Labeling annotations and IdentifyObjectsManually

Hi all,

Is there any way to label the regions of interest? For example, on an image, if I were to use IdentifyObjectsManually and Crop to isolate multiple regions on a single image, is there any way I could label one region “1,” then the next one as “2,” and so on and so forth? Thanks!


Hmmm, if you mean that you want to manually annotate objects to have an altogether different labeling, then CellProfiler doesn’t offer that ability.

CellProfiler already labels the objects numerically, but keeps those values “under the hood” since the user usually doesn’t need that information; I take that you just want to visually see the labels themselves? If that’s the case, you can use DisplayDataOnImage to display the object number. Select the desired objects as the input object, “Number” as the category and “Object_Number” as the measurement.


Thanks a ton for the reply, Mark! To clarify: there’s no way to label the regions of interest as “A,” or “B,” just the order they’re already in (as seen in DisplayDataOnImage).

Not to bother you so much, just one last question before I go. I’ve been reading the manual and trying to work this out on my own today; I’m currently attempting to work out a pipeline to capture the number of cells within each annotation. So far, I’m attempting to use RelateObjects (

The manual states that there’s an available measurement for “Count,” as in counting the number of child sub-objects (in my pipeline’s case, it would be the nuclei after using FilterObjects), for each parent sub-object. However, I can’t seem to find a Measure module that would allow me to do this.

I see that the manual states, “For every measurement that has been made of the children objects upstream in the pipeline, this module calculates the mean value of that measurement over all children and stores it as a measurement for the parent, as “Mean_”. For this reason, this module should be placed after all Measure modules that make measurements of the children objects.” Unfortunately, I’m not sure if I follow. I’ve attached an image just in case.

I’ve attached my pipeline for reference. Always really appreciate any kind of help, thanks!

Meeting Pipeline.cp (8.07 KB)

Never mind, solved it. Attached is a pipeline if anybody wants to know how to count the number of cells in a region of interest found by IdentifyObjectsManually.

The order I did was,

Meeting Pipeline 3.cp (11.5 KB)

Hi jgh.tam,

The output from RelateObjects gives you the count of children objects within each parent object. You don’t need to do the ClassifyObjects and CalculateMath (though maybe there were other reasons you are using these modules). Look in the CSV output of the RelateObjects parent object (in your case, the object named “Crop”, so a file probably called “DefaultOUT_Crop.csv”). There should be one row for each region that you defined manually (the parent). You should see a column labeled “Children_FilteredNuclei_Count” which contains the count of objects within each parent ROI.

Hope that helps!