Only count cells that contain nuclei (or holes in the binarized image)

Posted by kirbyfloss on Oct 15, 2015; 3:38pm
URL: http://imagej.273.s1.nabble.com/Only-count-cells-that-contain-nuclei-or-holes-in-the-binarized-image-tp5014650.html

Hi - is there a way to only count the cells in the attached binarized image that contain "holes"?


I am trying to analyze slides with muscle stained with H&E - and would like to count the number of regenerating muscle fibers, which are distinguished by dark nuclei in the interior of the cell bodies (rather than on the periphery).

This is the pipeline I have set up thus far:
1) Apply colour deconvolution (using plugin by G. Landini)
2) Set threshold to binarize the resulting image in channel 2
3) Analyze particles

This works reasonably well to count all the cells in an image, but is there any way to only count the cells that contain a hole (or multiple holes) automatically? I'm aware of more manual tools, like Cell Counter, but was hoping for the most automated solution possible.

Thanks!