Leprechauns on the Brain

by Michael Mullaney on June 1, 2009

If the human brain was a box of Lucky Charms, the above picture would be on the cover and the jingle would go like this:

“Blue nuclei, purple neurons, green vessels, red astrocytes, and yellow microglia.”

The picture is an actual scan of a human brain, which clearly shows multiple cell types and vasculature (all correctly identified in the jingle). Brain tissue is, by far, the most complex living tissue. The components are intimately intertwined and interact with amazing synergy. Because everything is so interconnected, it’s been a major challenge to study individual cells and understand exactly how they live, work, and play with their neighbors.

Professor Badri Roysam is at the forefront of tackling this challenge. He is leading an international effort, called FARSIGHT, to develop an open-source software program for high-throughput analysis of 3-D brain images like the one above.

Powered by a supercomputer, the program will use machine vision and artificial intelligence to analyze large sets of brain scans and other data, and create a robust map of the human brain that identifies the structural and functional relationships of its different components. Such a scan would include all of the juicy gossip about the private lives of these brain cells, and show what they really think about their fellow cells – which is exactly the kind of ellusive data researchers are seeking.

The end goal, Badri says, is to have the ability to quickly map a human brain so researchers can create a model and run simulations that will detail how the brain will react to different implants. These types of models exist today, but can take days or weeks to render. Shrinking this time down to hours will expedite the process and move the state-of-the-art forward at a brisk pace.

Today’s brain implants, or neuroprosthetics, are always quickly rejected and rendered useless by the surrounding brain tissue. But if FARSIGHT proceeds as planned, neuroprosthetic research should accelerate and will ultimately yield data critical for better understanding the brain and creating a longer-lasting – if not permanent – brain implant, which could potentially benefit countless people around the world who have suffered brain trauma.

Above are two FARSIGHT mosaics of the surface of a human brain. The top is a 5-color mosaic, and the lower is a rendered 3-D object mosaic showing neurons (purple), vessels (green), astrocytes (red), and microglia (yellow).

You can read more about Badri’s work and FARSIGHT here. Technical types may enjoy a quick look at a pair of posters – Segmentation and Tracking Algorithms on Parallel Hardware, and FARSIGHT: A Framework for Automated Quantification of 2D and 3D Multi-Parameter Images of Biological Tissues – created by Badri’s students and presented this past April to the NSF.