FAFBseg tools#

fafbseg is a set of Python tools to work with various kinds of segmentation data in the “full adult fly brain” (FAFB) dataset:

  1. FlyWire by the Seung/Murthy labs in Princeton

  2. Google’s auto-segmentation

  3. Buhmann et al. (2021) synapse predictions

  4. Eckstein et al. (2023) neurotransmitter predictions

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


Here are just some of the things you can do with fafbseg:

  • map locations or supervoxels to segmentation IDs

  • load neuron meshes and skeletons

  • generate high quality neuron meshes and skeletons from scratch

  • query connectivity and annotations

  • parse and generate FlyWire neuroglancer URLs

  • transform neurons from FAFB/FlyWire space to other brains spaces (e.g. hemibrain)

For a full list of features please see the API documentation.


fafbseg is built on top of navis, a library for general neuroanatomical analyses and visualisation. Objects (i.e. skeletons, meshes, etc.) can be directly plugged into navis’ functions. This in turn enables you among other things to:

  • extract morphometrics (length, Strahler order, etc.)

  • split neurons into axon and dendrites

  • run morphological clustering/matching using NBLAST

  • plot neurons in 2D and 3D

  • import neurons into Blender 3D e.g. for making high quality renderings

  • export to various file formats

See the navis tutorials for examples.

How to cite#

If you use fafbseg for your publication, please cite the two FlyWire papers and the original FAFB dataset publication.

  1. Whole-brain annotation and multi-connectome cell typing quantifies circuit stereotypy in Drosophila” Schlegel et al., bioRxiv (2023); https://doi.org/10.1101/2023.06.27.546055

  2. Neuronal wiring diagram of an adult brain” Dorkenwald et al., bioRxiv (2023); https://doi.org/10.1101/2023.06.27.546656

  3. A Complete Electron Microscopy Volume of the Brain of Adult Drosophila melanogaster” Zheng et al., Cell (2018); https://doi.org/10.1016/j.cell.2018.06.019


Open an issue in fafbseg’s Github repository.