Object Neightbor Question

Hi guys, I hope all goes well. I’d like to thank you for all your replies and help, and apologize for my lack of timely responses. I’ll aim to improve those numbers in time to come.

I have a case where I get what appears to be incorrect neightbor counts and wondered if I have things set wrong. I have two primary objects, Nuc and F480 marker, and I want to highlight the F480 objects touching the nuclei.
Here are the outlines:

Here are my settings:

And here is the result:

I would expect only some of the nuclei to have neighbors…? Where am I going wrong?

Thanks for your time.

Hey! If you could upload the pipeline and provide example images, I could look over it! There’s definitely a problem (I often get confused when using the neighbors module) but its hard to tell without this information.

Hi Fabba, thanks for the assistance.

The strange thing is that it now works, but I didn’t change anything. I pulled an image from the lif file to test and ran the test on a different computer, without changing the project file details (bar the file and update buttons), and it works… ??
The outlines shows something that looks very similar to the other image (I’ll look to see if I can find that image, but I don’t see how this one should be any different)

And now I get neighbors values of 1 for those that should be neighbors. Great stuff!

Alas, now I don’t know if I can trust CP on some PC’s…? This is a real concern if it is the case. Does anybody know of a good way to completely wipe the CP install and reinstall?

I’ll get back to the other machine and find the exact image I was working with and work from there for completeness.

Thanks in advance for your time.

Good to see that problems still do resolve themselves, right?

I think you might not have to uninstall CP. I’m no programmer but I believe if you recreate your functioning pipeline on your other PC (or you transfer the project file and the images) your pipeline will work.

As long as your having fun - are you working with spreadsheets or databases? I strongly recommend getting to know how to work with CP Analyst, use the ExportToDatabase module (where you can choose to create a properties file), and take a glanze at the CPA manual. It’s very useful to quickly visualise data from lots of measurements (you could compare neighbor+ and neighbor- objects)

Hi Fabba,
Alas, if I return to the original machine, after recreating a fresh duplicate project it still shows an incorrect number of neighbors…
I’ll continue testing with different files etc and see if I can get more info.


Interesting. Have you ensured that both PC’s are running the same version of CP, and then tried to run the same project file? If in doubt, give both a fresh install with the current version.


Any idea how to uninstall CP on linux?