Gap Filling of 3-D Microvascular Networks by Tensor Voting

We present a new algorithm which merges discontinuities in 3-D images of tubular structures presenting undesirable gaps. The application of the proposed method is mainly associated to large 3-D images of microvascular networks. In order to recover the real network topology, we need to fill the gaps between the closest discontinuous vessels. The algorithm presented in this paper aims at achieving this goal. This algorithm is based on the skeletonization of the segmented network followed by a tensor voting method. It permits to merge the most common kinds of discontinuities found in microvascular networks. It is robust, easy to use, and relatively fast. The microvascular network images were obtained using synchrotron tomography imaging at the European Synchrotron Radiation Facility. These images exhibit samples of intracortical networks. Representative results are illustrated

ART-VENA: Retinal Vaseular Caliber Measurement

The size of retinal vascular caliber in eye fundus images is a fundamental diagnosis parameter in the study of systemic vascular pathologies, like arterial hypertension or arteriosclerosis. ART-VENA is a semiautomatic system to measure the retinal vascular caliber. From the medical point of view, its repeatability (coefficients of variation under 1.5%) turns it into a reliable tool to objectify vascular changes which previously depended an the observer’s subjectivity

Motion Calculations on Stent Grafts in AAA

Endovascular aortic repair (EVAR) is a technique which uses stent grafts to treat aortic aneurysms in patients at risk of aneurysm rupture. Although this technique has been shown to be very successful on the short term, the long term results are less optimistic due to failure of the stent graft. The pulsating blood flow applies stresses and forces to the stent graft, which can cause problems such as breakage, leakage, and migration. Therefore it is of importance to gain more insight into the in vivo motion behavior of these devices. If we know more about the motion patterns in well-behaved stent graft as well as ill-behaving devices, we shall be better able to distinguish between these type of behaviors These insights will enable us to detect stent-related problems and might even be used to predict problems beforehand. Further, these insights will help in designing the next generation stent grafts. Firstly, this work discusses the applicability of ECG-gated CT for measuring the motions of stent grafts in AAA. Secondly, multiple methods to segment the stent graft from these data are discussed. Thirdly, this work proposes a method that uses image registration to apply motion to the segmented stent mode

