Curvilinear Structure Enhancement in Biomedical Images

Curvilinear structures can appear in many different areas and at a variety of scales. They can be axons and dendrites in the brain, blood vessels in the fundus, streets, rivers or fractures in buildings, and others. So, it is essential to study curvilinear structures in many fields such as neuroscience, biology, and cartography regarding image processing. Image processing is an important field for the help to aid in biomedical imaging especially the diagnosing the disease. Image enhancement is the early step of image analysis. In this thesis, I focus on the research, development, implementation, and validation of 2D and 3D curvilinear structure enhancement methods, recently established. The proposed methods are based on phase congruency, mathematical morphology, and tensor representation concepts. First, I have introduced a 3D contrast independent phase congruency-based enhancement approach. The obtained results demonstrate the proposed approach is robust against the contrast variations in 3D biomedical images. Second, I have proposed a new mathematical morphology-based approach called the bowler-hat transform. In this approach, I have combined the mathematical morphology with a local tensor representation of curvilinear structures in images. The bowler-hat transform is shown to give better results than comparison methods on challenging data such as retinal/fundus images. The bowler-hat transform is shown to give better results than comparison methods on challenging data such as retinal/fundus images. Especially the proposed method is quite successful while enhancing of curvilinear structures at junctions. Finally, I have extended the bowler-hat approach to the 3D version to prove the applicability, reliability, and ability of it in 3D

Road Feature Extraction from High Resolution Aerial Images Upon Rural Regions Based on Multi-Resolution Image Analysis and Gabor Filters

Accurate, detailed and up-to-date road information is of special importance in geo-spatial databases as it is used in a variety of applications such as vehicle navigation, traffic management and advanced driver assistance systems (ADAS). The commercial road maps utilized for road navigation or the geographical information system (GIS) today are based on linear road centrelines represented in vector format with poly-lines (i.e., series of nodes and shape points, connected by segments), which present a serious lack of accuracy, contents, and completeness for their applicability at the sub-road level. For instance, the accuracy level of the present standard maps is around 5 to 20 meters. The roads/streets in the digital maps are represented as line segments rendered using different colours and widths. However, the widths of line segments do not necessarily represent the actual road widths accurately. Another problem with the existing road maps is that few precise sub-road details, such as lane markings and stop lines, are included, whereas such sub-road information is crucial for applications such as lane departure warning or lane-based vehicle navigation. Furthermore, the vast majority of roadmaps aremodelled in 2D space, whichmeans that some complex road scenes, such as overpasses and multi-level road systems, cannot be effectively represented. In addition, the lack of elevation information makes it infeasible to carry out applications such as driving simulation and 3D vehicle navigation

Automating the Reconstruction of Neuron Morphological Models: the Rivulet Algorithm Suite

The automatic reconstruction of single neuron cells is essential to enable large-scale data-driven investigations in computational neuroscience. The problem remains an open challenge due to various imaging artefacts that are caused by the fundamental limits of light microscopic imaging. Few previous methods were able to generate satisfactory neuron reconstruction models automatically without human intervention. The manual tracing of neuron models is labour heavy and time-consuming, making the collection of large-scale neuron morphology database one of the major bottlenecks in morphological neuroscience. This thesis presents a suite of algorithms that are developed to target the challenge of automatically reconstructing neuron morphological models with minimum human intervention. We first propose the Rivulet algorithm that iteratively backtracks the neuron fibres from the termini points back to the soma centre. By refining many details of the Rivulet algorithm, we later propose the Rivulet2 algorithm which not only eliminates a few hyper-parameters but also improves the robustness against noisy images. A soma surface reconstruction method was also proposed to make the neuron models biologically plausible around the soma body. The tracing algorithms, including Rivulet and Rivulet2, normally need one or more hyper-parameters for segmenting the neuron body out of the noisy background. To make this pipeline fully automatic, we propose to use 2.5D neural network to train a model to enhance the curvilinear structures of the neuron fibres. The trained neural networks can quickly highlight the fibres of interests and suppress the noise points in the background for the neuron tracing algorithms. We evaluated the proposed methods in the data released by both the DIADEM and the BigNeuron challenge. The experimental results show that our proposed tracing algorithms achieve the state-of-the-art results

