So, first, you will need to either export your images so they appear in grayscale; or you can try the example pipeline, ColorToGray. Then, once you have your grayscale images saved, you can start working on your pipeline. What you will need some of the following modules:
CorrectIllumination_Calculate (two of these-- one for the green channel and one for the red channel)
CorrectIllumination_Apply (two of these-- one for the green channel and one for the red channel)
IdentifyPrimAutomatic (to identify green cells)
IdentifyPrimAutomatic (to identify red cells)
MeasureObjectIntensity (same comment as above… for the measure modules)
You might need other modules, depending on whether you decide to measure different features of the images (ie: Texture, Area, etc). The ‘help’ for each module will be a good reference for setting up the parameters.
If you would like to see how some of the modules work when identifying or measuring object, be sure to download a few of the examples and test them out.