Accurate Simulation of Low-Intensity Transcranial Ultrasound Propagation for Neurostimulation

Neural stimulation with low-intensity ultrasound is a potentially transformative technology with applications in therapy and research. To develop, it will require ultrasound to be tightly focused on brain structures with accurate spatial targeting and fine control over the ultrasound amplitude at the target. However, the skull is an impediment to the effective focusing of ultrasound. Simulations of ultrasound propagation through acoustic property maps derived from medical images can be used to derive focusing drive signals for multi-element arrays. Focusing effectiveness is dependent on the fidelity of the numerical simulations. In combination with MRI based treatment verification, model based focusing has been used to focus high-intensity ultrasound onto the brain for ablation. This thesis presents a thorough and systematic study of the simulation parameters required to achieve effective transcranial focusing. The literature on ultrasonic neurostimulation, transcranial ultrasonic focusing, and the derivation of property maps from medical images is reviewed. The sampling criteria required to ensure numerical accuracy for the k-space pseudospectral time domain simulation scheme is established through testing of individual sources of numerical error, and convergence testing of a simulated time-reversal protocol. With numerical accuracy assured, the importance of acoustic property maps is examined through simulations to determine the sensitivity of intracranial fields to the properties of the skull layer. These results are corroborated by matching experimental measurements of ultrasound propagation through skull bone phantoms with spatially registered simulations. Finally, the impact of image related homogenisation and loss of internal bone structure is determined using simulations through co-registered clinical CT and micro-CT data of the skull

Mathematical Imaging Tools in Cancer Research - From Mitosis Analysis to Sparse Regularisation

This dissertation deals with customised image analysis tools in cancer research. In the field of biomedical sciences, mathematical imaging has become crucial in order to account for advancements in technical equipment and data storage by sound mathematical methods that can process and analyse imaging data in an automated way. This thesis contributes to the development of such mathematically sound imaging models in four ways: (i) automated cell segmentation and tracking. In cancer drug development, time-lapse light microscopy experiments are conducted for performance validation. The aim is to monitor behaviour of cells in cultures that have previously been treated with chemotherapy drugs, since atypical duration and outcome of mitosis, the process of cell division, can be an indicator of successfully working drugs. As an imaging modality we focus on phase contrast microscopy, hence avoiding phototoxicity and influence on cell behaviour. As a drawback, the common halo- and shade-off effect impede image analysis. We present a novel workflow uniting both automated mitotic cell detection with the Hough transform and subsequent cell tracking by a tailor-made level-set method in order to obtain statistics on length of mitosis and cell fates. The proposed image analysis pipeline is deployed in a MATLAB software package called MitosisAnalyser. For the detection of mitotic cells we use the circular Hough transform. This concept is investigated further in the framework of image regularisation in the general context of imaging inverse problems, in which circular objects should be enhanced, (ii) exploiting sparsity of first-order derivatives in combination with the linear circular Hough transform operation. Furthermore, (iii) we present a new unified higher-order derivative-type regularisation functional enforcing sparsity of a vector field related to an image to be reconstructed using curl, divergence and shear operators. The model is able to interpolate between well-known regularisers such as total generalised variation and infimal convolution total variation. Finally, (iv) we demonstrate how we can learn sparsity promoting parametrised regularisers via quotient minimisation, which can be motivated by generalised Eigenproblems. Learning approaches have recently become very popular in the field of inverse problems. However, the majority aims at fitting models to favourable training data, whereas we incorporate knowledge about both fit and misfit data. We present results resembling behaviour of well-established derivative-based sparse regularisers, introduce novel families of non-derivative-based regularisers and extend this framework to classification problems.NIHR Cambridge Biomedical Research Centre PhD Fellowshi

