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. 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.

I have two research goals in the near future:

  • To create a github-like way of distributing published data and allowing pull requests of changes from other researchers.
  • To develop interesting ways to visualize the richness of our nanometer-resolution, segmented image volumes.

Most of my time, though, is spent supporting the daily operations of our reconstruction effort. This includes building out a serverless data service (on Google Cloud Run) for our Clio platform.


  • 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



Senior 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.

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.



Aug 2003 – Present
Writertopia hosts the eligibility pages for the Astounding Award for Best New Sci-Fi/Fantasy Writer, some college workshops, and a few tools. Through Writertopia development, I’ve explored (from most recent to ancient): Javascript single page apps (Vue/React, Google Firebase) and static sites, Go web development, Amazon Web Services, Google App Engine and its python APIs, Ruby on Rails, PHP and various shared web hosting providers.

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)