Carragher

Categories

Electron Microscopy

Versions

• Linux 32: 5.7
• Linux 64: 5.7
• OSX Intel: 5.7

Citations

Whittaker. PHOELIX: a package for semi-automated helical reconstruction. Ultramicroscopy. 1995. 58(3-4):245-59.

• a graphical user interface for picking particles from image tilt pairs for such applications as random conical tilt (RCT) and orthogonal tilt reconstruction (OTR). TiltPicker borrows its interface from Leginon and re-implements many of the tilt picking features of SPIDER WEB that can be run on modern computers.

Developers

Automated Molecular Imaging Group

Bridget Carragher

Neil Voss

Clint Potter

Categories

Electron Microscopy

Versions

• Linux 32: 2.0b13
• Linux 64: 2.0b13

Citations

Voss et al. DoG Picker and TiltPicker: software tools to facilitate particle selection in single particle electron microscopy. 2009. J Struct Biol. 166(2): 205-13.

• designed for interactive fitting of high-resolution models (e.g, obtained by X-Ray crystallography) into Electron Microscopy reconstructions. It can also be used to fit two maps together (e.g., in tomography), or to perform Normal-modes calculations.

Developers

Xavier Siebert

Categories

Electron Microscopy

Versions

• Linux 32: 2.0.2
• Linux 64: 2.0.2

Citations

Siebert and Navaza. UROX 2.0 : An interactive tool for fitting atomic models into Electron Microscopy reconstructions. Acta. Crys. 2009. D65: 651-658. Navaza et al. On the fitting of model electron densities into EM reconstructions: a reciprocal-space formulation. Acta. Cryst. 2002. D58: 1820-1825.

• used for processing Electron Diffraction data. Previously available only on DEC Alpha.

Developers

Kaoru Mitsuoka

Categories

2D Crystallography

Electron Microscopy

Versions

• OSX PPC: 2000

Technical Notes

Andreas D. Schenk, Daniel Castaño-Díez, Bryant Gipson, Marcel Arheit, Xiangyan Zeng, Henning Stahlberg. Methods in Enzymology. (2010) Vol 482: 101–129 Cryo-EM, Part B: 3-D Reconstruction. Chapter Four – 3D Reconstruction from 2D Crystal Image and Diffraction Data.

• (X-Window-based Microscopy Image Processing Package) a suite of image processing programs primarily aimed at single-particle 3D electron microscopy.

Developers

Biocomputing Unit CNB-CSIC

Categories

Electron Microscopy

Versions

• Linux 32: 3.0
• Linux 64: 3.0
• OSX Intel: 3.0
• OSX PPC: 2.3

Citations

Scheres SHW et al. Image processing for electron microscopy single-particle analysis using Xmipp. Nat. Protoc. 2008. 3: 977-990. Sorzano COS et al. XMIPP: a new generation of an open-source image processing package for Electron Microscopy. J. Struct. Biol. 2004. 148(2): 194-204. Marabini R et al. Xmipp: An image processing package for electron microscopy. J. Struct. Biol. 1996. 116:. 237-240.

Technical Notes

To configure the installation for submission to a local cluster, you should:

• put your config_launch.py or config_launch_sge.py file in /programs/local/xmipp.
• add the XMIPP_PARALLEL_LAUNCH environment variable pointing to your local cluster submission configuration.

• a tool for analyzing and manipulating images, especially those generated for electron microscopy. Zephyr is scriptable in Python, easy to extend, and easy to link to other programs. Zephyr was written (is being written) by Alex Stewart and Donald J. Olbris in the laboratories of Prof. David J. DeRosier and Prof. Niko Grigorieff at the Rosenstiel Basic Medical Sciences Research Center at Brandeis University in Waltham, Massachusetts, USA.

Developers

David DeRosier

Niko Grigorieff

Categories

Electron Microscopy

Versions

• Linux 32: 0.8.9
• Linux 64: 0.8.9