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

3D shape matching and registration : a probabilistic perspective

Dense correspondence is a key area in computer vision and medical image analysis. It has applications in registration and shape analysis. In this thesis, we develop a technique to recover dense correspondences between the surfaces of neuroanatomical objects over heterogeneous populations of individuals. We recover dense correspondences based on 3D shape matching. In this thesis, the 3D shape matching problem is formulated under the framework of Markov Random Fields (MRFs). We represent the surfaces of neuroanatomical objects as genus zero voxel-based meshes. The surface meshes are projected into a Markov random field space. The projection carries both geometric and topological information in terms of Gaussian curvature and mesh neighbourhood from the original space to the random field space. Gaussian curvature is projected to the nodes of the MRF, and the mesh neighbourhood structure is projected to the edges. 3D shape matching between two surface meshes is then performed by solving an energy function minimisation problem formulated with MRFs. The outcome of the 3D shape matching is dense point-to-point correspondences. However, the minimisation of the energy function is NP hard. In this thesis, we use belief propagation to perform the probabilistic inference for 3D shape matching. A sparse update loopy belief propagation algorithm adapted to the 3D shape matching is proposed to obtain an approximate global solution for the 3D shape matching problem. The sparse update loopy belief propagation algorithm demonstrates significant efficiency gain compared to standard belief propagation. The computational complexity and convergence property analysis for the sparse update loopy belief propagation algorithm are also conducted in the thesis. We also investigate randomised algorithms to minimise the energy function. In order to enhance the shape matching rate and increase the inlier support set, we propose a novel clamping technique. The clamping technique is realized by combining the loopy belief propagation message updating rule with the feedback from 3D rigid body registration. By using this clamping technique, the correct shape matching rate is increased significantly. Finally, we investigate 3D shape registration techniques based on the 3D shape matching result. Based on the point-to-point dense correspondences obtained from the 3D shape matching, a three-point based transformation estimation technique is combined with the RANdom SAmple Consensus (RANSAC) algorithm to obtain the inlier support set. The global registration approach is purely dependent on point-wise correspondences between two meshed surfaces. It has the advantage that the need for orientation initialisation is eliminated and that all shapes of spherical topology. The comparison of our MRF based 3D registration approach with a state-of-the-art registration algorithm, the first order ellipsoid template, is conducted in the experiments. These show dense correspondence for pairs of hippocampi from two different data sets, each of around 20 60+ year old healthy individuals

HIGH QUALITY HUMAN 3D BODY MODELING, TRACKING AND APPLICATION

Geometric reconstruction of dynamic objects is a fundamental task of computer vision and graphics, and modeling human body of high fidelity is considered to be a core of this problem. Traditional human shape and motion capture techniques require an array of surrounding cameras or subjects wear reflective markers, resulting in a limitation of working space and portability. In this dissertation, a complete process is designed from geometric modeling detailed 3D human full body and capturing shape dynamics over time using a flexible setup to guiding clothes/person re-targeting with such data-driven models. As the mechanical movement of human body can be considered as an articulate motion, which is easy to guide the skin animation but has difficulties in the reverse process to find parameters from images without manual intervention, we present a novel parametric model, GMM-BlendSCAPE, jointly taking both linear skinning model and the prior art of BlendSCAPE (Blend Shape Completion and Animation for PEople) into consideration and develop a Gaussian Mixture Model (GMM) to infer both body shape and pose from incomplete observations. We show the increased accuracy of joints and skin surface estimation using our model compared to the skeleton based motion tracking. To model the detailed body, we start with capturing high-quality partial 3D scans by using a single-view commercial depth camera. Based on GMM-BlendSCAPE, we can then reconstruct multiple complete static models of large pose difference via our novel non-rigid registration algorithm. With vertex correspondences established, these models can be further converted into a personalized drivable template and used for robust pose tracking in a similar GMM framework. Moreover, we design a general purpose real-time non-rigid deformation algorithm to accelerate this registration. Last but not least, we demonstrate a novel virtual clothes try-on application based on our personalized model utilizing both image and depth cues to synthesize and re-target clothes for single-view videos of different people

Essential techniques for improving visual realism of laparoscopic surgery simulation.

