I’ve been using Cell Profiler for a while and I’m using a pipeline that measure object intensity. The problem I’m having is that I can check cells average intensity in Fiji and find that there are great discrepancies between what I measure in Fiji and Cell profiler. I understand that cell profiler normalizes the images intensities but I can easily find value in the thousands for mean intensity in Fiji and only get mean fluorescence less than 1 in cell profiler ( and in the hundreds for integrated intensity) even after rescaling to full intensity range. I’ve tried rescaling image intensity with no avail. Is there something I’m missing?
P.S. I’m using version 2.2