Python port of bombcell. Automated quality control, curation and neuron classification of spike-sorted electrophysiology data.
Project description
Bombcell
Python port of BombCell. Automated quality control, curation and neuron classification of spike-sorted electrophysiology data.
Installation
To install the latest stable version:
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):
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
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 for more information
License
GPL-3.0 License
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