Accessing putative cell type in neuropixel dataset

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?

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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.

Thanks for the information Josh. Do you know approximately when that module will be released? I’ll probably just wait and write my analysis without cell-type information for now.

Hopefully in January or February…and if we don’t have a completed module by then, we’ll at least create a tutorial with the example code required for this analysis.

Hey Josh, any updates on this code? Thanks again.

This is on my to-do list for next week. I’ll send an update then!

Hi! I created an example notebook that demonstrates how to identify Cre+ neurons in our Neuropixels recordings:

It hasn’t been merged into the main docs page yet, but that should happen soon.

In any case, please take a look and let me know if anything is unclear!

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Thanks so much Josh! I hope you and the team are doing well!

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