I am using Cell Profiler to count foci within cells in my images. I was wondering if I could also use Cell Profiler to discern the total area of the foci per image. I see that line 430 in the Image output file is called “Area (Foci, AreaShape).” Would this be the correct line to look at?
Yes, you are correct. That column will give the area of the Foci.
In addition, as we (including Anne) discussed personally but others may find useful, if you want to get the total area of foci in the entire image, the CellProfiler measurements that are exported in the Image.xls file will report the mean (that is, the average) area of foci in each image in the column you mention, “Area (Foci, AreaShape)". So it is a simple matter to multiply the number of foci times this mean area to get the total area of foci in the entire image.