Anisotropy and SMI in BoneJ

Hi all,
I am comparing histomorphometry results from commercial and BoneJ software.
Except Anisotropy and SMI, all other values look similar.
Is there a manual how to properly prepare your stack for BoneJ analysis, since I am missing something definitely?

update: I try to evaluate cylindrical models, and somehow I think that my circular selection is not evaluated but the whole square instead. How can I make sure that only my ROI is analysed, not the whole window?


Hello Nikola,

The documentation for these BoneJ plugins is available at:

At the moment they don’t support an option to limit the calculations to ROIs. I guess what you could try to do is call Edit > Clear Outside once you’ve drawn your circular selection.

Best Regards,
Richard Domander

P.S. @mdoube any advice?

1 Like

Edit > Clear Outside is exactly what I did, and it worked for Tb.Sp.
It could just be that algorithm works a bit different compared to commercial one, and that both results are correct at some extent.