Human perception-oriented segmentation for triangle meshes

A segmentação de malhas é um tópico importante de investigação em computação gráfica, em particular em modelação geométrica. Isto deve-se ao facto de as técnicas de segmentaçãodemalhasteremváriasaplicações,nomeadamentenaproduçãodefilmes, animaçãoporcomputador, realidadevirtual, compressãodemalhas, assimcomoemjogosdigitais. Emconcreto, asmalhastriangularessãoamplamenteusadasemaplicações interativas, visto que sua segmentação em partes significativas (também designada por segmentação significativa, segmentação perceptiva ou segmentação perceptualmente significativa ) é muitas vezes vista como uma forma de acelerar a interação com o utilizador ou a deteção de colisões entre esses objetos 3D definidos por uma malha, bem como animar uma ou mais partes significativas (por exemplo, a cabeça de uma personagem) de um dado objeto, independentemente das restantes partes. Acontece que não se conhece nenhuma técnica capaz de segmentar correctamente malhas arbitrárias −ainda que restritas aos domínios de formas livres e não-livres− em partes significativas. Algumas técnicas são mais adequadas para objetos de forma não-livre (por exemplo, peças mecânicas definidas geometricamente por quádricas), enquanto outras são mais talhadas para o domínio dos objectos de forma livre. Só na literatura recente surgem umas poucas técnicas que se aplicam a todo o universo de objetos de forma livre e não-livre. Pior ainda é o facto de que a maioria das técnicas de segmentação não serem totalmente automáticas, no sentido de que quase todas elas exigem algum tipo de pré-requisitos e assistência do utilizador. Resumindo, estes três desafios relacionados com a proximidade perceptual, generalidade e automação estão no cerne do trabalho descrito nesta tese. Para enfrentar estes desafios, esta tese introduz o primeiro algoritmo de segmentação baseada nos contornos ou fronteiras dos segmentos, cuja técnica se inspira nas técnicas de segmentação baseada em arestas, tão comuns em análise e processamento de imagem,porcontraposiçãoàstécnicasesegmentaçãobaseadaemregiões. Aideiaprincipal é a de encontrar em primeiro lugar a fronteira de cada região para, em seguida, identificar e agrupar todos os seus triângulos internos. As regiões da malha encontradas correspondem a saliências e reentrâncias, que não precisam de ser estritamente convexas, nem estritamente côncavas, respectivamente. Estas regiões, designadas regiões relaxadamenteconvexas(ousaliências)eregiõesrelaxadamentecôncavas(oureentrâncias), produzem segmentações que são menos sensíveis ao ruído e, ao mesmo tempo, são mais intuitivas do ponto de vista da perceção humana; por isso, é designada por segmentação orientada à perceção humana (ou, human perception- oriented (HPO), do inglês). Além disso, e ao contrário do atual estado-da-arte da segmentação de malhas, a existência destas regiões relaxadas torna o algoritmo capaz de segmentar de maneira bastante plausível tanto objectos de forma não-livre como objectos de forma livre. Nesta tese, enfrentou-se também um quarto desafio, que está relacionado com a fusão de segmentação e multi-resolução de malhas. Em boa verdade, já existe na literatura uma variedade grande de técnicas de segmentação, bem como um número significativo de técnicas de multi-resolução, para malhas triangulares. No entanto, não é assim tão comum encontrar estruturas de dados e algoritmos que façam a fusão ou a simbiose destes dois conceitos, multi-resolução e segmentação, num único esquema multi-resolução que sirva os propósitos das aplicações que lidam com malhas simples e segmentadas, sendo que neste contexto se entende que uma malha simples é uma malha com um único segmento. Sendo assim, nesta tese descreve-se um novo esquema (entenda-seestruturasdedadosealgoritmos)demulti-resoluçãoesegmentação,designado por extended Ghost Cell (xGC). Este esquema preserva a forma das malhas, tanto em termos globais como locais, ou seja, os segmentos da malha e as suas fronteiras, bem como os seus vincos e ápices são preservados, não importa o nível de resolução que usamos durante a/o simplificação/refinamento da malha. Além disso, ao contrário de outros esquemas de segmentação, tornou-se possível ter segmentos adjacentes com dois ou mais níveis de resolução de diferença. Isto é particularmente útil em animação por computador, compressão e transmissão de malhas, operações de modelação geométrica, visualização científica e computação gráfica. Em suma, esta tese apresenta um esquema genérico, automático, e orientado à percepção humana, que torna possível a simbiose dos conceitos de segmentação e multiresolução de malhas trianguladas que sejam representativas de objectos 3D.The mesh segmentation is an important topic in computer graphics, in particular in geometric computing. This is so because mesh segmentation techniques find many applications in movies, computer animation, virtual reality, mesh compression, and games. Infact, trianglemeshesarewidelyusedininteractiveapplications, sothattheir segmentation in meaningful parts (i.e., human-perceptually segmentation, perceptive segmentationormeaningfulsegmentation)isoftenseenasawayofspeedinguptheuser interaction, detecting collisions between these mesh-covered objects in a 3D scene, as well as animating one or more meaningful parts (e.g., the head of a humanoid) independently of the other parts of a given object. It happens that there is no known technique capable of correctly segmenting any mesh into meaningful parts. Some techniques are more adequate for non-freeform objects (e.g., quadricmechanicalparts), whileothersperformbetterinthedomainoffreeform objects. Only recently, some techniques have been developed for the entire universe of objects and shapes. Even worse it is the fact that most segmentation techniques are not entirely automated in the sense that almost all techniques require some sort of pre-requisites and user assistance. Summing up, these three challenges related to perceptual proximity, generality and automation are at the core of the work described in this thesis. In order to face these challenges, we have developed the first contour-based mesh segmentation algorithm that we may find in the literature, which is inspired in the edgebased segmentation techniques used in image analysis, as opposite to region-based segmentation techniques. Its leading idea is to firstly find the contour of each region, and then to identify and collect all of its inner triangles. The encountered mesh regions correspond to ups and downs, which do not need to be strictly convex nor strictly concave, respectively. These regions, called relaxedly convex regions (or saliences) and relaxedly concave regions (or recesses), produce segmentations that are less-sensitive to noise and, at the same time, are more intuitive from the human point of view; hence it is called human perception- oriented (HPO) segmentation. Besides, and unlike the current state-of-the-art in mesh segmentation, the existence of these relaxed regions makes the algorithm suited to both non-freeform and freeform objects. In this thesis, we have also tackled a fourth challenge, which is related with the fusion of mesh segmentation and multi-resolution. Truly speaking, a plethora of segmentation techniques, as well as a number of multiresolution techniques, for triangle meshes already exist in the literature. However, it is not so common to find algorithms and data structures that fuse these two concepts, multiresolution and segmentation, into a symbiotic multi-resolution scheme for both plain and segmented meshes, in which a plainmeshisunderstoodasameshwithasinglesegment. So, weintroducesuchanovel multiresolution segmentation scheme, called extended Ghost Cell (xGC) scheme. This scheme preserves the shape of the meshes in both global and local terms, i.e., mesh segments and their boundaries, as well as creases and apices are preserved, no matter the level of resolution we use for simplification/refinement of the mesh. Moreover, unlike other segmentation schemes, it was made possible to have adjacent segments with two or more resolution levels of difference. This is particularly useful in computer animation, mesh compression and transmission, geometric computing, scientific visualization, and computer graphics. In short, this thesis presents a fully automatic, general, and human perception-oriented scheme that symbiotically integrates the concepts of mesh segmentation and multiresolution

