How do I create a 3d skeleton map from a 3d image? the skeleton should be represented by 2d planes.

I have a problem that I hope someone can answer of at least point me in the right direction. For some background, I am trying to analyze some images and am hoping to create a 3D skeleton of a binary mapping of the images. The goal is to create a skeleton that truncates a binary 3d array to a series of skeleton branches/planes. Our hope is to generate 2d skeleton sheets from our scan data. Here is what I have tried so far:

1. Accurate Fast Marching by Drik-Jan Kroon. Although this was a very helpful program for generating a skeleton of a 2d slice and even 3d data, it maps a skeleton to a single line. Our hope is to get a 3d image mapped to a series of 2d planes.

2. skeleton in 3D by Gianni Schena. Although this program looks promising, I cannot understand how to use it due to lack of documentation. If ANYONE has used this, has found it useful and knows how to operate it I would be very grateful to any information

3. SDC Morphology Toolbox. I found this online and am looking at the trial version. Unfortunately from my initial research, it looks like this can only do a 2d skeleton from a 2d image. Am I correct in this understanding or can it create a 3d image?

On top of this, I am a relative MATLAB novice and am still learning to nuances of the program and its functions. This only complicates things so if anyone would be able to give some additional pointers on programming tips for constructing a 3d skeleton I would appreciate. Thank you.

-Erik V

[Sean de Wolski]

Perhaps you could show us a sample image, perhaps with a line showing what you expect (drawn in paint or whatever..)