Mon, 01 Jan 0001 00:00:00 +0000

I like working at the intersection of computer science and biomedical research.

I’m a research scientist on the FlyEM Team at the Howard Hughes Medical Institute’s Janelia Research Campus. We use cutting-edge electron microscopy to image fruit fly brains at nanometer resolution. After extracting likely neurons from the 25+ Teravoxel image volumes (through our collaboration with Google Research), our team of bio experts proofread the results. The result is a connectome, a map of the neural circuits. Our work has been profiled in the NY Times, the Simons Foundation, and other media.

I’ve been designing the data systems that allow us to flexibly capture versions of our proofreading and all the data we generate while reconstructing the connectome. Here’s a post that gives an overview of our data management strategy. We’ve opened a few of our datasets to the public on our Clio platform, which is backed by a serverless data service built on Google Cloud Run with some proxying to Janelia-based DVID servers.

I have three research goals in the near future:

Allow “chained” datastores where local changes are applied on top of large-scale (terabytes to petabyte) published data, and allowing git-like pull requests from other researchers.
Develop interesting ways to visualize the richness of our nanometer-resolution, segmented image volumes.
Investigate ways to use deep learning for compressed representation and accelerated proofreading of our data.

I’m an organizer of the Janelia Scientific Visualization Interest Group. Feel free to watch our invited talks at YouTube.

Authors | Bill Katz