Visualizing projections with new connectivity map from Allen Brain Institute

July 15, 2012

Last June, the Allen Institute for Brain Science released a map of mouse connectivity. They took a classic technique, injection of anterogradely transported viruses, and used it on a large scale. They made injections in multiple brain areas, scanned all the images with a 2-photon and put them on their website. This is an incredibly useful tool: all of the injections were done by the same group in the same way, making it feasible to compare the projections from one area with projections from another area. I am primarily interested in the posterior parietal cortex, so, with the help of my Cold Spring Harbor colleague Petr Znamenskiy, I did the following: I downloaded all the parietal injection images from the Allen Institute’s website, changed the color so that only the projections were visible, and then used tools on ImageJ to interpolate between slices and make the images into a 3-d movie. You can see it in this post: the white lines are projections coming from posterior parietal cortex and going to many regions of the brain.

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