We seem to have an uploading problem right now, since I can’t fully upload either. We’ll check into that.
As for your science question, measurements are either Per_Image (e.g. the “Image” sheet) or Per_Object (e.g. “cytoplasm”, and any other objects you defined in the pipeline). Per_Image measurements are any measurements defined across the whole image, like image thresholds or object counts. Object measurements in the Per_Object tables are measurements across each individual object, like area or that object’s intensity. So it’s up to you to determine what measurement you want to analyze. You say you want “to measure nuclei and cytoplasm fluorescence”, then I assume you want to use MeasureObjectIntensity and then look in the nucleus and cytoplasm spreadsheets for the, say, mean intensity columns. You can average them per image or across the whole experiment depending on your protocol.
You should think of objects like nucleus and cytoplasm separately from the channels that typically define them. You might only care about the DAPI intensity in the nucleus object and the alexa intensity in the cytoplasm, but one can certainly measure the DAPI channel intensity in the cytoplasm and vice versa, though you might not care about this somewhat non-intuitive measure. Maybe there will even be some translocation that you didn’t expect and then you could measure the intensity change. The point is, you can measure any channel’s properties in any defined object. Hope that helps!