Re: Voronoi plugin not adjusted

Posted by Adrián Villalba on Feb 08, 2018; 10:39pm
URL: http://imagej.273.s1.nabble.com/Voronoi-plugin-not-adjusted-tp5020029p5020035.html

Dear Kenneth,

Thank you for your hint. I achieve to perform now the Voronoi to the whole
image (as i understand you suggested). Do you know at this point how can i
restrict it to to my green positive are and even measure the area of each
ROI of interest?

Thank you

Macro:
run("Duplicate...", " ");
title = getTitle();
run("Split Channels");

selectWindow(title+" (green)");
// process the green channel;
setAutoThreshold("Moments dark");
//run("Threshold...");
//setThreshold(69, 255);
setOption("BlackBackground", false);
run("Convert to Mask");
run("Close-");
run("Fill Holes");
run("Dilate");
run("Remove Outliers...", "radius=50 threshold=50 which=Bright");
run("Create Selection");


selectWindow(title+" (blue)");
// process the blue channel;

run("Unsharp Mask...", "radius=5 mask=0.90");
run("Remove Outliers...", "radius=3 threshold=2 which=Bright");
run("Find Maxima...", "noise=50 output=[Maxima Within Tolerance]");
run("Delaunay Voronoi", "mode=Voronoi interactive");
run("Close-");
run("Fill Holes");
run("Watershed");
run("Find Maxima...", "noise=1 output=[Point Selection] light");
run("Delaunay Voronoi", "mode=Voronoi interactive");


2018-02-08 22:38 GMT+01:00 Kenneth Sloan <[hidden email]>:

> I usually do this sort of restriction by limiting the analysis to Voronoi
> regions which are completely in the ROI (your "green region").  But, I also
> always roll my own Voronoi computations, and have no clue how to do that
> using the standard tool, and especially not in the macro language.
>
> Even so, I thought this hint might be useful.
>
> You WANT the Voronoi computation to include the entire image, because
> those half-infinite regions provide boundaries for the ones you want to
> analyze.  Use as much area as possible to create the Voronoi Diagram, and
> then clip out and reject any Voronoi region that is not entirely contained
> inside your ROI.  In practice, this means computing the Voronoi vertices
> and checking that each one is inside the ROI,
>
> --
> Kenneth Sloan
> [hidden email]
> Vision is the art of seeing what is invisible to others.
>
>
>
>
>
> > On 8 Feb 2018, at 10:08 , Adrián Villalba <[hidden email]> wrote:
> >
> > Dear all,
> >
> > Thank you all for your help. I am trying to perform Voronoi - using the
> > DelaunayVoronoi plugin in Plugin>Analyze) to calculte (aproximately) the
> > area of positive staining in each cell.
> >
> > I used a homemade macro:
> >
> > run("Duplicate...", " ");
> > title = getTitle();
> > run("Split Channels");
> >
> > selectWindow(title+" (green)");
> > // process the green channel;
> > setAutoThreshold("Moments dark");
> > //run("Threshold...");
> > //setThreshold(69, 255);
> > setOption("BlackBackground", false);
> > run("Convert to Mask");
> > run("Close-");
> > run("Fill Holes");
> > run("Dilate");
> > run("Remove Outliers...", "radius=50 threshold=50 which=Bright");
> > run("Create Selection");
> >
> >
> > selectWindow(title+" (blue)");
> > // process the blue channel;
> > run("Restore Selection");
> > run("Unsharp Mask...", "radius=5 mask=0.90");
> > run("Remove Outliers...", "radius=3 threshold=2 which=Bright");
> > run("Find Maxima...", "noise=50 output=[Maxima Within Tolerance]");
> > run("Delaunay Voronoi", "mode=Voronoi interactive");
> > run("Close-");
> > run("Fill Holes");
> > run("Watershed");
> > run("Find Maxima...", "noise=1 output=[Point Selection] light");
> > run("Delaunay Voronoi", "mode=Voronoi interactive");
> >
> >
> > The point is that the surrounding nuclei of my section has a Voronoi area
> > to the boundaries of the image and i only want to perform that in the
> > green-positive selection. I can not restore in the same image the find
> > maxima output to locate the nuclei and the selection i previously used in
> > my green channel. Does anyone know how can i apply Voronoi with my
> > selection boundaries instead of performing Voroni to the whole picture?
> And
> > if it is possible, how can i measure the area of each Voronoi-region?
> >
> > Thank you in advance!
> >
> >
> > --
> >
> >   - Adrián Villalba Felipe.
> >   https://es.linkedin.com/in/adrianvillalba
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > <input_Voronoi.tif><Voronoi output.tif>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--

   - Adrián Villalba Felipe.
   https://es.linkedin.com/in/adrianvillalba

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