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Mapping behavior to neural anatomy using machine vision and thermogenetic - Kristin Branson

February 18, 2016 - 12:00pm to 1:00pm
Clark Center S360

Stanford Neurosciences Institute Seminar Series Presents

Mapping behavior to neural anatomy using machine vision and thermogenetics  Kristin Branson, PhD Janelia Group Leader Computational Biology, Janelia HHMI

Host: Jin Billy Li


To understand the relationship between neural anatomy and behavior, the ultimate output of the nervous system, we performed a high-throughput, thermogenetic screen of 2,200 transgenic lines of Drosophila from the Janelia GAL4 collection. Each GAL4 line drives expression in a different, sparse subset of neurons in the fly nervous system. Using UAS dTrpa1, we selectively activated these sparse subsets of neurons, and measured the behavioral effects. For this screen, we developed a complete, high-throughput, automated system for measuring the locomotion and social behavior of flies with both breadth and depth. We recorded 20,000 videos of groups of flies freely behaving in an open-field walking arena, totaling about 400 TB of raw data. From the video, we tracked the flies' body positions and wings using our tracking software, Ctrax. We used our machine learning-based behavior classification system, JAABA (The Janelia Automatic Animal Behavior Annotator), to create 15 behavior classifiers (e.g. walking, grooming, chasing) that input the trajectories created by Ctrax and output predictions, for each frame and each fly, of the flies' behaviors (totaling ~175 billion annotations of fly behavior). For each line of flies, we compute a set of ~800 behavior statistics, such as the frac+on of +me spent chasing, or the average speed while walking, summarizing the behavioral effects of activating the targeted neurons in a concise yet interpretable manner. Concurrent with our screen, the Janelia Fly Light project has imaged the expression padern of each GAL4 line, producing image stacks indicating which neurons are likely being activated in each line. By mining our behavior data set in conjunction with the Fly Light imagery data, we have identified novel sets of neurons potentially involved in jumping, female chasing, and wing flicking behavior. 

Recent Papers:

[1] JAABA: Interactive machine learning for automatic annotation of animal behavior Mayank Kabra, Alice A. Robie, Marta Rivera-Alba, Steven Branson, Kristin Branson Nature Methods. 2012 Jun 16;10(1):64-7. doi:10.1038/nmeth.2281

[2] Cortex commands the performance of skilled movement Jian-Zhong Guo, Austin R. Graves, Wendy W. Guo, Jihong Zheng, Allen Lee, Juan Rodríquez-González, Nuo Li, John J. Macklin, James W. Phillips, Brett D. Mensh, Kristin Branson, Adam W. Hantman eLife. 2015 Dec 2;4:1-18. doi:10.7554/eLife.10774

Curriculum Vitae

A conversation with Kristin Branson and the Stanford group NeuWrite West can be streamed or downloaded: Branson Conversation

Lab Website

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Stanford Neurosciences Institute
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