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Deep learning (DL) approaches are state-of-the-art for many medical image segmentation tasks. They offer a number of advantages: they can be trained for specific tasks, computations are fast at test time, and segmentation quality is typically high. In contrast, previously popular multi-atlas segmentation (MAS) methods are relatively slow (as they rely on costly registrations) and even though sophisticated label fusion strategies have been proposed, DL approaches generally outperform MAS. In this work, we propose a DL-based label fusion strategy (VoteNet) which locally selects a set of reliable atlases whose labels are then fused via plurality voting. Experiments on 3D brain MRI data show that by selecting a good initial atlas set MAS with VoteNet significantly outperforms a number of other label fusion strategies as well as a direct DL segmentation approach. We also provide an experimental analysis of the upper performance bound achievable by our method. While unlikely achievable in practice, this bound suggests room for further performance improvements. Lastly, to address the runtime disadvantage of standard MAS, all our results make use of a fast DL registration approach.

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, preprocessing, training and inference. These choices are not independent of each other and substantially impact the overall performance. The present paper introduces the nnU-Net ('no-new-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.

In this paper, we focus on three problems in deep learning based medical image segmentation. Firstly, U-net, as a popular model for medical image segmentation, is difficult to train when convolutional layers increase even though a deeper network usually has a better generalization ability because of more learnable parameters. Secondly, the exponential ReLU (ELU), as an alternative of ReLU, is not much different from ReLU when the network of interest gets deep. Thirdly, the Dice loss, as one of the pervasive loss functions for medical image segmentation, is not effective when the prediction is close to ground truth and will cause oscillation during training. To address the aforementioned three problems, we propose and validate a deeper network that can fit medical image datasets that are usually small in the sample size. Meanwhile, we propose a new loss function to accelerate the learning process and a combination of different activation functions to improve the network performance. Our experimental results suggest that our network is comparable or superior to state-of-the-art methods.

In this work, we evaluate the use of superpixel pooling layers in deep network architectures for semantic segmentation. Superpixel pooling is a flexible and efficient replacement for other pooling strategies that incorporates spatial prior information. We propose a simple and efficient GPU-implementation of the layer and explore several designs for the integration of the layer into existing network architectures. We provide experimental results on the IBSR and Cityscapes dataset, demonstrating that superpixel pooling can be leveraged to consistently increase network accuracy with minimal computational overhead. Source code is available at //github.com/bermanmaxim/superpixPool

Weak supervision, e.g., in the form of partial labels or image tags, is currently attracting significant attention in CNN segmentation as it can mitigate the lack of full and laborious pixel/voxel annotations. Enforcing high-order (global) inequality constraints on the network output, for instance, on the size of the target region, can leverage unlabeled data, guiding training with domain-specific knowledge. Inequality constraints are very flexible because they do not assume exact prior knowledge. However,constrained Lagrangian dual optimization has been largely avoided in deep networks, mainly for computational tractability reasons.To the best of our knowledge, the method of Pathak et al. is the only prior work that addresses deep CNNs with linear constraints in weakly supervised segmentation. It uses the constraints to synthesize fully-labeled training masks (proposals)from weak labels, mimicking full supervision and facilitating dual optimization.We propose to introduce a differentiable term, which enforces inequality constraints directly in the loss function, avoiding expensive Lagrangian dual iterates and proposal generation. From constrained-optimization perspective, our simple approach is not optimal as there is no guarantee that the constraints are satisfied. However, surprisingly,it yields substantially better results than the proposal-based constrained CNNs, while reducing the computational demand for training.In the context of cardiac images, we reached a segmentation performance close to full supervision using a fraction (0.1%) of the full ground-truth labels and image-level tags.While our experiments focused on basic linear constraints such as the target-region size and image tags, our framework can be easily extended to other non-linear constraints.Therefore, it has the potential to close the gap between weakly and fully supervised learning in semantic image segmentation.

Image foreground extraction is a classical problem in image processing and vision, with a large range of applications. In this dissertation, we focus on the extraction of text and graphics in mixed-content images, and design novel approaches for various aspects of this problem. We first propose a sparse decomposition framework, which models the background by a subspace containing smooth basis vectors, and foreground as a sparse and connected component. We then formulate an optimization framework to solve this problem, by adding suitable regularizations to the cost function to promote the desired characteristics of each component. We present two techniques to solve the proposed optimization problem, one based on alternating direction method of multipliers (ADMM), and the other one based on robust regression. Promising results are obtained for screen content image segmentation using the proposed algorithm. We then propose a robust subspace learning algorithm for the representation of the background component using training images that could contain both background and foreground components, as well as noise. With the learnt subspace for the background, we can further improve the segmentation results, compared to using a fixed subspace. Lastly, we investigate a different class of signal/image decomposition problem, where only one signal component is active at each signal element. In this case, besides estimating each component, we need to find their supports, which can be specified by a binary mask. We propose a mixed-integer programming problem, that jointly estimates the two components and their supports through an alternating optimization scheme. We show the application of this algorithm on various problems, including image segmentation, video motion segmentation, and also separation of text from textured images.

