A common task I want to perform is measure GFP intensity (green channel) in areas defined by RFP (red channel). In ImageJ and other software I generate a binary mask (0-1) using the Red channel and then multiply it by the green image.
For example in this instance I am interested only in the green vessels (w1) within the red yolk sack (w2).
How can I do this using CellProfiler?
I would recommend using IdentifyPrimaryObjects on the w2 channel to identify the yolk sac, then MeasureObjectIntensity to make measurements on the w1 channel using the yolk sac object. Only the region within the yolk sac will be used for the intensity measurement; areas outside of this will be ignored.