Metadata-Version: 2.4
Name: bombcell
Version: 0.41
Summary: Python port of bombcell. Automated quality control, curation and neuron classification of spike-sorted electrophysiology data.
Author: Sam Dodgson, Maxime Beau
Author-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

# BombCell

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

## Installation

```bash
pip install bombcell
```

For full functionality including optional features:

```bash
pip install bombcell[all]
```

## Quick Start

```python
import bombcell as bc

# Set up parameters
param = bc.get_default_parameters("path/to/kilosort_output")

# Run quality metrics
quality_metrics, param, unit_type, unit_type_string = bc.run_bombcell(
    "path/to/kilosort_output", 
    "path/to/bombcell_output", 
    param
)

# Launch GUI for manual inspection
gui = bc.unit_quality_gui(
    ks_dir="path/to/kilosort_output",
    quality_metrics=quality_metrics,
    unit_types=unit_type,
    param=param,
    save_path="path/to/bombcell_output"
)
```

## 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.

## License

GPL-3.0 License