Robust Cardiac Motion Estimation using Ultrafast Ultrasound Data: A Low-Rank-Topology-Preserving Approach

Cardiac motion estimation is an important diagnostic tool to detect heart diseases and it has been explored with modalities such as MRI and conventional ultrasound (US) sequences. US cardiac motion estimation still presents challenges because of the complex motion patterns and the presence of noise. In this work, we propose a novel approach to estimate the cardiac motion using ultrafast ultrasound data. -- Our solution is based on a variational formulation characterized by the L2-regularized class. The displacement is represented by a lattice of b-splines and we ensure robustness by applying a maximum likelihood type estimator. While this is an important part of our solution, the main highlight of this paper is to combine a low-rank data representation with topology preservation. Low-rank data representation (achieved by finding the k-dominant singular values of a Casorati Matrix arranged from the data sequence) speeds up the global solution and achieves noise reduction. On the other hand, topology preservation (achieved by monitoring the Jacobian determinant) allows to radically rule out distortions while carefully controlling the size of allowed expansions and contractions. Our variational approach is carried out on a realistic dataset as well as on a simulated one. We demonstrate how our proposed variational solution deals with complex deformations through careful numerical experiments. While maintaining the accuracy of the solution, the low-rank preprocessing is shown to speed up the convergence of the variational problem. Beyond cardiac motion estimation, our approach is promising for the analysis of other organs that experience motion.Comment: 15 pages, 10 figures, Physics in Medicine and Biology, 201

