I have con-focal z-stacked images (obi)of red and DAPI channels that I can load onto the cell profiler, as per the manual. However, I have been unable to run an analysis on the loaded metadata. I want to see if I can measure doxorubicin (red) penetration within my 3D tumor spheroids (DAPI stained) and I am using the ‘speckles’ pipeline to analyze the data. It has been a total failure. Any suggestions as to how I can go about measuring the DOX intensity in my DAPI image?