Use filtered secondary objects in CPA




I created a pipeline where I identify cells with Hoechst (Primary) and a cytoplasmic GFP (secondary). Then I filter the secondary objects based on size, because some of the cells are too big or too small. Then I would like to classify these filtered secondary objects for their intensity from a third channel in CPA.

I could get CPA to work to show me all objects with Hoechst. Can I tell CPA to just use the filtered secondary objects?

Thank you!

transfer_analysis.cppipe (15.9 KB)


Hi Dominik,

In the ExportToDatabase module it asks you “Which objects should be used for locations?”

You currently have that set to Nuclei but I think selecting “FO_DCs” (your filtered secondary objects) should give you the result you desire.


Edit: re-reading this I just wanted to also say that you could use MeasureObjectIntensity to measure the objects intensity in your third channel and then FilterObjects again to sort your objects based on their intensity. Maybe there is a specific reason you want to use CPA for this but just wanted to make sure you knew this was an option.