Re: need help on various watershed segmentation algorithms

Posted by Michael Schmid on
URL: http://imagej.273.s1.nabble.com/need-help-on-various-watershed-segmentation-algorithms-tp3697689p3697691.html

Hi Chistine,

to increase your confusion, there is at least one more:
Process>Binary>Find Maxima can do Watershed segmentation based
on *pixel values* (as the watershed command by Daniel Sage,
without preprocessing).
With Process>Binary>Find Maxima one can avoid oversegmentation by
using a proper value of the noise tolerance.

If you want watershed segmentation of the distance map, it is only
the outline of the particles that matters, not the pixel values.
In this case, the built-in Process>Binary>Watershed command has a
slight advantage over other algorithms that do watershed
segmentation of the EDM (Euclidian Distance Map):
The algorithm is aware of the limitations of an EDM caused by
finite resolution (i.e., pixels) and corrects for these (an EDM
with sub-pixel resolution is used internally).
Thus, it will usually perform better with respect to avoiding
false segmentations while on the other hand keeping the maximum
sensitivity towards particles with a waist not much narrower than
the remaining particle.

Anyhow, finding the best algorithm for your problem will probably be
a matter of trial and error.

Michael
____________________________________________________________________

On Fri, 28 Dec 2007 19:08:12 +0800 Chris Clarin
<[hidden email]> wrote:

>Hello,
>
>I am looking for effective watershed segmentation algorithms that I can use
>for my objective which is to segment clustered cells in a microscope image.
>As of the moment, I am using these three options:
>
>1) process->binary->watershed
>2) process->binary->Distance Map->daniel sage's plugin (Watershed Algorithm)
>3) blur->binary->Distance Map->daniel sage's plugin (Watershed Algorithm)
>
>but somehow I think there are still other ways to segment properly. I have
>come across this: Watershed Segmentation (
>http://bigwww.epfl.ch/sage/soft/watershed/) again by Daniel Sage and I am
>getting a little confused on the differences among all of the three
>algorithms available: the one built in imagej (process->binary->watershed),
>the watershed immersion algorithm created by daniel sage (the translation of
>the one by Lee Vincent and Pierre Soille) and the new one I discovered
>today, the watershed segmentation algorithm. can anyone explain to me their
>differences? and what do you think is the most feasible that I could use for
>segmenting badly clustered cells.
>
>Thank you very much. Any help would be greatly appreciated.
>
>Best regards,
>Christine
>
>-------------------------------------------------------------------
>Christine T. Clarin
>UP Department of Computer Science
>Work/Fax: [phone]
>Mobile: [phone]
>Email: [hidden email]
>