JohAn 90a1c8fe02 git-annex in jveith@Jlabs-MacBook-Pro.local | 6 months ago | |
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200814 | 6 months ago | |
200814_processing | 6 months ago | |
200930 | 6 months ago | |
200930_processing | 6 months ago | |
.DS_Store | 6 months ago | |
README.md | 6 months ago |
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
Veith_et_al_2024/200930/Acq12h03_doubleSineShifted_phaseNamp1000line2line_zoom0315_4096x1024_unidir/...
acqParam.mat stores acquisition parameters
acqWphaseShift0001.mat stores vibrometry data
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
For 200930_processing/Acq14h21[...]/masks: stores masks defining regions of interest to compute displacement of tissue and lapillus in Fig.3e, and related data
Two Matlab scripts are used to generate these figures:
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).
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 | |
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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 |