Stratified decision forests for accurate anatomical landmark localization in cardiac images

Accurate localization of anatomical landmarks is an important step in medical imaging, as it provides useful prior information for subsequent image analysis and acquisition methods. It is particularly useful for initialization of automatic image analysis tools (e.g. segmentation and registration) and detection of scan planes for automated image acquisition. Landmark localization has been commonly performed using learning based approaches, such as classifier and/or regressor models. However, trained models may not generalize well in heterogeneous datasets when the images contain large differences due to size, pose and shape variations of organs. To learn more data-adaptive and patient specific models, we propose a novel stratification based training model, and demonstrate its use in a decision forest. The proposed approach does not require any additional training information compared to the standard model training procedure and can be easily integrated into any decision tree framework. The proposed method is evaluated on 1080 3D highresolution and 90 multi-stack 2D cardiac cine MR images. The experiments show that the proposed method achieves state-of-theart landmark localization accuracy and outperforms standard regression and classification based approaches. Additionally, the proposed method is used in a multi-atlas segmentation to create a fully automatic segmentation pipeline, and the results show that it achieves state-of-the-art segmentation accuracy

ROAM: a Rich Object Appearance Model with Application to Rotoscoping

Rotoscoping, the detailed delineation of scene elements through a video shot, is a painstaking task of tremendous importance in professional post-production pipelines. While pixel-wise segmentation techniques can help for this task, professional rotoscoping tools rely on parametric curves that offer the artists a much better interactive control on the definition, editing and manipulation of the segments of interest. Sticking to this prevalent rotoscoping paradigm, we propose a novel framework to capture and track the visual aspect of an arbitrary object in a scene, given a first closed outline of this object. This model combines a collection of local foreground/background appearance models spread along the outline, a global appearance model of the enclosed object and a set of distinctive foreground landmarks. The structure of this rich appearance model allows simple initialization, efficient iterative optimization with exact minimization at each step, and on-line adaptation in videos. We demonstrate qualitatively and quantitatively the merit of this framework through comparisons with tools based on either dynamic segmentation with a closed curve or pixel-wise binary labelling

Topomap: Topological Mapping and Navigation Based on Visual SLAM Maps

Visual robot navigation within large-scale, semi-structured environments deals with various challenges such as computation intensive path planning algorithms or insufficient knowledge about traversable spaces. Moreover, many state-of-the-art navigation approaches only operate locally instead of gaining a more conceptual understanding of the planning objective. This limits the complexity of tasks a robot can accomplish and makes it harder to deal with uncertainties that are present in the context of real-time robotics applications. In this work, we present Topomap, a framework which simplifies the navigation task by providing a map to the robot which is tailored for path planning use. This novel approach transforms a sparse feature-based map from a visual Simultaneous Localization And Mapping (SLAM) system into a three-dimensional topological map. This is done in two steps. First, we extract occupancy information directly from the noisy sparse point cloud. Then, we create a set of convex free-space clusters, which are the vertices of the topological map. We show that this representation improves the efficiency of global planning, and we provide a complete derivation of our algorithm. Planning experiments on real world datasets demonstrate that we achieve similar performance as RRT* with significantly lower computation times and storage requirements. Finally, we test our algorithm on a mobile robotic platform to prove its advantages.Comment: 8 page

Interactive object contour extraction for shape modeling

In this paper we present a semi-automatic segmentation approach suitable for extracting object contours as a precursor to 2D shape modeling. The approach is a modified and extended version of an existing state-of-the-art approach based on the concept of a Binary Partition Tree (BPT) [1]. The resulting segmentation tool facilitates quick and easy extraction of an object’s contour via a small amount of user interaction that is easy to perform, even in complicated scenes. Illustrative segmentation results are presented and the usefulness of the approach in generating object shape models is discussed

Automatic 3D bi-ventricular segmentation of cardiac images by a shape-refined multi-task deep learning approach

Deep learning approaches have achieved state-of-the-art performance in cardiac magnetic resonance (CMR) image segmentation. However, most approaches have focused on learning image intensity features for segmentation, whereas the incorporation of anatomical shape priors has received less attention. In this paper, we combine a multi-task deep learning approach with atlas propagation to develop a shape-constrained bi-ventricular segmentation pipeline for short-axis CMR volumetric images. The pipeline first employs a fully convolutional network (FCN) that learns segmentation and landmark localisation tasks simultaneously. The architecture of the proposed FCN uses a 2.5D representation, thus combining the computational advantage of 2D FCNs networks and the capability of addressing 3D spatial consistency without compromising segmentation accuracy. Moreover, the refinement step is designed to explicitly enforce a shape constraint and improve segmentation quality. This step is effective for overcoming image artefacts (e.g. due to different breath-hold positions and large slice thickness), which preclude the creation of anatomically meaningful 3D cardiac shapes. The proposed pipeline is fully automated, due to network's ability to infer landmarks, which are then used downstream in the pipeline to initialise atlas propagation. We validate the pipeline on 1831 healthy subjects and 649 subjects with pulmonary hypertension. Extensive numerical experiments on the two datasets demonstrate that our proposed method is robust and capable of producing accurate, high-resolution and anatomically smooth bi-ventricular 3D models, despite the artefacts in input CMR volumes