3D Watershed Plugin?

Posted by Zwick, Ari A. on Apr 05, 2010; 10:47pm
URL: http://imagej.273.s1.nabble.com/3D-Watershed-Plugin-tp3688059.html

Dear ImageJ Community,

 

This is a continuation of a previous question, whereby I need one final
push to the finish.  I have multiple stacks of grayscale images that
require 3D watershed segmentation in order for me to obtain volume and
radii of pore space in soil aggregates.  Michael Doube and Robert
Dougherty were very helpful in providing their plugins: local thickness,
and BoneJ.  I have since decided to go with the particle analyzer in
BoneJ, but the final requirement is that I separate pores in 3D before I
use the particle analyzer.  It turns out that many of my pores are
connected and it becomes impossible to obtain the feret diameter with
such large networks.  2D watershed doesn't work because it thresholds at
different spots in different slices.  I tried using the IFT-3D plugin in
Fiji, which works on grayscale images, but it hasn't given me the
results I'm looking for and I can't find any documentation on it.  I was
able to find a 3D RGB watershed plugin, but that doesn't do me any good
with grayscale images.  Does anyone know of a 3D watershed plugin that
works on greyscales, or have any other ideas of how I could get around
this?

 

One more alternative I thought of was finding a Maximal Balls algorithm,
for which even if it just made spheres I could still use the particle
analyzer to get the radius.  I haven't seen any ImageJ plugins that do
that though, has anyone else?

 

Thanks in advance, I really appreciate any and all help that I've had in
the past, and hopefully in the future.

 

Ari Zwick