3D Mouse Brain Data Library Now Available Online

A multi-institutional consortium has created incredibly sharp three-dimensional (3D) microscopic views of tiny mouse brains--revealed layer by layer--by extending the capabilities of conventional magnetic resonance imaging (MRI).

"These images can be more than 100,000 times higher resolution than a clinical MRI scan,” said Dr. G. Allan Johnson, a professor of radiology and professor of biomedical engineering and physics at Duke University (Durham, NC, USA). He is first author of a report describing the innovations set for publication in the research journal NeuroImage.

Images on the website for Duke's Center for In Vivo Microscopy, which Johnson directs, reveal examples of these developments in action. In one video two different mouse brains--one from a normal animal and the other from a rodent missing a gene linked to mental abnormalities--seem to assemble themselves before the viewer's eyes, structure by structure.

After building up like time-lapse photos of opening flowers, the side-by-side brain images begin revolving as overlying tissues dissolve into computer-rendered transparency. What remains visible, seemingly floating over the bases of the animals' skulls, are two color-coded brain structures--the ventricles and hippocampus--demonstrating different volumes resulting from specific genetic differences.

The six U.S. schools involved in the project--Duke, the California Institute of Technology (Pasadena), the University of Tennessee at Memphis, the University of California at Los Angeles, Drexel College of Medicine (Philadelphia. PA), and the University of California at San Diego--are connected via a very high speed network with each other as well as with the San Diego Supercomputing Center.

The consortium has developed the computer infrastructure to collect a rapidly growing library of 3D mouse brain data, and make all the data available on the web. The aim of the researchers is to use mouse brains as surrogates for human brains to study the connections between genes and brain structure. Investigators worldwide are sending their models to Duke where the 3D images are acquired in a standardized fashion and made available via high speed web connections.

High resolution MRI, which the researchers call "MRI histology,” provides distortion-free 3D images with an ability to differentiate slight tissue differences in the brain, according to Dr. Johnson. "The specimen is still actually in the skull,” he said. "It hasn't been cut by a knife. It has not been dehydrated and distorted as it would be in conventional histological techniques.”

Using computer-guided statistical methods, the data can be segmented into more than 30 anatomic structures with quantitative volume measurements. These structures can then be computer-enhanced to produce color-coded and labeled volume renderings of selected anatomic features in 3D, seen at any angle. MRI scanning is also faster and is less expensive than conventional histology, according to Dr. Johnson. MRI histology permits the evaluation of an entire brain, which would be prohibitively costly using traditional methods.


Related Links:
Duke University Center for In Vivo Microscopy
3D Mouse data library