Re: 3D Watershed Plugin?

Posted by Teresa W on Jun 05, 2010; 6:31am
URL: http://imagej.273.s1.nabble.com/3D-Watershed-Plugin-tp3688059p3688060.html

Hi Avi

I'm interested in this as well, as I want to quantify the void size distributions for my highly interconnected porous bread samples. Please, if you could pass on what you decided to do regarding 3d watershedding, that would be very helpful.

If you haven't found a solution, I worked out a way to watershed particles/voids in stacks for 2D counting. The approach arbitarily cuts off intersecting voids at necks close to the edge of the counting frame. As I wanted to get an unbiased count of particle size categories, I used different counting frames to exclude particles intersecting two sides of the final count frame, while stitching back the spillover of particles on the other two sides. See Disector Counting Frame post Jun 11, 2008 for the details, my post's towards the end.

I also wanted to count the particles with watershedding removed (Coaleseced/interconnected). For this
* Subtracted watershedded whole image from original binary image to get watershed lines
* ANDed the lines with a mask of the counted particles which had undergone Erode/Dilate,
* Added back into stack to remove watershed lines from my binary counting image.
* Recounted reconnected image.

I think this approach would work in 3D as well
* Follow process in 2D
* Check stack, flicking through to erase the occasional extra particle that appears on the edges.

I think it would be useful also to quantify the number of 'necks' intersecting the count volume where the voids were cut off, as part of defining the counted unit within the sample.

Anyway, I am going to give it a go myself now.

Teresa Wegrzyn
Food Tecnology
Massey University
Palmerston North
New Zealand