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

Technologies for Biomechanically-Informed Image Guidance of Laparoscopic Liver Surgery

Laparoscopic surgery for liver resection has a number medical advantages over open surgery, but also comes with inherent technical challenges. The surgeon only has a very limited field of view through the imaging modalities routinely employed intra-operatively, laparoscopic video and ultrasound, and the pneumoperitoneum required to create the operating space and gaining access to the organ can significantly deform and displace the liver from its pre-operative configuration. This can make relating what is visible intra-operatively to the pre-operative plan and inferring the location of sub-surface anatomy a very challenging task. Image guidance systems can help overcome these challenges by updating the pre-operative plan to the situation in theatre and visualising it in relation to the position of surgical instruments. In this thesis, I present a series of contributions to a biomechanically-informed image-guidance system made during my PhD. The most recent one is work on a pipeline for the estimation of the post-insufflation configuration of the liver by means of an algorithm that uses a database of segmented training images of patient abdomens where the post-insufflation configuration of the liver is known. The pipeline comprises an algorithm for inter and intra-subject registration of liver meshes by means of non-rigid spectral point-correspondence finding. My other contributions are more fundamental and less application specific, and are all contained and made available to the public in the NiftySim open-source finite element modelling package. Two of my contributions to NiftySim are of particular interest with regards to image guidance of laparoscopic liver surgery: 1) a novel general purpose contact modelling algorithm that can be used to simulate contact interactions between, e.g., the liver and surrounding anatomy; 2) membrane and shell elements that can be used to, e.g., simulate the Glisson capsule that has been shown to significantly influence the organ’s measured stiffness

Soft volume simulation using a deformable surface model

The aim of the research is to contribute to the modelling of deformable objects, such as soft tissues in medical simulation. Interactive simulation for medical training is a concept undergoing rapid growth as the underlying technologies support the increasingly more realstic and functional training environments. The prominent issues in the deployment of such environments centre on a fine balance between the accuracy of the deformable model and real-time interactivity. Acknowledging the importance of interacting with non-rigid materials such as the palpation of a breast for breast assessment, this thesis has explored the physics-based modelling techniques for both volume and surface approach. This thesis identified that the surface approach based on the mass spring system (MSS) has the benefits of rapid prototyping, reduced mesh complexity, computational efficiency and the support for large material deformation compared to the continuum approach. However, accuracy relative to real material properties is often over looked in the configuration of the resulting model. This thesis has investigated the potential and the feasibility of surface modelling for simulating soft objects regardless of the design of the mesh topology and the non-existence of internal volume discretisation. The assumptions of the material parameters such as elasticity, homogeneity and incompressibility allow a reduced set of material values to be implemented in order to establish the association with the surface configuration. A framework for a deformable surface model was generated in accordance with the issues of the estimation of properties and volume behaviour corresponding to the material parameters. The novel extension to the surface MSS enables the tensile properties of the material to be integrated into an enhanced configuration despite its lack of volume information. The benefits of the reduced complexity of a surface model are now correlated with the improved accuracy in the estimation of properties and volume behaviour. Despite the irregularity of the underlying mesh topology and the absence of volume, the model reflected the original material values and preserved volume with minimal deviations. Global deformation effect which is essential to emulate the run time behaviour of a real soft material upon interaction, such as the palpation of a generic breast, was also demonstrated, thus indicating the potential of this novel technique in the application of soft tissue simulation

Soft volume simulation using a deformable surface model

The aim of the research is to contribute to the modelling of deformable objects, such as soft tissues in medical simulation. Interactive simulation for medical training is a concept undergoing rapid growth as the underlying technologies support the increasingly more realstic and functional training environments. The prominent issues in the deployment of such environments centre on a fine balance between the accuracy of the deformable model and real-time interactivity. Acknowledging the importance of interacting with non-rigid materials such as the palpation of a breast for breast assessment, this thesis has explored the physics-based modelling techniques for both volume and surface approach. This thesis identified that the surface approach based on the mass spring system (MSS) has the benefits of rapid prototyping, reduced mesh complexity, computational efficiency and the support for large material deformation compared to the continuum approach. However, accuracy relative to real material properties is often over looked in the configuration of the resulting model. This thesis has investigated the potential and the feasibility of surface modelling for simulating soft objects regardless of the design of the mesh topology and the non-existence of internal volume discretisation. The assumptions of the material parameters such as elasticity, homogeneity and incompressibility allow a reduced set of material values to be implemented in order to establish the association with the surface configuration. A framework for a deformable surface model was generated in accordance with the issues of the estimation of properties and volume behaviour corresponding to the material parameters. The novel extension to the surface MSS enables the tensile properties of the material to be integrated into an enhanced configuration despite its lack of volume information. The benefits of the reduced complexity of a surface model are now correlated with the improved accuracy in the estimation of properties and volume behaviour. Despite the irregularity of the underlying mesh topology and the absence of volume, the model reflected the original material values and preserved volume with minimal deviations. Global deformation effect which is essential to emulate the run time behaviour of a real soft material upon interaction, such as the palpation of a generic breast, was also demonstrated, thus indicating the potential of this novel technique in the application of soft tissue simulation.EThOS - Electronic Theses Online ServiceUniversiti Malaysia Sarawak (UMS)Malaysia. Jabatan Perkhidmatan Awam (JPA)Malaysia. Kementerian Pengajian Tinggi (KPT)GBUnited Kingdo

