Tackling the class imbalance problem of deep learning-based head and neck organ segmentation

PURPOSE: The segmentation of organs at risk (OAR) is a required precondition for the cancer treatment with image- guided radiation therapy. The automation of the segmentation task is therefore of high clinical relevance. Deep learning (DL)-based medical image segmentation is currently the most successful approach, but suffers from the over-presence of the background class and the anatomically given organ size difference, which is most severe in the head and neck (HAN) area. METHODS: To tackle the HAN area-specific class imbalance problem, we first optimize the patch size of the currently best performing general-purpose segmentation framework, the nnU-Net, based on the introduced class imbalance measurement, and second introduce the class adaptive Dice loss to further compensate for the highly imbalanced setting. RESULTS: Both the patch size and the loss function are parameters with direct influence on the class imbalance, and their optimization leads to a 3% increase in the Dice score and 22% reduction in the 95% Hausdorff distance compared to the baseline, finally reaching [Formula: see text] and [Formula: see text] mm for the segmentation of seven HAN organs using a single and simple neural network. CONCLUSION: The patch size optimization and the class adaptive Dice loss are both simply integrable in current DL-based segmentation approaches and allow to increase the performance for class imbalance segmentation tasks.