VMD (Visual Molecular Dynamics) is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer. VMD uses OpenGL and OpenGL Programmable Shading Language for high performance rendering of large structures.
Jmol is a Free, Open Source molecule viewer and editor. It is a collaboratively developed visualization and measurement tool for chemical scientists. Jmol is an active project, and there are new features being added to it on a daily basis. Users are encouraged to modify it to fit their needs and to contribute their changes to the project.
BALLView is an extensible viewer for bio-molecular structures. It provides all standard models and offers rich functionality for molecular modeling and simulation, including molecular mechanics methods (AMBER, CHARMM, and MMFF94 force fields), continuum electrostatics methods employing a Finite-Difference Poisson Boltzmann solver, secondary structure calculation, molecular editing and docking. Since BALLView is based on BALL (the Biochemical ALgorithms Library), it is easily extensible on the level of C++ code. In addition, it provides a Python interface with Integrated Development Environment features to allow interactive rapid prototyping.
The National Library of Medicine Insight Segmentation and Registration Toolkit (ITK) is a software system to support the Visible Human Project. Segmentation is the process of identifying and classifying data found in a digitally sampled representation. Registration is the task of aligning or developing correspondences between data. For example, in the medical environment, a CT scan may be aligned with an MRI scan in order to combine the information contained in both.
ImLib3D is a C++ library and visualization system for 3D (volumetric) image processing. It contains most basic image processing algorithms, as well as some more sophisticated ones. Its images are STL-compliant templated containers. It inculdes a viewer that features multiplanar views, interactive image processing, animations, vector field views, and 3D (OpenGL) multiplanar. Its main application is medical image processing.
FastVox is an API for volume visualization that can be embedded into OpenGL displays. It features a multi-threaded realtime volume rendering engine which is based on a set of plugins that range from high-speed software-based renderers to hardware-accelerated renderers designed for current generation graphics hardware.
The OpenVL library is a framework for working with 3D volumetric datasets. It provides a standard and uniform API to volumetric data access, storage, and processing. It is designed and built to be fast, extensible, flexible, and easy to use. The library is completely open-sourced and encourages contribution. This library is an ideal choice if you want to write applications that deal with 3D volumes.
Julius MV1 is a showcase application for the Julius framework. It can be used as a fully functional DICOM 3.0 or RAW volume viewer as well as a viewer for large polymesh datasets. It also provides basic data processing features such as volume segmentation or polymesh decimation. Julius MV1 can be used as a basis and testbed for other applications developed with the Julius Framework. The Julius Framework (which comes bundled with MV1) is a general software architecture for medical visualization, simulation, and navigation.
Seg3D is a volume editing and processing tool that combines a flexible manual segmentation interface with powerful higher-dimensional image processing and segmentation algorithms from the Insight Toolkit. DICOM, VFF, META, NRRD, and many other volume formats are supported. Users can explore and label image volumes using configurable, orthogonal slice view windows and 3D volume rendering.
OsiriX is an image processing software dedicated to DICOM images produced by medical equipment (such as MRI, CT, PET, and PET-CT) and confocal microscopy (LSM and BioRAD-PIC format). It can also read many other file formats: TIFF, JPEG, PDF, AVI, MPEG, and Quicktime. OsiriX is able to receive images transferred by DICOM communication protocol from any PACS or medical imaging modality. OsiriX has been specifically designed for navigation and visualization of multimodality and multidimensional images.