Improvements to physically based cloth simulation

Physically based cloth simulation in computer graphics has come a long way since the 1980s. Although extensive methods have been developed, physically based cloth animation remains challenging in a number of aspects, including the efficient simulation of complex internal dynamics, better performance and the generation of more effects of friction in collisions, to name but a few. These opportunities motivate the work presented in this thesis to improve on current state of the art in cloth simulation by proposing methods for cloth bending deformation simulation, collision detection and friction in collision response. The structure of the thesis is as follows. A literature review of work related to physically based cloth simulation including aspects of internal dynamics, collision handling and GPU computing for cloth simulation is given in Chapter 2. In order to provide a basis for understanding of the work of the subsequent chapters of the thesis, Chapter 3 describes and discusses main components of our physically based cloth simulation framework which can be seen as the basis of our developments, as methods presented in the following chapters use this framework. Chapter 4 presents an approach that effectively models cloth non-linear features in bending behaviour, such as energy dissipation, plasticity and fatigue weakening. This is achieved by a simple mathematical approximation to an ideal hysteresis loop at a high level, while in textile research bending non-linearity is computed using complex internal friction models at the geometric structure level. Due to cloth flexibility and the large quantity of triangles, in a robust cloth system collision detection is the most time consuming task. The approach proposed in Chapter 5 improves performance of collision detection using a GPU-based approach employing spatial subdivision. It addresses a common issue, uneven triangle sizes, which can easily impair the spatial subdivision efficiency. To achieve this, a virtual subdivision scheme with a uniform grid is used to virtually subdivide large triangles, resulting in a more appropriate cell size and thus a more efficient subdivision. The other common issue that limits the subdivision efficiency is uneven triangle spatial distributions, and is difficult to tackle via uniform grids because areas with different triangle densities may require different cell sizes. In order to address this problem, Chapter 6 shows how to build an octree grid to adaptively partition space according to triangle spatial distribution on a GPU, which delivers further improvements in the performance of collision detection. Friction is an important component in collision response. Frictional effects include phenomena that are velocity dependent, such as stiction, Stribeck friction, viscous friction and the stick-slip phenomenon, which are not modelled by the classic Coulomb friction model adopted by existing cloth systems. Chapter 7 reports a more comprehensive friction model to capture these additional effects. Chapter 8 concludes this thesis and briefly discusses potential avenues for future work

Modelling and simulation of flexible instruments for minimally invasive surgical training in virtual reality

Improvements in quality and safety standards in surgical training, reduction in training hours and constant technological advances have challenged the traditional apprenticeship model to create a competent surgeon in a patient-safe way. As a result, pressure on training outside the operating room has increased. Interactive, computer based Virtual Reality (VR) simulators offer a safe, cost-effective, controllable and configurable training environment free from ethical and patient safety issues. Two prototype, yet fully-functional VR simulator systems for minimally invasive procedures relying on flexible instruments were developed and validated. NOViSE is the first force-feedback enabled VR simulator for Natural Orifice Transluminal Endoscopic Surgery (NOTES) training supporting a flexible endoscope. VCSim3 is a VR simulator for cardiovascular interventions using catheters and guidewires. The underlying mathematical model of flexible instruments in both simulator prototypes is based on an established theoretical framework – the Cosserat Theory of Elastic Rods. The efficient implementation of the Cosserat Rod model allows for an accurate, real-time simulation of instruments at haptic-interactive rates on an off-the-shelf computer. The behaviour of the virtual tools and its computational performance was evaluated using quantitative and qualitative measures. The instruments exhibited near sub-millimetre accuracy compared to their real counterparts. The proposed GPU implementation further accelerated their simulation performance by approximately an order of magnitude. The realism of the simulators was assessed by face, content and, in the case of NOViSE, construct validity studies. The results indicate good overall face and content validity of both simulators and of virtual instruments. NOViSE also demonstrated early signs of construct validity. VR simulation of flexible instruments in NOViSE and VCSim3 can contribute to surgical training and improve the educational experience without putting patients at risk, raising ethical issues or requiring expensive animal or cadaver facilities. Moreover, in the context of an innovative and experimental technique such as NOTES, NOViSE could potentially facilitate its development and contribute to its popularization by keeping practitioners up to date with this new minimally invasive technique.Open Acces

Real-time Biomechanical Modeling for Intraoperative Soft Tissue Registration

Computer assisted surgery systems intraoperatively support the surgeon by providing information on the location of hidden risk and target structures during surgery. However, soft tissue deformations make intraoperative registration (and thus intraoperative navigation) difficult. In this work, a novel, biomechanics based approach for real-time soft tissue registration from sparse intraoperative sensor data such as stereo endoscopic images is presented to overcome this problem

A computational neuromuscular model of the human upper airway with application to the study of obstructive sleep apnoea

