Codes and Data used in "Vortex reversal is a precursor of confined bacterial turbulence"

This repository contains the scripts and data used for our paper "Vortex reversal is a precursor of confined bacterial turbulence".

Contents:

Directories

20231016_WellD60-H30_Bacillus1085_10x_Exp1ms_50fps_3.zip: Experimental data and analysis results for smaller wells, with incoherent random motion (Supplementary Movie 9)

20231016_WellD60-H30_Bacillus1085_10x_Exp1ms_50fps_4.zip: Experimental data and analysis mainly presented in the paper.

NumericalCode.zip: Numerical code used for TTSHE simulations and the analysis of numerical data.

TTSHNumerical.zip: Numerically obtained velocity and vorticity field from TTSH simulation used for testing parameter regression.

SupplementalMovies.zip: Supplemental Movies SM1-SM19 are contained.

MATLAB code for experimental analysis

WellConfinementExpAnalysis.m(.mlx): Main analysis code, including 3D Gaussian filtering, Spin analysis, Fourier mode analysis etc.

ModeAntiphase_ExpData.m(.mlx): Code to make a plot of antiphase oscillation of modes n=1 & n=2 (Fig.1g)

TTSHParameterEstimation_NumericalData.m(.mlx): Regression analysis of numerical data

TTSHParameterEstimation_ExpData.m(.mlx): Regression analysis of experimental data

GenerateFig2_Subplot.m: Code to generate Fig.2

FigureSetSave.m: A custom-made function to generate figures, frequently used in the above codes.

Mathematica code for analytical theory

normal_form_eqs.nb: Code used for the weakly nonlinear analysis

Remarks

All the relevant data and codes are included. However, due to the size limit of the repository, we were unable to upload all the raw images (150GB x 2 data sets) and all the numerical outputs. Only the first 101 frames () out of 7500 frames of each experimental movie (20231016_WellD60-H30_Bacillus1085_10x_Exp1ms_50fps_3.zip and 20231016_WellD60-H30_Bacillus1085_10x_Exp1ms_50fps_4.zip) were included. The entire raw image sequences can be obtained from the authors upon request.