Robust Algorithms for Registration of 3D Images of Human Brain

This thesis is concerned with the process of automatically aligning 3D medical images of human brain. It concentrates on rigid-body matching of Positron Emission Tomography images (PET) and Magnetic Resonance images (MR) within one patient and on non-linear matching of PET images of different patients. In recent years, mutual information has proved to be an excellent criterion for automatic registration of intra-individual images from different modalities. We propose and evaluate a method that combines a multi-resolution optimization of mutual information with an efficient segmentation of background voxels and a modified principal axes algorithm. We show that an acceleration factor of 6-7 can be achieved without loss of accuracy and that the method significantly reduces the rate of unsuccessful registrations. Emphasis was also laid on creation of an automatic registration system that could be used routinely in clinical environment. Non-linear registration tries to reduce the inter-individual variability of shape and structure between two brain images by deforming one image so that homologous regions in both images get aligned. It is an important step of many procedures in medical image processing and analysis. We present a novel algorithm for an automatic non-linear registration of PET images based on hierarchical volume subdivisions and local affine optimizations. It produces a C2-continuous deformation function and guarantees that the deformation is one-to-one. Performance of the algorithm was evaluated on more than 600 clinical PET images

Automated boundary detection of echocardiograms

Two-dimensional echocardiograms of the left ventricle of the heart have been used to produce three-dimensional wire frame reconstructions of the inner wall of the left ventricle chamber. Currently, this process is accomplished by tracing the boundary of the images manually after applying simple image processing algorithms. This manual interaction is a very tedious and time consuming step in the three-dimensional and four-dimensional reconstruction process. It would be desirable to remove as much operator interaction as possible from the process to improve repeatability and decrease throughput time. This thesis investigated and implemented several basic and novel image processing algorithms which automatically preprocessed the echo images and extracted the boundary information necessary for a reconstruction process. Among the algorithms investigated are common spatial kernel operators such as the Gaussian Convolution Kernel and the Standard Deviation Kernel. Also implemented and discussed are the Robust Automatic Threshold Selector (RATS), a Contour Following Algorithm and a variation of a QUAD-TREE/Pyramid Resolution data structure. Morphological operations of erosion and dilation were applied to give the closing effect necessary in handling boundary dropouts found in some echo images. An effort has been made to utilize the Gould/Deanza image processing system to execute the algorithms in order to take advantage of its unique architecture. The accuracy of the final sequence of algorithms was tested on actual images and a comparison made between hand drawn borders and the computer generated borders traced on actual echo images

A comparative evaluation for liver segmentation from spir images and a novel level set method using signed pressure force function

Thesis (Doctoral)--Izmir Institute of Technology, Electronics and Communication Engineering, Izmir, 2013Includes bibliographical references (leaves: 118-135)Text in English; Abstract: Turkish and Englishxv, 145 leavesDeveloping a robust method for liver segmentation from magnetic resonance images is a challenging task due to similar intensity values between adjacent organs, geometrically complex liver structure and injection of contrast media, which causes all tissues to have different gray level values. Several artifacts of pulsation and motion, and partial volume effects also increase difficulties for automatic liver segmentation from magnetic resonance images. In this thesis, we present an overview about liver segmentation methods in magnetic resonance images and show comparative results of seven different liver segmentation approaches chosen from deterministic (K-means based), probabilistic (Gaussian model based), supervised neural network (multilayer perceptron based) and deformable model based (level set) segmentation methods. The results of qualitative and quantitative analysis using sensitivity, specificity and accuracy metrics show that the multilayer perceptron based approach and a level set based approach which uses a distance regularization term and signed pressure force function are reasonable methods for liver segmentation from spectral pre-saturation inversion recovery images. However, the multilayer perceptron based segmentation method requires a higher computational cost. The distance regularization term based automatic level set method is very sensitive to chosen variance of Gaussian function. Our proposed level set based method that uses a novel signed pressure force function, which can control the direction and velocity of the evolving active contour, is faster and solves several problems of other applied methods such as sensitivity to initial contour or variance parameter of the Gaussian kernel in edge stopping functions without using any regularization term

