DOI: 10.5281/zenodo.3814726
title: A VTA to basal amygdala dopamine projection contributes to signal salient somatosensory events during fear learning

description: This dataset represents the raw data that gave rise to the study by Tang et al., J. Neuroscience 2020 (DOI: 10.1523/JNEUROSCI.1796-19.2020). 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), and essential details on the specific data formats. raw data is organized in the datasets related to the Figs. 1H-L, 1M, 3B-C, 2, 4G-H, 5D-E, 5H-I of the paper (Tang et al., 2020); the metadata for each individual dataset, which lists individual data filenames from the respective dataset, are stored in separate “.csv” files, one per each dataset. Field separator: comma; individual metadata files for each dataset are described in the master metadata file “metadata_master.csv”. Field separator: comma; widefield fluorescent images of single coronal slices containing VTA (Fig. 1H-M) 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). Image stacks covering the injection area of CTB into BA are provided in single multi-plane TIFF files, one per animal. Unless specified in the metadata file, 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 files; AP positions refer to Franklin KB, Paxinos G (2016) The mouse brain in stereotaxic coordinates, Ed 4. San Diego: Elsevier/Academic; confocal fluorescent image stacks acquired from single coronal slices containing VTA (Fig. 3B-C) are provided in the original format “.lsm” written by a confocal software Zen (Carl Zeiss). Besides the original Zen software, this format can be readily imported into FIJI/ImageJ using built-in converters “LSM…” or “Bio-Formats”. All the metadata containing imaging parameters is embedded in this format and can be accessed from FIJI/ImageJ after importing the stack. Attribution of fluorescent probes to the color channels is given in the corresponding “.csv” metadata file; AP positions refer to Franklin and Paxinos (2016); video recordings of animal behavior are provided as “.wmv” files, unmodified from the original version created by the acquisition software VideoFreeze (MedAssociates Inc). Video stream parameters: wmv3 codec, color space yuv420p, 320x240 pixels, bitrate 300 kb/s, 30 fps; timing patterns of the sound (CS) and of the footshock (US) applications during each day of fear conditioning protocol are provided in the respective “.csv” files: “day1_CS_timing.csv”, “day2_CS_timing.csv”, “day2_US_timing.csv”, “day3_CS_timing.csv”. The timestamps in these files are expressed in seconds relative to the start of the VideoFreeze video recordings (see p. 4 above). These patterns are in common for all the video recordings done on respective training days in every data subset (Figs. 2, 4-5); extracellular optrode recording data (Fig. 2) were converted from the original proprietary “.mcd” format of the MC_Rack software (Multichannel Systems) into the open HDF5 format “.h5” using the Multi Channel DataManager software (Multichannel Systems). We provide both the continuous recording data acquired during behavior sessions on days 1-3 of the fear learning protocol, as well as recordings of light-evoked spiking acquired during the opto-tagging sessions on each experimental day. In the latter, each of 8-10 consequently recorded data files contains individual triggered sweeps (from -50 to +50 ms), each centered around a single laser pulse (t=0 ms); the raw unfiltered electrode data is stored as a 32-bit integer matrix 16xN (16 - number of electrodes, N - number of sampling points @ 40 kHz) in the container Data-&gt;Recording_0-&gt;AnalogStream-&gt;Stream_1-&gt;ChannelData of the HDF5 files. Conversion factor to the units of volts for the raw values is 1.25e-6. Correspondence of the rows of the data matrix to the electrodes “E1”-“E16” is indexed by the string array Data-&gt;Recording_0-&gt;AnalogStream-&gt;Stream_1-&gt;I_Label. The electrodes were physically arranged into four tetrodes in following groups: E1-E4, E5-E8, E9-E12, E13-E16; timestamps for the continuous recordings, or for each of the triggered sweeps in case of opto-tagging, are stored in the 2D floating point array Data-&gt;Recording_0-&gt;AnalogStream-&gt;Stream_1-&gt;ChannelDataTimeStamps; the timestamp values are in microseconds; the timing of CS and US stimuli produced by the VideoFreeze software (see p. 5 above) was sampled as input digital triggers by the amplifier for extracellular recordings for precise synchronization between the optrode- and video recordings. These signals are stored as single bit changes in the 32-bits integer N-samples array Data-&gt;Recording_0-&gt;AnalogStream-&gt;Stream_0-&gt;ChannelData of the corresponding HDF5 files.
description: This work was supported by Swiss National Science Foundation (SNSF) 31003A_176332/1 to Ralf Schneggenburger, SNSF National Competence Center for Research Synapsy, Synaptic Bases of Mental Disease Project #28 to Ralf Schneggenburger, and EMBO Fellowship ALTF 224-2015 to Michael Kintscher. Image acquisition was done at the Bioimaging and Optics Platform (BIOP) of École Polytechnique Fédérale de Lausanne (EPFL).