Computerized analysis of coronary artery disease: Performance evaluation of segmentation and tracking of coronary arteries in CT angiograms

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/134780/1/mp0294.pd

간 조영술을 위한 혈관 모델 기반의 국부 적응 2D-3D 정합 알고리즘 기법 연구

학위논문 (박사)-- 서울대학교 대학원 : 전기·컴퓨터공학부, 2017. 2. 신영길.Two-dimensional–three-dimensional (2D–3D) registration between intra-operative 2D digital subtraction angiography (DSA) and pre-operative 3D computed tomography angiography (CTA) can be used for roadmapping purposes. However, through the projection of 3D vessels, incorrect intersections and overlaps between vessels are produced because of the complex vascular structure, which make it difficult to obtain the correct solution of 2D–3D registration. To overcome these problems, we propose a registration method that selects a suitable part of a 3D vascular structure for a given DSA image and finds the optimized solution to the partial 3D structure. The proposed algorithm can reduce the registration errors because it restricts the range of the 3D vascular structure for the registration by using only the relevant 3D vessels with the given DSA. To search for the appropriate 3D partial structure, we first construct a tree model of the 3D vascular structure and divide it into several subtrees in accordance with the connectivity. Then, the best matched subtree with the given DSA image is selected using the results from the coarse registration between each subtree and the vessels in the DSA image. Finally, a fine registration is conducted to minimize the difference between the selected subtree and the vessels of the DSA image. In experimental results obtained using 10 clinical datasets, the average distance errors in the case of the proposed method were 2.34 ± 1.94 mm. The proposed algorithm converges faster and produces more correct results than the conventional method in evaluations on patient datasets.Chapter 1 Introduction 1 1.1 Background 1 1.2 Problem statement 6 1.3 Main contributions 8 1.4 Contents organization 10 Chapter 2 Related Works 12 2.1 Overview 12 2.1.1 Definitions 14 2.1.2 Intensity-based and feature-based registration 17 2.2 Neurovascular applications 19 2.3 Liver applications 22 2.4 Cardiac applications 27 2.4.1 Rigid registration 27 2.4.2 Non-rigid registration 31 Chapter 3 3D Vascular Structure Model 33 3.1 Vessel segmentation 34 3.1.1 Overview 34 3.1.2 Vesselness filter 36 3.1.3 Vessel segmentation 39 3.2 Skeleton extraction 40 3.2.1 Overview 40 3.2.2 Skeleton extraction based on fast marching method 41 3.3 Graph construction 45 3.4 Generation of subtree structures from 3D tree model 46 Chapter 4 Locally Adaptive Registration 52 4.1 2D centerline extraction 53 4.1.1 Extraction from a single DSA image 54 4.1.2 Extraction from angiographic image sequence 55 4.2 Coarse registration for the detection of the best matched subtree 58 4.3 Fine registration with selected 3D subtree 61 Chapter 5 Experimental Results 63 5.1 Materials 63 5.2 Phantom study 65 5.3 Performance evaluation 69 5.3.1 Evaluation for a single DSA image 69 5.3.2 Evaluation for angiographic image sequence 75 5.4 Comparison with other methods 77 5.5 Parameter study 87 Chapter 6 Conclusion 90 Bibliography 92 초록 109Docto

Developing Photoacoustic Tomography Devices for Translational Medicine and Basic Science Research

Photoacoustic (PA) tomography (PAT) provides volumetric images of biological tissue with scalable spatial resolutions and imaging depths, while preserving the same imaging contrast—optical absorption. Taking the advantage of its 100% sensitivity to optical absorption, PAT has been widely applied in structural, functional, and molecular imaging, with both endogenous and exogenous contrasts, at superior depths than pure optical methods. Intuitively, hemoglobin has been the most commonly studied biomolecule in PAT due to its strong absorption in the visible wavelength regime. One of the main focuses of this dissertation is to investigate an underexplored wavelength regime—ultraviolet (UV), which allows us to image cell nuclei without labels and generate histology-like images naturally from unprocessed biological tissue. These preparation-free and easy-to-interpret characteristics open up new possibilities for PAT to become readily applicable to other important biomedical problems (e.g., surgical margin analysis, Chapter 2) or basic science studies (e.g., whole-organ imaging, Chapter 3). For instance, we developed and optimized a PA microscopy system with UV laser illumination (UV-PAM) to achieve fast, label-free, multilayered, and histology-like imaging of human breast cancer in Chapter 2. These imaging abilities are essential to intraoperative surgical margin analysis, which enables promptly directed re-excision and reduces the number of repeat surgeries. We have incorporated the Grüneisen relaxation (GR) effect with UV-PAM to improve the performance of our UV-PAM system (e.g., the axial resolution), thus providing more accurate three-dimensional (3D) information (Chapter 4). The nonlinear PA signals caused by the GR effect enable optical sectioning capability, revealing important 3D cell nuclear distributions and internal structures for cancer diagnosis. In the final focus of this dissertation, we have implemented a low-cost PA computed tomography (PACT) system with a single xenon flash lamp as the illumination source (Chapter 5). Lasers have been commonly used as illumination light sources in PACT. However, lasers are usually expensive and bulky, limiting their applicability in many clinical usages. Therefore, the use of a single xenon flash lamp as an alternative light source was explored. We found that PACT images acquired with flash lamp illumination were comparable to those acquired with laser illumination. This low-cost and portable PACT system opens up new potentials, such as low-cost skin melanoma imaging in undeveloped countries

