Spots (or speckles) per cell


I want to count spots per cell. I have managed to use the speckle counting pipeline and tweak it a bit and it seems to be working fine. My question is - is there a module or a setting that would allow me to get a number of spots per cell? I relate the spots to the cell but in my excel file it never gives me a total number for the spots per cell. It lists the intensity for every spot and next to it the number of the cell it comes from. I can then sum all these in excel but I feel like I am missing something. Is there a simpler way to get the total number of spots per cell?


Hi Henriette,

This information should be in the Parent object’s output file (if using ExportToExcel?). So look in the “Cell” output file, or whatever you called the cell object, and there should be a measurement named ChildrenCount (or some such name).

Hope this helps!

Hi David,

I want to count spots per cell too. But i couldn’t find this information in output file, and i am using EportToSpreadsSheet module. What do you think i should do ?

Thanks a lot,


Hi @Isabela_Possebom,

Did you use the RelateObjects module prior to making measurements? The Speckle Counting example on this website may be helpful:

If you’re new to CellProfiler, I recommend starting with this video tutorial from the Center for Open Bioimage Analysis YouTube channel:

The tutorial materials are available for download at this link:

Good luck!