Segmentation and reconstruction of 3D artery models for surgical planning

Master'sMASTER OF SCIENC

복부 CT에서 간과 혈관 분할 기법

학위논문(박사)--서울대학교 대학원 :공과대학 컴퓨터공학부,2020. 2. 신영길.복부 전산화 단층 촬영 (CT) 영상에서 정확한 간 및 혈관 분할은 체적 측정, 치료 계획 수립 및 추가적인 증강 현실 기반 수술 가이드와 같은 컴퓨터 진단 보조 시스템을 구축하는데 필수적인 요소이다. 최근 들어 컨볼루셔널 인공 신경망 (CNN) 형태의 딥 러닝이 많이 적용되면서 의료 영상 분할의 성능이 향상되고 있지만, 실제 임상에 적용할 수 있는 높은 일반화 성능을 제공하기는 여전히 어렵다. 또한 물체의 경계는 전통적으로 영상 분할에서 매우 중요한 요소로 이용되었지만, CT 영상에서 간의 불분명한 경계를 추출하기가 어렵기 때문에 현대 CNN에서는 이를 사용하지 않고 있다. 간 혈관 분할 작업의 경우, 복잡한 혈관 영상으로부터 학습 데이터를 만들기 어렵기 때문에 딥 러닝을 적용하기가 어렵다. 또한 얇은 혈관 부분의 영상 밝기 대비가 약하여 원본 영상에서 식별하기가 매우 어렵다. 본 논문에서는 위 언급한 문제들을 해결하기 위해 일반화 성능이 향상된 CNN과 얇은 혈관을 포함하는 복잡한 간 혈관을 정확하게 분할하는 알고리즘을 제안한다. 간 분할 작업에서 우수한 일반화 성능을 갖는 CNN을 구축하기 위해, 내부적으로 간 모양을 추정하는 부분이 포함된 자동 컨텍스트 알고리즘을 제안한다. 또한, CNN을 사용한 학습에 경계선의 개념이 새롭게 제안된다. 모호한 경계부가 포함되어 있어 전체 경계 영역을 CNN에 훈련하는 것은 매우 어렵기 때문에 반복되는 학습 과정에서 인공 신경망이 스스로 예측한 확률에서 부정확하게 추정된 부분적 경계만을 사용하여 인공 신경망을 학습한다. 실험적 결과를 통해 제안된 CNN이 다른 최신 기법들보다 정확도가 우수하다는 것을 보인다. 또한, 제안된 CNN의 일반화 성능을 검증하기 위해 다양한 실험을 수행한다. 간 혈관 분할에서는 간 내부의 관심 영역을 지정하기 위해 앞서 획득한 간 영역을 활용한다. 정확한 간 혈관 분할을 위해 혈관 후보 점들을 추출하여 사용하는 알고리즘을 제안한다. 확실한 후보 점들을 얻기 위해, 삼차원 영상의 차원을 먼저 최대 강도 투영 기법을 통해 이차원으로 낮춘다. 이차원 영상에서는 복잡한 혈관의 구조가 보다 단순화될 수 있다. 이어서, 이차원 영상에서 혈관 분할을 수행하고 혈관 픽셀들은 원래의 삼차원 공간상으로 역 투영된다. 마지막으로, 전체 혈관의 분할을 위해 원본 영상과 혈관 후보 점들을 모두 사용하는 새로운 레벨 셋 기반 알고리즘을 제안한다. 제안된 알고리즘은 복잡한 구조가 단순화되고 얇은 혈관이 더 잘 보이는 이차원 영상에서 얻은 후보 점들을 사용하기 때문에 얇은 혈관 분할에서 높은 정확도를 보인다. 실험적 결과에 의하면 제안된 알고리즘은 잘못된 영역의 추출 없이 다른 레벨 셋 기반 알고리즘들보다 우수한 성능을 보인다. 제안된 알고리즘은 간과 혈관을 분할하는 새로운 방법을 제시한다. 제안된 자동 컨텍스트 구조는 사람이 디자인한 학습 과정이 일반화 성능을 크게 향상할 수 있다는 것을 보인다. 그리고 제안된 경계선 학습 기법으로 CNN을 사용한 영상 분할의 성능을 향상할 수 있음을 내포한다. 간 혈관의 분할은 이차원 최대 강도 투영 기반 이미지로부터 획득된 혈관 후보 점들을 통해 얇은 혈관들이 성공적으로 분할될 수 있음을 보인다. 본 논문에서 제안된 알고리즘은 간의 해부학적 분석과 자동화된 컴퓨터 진단 보조 시스템을 구축하는 데 매우 중요한 기술이다.Accurate liver and its vessel segmentation on abdominal computed tomography (CT) images is one of the most important prerequisites for computer-aided diagnosis (CAD) systems such as volumetric measurement, treatment planning, and further augmented reality-based surgical guide. In recent years, the application of deep learning in the form of convolutional neural network (CNN) has improved the performance of medical image segmentation, but it is difficult to provide high generalization performance for the actual clinical practice. Furthermore, although the contour features are an important factor in the image segmentation problem, they are hard to be employed on CNN due to many unclear boundaries on the image. In case of a liver vessel segmentation, a deep learning approach is impractical because it is difficult to obtain training data from complex vessel images. Furthermore, thin vessels are hard to be identified in the original image due to weak intensity contrasts and noise. In this dissertation, a CNN with high generalization performance and a contour learning scheme is first proposed for liver segmentation. Secondly, a liver vessel segmentation algorithm is presented that accurately segments even thin vessels. To build a CNN with high generalization performance, the auto-context algorithm is employed. The auto-context algorithm goes through two pipelines: the first predicts the overall area of a liver and the second predicts the final liver using the first prediction as a prior. This process improves generalization performance because the network internally estimates shape-prior. In addition to the auto-context, a contour learning method is proposed that uses only sparse contours rather than the entire contour. Sparse contours are obtained and trained by using only the mispredicted part of the network's final prediction. Experimental studies show that the proposed network is superior in accuracy to other modern networks. Multiple N-fold tests are also performed to verify the generalization performance. An algorithm for accurate liver vessel segmentation is also proposed by introducing vessel candidate points. To obtain confident vessel candidates, the 3D image is first reduced to 2D through maximum intensity projection. Subsequently, vessel segmentation is performed from the 2D images and the segmented pixels are back-projected into the original 3D space. Finally, a new level set function is proposed that utilizes both the original image and vessel candidate points. The proposed algorithm can segment thin vessels with high accuracy by mainly using vessel candidate points. The reliability of the points can be higher through robust segmentation in the projected 2D images where complex structures are simplified and thin vessels are more visible. Experimental results show that the proposed algorithm is superior to other active contour models. The proposed algorithms present a new method of segmenting the liver and its vessels. The auto-context algorithm shows that a human-designed curriculum (i.e., shape-prior learning) can improve generalization performance. The proposed contour learning technique can increase the accuracy of a CNN for image segmentation by focusing on its failures, represented by sparse contours. The vessel segmentation shows that minor vessel branches can be successfully segmented through vessel candidate points obtained by reducing the image dimension. The algorithms presented in this dissertation can be employed for later analysis of liver anatomy that requires accurate segmentation techniques.Chapter 1 Introduction 1 1.1 Background and motivation 1 1.2 Problem statement 3 1.3 Main contributions 6 1.4 Contents and organization 9 Chapter 2 Related Works 10 2.1 Overview 10 2.2 Convolutional neural networks 11 2.2.1 Architectures of convolutional neural networks 11 2.2.2 Convolutional neural networks in medical image segmentation 21 2.3 Liver and vessel segmentation 37 2.3.1 Classical methods for liver segmentation 37 2.3.2 Vascular image segmentation 40 2.3.3 Active contour models 46 2.3.4 Vessel topology-based active contour model 54 2.4 Motivation 60 Chapter 3 Liver Segmentation via Auto-Context Neural Network with Self-Supervised Contour Attention 62 3.1 Overview 62 3.2 Single-pass auto-context neural network 65 3.2.1 Skip-attention module 66 3.2.2 V-transition module 69 3.2.3 Liver-prior inference and auto-context 70 3.2.4 Understanding the network 74 3.3 Self-supervising contour attention 75 3.4 Learning the network 81 3.4.1 Overall loss function 81 3.4.2 Data augmentation 81 3.5 Experimental Results 83 3.5.1 Overview 83 3.5.2 Data configurations and target of comparison 84 3.5.3 Evaluation metric 85 3.5.4 Accuracy evaluation 87 3.5.5 Ablation study 93 3.5.6 Performance of generalization 110 3.5.7 Results from ground-truth variations 114 3.6 Discussion 116 Chapter 4 Liver Vessel Segmentation via Active Contour Model with Dense Vessel Candidates 119 4.1 Overview 119 4.2 Dense vessel candidates 124 4.2.1 Maximum intensity slab images 125 4.2.2 Segmentation of 2D vessel candidates and back-projection 130 4.3 Clustering of dense vessel candidates 135 4.3.1 Virtual gradient-assisted regional ACM 136 4.3.2 Localized regional ACM 142 4.4 Experimental results 145 4.4.1 Overview 145 4.4.2 Data configurations and environment 146 4.4.3 2D segmentation 146 4.4.4 ACM comparisons 149 4.4.5 Evaluation of bifurcation points 154 4.4.6 Computational performance 159 4.4.7 Ablation study 160 4.4.8 Parameter study 162 4.5 Application to portal vein analysis 164 4.6 Discussion 168 Chapter 5 Conclusion and Future Works 170 Bibliography 172 초록 197Docto

