610 research outputs found

    Robust Anatomical Correspondence Detection by Hierarchical Sparse Graph Matching

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    Robust anatomical correspondence detection is a key step in many medical image applications such as image registration and motion correction. In the computer vision field, graph matching techniques have emerged as a powerful approach for correspondence detection. By considering potential correspondences as graph nodes, graph edges can be used to measure the pairwise agreement between possible correspondences. In this paper, we present a novel, hierarchical graph matching method with sparsity constraint to further augment the power of conventional graph matching methods in establishing anatomical correspondences, especially for the cases of large inter-subject variations in medical applications. Specifically, we first propose to measure the pairwise agreement between potential correspondences along a sequence of intensity profiles which reduces the ambiguity in correspondence matching. We next introduce the concept of sparsity on the fuzziness of correspondences to suppress the distraction from misleading matches, which is very important for achieving the accurate, one-to-one correspondences. Finally, we integrate our graph matching method into a hierarchical correspondence matching framework, where we use multiple models to deal with the large inter-subject anatomical variations and gradually refine the correspondence matching results between the tentatively deformed model images and the underlying subject image. Evaluations on both synthetic data and public hand X-ray images indicate that the proposed hierarchical sparse graph matching method yields the best correspondence matching performance in terms of both accuracy and robustness when compared with several conventional graph matching methods

    Building dynamic population graph for accurate correspondence detection

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    AbstractIn medical imaging studies, there is an increasing trend for discovering the intrinsic anatomical difference across individual subjects in a dataset, such as hand images for skeletal bone age estimation. Pair-wise matching is often used to detect correspondences between each individual subject and a pre-selected model image with manually-placed landmarks. However, the large anatomical variability across individual subjects can easily compromise such pair-wise matching step. In this paper, we present a new framework to simultaneously detect correspondences among a population of individual subjects, by propagating all manually-placed landmarks from a small set of model images through a dynamically constructed image graph. Specifically, we first establish graph links between models and individual subjects according to pair-wise shape similarity (called as forward step). Next, we detect correspondences for the individual subjects with direct links to any of model images, which is achieved by a new multi-model correspondence detection approach based on our recently-published sparse point matching method. To correct those inaccurate correspondences, we further apply an error detection mechanism to automatically detect wrong correspondences and then update the image graph accordingly (called as backward step). After that, all subject images with detected correspondences are included into the set of model images, and the above two steps of graph expansion and error correction are repeated until accurate correspondences for all subject images are established. Evaluations on real hand X-ray images demonstrate that our proposed method using a dynamic graph construction approach can achieve much higher accuracy and robustness, when compared with the state-of-the-art pair-wise correspondence detection methods as well as a similar method but using static population graph

    Landmark Localization, Feature Matching and Biomarker Discovery from Magnetic Resonance Images

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    The work presented in this thesis proposes several methods that can be roughly divided into three different categories: I) landmark localization in medical images, II) feature matching for image registration, and III) biomarker discovery in neuroimaging. The first part deals with the identification of anatomical landmarks. The motivation stems from the fact that the manual identification and labeling of these landmarks is very time consuming and prone to observer errors, especially when large datasets must be analyzed. In this thesis we present three methods to tackle this challenge: A landmark descriptor based on local self-similarities (SS), a subspace building framework based on manifold learning and a sparse coding landmark descriptor based on data-specific learned dictionary basis. The second part of this thesis deals with finding matching features between a pair of images. These matches can be used to perform a registration between them. Registration is a powerful tool that allows mapping images in a common space in order to aid in their analysis. Accurate registration can be challenging to achieve using intensity based registration algorithms. Here, a framework is proposed for learning correspondences in pairs of images by matching SS features and random sample and consensus (RANSAC) is employed as a robust model estimator to learn a deformation model based on feature matches. Finally, the third part of the thesis deals with biomarker discovery using machine learning. In this section a framework for feature extraction from learned low-dimensional subspaces that represent inter-subject variability is proposed. The manifold subspace is built using data-driven regions of interest (ROI). These regions are learned via sparse regression, with stability selection. Also, probabilistic distribution models for different stages in the disease trajectory are estimated for different class populations in the low-dimensional manifold and used to construct a probabilistic scoring function.Open Acces

    Expanded Parts Model for Semantic Description of Humans in Still Images

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    We introduce an Expanded Parts Model (EPM) for recognizing human attributes (e.g. young, short hair, wearing suit) and actions (e.g. running, jumping) in still images. An EPM is a collection of part templates which are learnt discriminatively to explain specific scale-space regions in the images (in human centric coordinates). This is in contrast to current models which consist of a relatively few (i.e. a mixture of) 'average' templates. EPM uses only a subset of the parts to score an image and scores the image sparsely in space, i.e. it ignores redundant and random background in an image. To learn our model, we propose an algorithm which automatically mines parts and learns corresponding discriminative templates together with their respective locations from a large number of candidate parts. We validate our method on three recent challenging datasets of human attributes and actions. We obtain convincing qualitative and state-of-the-art quantitative results on the three datasets.Comment: Accepted for publication in IEEE Transactions on Pattern Analysis and Machine Intelligence (TPAMI

