I have been using bonej to assess trabecular structure of mouse tibia. Images are obtained with Bruker microCT, reconstructed at 10microns.
I have been using BoneJ1 as I can generate a 3D reconstruction of the trabecular bone surface.
I have noticed that default ImageJ threshold is often to strict. (Not picking up thin segments of bone). Huang seems to be the best option. (Although it probably over estimates bone thickness)
I use do the thresholding across the entire stack. (Stack Histogram option). Also I try crop the image to reduce the amount of “background”.
I was wondering if there is any hard or fast rules in terms of ideal thresholding methods for trabecular bone analysis.