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: *********************************************************************************************** Name Feeding Concentration [in units of 0.195mM PCA] nd004_series1 0.5 nd004_series2 0.5 nd004_series3 0.5 nd004_series4 2.0 nd004_series5 2.0 nd004_series6 2.0 nd004_series7 3.0 nd004_series8 3.0 nd112_series2 0.25 nd112_series3 0.25 nd112_series7 3.0 nd112_series8 3.0 Every folder contains: - a tif-file with captured image series - 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. 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: x y ux1 uy1 mag1 ang1 p1 ux2 uy2 mag2 ang2 p2 ux0 uy0 mag0 flag -- (x,y) is the position of the vector (center of the interrogation window). -- ux1, uy1 are the x and y component of the vector (displacement) obtained from the 1st correlation peak. -- mag1 is the magnitude (norm) of the vector. -- ang1, is the angle between the current vector and the vector interpolated from previous PIV iteration. -- p1 is the correlation value of the 1st peak. -- ux2,uy2,mag2,ang2,p2 are the values for the vector obtained from the 2nd correlation peak. -- ux0, uy0, mag0 are the vector value at (x,y) interpolated from previous PIV iteration. -- 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). According to the PIV-Fiji-plugin as provided by Qingzong Tseng, used also in : Tseng, Q. et al. Spatial organization of the extracellular matrix regulates cell-cell junction positioning. Proc. Natl. Acad. Sci. 109, 1506–1511 (2012) - two traj*.dat files, belonging to particle positions of the corresponding simulation with monod/teissier uptake. Columns correspond to 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) | -- rx,ry,rz 3D coordinates of particle -- species is either 0 (living cell) or 1 (wall-particle) -- vx,vy,vz 3D velocity of particle -- fx,fy,fz 3D force of particle -- B(g) growth force constant dependent on local g-concentration Note that due to the simulation being 2D, rx=constant and vx=0=fx. - two g*.dat files, belonging to nutrient concentrations of the corresponding simulation with monod/teissier uptake. Columns correspond to 1 : time | 2 : gridx | 3 : gridy | 4 : gridz | 5 : g-conc | 6: kcons | 7 : kprod | 8: Dlocal | -- gridx,gridy,gridz coordinates of lattice side -- kcons local nutrient consumption rate -- kprod local nutrient production rate (always zero) -- Dlocal local diffusion constant GrowthChamberExperiments contains the the data-folders of the following growth chamber experiments: *************************************************************************************************** Name Feeding Concentration [in units of 0.195mM PCA] nd143_xy009 1.0 nd143_xy013 1.0 nd143_xy025 1.0 nd143_xy032 1.0 nd143_xy059 1.0 nd143_xy060 1.0 nd143_xy061 1.0 nd143_xy165 0.1 nd143_xy184 0.1 nd143_xy214 0.1 Every folder contains: - a tif-file with captured image series - 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. - 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.