CellProfiler: discard secondary object if it contains >1 primary objects



Hi Image.sc forums,

I am using cell profiler to process image masks for nuclei and cytoplasm (generated in Image J) to measure protein concentration.

A certain number of cells are showing two nuclei for a single cell, which is in error. This is due to tissue artifacts and is produced by the process of generating masks in Image J.

Is there any way to tell CellProfiler to discard the object if the a secondary objects contains two or more primary objects?




Hi Michael,

My understanding was that you couldn’t end up with more PrimaryObjects than SecondaryObjects but I guess your ImageJ process bypasses this somehow?

If you go to FilterObjects and try to filter your cell objects is it possible to set the below measurements

Filtering mode - Measurements
Filtering method - Limits
Catgory: Children
Measurement: Nuclei_Count (or something similar)

And then set a maxiumum of 1 to allow for no more than one child?

If that isn’t being shown you might have to try and use a RelateObjects module to relate your Cells and Nuclei (this method allows for not just a 1:1 object relationship) and then try FilterObjects again?

Hope that helps?


Hi Laura,

Thanks for your help.

I will test this out. The process with Image J mostly works but if there is a very dim area in cytoplasm or a dark artifact then the algorithm will detect that area as a nuclei.

I will try this out asap and report back.




I just realized something. I would like to eliminate individual cell objects with an erroneous nuclei but I cannot do it this way. There are even more cell objects that are actually two cells identified as one larger cell which have two nuclei (one for each cell) and CellProfiler divides these up because the nuclei are primary objects, which is ideal.

So, if I begin eliminating cell objects with two nuclei then I will end up losing more positive cells than erroneous ones. Thanks for your help Laura. I enjoyed learning about that useful module and now know about it for future use.