http://imagej.273.s1.nabble.com/simple-thresholding-problem-tp5015481p5015487.html
I would also look into a Hough-like transform for detecting circles, perhaps extended to handle ellipses. This would depend critically on being able to find good edges (preferably with good orientations).
but first Local Thresholding. I have been using Phansalkar to good effect.
> On Jan 29, 2016, at 07:17, Straub, Volko A. (Dr.) <
[hidden email]> wrote:
>
> For what it is worth this looked to me like a problem for local thresholding. Using the 'Niblack' method in the 'Auto Local Threshold' menu followed by a watershed segmentation appeared to produce some reasonable results for your sample image.
> Hope this helps,
> Volko
>
>
>
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of Gensch, Thomas
> Sent: 29 January 2016 08:38
> To:
[hidden email]
> Subject: simple thresholding problem
>
> dear all,
>
> i have a (rather simple?) problem of identifying circular and elliptical objects in a fluorescence image (see the attached sample picture). i want to generate a mask, that i can use in a second image (different fluorophore and color, different structures) to select the interesting areas.
>
> while by eye and freehand drawing one can nicely mark the limits of the object, with all the thresholding tools in imagej (i tried "threshold in "adjust" and the "autothreshold plugin") i obtained only mediocre results (one of the best examples is attached). i can see the problem (in some parts due to close localization and very different fluorescence intensities by neighbouring objects the space between objects has intensity values larger than some of the weaker fluorescent elliptical objects.
>
> i wouId appreciate very much, if one of you could help me or suggest a better approach,
>
> thanks a lot,
>
>
> thomas
>
>
> Dr. Thomas Gensch
> Institute of Complex Systems 4 (ICS-4), Cellular Biophysics/Institut fuer Komplexe Systeme 4, Zelluläre Biophysik Forschungszentrum Juelich (Research Centre Juelich)
> 52425 Juelich
> Tel:+49-2461-618068
> Tel:+49-2461-614216
> email:
[hidden email]
>
>
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