동적 환경 디블러링을 위한 새로운 모델, 알로기즘, 그리고 해석에 관한 연구

학위논문 (박사)-- 서울대학교 대학원 : 전기·컴퓨터공학부, 2016. 8. 이경무.Blurring artifacts are the most common flaws in photographs. To remove these artifacts, many deblurring methods which restore sharp images from blurry ones have been studied considerably in the field of computational photography. However, state-of-the-art deblurring methods are based on a strong assumption that the captured scenes are static, and thus a great many things still remain to be done. In particular, these conventional methods fail to deblur blurry images captured in dynamic environments which have spatially varying blurs caused by various sources such as camera shake including out-of-plane motion, moving objects, depth variation, and so on. Therefore, the deblurring problem becomes more difficult and deeply challenging for dynamic scenes. Therefore, in this dissertation, addressing the deblurring problem of general dynamic scenes is a goal, and new solutions are introduced, that remove spatially varying blurs in dynamic scenes unlike conventional methods built on the assumption that the captured scenes are static. Three kinds of dynamic scene deblurring methods are proposed to achieve this goal, and they are based on: (1) segmentation, (2) sharp exemplar, (3) kernel-parametrization. The proposed approaches are introduced from segment-wise to pixel-wise approaches, and pixel-wise varying general blurs are handled in the end. First, the segmentation-based deblurring method estimates the latent image, multiple different kernels, and associated segments jointly. With the aid of the joint approach, segmentation-based method could achieve accurate blur kernel within a segment, remove segment-wise varying blurs, and reduce artifacts at the motion boundaries which are common in conventional approaches. Next, an \textit{exemplar}-based deblurring method is proposed, which utilizes a sharp exemplar to estimate highly accurate blur kernel and overcomes the limitations of the segmentation-based method that cannot handle small or texture-less segments. Lastly, the deblurring method using kernel-parametrization approximates the locally varying kernel as linear using motion flows. Thus the proposed method based on kernel-parametrization is generally applicable to remove pixel-wise varying blurs, and estimates the latent image and motion flow at the same time. With the proposed methods, significantly improved deblurring qualities are achieved, and intensive experimental evaluations demonstrate the superiority of the proposed methods in dynamic scene deblurring, in which state-of-the-art methods fail to deblur.Chapter 1 Introduction 1 Chapter 2 Image Deblurring with Segmentation 7 2.1 Introduction and Related Work 7 2.2 Segmentation-based Dynamic Scene Deblurring Model 11 2.2.1 Adaptive blur model selection 13 2.2.2 Regularization 14 2.3 Optimization 17 2.3.1 Sharp image restoration 18 2.3.2 Weight estimation 19 2.3.3 Kernel estimation 23 2.3.4 Overall procedure 25 2.4 Experiments 25 2.5 Summary 27 Chapter 3 Image Deblurring with Exemplar 33 3.1 Introduction and Related Work 35 3.2 Method Overview 37 3.3 Stage I: Exemplar Acquisition 38 3.3.1 Sharp image acquisition and preprocessing 38 3.3.2 Exemplar from blur-aware optical flow estimation 40 3.4 Stage II: Exemplar-based Deblurring 42 3.4.1 Exemplar-based latent image restoration 43 3.4.2 Motion-aware segmentation 44 3.4.3 Robust kernel estimation 45 3.4.4 Unified energy model and optimization 47 3.5 Stage III: Post-processing and Refinement 47 3.6 Experiments 49 3.7 Summary 53 Chapter 4 Image Deblurring with Kernel-Parametrization 57 4.1 Introduction and Related Work 59 4.2 Preliminary 60 4.3 Proposed Method 62 4.3.1 Image-statistics-guided motion 62 4.3.2 Adaptive variational deblurring model 64 4.4 Optimization 69 4.4.1 Motion estimation 70 4.4.2 Latent image restoration 72 4.4.3 Kernel re-initialization 73 4.5 Experiments 75 4.6 Summary 80 Chapter 5 Video Deblurring with Kernel-Parametrization 87 5.1 Introduction and Related Work 87 5.2 Generalized Video Deblurring 93 5.2.1 A new data model based on kernel-parametrization 94 5.2.2 A new optical flow constraint and temporal regularization 104 5.2.3 Spatial regularization 105 5.3 Optimization Framework 107 5.3.1 Sharp video restoration 108 5.3.2 Optical flows estimation 109 5.3.3 Defocus blur map estimation 110 5.4 Implementation Details 111 5.4.1 Initialization and duty cycle estimation 112 5.4.2 Occlusion detection and refinement 113 5.5 Motion Blur Dataset 114 5.5.1 Dataset generation 114 5.6 Experiments 116 5.7 Summary 120 Chapter 6 Conclusion 127 Bibliography 131 국문 초록 141Docto