The mitral valve computational anatomy and geometry analysis

We present a novel methodology to characterize and quantify the Mitral Valve (MV) geometry and physical attributes in a multi-resolution framework. A multi-scale decomposition was implemented to model the MV geometry by using superquadric shape primitives and spectral reconstruction of the finer-scale geometric details. Superquadrics provide a basis to normalize the size and approximate a basic model of the MV geometry. The point-wise difference between the original geometry and the superquadric model denotes the finer-scale geometric details, which can be modeled as a scalar attribute for the MV model development. The additive decomposition of the basic MV geometry from geometric details (attributes) allows recovering the actual geometry by superposition of the superquadric approximation and the finer-details model. We implemented a lasso optimization algorithm to perform spectral analysis and develop the Fourier reconstruction of the geometric details. The spectral modeling enabled us to resample the geometric details or use spectral filters in order to adjust the spatial resolution in the model reconstruction. It also provides the basis to control the level of detail in the final model reconstruction by applying low-pass filters in the frequency domain. The higher-order attributes such as internal fiber architecture can be integrated with the geometric models using the same framework. We applied our pipeline to create models of three ovine MVs based on computed-tomography 3D images with micrometer resolution. We were able to quantify the MV leaflet geometry, reconstruct models with custom level of geometric details, and develop medial representation of the MV leaflet structure. The results show that our methodology for geometry analysis provides a basis for assessing patient-specific geometries and facilitates developing population-averaged models. Ultimately, this approach allows building personalized image-based computational models for medical device design and surgical treatment simulations.Mechanical Engineerin

Automatic generation of synthetic datasets for digital pathology image analysis

The project is inspired by an actual problem of timing and accessibility in the analysis of histological samples in the health-care system. In this project, I address the problem of synthetic histological image generation for the purpose of training Neural Networks for the segmentation of real histological images. The collection of real histological human-labeled samples is a very time consuming and expensive process and often is not representative of healthy samples, for the intrinsic nature of the medical analysis. The method I propose is based on the replication of the traditional specimen preparation technique in a virtual environment. The first step is the creation of a 3D virtual model of a region of the target human tissue. The model should represent all the key features of the tissue, and the richer it is the better will be the yielded result. The second step is to perform a sampling of the model through a virtual tomography process, which produces a first completely labeled image of the section. This image is then processed with different tools to achieve a histological-like aspect. The most significant aesthetical post-processing is given by the action of a style transfer neural network that transfers the typical histological visual texture on the synthetic image. This procedure is presented in detail for two specific models: one of pancreatic tissue and one of dermal tissue. The two resulting images compose a pair of images suitable for a supervised learning technique. The generation process is completely automatized and does not require the intervention of any human operator, hence it can be used to produce arbitrary large datasets. The synthetic images are inevitably less complex than the real samples and they offer an easier segmentation task to solve for the NN. However, the synthetic images are very abundant, and the training of a NN can take advantage of this feature, following the so-called curriculum learning strategy

Segmentation of 3D Carotid Ultrasound Images Using Weak Geometric Priors

Vascular diseases are among the leading causes of death in Canada and around the globe. A major underlying cause of most such medical conditions is atherosclerosis, a gradual accumulation of plaque on the walls of blood vessels. Particularly vulnerable to atherosclerosis is the carotid artery, which carries blood to the brain. Dangerous narrowing of the carotid artery can lead to embolism, a dislodgement of plaque fragments which travel to the brain and are the cause of most strokes. If this pathology can be detected early, such a deadly scenario can be potentially prevented through treatment or surgery. This not only improves the patient's prognosis, but also dramatically lowers the overall cost of their treatment. Medical imaging is an indispensable tool for early detection of atherosclerosis, in particular since the exact location and shape of the plaque need to be known for accurate diagnosis. This can be achieved by locating the plaque inside the artery and measuring its volume or texture, a process which is greatly aided by image segmentation. In particular, the use of ultrasound imaging is desirable because it is a cost-effective and safe modality. However, ultrasonic images depict sound-reflecting properties of tissue, and thus suffer from a number of unique artifacts not present in other medical images, such as acoustic shadowing, speckle noise and discontinuous tissue boundaries. A robust ultrasound image segmentation technique must take these properties into account. Prior to segmentation, an important pre-processing step is the extraction of a series of features from the image via application of various transforms and non-linear filters. A number of such features are explored and evaluated, many of them resulting in piecewise smooth images. It is also proposed to decompose the ultrasound image into several statistically distinct components. These components can be then used as features directly, or other features can be obtained from them instead of the original image. The decomposition scheme is derived using Maximum-a-Posteriori estimation framework and is efficiently computable. Furthermore, this work presents and evaluates an algorithm for segmenting the carotid artery in 3D ultrasound images from other tissues. The algorithm incorporates information from different sources using an energy minimization framework. Using the ultrasound image itself, statistical differences between the region of interest and its background are exploited, and maximal overlap with strong image edges encouraged. In order to aid the convergence to anatomically accurate shapes, as well as to deal with the above-mentioned artifacts, prior knowledge is incorporated into the algorithm by using weak geometric priors. The performance of the algorithm is tested on a number of available 3D images, and encouraging results are obtained and discussed

