Image Processing & Analysis

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

Signature   A particle data analysis system for macromolecule EM. 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

Image Processing & Analysis of Helical Complexes

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 No longer maintained.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

Molecular Visualization of Volumetric Densities

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

Molecular Visualization of Atomic Structures

PyMOL   A molecular graphics program with many features, including a high quality ray-tracer. Free for some applications. $$$

Chimera   A highly extensible, interactive molecular graphics program. FREE

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

3D Modeling, Visualization & Animation

IRIS Explorer   A visual programming environment for 3D data visualisation, animation and manipulation. $$$

Amira   An advanced 3D visualization and volume modeling package. $$$

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

Programming Tools

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

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