Learned boundary maps are known to outperform hand- crafted ones as a basis for the watershed algorithm. We show, for the first time, how to train watershed computation jointly with boundary map prediction. The estimator for the merging priorities is cast as a neural network that is con- volutional (over space) and recurrent (over iterations). The latter allows learning of complex shape priors. The method gives the best known seeded segmentation results on the CREMI segmentation challenge.
Reference EPFL-ARTICLE-226946doi:10.1038 nmeth.4151View record in Web of Science Record created on 2017-03-27, modified on 2017-07-13 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 this http URL . Most contemporary approaches to instance segmentation use complex pipelines involving conditional random fields, recurrent neural networks, object proposals, or template matching schemes. In this paper, we present a simple yet powerful end-to-end convolutional neural network to tackle this task. Our approach combines intuitions from the classical watershed transform and modern deep learning to produce an energy map of the image where object instances are unambiguously represented as energy basins. We then perform a cut at a single energy level to directly yield connected components corresponding to object instances. Our model achieves more than double the performance over the state-of-the-art on the challenging Cityscapes Instance Level Segmentation task.