With the prevalence of laparoscopic surgery, the request for reliable training and assessment is becoming increasingly important. The traditional way of training is both time consuming and cost intensive, and may cause ethical or moral issues. With the development of computer technologies, virtual reality has entered the world of consumer electronics as a new way to enhance tactile and visual sensory experiences. Virtual reality based surgical skill training gradually becomes an effective supplementary to the traditional laparoscopic skill training in many surgical theatres. To provide high fidelity virtual surgery training experiences, the presentation of the virtual world should have the same level of realism as what surgeons see and feel during real operations. However, the weak computing power limits the potential level of details on the graphics presentation and physical behaviour of virtual objects, which will further influence the fidelity of tactile interaction. Achieving visual realism (realistic graphics presentation and accurate physical behaviour) and good user experience using limited computing resources is the main challenge for laparoscopic surgery simulation. The topic of visual realism in laparoscopic surgery simulation has not been well researched. This topic mainly relates to the area of 3D anatomy modeling, soft body simulation and rendering. Current researches in computer graphics and game communities are not tailored for laparoscopic surgery simulation. The direct use of those techniques in developing surgery simulators will often result in poor quality anatomy model, inaccurate simulation, low fidelity visual effect, poor user experience and inefficient production pipeline, which significantly influence the visual realism of the virtual world. The development of laparoscopic surgery simulator is an interdiscipline of computer graphics, computational physics and haptics. However, current researches barely focus on the study of tailored techniques and efficient production pipeline which often result in the long term research cycle and daunting cost for simulator development. This research is aiming at improving the visual realism of laparoscopic surgery simulation from the perspective of computer graphics. In this research, a set of tailor techniques have been proposed to improve the visual realism for laparoscopic surgery simulation. For anatomy modeling, an automatic and efficient 3D anatomy conversion pipeline is proposed which can convert bad quality 3D anatomy into simulation ready state while preserving the original model’s surface parameterization property. For simulation, a soft tissue simulation pipeline is pro- posed which can provide multi-layer heterogeneous soft tissue modeling and intuitive physically editable simulation based on uniform polynomial based hyperelastic material representation. For interaction, a collision detection and interaction system based on adaptive circumphere structure is proposed which supports robust and efficient sliding con- tact, energized dissection and clip. For rendering, a multi-layer soft tissue rendering pipeline is proposed which decomposed the multi-layer structure of soft tissue into corresponding material asset required by state-of-art rendering techniques. Based on this research, a system framework for building a laparoscopic surgery simulator is also proposed to test the feasibility of those tailored techniques

Automatic skeletonization and skin attachment for realistic character animation.

The realism of character animation is associated with a number of tasks ranging from modelling, skin defonnation, motion generation to rendering. In this research we are concerned with two of them: skeletonization and weight assignment for skin deformation. The fonner is to generate a skeleton, which is placed within the character model and links the motion data to the skin shape of the character. The latter assists the modelling of realistic skin shape when a character is in motion. In the current animation production practice, the task of skeletonization is primarily undertaken by hand, i.e. the animator produces an appropriate skeleton and binds it with the skin model of a character. This is inevitably very time-consuming and costs a lot of labour. In order to improve this issue, in this thesis we present an automatic skeletonization framework. It aims at producing high-quality animatible skeletons without heavy human involvement while allowing the animator to maintain the overall control of the process. In the literature, the tenn skeletonization can have different meanings. Most existing research on skeletonization is in the remit of CAD (Computer Aided Design). Although existing research is of significant reference value to animation, their downside is the skeleton generated is either not appropriate for the particular needs of animation, or the methods are computationally expensive. Although some purpose-build animation skeleton generation techniques exist, unfortunately they rely on complicated post-processing procedures, such as thinning and pruning, which again can be undesirable. The proposed skeletonization framework makes use of a new geometric entity known as the 3D silhouette that is an ordinary silhouette with its depth information recorded. We extract a curve skeleton from two 3D silhouettes of a character detected from its two perpendicular projections. The skeletal joints are identified by down sampling the curve skeleton, leading to the generation of the final animation skeleton. The efficiency and quality are major performance indicators in animation skeleton generation. Our framework achieves the former by providing a 2D solution to the 3D skeletonization problem. Reducing in dimensions brings much faster performances. Experiments and comparisons are carried out to demonstrate the computational simplicity. Its accuracy is also verified via these experiments and comparisons. To link a skeleton to the skin, accordingly we present a skin attachment framework aiming at automatic and reasonable weight distribution. It differs from the conventional algorithms in taking topological information into account during weight computation. An effective range is defined for a joint. Skin vertices located outside the effective range will not be affected by this joint. By this means, we provide a solution to remove the influence of a topologically distant, hence highly likely irrelevant joint on a vertex. A user-defined parameter is also provided in this algorithm, which allows different deformation effects to be obtained according to user's needs. Experiments and comparisons prove that the presented framework results in weight distribution of good quality. Thus it frees animators from tedious manual weight editing. Furthermore, it is flexible to be used with various deformation algorithms

