Re: Segmenting Circular Objects that are touching multiple other objects

Posted by Straub, Volko A. (Dr.) on Apr 30, 2016; 4:08am
URL: http://imagej.273.s1.nabble.com/Segmenting-Circular-Objects-that-are-touching-multiple-other-objects-tp5016288p5016289.html

Have you tried applying a watershed segmentation after your initial
thresholding to separate touching particles? I just tried it with your
image after thresholding the image with the default settings and it
appeared to do a good job.

You can then use 'Analyse Particle' to add all your particles to the ROI
manager and measure them. If you select 'Fit ellipse' in the measure
option you will also get the length of the two main axes of the
particle, while 'Centroid' or 'Centre of mass' provide the coordinates
of the centre of each particle. Based on the measurements, it would be
easy to draw a smooth circle/ellipse for each particle if that is needed
(I didn't include this in the macro code below that illustrate what I did).

Hope this helps,
Volko


run("Duplicate...", " ");
run("8-bit");
setAutoThreshold("Default");
setOption("BlackBackground", true);
run("Convert to Mask");
run("Watershed");
run("Set Measurements...", "centroid center fit shape redirect=None
decimal=3");
run("Analyze Particles...", "display exclude clear add");




On 29/04/2016 22:21, smithd10 wrote:

> Hello,
>
> I am attempting to size microspheres that I have imaged on TEM. The
> microspheres are touching multiple other microspheres and I am having
> difficulty segmenting/thresholding the objects to maintain the original size
> of the microsphere. I either have the problem of the negative space becoming
> the main focus of the particle analysis, or I have thresholded the image so
> much that the particle size is no longer accurately measured.
>
> In other programs, there is the ability to automatically draw circles around
> an object based on the circularity of part of that that object. Is that
> ability available in ImageJ?
>
> Thank you.
>
> <http://imagej.1557.x6.nabble.com/file/n5016288/Pic13.gif>
>
>
>
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> View this message in context: http://imagej.1557.x6.nabble.com/Segmenting-Circular-Objects-that-are-touching-multiple-other-objects-tp5016288.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
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