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?



What do you mean exactly by “run an analysis on the loaded metadata”? Can you extract the metadata? Does CP run but not attach the metadata?

Would you post, or link to, a sample image stack, plus your pipeline attempt? Note that CellProfiler does not do 3D segmentation (yet), so you should think about what software tool is the best for this (ImageJ?, do z-projection?).