Development of an Atlas-Based Segmentation of Cranial Nerves Using Shape-Aware Discrete Deformable Models for Neurosurgical Planning and Simulation

Twelve pairs of cranial nerves arise from the brain or brainstem and control our sensory functions such as vision, hearing, smell and taste as well as several motor functions to the head and neck including facial expressions and eye movement. Often, these cranial nerves are difficult to detect in MRI data, and thus represent problems in neurosurgery planning and simulation, due to their thin anatomical structure, in the face of low imaging resolution as well as image artifacts. As a result, they may be at risk in neurosurgical procedures around the skull base, which might have dire consequences such as the loss of eyesight or hearing and facial paralysis. Consequently, it is of great importance to clearly delineate cranial nerves in medical images for avoidance in the planning of neurosurgical procedures and for targeting in the treatment of cranial nerve disorders. In this research, we propose to develop a digital atlas methodology that will be used to segment the cranial nerves from patient image data. The atlas will be created from high-resolution MRI data based on a discrete deformable contour model called 1-Simplex mesh. Each of the cranial nerves will be modeled using its centerline and radius information where the centerline is estimated in a semi-automatic approach by finding a shortest path between two user-defined end points. The cranial nerve atlas is then made more robust by integrating a Statistical Shape Model so that the atlas can identify and segment nerves from images characterized by artifacts or low resolution. To the best of our knowledge, no such digital atlas methodology exists for segmenting nerves cranial nerves from MRI data. Therefore, our proposed system has important benefits to the neurosurgical community