The image ray transform

Image feature extraction is a fundamental area of image processing and computer vision. There are many ways that techniques can be created that extract features and particularly novel techniques can be developed by taking influence from the physical world. This thesis presents the Image Ray Transform (IRT), a technique based upon an analogy to light, using the mechanisms that define how light travels through different media and analogy to optical fibres to extract structural features within an image. Through analogising the image as a transparent medium we can use refraction and reflection to cast many rays inside the image and guide them towards features, transforming the image in order to emphasise tubular and circular structures.The power of the transform for structural feature detection is shown empirically in a number of applications, especially through its ability to highlight curvilinear structures. The IRT is used to enhance the accuracy of circle detection through use as a preprocessor, highlighting circles to a greater extent than conventional edge detection methods. The transform is also shown to be well suited to enrolment for ear biometrics, providing a high detection and recognition rate with PCA, comparable to manual enrolment. Vascular features such as those found in medical images are also shown to be emphasised by the transform, and the IRT is used for detection of the vasculature in retinal fundus images.Extensions to the basic image ray transform allow higher level features to be detected. A method is shown for expressing rays in an invariant form to describe the structures of an object and hence the object itself with a bag-of-visual words model. These ray features provide a complementary description of objects to other patch-based descriptors and have been tested on a number of object categorisation databases. Finally a different analysis of rays is provided that can produce information on both bilateral (reflectional) and rotational symmetry within the image, allowing a deeper understanding of image structure. The IRT is a flexible technique, capable of detecting a range of high and low level image features, and open to further use and extension across a range of applications

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

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

Current state of the art of regional hyperthermia treatment planning: A review

Locoregional hyperthermia, i.e. increasing the tumor temperature to 40-45 °C using an external heating device, is a very effective radio and chemosensitizer, which significantly improves clinical outcome. There is a clear thermal dose-effect relation, but the pursued optimal thermal dose of 43 °C for 1 h can often not be realized due to treatment limiting hot spots in normal tissue. Modern heating devices have a large number of independent antennas, which provides flexible power steering to optimize tumor heating and minimize hot spots, but manual selection of optimal settings is difficult. Treatment planning is a very valuable tool to improve locoregional heating. This paper reviews the developments in treatment planning software for tissue segmentation, electromagnetic field calculations, thermal modeling and optimization techniques. Over the last decade, simulation tools have become more advanced. On-line use has become possible by implementing algorithms on the graphical processing unit, which allows real-time computations. The number of applications using treatment planning is increasing rapidly and moving on from retrospective analyses towards assisting prospective clinical treatment strategies. Some clinically relevant applications will be discussed

Metabolomic profiling of macrophages determines the discrete metabolomic signature and metabolomic interactome triggered by polarising immune stimuli

Priming and activating immune stimuli have profound effects on macrophages, however, studies generally evaluate stimuli in isolation rather than in combination. In this study we have investigated the effects of pro-inflammatory and anti-inflammatory stimuli either alone or in combination on macrophage metabolism. These stimuli include host factors such as IFNγ and ovalbumin-immunoglobulin immune complexes, or pathogen factors such as LPS. Untargeted LC-MS based metabolomics provided an in-depth profile of the macrophage metabolome, and revealed specific changes in metabolite abundance upon either individual stimuli or combined stimuli. Here, by factoring in an interaction term in the linear model, we define the metabolome interactome. This approach allowed us to determine whether stimuli interact in a synergistic or antagonistic manner. In conclusion this study demonstrates a robust approach to interrogate immune-metabolism, especially systems that model host-pathogen interactions

Coronary Artery Segmentation and Motion Modelling

Conventional coronary artery bypass surgery requires invasive sternotomy and the use of a cardiopulmonary bypass, which leads to long recovery period and has high infectious potential. Totally endoscopic coronary artery bypass (TECAB) surgery based on image guided robotic surgical approaches have been developed to allow the clinicians to conduct the bypass surgery off-pump with only three pin holes incisions in the chest cavity, through which two robotic arms and one stereo endoscopic camera are inserted. However, the restricted field of view of the stereo endoscopic images leads to possible vessel misidentification and coronary artery mis-localization. This results in 20-30% conversion rates from TECAB surgery to the conventional approach. We have constructed patient-specific 3D + time coronary artery and left ventricle motion models from preoperative 4D Computed Tomography Angiography (CTA) scans. Through temporally and spatially aligning this model with the intraoperative endoscopic views of the patient's beating heart, this work assists the surgeon to identify and locate the correct coronaries during the TECAB precedures. Thus this work has the prospect of reducing the conversion rate from TECAB to conventional coronary bypass procedures. This thesis mainly focus on designing segmentation and motion tracking methods of the coronary arteries in order to build pre-operative patient-specific motion models. Various vessel centreline extraction and lumen segmentation algorithms are presented, including intensity based approaches, geometric model matching method and morphology-based method. A probabilistic atlas of the coronary arteries is formed from a group of subjects to facilitate the vascular segmentation and registration procedures. Non-rigid registration framework based on a free-form deformation model and multi-level multi-channel large deformation diffeomorphic metric mapping are proposed to track the coronary motion. The methods are applied to 4D CTA images acquired from various groups of patients and quantitatively evaluated

