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

Posted by G. Esteban Fernandez on Oct 15, 2015; 8:51pm
URL: http://imagej.273.s1.nabble.com/Only-count-cells-that-contain-nuclei-or-holes-in-the-binarized-image-tp5014654p5014656.html

You can try the "Add to Manager" option in Analyze Particles, then go
through the list of ROIs and draw only those with holes onto a new
blank image.

-Esteban

On Thu, Oct 15, 2015 at 12:11 PM, kirbyfloss <[hidden email]> wrote:

> Thanks so much! I tested the code and it runs perfectly - the solution of
> using include/exclude to distinguish the two populations is great.
>
> Just one more thing, is it possible to show outlines for just the particles
> that contained holes? So I know which particles were counted.
>
> This is the macro I have set up so far with the helpful suggestions of the
> community:
> // run on the original image
> run("Duplicate...", "title=workingCopy.png");
> selectWindow("workingCopy.png");
> run("Colour Deconvolution", "vectors=[H&E 2]");
> selectWindow("workingCopy.png-(Colour_2)");
> setAutoThreshold("Minimum");
> run("Convert to Mask");
> run("Set Measurements...", "area redirect=None decimal=5");
> run("Analyze Particles...", "size=100-Infinity display exclude clear");
> noHoles = newArray(nResults);
> holes = newArray(nResults);
> for (i = 0; i < nResults; i++) noHoles[i] = getResult("Area", i);
> run("Analyze Particles...", "size=100-Infinity display exclude clear
> include");
> print("Particles Containing Holes");
> for (i = 0; i < nResults; i++) {
>         n = i+1;
>         holes[i] = getResult("Area", i);
>         a = holes[i] - noHoles[i];
>         if(a > 0) print(n + " area of hole = " + a);
> }
>
>
>
>
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>
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