Good question. I would probably use the Relate module to relate B (children) to A (parents). Then, in the output, you will have a feature which is how many of B are in each of A. You can then filter out A’s that don’t contain any B’s. There is currently no way within CellProfiler to filter existing objects based on this criteria and do analysis on only those objects, so the downfall is that you will be making measurements on objects you don’t care about. We have been developing some Mask modules and soon this task should be easier to accomplish.
Another option is to use FilterByObjectMeasurement and filter by something like max intensity within object A using the image for object B. If there are any objects (B’s) present, you will have a much higher max intensity then an object A without any B’s.