Exploring the Bioinformatics-Enabled 3D CAVE

It’s a triumph of three-dimensional imagery.

Bioinformatics is giving researchers an entirely different view of the human anatomy - from the top, outside and within.

The University of Calgary's Sun Centre of Excellence for Visual Genomics (COE) has pioneered the development of the world's first Java 3D-enabled Cave Automatic Virtual Environment (CAVE), which allows researchers to view, analyze and manipulate images and data in virtual reality.

"It allows the user to play with images in a pretty unprecedented [fashion]," said Dr. Andrei Turinsky, research associate at the COE. He added the center's CAVE technology is not even comparable to a regular two-dimensional screen.

CAVE technology was originally researched and developed by the Electronic Visualization Laboratory at the University of Illinois in Chicago. COE adopted the technology three years ago and modified it for use in bioinformatics.

The Calgary researchers used Java's 3D API for the CAVE's 3D component. Java is one of the major programming languages in bioinformatics and provides the added benefit of unlinking the development environment from the execution of the fully developed system, according to a COE white paper.

Developed in collaboration with Fakespace Systems Inc. and Sun Microsystems, the CAVE consists of four Marquee 8500 CRT projectors operating at a full resolution of 1280 x 1024. Users wear a pair of electronic LCD shutter glasses that operate at a frequency of 112 Hz, with rapidly alternating left and right eye perspective views. At a speed of 56 frames per second, per eye, the brain is able to "fuse" alternating pictures into one image.

"Virtually you are communicating with the object as it is moving towards you and around you. You can (either) manipulate the object using a joystick device, or you can walk around it and the CAVE tracks your movement. The object (being analyzed) stays still and you can walk into it," Turinsky said.

The CAVE provides anatomical and molecular images ranging from human organs down to the level of individual molecules such as DNA and protein.

The Sun Centre loads images provided by biologists on to the CAVE for viewing and analysis, said Turinsky. "We don’t really care what area on this hierarchy of scale we are working in, as long as we can get the pictures from the biologist, process them, visualize them and make sure they happen in the CAVE."

Currently, the CAVE can take images in various 3D, tiff, and vrml (virtual reality markup language) formats, said Turinsky. COE is working on expanding its capabilities to enable the CAVE to load volumetric data, including medical images such as MRI (magnetic resonance image) and CAT scans.

The ability to have a three-dimension view and analysis of the images in virtual reality provides benefits that two-dimensional screens cannot, said Turinsky. "Typically on a 2D screen you deal with images that look like a bowl of spaghetti, it is hard to distinguish what the parts are and where they go. In the CAVE, you will see the object like you would see it in real life, extended."

The CAVE does not only provide viewing pleasure for researchers. It runs image analysis algorithms "to create automatic measurements and quantification of anatomical issues", so when an image is placed in the CAVE the researcher could see if the algorithm is computing correctly, Turinsky said.

COE also hopes to add the element of time into the CAVE. Turinsky said the time equation would allow researchers to view images changing through time.

"If a disease (for example) takes two years (to progress), you can view the time series in two minutes. It would compress progress of a biomedical process and see it in three dimension changing through time."

The ability to provide complete and comprehensive data in a single view is another element COE wants to add to the CAVE's capabilities, according to the Calgary researcher.

By mapping different types of data into the same CAVE space, the user can view the anatomy "but at the same time you can see what genes are active or inactive at each moment and each place of your brain."

Last April, the Sun Centre received funding to undertake planned expansion of CAVE capabilities. It will be a two-year project in collaboration with graphics firm Kasterstener Publications Inc., which will develop a 3D atlas of the human anatomy, according to Turinsky.