Thanks for the quick reply.
Indeed, that helps, but I have a followup question.
When I open my 'sample' images (they are .tif files) in matlab, my 'positive' intensities (i.e. intensities when the pixel belongs to a nucleus - which have been stained, as opposed to a background) are approximately 60,000.
Does this mean my microscope is illuminating uniformly, because the background values seem to be very small compared to positive values?
Or does cell profiler change the image intensity values to a different scale of its own?