Compatibility with phy

Bombcell has an optional compatibility with phy. If param.saveAsTSV is true, bombcell saves 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. When using phy, there will then be a column per quality metric in the ClusterView view. Note that this just loads pre-calculated metrics, so any units you split or merge will not have quality metrics displayed.

All the columns can get crowded. We recommend removing some of phy's default ones (e.g. KSlabel, ..). To do this, you can take a look at the phyPlugins here - in particular the plugin removeUselessColumnsPlugin. To use them:

Copy the plugins to your .phy/plugins/ folder (usually located at C:/Users/You/.phy/plugins/ for windows users, or ~/.phy for Linux users), and modify your phy_config file located in your .phy folder to add the following lines:

c = get_config()
c.Plugins.dirs = ['C:/Users/Julie/.phy/plugins/']
c.TemplateGUI.plugins = ['MyPlugin', 'removeUselessColumnsPlugin', 'clusterViewStylingPlugin']

In the plugin removeUselessColumnsPlugin you can define which column names you want to keep. For bombcell, you could for instance choose these columns:

controller.supervisor.columns = ['id', 'depth', 'fr', 'Amplitude', 'n_spikes', 'fractionRPV', 'percentSpikesMissing', 
                                             '%_spikes_missing', 'presence_ratio', 'max_drift', 'n_peaks', 'n_troughs', 
                                             'is_somatic','waveform_dur', 'spatial_decay_slope','wv_baseline_flatness',
                                             'SNR','frac_RPVs']