fiber orientation

[jm]

Hello!

I am trying to determine the orientation/ angle of fibers (from microscopic images) in 3D. Is this possible with ImageJ, and if so, how?
Thanks for your reply!

[jm]

Thanks!
I did that and it's perfectly working.
But I have more than 2000 slices (image stack) of which I'd like to generate a 3D model and determine the fiber orientation (the angle) in z-direction. How am I gonna do that?

[Russ Taylor]

You can take a look at our semi-automatic fiber extraction and orientation-reporting software available at http://cismm.cs.unc.edu/downloads/ under the "Network Extractor" topic.  There is a tutorial there and a Windows installer.  Not ImageJ, but aimed at your issue.

[jm]

Thanks a lot Russ!
The only problem I have now is that I do not have images (SHG microscopy) with objects being on a darker background, the fibers are continuous.. so the software doesn't detect the fibers. I already tried to change the contrast etc., but so far I wasn't successful. Any idea how I can solve this problem?