The pipeline of the methodology. First, the osteochondral cores were prepared from the tibiae and cut in half. The first half was subjected to histology (OARSI grading), and the second half to μCT. Based on the OARSI grades, 12 samples were selected for this study: six samples with OARSI grades 0–1.0, and six samples with OARSI grades 3–3.5. After the HMDS-based sample processing protocol, the samples were imaged with the μCT device, followed by image reconstructions and VOI selection. The chondron selection and segmentation algorithm was then applied to the VOIs, and finally, chondron analysis were performed.