Automatic region-of-interest extraction in low depth-of-field images

PhD ThesisAutomatic extraction of focused regions from images with low depth-of-field (DOF) is a problem without an efficient solution yet. The capability of extracting focused regions can help to bridge the semantic gap by integrating image regions which are meaningfully relevant and generally do not exhibit uniform visual characteristics. There exist two main difficulties for extracting focused regions from low DOF images using high-frequency based techniques: computational complexity and performance. A novel unsupervised segmentation approach based on ensemble clustering is proposed to extract the focused regions from low DOF images in two stages. The first stage is to cluster image blocks in a joint contrast-energy feature space into three constituent groups. To achieve this, we make use of a normal mixture-based model along with standard expectation-maximization (EM) algorithm at two consecutive levels of block size. To avoid the common problem of local optima experienced in many models, an ensemble EM clustering algorithm is proposed. As a result, relevant blocks, i.e., block-based region-of-interest (ROI), closely conforming to image objects are extracted. In stage two, two different approaches have been developed to extract pixel-based ROI. In the first approach, a binary saliency map is constructed from the relevant blocks at the pixel level, which is based on difference of Gaussian (DOG) and binarization methods. Then, a set of morphological operations is employed to create the pixel-based ROI from the map. Experimental results demonstrate that the proposed approach achieves an average segmentation performance of 91.3% and is computationally 3 times faster than the best existing approach. In the second approach, a minimal graph cut is constructed by using the max-flow method and also by using object/background seeds provided by the ensemble clustering algorithm. Experimental results demonstrate an average segmentation performance of 91.7% and approximately 50% reduction of the average computational time by the proposed colour based approach compared with existing unsupervised approaches

Recognition of leishmania parasite and macrophage infection rate using image processing techniques

Dissertação de mestrado, Ciências da Computação (Processamento de Imagem), Faculdade de Ciência e Tecnologia, Universidade do Algarve, 2013Leishmaniasis is an epidemic dangerous disease in tropical and sub tropical regions of the world and if it is not treated conveniently, it may cause several health infections and could even lead to the death of patients. Currently, there is no efficient vaccine for the disease and available treatments cause serious side effects such as toxicity and parasite resistance. Therefore, ongoing research in Drug Discovery and other related biological areas concentrate on finding adequate drug candidates for the disease. Drug discovery pipeline for Leishmaniasis disease facilitates so many biological techniques till now to understand level of effectiveness of different drug candidates for treating the disease. The accuracy and reliability of such techniques, however, highly depends on manual process of detecting, extracting, counting and analyzing components of interest such as cells, parasites and cytoplasm regions by expert biologists. Such kind of activities is subjected to so many human-made errors and is often considered to be too time and energy consuming. The existing computational based solutions, which are reduced, also suffer from limited level of analysis and in some cases inaccuracy of the results are evident. For instance, there is no package dedicated to Intracellular Parasites Counting, which is a central operation when researching drug candidates’ effects. The current research aims at addressing the urgent need to find a solution to the problem of investigating Infection Ratio of cells more accurately, which is in fact still lacking. A computational framework which fulfills all those mentioned tasks automatically, in an acceptable time range with maximum possible accuracy of the results is suggested. The proposed solution mainly uses Image Processing approaches to process clinical images and analyze the results. The visual and statistical results then could be used independently or as a complementary tool for laboratories to investigate infection ratio of drug candidates and even at a higher level introduce vaccines for the disease

Comparison of Deep Convolutional Neural Networks and Edge Detectors for Image-Based Crack Detection in Concrete

