You can do this in the same pipeline! If you have images of nuclei and of your foci, you can have one pipeline that loads both images, identifies both the nucleus and the foci, and get quantitation for both. Better yet, you can also identify “cells” (arbitrary rings around nucleus) and correlate these to your foci to automatically get average foci/cell! Here is what I would do:
LoadImages (load Foci and Nuclei image)
IdentifyPrimAutomatic (Identify your Nuclei)
IdentifySecondary (Identify Cells around Nuclei using Distance - N)
METHOD OF IDENTIFYING FOCI (I showed you two methods, so use the one which works better here)
Relate (Have foci be the children of Cells)
Now when you analyze your images, the relate module will calculate how many foci are in each cell. You can make these cells expand as far as you want from each nucleus, to cover all of the foci. When you export your data using the data tool “ExportData”, the image output file will contain a field which is the average foci per cell.
Give it a try and if you run in to problems, please ask for help.