Accessing putative cell type in neuropixel dataset

dwyrick · December 11, 2019, 8:28pm

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?
Thanks!

joshs · December 12, 2019, 9:37pm

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.

dwyrick · December 13, 2019, 7:41pm

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.

joshs · December 13, 2019, 11:12pm

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.

dwyrick · February 6, 2020, 5:39am

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

joshs · February 6, 2020, 7:07pm

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

joshs · February 21, 2020, 6:45pm

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

github.com

jsiegle/AllenSDK/blob/opto-tutorial/doc_template/examples_root/examples/nb/ecephys_optotagging.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Optotagging Analysis\n",
    "\n",
    "## Tutorial overview\n",
    "\n",
    "This Jupyter notebook will demonstrate how to analyze responses to optotagging stimuli in Neuropixels Brain Observatory datasets. Optotagging makes it possible to link _in vivo_ spike trains to genetically defined cell classes. By expressing a light-gated ion channel (in this case, ChR2) in a Cre-dependent manner, we can activate Cre+ neurons with light pulses delivered to the cortical surface. Units that fire action potentials in response to these light pulses are likely to express the gene of interest.\n",
    "\n",
    "Of course, there are some shortcomings to this approach, most notably that the presence of light artifacts can create the appearance of false positives, and that false negatives (cells that are Cre+ but do not respond to light) are nearly impossible to avoid. We will explain how to deal with these caveats in order to incorporate the available cell type information into your analyses.\n",
    "\n",
    "This tutorial will cover the following topics:\n",
    "\n",
    "* <a href='#Finding-datasets-of-interest'>Finding datasets of interest</a>\n",
    "* <a href='#Types-of-optotagging-stimuli'>Types of optotagging stimuli</a>\n",
    "* <a href='#Aligning-spikes-to-light-pulses'>Aligning spikes to light pulses</a>\n",
    "* <a href='#Identifying-Cre+-units'>Identifying Cre+ units</a>\n",

This file has been truncated. show original

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!

EricKenjiLee · February 22, 2020, 5:31am

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

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Accessing putative cell type in neuropixel dataset

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