Veith_et_al_2024/vibrometry

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