First of all, thanks for the great work on CellProfiler. Since our lab switched to using it, we haven’t looked back.
I would like to suggest that the calculation of a threshold include an option to take the log of the image prior to thresholding. I believe this would be particularly helpful in identifying objects.
My fluorescence images often have a background of relatively low variance and a foreground (often the nuclei) of considerably higher variance. Without a log transform, the threshold (regardless of the method used) tends to be too high, and dim nuclei are missed, even if they are clearly brighter than the true background. I have found the calculation of the threshold to be significantly improved by a log transform, which narrows the distribution of the foreground pixels. I would imagine this is a common scenario, and that the log transform would be useful to many people. Such an option would probably save people from having to fiddle around with the threshold correction factor.
At the moment, in my IdentifyPrimaryObjects module, I’ve resorted to setting a maximum value for the threshold based on manual inspection of the images, but this is the definition of a hack.