https://doi.org/10.5061/dryad.vmcvdnd0m

Description of the data and file structure

Brainstem control of vocalization and its coordination with respiration

https://doi.org/10.5061/dryad.vmcvdnd0m

DATA used in this study is shared in this depository.

Description of the data and file structure

Each jupyter notebook and .jl file has description regarding data and file structure

USV stands for Ultrasonic Vocalization

Folders

Codes

Julia programming codes for data acquisition and analysis used in this study.

: for acquisition

Nidaq_read.jl, plot_functions.jl 

: for analysis

respiration.jl, usvanalysis.jl, usvdetection.jl, USVpreprocess.jl, usv_temp.jl

Fig. 1

This folder is empty (nothing shared)

Fig. 2

Fig. 2C

• Fig. 2C - RAmVOC - preLMN - AllenCCF.ipynb : jupyter notebook for creating data here
• NS-RV1, NS-RV2, NS-RV3.txt: .csv files include name (brain region names), acronym, AP (anterior-posterior)_location, DV (dorsal-ventral)_location, ML (middle-lateral)_location, avIndex (arbitrary number) for 3d Coordinates, units in (mm)

Fig. 2E

• Fig_2_E_RAmVOC-HCR.xlsx: the number of counts for in-situ data (the total numbers of cells (e.g., 24 cells) used in the analysis)
• RAmVOC HCR.ipynb: jupyter notebook file for creating data here

Fig. 2G

• Fig_2_G_GFP_TeLC.h5: .h5 file includes 2d matrix of floats number
• Fig. 2G - representative spectrogram - control - TeLC:  jupyter notebook file for creating data here

Fig. 2H

• Analyze_vocalizations_KAT_noStops, ImportWAV_Katie_filter25to110kHz.m: MATLAB codes for analysis here.
• Control_after, Control_before, TeLC_after, TeLC_before.mat : for processed data from MATLAB
• Fig. 2H-I.ipynb:  jupyter notebook file for creating data here
• Raw_audio (folder): containing raw .wav files for each group (GFP vs TeLC)

Fig. 2KL

• Fig. 2KL - Squeak - headfix - tailpinch.ipynb: jupyter notebook file for creating data here
• DATA (folder): .jld files containing 1d audio signals

Fig. 3

• Fig. 3GI: jupyter notebook file for creating data here

Fig. 3GI

• DATA (folder) 
  1. female: 
     • .jld files includes bound information (rectangle; x scale, y scale)
     • .h5 files for raw data including 1d audio signal
  2. Rs:
     • .jld files includes bound information (rectangle; x scale, y scale)
  3. utf: 
     • .jld files includes bound information (rectangle; x scale, y scale)

Fig. 3H

• USVs: a folder of images of ultrasonic vocalization syllables

Fig. 4

• Fig. 4 DE, Fig. 4 IK.ipynb: jupyter notebook files for creating data here

Fig. 4DE

• PostIns (folder):
  • .h5 files containing raw data
• USV (folder)
  • .h5 files containing raw data of breathing and audio signals
  • .jld files containing bounding boxes for USV detection

Fig. 4GH

• Fig4GH.jl: .jl file for creating data here

DATA (folder)

• .h5 files containing raw data of breathing and audio signals
• .jld files containing bounding boxes for USV detection

Fig. 4IK

• group (folder)
  • Rs (folder): 
  • .h5 files containing raw data of breathing and audio signals
  • Rs_utfs (folder):
  • jld files containing bounding boxes for USV detection
• single (folder)
  • .h5 files containing raw data of breathing and audio signals
  • jld files containing bounding boxes for USV detection

Fig. 5

• Fig. 5 - GFE3 experiments.ipynb: jupyter notebook files for creating data here

Fig. 5 DATA

• GFE3 (folder): each folder (1-5) contains:
  • .h5 files containing raw data of breathing and audio signals
  • jld files containing bounding boxes for USV detection
• GFP (folder): each folder (1-4) contains:
  • .h5 files containing raw data of breathing and audio signals
  • jld files containing bounding boxes for USV detection

annotation_volume_10um_by_index.npy: numpy files containing Allen Atlas data frames

Files and variables

File: DATA_deposition.zip

Description: details are available in the README.md

File: README.md

Description: details for DATA_deposition.zip

Access information

Other publicly accessible locations of the data:

• n/a

Data was derived from the following sources:

• n/a