[](https://fafbseg-py.readthedocs.io/en/latest/?badge=latest) [](https://github.com/navis-org/fafbseg-py/actions/workflows/test-package.yml) [](https://zenodo.org/badge/latestdoi/197735091)
<img src="https://github.com/navis-org/fafbseg-py/blob/master/docs/_static/logo2.png?raw=true" height="60">
Tools to work with the [FlyWire](https://flywire.ai/) and [Google](https://fafb-ffn1.storage.googleapis.com/landing.html) segmentations of the FAFB EM dataset. Fully interoperable with [navis](https://github.com/navis-org/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](https://fafbseg-py.readthedocs.io/en/latest/).
## Quickstart
Install latest stable version
```bash
pip3 install fafbseg -U
```
Install from Github
```bash
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](https://codex.flywire.ai/about_flywire) on Codex.
Raw data
{
"_id": null,
"home_page": "https://fafbseg-py.readthedocs.io",
"name": "fafbseg",
"maintainer": null,
"docs_url": null,
"requires_python": ">=3.8",
"maintainer_email": null,
"keywords": "FAFB neuron segmentation FlyWire Google synapses connectome fly brain navis cave",
"author": "Philipp Schlegel",
"author_email": "pms70@cam.ac.uk",
"download_url": "https://files.pythonhosted.org/packages/c8/f9/5f02d0f97dba8fd4cbe6024cd9a9d29aaa1bcd053f41e857b10e792742b6/fafbseg-3.0.9.tar.gz",
"platform": null,
"description": "[](https://fafbseg-py.readthedocs.io/en/latest/?badge=latest) [](https://github.com/navis-org/fafbseg-py/actions/workflows/test-package.yml) [](https://zenodo.org/badge/latestdoi/197735091)\n\n<img src=\"https://github.com/navis-org/fafbseg-py/blob/master/docs/_static/logo2.png?raw=true\" height=\"60\">\n\nTools to work with the [FlyWire](https://flywire.ai/) and [Google](https://fafb-ffn1.storage.googleapis.com/landing.html) segmentations of the FAFB EM dataset. Fully interoperable with [navis](https://github.com/navis-org/navis).\n\n## Features\nHere are just some of the things you can do with ``fafbseg``:\n\n* map locations or supervoxels to segmentation IDs\n* load neuron meshes and skeletons\n* generate high quality neuron meshes and skeletons from scratch\n* query connectivity and annotations\n* parse and generate FlyWire neuroglancer URLs\n* transform neurons from FAFB/FlyWire space to other brains spaces (e.g. hemibrain)\n\n## Documentation\nFAFBseg is on [readthedocs](https://fafbseg-py.readthedocs.io/en/latest/).\n\n## Quickstart\nInstall latest stable version\n\n```bash\npip3 install fafbseg -U\n```\n\nInstall from Github\n```bash\npip3 install git+https://github.com/flyconnectome/fafbseg-py.git\n```\n\n## How to cite\nIf you use `fafbseg` for your publication, please cite the two FlyWire papers:\n\n1. \"_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\n2. \"_Neuronal wiring diagram of an adult brain_\" Dorkenwald _et al._, bioRxiv (2023); doi: https://doi.org/10.1101/2023.06.27.546656\n\nDepending on what data you used (e.g. neurotransmitter predictions) you might need to cite additional publications. Please see the [Citation Guidelines](https://codex.flywire.ai/about_flywire) on Codex.\n",
"bugtrack_url": null,
"license": "GNU GPL V3",
"summary": "Tools to work with the FlyWire and Google segmentations of the FAFB EM dataset",
"version": "3.0.9",
"project_urls": {
"Changelog": "https://github.com/navis-org/fafbseg-py/releases",
"Documentation": "https://fafbseg-py.readthedocs.io",
"Homepage": "https://fafbseg-py.readthedocs.io",
"Source": "https://github.com/navis-org/fafbseg-py"
},
"split_keywords": [
"fafb",
"neuron",
"segmentation",
"flywire",
"google",
"synapses",
"connectome",
"fly",
"brain",
"navis",
"cave"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "3c196f14495defa8a9566aa9cf8ac7d4eb2acb280f80fb61f95889e8ac3d5190",
"md5": "04dbfc2788e00bf754c552b61015268b",
"sha256": "33150cdb7374628945332a330b859ae8d502b3493836089c24d1b268a85e075d"
},
"downloads": -1,
"filename": "fafbseg-3.0.9-py3-none-any.whl",
"has_sig": false,
"md5_digest": "04dbfc2788e00bf754c552b61015268b",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.8",
"size": 9268250,
"upload_time": "2024-07-20T07:57:41",
"upload_time_iso_8601": "2024-07-20T07:57:41.699271Z",
"url": "https://files.pythonhosted.org/packages/3c/19/6f14495defa8a9566aa9cf8ac7d4eb2acb280f80fb61f95889e8ac3d5190/fafbseg-3.0.9-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "c8f95f02d0f97dba8fd4cbe6024cd9a9d29aaa1bcd053f41e857b10e792742b6",
"md5": "92fb39c6577db1dd9dfd05d3b2a4ef13",
"sha256": "869c92399b473fb872ee618dd97104640afa9f5ba9ead4b984a1f3f3059ed045"
},
"downloads": -1,
"filename": "fafbseg-3.0.9.tar.gz",
"has_sig": false,
"md5_digest": "92fb39c6577db1dd9dfd05d3b2a4ef13",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.8",
"size": 9240325,
"upload_time": "2024-07-20T07:57:44",
"upload_time_iso_8601": "2024-07-20T07:57:44.691853Z",
"url": "https://files.pythonhosted.org/packages/c8/f9/5f02d0f97dba8fd4cbe6024cd9a9d29aaa1bcd053f41e857b10e792742b6/fafbseg-3.0.9.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2024-07-20 07:57:44",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "navis-org",
"github_project": "fafbseg-py",
"travis_ci": false,
"coveralls": false,
"github_actions": true,
"requirements": [],
"lcname": "fafbseg"
}
JSON
