Posted by
Michael Schmid on
URL: http://imagej.273.s1.nabble.com/Particle-Analysis-and-Watershed-tp3690122p3690123.html
Hi Florian,
concerning Process>Binary>Watershed: You can have a 'watershed
segmentation' function of binary images with less sensitivity:
If you have small particles, for better accuracy, select 32-bit EDM
output in the binary options.
Run Process>Binary>Distance Map on your binary image
Threshold between 1 and 255
Run Process>Binary>Find Maxima with 'Above lower threshold', output
type 'Segmented particles' and use preview to adjust the tolerance in
a way that each of your kidney particles gets only one maximum. (use
'light background' if your distance map has a white background)
With a proper value, you can still split particles that are slightly
touching.
The Process>Binary>Watershed command does essentially the same, with
the only difference that it uses a special algorithm to reduce
quantization noise caused by the finite pixel spacing. This is
important at low values of the tolerance (say, below 1).
Michael
________________________________________________________________
On 10 Dec 2009, at 19:38, 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?
>
> Thank you and best regards.
> Florian