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!

Good Afternoon Pearl,

Thanks a lot for the answer. I’am a new user of CellProfiler and CPA, and still in learning process.

I managed to create a pipeline able to count spots per cell using the RelateObjects module, because I work with images of cells infected with Trypanosoma cruzi parasites. Althouhg, now i want generate a properties file to work with these found parameters in CellProfiler Analyst. I would like to classifier the cells based in how much parasites they have inside.

However, i have been trying to build this properties, but i couldn’t make it work. A error occurs in the module ExportToDatabase ( “Granulos is not in a 1:1 relationship with the objects, wich may cause downstream problems. You may want chose another object container” ).

Do you know what i should do to deal with this problem ?

Thank you so much,


If your data is 2D and spots inside the cell you can make use this tool

Count cells in 2D

You have to create a rectangle selection around each cell, the roi manager will update with all the spots it finds in that region and then you can move the rectangle to another cell, adjust parameters if needed and then get a count of cells in that region as well.


Regarding the 1:1 relationship error, please see the post below – for your CellProfilerAnalyst database, you’ll want to export each object into its own table. Good luck!

Good morning Pearl,

Thanks a lot. I changed the option to One table per object type, then it worked. The properties file open in CPA.

Now I am having problems with the classifier, I am not sure if he is training well, because it lasts for a short time (like 0.02s at most). Could it be the volume of images ?



Do you mean that the classifier trains very quickly? That would be expected and is not an indication of training quality.

You can use the “evaluate” option to get a better sense of how your classifier is performing – see the CellProfiler Analyst tutorial: CellProfiler-Analyst Workshop - YouTube

Good luck and I’m glad it helped!