    Scalable High-Performance Image Registration Framework by Unsupervised Deep Feature Representations Learning

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    Feature selection is a critical step in deformable image registration. In particular, selecting the most discriminative features that accurately and concisely describe complex morphological patterns in image patches improves correspondence detection, which in turn improves image registration accuracy. Furthermore, since more and more imaging modalities are being invented to better identify morphological changes in medical imaging data,, the development of deformable image registration method that scales well to new image modalities or new image applications with little to no human intervention would have a significant impact on the medical image analysis community. To address these concerns, a learning-based image registration framework is proposed that uses deep learning to discover compact and highly discriminative features upon observed imaging data. Specifically, the proposed feature selection method uses a convolutional stacked auto-encoder to identify intrinsic deep feature representations in image patches. Since deep learning is an unsupervised learning method, no ground truth label knowledge is required. This makes the proposed feature selection method more flexible to new imaging modalities since feature representations can be directly learned from the observed imaging data in a very short amount of time. Using the LONI and ADNI imaging datasets, image registration performance was compared to two existing state-of-the-art deformable image registration methods that use handcrafted features. To demonstrate the scalability of the proposed image registration framework image registration experiments were conducted on 7.0-tesla brain MR images. In all experiments, the results showed the new image registration framework consistently demonstrated more accurate registration results when compared to state-of-the-art

    Generative-Discriminative Low Rank Decomposition for Medical Imaging Applications

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    In this thesis, we propose a method that can be used to extract biomarkers from medical images toward early diagnosis of abnormalities. Surge of demand for biomarkers and availability of medical images in the recent years call for accurate, repeatable, and interpretable approaches for extracting meaningful imaging features. However, extracting such information from medical images is a challenging task because the number of pixels (voxels) in a typical image is in order of millions while even a large sample-size in medical image dataset does not usually exceed a few hundred. Nevertheless, depending on the nature of an abnormality, only a parsimonious subset of voxels is typically relevant to the disease; therefore various notions of sparsity are exploited in this thesis to improve the generalization performance of the prediction task. We propose a novel discriminative dimensionality reduction method that yields good classification performance on various datasets without compromising the clinical interpretability of the results. This is achieved by combining the modelling strength of generative learning framework and the classification performance of discriminative learning paradigm. Clinical interpretability can be viewed as an additional measure of evaluation and is also helpful in designing methods that account for the clinical prior such as association of certain areas in a brain to a particular cognitive task or connectivity of some brain regions via neural fibres. We formulate our method as a large-scale optimization problem to solve a constrained matrix factorization. Finding an optimal solution of the large-scale matrix factorization renders off-the-shelf solver computationally prohibitive; therefore, we designed an efficient algorithm based on the proximal method to address the computational bottle-neck of the optimization problem. Our formulation is readily extended for different scenarios such as cases where a large cohort of subjects has uncertain or no class labels (semi-supervised learning) or a case where each subject has a battery of imaging channels (multi-channel), \etc. We show that by using various notions of sparsity as feasible sets of the optimization problem, we can encode different forms of prior knowledge ranging from brain parcellation to brain connectivity

