Workshop on the dynamic brain highlights tools from the Allen Institute that make it easy to visualize neural connectivity

September 4, 2014

I have just returned from a week-long Workshop on the Dynamic Brain, led by Adrienne Fairhall (University of Washington) and Christof Koch (Allen Institute for Brain Science). The course brought in students from around the country including graduate programs at the University of Washington, UCSD and the University of Michigan. Lectures brought students up to speed on emerging approaches for understanding brain function, especially those using tools developed by the Allen Institute. For my part, I gave 2 lectures and then took advantage of the opportunity to learn about the ins and outs of the tools from some of the local experts, most notably Lydia Ng who is my new hero.

I already had some experience with the Allen Brain Connectivity Atlas, but its new developments really blew me away. The atlas is based on systematic injections of AAV across cortical and subcortical structures. One feature I particularly liked is the ability to visualize injections not just based on the injection location, but based on a target location for which the user wants to know all the inputs (this is called a “spatial search”). I did such a search for the posterior parietal region. Because this approach allowed me to see all the areas into which injections led to parietal label, it is kind of equivalent to seeing a retrograde injection from the posterior parietal cortex. As the image below shows, there is clear label in visual areas (the blue dots at the posterior region of the gray brain, one of which is shown in more detail at the right). Injections to secondary motor and orbital areas (the green dots at the anterior region) likewise innervate the posterior parietal area. Being able to easily visualize many injections from many different vantage points gives a much clearer pictures of the overall connectivity, and the tools are really fun to play around with.


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