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

Posted by G. Esteban Fernandez on Oct 15, 2015; 5:11pm
URL: http://imagej.273.s1.nabble.com/Only-count-cells-that-contain-nuclei-or-holes-in-the-binarized-image-tp5014650p5014651.html

I'd run Analyze Particles WITHOUT "Include holes" then again WITH
"Include holes" activated and compare the Results to count the ones
for which the Area changed.

-Esteban

On Thu, Oct 15, 2015 at 8:38 AM, kirbyfloss <[hidden email]> wrote:

> Hi - is there a way to only count the cells in the attached binarized image
> that contain "holes"?
> <http://imagej.1557.x6.nabble.com/file/n5014650/workingCopy.png>
>
> 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!
>
>
>
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