yousafkhan55 / bombcell

Automated manual curation and cell classification of spike-sorted electrophysiology data. Fine-tuned for kilosorted neuropixels data.

💣 BombCell: find bombshell cells! 💣

Bombcell is a powerful toolbox designed to evaluate the quality of recorded units and extract essential electrophysiological properties. It is specifically tailored for units recorded with Neuropixel probes (3A, 1.0, and 2.0) using SpikeGLX or OpenEphys and spike-sorted with Kilosort.

📖 Bombcell wiki

Documentation and guides to using and troubleshooting bombcell can be found on the dedicated wiki

🏁 Quick start guide

Overview

Bombcell extracts relevant quality metrics to categorize units into three categories: single somatic units, multi-units, noise units and non-somatic units.

The script bc_qualityMetrics_pipeline provides an example workflow to get started.

Installation

To begin using Bombcell,

• clone the repository and the dependancies.
• add bombcell's and the dependancies' folders to MATLAB's path
• in addition, if you want to compute ephys properties, change your working directory to bombcell\ephysProperties\helpers in matlab and run mex -O CCGHeart.c to able to compute fast ACGs.

Dependancies

• https://github.com/kwikteam/npy-matlab (to load .npy data in)
• If you have z-lib compressed ephys data, compressed with mtscomp, you will additionally need the zmat toolbox. More information about compressing ephys data here.

🤗 Support and citing

Please note that Bombcell is currently unpublished. If you find Bombcell useful in your work, we kindly request that you acknowledge its contribution by citing xxx (citation reference coming soon).

📬 Contact us

If you run into any issues or if you have any suggestions, please raise a github issue or alternatively email us.