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

Feature-based hybrid inspection planning for complex mechanical parts

Globalization and emerging new powers in the manufacturing world are among many challenges, major manufacturing enterprises are facing. This resulted in increased alternatives to satisfy customers\u27 growing needs regarding products\u27 aesthetic and functional requirements. Complexity of part design and engineering specifications to satisfy such needs often require a better use of advanced and more accurate tools to achieve good quality. Inspection is a crucial manufacturing function that should be further improved to cope with such challenges. Intelligent planning for inspection of parts with complex geometric shapes and free form surfaces using contact or non-contact devices is still a major challenge. Research in segmentation and localization techniques should also enable inspection systems to utilize modern measurement technologies capable of collecting huge number of measured points. Advanced digitization tools can be classified as contact or non-contact sensors. The purpose of this thesis is to develop a hybrid inspection planning system that benefits from the advantages of both techniques. Moreover, the minimization of deviation of measured part from the original CAD model is not the only characteristic that should be considered when implementing the localization process in order to accept or reject the part; geometric tolerances must also be considered. A segmentation technique that deals directly with the individual points is a necessary step in the developed inspection system, where the output is the actual measured points, not a tessellated model as commonly implemented by current segmentation tools. The contribution of this work is three folds. First, a knowledge-based system was developed for selecting the most suitable sensor using an inspection-specific features taxonomy in form of a 3D Matrix where each cell includes the corresponding knowledge rules and generate inspection tasks. A Travel Salesperson Problem (TSP) has been applied for sequencing these hybrid inspection tasks. A novel region-based segmentation algorithm was developed which deals directly with the measured point cloud and generates sub-point clouds, each of which represents a feature to be inspected and includes the original measured points. Finally, a new tolerance-based localization algorithm was developed to verify the functional requirements and was applied and tested using form tolerance specifications. This research enhances the existing inspection planning systems for complex mechanical parts with a hybrid inspection planning model. The main benefits of the developed segmentation and tolerance-based localization algorithms are the improvement of inspection decisions in order not to reject good parts that would have otherwise been rejected due to misleading results from currently available localization techniques. The better and more accurate inspection decisions achieved will lead to less scrap, which, in turn, will reduce the product cost and improve the company potential in the market

Multimodal Three Dimensional Scene Reconstruction, The Gaussian Fields Framework

The focus of this research is on building 3D representations of real world scenes and objects using different imaging sensors. Primarily range acquisition devices (such as laser scanners and stereo systems) that allow the recovery of 3D geometry, and multi-spectral image sequences including visual and thermal IR images that provide additional scene characteristics. The crucial technical challenge that we addressed is the automatic point-sets registration task. In this context our main contribution is the development of an optimization-based method at the core of which lies a unified criterion that solves simultaneously for the dense point correspondence and transformation recovery problems. The new criterion has a straightforward expression in terms of the datasets and the alignment parameters and was used primarily for 3D rigid registration of point-sets. However it proved also useful for feature-based multimodal image alignment. We derived our method from simple Boolean matching principles by approximation and relaxation. One of the main advantages of the proposed approach, as compared to the widely used class of Iterative Closest Point (ICP) algorithms, is convexity in the neighborhood of the registration parameters and continuous differentiability, allowing for the use of standard gradient-based optimization techniques. Physically the criterion is interpreted in terms of a Gaussian Force Field exerted by one point-set on the other. Such formulation proved useful for controlling and increasing the region of convergence, and hence allowing for more autonomy in correspondence tasks. Furthermore, the criterion can be computed with linear complexity using recently developed Fast Gauss Transform numerical techniques. In addition, we also introduced a new local feature descriptor that was derived from visual saliency principles and which enhanced significantly the performance of the registration algorithm. The resulting technique was subjected to a thorough experimental analysis that highlighted its strength and showed its limitations. Our current applications are in the field of 3D modeling for inspection, surveillance, and biometrics. However, since this matching framework can be applied to any type of data, that can be represented as N-dimensional point-sets, the scope of the method is shown to reach many more pattern analysis applications

