This readme.txt file was generated on 2020-12-18 by Valerie Michael
The files included in this dataset include the data and code required to reproduce the analyses included in Michael et al., “Circuit and synaptic organization of forebrain-to-midbrain pathways that promote and suppress vocalization” (doi: https://doi.org/10.1101/2019.12.12.874354).

GENERAL INFORMATION
1. Title of Dataset: Data and scripts from: Circuit and synaptic organization of forebrain-to-midbrain pathways that promote and suppress vocalization
2. Author Information
	A. First Author Contact Information
		Name: Valerie Michael
		Institution: Duke University
		OCRID ID:  0000-0003-3288-9409
		Email: Valerie.michael@duke.edu

	B. Co-corresponding Author Contact Information
		Name: Richard Mooney
		Institution: Duke University
		OCRID ID:  0000-0002-3308-1367
		Email: mooney@neuro.duke.edu

	C. Co-corresponding Author Contact Information
		Name: Katherine Tschida
		Institution: Cornell University
		OCRID ID: 0000-0002-8171-1722
		Email: kat227@cornell.edu

3. Date of data collection (single date, range, approximate date): 2018-2020 

4. Geographic location of data collection: Durham, NC, United States of America

SHARING/ACCESS INFORMATION

1. Licenses/restrictions placed on the data: Data are available under a CC0 waiver.

2. Links to publications that cite or use the data: Michael et al., “Circuit and synaptic organization of forebrain-to-midbrain pathways that promote and suppress vocalization” (doi: https://doi.org/10.1101/2019.12.12.874354).

DATA & FILE OVERVIEW

1. Folder overview: 
This dataset has four folders: (1) “Audio and Video” contains the audio files (and video files where applicable) of the mice included in the analyses shown in Figures 2, 3, 4, and supplemental figures associated with Figure 2 of Michael et al.; (2) “Confocal Images” contains confocal microscope image files of brain sections included in the in situ hybridization studies shown in Figures 1D, Figure 2C, and Figure 4C of Michael et al.; (3) “Slice Physiology” contains whole-cell electrophysiological recording files from the neurons included in the analyses of Figures 5, 6, and supplemental figures associated with Figure 6 of Michael et al.; and (4) “Matlab Codes” contains the codes used to analyze the audio, video, and slice physiology data in Michael et al.

METHODOLOGICAL INFORMATION

1. Description of methods used for collection/generation of data: 
See preprint at doi: https://doi.org/10.1101/2019.12.12.874354 for methodological description.

2. Methods for processing the data: 
See preprint at doi: https://doi.org/10.1101/2019.12.12.874354 for data processing description.

3. Instrument- or software-specific information needed to interpret the data: 
Audio files: Spike2 7.10 (CED) to open the native files, and we also include the Matlab code necessary to convert .smr format to .mat
Video files: Windows Media Player (Microsoft) or Quicktime (Apple)
Confocal microscope image files: ZEN (Zeiss) and/or ImageJ (NIH)
Slice physiology files: Igor Pro 8 (Wavemetrics)
Matlab codes: Matlab R2017a (Mathworks), including Image Processing toolbox

DATA-SPECIFIC INFORMATION FOR: all files contained within each main folder
Data files within the “Audio and Video”, “Confocal Images”, and “Slice Physiology” folders are named as follows:
FigureID_MouseID_Condition
FigureID refers to the figure from Michael et al. to which the file pertains
MouseID is the identifier information for each animal in our study
Condition refers to the viral strategy used to label neurons and/or additional relevant experimental information.
Each file within the “Matlab Codes” folder includes documentation in comments describing its function.