A striatal circuit balances learned fear in the presence and absence of sensory cues

This repository stores the raw data that gave rise to the study by Kintscher et al. 2023, published by eLife (eLife2023;12:e75703; DOI:https://doi.org/10.7554/eLife.75703), as well as a preprint at bioRxiv (doi: 10.1101/2021.12.09.471922). Please refer to the original publication regarding experimental design and methodological details of data acquisition and analysis. Below we supply information on the provided metadata files which, in turn, refer to individual raw data files.

General structure of the repository:

• the raw data is organized in 22 subsets defined by the figures or supplementary figures they contribute to. Each subset is documented by its own metadata file;
• the metadata files listing names of the individual data files were made in “.csv” format, one per data subset. Field separator: comma;
• all metadata are summarized in the main metadata file “metadata_master.csv”. Field separator: comma;
• the dataset expands into the second repository accessible at the following doi: 10.5281/zenodo.7522958

Description of the non-textual data formats:

• due to its excessive volume, the raw data for in-vivo microendoscopic Ca²⁺ recordings is not present in the current repository but will be made available upon request from the corresponding author;
• certain blocks of data, such as the output of CaImAn package, or slide scanner imaging projects, contained multiple smaller files and thus were compressed into encryption- and password-free .zip archives;
• video recordings of animal behavior during the fear conditioning protocol were provided as unmodified “.wmv” files created by the VideoFreeze acquisition software (Med Associates Inc). Video stream parameters: wmv3 codec, color space yuv420p, 320x240 pixels, 30 fps, bitrate 300 kb/s. Alternatively (Figure 4 – figure supplement 3), videos were stored by EthoVisionXT software as “.mpg” files with the following parameters: AVI container, mpeg4 codec, color space yuv420p, 1280x1024 pixels, 30 fps, bitrate 1206 kb/s;
• widefield fluorescent images of single coronal sections were either uploaded as original unmodified data in a proprietary .vsi format of Olympus slide scanning microscope (for Figure 1 – figure supplement 1, Figure 3 – figure supplement 1, Figure 7, Figure 7 – figure supplement 1), or were first binned and saved as a composite TIFF format at a resolution ~10.3 micrometers/pixel (for all the post-hoc images showing the virus expression and the fiber/lens placement). Both “.vsi” and TIFF formats are readable by Bioformats plugin working under open-source free software packages FIJI/ImageJ (https://fiji.sc/ , https://imagej.net/Fiji/Downloads), or QuPath (https://qupath.github.io/). Imaging metadata such as pixel resolution is embedded inside the individual .vsi or TIFF files. Correspondence between the fluorescent signals and image color channels is provided in the .csv metadata files;
• confocal fluorescent image stack underlying images in Figure 7B is provided in original proprietary “.lsm” format (Carl Zeiss). The imaging metadata is embedded in .lsm format, which can be read by the Bioformats plugin under FIJI/ImageJ or QuPath;
• data for patch clamp recordings (Figure 5 – figure supplement 2, Figure 8, Figure 8 – figure supplement 1, Figure 9) are provided as original .dat files from the acquisition software PatchMaster (HEKA Elektronik, Germany). These files can be imported using an Igor Pro extension “bpc_ReadHeka.xop” (for 32-bit Igor Pro versions 5.xx - 6.37) by Holger Taschenberger (https://www.wavemetrics.com/project/bpc_ReadHeka), or using a Python script by Luke Campagnola (https://github.com/campagnola/heka_reader), or using a Matlab script “HEKA PatchMaster Importer” by Christian Keine (https://github.com/ChristianKeine/HEKA_Patchmaster_Importer).