Submicron-resolution Photoacoustic Microscopy of Endogenous Light-absorbing Biomolecules

Photoacoustic imaging in biomedicine has the unique advantage of probing endogenous light absorbers at various length scales with a 100% relative sensitivity. Among the several modalities of photoacoustic imaging, optical-resolution photoacoustic microscopy (OR-PAM) can achieve high spatial resolution, on the order of optical wavelength, at \u3c1 mm depth in biological tissue (the optical ballistic regime). OR-PAM has been applied successfully to structural and functional imaging of blood vasculature and red blood cells in vivo. Any molecules which absorb sufficient light at certain wavelengths can potentially be imaged by PAM. Compared with pure optical imaging, which typically targets fluorescent markers, label-free PAM avoids the major concerns that the fluorescent labeling probes may disturb the function of biomolecules and may have an insufficient density. This dissertation aims to advance label-free OR-PAM to the subcellular scale. The first part of this dissertation describes the technological advancement of PAM yielding high spatial resolution in 3D. The lateral resolution was improved by using optical objectives with high numerical apertures for optical focusing. The axial resolution was improved by using broadband ultrasonic transducers for ultrasound detection. We achieved 220 nm lateral resolution in transmission mode, 0.43 µm lateral resolution in reflection mode, 7.6 µm axial resolution in normal tissue, and 5.8 µm axial resolution with silicone oil immersion/injection. The achieved lateral resolution and axial resolution were the finest reported at the time. With high-resolution in 3D, PAM was demonstrated to resolve cellular and subcellular structures in vivo, such as red blood cells and melanosomes in melanoma cells. Compared with previous PAM systems, our high-resolution PAM could resolve capillaries in mouse ears more clearly. As an example application, we demonstrated intracellular temperature imaging, assisted by fluorescence signal detection, with sub-degree temperature resolution and sub-micron lateral resolution. The second part of this dissertation describes the exploration of endogenous light-absorbing biomolecules for PAM. We demonstrated cytochromes and myoglobin as new absorption contrasts for PAM and identified the corresponding optimal wavelengths for imaging. Fixed fibroblasts on slides and mouse ear sections were imaged by PAM at 422 nm and 250 nm wavelengths to reveal cytoplasms and nuclei, respectively, as confirmed by standard hematoxylin and eosin (H&E) histology. By imaging a blood-perfused mouse heart at 532 nm down to 150 µm in depth, we derived the myocardial sheet thickness and the cleavage height from an undehydrated heart for the first time. The findings promote PAM at new wavelengths and open up new possibilities for characterizing biological tissue. Of particular interest, dual-wavelength PAM around 250 nm and 420 nm wavelengths is analogous to H&E histology. The last part of this dissertation describes the development of sectioning photoacoustic microscopy (SPAM), based on the advancement in spatial resolution and new contrasts for PAM, with applications in brain histology. Label-free SPAM, assisted by a microtome, acquires serial distortion-free images of a specimen on the surface. By exciting cell nuclei at 266 nm wavelength with high resolution, SPAM could pinpoint cell nuclei sensitively and specifically in the mouse brain section, as confirmed by H&E histology. SPAM was demonstrated to generate high-resolution 3D images, highlighting cell nuclei, of formalin-fixed paraffin-embedded mouse brains without tissue staining or clearing. SPAM can potentially serve as a high-throughput and minimal-artifact substitute for histology, probe many other biomolecules and cells, and become a universal tool for animal or human whole-organ microscopy, with diverse applications in life sciences

Amélioration des ouvertures par chemins pour l'analyse d'images à N dimensions et implémentations optimisées

