DOI: 10.5281/zenodo.15552692
title: Segregated auditory cortico-striatal pathways regulate distinct components of sensory-driven learning

description: This repository stores the raw data that gave rise to the study by Palchaudhuri et al. for the duration of the Postdoc.Mobility fellowship funded by the Swiss National Science Foundation. Please refer to the final scientific report regarding details of experimental design and methodology of data acquisition and analysis.

The data is indexed and described in the provided metadata (.csv) files which refer to individual .ZIP archives containing the raw and accessory data files.

This repository begins with data for Figures 1 and 2, and continues in squence to the follwoing repositories accessible with separate dois: 10.5281/zenodo.15552685, 10.5281/zenodo.15552733, 10.5281/zenodo.15545271, 10.5281/zenodo.15552675,  10.5281/zenodo.15552745, 10.5281/zenodo.15552772, 10.5281/zenodo.15553142, 10.5281/zenodo.15553129 and 10.5281/zenodo.15559234. The extension repositories contain no metadata files but .ZIP archives of the raw data beyond the space quota of the master repository. 

General structure of the repository:

·         The data is organized in 5 subsets, each referring to one figure of the study summary. Each subset contains multiple mice, grouped by the same experiment name that is suffixed in the zipped filename, and is referred to in the metedata.csv file.

Data formats of the raw data:

·        Figure 1: For anatomical characterization of cortico-striatal connectivity, widefield fluorescent images of coronal mouse brain sections were uploaded either as original unmodified datasets in a proprietary .vsi format of Olympus slide scanning microscope or were registered to the digital Allen Brain Atlas, binned, and uploaded as composite image stacks in TIFF format. Both “.vsi” and TIFF formats are readable by Bioformats plugin under open-source free software packages FIJI (https://fiji.sc/) and/or QuPath (https://qupath.github.io/). Imaging metadata such as microscope settings and/or pixel resolution is embedded inside the individual .vsi or TIFF files.

·       Figure 2: For  in-vivo fiber photometry recordings the raw data isolated from simultaneous recordings from 4 behavior boxes and 2 channels in each mouse, are provided as .mat files generated by the custom MATLAB scripts to isolate single channel Ca2+ traces from each fiber for each day of the auditory discrimination task training. We also provide the .csv files of timestamps of events (sounds, licks, video timestamps) needed for synchronization of the Ca2+ imaging data with the behavioral videos. 

·         Figure 3 and 4: Due to excessive data volume (~0.75 Tb), the raw data (videos) for in-vivo 2-photon Ca2+ imaging are not added to the repository. The data will be made available upon request. Here we provide output files generated by the Suite2p package from analysis of the miniature microscope Ca2+ imaging data, for 3 phases of the auditory discrimination task phases: Go-naive, NoGo-naive and expert. These include the fluorescence traces for each accepted and rejected cell, and outlines of the ROIs for each detected neuron. We also provide the .csv files of timestamps of events (Go tone, No go tone, licks) needed for synchronization of the Ca2+ imaging data with the behavioral videos.  

·         Figure 2, 3, 4 and 5: Video recordings of animal behavior during the auditory discrimination task and the open field test are provided as unmodified “.avi” files created by the Bonsai acquisition software. We also provide separate .csv files with the timestamps of events (sounds, licks, video timestamps) linked to the video timing.