DOI: 10.5281/zenodo.998797
title: Quantitative modelling of nutrient-limited growth of bacterial colonies in microfluidic cultivation

description: Data for "Quantitative modelling of nutrient-limited growth of bacterial colonies in microfluidic cultivation"

 

GrowthChannelExperiments contains the data-folders of the following growth channel experiments:<br>
***********************************************************************************************

Name            Feeding Concentration [in units of 0.195mM PCA]<br>
nd004_series1    0.5<br>
nd004_series2    0.5<br>
nd004_series3    0.5<br>
nd004_series4    2.0<br>
nd004_series5    2.0<br>
nd004_series6    2.0<br>
nd004_series7    3.0<br>
nd004_series8    3.0<br>
nd112_series2    0.25<br>
nd112_series3    0.25<br>
nd112_series7    3.0<br>
nd112_series8    3.0

Every folder contains:<br>
-    a tif-file with captured image series<br>
-    a PIV*-folder with four PIV-files for every frame pair. The four files belong to intermediate results of the multistep PIV. The final PIV-result is given in the file step2*.dat.nmt.<br>
        The PIV result will be stored in a plain text file. Each line in this file correspond to each PIV vector and comprised of 16 columns:<br>
        x     y     ux1     uy1     mag1     ang1     p1    ux2     uy2     mag2     ang2     p2     ux0     uy0     mag0     flag<br>
        -- (x,y) is the position of the vector (center of the interrogation window).<br>
        -- ux1, uy1 are the x and y component of the vector (displacement) obtained from the 1st correlation peak.<br>
        -- mag1 is the magnitude (norm) of the vector.<br>
        -- ang1, is the angle between the current vector and the vector interpolated from previous PIV iteration.<br>
        -- p1 is the correlation value of the 1st peak.<br>
        -- ux2,uy2,mag2,ang2,p2 are the values for the vector obtained from the 2nd correlation peak.<br>
        -- ux0, uy0, mag0 are the vector value at (x,y) interpolated from previous PIV iteration.<br>
        -- flag is a column used for mark whether this vector value is interpolated (marked as 999) or switched between 1st and 2nd peak (marked as 21), or invalid (-1). <br>
        According to the PIV-Fiji-plugin as provided by Qingzong Tseng, used also in : <br>
        Tseng, Q. et al. Spatial organization of the extracellular matrix regulates cell-cell junction positioning. Proc. Natl. Acad. Sci. 109, 1506–1511 (2012)<br>
-    two traj*.dat files, belonging to particle positions of the corresponding simulation with monod/teissier uptake. <br>
        Columns correspond to <br>
        1 : time | 2 : cellID | 3 : rx | 4 : ry | 5 : rz | 6: species | 7 : vx | 8 : vy | 9 : vz | 10 : fx | 11 : fy | 12 : fz | 13 : B(g) |<br>
        -- rx,ry,rz 3D coordinates of particle<br>
        -- species is either 0 (living cell) or 1 (wall-particle)<br>
        -- vx,vy,vz 3D velocity of particle<br>
        -- fx,fy,fz 3D force of particle<br>
        -- B(g) growth force constant dependent on local g-concentration<br>
        Note that due to the simulation being 2D, rx=constant and vx=0=fx.<br>
-    two g*.dat files, belonging to nutrient concentrations of the corresponding simulation with monod/teissier uptake. <br>
        Columns correspond to <br>
        1 : time | 2 : gridx | 3 : gridy | 4 : gridz | 5 : g-conc | 6: kcons | 7 : kprod | 8: Dlocal |<br>
        -- gridx,gridy,gridz coordinates of lattice side<br>
        -- kcons local nutrient consumption rate<br>
        -- kprod local nutrient production rate (always zero)<br>
        -- Dlocal local diffusion constant

 

GrowthChamberExperiments contains the the data-folders of the following growth chamber experiments:<br>
***************************************************************************************************

Name            Feeding Concentration [in units of 0.195mM PCA]<br>
nd143_xy009        1.0<br>
nd143_xy013        1.0<br>
nd143_xy025        1.0<br>
nd143_xy032        1.0<br>
nd143_xy059        1.0<br>
nd143_xy060        1.0<br>
nd143_xy061        1.0<br>
nd143_xy165        0.1<br>
nd143_xy184        0.1<br>
nd143_xy214        0.1

Every folder contains:<br>
-    a tif-file with captured image series<br>
-    five traj*.dat files, belonging to particle positions of the corresponding simulation with monod-uptake and five different ratios of the diffusion constants in- and outside the colony.<br>
-    five g*.dat files, belonging to nutrient concentrations of the corresponding simulation with monod-uptake and five different ratios of the diffusion constants in- and outside the colony.