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!