    Rekonstruktion, Analyse und Editierung dynamisch deformierter 3D-Oberflächen

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    Dynamically deforming 3D surfaces play a major role in computer graphics. However, producing time-varying dynamic geometry at ever increasing detail is a time-consuming and costly process, and so a recent trend is to capture geometry data directly from the real world. In the first part of this thesis, I propose novel approaches for this research area. These approaches capture dense dynamic 3D surfaces from multi-camera systems in a particularly robust and accurate way. This provides highly realistic dynamic surface models for phenomena like moving garments and bulging muscles. However, re-using, editing, or otherwise analyzing dynamic 3D surface data is not yet conveniently possible. To close this gap, the second part of this dissertation develops novel data-driven modeling and animation approaches. I first show a supervised data-driven approach for modeling human muscle deformations that scales to huge datasets and provides fine-scale, anatomically realistic deformations at high quality not attainable by previous methods. I then extend data-driven modeling to the unsupervised case, providing editing tools for a wider set of input data ranging from facial performance capture and full-body motion to muscle and cloth deformation. To this end, I introduce the concepts of sparsity and locality within a mathematical optimization framework. I also explore these concepts for constructing shape-aware functions that are useful for static geometry processing, registration, and localized editing.Dynamisch deformierbare 3D-Oberflächen spielen in der Computergrafik eine zentrale Rolle. Die Erstellung der für Computergrafik-Anwendungen benötigten, hochaufgelösten und zeitlich veränderlichen Oberflächengeometrien ist allerdings äußerst arbeitsintensiv. Aus dieser Problematik heraus hat sich der Trend entwickelt, Oberflächendaten direkt aus Aufnahmen der echten Welt zu erfassen. Dazu nötige 3D-Rekonstruktionsverfahren werden im ersten Teil der Arbeit entwickelt. Die vorgestellten, neuartigen Verfahren erlauben die Erfassung dynamischer 3D-Oberflächen aus Mehrkamera-Aufnahmen bei hoher Verlässlichkeit und Präzision. Auf diese Weise können detaillierte Oberflächenmodelle von Phänomenen wie in Bewegung befindliche Kleidung oder sich anspannende Muskeln erfasst werden. Aber auch die Wiederverwendung, Bearbeitung und Analyse derlei gewonnener 3D-Oberflächendaten ist aktuell noch nicht auf eine einfache Art und Weise möglich. Um diese Lücke zu schließen beschäftigt sich der zweite Teil der Arbeit mit der datengetriebenen Modellierung und Animation. Zunächst wird ein Ansatz für das überwachte Lernen menschlicher Muskel-Deformationen vorgestellt. Dieses neuartige Verfahren ermöglicht eine datengetriebene Modellierung mit besonders umfangreichen Datensätzen und liefert anatomisch-realistische Deformationseffekte. Es übertrifft damit die Genauigkeit früherer Methoden. Im nächsten Teil beschäftigt sich die Dissertation mit dem unüberwachten Lernen aus 3D-Oberflächendaten. Es werden neuartige Werkzeuge vorgestellt, die eine weitreichende Menge an Eingabedaten verarbeiten können, von aufgenommenen Gesichtsanimationen über Ganzkörperbewegungen bis hin zu Muskel- und Kleidungsdeformationen. Um diese Anwendungsbreite zu erreichen stützt sich die Arbeit auf die allgemeinen Konzepte der Spärlichkeit und Lokalität und bettet diese in einen mathematischen Optimierungsansatz ein. Abschließend zeigt die vorliegende Arbeit, wie diese Konzepte auch für die Konstruktion von oberflächen-adaptiven Basisfunktionen übertragen werden können. Dadurch können Anwendungen für die Verarbeitung, Registrierung und Bearbeitung statischer Oberflächenmodelle erschlossen werden

    Inferring Geodesic Cerebrovascular Graphs: Image Processing, Topological Alignment and Biomarkers Extraction

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    A vectorial representation of the vascular network that embodies quantitative features - location, direction, scale, and bifurcations - has many potential neuro-vascular applications. Patient-specific models support computer-assisted surgical procedures in neurovascular interventions, while analyses on multiple subjects are essential for group-level studies on which clinical prediction and therapeutic inference ultimately depend. This first motivated the development of a variety of methods to segment the cerebrovascular system. Nonetheless, a number of limitations, ranging from data-driven inhomogeneities, the anatomical intra- and inter-subject variability, the lack of exhaustive ground-truth, the need for operator-dependent processing pipelines, and the highly non-linear vascular domain, still make the automatic inference of the cerebrovascular topology an open problem. In this thesis, brain vessels’ topology is inferred by focusing on their connectedness. With a novel framework, the brain vasculature is recovered from 3D angiographies by solving a connectivity-optimised anisotropic level-set over a voxel-wise tensor field representing the orientation of the underlying vasculature. Assuming vessels joining by minimal paths, a connectivity paradigm is formulated to automatically determine the vascular topology as an over-connected geodesic graph. Ultimately, deep-brain vascular structures are extracted with geodesic minimum spanning trees. The inferred topologies are then aligned with similar ones for labelling and propagating information over a non-linear vectorial domain, where the branching pattern of a set of vessels transcends a subject-specific quantized grid. Using a multi-source embedding of a vascular graph, the pairwise registration of topologies is performed with the state-of-the-art graph matching techniques employed in computer vision. Functional biomarkers are determined over the neurovascular graphs with two complementary approaches. Efficient approximations of blood flow and pressure drop account for autoregulation and compensation mechanisms in the whole network in presence of perturbations, using lumped-parameters analog-equivalents from clinical angiographies. Also, a localised NURBS-based parametrisation of bifurcations is introduced to model fluid-solid interactions by means of hemodynamic simulations using an isogeometric analysis framework, where both geometry and solution profile at the interface share the same homogeneous domain. Experimental results on synthetic and clinical angiographies validated the proposed formulations. Perspectives and future works are discussed for the group-wise alignment of cerebrovascular topologies over a population, towards defining cerebrovascular atlases, and for further topological optimisation strategies and risk prediction models for therapeutic inference. Most of the algorithms presented in this work are available as part of the open-source package VTrails

