Space Between Primary Objects




I’m new to CellProfiler so this is likely a fairly dumb question. I’m identifying nuclei as primary objects in a fairly densely populated image, but I find that in many areas the gaps between nuclei are being identified as primary objects as well. I cut down the expected diameter to try and eliminate these areas because they’re usually a bit larger, but they are still identified as primary objects, just with divides that segment them into smaller units. The image has a fairly bright background which makes me think there’s in issue there, but I’m really not sure. If that were the case, is there anything I can do about it?

Any help is really appreciated, and thanks for your time.


Hello Nick Seyler,
If the gaps are brighter than the nuclei, then just invert the image. Otherwise send a sample image in PNG or Jpeg format if possible please.


Thank you for your reply, I couldn’t add images to the initial post because I’d just made my account and they restrict that, but I am able to now. The image is sort of small but if you zoom in you can see a few regions , one of the more noticeable a yellow region in the left center of the image, that were identified as nuclei that are really just gaps. The background is bright but I don’t think brighter than the nuclei in those areas.

Thanks again for the help


O.K. Nick,
I have your images and will work on them. Be back with you soon.



Sorry for late reply, thank you for taking a look!



One thing you can try doing the thresholding first and then use detect nuclei with primary object module. I hope that might help you