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

Project description

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

Features

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)

Documentation

FAFBseg is on readthedocs.

Quickstart

Install latest stable version

pip3 install fafbseg -U

Install from Github

pip3 install git+https://github.com/flyconnectome/fafbseg-py.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: https://doi.org/10.1101/2023.06.27.546055
  2. "Neuronal wiring diagram of an adult brain" Dorkenwald et al., bioRxiv (2023); doi: https://doi.org/10.1101/2023.06.27.546656

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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