Displaying 3D volume using Volume Fraction surface algorithm

[Emily Yap]

Hi all,

I am trying to determine the volume fraction of my 3D stacks. When I select the surface algorithm and to show the 3D result, there is no 3D image and no result. But if I select just the surface algorithm, then there will be a result.

I have installed 3D viewer and Java3D so I don't understand why it isn't producing a 3D image result through the BoneJ Volume Fraction option. If there's anyone who can help explain to me what I'm doing wrong that would be highly appreciated.

Thanks!

[Michael Doube]

Hi Emily,

It works here. How big is your image? Try on a small test volume (128 x 128 x 128) and see if you get a result.

Are you able to run the 3D Viewer by itself, and load a surface?

Michael

[Michael Doube]

Also check to see if BoneJ>Isosurface produces an image for you.

[Emily Yap]

Hi Michael,

My images are 500x500x500 which is smaller than when I previously tried and worked before. It can load the surface and volume in 3D viewer but not through Volume Fraction or Isosurface. I also tried with the smaller test volume as you suggested but arrived at the same result. Isosurface will produce results and it'll say that it is "adding mesh to 3D viewer" but then nothing happens. 

Thanks

[Michael Doube]

Hi Emily,

To comment further I'd really need to know:

ImageJ / Fiji version (Help > About ImageJ)
Java version (Help > About ImageJ)
BoneJ version (Help > About Plugins... > BoneJ)
3D Viewer Version (where did you get it, there's no easy way to see the version)
Your operating system
Your graphics card and driver version and whether you updated it recently

Nothing has changed in the Isosurface code in BoneJ for a couple of years, so if the bug has appeared recently, something else must have changed.

https://github.com/mdoube/BoneJ/commits/master/src/org/doube/bonej/MeasureSurface.java

In particular, if you are using Fiji you may find that behaviour changes unexpectedly when you apply updates (for now, BoneJ is tested against vanilla ImageJ and an older 3D viewer, a situation that will change I hope in the near future).

Michael