Extending nnU-Net is all you need

Abstract: Semantic segmentation is one of the most popular research areas in medical image computing. Perhaps surprisingly, despite its conceptualization dating back to 2018, nnU-Net continues to provide competitive out-of-the-box solutions for a broad variety of segmentation problems and is regularly used as a development framework for challenge-winning algorithms. Here we use nnU-Net to participate in the AMOS2022 challenge, which comes with a unique set of tasks: not only is the dataset one of the largest ever created and boasts 15 target structures, but the competition also requires submitted solutions to handle both MRI and CT scans. Through careful modification of nnU-net's hyperparameters, the addition of residual connections in the encoder and the design of a custom postprocessing strategy, we were able to substantially improve upon the nnU-Net baseline. Our final ensemble achieves Dice scores of 90.13 for Task 1 (CT) and 89.06 for Task 2 (CT+MRI) in a 5-fold cross-validation on the provided training cases.