Particle Analysis and Watershed

Posted by Florian Sedlmeir on
URL: http://imagej.273.s1.nabble.com/Particle-Analysis-and-Watershed-tp3690122.html

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