Cell Profiler Correlating Object # to the Particle Analysis Image (Identifying Primary Objects Image)

Hello Cell Imaging Community,

I have a question to anyone that has experience with cell profiler. I am a novice at cell profiler, but I have previous experience with Imaging software such as ImageJ by FIJI. I just wanted to ask, how do you correlate the object number to the image results in order to compare the numerical values with the image? The excel results give you coordinates as to which object the program is talking about, but the program does not label the objects in the image with a specific number. In ImageJ by FIJI they have something called an ROI manager to correlate which object they are talking about in comparison with the image. Since I am talking about this in terms of the “Identifying Primary Objects” part of the pipeline, I was wondering, is the “Identifying Primary Objects” labeling the same or different in terms of cell border analysis if they have this feature? If they do not have the feature of labeling objects with numbers, how does everybody go about in terms of comparing your numerical results with the image?

If anyone can please get back to me with an answer to my question, that would be greatly appreciated for my cell imaging journey.

Thank you,


Hi Brandon,

Welcome to the forum.

You should have a look at the module “DisplayDataOnImage”. I often use to mark images with the object number for the reasons you are talking about.

You’ll want to have set to display Object measurements and then the Category is called Number and the Measurement called “Object_Number”.

Good luck!


The WorkspaceViewer is also really helpful for this, if you’re talking about looking at object numbers “on the fly” (as opposed to saving out a version with the object numbers on it for later, for which @lmurphy is exactly right that DisplayDataOnImage is the best way to do)

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