I am a beginner in the use of the Cell Profiler and I need to compare the raw intensity values between the different images. If well understood, Cell Profiler usually rescales the intensity values between 0 to 1 by dividing the intensity values of each pixel by the maximum intensity value detected in each image. But if it is correct, I can’t compare the intensity values of different images because they depends from the maximum value detected inside each image, then they don’t reflect the real value of the intensity of the pixels.
I also tried to select “Image bit depth” as intensity range (“set range of intensity” in NameAndType Module) and to use the “ImageMath” module to multiply all the intensity values for 16384 (214 because my images are 14 bits), but the results don’t match with the real intensity values.
I absolutely need to have this information as soon as possible and it would be great if someone can suggest me what to do.
Thanks a lot.