I am a new user of cell profiler and I am creating outlines for nucleus and cytoplasm of neurons to be used in FISHquant. I figured that I was also able to identify the transcription sites using cell profiler.
Using primary objects, followed by measure image intensity and filter objects (maximal per object in the nucleus) I was able to identify and create an outline for one of the transcription site. But the problem is that it is giving me only THE brightest object in the nucleus and not the two brightest.
Can you please help me identify the function which can allow me to identify and create an outline for the two brightest objects in the nucleus?