Includes bibliographical references.Numerous challenges are faced in investigations aimed at developing a better understanding of the pathophysiology of obstructive sleep apnoea. The anatomy of the tongue and other upper airway tissues, and the ability to model their behaviour, is central to such investigations. In this thesis, details of the construction and development of a three-dimensional finite element model of soft tissues of the human upper airway, as well as a simplified fluid model of the airway, are provided. The anatomical data was obtained from the Visible Human Project, and its underlying micro-histological data describing tongue musculature were also extracted from the same source and incorporated into the model. An overview of the mathematical models used to describe tissue behaviour, both at a macro- and microscopic level, is given. Hyperelastic constitutive models were used to describe the material behaviour, and material incompressibility was accounted for. An active Hill three-element muscle model was used to represent the muscular tissue of the tongue. The neural stimulus for each muscle group to a priori unknown external forces was determined through the use of a genetic algorithm-based neural control model. The fundamental behaviour of the tongue under gravitational and breathing-induced loading is investigated. The response of the various muscles of the tongue to the complex loading developed during breathing is determined, with a particular focus being placed to that of the genioglossus. It is demonstrated that, when a time-dependent loading is applied to the tongue, the neural model is able to control the position of the tongue and produce a physiologically realistic response for the genioglossus. A comparison is then made to the response determined under quasi-static conditions using the pressure distribution extracted from computational fluid-dynamics results. An analytical model describing the time-dependent response of the components of the tongue musculature most active during oral breathing is developed and validated. It is then modified to simulate the activity of the tongue during sleep and under conditions relating to various possible neural and physiological pathologies. The retroglossal movement of the tongue resulting from the pathologies is quantified and their role in the potential to induce airway collapse is discussed

Generating anatomical substructures for physically-based facial animation.

Physically-based facial animation techniques are capable of producing realistic facial deformations, but have failed to find meaningful use outside the academic community because they are notoriously difficult to create, reuse, and art-direct, in comparison to other methods of facial animation. This thesis addresses these shortcomings and presents a series of methods for automatically generating a skull, the superficial musculoaponeurotic system (SMAS – a layer of fascia investing and interlinking the mimic muscle system), and mimic muscles for any given 3D face model. This is done toward (the goal of) a production-viable framework or rig-builder for physically-based facial animation. This workflow consists of three major steps. First, a generic skull is fitted to a given head model using thin-plate splines computed from the correspondence between landmarks placed on both models. Second, the SMAS is constructed as a variational implicit or radial basis function surface in the interface between the head model and the generic skull fitted to it. Lastly, muscle fibres are generated as boundary-value straightest geodesics, connecting muscle attachment regions defined on the surface of the SMAS. Each step of this workflow is developed with speed, realism and reusability in mind

Caractérisation et modélisation des propriétés mécaniques des biocomposites à fibres courtes aléatoires

Cette étude consiste à caractériser les propriétés mécaniques en traction, flexion et résistance au choc de trois matériaux biocomposites afin d'évaluer leur aptitude à remplacer des matériaux composites dans des applications automobiles. Les matériaux à caractériser sont constitués de la même matrice (polypropylène (PP) / élastomère polyoléfine (POE), PP/POE [95wt% : 5wt%]) renforcée par trois renforts différents. Les formulations (F1), (F2) et (F3) sont renforcées respectivement par 30wt% de biochar, 30wt% de miscanthus et le troisième renfort est un mélange entre 15wt% de biochar et 15wt% de miscanthus. Pour améliorer l'adhésion entre les renforts et la matrice, 3wt% d'anhydride polypropylène modifié (MAPP) ont été ajoutés aux composites. Les résultats expérimentaux ont montré que les trois renforts améliorent le module d'Young de la matrice. La formulation (F2) a présenté les meilleures propriétés en traction et en flexion par rapport aux deux autres matériaux. En effet les fibres de miscanthus ont augmenté le module d'Young de la matrice de 107% et la résistance en traction de 10,51%. Ces proprieties en traction sont meilleures que celles du matériau commercialisé RTP 132 UV. Le bicomposite hybride (F3) a aussi augmenté le module d'Young de la matrice de 70% et a maintenu Presque la même résistance en traction du PP/POE. Le biocomposite renforcé par le biochar (F1) a amélioré la rigidité de la matrice de 34% mais il a diminué sa résistance de 8%. Par contre, ces renforts ont diminué la résistance au choc de la matrice. En comparant les résultats expérimentaux de l'essai Izod sans entaille des trois biocomposites, la formulation renforcée par le biochar (F1) a présenté la meilleure résilience, mais elle reste toujours loin de celle du matériau commercialisé. L'homogénéisation numérique par la méthode des éléments finis a permis de prédire les modules d'Young de ces biocomposites aléatoirement renforcés. Le logiciel commercial Digimat® a été utilisé pour générer le volume élémentaire représentatif 3D (VER) et pour calculer les modules d'Young du composite. La taille critique du VER est environ deux fois la longueur de la fibre en utilisant les conditions aux limites périodiques. Les résultats numériques ont montré une bonne concordance avec les résultats expérimentaux des biocomposites de cette étude