Posted by
Thomas Boudier-4 on
Dec 01, 2016; 4:43am
URL: http://imagej.273.s1.nabble.com/3D-Region-of-Interest-tp5017648p5017662.html
Hi Xin,
The macro will basically cluster together closest objects. If A is
closest to B and B is closest to C, the algo will cluster A B and C.
This is a very simple algorithm but can be eventually useful to detect
clusters.
Can you send me directly some sample image to test this macro.
Best,
Thomas
On 29/11/2016 19:47, BirthingXS wrote:
> Hi Thomas,
>
> I'm having some trouble with loading some of the contents of the link, are
> you able to elaborate on what the function does (Sorry as I'm not a
> programmer myself). Also if it helps, this is the function I'm using for 2D
> and would like it to be translated to 3D.
>
> setOption("BlackBackground");
> original = getTitle();
> run("Invert");
>
> roiManager("reset");
>
> run("Create Selection");
> run("Enlarge...", "enlarge=2");
> roiManager("Add");
> roiManager("Split");
>
> roiManager("select", 0);
> roiManager("Delete");
>
> selectWindow(original);
>
> run("Invert");
> run("Set Measurements...", "area stack display redirect=None decimal=3");
> for(i=0; i<roiManager("count"); i++) {
> roiManager("Select", i);
> roiManager("Measure");
> //if the selection is empty (included holes) the measurement and result
> will be deleted
> if(getResult("%Area", nResults-1)==0) {
> roiManager("Delete");
> IJ.deleteRows(nResults-1, nResults-1);
> i--;
> //if there is a particle inside the selection the CRU and tne clusters will
> be analyzed
> } else {
> setResult("Label", nResults-1, getResultLabel(nResults-1) + "-CRU");
> run("Analyze Particles...", "display");
> }
> }
>
> Additionally, I've been in touch with Jan Brocher with some of these issues
> and he suggested you might be able to offer some insights. Do you mind if I
> get in touch with you via email?
>
> Cheers,
> Xin
>
>
>
> --
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>
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--
/***************************************************************/
Thomas Boudier, Associate Professor, UPMC,
Université Pierre et Marie Curie, Paris, France.
BioInformatics Institute (BII)/IPAL, Singapore.
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