Electron Microscopy

SBGrid supports 28 electron microscopy software titles. The following software packages are supported by SBGrid; availability of a specific software package may be limited based on license requirements.

Software Title Description Linux 32-bit Linux 64-bit OS X Intel Links

2dx

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

yes yes yes

AUTO3DEM

- 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).

yes yes yes

Bsoft

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

yes yes yes

Burnham-Brandeis Helical Package

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

yes yes yes

em2em

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

yes yes yes

EMAN

- 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.

yes yes yes

EMAN2

- 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.

yes yes yes

EM-BFACTOR

- 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.

yes yes yes

FREALIGN

- (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.

yes yes yes

Grigorieff Apps

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

yes yes yes

ImageJ

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.

yes yes yes

IMOD

- 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.

yes yes yes

MRC Cambridge Image Processing System

- 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.

yes yes yes

NORMA

- 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.

yes yes

PARTICLE

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.

yes yes

PFT3dr

- performs orientation searches and positional refinement of icosahedral viruses.

yes yes yes

Priism/IVE

- 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.

yes yes yes

SIGNATURE

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

yes yes yes

SITUS

- 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.

yes yes yes

SPARX

- (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.

yes yes yes

SPIDER

- (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.

yes yes yes

Spire

- 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.

yes yes yes

Suprim

- 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.

yes yes yes

Tiltpicker

- 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.

yes yes

UROX

- 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.

yes yes

XDP

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

yes yes

Xmipp

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

yes yes yes

Zephyr

- 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.

yes yes