    Registration of brain MR images in large-scale populations

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    Non-rigid image registration is fundamentally important in analyzing large-scale population of medical images, e.g., T1-weighted brain MRI data. Conventional pairwise registration methods involve only two images, as the moving subject image is deformed towards the space of the template for the maximization of their in-between similarity. The population information, however, is mostly ignored, with individual images in the population registered independently with the arbitrarily selected template. By contrast, this dissertation investigates the contributions of the entire population to image registration. First, the population can provide guidance to the pairwise registration between a certain subject and the template. If the subject and an intermediate image in the same population are similar in appearances, the subject shares a similar deformation field with the intermediate image. Thus, the guidance from the intermediate image can be beneficial to the subject, in that the pre-estimated deformation field of the intermediate image initiates the estimation of the subject deformation field when the two images are registered with the identical template. Second, all images in the population can be registered towards the common space of the population using the groupwise technique. Groupwise registration differs from the traditional design of pairwise registration in that no template is pre-determined. Instead, all images agglomerate to the common space of the population simultaneously. Moreover, the common space is revealed spontaneously during image registration, without introducing any bias towards the subsequent analyses and applications. This dissertation shows that population information can contribute to both pairwise registration and groupwise registration. In particular, by utilizing the guidance from the intermediate images in the population, the pairwise registration is more robust and accurate compared to the direct pairwise registration between the subject and the template. Also, for groupwise registration, all images in the population can be aligned more accurately in the common space, although the complexity of groupwise registration increases substantially.Doctor of Philosoph

    An image segmentation and registration approach to cardiac function analysis using MRI

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    Cardiovascular diseases (CVDs) are one of the major causes of death in the world. In recent years, significant progress has been made in the care and treatment of patients with such diseases. A crucial factor for this progress has been the development of magnetic resonance (MR) imaging which makes it possible to diagnose and assess the cardiovascular function of the patient. The ability to obtain high-resolution, cine volume images easily and safely has made it the preferred method for diagnosis of CVDs. MRI is also unique in its ability to introduce noninvasive markers directly into the tissue being imaged(MR tagging) during the image acquisition process. With the development of advanced MR imaging acquisition technologies, 3D MR imaging is more and more clinically feasible. This recent development has allowed new potentially 3D image analysis technologies to be deployed. However, quantitative analysis of cardiovascular system from the images remains a challenging topic. The work presented in this thesis describes the development of segmentation and motion analysis techniques for the study of the cardiac anatomy and function in cardiac magnetic resonance (CMR) images. The first main contribution of the thesis is the development of a fully automatic cardiac segmentation technique that integrates and combines a series of state-of-the-art techniques. The proposed segmentation technique is capable of generating an accurate 3D segmentation from multiple image sequences. The proposed segmentation technique is robust even in the presence of pathological changes, large anatomical shape variations and locally varying contrast in the images. Another main contribution of this thesis is the development of motion tracking techniques that can integrate motion information from different sources. For example, the radial motion of the myocardium can be tracked easily in untagged MR imaging since the epi- and endocardial surfaces are clearly visible. On the other hand, tagged MR imaging allows easy tracking of both longitudinal and circumferential motion. We propose a novel technique based on non-rigid image registration for the myocardial motion estimation using both untagged and 3D tagged MR images. The novel aspect of our technique is its simultaneous use of complementary information from both untagged and 3D tagged MR imaging. The similarity measure is spatially weighted to maximise the utility of information from both images. The thesis also proposes a sparse representation for free-form deformations (FFDs) using the principles of compressed sensing. The sparse free-form deformation (SFFD) model can capture fine local details such as motion discontinuities without sacrificing robustness. We demonstrate the capabilities of the proposed framework to accurately estimate smooth as well as discontinuous deformations in 2D and 3D CMR image sequences. Compared to the standard FFD approach, a significant increase in registration accuracy can be observed in datasets with discontinuous motion patterns. Both the segmentation and motion tracking techniques presented in this thesis have been applied to clinical studies. We focus on two important clinical applications that can be addressed by the techniques proposed in this thesis. The first clinical application aims at measuring longitudinal changes in cardiac morphology and function during the cardiac remodelling process. The second clinical application aims at selecting patients that positively respond to cardiac resynchronization therapy (CRT). The final chapter of this thesis summarises the main conclusions that can be drawn from the work presented here and also discusses possible avenues for future research
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