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Videogame Engine Serves Up Free Brain Imagery for All

Mark Ellisman wants neuroscientists to share. Typically, they don’t: Data on brain structures, painstakingly accumulated using neuroimaging technologies and dissections, usually belongs to individual researchers, labs, and journals. So Ellisman, a neuroscientist at UC San Diego, started working on the Whole Brain Catalog, an open source, open-access database of mouse brain imagery. Think of it as Google Earth for rodent neurology—if Google Earth were based on a videogame engine and could zoom from the scale of a continent to a ladybug. “That’s the range we traverse, but in 3-D,” Ellisman says.

Download the software and you get visualizations and videos ranging from the structure of the entire brain to individual neurons. And many of the renders link to the data they’re built from, like the massive (and massively well-funded) Allen Brain Atlas or the Neuroscience Information Framework, run by the National Institutes of Health. A handful of labs have also donated their work—the Salk Institute’s Fred Gage contributed a 2-D simulation of nerve cell growth in adult mice, and Ellisman’s team adjusted the pacing to run in real time, eventually posting it to the catalog as a “4-D simulation.”

Today the database totals 3,595 images and videos, including recently added views of the retina and optical nerve. A whole new version of the WBC is due out in December. Eventually the videogame engine—it’s Java Monkey, the underpinning of a bunch of addictive web games—will do even more. Nothing brings a research lab together like a fly-through of the hippocampus in PvP mode.

This post was written by: Franklin Manuel

Franklin Manuel is a professional blogger, web designer and front end web developer. Follow him on Twitter