MOTIVATION: While deep-learning algorithms have demonstrated outstanding performance in semantic image segmentation tasks, large annotation datasets are needed to create accurate models. Annotation of histology images is challenging due to the effort and experience required to carefully delineate tissue structures, and difficulties related to sharing and markup of whole-slide images. RESULTS: We recruited 25 participants, ranging in experience from senior pathologists to medical students, to delineate tissue regions in 151 breast cancer slides using the Digital Slide Archive. Inter-participant discordance was systematically evaluated, revealing low discordance for tumor and stroma, and higher discordance for more subjectively defined or rare tissue classes. Feedback provided by senior participants enabled the generation and curation of 20 000+ annotated tissue regions. Fully convolutional networks trained using these annotations were highly accurate (mean AUC=0.945), and the scale of annotation data provided notable improvements in image classification accuracy. AVAILABILITY AND IMPLEMENTATION: Dataset is freely available at: https://goo.gl/cNM4EL. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Image segmentation is, in general, an ill-posed problem and additional constraints need to be imposed in order to achieve the desired segmentation result. While segmenting organs in medical images, which is the topic of this paper, a significant amount of prior knowledge about the shape, appearance, and location of the organs is available that can be used to constrain the solution space of the segmentation problem. Among the various types of prior information, the incorporation of prior information about shape, in particular, is very challenging. In this paper, we present an explicit shape-constrained MAP-MRF-based contour evolution method for the segmentation of organs in 2-D medical images. Specifically, we represent the segmentation contour explicitly as a chain of control points. We then cast the segmentation problem as a contour evolution problem, wherein the evolution of the contour is performed by iteratively solving a MAP-MRF labeling problem. The evolution of the contour is governed by three types of prior information, namely: (i) appearance prior, (ii) boundary-edgeness prior, and (iii) shape prior, each of which is incorporated as clique potentials into the MAP-MRF problem. We use the master-slave dual decomposition framework to solve the MAP-MRF labeling problem in each iteration. In our experiments, we demonstrate the application of the proposed method to the challenging problem of heart segmentation in non-contrast computed tomography data.

In this paper, we present a graph-based image segmentation method (patch-cuts) that incorporates features and spatial relations obtained from image patches. In the first step, patch-cuts extracts a set of patches that can assume arbitrary shape and size. Patches are determined by a combination of intensity quantization and morphological operations and render the proposed method robust against noise. Upon patch extraction, a set of intensity, texture and shape features are computed for each patch. These features are integrated and minimized simultaneously in a tunable energy function. Patch-cuts explores the benefit of information theory-based measures such as the Kullback-Leibler and the Jensen-Shannon divergence in its energy terms. In our experiments, we applied patchcuts to general images as well as to non-contrast Computed Tomography heart scans. 1

In this paper, we present a knowledge-driven Markov Random Field (MRF) model for the segmentation of organs in medical images with particular emphasis on the incorporation of shape constraints into the segmentation problem. We cast the problem of image segmentation as the Maximum A Posteriori (MAP) estimation of a Markov Random Field which, in essence, is equivalent to the minimization of the corresponding Gibbs energy function. We then incorporate a set of constraints into the Gibbs energy function that collectively force the resulting segmentation contour/surface to have a shape similar to that of a given shape template. In particular, we introduce a flux-maximization constraint and a generalized template-based star-shape constraint that are encoded into the first- and second-order clique potentials of the Gibbs energy function, respectively. Our main contribution is in the translation of a set of global notions about the shape of the desired segmentation contour into a set of local measures that can be conveniently encoded into the Gibbs energy function and used in combination with other traditionally used constraints derived from image information. In our experiments, we demonstrate the application of the proposed method to the challenging problem of heart segmentation in non-contrast computed tomography (CT) data.

Image segmentation is, in general, an ill-posed problem and additional constraints need to be imposed in order to achieve the desired result. Particularly in the field of medical image segmentation, a significant amount of prior knowledge is available that can be used to constrain the solution space of the segmentation problem. However, most of this prior knowledge is, in general, vague or imprecise in nature, which makes it very difficult to model. This is the problem that is addressed in this paper. Specifically, in this paper, we present fuzzy-cuts, a novel, knowledge-driven, graph-based method for medical image segmentation. We cast the problem of image segmentation as the maximum a posteriori (MAP) estimation of a Markov random field (MRF) which, in essence, is equivalent to the minimization of the corresponding Gibbs energy function. Considering the inherent imprecision that is common in the a priori description of objects in medical images, we propose a fuzzy theoretic model to incorporate knowledge-driven constraints into the MAP-MRF formulation. In particular, we focus on prior information about the object's location, appearance and spatial connectivity to a known seed region inside the object. To that end, we introduce fuzzy connectivity and fuzzy location priors that are used in combination to define the first-order clique potential of the Gibbs energy function. In our experiments, we demonstrate the application of the proposed method to the challenging problem of heart segmentation in non-contrast computed tomography (CT) data.