intlist = meaninthist(cellList)

[intlist1,intlist2] = meaninthist(cellList1,cellList2)

This function plots a histogram of the mean intensity inside every cell in a population, i.e. total intensity divided by the area of the cell. 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.

  • <cellList1>, <cellList2> ˗ you can load two or more arrays, they will be plotted together for comparison.

  • <signal1>, <signal2> - the signal field which will be processed. Must be in single quotes and must start from the word 'signal'. The default is 'signal1'.

  • <xarray> ˗ array of x values for the histogram, which serve the centers of bins of the histogram (the boundaries will be in between, for example [1 2 3 4 5] to display all the cells with intensities less than 1.5 in the first bin, between 1.5 and 2.5 in the second, etc.).

  • <normfactor>, <normfactor1>, <normfactor2> ˗ conversion factors from image units. Use only if normalization is known.

  • 'overlap' ˗ indicate this if you wish the histograms to overlap, otherwise they will be displayed separately. The default colors for overlapping bars are red (first set), green (second set), and yellow (overlap).

  • <intlist>, <intlist1>, <intlist2> ˗ arrays containing the length of every cell to save and plot separately.

  • <nooutput> blocks standard text output (type of data processed, mean, and standard deviation; only a figure is displayed).

  • <nooutput> blocks figure output (only text output is produced).


>>% First load the data from two files and assign it to two different variables (here c1 and c2)
>>c1 = cellList;
>>c2 = cellList;
>>% Now plot a histogram

Mean intensity inside cells, image units
Processed 2 datasets
Set 1: mean 0.00011441, std 2.5648e-005
Set 1: mean 0.00010174, std 3.2709e-005

>>% Now plot an overlapping-style histogram also using a scaling factor 100

Mean intensity inside cells, normalized
Processed 2 datasets
Set 1: mean 0.011441, std 0.0025648
Set 1: mean 0.010174, std 0.0032709