Syntax:

intprofileall(cellList)

intprofileall(cellList,folder)

intprofileall(cellList,signal)

intprofileall(cellList,normalization)

intprofileall(cellList,pix2mu)

intprofileall(cellList,pix2mu,background)

intprofileall(cellList,[],background)

This function plots a intensity profile for a all cells in the list and will save them to the folder indicated as MATLAB figures. Note, the background has to be subtracted before detecting the signal in MicrobeTracker.

• <cellList> is an array that contains the meshes. You can drag and drop the file with the data into MATLAB workspace or open it using MATLAB Import Tool. The default name of the variable is cellList, but it can be renamed.

• <folder> - the name of the folder where the figures will be saved, e.g. 'c:\users\test\'. Default: current folder.

• <signal> - the signal channel in which the data is written, e.g. 'signal1', 'signal2', etc. Has to be in single quotes and start from the word 'signal'. Default: 'signal1'.

• <normalization> - the type of normalization of the plot, one of the words below:

•             'integrate' - full integral signal in each segment will be plotted

•             'area' (default) - the integral signal in each segment will be divided by the area of the segment.

•             'volume' - the total signal in the segment will be divided by the estimated volume of the segment assuming it's ideal cut cone shape (the height equal to the width).

• <pix2mu> - conversion factor from pixels to microns, the size of a pixel in microns.

• <background> - background level (usually obtained in a control experiment with a different strain not containing the signal), which will be plotted in addition to the signal profile.