Suggestions for "concentric" Segmentation

[Nicolas Chiaruttini]

Hi all,

I wonder if anyone has a good suggestion to automatically segment this sort of AFM images (ExAFM.tif). What I would like is to partition the image between independent concentric units (see ExAFMSegment.png).

I think I need to somehow extract a "concentricity" feature, but it looks quite tricky to me.

Thanks for suggestions,

Nicolas?



----------------------------------------
Nicolas Chiaruttini, PhD
Aurélien Roux lab,
Biochemistry Department
University of Geneva, Science II
30 quai Ernest Ansermet
CH-1211 Geneva 4, Switzerland


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[Straub, Volko A. (Dr.)]

On 18/08/2016 16:15, Nicolas Chiaruttini wrote:
> Hi all,
>
> I wonder if anyone has a good suggestion to automatically segment this sort of AFM images (ExAFM.tif). What I would like is to partition the image between independent concentric units (see ExAFMSegment.png).
>
> I think I need to somehow extract a "concentricity" feature, but it looks quite tricky to me.
>
> Thanks for suggestions,
>
> Nicolas?
Dear Nicolas,
It looks to me that this is a quite challenging task as the structures
that you want to separate are very tightly packed and the boundaries are
not always nicely defined. I had a quick go using local thresholding and
the particle analyser, which appeared to produce some reasonable results
for part of the image. Below is some macro code that shows what I did -
perhaps this might be some use as a starting point. Or perhaps somebody
else has a much more clever idea.
Good luck,
Volko

image=getTitle()
run("Duplicate...", " ");
run("8-bit");
run("Auto Local Threshold", "method=Median radius=15 parameter_1=0
parameter_2=0 white");
run("Duplicate...", " ");
run("Analyze Particles...", "size=3000-Infinity show=Masks include");
run("Invert LUT");
run("Watershed");
run("Analyze Particles...", "size=3000-Infinity show=Nothing add");
selectWindow(image);
roiManager("Show All");

>
>
>
> ----------------------------------------
> Nicolas Chiaruttini, PhD
> Aurélien Roux lab,
> Biochemistry Department
> University of Geneva, Science II
> 30 quai Ernest Ansermet
> CH-1211 Geneva 4, Switzerland
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html