Hello, I’m trying to utilize the neuropixel sessions that have inhibitory cell types identified via opto-tagging, but it doesn’t seem as if anything is written to take the responses during those optogenetic epochs and cluster cells into inhibitory / excitatory cell types. i.e. there’s no column within the unit DataFrame (cache.get_session_data(760693773).units) that indicates what celltype it is.
Do I need to take the start and end times from session.optogenetic_stimulation_epochs and look at the responses myself to identify the putative cell types? Or is there an easier way to do it?
Hi dwyrick, thanks for the question! For now, you’ll have to use the times in session.optogenetic_stimulation_epochs to align each unit’s spike times to the light pulses. We are working on a module that automatically identifies putative Cre+ units across the dataset, but it’s not ready yet.
A couple things to be aware of:
Some units are contaminated by light artifacts within ~1 ms of the pulse on/off times. We’ve gotten the most reliable results by using trials with 10 ms pulses and ignoring any spikes that occur at exactly 0 or 10 ms.
The prevalence of optotagged units will depend heavily on the mouse line. Parvalbumin+ units are the easiest to find, followed by somatostatin. Optotagged VIP+ units are very rare, with the best sessions having at most 5 units, and many having none.