A Generic Framework for Tracking Using Particle Filter With Dynamic Shape Prior

©2007 IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or distribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE. This material is presented to ensure timely dissemination of scholarly and technical work. Copyright and all rights therein are retained by authors or by other copyright holders. All persons copying this information are expected to adhere to the terms and constraints invoked by each author's copyright. In most cases, these works may not be reposted without the explicit permission of the copyright holder.DOI: 10.1109/TIP.2007.894244Tracking deforming objects involves estimating the global motion of the object and its local deformations as functions of time. Tracking algorithms using Kalman filters or particle filters (PFs) have been proposed for tracking such objects, but these have limitations due to the lack of dynamic shape information. In this paper, we propose a novel method based on employing a locally linear embedding in order to incorporate dynamic shape information into the particle filtering framework for tracking highly deformable objects in the presence of noise and clutter. The PF also models image statistics such as mean and variance of the given data which can be useful in obtaining proper separation of object and backgroun

An Automatic Level Set Based Liver Segmentation from MRI Data Sets

A fast and accurate liver segmentation method is a challenging work in medical image analysis area. Liver segmentation is an important process for computer-assisted diagnosis, pre-evaluation of liver transplantation and therapy planning of liver tumors. There are several advantages of magnetic resonance imaging such as free form ionizing radiation and good contrast visualization of soft tissue. Also, innovations in recent technology and image acquisition techniques have made magnetic resonance imaging a major tool in modern medicine. However, the use of magnetic resonance images for liver segmentation has been slow when we compare applications with the central nervous systems and musculoskeletal. The reasons are irregular shape, size and position of the liver, contrast agent effects and similarities of the gray values of neighbor organs. Therefore, in this study, we present a fully automatic liver segmentation method by using an approximation of the level set based contour evolution from T2 weighted magnetic resonance data sets. The method avoids solving partial differential equations and applies only integer operations with a two-cycle segmentation algorithm. The efficiency of the proposed approach is achieved by applying the algorithm to all slices with a constant number of iteration and performing the contour evolution without any user defined initial contour. The obtained results are evaluated with four different similarity measures and they show that the automatic segmentation approach gives successful results

State of the Art of Level Set Methods in Segmentation and Registration of Medical Imaging Modalities

Segmentation of medical images is an important step in various applications such as visualization, quantitative analysis and image-guided surgery. Numerous segmentation methods have been developed in the past two decades for extraction of organ contours on medical images. Low-level segmentation methods, such as pixel-based clustering, region growing, and filter-based edge detection, require additional pre-processing and post-processing as well as considerable amounts of expert intervention or information of the objects of interest. Furthermore the subsequent analysis of segmented objects is hampered by the primitive, pixel or voxel level representations from those region-based segmentation. Deformable models, on the other hand, provide an explicit representation of the boundary and the shape of the object. They combine several desirable features such as inherent connectivity and smoothness, which counteract noise and boundary irregularities, as well as the ability to incorporate knowledge about the object of interest. However, parametric deformable models have two main limitations. First, in situations where the initial model and desired object boundary differ greatly in size and shape, the model must be re-parameterized dynamically to faithfully recover the object boundary. The second limitation is that it has difficulty dealing with topological adaptation such as splitting or merging model parts, a useful property for recovering either multiple objects or objects with unknown topology. This difficulty is caused by the fact that a new parameterization must be constructed whenever topology change occurs, which requires sophisticated schemes. Level set deformable models, also referred to as geometric deformable models, provide an elegant solution to address the primary limitations of parametric deformable models. These methods have drawn a great deal of attention since their introduction in 1988. Advantages of the contour implicit formulation of the deformable model over parametric formulation include: (1) no parameterization of the contour, (2) topological flexibility, (3) good numerical stability, (4) straightforward extension of the 2D formulation to n-D. Recent reviews on the subject include papers from Suri. In this chapter we give a general overview of the level set segmentation methods with emphasize on new frameworks recently introduced in the context of medical imaging problems. We then introduce novel approaches that aim at combining segmentation and registration in a level set formulation. Finally we review a selective set of clinical works with detailed validation of the level set methods for several clinical applications

Statistical region-based active contours for segmentation: an overview

International audienceIn this paper we propose a brief survey on geometric variational approaches and more precisely on statistical region-based active contours for medical image segmentation. In these approaches, image features are considered as random variables whose distribution may be either parametric, and belongs to the exponential family, or non-parametric estimated with a kernel density method. Statistical region-based terms are listed and reviewed showing that these terms can depict a wide spectrum of segmentation problems. A shape prior can also be incorporated to the previous statistical terms. A discussion of some optimization schemes available to solve the variational problem is also provided. Examples on real medical images are given to illustrate some of the given criteria

Coupled PDEs for Non-Rigid Registration and Segmentation

In this paper we present coupled partial differential equations (PDEs) for the problem of joint segmentation and registration. The registration component of the method estimates a deformation field between boundaries of two structures. The desired coupling comes from two PDEs that estimate a common surface through segmentation and its non-rigid registration with a target image. The solutions of these two PDEs both decrease the total energy of the surface, and therefore aid each other in finding a locally optimal solution. Our technique differs from recently popular joint segmentation and registration algorithms, all of which assume a rigid transformation among shapes. We present both the theory and results that demonstrate the effectiveness of the approach

Coupled nonparametric shape priors for segmentation of multiple basal ganglia structures

This paper presents a new method for multiple structure segmentation, using a maximum a posteriori (MAP) estimation framework, based on prior shape densities involving nonparametric multivariate kernel density estimation of multiple shapes. Our method is motivated by the observation that neighboring or coupling structures in medical images generate configurations and co-dependencies which could potentially aid in segmentation if properly exploited. Our technique allows simultaneous segmentation of multiple objects, where highly contrasted, easy-to-segment structures can help improve the segmentation of weakly contrasted objects. We demonstrate the effectiveness of our method on both synthetic images and real magnetic resonance images (MRI) for segmentation of basal ganglia structures

Segmentation of image ensembles via latent atlases

Spatial priors, such as probabilistic atlases, play an important role in MRI segmentation. However, the availability of comprehensive, reliable and suitable manual segmentations for atlas construction is limited. We therefore propose a method for joint segmentation of corresponding regions of interest in a collection of aligned images that does not require labeled training data. Instead, a latent atlas, initialized by at most a single manual segmentation, is inferred from the evolving segmentations of the ensemble. The algorithm is based on probabilistic principles but is solved using partial differential equations (PDEs) and energy minimization criteria. We evaluate the method on two datasets, segmenting subcortical and cortical structures in a multi-subject study and extracting brain tumors in a single-subject multi-modal longitudinal experiment. We compare the segmentation results to manual segmentations, when those exist, and to the results of a state-of-the-art atlas-based segmentation method. The quality of the results supports the latent atlas as a promising alternative when existing atlases are not compatible with the images to be segmented.National Institutes of Health (U.S.) (National Institute for Biomedical Imaging and Bioengineering (U.S.)/National Alliance for Medical Image Computing (U.S.) U54-EB005149)National Institutes of Health (U.S.) (National Center for Research Resources (U.S.)/Neuroimaging Analysis Center (U.S.) P41-RR13218)National Institutes of Health (U.S.) (National Institute of Neurological Disorders and Stroke (U.S.) R01-NS051826)National Institutes of Health (U.S.) (National Center for Research Resources (U.S.)/Biomedical Informatics Research Network U24-RR021382)National Science Foundation (U.S.) (CAREER Award 0642971)German Academy of Sciences Leopoldina (Fellowship LPDS 2009-10)Academy of Finland (Grant 133611