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Tools to work with the FlyWire and Google segmentations of the FAFB EM dataset

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Tools to work with the FlyWire and Google segmentations of the FAFB EM dataset. Fully interoperable with navis.


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)


FAFBseg is on readthedocs.


Install latest stable version

pip3 install fafbseg -U

Install from Github

pip3 install git+

How to cite

If you use fafbseg for your publication, please cite the two FlyWire papers:

  1. "Whole-brain annotation and multi-connectome cell typing quantifies circuit stereotypy in Drosophila" Schlegel et al., bioRxiv (2023); doi:
  2. "Neuronal wiring diagram of an adult brain" Dorkenwald et al., bioRxiv (2023); doi:

Depending on what data you used (e.g. neurotransmitter predictions) you might need to cite additional publications. Please see the Citation Guidelines on Codex.

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