La détection de structures fines et orientées dans une image peut mener à un très large champ d'applications en particulier dans le domaine de l'imagerie médicale, des sciences des matériaux ou de la télédétection. Les ouvertures et fermetures par chemins sont des opérateurs morphologiques utilisant des chemins orientés et flexibles en guise d'éléments structurants. Ils sont utilisés de la même manière que les opérateurs morphologiques utilisant des segments orientés comme éléments structurants mais sont plus efficaces lorsqu'il s'agit de détecter des structures pouvant être localement non rigides. Récemment, une nouvelle implémentation des opérateurs par chemins a été proposée leur permettant d'être appliqués à des images 2D et 3D de manière très efficace. Cependant, cette implémentation est limitée par le fait qu'elle n'est pas robuste au bruit affectant les structures fines. En effet, pour être efficaces, les opérateurs par chemins doivent être suffisamment longs pour pouvoir correspondre à la longueur des structures à détecter et deviennent de ce fait beaucoup plus sensibles au bruit de l'image. La première partie de ces travaux est dédiée à répondre à ce problème en proposant un algorithme robuste permettant de traiter des images 2D et 3D. Nous avons proposé les opérateurs par chemins robustes, utilisant une famille plus grande d'éléments structurants et qui, donnant une longueur L et un paramètre de robustesse G, vont permettre la propagation du chemin à travers des déconnexions plus petites ou égales à G, rendant le paramètre G indépendant de L. Cette simple proposition mènera à une implémentation plus efficace en terme de complexité de calculs et d'utilisation mémoire que l'état de l'art. Les opérateurs développés ont été comparés avec succès avec d'autres méthodes classiques de la détection des structures curvilinéaires de manière qualitative et quantitative. Ces nouveaux opérateurs ont été par la suite intégrés dans une chaîne complète de traitement d'images et de modélisation pour la caractérisation des matériaux composite renforcés avec des fibres de verres. Notre étude nous a ensuite amenés à nous intéresser à des filtres morphologiques récents basés sur la mesure de caractéristiques géodésiques. Ces filtres sont une bonne alternative aux ouvertures par chemins car ils sont très efficaces lorsqu'il s'agit de détecter des structures présentant de fortes tortuosités ce qui est précisément la limitation majeure des ouvertures par chemins. La combinaison de la robustesse locale des ouvertures par chemins robustes et la capacité des filtres par attributs géodésiques à recouvrer les structures tortueuses nous ont permis de proposer un nouvel algorithme, les ouvertures par chemins robustes et sélectives.The detection of thin and oriented features in an image leads to a large field of applications specifically in medical imaging, material science or remote sensing. Path openings and closings are efficient morphological operators that use flexible oriented paths as structuring elements. They are employed in a similar way to operators with rotated line segments as structuring elements, but are more effective as they can detect linear structures that are not necessarily locally perfectly straight. While their theory has always allowed paths in arbitrary dimensions, de facto implementations were only proposed in 2D. Recently, a new implementation was proposed enabling the computation of efficient d-dimensional path operators. However this implementation is limited in the sense that it is not robust to noise. Indeed, in practical applications, for path operators to be effective, structuring elements must be sufficiently long so that they correspond to the length of the desired features to be detected. Yet, path operators are increasingly sensitive to noise as their length parameter L increases. The first part of this work is dedicated to cope with this limitation. Thus, we will propose an efficient d-dimensional algorithm, the robust path operators, which use a larger family of flexible structuring elements. Given an arbitrary length parameter G, path propagation is allowed if disconnections between two pixels belonging to a path is less or equal to G and so, render it independent of L. This simple assumption leads to a constant memory bookkeeping and results in a low complexity. The developed operators have been compared qualitatively and quantitatively to other efficient methods for the detection of line-like features. As an application, robust path openings have been integrated into a complete chain of image processing for the modelling and the characterization of glass fibers reinforced polymer. Our study has also led us to focus our interest on recent morphological connected filters based on geodesic measurements. These filters are a good alternative to path operators as they are efficient at detecting the so-called "tortuous" shapes in an image which is precisely the main limitation of path operators. Combining the local robustness of the robust path operators with the ability of geodesic attribute-based filters to recover "tortuous" shapes have enabled us to propose another original algorithm, the selective and robust path operators.SAVOIE-SCD - Bib.électronique (730659901) / SudocGRENOBLE1/INP-Bib.électronique (384210012) / SudocGRENOBLE2/3-Bib.électronique (384219901) / SudocSudocFranceF