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README.md

Vibrometry data used in Figure 3 and Extended Data Figure 11

Data

Fig.3a - Extended Data Fig.11a 200930/Acq12h03_doubleSineShifted_phaseNamp1000line2line_zoom0315_4096x1024_unidir

Fig.3d - Extended Data Fig.11b 200814/Acq15h19_doubleSineShifted_phaseNamp1000line2line_zoom025_4096x887_unidir

Fig.3e - Extended Data Fig.11c

200930/Acq14h21_doubleSineShifted_phaseNamp1000line2line_zoom0397_4096x1024_unidir

Data structure

  1. Veith_et_al_2024/200930/Acq12h03_doubleSineShifted_phaseNamp1000line2line_zoom0315_4096x1024_unidir/...

    • acqParam.mat stores acquisition parameters

    • acqWphaseShift0001.mat stores vibrometry data

  2. Veith_et_al_2024/200930_processing/Acq12h03_doubleSineShifted_phaseNamp1000line2line_zoom0315_4096x1024_unidir/...

    • cmdPIV_rolling_Pass_32_4_step1stPass16_Clahe500_minInt0_maxInt04.mat stores extracted velocity data

    • ./figures stores images as in Fig.3 and Extended Data Fig.11

  3. For 200930_processing/Acq14h21[...]/masks: stores masks defining regions of interest to compute displacement of tissue and lapillus in Fig.3e, and related data

Code

Two Matlab scripts are used to generate these figures:

  1. motionDetect_Veith2024.m

    • loads the data,

    • reshapes the data set to reconstruct the movie of mechanical tissue deformation in response to acoustic stimulation,

    • sets particle image velocimetry (PIV) parameters including image pre-processing,

    • computes local displacement from one frame to the next along x and y directions, using the PIVlab Matlab library (GitHub - Shrediquette/PIVlab: Particle Image Velocimetry for Matlab, official repository, tested with version 2.31 - to use 3.0, a few new parameters must be defined, see code).

  2. phaseMapping_Veith2024.m

    • loads the motion data (output from previous code)

    • computes the first Fourier component, and convert to proper unit (velocities in um/s and displacement amplitude in um)

    • plots the results

    • compute mean values of displacement amplitude and phase within region of interests

datacite.yml
Title The mechanism for directional hearing in fish
Authors Veith,Johannes;Einstein Center for Neurosciences, Charité – Universitätsmedizin Berlin, Germany - Institute for Biology, Humboldt University, Berlin, Germany
Chaigne,Thomas;Aix Marseille University, CNRS, Centrale Marseille, Institut Fresnel, Marseille, France - Einstein Center for Neurosciences, Charité – Universitätsmedizin Berlin, Germany
Svanidze,Ana;Einstein Center for Neurosciences, Charité – Universitätsmedizin Berlin, Germany
Dressler,Lena;Einstein Center for Neurosciences, Charité – Universitätsmedizin Berlin, Germany
Hoffmann,Maximilian;Einstein Center for Neurosciences, Charité – Universitätsmedizin Berlin, Germany
Gerhardt,Ben;Einstein Center for Neurosciences, Charité – Universitätsmedizin Berlin, Germany
Judkewitz,Benjamin;Einstein Center for Neurosciences, Charité – Universitätsmedizin Berlin, Germany
Description We provide trajectory data of directional acoustically evoked startles in adult Danionella cerebrum, Micro CT raw data and segmentation of the Danionella cerebrum hearing apparatus, and laser scanning confocal reflectance vibrometry data of inner ear structures.
License Creative Commons CC0 1.0 Public Domain Dedication (https://creativecommons.org/publicdomain/zero/1.0/)
References The mechanism for directional hearing in fish [doi:10.xxx/zzzz] (IsSupplementTo)
The mechanism for directional hearing in fish [url:https://github.com/danionella/veith_et_al_2024] (IsReferencedBy)
Funding
Keywords Neuroscience
Danionella cerebrum
Directional Hearing
Startle Behavior
Inner Ear Anatomy
Schuijf Model
Neuroethology
Particle Motion
Vibrometry
Fish Hearing
Resource Type Dataset