Hello BoneJ community,
We are a group of ophthalmology researchers, and we are investigating an ocular structure called “lamina cribrosa.”. It is a bone-like structure, and we are using OCT to image it. We were using BoneJ to obtain thickness measurements of collagen beams in this structure (it looks like tubercular bone), and we had some issues with the average values the code provides. When running the code on a file with only 2 white circles, we found that the average calculated is much closer to the large diameter circle (for example, 20 and 100 voxels, the average provided was 95.7). We thought that BoneJ assigns the large diameter value to every voxel in the large circle, and the small diameter to all the voxels in the small one then calculates the mean over all pore voxels.
Sample image attached in next post
We are trying to understand why this happens and if this is a bug or intentional. Additionally, we are hoping to find a way that the code will generate a true average of all the particles in the image rather than a weighted one.
Looking forward to hearing from you,
Yoav Glidai, MD