Gareth Funka-Lea

Graph Cuts and Efficient N-D Image Segmentation

Combinatorial graph cut algorithms have been successfully applied to a wide range of problems in vision and graphics. This paper focusses on possibly the simplest application of graph-cuts: segmentation of objects in image data. Despite its simplicity, this application epitomizes the best features of combinatorial graph cuts methods in vision: global optima, practical efficiency, numerical robustness, ability to fuse a wide range of visual cues and constraints, unrestricted topological properties of segments, and applicability to N-D problems. Graph cuts based approaches to object extraction have also been shown to have interesting connections with earlier segmentation methods such as snakes, geodesic active contours, and level-sets. The segmentation energies optimized by graph cuts combine boundary regularization with region-based properties in the same fashion as Mumford-Shah style functionals. We present motivation and detailed technical description of the basic combinatorial optimization framework for image segmentation via s/t graph cuts. After the general concept of using binary graph cut algorithms for object segmentation was first proposed and tested in Boykov and Jolly (2001), this idea was widely studied in computer vision and graphics communities. We provide links to a large number of known extensions based on iterative parameter re-estimation and learning, multi-scale or hierarchical approaches, narrow bands, and other techniques for demanding photo, video, and medical applications.

A review of 3D vessel lumen segmentation techniques: Models, features and extraction schemes

Vascular diseases are among the most important public health problems in developed countries. Given the size and complexity of modern angiographic acquisitions, segmentation is a key step toward the accurate visualization, diagnosis and quantification of vascular pathologies. Despite the tremendous amount of past and on-going dedicated research, vascular segmentation remains a challenging task. In this paper, we review state-of-the-art literature on vascular segmentation, with a particular focus on 3D contrast-enhanced imaging modalities (MRA and CTA). We structure our analysis along three axes: models, features and extraction schemes. We first detail model-based assumptions on the vessel appearance and geometry which can embedded in a segmentation approach. We then review the image features that can be extracted to evaluate these models. Finally, we discuss how existing extraction schemes combine model and feature information to perform the segmentation task. Each component (model, feature and extraction scheme) plays a crucial role toward the efficient, robust and accurate segmentation of vessels of interest. Along each axis of study, we discuss the theoretical and practical properties of recent approaches and highlight the most advanced and promising ones.

Multi-label Image Segmentation for Medical Applications Based on Graph-Theoretic Electrical Potentials

A novel method is proposed for performing multi-label, semi-automated image segmentation. Given a small number of pixels with user-defined labels, one can analytically (and quickly) determine the probability that a random walker starting at each unlabeled pixel will first reach one of the pre-labeled pixels. By assigning each pixel to the label for which the greatest probability is calculated, a high-quality image segmentation may be obtained. Theoretical properties of this algorithm are developed along with the corresponding connections to discrete potential theory and electrical circuits. This algorithm is formulated in discrete space (i.e., on a graph) using combinatorial analogues of standard operators and principles from continuous potential theory, allowing it to be applied in arbitrary dimension.

Automatic heart isolation for CT coronary visualization using graph-cuts

We describe a means to automatically and efficiently isolate the outer surface of the entire heart in computer tomography (CT) cardiac scans. Isolating the entire heart allows the coronary vessels on the surface of the heart to be easily visualized despite the proximity of surrounding organs such as the ribs and pulmonary blood vessels. Numerous techniques have been described for segmenting the left ventricle of the heart in images from various types of medical scanners but rarely has the entire heart been segmented. We make use of graph-cuts to do the segmentation and introduce a novel means of initiating and constraining the graph-cut technique for heart isolation. The technique has been tested on 70 patient data sets. Results are compares with hand labeled results

Combining color and geometry for the active, visual recognition of shadows

Shadows are a frequent occurrence, but they cannot be infallibly recognized until a scenes geometry and lighting are known. We present a number of cues which together strongly suggest the identification of a shadow and which can be examined with low cost. The techniques are: a color image segmentation method that recovers single material surfaces as single image regions irregardless of the surface partially in shadow, a method to recover the penumbra and umbra of shadow; a method for determining whether some object could be obstructing a light source. The last cue requires the examination of well understood shadows in the scene. Our observer is equipped with an extendable probe for casting its own shadows. Actively obtained shadows allow the observer to experimentally determine the location of the light sources in the scene. The system has been tested both indoors and out.<<ETX>>

