William T. Katz

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.


  • Systems for branched versioning of data
  • 3D visualization, particularly for image volumes
  • Deep Learning


  • PhD, Biomedical Engineering

    University of Virginia

  • MD (Medical Scientist Training Program)

    University of Virginia

  • MS coursework, Computer Science

    Stanford University

  • BS, Biological Sciences

    Stanford University

  • International Baccalaureate

    St. Mary's International, Tokyo, Japan



Principal Software Engineer

HHMI Janelia Research Campus

Jan 2010 – Present Virginia
Developing software tools for visualization, analysis, and storage of high-resolution neuroimaging. Chief areas of interest: multi-scale visualization of sparse volumes; distributed, versioned image-oriented datastores; machine learning. Architect and main developer of DVID.

Entrepreneur / Consultant


Nov 2007 – Dec 2009
Founder of the SF Bay Area Google App Engine Developer group with over 400 members. One of two Google-designated “Gurus” of the python App Engine API. Consultant for local web ventures and Stanford NIH Center for Physics-Based Simulation of Biological Structure.

Senior Scientist

Stanford University

Mar 2006 – Nov 2007 California
Development of open source, patient-specific cardiovascular simulation programs as part of Simbios, the NIH Center for Biocomputation at Stanford. Provided Ruby on Rails expertise during the development of Simbiome, an online directory of resources for physics-based simulation of biomedical structures.

Senior Scientist

Varian Medical Systems

Oct 1995 – Oct 2001 Charlottesville, Virginia
One of the founding software engineers of Multimedia Medical Systems, which was acquired by Varian Medical in June 1999. Designed, developed, and supported a software system for real-time radiotherapy planning in an intra-operative setting. Conducted site visits to gather feedback from practitioners. By October 2001, the VariSeed system was employed at over 600 hospitals and clinics. Created algorithms for the optimal positioning of radioisotope sources in the treatment of prostate cancer. Developed prototypes for dose-optimized source placement using both simulated annealing and a proprietary method for direct evaluation of user-defined rules. Led a side project as sole programmer and designer, creating the Digital Humans CD-ROM (Byte Magazine’s CD-ROM of the month), a 3d exploration of the Visible Human Project data using Flash and 3d glasses.

Assistant Professor of Research in Neurosurgery

University of Virginia

May 1995 – Oct 1995 Charlottesville, Virginia
Directed the Neurosurgical Visualization Lab, which explored the use of 3D image analysis and human-computer interfaces for neurosurgical planning. Recruited by mentor to start a company with other lab members. After departure to commercial sector, continued to serve as a resource for lab efforts.

Published Fiction

Plastic Soul of a Note

Science fiction story that won the 2004 Grand Prize (Golden Pen Award)