This paper compares the performance of common edge detectors and deep convolutional neural networks (DCNN) for image-based crack detection in concrete structures. A dataset of 19 high definition images (3420 sub-images, 319 with cracks and 3101 without) of concrete is analyzed using six common edge detection schemes (Roberts, Prewitt, Sobel, Laplacian of Gaussian, Butterworth, and Gaussian) and using the AlexNet DCNN architecture in fully trained, transfer learning, and classifier modes. The relative performance of each crack detection method is compared here for the first time on a single dataset. Edge detection methods accurately detected 53–79% of cracked pixels, but they produced residual noise in the final binary images. The best of these methods was useful in detecting cracks wider than 0.1 mm. DCNNs were used to label images, and accurately labeled them with 99% accuracy. In transfer learning mode, the network accurately detected about 86% of cracked images. DCNNs also detected much finer cracks than edge detection methods. In fully trained and classifier modes, the network detected cracks wider than 0.08 mm; in transfer learning mode, the network was able to detect cracks wider than 0.04 mm. Computational times for DCNN are shorter than the most efficient edge detection algorithms, not considering the training process. These results show significant promise for future adoption of DCNN methods for image-based damage detection in concrete. To reduce the residual noise, a hybrid method was proposed by combining the DCNN and edge detectors which reduced the noise by a factor of 24

Curve Skeleton and Moments of Area Supported Beam Parametrization in Multi-Objective Compliance Structural Optimization

