Merging objects that are touching


#1

I am using cell profiler to quantify TUNEL stains on high magnification images.
Just using grayscale/thresholding and size criteria I’m able to identify the stain +ve nucleii quite well.
The only problem is for some nucleii it is identifying them as 2-3 separate objects that are touching or very,very close.
Attached is the image w. objects.

The TUNEL+ve count would be more accurate if I could merge the touching/very close objects.
one of the previous posts mention ‘unify’ module in previous versions?
-is that available or are there any other ways to do this?

thanks for making this software available - I think it is going to save us a lot of mindless labour with more reproducible results.

Justin


#2

In your original image, are there objects that are actually touching? If not, you can ‘turn’ off the ‘declumping’ settings to “None”. Otherwise, you may want to try another ‘declumping’ method. To see all of the ‘declumping’ methods at one time, you can run the pipeline in ‘Test Mode.’ To do so, you should change the question, “Do you want to run in test mode where each method for distinguishing clumped objects is compared?” to “Yes.” Once you are finished deciding which method to use, change the setting back to “No” to avoid seeing the test mode figure windows.

~martha


#3

Thanks for your reply. Adjusting shape and maxima suppression settings was helpful.

To other users - I would suggest using the pdf or printed version of the identifyprimary module in the MANUAL - it is difficult to read on the screen and I think I missed some of of the information when I tried to read it within the software.


#4

Great, glad to hear that you were able to adjust the settings. Also, we are currently working on fixing the help windows, so that it is easier for users to scroll, which should solve the issue that you were having.

Thanks for the feedback.
martha