I’m using […] MeasureImageIntensity for the background
That’s fine in the theory, though I’d be very careful about precisely which measurement you’re choosing as your “background”, particularly about whether the objects will be masked out and how you can be sure you’re choosing a measurement that will be robust if some objects are missed, if there are more or fewer than expected, etc.
So I can subtract the background within the pipeline and still use the data for quantification?
You absolutely can quantify the data in processed images if you are careful to process them correctly. The first ~10 minutes of this video and this paper are good primers on some methods of illumination correction. That is routinely what we do in the lab, and I think is indeed a better strategy than doing it with math in the spreadsheet after-the-fact.
This was an error on my part, see the correction.
And how do I export my ImageAfterMath data? I can’t find it it in the ExportToSpreadsheet module.
ImageMath doesn’t make measurements, it creates an image. So you could theoretically subtract a value from an image using ImageMath and then measure in it with Measure(Object/Image)Intensity, but I’d suggest instead using CorrectIlluminationCalculate and CorrectIlluminationApply as in the paper I linked.