Potter, Bassi, & Runyan 2024 - Part 1 of 2
Description
In this study, we virally labeled somatostatin-expressing neurons with the fluorophore mCherry, parvalbumin-expressing neurons with the fluorophore tdTomato, and all neurons with the calcium indicator GCaMP6f. This was done in the posterior parietal cortex (PPC) of SOM-Flp x PV-Cre mice. We imaged the spike-related calcium activity of these neurons, and used their excitation spectra to identify them post hoc. The data posted includes 4 of 7 mice, and dated imaging sessions for each mouse.
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Steps to reproduce
See https://www.biorxiv.org/content/10.1101/2023.01.09.523298v2 for full description. Within each session three .mat files are provided: 'activity', 'clustering', and 'D_onsets'. 'activity.mat' includes the running velocity of the mouse (in 3 axes: pitch, roll, and yaw) and the simultaneously imaged activity of all neurons (dff - normalized fluorescence of n neurons x t imaging frames; deconv - deconvolved estimated spike rates for n neurons x t imaging frames; F - raw fluorescence of n neurons x t imaging frames; metaData - relevant metadata from imaging session). 'clustering.mat' includes information related to the k-means clustering applied to assign the cell type identities (cell ids) of the neurons, which were identified following the methods described in the manuscript, using the code at https://github.com/RunyanLab/Clustering-Pipeline. SOM neurons have cellid ==1, PV neurons have cellid ==2, and 'unlabeled' neurons that were only labeled with GCaMP have cellid==0, and these indices can be applied to 'combined_info.F, dff, or decent to access their activity traces. Also included is the silhouette score for each neuron & wavelength combination, to assess clustering performance. 'D_onsets.mat' is a structure with one entry per detected inhibitory interneuron population activity event.Fields report the cell type identity of the event (SOM, PV) and the activity of the imaged neurons aligned to the onset time of the event. Other fields (onset, event, peak) report the frame identities of the events in the full imaging time series (see activity.mat).
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Funding
Pew Charitable Trusts
Pew Biomedical Scholars Program
National Institute of Mental Health
DP2MH122404
National Institute of Neurological Disorders and Stroke
R01NS121913
Esther A. and Joseph Klingenstein Fund
Searle Scholars Program
National Institute of Mental Health
3DP2MH122404-01S1