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.
Documentation and guides to using and troubleshooting bombcell can be found on the dedicated wiki
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.
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\helpersin matlab and runmex -O CCGHeart.cto able to compute fast ACGs.
- 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.
Please note that Bombcell is currently unpublished.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).
If you run into any issues or if you have any suggestions, please raise a github issue or alternatively email us.