Shape analyses on pQCT images


I am new to ImageJ and would really appreciate some direction, specifically in terms of shape analyses.
I have 4 pQCT images of slices of the shank(4%, 14%,38% and 66% of tibial length). I want to be able to perform shape analysis on the tibia part of the image only, identifying the centre of the bone as well as outer coordinates (any other shape related analyses would also be beneficial) The aim is to be able to use this to influence a finite element model.
I have downloaded BoneJ as a plugin. I have managed to crop the image to just include the tibia portion, performing shape analyses based on a cropped image to get the centroid x and y coordinate. However I am unsure how to do anything else in terms of shape analyses, or indeed if this is the correct way of doing it.
Any help would be much appreciated.

Many Thanks,

If your ROI contains only the tibial cross-section, you can get some useful numbers like cross-sectional area, second moment of area, and section modulus using BoneJ’s Slice Geometry. Make sure you specify sensible upper and lower threshold values so that BoneJ knows which pixels to use and which to exclude.

@tjrantal might have other suggestions based on your use of pQCT, in addition to the notes we publish.

The published notes were really useful and helped me get to that point. :relaxed:
The image quality isn’t great so the grey scale is quite similar for different areas, would I have the upper and lower limit to include just those which would be cortical bone?

Many Thanks

Yes, if that is what you are interested in