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

Posted by gankaku on Oct 15, 2015; 5:47pm
URL: http://imagej.273.s1.nabble.com/Only-count-cells-that-contain-nuclei-or-holes-in-the-binarized-image-tp5014650p5014653.html

Hi kirbyfloss,

you can have a look at the "Binary Feature Extractor" in the BioVoxxel
Toolbox (http://imagej.net/BioVoxxel_Toolbox).
In the case you have a nuclear counterstain you can extract that one and
extract cells which have those nuclei and compare it to all extracted cells.

Or, as Esteban pointed out by referring to the solidity, the Extended
Particle Analyzer together with the Shape Descriptor Maps might give you a
tool at hand to separate specific shapes from each other.

Kind regards,
Jan

2015-10-15 17:38 GMT+02:00 kirbyfloss <[hidden email]>:

> 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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