bombcell 0.4

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

BombCell

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

Installation

pip install bombcell

For full functionality including optional features:

pip install bombcell[all]

Quick Start

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