Posted by
Michael Schmid on
Jan 22, 2019; 9:51am
URL: http://imagej.273.s1.nabble.com/Particle-segmentation-tp5021680p5021681.html
Hi James,
you can try the Adjustable Watershed. It does not get it 100% correct,
but most of the rods are separated correctly.
http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:adjustable_watershed:startAs a preprocessing step (before thresholding) you could duplicate the
image, run Find Edges, and add it to the original. This makes the edges
stand out more clearly. Then, after thresholding, the Adjustable
Watershed gets it almost perfect.
I also tried various methods based on grayscale (edge-preserving blur
plus Find Maxima, which can also do a segmentation). In several places,
the contrast within the particles is higher than the contrast between
the particle and the gap in between two particles, so this does not help.
For a perfect result, I fear that one would need some algorithm that
takes the expected shape of the nanorods into account. (I am not aware
of any; maybe others know more.)
Michael
________________________________________________________________
On 22.01.19 08:30, Jaime Wesley-Smith wrote:
> Me again.
>
> To familiarise myself further with FIJI, I deliberately chose gold
> nanorods for their electron opacity and thus contrast, but I am struggling
> to segment them. Thresholding successfully separates them from the
> background, but I have tried various settings of erode / dilate and open /
> close routines to no avail - just cannot separate them completely. I even
> looked for watershed segmentation, which tends to "over segment". I also
> looked at answers to previous questions posted on this listserver without
> much success.
>
> Where am I going wrong? What segmentation steps would you suggest I follow
> for this sort of sample (attached)?
>
> Thanks again!
>
> Best regards,
>
> James
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