Data registration and fusion for cardiac applications

The registration and fusion of information from multiple cardiac image modalities such as magnetic resonance imaging (MRI), X-ray computed tomography (CT), positron emission tomography (PET) and single photon emission computed tomography (SPECT) has been of increasing interest to the medical community as tools for furthering physiological understanding and for diagnostic of ischemic heart diseases. Ischemic heart diseases and their consequence, myocardial infarct, are the leading cause of mortality in industrial countries. In cardiac image registration and data fusion, the combination of structural information from MR images and functional information from PET and SPECT is of special interest in the estimation of myocardial function and viability. Cardiac image registration is a more complex problem than brain image registration. The non-rigid motion of the heart and the thorax structures introduce additional difficulties in registration. In this thesis the goal was develop methods for cardiac data registration and fusion. A rigid registration method was developed to register cardiac MR and PET images. The method was based on the registration of the segmented thorax structures from MR and PET transmission images. The thorax structures were segmented from images using deformable models. A MR short axis registration with PET emission image was also derived. The rigid registration method was evaluated using simulated images and clinical MR and PET images from ten patients with multivessel coronary artery diseases. Also an elastic registration method was developed to register intra-patient cardiac MR and PET images and inter-patient head MR images. In the elastic registration method, a combination of mutual information, gradient information and smoothness of transformation was used to guide the deformation of one image towards another image. An approach for the creation of 3-D functional maps of the heart was also developed. An individualized anatomical heart model was extracted from the MR images. A rigid registration of anatomical MR images and PET metabolic images was carried out using surface based registration, and the registration of MR images with magnetocardiography (MCG) data using external markers. The method resulted in a 3-D anatomical and functional model of the heart that included structural information from the MRI and functional information from the PET and MCG. Different error sources in the registration method of the MR images and MCG data was also evaluated in this thesis. The results of the rigid MR-PET registration method were also used in the comparison of multimodality MR imaging methods to PET.reviewe

NeRF: Neural Radiance Field in 3D Vision, A Comprehensive Review

Neural Radiance Field (NeRF), a new novel view synthesis with implicit scene representation has taken the field of Computer Vision by storm. As a novel view synthesis and 3D reconstruction method, NeRF models find applications in robotics, urban mapping, autonomous navigation, virtual reality/augmented reality, and more. Since the original paper by Mildenhall et al., more than 250 preprints were published, with more than 100 eventually being accepted in tier one Computer Vision Conferences. Given NeRF popularity and the current interest in this research area, we believe it necessary to compile a comprehensive survey of NeRF papers from the past two years, which we organized into both architecture, and application based taxonomies. We also provide an introduction to the theory of NeRF based novel view synthesis, and a benchmark comparison of the performance and speed of key NeRF models. By creating this survey, we hope to introduce new researchers to NeRF, provide a helpful reference for influential works in this field, as well as motivate future research directions with our discussion section

Integrated Frequency Combs for Applications in Optical Communications & Microwave Photonics

This dissertation reviews the advancements made in chip-scale optical frequency combs and their applications towards optical communications and optical to RF links. We review different chip-scale comb sources and in particular, chip-scale Kerr microresonator frequency combs. Then, we establish the theoretical background in nonlinear optics which allows the formation and stabilization of Kerr solitons in nonlinear cavities. We also discuss the concept of optical injection locking and in particular, multi-tone injection locking which precedes the idea of regenerative harmonic injection locking. We then go on to show the experimental work involved in soliton generation and characterization. We show efforts towards developing an on-chip massive electronic-photonic optical communications link using Kerr soliton frequency combs as equidistant optical carriers in a DWDM based system using a PAM-4 data modulation format. Potential methods for pushing the limits of communication speeds are also highlighted involving the implementation of other degrees of multiplexing such as space division multiplexing and polarization multiplexing. The second application we explore is based on the synchronization of two pulsed sources via regenerative harmonic injection locking, one with a repetition rate in the microwave regime (10s of GHz) and the other in the mm wave domain (100s of GHz). The two sources we use here are an InP based mode locked laser PIC and the Kerr microresonator. Future goals are discussed which involve techniques for the improvement in long-term stability and chip-scale integrability. This proposal envisions future work to achieve high-capacity optical communication links and optical to RF links utilizing chip-scale Kerr microresonator frequency combs

