The U-Net was presented in 2015. With its straight-forward and successful architecture it quickly evolved to a commonly used benchmark in medical image segmentation. The adaptation of the U-Net to novel problems, however, comprises several degrees of freedom regarding the exact architecture, pre-processing, training and inference. These choices are not independent of each other and substantially impact the overall performance. The present paper introduces the nnU-Net ("nonew-Net"), which refers to a robust and self-adapting framework on the basis of 2D and 3D vanilla U-Nets. We argue the strong case for taking away superfluous bells and whistles of many proposed network designs and instead focus on the remaining aspects that make out the performance and generalizability of a method. We evaluate the nnU-Net in the context of the Medical Segmentation Decathlon challenge, which measures segmentation performance in ten disciplines comprising distinct entities, image modalities, image geometries and dataset sizes, with no manual adjustments between datasets allowed. At the time of manuscript submission, nnU-Net achieves the highest mean dice scores across all classes and seven phase 1 tasks (except class 1 in BrainTumour) in the online leaderboard of the challenge.
For many applications, in particular in natural science, the task is to determine hidden system parameters from a set of measurements. Often, the forward process from parameter-to measurement-space is well-defined, whereas the inverse problem is ambiguous: multiple parameter sets can result in the same measurement. To fully characterize this ambiguity, the full posterior parameter distribution, conditioned on an observed measurement, has to be determined. We argue that a particular class of neural networks is well suited for this task -so-called Invertible Neural Networks (INNs). Unlike classical neural networks, which attempt to solve the ambiguous inverse problem directly, INNs focus on learning the forward process, using additional latent output variables to capture the information otherwise lost. Due to invertibility, a model of the corresponding inverse process is learned implicitly. Given a specific measurement and the distribution of the latent variables, the inverse pass of the INN provides the full posterior over parameter space. We prove theoretically and verify experimentally, on artificial data and real-world problems from medicine and astrophysics, that INNs are a powerful analysis tool to find multi-modalities in parameter space, uncover parameter correlations, and identify unrecoverable parameters.
PurposeMultispectral imaging can provide reflectance measurements at multiple spectral bands for each image pixel. These measurements can be used for estimation of important physiological parameters, such as oxygenation, which can provide indicators for the success of surgical treatment or the presence of abnormal tissue. The goal of this work was to develop a method to estimate physiological parameters in an accurate and rapid manner suited for modern high-resolution laparoscopic images.MethodsWhile previous methods for oxygenation estimation are based on either simple linear methods or complex model-based approaches exclusively suited for off-line processing, we propose a new approach that combines the high accuracy of model-based approaches with the speed and robustness of modern machine learning methods. Our concept is based on training random forest regressors using reflectance spectra generated with Monte Carlo simulations.ResultsAccording to extensive in silico and in vivo experiments, the method features higher accuracy and robustness than state-of-the-art online methods and is orders of magnitude faster than other nonlinear regression based methods.ConclusionOur current implementation allows for near real-time oxygenation estimation from megapixel multispectral images and is thus well suited for online tissue analysis.
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