Weakly supervised instance segmentation with image-level labels, instead of expensive pixel-level masks, remains unexplored. In this paper, we tackle this challenging problem by exploiting class peak responses to enable a classification network for instance mask extraction. With image labels supervision only, CNN classifiers in a fully convolutional manner can produce class response maps, which specify classification confidence at each image location. We observed that local maximums, i.e., peaks, in a class response map typically correspond to strong visual cues residing inside each instance. Motivated by this, we first design a process to stimulate peaks to emerge from a class response map. The emerged peaks are then back-propagated and effectively mapped to highly informative regions of each object instance, such as instance boundaries. We refer to the above maps generated from class peak responses as Peak Response Maps (PRMs). PRMs provide a fine-detailed instance-level representation, which allows instance masks to be extracted even with some off-the-shelf methods. To the best of our knowledge, we for the first time report results for the challenging image-level supervised instance segmentation task. Extensive experiments show that our method also boosts weakly supervised pointwise localization as well as semantic segmentation performance, and reports state-of-the-art results on popular benchmarks, including PASCAL VOC 2012 and MS COCO.

The Normalized Cut (NCut) objective function, widely used in data clustering and image segmentation, quantifies the cost of graph partitioning in a way that biases clusters or segments that are balanced towards having lower values than unbalanced partitionings. However, this bias is so strong that it avoids any singleton partitions, even when vertices are very weakly connected to the rest of the graph. Motivated by the B\"uhler-Hein family of balanced cut costs, we propose the family of Compassionately Conservative Balanced (CCB) Cut costs, which are indexed by a parameter that can be used to strike a compromise between the desire to avoid too many singleton partitions and the notion that all partitions should be balanced. We show that CCB-Cut minimization can be relaxed into an orthogonally constrained $\ell_{\tau}$-minimization problem that coincides with the problem of computing Piecewise Flat Embeddings (PFE) for one particular index value, and we present an algorithm for solving the relaxed problem by iteratively minimizing a sequence of reweighted Rayleigh quotients (IRRQ). Using images from the BSDS500 database, we show that image segmentation based on CCB-Cut minimization provides better accuracy with respect to ground truth and greater variability in region size than NCut-based image segmentation.

We propose a new nonlinear embedding -- Piecewise Flat Embedding (PFE) -- for image segmentation. Based on the theory of sparse signal recovery, piecewise flat embedding attempts to recover a piecewise constant image representation with sparse region boundaries and sparse cluster value scattering. The resultant piecewise flat embedding exhibits interesting properties such as suppressing slowly varying signals, and offers an image representation with higher region identifiability which is desirable for image segmentation or high-level semantic analysis tasks. We formulate our embedding as a variant of the Laplacian Eigenmap embedding with an $L_{1,p} (0<p\leq1)$ regularization term to promote sparse solutions. First, we devise a two-stage numerical algorithm based on Bregman iterations to compute $L_{1,1}$-regularized piecewise flat embeddings. We further generalize this algorithm through iterative reweighting to solve the general $L_{1,p}$-regularized problem. To demonstrate its efficacy, we integrate PFE into two existing image segmentation frameworks, segmentation based on clustering and hierarchical segmentation based on contour detection. Experiments on four major benchmark datasets, BSDS500, MSRC, Stanford Background Dataset, and PASCAL Context, show that segmentation algorithms incorporating our embedding achieve significantly improved results.

Superpixel segmentation has become an important research problem in image processing. In this paper, we propose an Iterative Spanning Forest (ISF) framework, based on sequences of Image Foresting Transforms, where one can choose i) a seed sampling strategy, ii) a connectivity function, iii) an adjacency relation, and iv) a seed pixel recomputation procedure to generate improved sets of connected superpixels (supervoxels in 3D) per iteration. The superpixels in ISF structurally correspond to spanning trees rooted at those seeds. We present five ISF methods to illustrate different choices of its components. These methods are compared with approaches from the state-of-the-art in effectiveness and efficiency. The experiments involve 2D and 3D datasets with distinct characteristics, and a high level application, named sky image segmentation. The theoretical properties of ISF are demonstrated in the supplementary material and the results show that some of its methods are competitive with or superior to the best baselines in effectiveness and efficiency.