DOI: 10.5061/dryad.6djh9w108
title: ZETA benchmarking neuropixels data

description: Pre-processed matlab data files containing clustered spiking data of cells
 recorded across various visually-responsive regions with Neuropixels. The
 data can be accessed using the files provided at
 https://github.com/JorritMontijn/ZETA_analysis_repository.
 Neurophysiological studies depend on a reliable quantification of whether
 and when a neuron responds to stimulation. Current methods to determine
 responsiveness require arbitrary parameter choices, such as binning size.
 These choices can change the results, which invites bad statistical
 practice and reduces the replicability. Moreover, many methods only detect
 mean-rate modulated cells. New recording techniques that yield
 increasingly large numbers of cells would benefit from a test for
 cell-inclusion that requires no manual curation. Here, we present the
 parameter-free ZETA-test, which outperforms t-tests and ANOVAs by
 including more cells at a similar false-positive rate. We show that our
 procedure works across brain regions and recording techniques, including
 calcium imaging and Neuropixels data. Furthermore, in illustration of the
 method, we show in mouse visual cortex that 1) visuomotor-mismatch and
 spatial location are encoded by different neuronal subpopulations; and 2)
 optogenetic stimulation of VIP cells leads to early inhibition and
 subsequent disinhibition.
description: Data were recorded using SpikeGLX and pre-processed with
 Kilosort2. More information can be found here:
 https://www.biorxiv.org/content/10.1101/2020.09.24.311118v1.
description: Each data file contains a separate recording. The data structure
 is as follows: <b>sAP</b> – main structure
 containing the following fields:  
 <b>sAP.sMetaNI</b> – National Instruments and
 SpikeGLX metadata
 <b>sAP.vecChannelDepth</b> – Depth in microns per
 channel <b>sAP.vecBregmaCoords</b> –
 Coordinates of Bregma <b>sAP.cellStim</b> –
 Stimulus data (see below)
 <b>sAP.sCluster</b> – Single cluster data (see
 below)  
 <b>sAP.cellStim</b> – cell array, with each cell
 corresponding to a separate stimulus presentation block. Each block i
 contains two variables:  
 <b>cellStim{i}.sParamsSGL</b> – SpikeGLX
 metadata <b>cellStim{i}.structEP</b> –
 Stimulus data. The most important variables are:
 <b>structEP.strFile</b> – Source file
 identifier; “RunDriftingGratings” or
 “RunNaturalMovie”
 <b>structEP.vecStimOnTime</b> –
 Timestamps for stimulus onsets
 <b>structEP.vecStimOffTime</b> –
 Timestamps for stimulus offsets
 <b>structEP.Orientation</b> – Stimulus
 orientation (if drifting grating)
   In case of a natural movie, the
 movie loops every 20 seconds and is presented at
 60Hz.  
 <b>sAP.sCluster</b> – structure array, with each
 structure corresponding to a single cluster. Each structure j contains
 several variables, of which the following are most important:
   <b>.Area</b> – Brain area in
 which this cluster was found
 <b>.SpikeTimes</b> – Spikes synchronized to structEP
 timestamps <b>.Contamination</b> <i>–
 </i>Spike contamination to determine whether to include this cluster
 in further analyses <b>.KilosortGood</b> –
 Boolean indicating whether Kilosort determined this cluster to be of
 sufficient quality   Default
 inclusion criteria were: (KilosortGood == 1) OR (Contamination &lt;
 0.1).