DOI: 10.5281/zenodo.4311847
title: Stimulation of medial amygdala GABA neurons with kinetically different channelrhodopsins yields opposite behavioral outcomes

description: This dataset represents the raw data that gave rise to the study by Baleisyte et al., Cell Reports 2022 (DOI: 10.1016/j.celrep.2022.110850), previously published as a preprint at bioRxiv (DOI: 10.1101/2021.06.30.450543). 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. <strong>General repository structure:</strong> the raw data is organized in 11 datasets related to the Figures 1, S1, 2, S2, 3A-H, 3I-K, 3L-N, S3A-I, S3J-P, 4A;C-G;H_top;I-J;S4, 4B;C-G;H_bottom;I-J;S4; the metadata listing individual data filenames from the individual dataset are stored in separate “.csv” files, one per dataset. Field separator: comma; the custom script for the reconstruction of the optic fiber placement is described in a separate metadata file “script_metadata.csv”. Field separator: comma; all individual metadata files are summarized in a master metadata file “metadata_master.csv”. Field separator: comma. the data files related to Figures 2, S2, S3A-I are continued in a separate linked repository accessible by the following doi: 10.5281/zenodo.6489354 <strong>Description of the data formats:</strong> video recordings of resident-intruder test experiments (Figures 1, 3, S1) are provided as unmodified “.mpg” files created by the acquisition software EthoVision (Noldus Information Technology). The files were, however, renamed for convenience. Video stream parameters: MPEG-4 (DIVX) codec, color space yuv420p, 1280x512 pixels, 30 fps. Along with each video file, there is an associated text file (“.txt”) containing the metadata of video recording and the timestamps of hardware state changes. In these files, unmodified after creation by the EthoVision software, the status of hardware TTL inputs was logged whenever a change of state of these inputs was detected. Typically, “input 2” was sampling the gating signal from the Master-8 pulse generator, with the "high" signal level indicating the application of train of light pulses. This hardware state, signaling the presence of the light train, is noted in the individual metadata files; widefield fluorescent images of single coronal sections containing the MeApd (Figures 2, S2) were converted from the proprietary format of Olympus slide scanning microscope into composite TIFF format, readable by FIJI/ImageJ (https://fiji.sc/ or https://imagej.net/Fiji/Downloads). The information on pixel resolution and inter-section distance is embedded in the individual image files as TIFF metadata. Attribution of fluorescent probes to the color channels is given in the corresponding metadata files. confocal fluorescent image stacks acquired from single coronal sections containing MeApd (Figure S3) are provided in composite TIFF format after stitching the tiles (originally stored as “lsm” format; Carl Zeiss) using a stitching plugin (Preibisch et al., Bioinformatics 2009) in FIJI. The information on pixel resolution is embedded inside the individual image files as TIFF metadata. Attribution of fluorescent probes to the color channels is given in the corresponding metadata file. For each stack, a region of interest (ROI) highlighting the borders of the MeApd is provided as a separate file in a “.roi“ format (FIJI). patch clamp recordings (Figures 4, S4) are provided as “.dat” files, unmodified from the original version created by the acquisition software PatchMaster (HEKA Elektronik, Germany). Besides by the original PatchMaster software, these files can be imported using one of the following methods: I) via 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); II) via Python script by Luke Campagnola (https://github.com/campagnola/heka_reader); III) via Matlab script HEKA PatchMaster Importer by Christian Keine (https://github.com/ChristianKeine/HEKA_Patchmaster_Importer).
description: This work was supported by Swiss National Science Foundation (SNSF) National Competence Center for Research Synapsy, Synaptic Bases of Mental Disease Project #28 to Ralf Schneggenburger. Image acquisition was done at the Bioimaging and Optics Platform (BIOP) of École Polytechnique Fédérale de Lausanne (EPFL).