I am using BoneJ, the imageJ’s plugin in order to quantify bone’s porosity with BV/TV ratio. The probleme that I m facing is that it’s calculating the BV/TV of all the whole image and not only my selection (or the region of interest made with wand tool). How to fix it ?
That is a big question. We were hoping for better ROI handling in ImageJ2 that we could use for all the plugins, but it did not happen in time. So unfortunately in this case BoneJ1 handles ROIs better than BoneJ2.
You have a couple of options. What I normally do is make a rectangular ROI, then duplicate the stack restricted to the ROI then delete the slices above and below the region I am interested in (or just duplicate the slice range that you want to analyse). In that way I get a stack filled with bone and marrow space only.
For irregular ROIs it’s a bit trickier. You can clear outside the ROI, measure the ROI area (in pixels), then measure the BV of the whole stack with the plugin. Ignore the TV from the plugin and use the sum of ROI areas (≃ volume) as TV instead to calculate BV/TV yourself.