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

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

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 No longer maintained.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

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

3D Modeling, Visualization & Animation

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

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

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