Suggestion for background subtraction

Dear Developers,

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!!

Cheers,
Tischi

[quote=“tischer”]i think it would be great to put steps (ii) and (iii) into one of the Illumination correction modules.
[/quote]

Agreed. There is an option called Median under the CorrectIlluminationCalculate rescaling methods that I’ve been playing with this week, but I don’t think it quite does what it ought, or it’s not terribly intuitive as to how it should be used. Indeed, it was added as an experimental feature, but none of us have really used it that much! I’ll see about adding this to our to-do list.

Thanks!
-Mark

Actually, I stand (somewhat) corrected. A new feature that was snuck in was the ability to threshold on the basis of a measurement. So you can use ApplyThreshold on the image and select “Measurement” as the method, enter the prior intensity measurement, and check the “Subtract threshold…” setting box. I believe this will have the same effect.
-Mark