Problems with segmenting nuclei


Currently I am analyzing nuclei of plant cells (stained with DAPI) taken in 63x magnification. For whatever reason, there are holes in the nuclei. Subsequently one nucleus is identified as two nuclei leading to artifacts which I want to avoid.
Is there, perhaps in the image processing chapter, a way to virtually fill those holes in the nuclei? Just for a proper segmentation in order to enable an accuarate analysis of the whole nucleus without dividing it in two parts?
I already tried the smooth algorithm using the median filter but I could not solve the described problem.
Thanks for your advise,



Hello Dominik,
The issue that you describe is a common problem with identifying objects. In the IdentifyPrimAutomatic module, you can set the “Do you want to fill holes in identified objects?” to “Yes.”

Additionally, if you are having problems with the identified nuclei being segmented into multiple objects, you can modify the method for distinguishing clumped objects (also in the IdentifyPrimAutomatic module). If you are interested in running the various methods for distinguishing clumped objects, set the last question (“Do you want to run in test mode where each method for distinguishing clumped objects is compared?”) to “Yes,” which will give you a figure window showing you the results of the methods for clumped objects.

Good luck!