Monday, November 23, 2009
Software Links
SPIDER A system for processing image data in electron microscopy and related fields. FREE
IMAGIC An advanced scientific image processing package. $$$
EMAN A complete suite of software for single particle analysis. FREE
FREALIGN An alignment program for single-particle reconstruction. FREE
SPARX A new environment for Cryo-EM image processing. See doi:10.1016/j.jsb.2006.07.003 FREE
Signature A particle data analysis system for macromolecule EM. FREE
Adapt An image classification program developed by Vince Ramey of the Nogales Lab, based on the work of Ogura et al. FREE
SUPRIM A supervisor for the processing of images. FREE
Situs Allows modeling of atomic resolution structures into low-resolution density maps. FREE
Bsoft A package of programs for data manipulation, including many image processing tools. FREE
Priism A collection of tools for processing, analyzing, and visualizing multidimensional imagery with a focus on 3D wide-field optical microscopy and EM tomography. FREE
Xmipp An X11 based microscopy image processing package. FREE
PTool A software package for particle selection. FREE
PHOELIX Software package for image processing of helical macromolecular complexes. FREE
Brandeis Helical Package (Currently unavailable) A group of programs for the analysis of electron micrographs of helical objects. No longer maintained. FREE
Chimera A highly extensible, interactive molecular graphics program. FREE
Vis5d+ An OpenGL-based volumetric visualization program. FREE
Web An interface for interacting with 2D and 3D SPIDER images. $$$
O A macromolecular crystallographic modeling tool. $$$
VMD A program for displaying, animating, and analyzing large biomolecular systems. FREE
Chimera A highly extensible, interactive molecular graphics program. FREE
PyMOL A molecular graphics program with many features, including a high quality ray-tracer. Free for some applications. $$$
O A macromolecular crystallographic modeling tool. $$$
VMD A program for displaying, animating, and analyzing large biomolecular systems. FREE
PMV Python Molecular Viewer. ???
Molscript A program for rendering 3D atomic molecular structures and creating figures. FREE
Rasmol An older program for rendering 3D atomic molecular structures in PDB format. FREE
Amira An advanced 3D visualization and volume modeling package. $$$
IRIS Explorer A visual programming environment for 3D data visualisation, animation and manipulation. $$$
AVS An advanced data visualization package. $$$
DINO A realtime 3D visualization program for structural biology data. FREE
VISION A visual programming environment & data-vis package in development at Scripps. FREE
POV-Ray A free ray-tracing tool for creating high-quality three-dimensional graphics. FREE
The Visualization Toolkit An open source, freely available software system for 3D computer graphics, image processing, and visualization. FREE
CygWin A Linux-like environment for Windows. FREE
SciPy A library of scientific tools for Python. FREE
MMTK Molecular Modeling Toolkit. A Python program library for molecular simulation applications. FREE
NCMIDB (EMEN) A web based Zope database system for project management and long term data storage and search. FREE
Raw Raw image loader plug-in for The Gimp (GNU Image Manipulation Tool). FREE