Graphics and Visualization


The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data in a very efficient way. Having the data defined as a set of objects, specialized storage methods are used to get direct access to the separate attributes of the selected objects, without having to touch the bulk of the data.

ePMV (DISABLED - will be removed on 12/21/17)

Note: Due to lack of use, this software module has been disabled and will be removed from MSI systems on 12/21/17. If you need this software, please contact


The Embedded Python Molecular Viewer (ePMV) works with a variety of software applications to provide visualization of  molecular structures.

Enthought Canopy Python Distribution

Python is a high level programming language that aims to combine remarkable power with very clear syntax. The Enthought Python Distribution is a cross-platform environment for scientific computing in Python, and includes the Canopy IDE and package manager. MSI has installed an academic-licensed version that includes hundreds of modules, including tools that enable efficient parallel computations.


Slicer, or 3D Slicer, is a free, open source software package for visualization and image analysis. It includes tools for segmentation, rendering, registration of MRI, CT, US, nuclear medicine, and microscopy images.


FSL is a library of analysis tools for FMRI, MRI and DTI brain imaging data. It has both command line and graphical user interface.


trackd® is the standard device driver software for leading virtual reality applications, developers, display manufacturers, motion tracking companies, and input device manufacturers in the immersive 3D display industry. It is a small "daemon" application that takes information from a variety of motion tracking and input devices and makes that information available for other applications to use. Used with large and small immersive 3D displays, trackd allows applications to take advantage of six degrees of freedom interaction tools.


Python is a high level programming language that aims to combine remarkable power with very clear syntax. Its success in these areas has led to strong adoption by the scientific community, resulting in numerous math, physics, chemistry, and biology libraries being contributed from the community of users.



The Persistence of Vision Raytracer is a high-quality, totally free tool for creating stunning three-dimensional graphics. Many biology and chemistry programs export files that can be read by POVRay which is then used to render extremely high quality images.


HKL-2000 program package is based on the extended versions of Denzo, Xdisplayf and Scalepack. It consists of several subprograms coordinated by the graphical command center. The most important new elements are: strategy and simulation, 3-D processing, mosaicity refinement during processing, variable spot size, easy change of the space group, report generation, etc. The software is driven by the graphical user interface, which greatly improves convenience of working with various data sets.


Matlab is a high level technical computing language and interactive environment for data visualization, data analysis, numerical computation, and algorithm development.