This work addresses the end-to-end virtual automation of structural optimization up to the derivation of a parametric geometry model that can be used for application areas such as additive manufacturing or the verification of the structural optimization result with the finite element method. A holistic design in structural optimization can be achieved with the weighted sum method, which can be automatically parameterized with curve skeletonization and cross-section regression to virtually verify the result and control the local size for additive manufacturing. is investigated in general. In this paper, a holistic design is understood as a design that considers various compliances as an objective function. This parameterization uses the automated determination of beam parameters by so-called curve skeletonization with subsequent cross-section shape parameter estimation based on moments of area, especially for multi-objective optimized shapes. An essential contribution is the linking of the parameterization with the results of the structural optimization, e.g., to include properties such as boundary conditions, load conditions, sensitivities or even density variables in the curve skeleton parameterization. The parameterization focuses on guiding the skeletonization based on the information provided by the optimization and the finite element model. In addition, the cross-section detection considers circular, elliptical, and tensor product spline cross-sections that can be applied to various shape descriptors such as convolutional surfaces, subdivision surfaces, or constructive solid geometry. The shape parameters of these cross-sections are estimated using stiffness distributions, moments of area of 2D images, and convolutional neural networks with a tailored loss function to moments of area. Each final geometry is designed by extruding the cross-section along the appropriate curve segment of the beam and joining it to other beams by using only unification operations. The focus of multi-objective structural optimization considering 1D, 2D and 3D elements is on cases that can be modeled using equations by the Poisson equation and linear elasticity. This enables the development of designs in application areas such as thermal conduction, electrostatics, magnetostatics, potential flow, linear elasticity and diffusion, which can be optimized in combination or individually. Due to the simplicity of the cases defined by the Poisson equation, no experts are required, so that many conceptual designs can be generated and reconstructed by ordinary users with little effort. Specifically for 1D elements, a element stiffness matrices for tensor product spline cross-sections are derived, which can be used to optimize a variety of lattice structures and automatically convert them into free-form surfaces. For 2D elements, non-local trigonometric interpolation functions are used, which should significantly increase interpretability of the density distribution. To further improve the optimization, a parameter-free mesh deformation is embedded so that the compliances can be further reduced by locally shifting the node positions. Finally, the proposed end-to-end optimization and parameterization is applied to verify a linear elasto-static optimization result for and to satisfy local size constraint for the manufacturing with selective laser melting of a heat transfer optimization result for a heat sink of a CPU. For the elasto-static case, the parameterization is adjusted until a certain criterion (displacement) is satisfied, while for the heat transfer case, the manufacturing constraints are satisfied by automatically changing the local size with the proposed parameterization. This heat sink is then manufactured without manual adjustment and experimentally validated to limit the temperature of a CPU to a certain level.:TABLE OF CONTENT III I LIST OF ABBREVIATIONS V II LIST OF SYMBOLS V III LIST OF FIGURES XIII IV LIST OF TABLES XVIII 1. INTRODUCTION 1 1.1 RESEARCH DESIGN AND MOTIVATION 6 1.2 RESEARCH THESES AND CHAPTER OVERVIEW 9 2. PRELIMINARIES OF TOPOLOGY OPTIMIZATION 12 2.1 MATERIAL INTERPOLATION 16 2.2 TOPOLOGY OPTIMIZATION WITH PARAMETER-FREE SHAPE OPTIMIZATION 17 2.3 MULTI-OBJECTIVE TOPOLOGY OPTIMIZATION WITH THE WEIGHTED SUM METHOD 18 3. SIMULTANEOUS SIZE, TOPOLOGY AND PARAMETER-FREE SHAPE OPTIMIZATION OF WIREFRAMES WITH B-SPLINE CROSS-SECTIONS 21 3.1 FUNDAMENTALS IN WIREFRAME OPTIMIZATION 22 3.2 SIZE AND TOPOLOGY OPTIMIZATION WITH PERIODIC B-SPLINE CROSS-SECTIONS 27 3.3 PARAMETER-FREE SHAPE OPTIMIZATION EMBEDDED IN SIZE OPTIMIZATION 32 3.4 WEIGHTED SUM SIZE AND TOPOLOGY OPTIMIZATION 36 3.5 CROSS-SECTION COMPARISON 39 4. NON-LOCAL TRIGONOMETRIC INTERPOLATION IN TOPOLOGY OPTIMIZATION 41 4.1 FUNDAMENTALS IN MATERIAL INTERPOLATIONS 43 4.2 NON-LOCAL TRIGONOMETRIC SHAPE FUNCTIONS 45 4.3 NON-LOCAL PARAMETER-FREE SHAPE OPTIMIZATION WITH TRIGONOMETRIC SHAPE FUNCTIONS 49 4.4 NON-LOCAL AND PARAMETER-FREE MULTI-OBJECTIVE TOPOLOGY OPTIMIZATION 54 5. FUNDAMENTALS IN SKELETON GUIDED SHAPE PARAMETRIZATION IN TOPOLOGY OPTIMIZATION 58 5.1 SKELETONIZATION IN TOPOLOGY OPTIMIZATION 61 5.2 CROSS-SECTION RECOGNITION FOR IMAGES 66 5.3 SUBDIVISION SURFACES 67 5.4 CONVOLUTIONAL SURFACES WITH META BALL KERNEL 71 5.5 CONSTRUCTIVE SOLID GEOMETRY 73 6. CURVE SKELETON GUIDED BEAM PARAMETRIZATION OF TOPOLOGY OPTIMIZATION RESULTS 75 6.1 FUNDAMENTALS IN SKELETON SUPPORTED RECONSTRUCTION 76 6.2 SUBDIVISION SURFACE PARAMETRIZATION WITH PERIODIC B-SPLINE CROSS-SECTIONS 78 6.3 CURVE SKELETONIZATION TAILORED TO TOPOLOGY OPTIMIZATION WITH PRE-PROCESSING 82 6.4 SURFACE RECONSTRUCTION USING LOCAL STIFFNESS DISTRIBUTION 86 7. CROSS-SECTION SHAPE PARAMETRIZATION FOR PERIODIC B-SPLINES 96 7.1 PRELIMINARIES IN B-SPLINE CONTROL GRID ESTIMATION 97 7.2 CROSS-SECTION EXTRACTION OF 2D IMAGES 101 7.3 TENSOR SPLINE PARAMETRIZATION WITH MOMENTS OF AREA 105 7.4 B-SPLINE PARAMETRIZATION WITH MOMENTS OF AREA GUIDED CONVOLUTIONAL NEURAL NETWORK 110 8. FULLY AUTOMATED COMPLIANCE OPTIMIZATION AND CURVE-SKELETON PARAMETRIZATION FOR A CPU HEAT SINK WITH SIZE CONTROL FOR SLM 115 8.1 AUTOMATED 1D THERMAL COMPLIANCE MINIMIZATION, CONSTRAINED SURFACE RECONSTRUCTION AND ADDITIVE MANUFACTURING 118 8.2 AUTOMATED 2D THERMAL COMPLIANCE MINIMIZATION, CONSTRAINT SURFACE RECONSTRUCTION AND ADDITIVE MANUFACTURING 120 8.3 USING THE HEAT SINK PROTOTYPES COOLING A CPU 123 9. CONCLUSION 127 10. OUTLOOK 131 LITERATURE 133 APPENDIX 147 A PREVIOUS STUDIES 147 B CROSS-SECTION PROPERTIES 149 C CASE STUDIES FOR THE CROSS-SECTION PARAMETRIZATION 155 D EXPERIMENTAL SETUP 15

