nnU-Net: Breaking the Spell on Successful Medical Image Segmentation

Fueled by the diversity of datasets, semantic segmentation is a popular subfield in medical image analysis with a vast number of new methods being proposed each year. This ever-growing jungle of methodologies, however, becomes increasingly impenetrable. At the same time, many proposed methods fail to generalize beyond the experiments they were demonstrated on, thus hampering the process of developing a segmentation algorithm on a new dataset. Here we present nnU-Net ('no-new-Net'), a framework that automatically adapts itself to any given new dataset. While this process was completely human-driven so far, we make a first attempt to automate necessary adaptations such as preprocessing, the exact patch size, batch size, and inference settings based on the properties of a given dataset. Remarkably, nnU-Net strips away the architectural bells and whistles that are typically proposed in the literature and relies on just a simple U-Net architecture embedded in a robust training scheme. Out of the box, nnU-Net achieves state of the art performance on six well-established segmentation challenges. Source code is available at https://github.com/MIC-DKFZ/nnunet.