Segmentation of the left ventricle in cardiac MR images

This paper describes a segmentation technique to automatically extract the myocardium in 4D cardiac MR images for quantitative cardiac analysis and the diagnosis of patients. Three different modules are presented. The automatic localization algorithm is able to approximately locate the left ventricle in an image using a maximum discrimination technique. Then, the local deformation algorithm can deform active contours so that they align to the edges in the image to produce the desired outlining of the myocardium. Finally, the global localization algorithm is able to propagate segmented contours from one image in the data set to all the others. We have experimented with the proposed method on a large number of patients and present some examples to show the strengths and pitfalls of our algorithm.

Liver segmentation using sparse 3D prior models with optimal data support

Volume segmentation is a relatively slow process and, in certain circumstances, the enormous amount of prior knowledge available is underused. Model-based liver segmentation suffers from the large shape variability of this organ, and from structures of similar appearance that juxtapose the liver. The technique presented in this paper is devoted to combine a statistical analysis of the data with a reconstruction model from sparse information: only the most reliable information in the image is used, and the rest of the livers shape is inferred from the model and the sparse observation. The resulting process is more efficient than standard segmentation since most of the workload is concentrated on the critical points, but also more robust, since the interpolated volume is consistent with the prior knowledge statistics. The experimental results on liver datasets prove the sparse information model has the same potential as PCA, if not better, to represent the shape of the liver. Furthermore, the performance assessment from measurement statistics on the livers volume, distance between reconstructed surfaces and ground truth, and inter-observer variability demonstrates the liver is efficiently segmented using sparse information.

4D shape priors for a level set segmentation of the left myocardium in SPECT sequences

We develop a 4D (3D plus time) statistical shape model for implicit level set based shape representations. To this end, we represent hand segmented training sequences of the left ventricle by respective 4-dimensional embedding functions and approximate these by a principal component analysis. In contrast to recent 4D models on explicit shape representations, the implicit shape model developed in this work does not require the computation of point correspondences which is known to be quite challenging, especially in higher dimensions. Experimental results on the segmentation of SPECT sequences of the left myocardium confirm that the 4D shape model outperforms respective 3D models, because it takes into account a statistical model of the temporal shape evolution.

An energy minimization approach to the data driven editing of presegmented images/volumes

Fully automatic, completely reliable segmentation in medical images is an unrealistic expectation with todays technology. However, many automatic segmentation algorithms may achieve a near-correct solution, incorrect only in a small region. For these situations, an interactive editing tool is required, ideally in 3D, that is usually left to a manual correction. We formulate the editing task as an energy minimization problem that may be solved with a modified version of either graph cuts or the random walker 3D segmentation algorithms. Both algorithms employ a seeded user interface, that may be used in this scenario for a user to seed erroneous voxels as belonging to the foreground or the background. In our formulation, it is unnecessary for the user to specify both foreground and background seeds.

Robust and Accurate Coronary Artery Centerline Extraction in CTA by Combining Model-Driven and Data-Driven Approaches

Various methods have been proposed to extract coronary artery centerlines from computed tomography angiography (CTA) data. Almost all previous approaches are data-driven, which try to trace a centerline from an automatically detected or manually specified coronary ostium. No or little high level prior information is used; therefore, the centerline tracing procedure may terminate early at a severe occlusion or an anatomically inconsistent centerline course may be generated. Though the connectivity of coronary arteries exhibits large variations, the position of major coronary arteries relative to the heart chambers is quite stable. In this work, we propose to exploit the automatically segmented chambers to 1) predict the initial position of the major coronary centerlines and 2) define a vessel-specific region-of-interest (ROI) to constrain the following centerline refinement. The proposed prior constraints have been integrated into a model-driven algorithm for the extraction of three major coronary centerlines, namely the left anterior descending artery (LAD), left circumflex artery (LCX), and right coronary artery (RCA). After extracting the major coronary arteries, the side branches are traced using a data-driven approach to handle large anatomical variations in side branches. Experiments on the public Rotterdam coronary CTA database demonstrate the robustness and accuracy of the proposed method. We achieve the best average ranking on overlap metrics among automatic methods and our accuracy metric outperforms all other 22 methods (including both automatic and semi-automatic methods).