Medical imaging analysis with artificial neural networks

Given that neural networks have been widely reported in the research community of medical imaging, we provide a focused literature survey on recent neural network developments in computer-aided diagnosis, medical image segmentation and edge detection towards visual content analysis, and medical image registration for its pre-processing and post-processing, with the aims of increasing awareness of how neural networks can be applied to these areas and to provide a foundation for further research and practical development. Representative techniques and algorithms are explained in detail to provide inspiring examples illustrating: (i) how a known neural network with fixed structure and training procedure could be applied to resolve a medical imaging problem; (ii) how medical images could be analysed, processed, and characterised by neural networks; and (iii) how neural networks could be expanded further to resolve problems relevant to medical imaging. In the concluding section, a highlight of comparisons among many neural network applications is included to provide a global view on computational intelligence with neural networks in medical imaging

ToScA North America (6 – 8 June 2017, The University of Texas, Austin, TX) Program

ToScA North America will address key areas of science, including Multi-modal Imaging, Geosciences, Forensics, Increasing Contrast, Educational Outreach, Data, Materials Science and Medical and Biological Science.University of Texas High-Resolution X-ray CT Facility (UTCT); Jackson School of Geosciences, The University of Texas at Austin; Natural History Museum (London); Royal Microscopical Society (Oxford, UK)Geological Science

State of the Art of Level Set Methods in Segmentation and Registration of Medical Imaging Modalities

Segmentation of medical images is an important step in various applications such as visualization, quantitative analysis and image-guided surgery. Numerous segmentation methods have been developed in the past two decades for extraction of organ contours on medical images. Low-level segmentation methods, such as pixel-based clustering, region growing, and filter-based edge detection, require additional pre-processing and post-processing as well as considerable amounts of expert intervention or information of the objects of interest. Furthermore the subsequent analysis of segmented objects is hampered by the primitive, pixel or voxel level representations from those region-based segmentation. Deformable models, on the other hand, provide an explicit representation of the boundary and the shape of the object. They combine several desirable features such as inherent connectivity and smoothness, which counteract noise and boundary irregularities, as well as the ability to incorporate knowledge about the object of interest. However, parametric deformable models have two main limitations. First, in situations where the initial model and desired object boundary differ greatly in size and shape, the model must be re-parameterized dynamically to faithfully recover the object boundary. The second limitation is that it has difficulty dealing with topological adaptation such as splitting or merging model parts, a useful property for recovering either multiple objects or objects with unknown topology. This difficulty is caused by the fact that a new parameterization must be constructed whenever topology change occurs, which requires sophisticated schemes. Level set deformable models, also referred to as geometric deformable models, provide an elegant solution to address the primary limitations of parametric deformable models. These methods have drawn a great deal of attention since their introduction in 1988. Advantages of the contour implicit formulation of the deformable model over parametric formulation include: (1) no parameterization of the contour, (2) topological flexibility, (3) good numerical stability, (4) straightforward extension of the 2D formulation to n-D. Recent reviews on the subject include papers from Suri. In this chapter we give a general overview of the level set segmentation methods with emphasize on new frameworks recently introduced in the context of medical imaging problems. We then introduce novel approaches that aim at combining segmentation and registration in a level set formulation. Finally we review a selective set of clinical works with detailed validation of the level set methods for several clinical applications

Multiperspective mosaics and layered representation for scene visualization

This thesis documents the efforts made to implement multiperspective mosaicking for the purpose of mosaicking undervehicle and roadside sequences. For the undervehicle sequences, it is desired to create a large, high-resolution mosaic that may used to quickly inspect the entire scene shot by a camera making a single pass underneath the vehicle. Several constraints are placed on the video data, in order to facilitate the assumption that the entire scene in the sequence exists on a single plane. Therefore, a single mosaic is used to represent a single video sequence. Phase correlation is used to perform motion analysis in this case. For roadside video sequences, it is assumed that the scene is composed of several planar layers, as opposed to a single plane. Layer extraction techniques are implemented in order to perform this decomposition. Instead of using phase correlation to perform motion analysis, the Lucas-Kanade motion tracking algorithm is used in order to create dense motion maps. Using these motion maps, spatial support for each layer is determined based on a pre-initialized layer model. By separating the pixels in the scene into motion-specific layers, it is possible to sample each element in the scene correctly while performing multiperspective mosaicking. It is also possible to fill in many gaps in the mosaics caused by occlusions, hence creating more complete representations of the objects of interest. The results are several mosaics with each mosaic representing a single planar layer of the scene