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 0.8 +/- 0.15 and 3.17 +/- 1.7 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.