Re: 3D Watershed Plugin?

Posted by Michael Schmid on Apr 06, 2010; 8:50am
URL: http://imagej.273.s1.nabble.com/3D-Watershed-Plugin-tp3688059p3688061.html

Hi Ari,

if you have a 3D Euclidian Distance Map (EDM), you can simply search  
for the local maxima of this EDM. They will be the centers of the  
largest inscribed spheres, with the value equal to the radius.
There might be multiple nearby maxima (e.g. imagine a tube where you  
can inscribe many spheres with similar radius). You will probably  
need some type of post-processing to get rid of this.

Michael
________________________________________________________________

On 6 Apr 2010, at 00:47, Zwick, Ari A. wrote:

> 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
>
>