i would like to make a suggestion for a background intensity subtraction algorithm:
(i) identify objects (e.g. cells)
(ii) compute the median or lower quartile intensity of all pixels intensities OUTSIDE any objects (it is even safer to dilate the objects before doing this in order to ensure that one really only takes background pixels).
(iii) subtract this value from the image
in fact, even combining a number of different modules i could not realize this within the current version of CellProfiler2.0, because i did not figure out how to subtract a measurement value from an image.
i think it would be great to put steps (ii) and (iii) into one of the Illumination correction modules.
my point here is that the proposed algorithm is very simple and, in my experience, applies to a lot of commonly encountered images!
Would be super awesome if you guys could implement this!!