How to get Intensity Row Value

Hello people,

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.

That’s not actually true. When images are loaded in NamesAndTypes it rescales the images to be 0-1 on either
a) the metadata, which determines what bit depth your camera allows and rescales it 0-1 based on that (so assuming your metadata were read in correctly 4096 would be 0.25 in your 14-bit image, even if it is the brightest pixel)
b) the bit depth, which is either 8 bit or 16 bit (so I’m not surprised that it didn’t return the expected values when you multiplied by 16384 after using this setting, you’d have to multiply by 65535 instead)
c) a value the user manually provides. You could force a 14-bit scaling here by using 16383 (convention is that the values go from 0 to (2^n)-1)

You can read the help module for NamesAndTypes for more information.

Thank you very much for your reply. Now I understand what was wrong in my pipeline. Thanks a lot.

1 Like