Correspondence of three-dimensional objects

First many thanks go to Prof. Hans du Buf, for his supervision based on his experience, for providing a stimulating and cheerful research environment in his laboratory, for letting me participate in the projects that produced results for papers, thus made me more aware of the state of the art in Computer Vision, especially in the area of 3D recognition. Also for his encouraging support and his way to always nd time for discussions, and last but not the least for the cooking recipes... Many thanks go also to my laboratory fellows, to Jo~ao Rodrigues, who invited me to participate in FCT and QREN projects, Jaime Carvalho Martins and Miguel Farrajota, for discussing scienti c and technical problems, but also almost all problems in the world. To all persons, that worked in, or visited the Vision Laboratory, especially those with whom I have worked with, almost on a daily basis. A special thanks to the Instituto Superior de Engenharia at UAlg and my colleagues at the Department of Electrical Engineering, for allowing me to suspend lectures in order to be present at conferences. To my family, my wife and my kids

High-performance geometric vascular modelling

Image-based high-performance geometric vascular modelling and reconstruction is an essential component of computer-assisted surgery on the diagnosis, analysis and treatment of cardiovascular diseases. However, it is an extremely challenging task to efficiently reconstruct the accurate geometric structures of blood vessels out of medical images. For one thing, the shape of an individual section of a blood vessel is highly irregular because of the squeeze of other tissues and the deformation caused by vascular diseases. For another, a vascular system is a very complicated network of blood vessels with different types of branching structures. Although some existing vascular modelling techniques can reconstruct the geometric structure of a vascular system, they are either time-consuming or lacking sufficient accuracy. What is more, these techniques rarely consider the interior tissue of the vascular wall, which consists of complicated layered structures. As a result, it is necessary to develop a better vascular geometric modelling technique, which is not only of high performance and high accuracy in the reconstruction of vascular surfaces, but can also be used to model the interior tissue structures of the vascular walls.This research aims to develop a state-of-the-art patient-specific medical image-based geometric vascular modelling technique to solve the above problems. The main contributions of this research are:- Developed and proposed the Skeleton Marching technique to reconstruct the geometric structures of blood vessels with high performance and high accuracy. With the proposed technique, the highly complicated vascular reconstruction task is reduced to a set of simple localised geometric reconstruction tasks, which can be carried out in a parallel manner. These locally reconstructed vascular geometric segments are then combined together using shape-preserving blending operations to faithfully represent the geometric shape of the whole vascular system.- Developed and proposed the Thin Implicit Patch method to realistically model the interior geometric structures of the vascular tissues. This method allows the multi-layer interior tissue structures to be embedded inside the vascular wall to illustrate the geometric details of the blood vessel in real world