Open Fly - data licence and citations
=====================================

The brain data in this folder is not Open Fly's code. It is derived from the
FlyWire connectome, and it has its own licence.

  connectome.bin (and its connectome.bin.part.* parts) who connects to whom, and how strongly
  brain.bin                                            neuron positions and classes, for the 3D view
  brain.json                                           sensory and descending neurons, as indices

LICENCE

  These files are licensed under Creative Commons Attribution-NonCommercial 4.0
  International (CC BY-NC 4.0): https://creativecommons.org/licenses/by-nc/4.0/

  Source: FlyWire public release 783, https://flywire.ai - Princeton University
  and collaborators. "FlyWire's public release data is made available under
  license CC BY-NC 4.0" (https://flywire.ai/guidelines).

  NON-COMMERCIAL. You may copy, share and adapt these files, with credit, for any
  purpose that is not commercial. Open Fly asks for no money and carries no ads
  for this reason.

CHANGES MADE (tools/export_web_brain.py and open_fly/live.py)

  - Connectivity_783.parquet and Completeness_783.csv, as prepared from FlyWire 783
    by Shiu et al. (signed synapse counts, where the sign comes from FlyWire's
    neurotransmitter predictions), were re-encoded as a binary compressed sparse
    row table (connectome.bin).
  - Positions and super classes from flyconnectome/flywire_annotations
    (Supplemental_file1_neuron_annotations.tsv) were re-encoded for the 3D view
    (brain.bin).
  - Descending neurons from the same annotations, and sensory neurons listed in
    Shiu et al.'s notebooks, were converted to indices. The descending neurons were
    dealt into the game's 39 action groups (brain.json).
  - For Cloudflare Pages, the large files are served gzip-compressed and split
    into parts.

CITATIONS

  Following FlyWire's citation table, for the parts of the data used here:

  Dorkenwald et al. (2024). Neuronal wiring diagram of an adult brain. Nature 634, 124-138.
    https://doi.org/10.1038/s41586-024-07558-y
  Schlegel et al. (2024). Whole-brain annotation and multi-connectome cell typing of Drosophila.
    Nature 634, 139-152. https://doi.org/10.1038/s41586-024-07686-5
  Zheng et al. (2018). A complete electron microscopy volume of the brain of adult
    Drosophila melanogaster. Cell 174, 730-743. https://doi.org/10.1016/j.cell.2018.06.019
  Buhmann et al. (2021). Automatic detection of synaptic partners in a whole-brain
    Drosophila electron microscopy data set. Nature Methods 18, 771-774.
    https://doi.org/10.1038/s41592-021-01183-7
  Heinrich et al. (2018). Synaptic cleft segmentation in non-isotropic volume electron
    microscopy of the complete Drosophila brain. MICCAI 2018, LNCS 11071, 317-325.
    https://doi.org/10.1007/978-3-030-00934-2_36
  Eckstein, Bates et al. (2024). Neurotransmitter classification from electron microscopy
    images at synaptic sites in Drosophila melanogaster. Cell 187, 2574-2594.
    https://doi.org/10.1016/j.cell.2024.03.016

  For the annotations (flywire_annotations v3):
  Matsliah, Yu et al. (2024). Neuronal parts list and wiring diagram for a visual system.
    Nature 634, 166-180. https://doi.org/10.1038/s41586-024-07981-1
  Berg et al. (2025). Sexual dimorphism in the complete connectome of the Drosophila male
    central nervous system. bioRxiv. https://doi.org/10.1101/2025.10.09.680999

  The brain model that runs on this data:
  Shiu et al. (2024). A Drosophila computational brain model reveals sensorimotor
    processing. Nature 634, 210-219. https://doi.org/10.1038/s41586-024-07763-9
    Code: https://github.com/philshiu/Drosophila_brain_model, MIT License,
    Copyright (c) 2023 Philip Shiu and Nico Spiller.