U-Net: Convolutional Networks for Biomedical Image Segmentation
There is large consent that successful training of deep networks requires many thousand annotated training samples. In this paper, we present a network and training strategy that relies on the strong use of data augmentation to use the available annotated
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Abstract. There is large consent that successful training of deep networks requires many thousand annotated training samples. In this paper, we present a network and training strategy that relies on the strong use of data augmentation to use the available annotated samples more efficiently. The architecture consists of a contracting path to capture context and a symmetric expanding path that enables precise localization. We show that such a network can be trained end-to-end from very few images and outperforms the prior best method (a sliding-window convolutional network) on the ISBI challenge for segmentation of neuronal structures in electron microscopic stacks. Using the same network trained on transmitted light microscopy images (phase contrast and DIC) we won the ISBI cell tracking challenge 2015 in these categories by a large margin. Moreover, the network is fast. Segmentation of a 512x512 image takes less than a second on a recent GPU. The full implementation (based on Caffe) and the trained networks are available at http://lmb.informatik.uni-freiburg.de/people/ronneber/u-net.
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Introduction
In the last two years, deep convolutional networks have outperformed the state of the art in many visual recognition tasks, e.g. [7]. While convolutional networks have already existed for a long time [8], their success was limited due to the size of the available training sets and the size of the considered networks. The breakthrough by Krizhevsky et al. [7] was due to supervised training of a large network with 8 layers and millions of parameters on the ImageNet dataset with 1 million training images. Since then, even larger and deeper networks have been trained [12]. The typical use of convolutional networks is on classification tasks, where the output to an image is a single class label. However, in many visual tasks, especially in biomedical image processing, the desired output should include localization, i.e., a class label is supposed to be assigned to each pixel. Moreover, thousands of training images are usually beyond reach in biomedical tasks. Hence, Ciresan et al. [2] trained a network in a sliding-window setup to predict the class label of each pixel by providing a local region (patch) around that pixel c Springer International Publishing Switzerland 2015 N. Navab et al. (Eds.): MICCAI 2015, Part III, LNCS 9351, pp. 234–241, 2015. DOI: 10.1007/978-3-319-24574-4_28
U-Net: Convolutional Networks for Biomedical Image Segmentation
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Fig. 1. U-net architecture (example for 32x32 pixels in the lowest resolution). Each blue box corresponds to a multi-channel feature map. The number of channels is denoted on top of the box. The x-y-size is provided at the lower left edge of the box. White boxes represent copied feature maps. The arrows denote the different operations.
as input. First, this network can localize. Secondly, the training data in terms of patches is much larger than the number of training images. The resulting network won the EM segmentation challenge at ISBI 2012 by a large margin. Obviously, the
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