Modern Applications in Optics and Photonics: From Sensing and Analytics to Communication

Optics and photonics are among the key technologies of the 21st century, and offer potential for novel applications in areas such as sensing and spectroscopy, analytics, monitoring, biomedical imaging/diagnostics, and optical communication technology. The high degree of control over light fields, together with the capabilities of modern processing and integration technology, enables new optical measurement systems with enhanced functionality and sensitivity. They are attractive for a range of applications that were previously inaccessible. This Special Issue aims to provide an overview of some of the most advanced application areas in optics and photonics and indicate the broad potential for the future

From small to large baseline multiview stereo : dealing with blur, clutter and occlusions

This thesis addresses the problem of reconstructing the three-dimensional (3D) digital model of a scene from a collection of two-dimensional (2D) images taken from it. To address this fundamental computer vision problem, we propose three algorithms. They are the main contributions of this thesis. First, we solve multiview stereo with the o -axis aperture camera. This system has a very small baseline as images are captured from viewpoints close to each other. The key idea is to change the size or the 3D location of the aperture of the camera so as to extract selected portions of the scene. Our imaging model takes both defocus and stereo information into account and allows to solve shape reconstruction and image restoration in one go. The o -axis aperture camera can be used in a small-scale space where the camera motion is constrained by the surrounding environment, such as in 3D endoscopy. Second, to solve multiview stereo with large baseline, we present a framework that poses the problem of recovering a 3D surface in the scene as a regularized minimal partition problem of a visibility function. The formulation is convex and hence guarantees that the solution converges to the global minimum. Our formulation is robust to view-varying extensive occlusions, clutter and image noise. At any stage during the estimation process the method does not rely on the visual hull, 2D silhouettes, approximate depth maps, or knowing which views are dependent(i.e., overlapping) and which are independent( i.e., non overlapping). Furthermore, the degenerate solution, the null surface, is not included as a global solution in this formulation. One limitation of this algorithm is that its computation complexity grows with the number of views that we combine simultaneously. To address this limitation, we propose a third formulation. In this formulation, the visibility functions are integrated within a narrow band around the estimated surface by setting weights to each point along optical rays. This thesis presents technical descriptions for each algorithm and detailed analyses to show how these algorithms improve existing reconstruction techniques

Simulating molecular docking with haptics

Intermolecular binding underlies various metabolic and regulatory processes of the cell, and the therapeutic and pharmacological properties of drugs. Molecular docking systems model and simulate these interactions in silico and allow the study of the binding process. In molecular docking, haptics enables the user to sense the interaction forces and intervene cognitively in the docking process. Haptics-assisted docking systems provide an immersive virtual docking environment where the user can interact with the molecules, feel the interaction forces using their sense of touch, identify visually the binding site, and guide the molecules to their binding pose. Despite a forty-year research e�ort however, the docking community has been slow to adopt this technology. Proprietary, unreleased software, expensive haptic hardware and limits on processing power are the main reasons for this. Another signi�cant factor is the size of the molecules simulated, limited to small molecules. The focus of the research described in this thesis is the development of an interactive haptics-assisted docking application that addresses the above issues, and enables the rigid docking of very large biomolecules and the study of the underlying interactions. Novel methods for computing the interaction forces of binding on the CPU and GPU, in real-time, have been developed. The force calculation methods proposed here overcome several computational limitations of previous approaches, such as precomputed force grids, and could potentially be used to model molecular exibility at haptic refresh rates. Methods for force scaling, multipoint collision response, and haptic navigation are also reported that address newfound issues, particular to the interactive docking of large systems, e.g. force stability at molecular collision. The i ii result is a haptics-assisted docking application, Haptimol RD, that runs on relatively inexpensive consumer level hardware, (i.e. there is no need for specialized/proprietary hardware)