Methods for Automated Neuron Image Analysis

Knowledge of neuronal cell morphology is essential for performing specialized analyses in the endeavor to understand neuron behavior and unravel the underlying principles of brain function. Neurons can be captured with a high level of detail using modern microscopes, but many neuroscientific studies require a more explicit and accessible representation than offered by the resulting images, underscoring the need for digital reconstruction of neuronal morphology from the images into a tree-like graph structure. This thesis proposes new computational methods for automated detection and reconstruction of neurons from fluorescence microscopy images. Specifically, the successive chapters describe and evaluate original solutions to problems such as the detection of landmarks (critical points) of the neuronal tree, complete tracing and reconstruction of the tree, and the detection of regions containing neurons in high-content screens

Computerized Analysis of Magnetic Resonance Images to Study Cerebral Anatomy in Developing Neonates

The study of cerebral anatomy in developing neonates is of great importance for the understanding of brain development during the early period of life. This dissertation therefore focuses on three challenges in the modelling of cerebral anatomy in neonates during brain development. The methods that have been developed all use Magnetic Resonance Images (MRI) as source data. To facilitate study of vascular development in the neonatal period, a set of image analysis algorithms are developed to automatically extract and model cerebral vessel trees. The whole process consists of cerebral vessel tracking from automatically placed seed points, vessel tree generation, and vasculature registration and matching. These algorithms have been tested on clinical Time-of- Flight (TOF) MR angiographic datasets. To facilitate study of the neonatal cortex a complete cerebral cortex segmentation and reconstruction pipeline has been developed. Segmentation of the neonatal cortex is not effectively done by existing algorithms designed for the adult brain because the contrast between grey and white matter is reversed. This causes pixels containing tissue mixtures to be incorrectly labelled by conventional methods. The neonatal cortical segmentation method that has been developed is based on a novel expectation-maximization (EM) method with explicit correction for mislabelled partial volume voxels. Based on the resulting cortical segmentation, an implicit surface evolution technique is adopted for the reconstruction of the cortex in neonates. The performance of the method is investigated by performing a detailed landmark study. To facilitate study of cortical development, a cortical surface registration algorithm for aligning the cortical surface is developed. The method first inflates extracted cortical surfaces and then performs a non-rigid surface registration using free-form deformations (FFDs) to remove residual alignment. Validation experiments using data labelled by an expert observer demonstrate that the method can capture local changes and follow the growth of specific sulcus

Variational methods and its applications to computer vision

Many computer vision applications such as image segmentation can be formulated in a ''variational'' way as energy minimization problems. Unfortunately, the computational task of minimizing these energies is usually difficult as it generally involves non convex functions in a space with thousands of dimensions and often the associated combinatorial problems are NP-hard to solve. Furthermore, they are ill-posed inverse problems and therefore are extremely sensitive to perturbations (e.g. noise). For this reason in order to compute a physically reliable approximation from given noisy data, it is necessary to incorporate into the mathematical model appropriate regularizations that require complex computations. The main aim of this work is to describe variational segmentation methods that are particularly effective for curvilinear structures. Due to their complex geometry, classical regularization techniques cannot be adopted because they lead to the loss of most of low contrasted details. In contrast, the proposed method not only better preserves curvilinear structures, but also reconnects some parts that may have been disconnected by noise. Moreover, it can be easily extensible to graphs and successfully applied to different types of data such as medical imagery (i.e. vessels, hearth coronaries etc), material samples (i.e. concrete) and satellite signals (i.e. streets, rivers etc.). In particular, we will show results and performances about an implementation targeting new generation of High Performance Computing (HPC) architectures where different types of coprocessors cooperate. The involved dataset consists of approximately 200 images of cracks, captured in three different tunnels by a robotic machine designed for the European ROBO-SPECT project.Open Acces

Automatic road network extraction from high resolution satellite imagery using spectral classification methods

Road networks play an important role in a number of geospatial applications, such as cartographic, infrastructure planning and traffic routing software. Automatic and semi-automatic road network extraction techniques have significantly increased the extraction rate of road networks. Automated processes still yield some erroneous and incomplete results and costly human intervention is still required to evaluate results and correct errors. With the aim of improving the accuracy of road extraction systems, three objectives are defined in this thesis: Firstly, the study seeks to develop a flexible semi-automated road extraction system, capable of extracting roads from QuickBird satellite imagery. The second objective is to integrate a variety of algorithms within the road network extraction system. The benefits of using each of these algorithms within the proposed road extraction system, is illustrated. Finally, a fully automated system is proposed by incorporating a number of the algorithms investigated throughout the thesis. CopyrightDissertation (MSc)--University of Pretoria, 2010.Computer Scienceunrestricte