Locally Adaptive Frames in the Roto-Translation Group and their Applications in Medical Imaging

Locally adaptive differential frames (gauge frames) are a well-known effective tool in image analysis, used in differential invariants and PDE-flows. However, at complex structures such as crossings or junctions, these frames are not well-defined. Therefore, we generalize the notion of gauge frames on images to gauge frames on data representations $U:\mathbb{R}^{d} \rtimes S^{d-1} \to \mathbb{R}$ defined on the extended space of positions and orientations, which we relate to data on the roto-translation group $SE(d)$, $d=2,3$. This allows to define multiple frames per position, one per orientation. We compute these frames via exponential curve fits in the extended data representations in $SE(d)$. These curve fits minimize first or second order variational problems which are solved by spectral decomposition of, respectively, a structure tensor or Hessian of data on $SE(d)$. We include these gauge frames in differential invariants and crossing preserving PDE-flows acting on extended data representation $U$ and we show their advantage compared to the standard left-invariant frame on $SE(d)$. Applications include crossing-preserving filtering and improved segmentations of the vascular tree in retinal images, and new 3D extensions of coherence-enhancing diffusion via invertible orientation scores

Surface and Volumetric Segmentation of Complex 3-D Objects Using Parametric Shape Models

The problem of part definition, description, and decomposition is central to the shape recognition systems. In this dissertation, we develop an integrated framework for segmenting dense range data of complex 3-D scenes into their constituent parts in terms of surface and volumetric primitives. Unlike previous approaches, we use geometric properties derived from surface, as well as volumetric models, to recover structured descriptions of complex objects without a priori domain knowledge or stored models. To recover shape descriptions, we use bi-quadric models for surface representation and superquadric models for object-centered volumetric representation. The surface segmentation uses a novel approach of searching for the best piecewise description of the image in terms of bi-quadric (z = f(x,y)) models. It is used to generate the region adjacency graphs, to localize surface discontinuities, and to derive global shape properties of the surfaces. A superquadric model is recovered for the entire data set and residuals are computed to evaluate the fit. The goodness-of-fit value based on the inside-outside function, and the mean-squared distance of data from the model provide quantitative evaluation of the model. The qualitative evaluation criteria check the local consistency of the model in the form of residual maps of overestimated and underestimated data regions. The control structure invokes the models in a systematic manner, evaluates the intermediate descriptions, and integrates them to achieve final segmentation. Superquadric and bi-quadric models are recovered in parallel to incorporate the best of the coarse-to-fine and fine-to-coarse segmentation strategies. The model evaluation criteria determine the dimensionality of the scene, and decide whether to terminate the procedure, or selectively refine the segmentation by following a global-to-local part segmentation approach. The control module generates hypotheses about superquadric models at clusters of underestimated data and performs controlled extrapolation of the part-model by shrinking the global model. As the global model shrinks and the local models grow, they are evaluated and tested for termination or further segmentation. We present results on real range images of scenes of varying complexity, including objects with occluding parts, and scenes where surface segmentation is not sufficient to guide the volumetric segmentation. We analyze the issue of segmentation of complex scenes thoroughly by studying the effect of missing data on volumetric model recovery, generating object-centered descriptions, and presenting a complete set of criteria for the evaluation of the superquadric models. We conclude by discussing the applications of our approach in data reduction, 3-D object recognition, geometric modeling, automatic model generation. object manipulation, and active vision

Contributions of Continuous Max-Flow Theory to Medical Image Processing

Discrete graph cuts and continuous max-flow theory have created a paradigm shift in many areas of medical image processing. As previous methods limited themselves to analytically solvable optimization problems or guaranteed only local optimizability to increasingly complex and non-convex functionals, current methods based now rely on describing an optimization problem in a series of general yet simple functionals with a global, but non-analytic, solution algorithms. This has been increasingly spurred on by the availability of these general-purpose algorithms in an open-source context. Thus, graph-cuts and max-flow have changed every aspect of medical image processing from reconstruction to enhancement to segmentation and registration. To wax philosophical, continuous max-flow theory in particular has the potential to bring a high degree of mathematical elegance to the field, bridging the conceptual gap between the discrete and continuous domains in which we describe different imaging problems, properties and processes. In Chapter 1, we use the notion of infinitely dense and infinitely densely connected graphs to transfer between the discrete and continuous domains, which has a certain sense of mathematical pedantry to it, but the resulting variational energy equations have a sense of elegance and charm. As any application of the principle of duality, the variational equations have an enigmatic side that can only be decoded with time and patience. The goal of this thesis is to show the contributions of max-flow theory through image enhancement and segmentation, increasing incorporation of topological considerations and increasing the role played by user knowledge and interactivity. These methods will be rigorously grounded in calculus of variations, guaranteeing fuzzy optimality and providing multiple solution approaches to addressing each individual problem