What is the image format for analysing fluorescent intensity



Hi all

I am new to Cell Profiler and so have a very basic question to ask. For analysing fluorescent intensity, do I need to change all colour images to grey beforehand?

Thank you for your help!



Hello there,

Yes, you’d need to convert to grayscale.
If you already have each color channel separately, then in the “NamesAndTypes” module, you can simply “Select image type” as “Grayscale”

If you have multi color images, then in the “NamesAndTypes” module > “Select image type” as "Color"
then add module “ColorToGray”, and split each color channel to grayscale, as shown below:


Thanks Minh. Appreciate your help!


One thing just to add to what Minh said-
Fluorescence images are typically actually stored as greyscale, but sometimes ImageJ or your microscope program will “pseudocolor” them- it’s actually still a grey image, but it’s shown in shades of blue or green or red. If THAT’S the case, no, you don’t need to use ColorToGrey- if you try ColorToGrey and it fails, that’s likely the reason.


Thanks! Yes you are right, I checked my fluorescence images and they are in fact grey but just showing in colour for viewing on screen.