Re: Particle Analysis and Watershed

Posted by Johan Henriksson-2 on
URL: http://imagej.273.s1.nabble.com/Particle-Analysis-and-Watershed-tp3690122p3690124.html

Florian Sedlmeir wrote:

> Hi,
>
> Now I have started to use the auto-threshold and local-auto-threshold
> plugins for my particles (problem was: the particles are locally
> distinguishable against the background due to their contrast, but
> globally, there is always a long range gradient in grey values which i
> can´t substract sufficiently)
> The new problem with local thresholding algorithms is: My particles
> are very close together and their edges are darker then the middle. So
> there seems to be no optimal radius for local thresholding. Usually i
> get only the edges thresholded (of course not completly... )
>
> Question about watershed: After thresholding i have to use the
> watershed tool as the particles are very close together and touch each
> other sometimes. The probem is, that the particles are not totally
> konvex, they have roughly the form of a kidney. So the watershed tool
> always divides the particles in two halfes.  Of course i can correct
> this manually (drawing one line is enough) but that´s not very funny
> for many particles. Does anyone know a solution of this problem?

pictures always help but I see where this issue is coming from. you
might be able to recombine the particles afterwards with some heuristics
(if two areas are too circular and they have the least color difference
in the "bridge" as opposed to other combinations).

another approach would be with active contours with prior shape information

/Johan


>
> Thank you and best regards.
> Florian