DOI: 10.5061/dryad.vmcvdnd0m
title: Brainstem control of vocalization and its coordination with respiration

description: Phonation critically depends on precise controls of laryngeal muscles in
 coordination with ongoing respiration. However, the neural circuit
 mechanisms governing these processes remain unclear. Here, we identified
 excitatory vocalization-specific laryngeal premotor neurons located in the
 retroambiguus nucleus (RAmVOC) in adult mice as both necessary and
 sufficient for driving vocal-cord closure and eliciting mouse ultrasonic
 vocalizations (USVs). The duration of RAmVOC-activation can determine the
 lengths of both USV syllables and concurrent expiration periods, with the
 impact of RAmVOC-activation depending on respiration phases.
 RAmVOC-neurons receive inhibition from the preBötzinger complex, and
 inspiration-needs override RAmVOC-mediated-vocal-cord closure. Ablating
 inhibitory synapses in RAmVOC-neurons compromised this inspiration gating
 of laryngeal adduction, resulting in discoordination of vocalization with
 respiration. Our study revealed the hitherto unknown circuits for vocal
 production and vocal-respiratory coordination.
description: # Brainstem control of vocalization and its coordination with respiration
 [https://doi.org/10.5061/dryad.vmcvdnd0m](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](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