Re: Watershed question

Posted by Du, Guanghua on
URL: http://imagej.273.s1.nabble.com/Watershed-question-tp3685658p3685664.html

Hi, Natashaw,
have you tried the FociPicker3D plugin? you can have a look at
http://rsbweb.nih.gov/ij/plugins/foci-picker3d/index.html
I wrote the plugin for foci analysis.

guanghua

NatashaW wrote:

> Karsten,
>
> Many thanks for your explanation; you have exactly mentioned the most
> problems that I have found during my work!!
> I’m really working to count/measuring some particles (foci) inside the
> nuclei. Daniel’s algorithm gives me good results when I work on the foci
> images (gray-level values).
>
> But during this work, I found some problems:
>
> 1-When I smoothed the input image, the oversegmentation problem has been
> solved.. But watershed didn’t separate all the desired objects. I’m still
> looking for a better threshold value. Indeed, I didn’t find yet the best
> criteria to control the MIN and MAX values..
>
> 2-The detected particles are bigger than their real size. This may cause a
> problem during the measurement (like the mean and IntDen..) because the
> boundaries of the detected objects don’t match exactly their real size..
> Maybe because of the chosen MIN value??
>
> 3-Is Daniel’s watershed algorithm an implementation of this article:
> Vincent, Lee & Soille, Pierre, "Watersheds in digital spaces: An efficient
> algorithm based on immersion simulations", IEEE PAMI13 (6): 583-598
> If not, could someone tell me which one? I want to understand how the
> algorithm works Please..
>
> Thank you so much for your help
>

--
best wishes!
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Guanghua Du, PhD
James-Franck Str. 1
Physik Dept, E12, TUM
85748, Garching b. Muenchen
Germany

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E-mail: [hidden email]
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