New Program Maps Virtual Rat Brain In 3D The prototype BrainNavigator lets scientists travel through the rat brain — in three dimensions — and link the digital maps to pictures of real brain tissue.
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New Program Maps Virtual Rat Brain In 3D

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New Program Maps Virtual Rat Brain In 3D

New Program Maps Virtual Rat Brain In 3D

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This is All Things Considered from NPR News. I'm Melissa Block.


And I'm Robert Siegel. A rat's brain is about the size of a marble, but researchers often get lost inside that tiny universe. That slows down their experiments - experiments that could help find treatments for brain diseases such as Alzheimer's and Parkinson's. NPR's Jon Hamilton reports, though, help is on the way.

JON HAMILTON: Scientists do a lot of experiments with rat brains because you can't mess around with human brains. So you'd think these folks would be pretty good at navigating inside a rat's skull. There were lots of brain researchers in town this week at the annual meeting of the Society for Neuroscience. I asked several of them a question. Is it possible to get lost in there?

Dr. JEAN-MARC FELLOUS (Associate Professor of Psychology & Research Scientist, ARL Division of Neural Systems, Memory and Aging, University of Arizona): It's very possible.

HAMILTON: Jean-Marc Fellous is from the University of Arizona. He said pretty much what the other researchers said.

Dr. FELLOUS: All the structures are very compact, very mixed together. They are the same - basically the same structures as humans, but in ten times less of a volume, or even more.

HAMILTON: Brain researchers face two navigational challenges. The first is placing probes or electrodes into a precise spot in the brain. There are maps, massive printed atlases, but they only show the brain in two dimensions. Fellous says the hard part is figuring out the third dimension, how deep to go. He guides his electrodes by listening to the electrical noises produced by neurons. He says it's a bit like using sonar to steer a submarine.

Dr. FELLOUS: When you go down from the surface of the brain to where the target is, you go through all kinds of other structures that all sound the same as the target.

HAMILTON: Which means you simply have to guess. The other big challenge for brain researchers is studying slices of rat brains under the microscope. Again, it's really hard to know what you're looking at. So Elsevier, a scientific publishing company, decided there was an opportunity here. It teamed up with the Allen Institute for Brain Science to create a brain atlas for the digital age. It's called the BrainNavigator. Johannes Menzel is in charge of the project. He showed me a prototype on his laptop. It starts with a ghostly image of the entire rat brain.

Dr. JOHANNES MENZEL (Publisher for Science and Technology, Elsevier): So this is just kind of browsing, finding where you want to start. So let's say...

HAMILTON: Menzel zooms through the brain to one particular structure, the hippocampus. With a click, he pulls up a highly magnified photograph of cells from that part of the brain. They look a lot like brain cells from other parts of the brain.

Dr. MENZEL: This is like looking at an aerial photograph of Arizona and not knowing where you are.

HAMILTON: And this is where the BrainNavigator can help.

Mr. MENZEL: Just click on it, and it will tell you, OK, this is Casa Grande.

HAMILTON: OK, that helps you figure out where you are. But how about getting there? The BrainNavigator offers a sort of GPS system. Menzel switches to a three-dimensional model of the hippocampus. It appears green inside a gray outline of the entire brain.

Dr. MENZEL: And then you can do, you know, what you do with 3D structures. You can rotate it. There's a little compass-type mark that allows - that tells you where you are in this environment.

HAMILTON: I wonder whether the program could help Jean-Marc Fellous, the scientist who said he got lost. I bring him to the BrainNavigator exhibit, and Menzel gives him a demonstration. So, what do you think?

Dr. FELLOUS: I'll buy it.

(Soundbite of laughter)

Dr. MENZEL: There you go, I wanted to hear that.

HAMILTON: But Fellous says threading electrodes is still going to require some guesswork.

Mr. FELLOUS: Well, that is always going to be a problem. I mean, atlases are abstractions of the brain, and from rat to rat things are a little bit different. But this will reduce the amount of errors, probably.

HAMILTON: And rescue a few lost scientists. Elsevier has already started work on a navigator for the human brain. Jon Hamilton, NPR News.

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