Numerical simulation of combustion instability: flame thickening and boundary conditions

Combustion-driven instabilities are a significant barrier for progress for many avenues of immense practical relevance in engineering devices, such as next generation gas turbines geared towards minimising pollutant emissions being susceptible to thermoacoustic instabilities. Numerical simulations of such reactive systems must try to balance a dynamic interplay between cost, complexity, and retention of system physics. As such, new computational tools of relevance to Large Eddy Simulation (LES) of compressible, reactive flows are proposed and evaluated. High order flow solvers are susceptible to spurious noise generation at boundaries which can be very detrimental for combustion simulations. Therefore Navier-Stokes Characteristic Boundary conditions are also reviewed and an extension to axisymmetric configurations proposed. Limitations and lingering open questions in the field are highlighted. A modified Artificially Thickened Flame (ATF) model coupled with a novel dynamic formulation is shown to preserve flame-turbulence interaction across a wide range of canonical configurations. The approach does not require efficiency functions which can be difficult to determine, impact accuracy and have limited regimes of validity. The method is supplemented with novel reverse transforms and scaling laws for relevant post-processing from the thickened to unthickened state. This is implemented into a wider Adaptive Mesh Refinement (AMR) context to deliver a unified LES-AMR-ATF framework. The model is validated in a range of test case showing noticeable improvements over conventional LES alternatives. The proposed modifications allow meaningful inferences about flame structure that conventionally may have been restricted to the domain of Direct Numerical Simulation. This allows studying the changes in small-scale flow and scalar topologies during flame-flame interaction. The approach is applied to a dual flame burner setup, where simulations show inclusion of a neighbouring burner increases compressive flow topologies as compared to a lone flame. This may lead to favouring convex scalar structures that are potentially responsible for the increase in counter-normal flame-flame interactions observed in experiments.Open Acces

Learning with Contexts

Ph.DDOCTOR OF PHILOSOPH

CHAOS: A multi-GPU PIC-DSMC solver for modeling gas and plasma flows

Numerical modeling of gas and plasma-surface interactions is critical to understanding the complex kinetic processes that dominate the extreme environments of planetary entry and in-space propulsion. However, simulations of these systems that evolve over multiple length- and time-scales is computationally expensive. Until recently, approximations were used to keep computational costs tenable, which in turn, increased the uncertainty in predictions and offered limited insights into the micro-scale flow properties and electron kinetics that dominate the macroscale processes. The need to perform high-fidelity physics-based gas and plasma simulations has led to the development of a three-dimensional, multi-GPU, Particle-in-cell (PIC)-direct simulation Monte Carlo (DSMC) solver called Cuda-based Hybrid Approach for Octree Simulations (CHAOS) that is presented in this work. This computational tool has been applied to candidate PICA-like TPS materials that consist of an irregular porous network of fibers to allow high-temperature boundary layer gases as well as pyrolysis by-products to penetrate in and flow out of the material. Quantifying bulk transport properties of these materials is essential for accurate prediction of the macroscopic ablation rate. The second application that CHAOS is being used with is the modeling of ion thruster plumes that consist of fast beam ions and slow neutrals that undergo charge-exchange (CEX) reactions to produce slow ions and fast neutrals. These slow CEX ions are strongly influenced by the electric field induced between the ion plume and the thruster surface, resulting in a backflow of ions towards the critical solar panel and thruster surfaces. Three backflow quantities, namely, ion flux, incidence angle, and incidence energy affect the macroscopic sputtering rate of the solar panel surfaces over extended operational times and are predicted from the PIC-DSMC simulations