Metadata-Version: 2.4
Name: bombcell
Version: 0.61
Summary: Python port of bombcell. Automated quality control, curation and neuron classification of spike-sorted electrophysiology data.
Author: Julie Fabre, Sam Dodgson, Maxime Beau
Maintainer-email: Julie Fabre <julie.m.fabre@gmail.com>
License: GPL-3.0
Project-URL: Homepage, https://github.com/Julie-Fabre/bombcell
Project-URL: Repository, https://github.com/Julie-Fabre/bombcell
Project-URL: Issues, https://github.com/Julie-Fabre/bombcell/issues
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.8
Description-Content-Type: text/markdown
Requires-Dist: numpy>=1.19.0
Requires-Dist: scipy>=1.7.0
Requires-Dist: matplotlib>=3.3.0
Requires-Dist: pandas>=1.3.0
Requires-Dist: ipywidgets>=7.6.0
Requires-Dist: joblib>=1.0.0
Requires-Dist: tqdm>=4.50.0
Requires-Dist: pyarrow>=5.0.0
Requires-Dist: numba>=0.58.1
Requires-Dist: upsetplot
Requires-Dist: mtscomp
Requires-Dist: cachecache

# Bombcell

Python port of BombCell. Automated quality control, curation and neuron classification of spike-sorted electrophysiology data.

## Installation

To install the latest stable version:
```bash
conda create -n bombcell python=3.11
conda activate bombcell
pip install uv
uv pip install bombcell # you could do `pip install .`, but uv is much quicker!
```
To install the dev version (with the latest updates): 
```bash
conda create -n bombcell python=3.11
conda activate bombcell
git clone https://github.com/Julie-Fabre/bombcell.git
cd bombcell/pyBombCell
pip install uv
uv pip install -e .
```

## Quick Start

See the [demo script](https://github.com/Julie-Fabre/bombcell/blob/main/py_bombcell/demos/BC_demo.ipynb) 

## Features

- Automated quality control for spike-sorted data
- Interactive GUI for manual curation
- Cell type classification (cortical and striatal neurons)
- Comprehensive quality metrics computation
- Parameter optimization tools

## Documentation

See the demo notebooks in the `Demos/` directory for detailed examples, and see the [wiki](https://github.com/Julie-Fabre/bombcell/wiki) for more information

## License

GPL-3.0 License
