Compatibility with phy

If you wish to manually curate your units with phy, bombcell can assist you by displaying quality metrics for each unit in phy's Cluster view. This is automatic, and does not require any modifications to phy.

To enable this, simply set param.saveAsTSV to 1. Bombcell will then save a tsv file per quality metric in the param.ephysKilosortPath path. This needs to be the same path as where all your kilosort output paths are saved. Note that this just loads pre-calculated metrics, so any units you split or merge will not have quality metrics displayed.

All the columns in the Cluster view can get crowded. We recommend removing some of phy and bombcell's default ones if you don't use them. To do this, you can take a look at the phyPlugins here - in particular the plugin removeColumnsPlugin.

To use bombcell after having split/merged clusters, take a look at the phy_compatibility branch. We are working on integrating it into the main branch.