HexBox: Interactive Box Modeling of Hexahedral Meshes

We introduce HexBox, an intuitive modeling method and interactive tool for creating and editing hexahedral meshes. Hexbox brings the major and widely validated surface modeling paradigm of surface box modeling into the world of hex meshing. The main idea is to allow the user to box-model a volumetric mesh by primarily modifying its surface through a set of topological and geometric operations. We support, in particular, local and global subdivision, various instantiations of extrusion, removal, and cloning of elements, the creation of non-conformal or conformal grids, as well as shape modifications through vertex positioning, including manual editing, automatic smoothing, or, eventually, projection on an externally-provided target surface. At the core of the efficient implementation of the method is the coherent maintenance, at all steps, of two parallel data structures: a hexahedral mesh representing the topology and geometry of the currently modeled shape, and a directed acyclic graph that connects operation nodes to the affected mesh hexahedra. Operations are realized by exploiting recent advancements in grid- based meshing, such as mixing of 3-refinement, 2-refinement, and face-refinement, and using templated topological bridges to enforce on-the-fly mesh conformity across pairs of adjacent elements. A direct manipulation user interface lets users control all operations. The effectiveness of our tool, released as open source to the community, is demonstrated by modeling several complex shapes hard to realize with competing tools and techniques

Automatic generation of dynamic skin deformation for animated characters

© 2018 by the authors. Since non-automatic rigging requires heavy human involvements, and various automatic rigging algorithms are less efficient in terms of computational efficiency, especially for current curve-based skin deformation methods, identifying the iso-parametric curves and creating the animation skeleton requires tedious and time-consuming manual work. Although several automatic rigging methods have been developed, but they do not aim at curve-based models. To tackle this issue, this paper proposes a new rigging algorithm for automatic generation of dynamic skin deformation to quickly identify iso-parametric curves and create an animation skeleton in a few milliseconds, which can be seamlessly used in curve-based skin deformation methods to make the rigging process fast enough for highly efficient computer animation applications

Statistical Medial Model dor Cardiac Segmentation and Morphometry

In biomedical image analysis, shape information can be utilized for many purposes. For example, irregular shape features can help identify diseases; shape features can help match different instances of anatomical structures for statistical comparison; and prior knowledge of the mean and possible variation of an anatomical structure\u27s shape can help segment a new example of this structure in noisy, low-contrast images. A good shape representation helps to improve the performance of the above techniques. The overall goal of the proposed research is to develop and evaluate methods for representing shapes of anatomical structures. The medial model is a shape representation method that models a 3D object by explicitly defining its skeleton (medial axis) and deriving the object\u27s boundary via inverse-skeletonization . This model represents shape compactly, and naturally expresses descriptive global shape features like thickening , bending , and elongation . However, its application in biomedical image analysis has been limited, and it has not yet been applied to the heart, which has a complex shape. In this thesis, I focus on developing efficient methods to construct the medial model, and apply it to solve biomedical image analysis problems. I propose a new 3D medial model which can be efficiently applied to complex shapes. The proposed medial model closely approximates the medial geometry along medial edge curves and medial branching curves by soft-penalty optimization and local correction. I further develop a scheme to perform model-based segmentation using a statistical medial model which incorporates prior shape and appearance information. The proposed medial models are applied to a series of image analysis tasks. The 2D medial model is applied to the corpus callosum which results in an improved alignment of the patterns of commissural connectivity compared to a volumetric registration method. The 3D medial model is used to describe the myocardium of the left and right ventricles, which provides detailed thickness maps characterizing different disease states. The model-based myocardium segmentation scheme is tested in a heterogeneous adult MRI dataset. Our segmentation experiments demonstrate that the statistical medial model can accurately segment the ventricular myocardium and provide useful parameters to characterize heart function

Solid NURBS Conforming Scaffolding for Isogeometric Analysis

This work introduces a scaffolding framework to compactly parametrise solid structures with conforming NURBS elements for isogeometric analysis. A novel formulation introduces a topological, geometrical and parametric subdivision of the space in a minimal plurality of conforming vectorial elements. These determine a multi-compartmental scaffolding for arbitrary branching patterns. A solid smoothing paradigm is devised for the conforming scaffolding achieving higher than positional geometrical and parametric continuity. Results are shown for synthetic shapes of varying complexity, for modular CAD geometries, for branching structures from tessellated meshes and for organic biological structures from imaging data. Representative simulations demonstrate the validity of the introduced scaffolding framework with scalable performance and groundbreaking applications for isogeometric analysis