Biomedical imaging is a driver of scientific discovery and a core component of medical care and is being stimulated by the field of deep learning. While semantic segmentation algorithms enable image analysis and quantification in many applications, the design of respective specialized solutions is non-trivial and highly dependent on dataset properties and hardware conditions. We developed nnU-Net, a deep learning-based segmentation method that automatically configures itself, including preprocessing, network architecture, training and post-processing for any new task. The key design choices in this process are modeled as a set of fixed parameters, interdependent rules and empirical decisions. Without manual intervention, nnU-Net surpasses most existing approaches, including highly specialized solutions on 23 public datasets used in international biomedical segmentation competitions. We make nnU-Net publicly available as an out-of-the-box tool, rendering state-of-the-art segmentation accessible to a broad audience by requiring neither expert knowledge nor computing resources beyond standard network training.

nnU-Net: a self-configuring method for deep learning-based biomedical image segmentation

Biomedical imaging is a driver of scientific discovery and core component of medical care, currently stimulated by the field of deep learning. While semantic segmentation algorithms enable 3D image analysis and quantification in many applications, the design of respective specialised solutions is non-trivial and highly dependent on dataset properties and hardware conditions. We propose nnU-Net, a deep learning framework that condenses the current domain knowledge and autonomously takes the key decisions required to transfer a basic architecture to different datasets and segmentation tasks. Without manual tuning, nnU-Net surpasses most specialised deep learning pipelines in 19 public international competitions and sets a new state of the art in the majority of the 49 tasks. The results demonstrate a vast hidden potential in the systematic adaptation of deep learning methods to different datasets. We make nnU-Net publicly available as an open-source tool that can effectively be used out-of-the-box, rendering state of the art segmentation accessible to non-experts and catalyzing scientific progress as a framework for automated method design.

Automated Design of Deep Learning Methods for Biomedical Image Segmentation

Exploring uncertainty measures in deep networks for Multiple sclerosis lesion detection and segmentation.

Deep learning with noisy labels: exploring techniques and remedies in medical image analysis

Deep convolutional neural networks for brain image analysis on magnetic resonance imaging: a review.

https://www.hal.inserm.fr/inserm-01480156/document

Laurence Catanese

Papers

Longitudinal multiple sclerosis lesion segmentation: Resource and challenge.