I have a question about how CellProfiler loads images and presents pixel intensities. I am using 16-bit images. When I open these images in ImageJ, pixel intensities range from 0-300. However, when I open the same image in CellProfiler, pixel intensities range between 0-003. It seems cellprofiler is rescaling the image by dividing each pixel intensity with 65536. Is there any way to make cell profiler not do this rescaling and show the raw data?
Also, I did all my analysis with this default ‘rescaling.’ I am wondering if this rescaling has rendered my analysis meaningless. It seems that all intensities were scaled by a common factor. Do you think this will be a big deal if you are doing quantitative microscopy?
Thanks for helping with this.