Metadata-Version: 2.1
Name: fafbseg
Version: 3.0.6
Summary: Tools to work with the FlyWire and Google segmentations of the FAFB EM dataset
Home-page: https://fafbseg-py.readthedocs.io
Author: Philipp Schlegel
Author-email: pms70@cam.ac.uk
License: GNU GPL V3
Project-URL: Documentation, https://fafbseg-py.readthedocs.io
Project-URL: Source, https://github.com/navis-org/fafbseg-py
Project-URL: Changelog, https://github.com/navis-org/fafbseg-py/releases
Keywords: FAFB neuron segmentation FlyWire Google synapses connectome fly brain navis cave
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: caveclient >=5.4.2
Requires-Dist: cloud-volume >=8.20
Requires-Dist: diskcache
Requires-Dist: fastremap
Requires-Dist: inquirer >=2.6
Requires-Dist: ipython
Requires-Dist: navis >=0.6.1
Requires-Dist: numpy
Requires-Dist: pandas >=1.1.0
Requires-Dist: pyarrow >=3.0.0
Requires-Dist: pyperclip
Requires-Dist: python-catmaid >=2.0.2
Requires-Dist: requests
Requires-Dist: requests-futures
Requires-Dist: skeletor >=1.0.0
Requires-Dist: trimesh
Requires-Dist: tqdm
Requires-Dist: fuzzywuzzy

[![Documentation Status](https://readthedocs.org/projects/fafbseg-py/badge/?version=latest)](https://fafbseg-py.readthedocs.io/en/latest/?badge=latest) [![Tests](https://github.com/navis-org/fafbseg-py/actions/workflows/test-package.yml/badge.svg)](https://github.com/navis-org/fafbseg-py/actions/workflows/test-package.yml) [![DOI](https://zenodo.org/badge/197735091.svg)](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

