Syntax:

spotinthist(cellList)

spotinthist(cellList1,cellList2,...)

spotinthist(cellList,xarray)

spotinthist(cellList1,cellList2,xarray)

spotinthist(cellList1,normfactor)

spotinthist(cellList1,normfactor1,cellList2,normfactor2)

spotinthist(cellList1,cellList2,'overlap') 

[intlist] = spotinthist(cellList)

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

spotinthist(...'nooutput') 

This function plots a histogram of the intensities of all spots in every cell in a population. Note, the cells manually detected with spotfinderM will all have zero intensity.

• <cellList> - an array that contains cell 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 arrays, they will be plotted together for comparison.
• <xarray> - an 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 spots 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.
• <intlist>, <intlist1>, <intlist2> - arrays containing the intensity of every spot to save and plot separately.
• <nooutput> - blocks standard output (type of data processed, mean, and standard deviation).