Hello,
I would like to use the ellipsoid factor on CT images. The voxel resolution is 80 μm.
Even when I raise the Vectors (up to 500), I decrease the Sampling increment (down to 0.02) and I use only one point per ellipsoid, the results are bad.
Is the resolution too high, compared to the size of trabecular elements, or is it because of the parameters ? I precise that the samples come from bovine femurs, the structure is a mix of plates and rodes.
Thank you,
Nicolas Rogalski
Hi Nicolas,
Do you know the trabecular thickness in pixels of your images? Is there a (cropped-down) individual sample you could provide us for testing?
Estimating the trabecular thickness of cattle from two samples measured in Doube et al 2011 (see supplemental material) suggests 240-340 um, so 3-4 pixels at your resolution, average trabecular thickness. In my view, that’s just a little bit too low resolution for any trabecular analysis, so unfortunately, I doubt it’s worth trying.
Should you still want to go ahead with Ellipsoid Factor, in the latest BoneJ, there are some additional EF parameters that you can attempt to tune, and some recommendations for how to do this should be in this preprint.
You might in particular want to try adding more distance-ridge based seeds (i.e. tick the distance-ridge seed box and, from my experience, experiment with thresholds between 0.6 and 0.9 or so). For what it’s worth, 500 vectors and 0.02 step seem excessive to me - in my experience 100 vectors and as step between 0.5 and 0.8 should be OK.
Hope this helps!
Hi Alessandro,
thank you very much for this answer. The Tb.Th values of my samples are indeed in this range.
I will try to tune the other parameters.
What is the minimum resolution you believe is enough to run the EF ? (For the same range of thicknesses).
You’re welcome!
For me, in an ideal scenario, you’d have >10 pixels across a trabecula, so a good resolution in your case would be ~20-30 um or better. I think it’s worth trying while acknowledging the limits of your resolution if you get to >5 pixels across a trabeculae, so that would be ~50um or lower voxel size in your case.