Space Between Primary Objects

cellprofiler

#1

Hello,

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.


#2

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.
Bob


#3

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


#4

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

Bob


#5

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


#6

Hi,

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

Hamdah