Flow pattern analysis for magnetic resonance velocity imaging

Blood flow in the heart is highly complex. Although blood flow patterns have been investigated by both computational modelling and invasive/non-invasive imaging techniques, their evolution and intrinsic connection with cardiovascular disease has yet to be explored. Magnetic resonance (MR) velocity imaging provides a comprehensive distribution of multi-directional in vivo flow distribution so that detailed quantitative analysis of flow patterns is now possible. However, direct visualisation or quantification of vector fields is of little clinical use, especially for inter-subject or serial comparison of changes in flow patterns due to the progression of the disease or in response to therapeutic measures. In order to achieve a comprehensive and integrated description of flow in health and disease, it is necessary to characterise and model both normal and abnormal flows and their effects. To accommodate the diversity of flow patterns in relation to morphological and functional changes, we have described in this thesis an approach of detecting salient topological features prior to analytical assessment of dynamical indices of the flow patterns. To improve the accuracy of quantitative analysis of the evolution of topological flow features, it is essential to restore the original flow fields so that critical points associated with salient flow features can be more reliably detected. We propose a novel framework for the restoration, abstraction, extraction and tracking of flow features such that their dynamic indices can be accurately tracked and quantified. The restoration method is formulated as a constrained optimisation problem to remove the effects of noise and to improve the consistency of the MR velocity data. A computational scheme is derived from the First Order Lagrangian Method for solving the optimisation problem. After restoration, flow abstraction is applied to partition the entire flow field into clusters, each of which is represented by a local linear expansion of its velocity components. This process not only greatly reduces the amount of data required to encode the velocity distribution but also permits an analytical representation of the flow field from which critical points associated with salient flow features can be accurately extracted. After the critical points are extracted, phase portrait theory can be applied to separate them into attracting/repelling focuses, attracting/repelling nodes, planar vortex, or saddle. In this thesis, we have focused on vortical flow features formed in diastole. To track the movement of the vortices within a cardiac cycle, a tracking algorithm based on relaxation labelling is employed. The constraints and parameters used in the tracking algorithm are designed using the characteristics of the vortices. The proposed framework is validated with both simulated and in vivo data acquired from patients with sequential MR examination following myocardial infarction. The main contribution of the thesis is in the new vector field restoration and flow feature abstraction method proposed. They allow the accurate tracking and quantification of dynamic indices associated with salient features so that inter- and intra-subject comparisons can be more easily made. This provides further insight into the evolution of blood flow patterns and permits the establishment of links between blood flow patterns and localised genesis and progression of cardiovascular disease.Open acces

Discovery of retinal biomarkers for vascular conditions through advancement of artery-vein detection and fractal analysis

Research into automatic retina image analysis has become increasingly important, not just in ophthalmology but also in other clinical specialities such as cardiology and neurology. In the retina, blood vessels can be directly visualised non-invasively in-vivo, and hence it serves as a "window" to cardiovascular and neurovascular complications. Biomarker research, i.e. investigating associations between the morphology of the retinal vasculature (as a means of revealing microvascular health or disease) and particular conditions affecting the body or brain could play an important role in detecting disease early enough to impact on patient treatment and care. A fundamental requirement of biomarker research is access to large datasets to achieve sufficient power and significance when ascertaining associations between retinal measures and clinical characterisation of disease. Crucially, the vascular changes that appear can affect arteries and veins differently. An essential part of automatic systems for retinal morphology quantification and biomarker extraction is, therefore, a computational method for classifying vessels into arteries and veins. Artery-vein classification enables the efficient extraction of biomarkers such as the Arteriolar to Venular Ratio, which is a well-established predictor of stroke and other cardiovascular events. While structural parameters of the retinal vasculature such as vessels calibre, branching angle, and tortuosity may individually convey some information regarding specific aspects of the health of the retinal vascular network, they do not convey a global summary of the branching pattern and its state or condition. The retinal vascular tree can be considered a fractal structure as it has a branching pattern that exhibits the property of self-similarity. Fractal analysis, therefore, provides an additional means for the quantitative study of changes to the retinal vascular network and may be of use in detecting abnormalities related to retinopathy and systemic diseases. In this thesis, new developments to fully automated retinal vessel classification and fractal analysis were explored in order to extract potential biomarkers. These novel processes were tested and validated on several datasets of retinal images acquired with fundus cameras. The major contributions of this thesis include: 1) developing a fully automated retinal blood vessel classification technique, 2) developing a fractal analysis technique that quantifies regional as well as global branching complexity, 3) validating the methods using multiple datasets, and 4) applying the proposed methods in multiple retinal vasculature analysis studies

Evaluation of pulse wave analysis to assess coronary artery disease

Conventional risk factors for cardiovascular disease, such as age, gender, hyperlipidaemia and hypertension are useful clinical markers of coronary artery disease (CAD) in asymptomatic patients or those without a prior history of atherosclerosis. In patients referred for a cardiology opinion, modification of risk factors by lifestyle changes and cardiac medications as well as confounding co-morbidities limit the value of these markers. Patients are often referred for diagnostic coronary angiography to determine the presence and severity of CAD, stratify the risk of future events and determine appropriate management. Despite the use of a variety of tests to best identify those requiring angiography, up to half of all patients referred do not have significant disease. Pulse wave analysis (PWA) is a novel method to derive indices of central (aortic) blood pressure and arterial stiffness. Pressure waveforms are obtained non-invasively from the radial artery using a simple tonometry method and have been shown to correlate with clinical outcomes and cardiovascular events in selected populations. This thesis will explore, for the first time, the clinical potential for PWA as a non-invasive marker of CAD in an unselected contemporary cohort of patients referred for elective coronary angiography. The main hypotheses tested are first that PWA is a suitable tool for clinical use, including those with cardiac and non-cardiac co-morbidities and second that abnormalities of PWA are independent predictors of the presence and severity of CAD. Data have been derived from a prospective, protocol-driven, multi-centre cohort of 550 patients recruited from 2006-8. Results suggest that PWA has a useful clinical role in stratifying the risk of coronary disease. PWA variables were independent of conventional blood pressure measurement and superior to baseline risk factors, biomarkers and other non-invasive tests