Automated analysis of rabbit knee calcified cartilage morphology using micro-computed tomography and deep learning segmentation

Purpose Only little is known how calcified cartilage (CC) structure changes during exercise, aging and disease. CC thickness (CC.Th) can be analyzed using conventional histological sections. Micro-computed tomography (μCT) allows for three-dimensional (3D) imaging of mineralized tissues, however, the segmentation between bone and CC is challenging. Here, we present state-of-the-art deep learning segmentation for μCT images to enable assessment of CC morphology. Methods Sixteen knees from twelve New Zealand White rabbits were dissected into osteochondral samples from six anatomical regions: lateral and medial femoral condyles, lateral and medial tibial plateaus, femoral groove and patella ( n = 96). Samples were imaged with μCT and processed for conventional histology. Manually segmented CC from the histology and reconstructed μCT images was used as the gold standard to train segmentation models with different encoder-decoder architectures. The models with the greatest out-of-fold evaluation Dice score were used for automated CC.Th analysis. Subsequently, the automated CC.Th analysis was compared across a total of 24 regions, co-registered between the imaging modalities, using Pearson correlation and Bland-Altman analyses. Finally, the anatomical variation in CC.Th was assessed via a Linear Mixed Model analysis. Results The best segmentation models yielded average Dice scores of 0.891 and 0.807 for histology and μCT segmentation, respectively. The correlation between the co-registered regions across the modalities was strong ( r = 0.897). The Bland-Altman analysis yielded a bias of 21.9 μm and a standard deviation of 21.5 μm between the methods. Finally, both methods could separate the CC morphology between the patella, femoral, and tibial regions ( p < 0.001). Conclusion The presented method allows for ex vivo 3D assessment of CC.Th in an automated and non-destructive manner. We demonstrated its utility by quantifying CC.Th in different anatomical regions. CC.Th was the thickest in the patella and the thinnest in the tibial plateau. ![Figure][1] Graphical abstract We present a μCT-based method with deep learning segmentation for analyzing calcified cartilage thickness (CC.Th). The method is compared throughout the study against conventional histology. The comparison against co-registered regions yielded a strong Pearson correlation (r = 0.90). Both methods were able to separate the CC.Th properties between tibia, femur, and patella. ### Competing Interest Statement Details are given in disclosures and acknowledgments sections of the manuscript. [1]: pending:yes