Written by Notbohm Research Group, University of Wisconsin-Madison. https://notbohm.ep.wisc.edu
This document gives information about representative code to plot results of traction force microscopy, monolayer stress microscopy, and computed cell velocities. Scripts to compute tractions, stresses, and velocities are in the repository Cell-Traction-Stress ( https://github.com/jknotbohm/Cell-Traction-Stress ).
IMPORTANT: These scripts give examples of how to plot outputs. You will have to modify them or write your own scripts to analyze the quantity of interest in your experiment.
plot_cell_vel.m: Plots cell velocities using both a color map showing magnitudes and quivers showing relative magnitudes and directions.
compute_cell_trajectories.m: Interpolates image correlation data to stitch together approximate trajectories traveled by different cells.
plot_displ_tractions.m: Plots substrate displacements computed by image correlation and tractions computed by traction force microscopy.
plot_stress.m: Plots principal stresses, mean of prinipal stresses, max in-plane shear stress, and prinicpal orientations computed by monolayer stress microscopy.
Comments in all files state required inputs.
make_fig.m: Subfunction used to make figure window with desired size and settings.
map_cold-hot.dat: Text file containing colormap of cold colors -> black -> hot colors. Use Colormaps like this one for data having positive and negative numbers, setting black to 0.
map_cold-hot-wrap.dat: Text file containing colormap of colors that wrap from blue to black to red to white. Useful for plotting angles.
Some scripts require m files available from the Matlab file repository. See comments of each script for more information.
This software was tested on Matlab version R2019b, though other recent versions should work. Note that versions earlier than 2014b will not work, because graphics functions changed significantly in that version.