FAFBseg tools

FAFBseg is a set of Python tools to work with various kinds of segmentation data in the FAFB dataset:

  1. Google’s auto-segmentation

  2. FlyWire by the Seung/Murthy labs

  3. Buhmann et al. 2020 synapse predictions

A lot of this library depends on services hosted by Eric Perlman and Davi Bock. So if you happen to bump into them, buy them a beer or a whiskey.

Check out the introduction for a brief overview of FAFB data and the tutorials for code examples.


If you are coming from fafbseg prior to version 1.0.0: We have made major changes to better organize the diverse landscape of FAFB segmentation data. Function names and their locations have changed! See the API for an overview.


  • map locations to Google segmentation / FlyWire root IDs

  • transform neurons between FAFB and FlyWire space

  • merge neurons from Google autoseg into v14 main CATMAID instance

  • load FlyWire neurons and skeletonize them

  • generate connectivity tables using the Buhmann et al. synapse predictions

  • parse and generate FlyWire URLs