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:
- "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
- "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.
1 maintainer
Metadata
1 maintainer
Release files for fafbseg 3.2.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| fafbseg-3.2.2.tar.gz | 7.9 MB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| fafbseg-3.2.2-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 15.8 MB
Release files / fafbseg-3.2.2.tar.gz
| Download URL | fafbseg-3.2.2.tar.gz |
|---|---|
| Size | 7.9 MB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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No |
| Uploaded via |
twine/6.1.0 CPython/3.12.8
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Release files / fafbseg-3.2.2-py3-none-any.whl
| Download URL | fafbseg-3.2.2-py3-none-any.whl |
|---|---|
| Size | 7.9 MB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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No |
| Uploaded via |
twine/6.1.0 CPython/3.12.8
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