Thanks a lot for your answer @mdoube, and more generally thank you for the great work you’re doing with BoneJ.
I did give BoneJ2 a try, but considered that it was preferable for now to wait before ‘committing’ completely based the (probably simplistic) observation that the BoneJ2 website describes several tools as ‘work in progress’. The first tool one uses is usually ‘Optimise threshold’ (as binary images are required for most calculations). But this tool does not seem to be included yet.
Furthermore, I also tried to the new Anisotropy tool of BoneJ2 on one of my test stacks anisoPPP.tif (30.0 KB), which is basically ‘five simple trabeculae perfectly aligned positively along x, y, and z’. While BoneJ1’s routine yields a degree of anisotropy of almost 1, BoneJ2’s value is roughly 0.6 (whether or not the ‘Recommended minimum’ option is used). Furthermore, I did not see how to retrieve the direction of anisotropy in BoneJ2 (given as Eigen matrices in BoneJ1), which is a parameter of great interest to me.
Again, I’d like to warmly thank you @mdoube for your continuous effort with BoneJ!
All the best,