Geometric reconstruction methods for electron tomography

Electron tomography is becoming an increasingly important tool in materials science for studying the three-dimensional morphologies and chemical compositions of nanostructures. The image quality obtained by many current algorithms is seriously affected by the problems of missing wedge artefacts and nonlinear projection intensities due to diffraction effects. The former refers to the fact that data cannot be acquired over the full $180^\circ$ tilt range; the latter implies that for some orientations, crystalline structures can show strong contrast changes. To overcome these problems we introduce and discuss several algorithms from the mathematical fields of geometric and discrete tomography. The algorithms incorporate geometric prior knowledge (mainly convexity and homogeneity), which also in principle considerably reduces the number of tilt angles required. Results are discussed for the reconstruction of an InAs nanowire

Lesion detection in demoscopy images with novel density-based and active contour approaches

<p>Abstract</p> <p>Background</p> <p>Dermoscopy is one of the major imaging modalities used in the diagnosis of melanoma and other pigmented skin lesions. Automated assessment tools for dermoscopy images have become an important field of research mainly because of inter- and intra-observer variations in human interpretation. One of the most important steps in dermoscopy image analysis is the detection of lesion borders, since many other features, such as asymmetry, border irregularity, and abrupt border cutoff, rely on the boundary of the lesion. </p> <p>Results</p> <p>To automate the process of delineating the lesions, we employed Active Contour Model (ACM) and boundary-driven density-based clustering (BD-DBSCAN) algorithms on 50 dermoscopy images, which also have ground truths to be used for quantitative comparison. We have observed that ACM and BD-DBSCAN have the same border error of 6.6% on all images. To address noisy images, BD-DBSCAN can perform better delineation than ACM. However, when used with optimum parameters, ACM outperforms BD-DBSCAN, since ACM has a higher recall ratio.</p> <p>Conclusion</p> <p>We successfully proposed two new frameworks to delineate suspicious lesions with i) an ACM integrated approach with sharpening and ii) a fast boundary-driven density-based clustering technique. ACM shrinks a curve toward the boundary of the lesion. To guide the evolution, the model employs the exact solution <abbrgrp><abbr bid="B27">27</abbr></abbrgrp> of a specific form of the Geometric Heat Partial Differential Equation <abbrgrp><abbr bid="B28">28</abbr></abbrgrp>. To make ACM advance through noisy images, an improvement of the model’s boundary condition is under consideration. BD-DBSCAN improves regular density-based algorithm to select query points intelligently.</p

Gravity optimised particle filter for hand tracking

This paper presents a gravity optimised particle filter (GOPF) where the magnitude of the gravitational force for every particle is proportional to its weight. GOPF attracts nearby particles and replicates new particles as if moving the particles towards the peak of the likelihood distribution, improving the sampling efficiency. GOPF is incorporated into a technique for hand features tracking. A fast approach to hand features detection and labelling using convexity defects is also presented. Experimental results show that GOPF outperforms the standard particle filter and its variants, as well as state-of-the-art CamShift guided particle filter using a significantly reduced number of particles

Automated Morphology Analysis of Nanoparticles

The functional properties of nanoparticles highly depend on the surface morphology of the particles, so precise measurements of a particle's morphology enable reliable characterizing of the nanoparticle's properties. Obtaining the measurements requires image analysis of electron microscopic pictures of nanoparticles. Today's labor-intensive image analysis of electron micrographs of nanoparticles is a significant bottleneck for efficient material characterization. The objective of this dissertation is to develop automated morphology analysis methods. Morphology analysis is comprised of three tasks: separate individual particles from an agglomerate of overlapping nano-objects (image segmentation); infer the particle's missing contours (shape inference); and ultimately, classify the particles by shape based on their complete contours (shape classification). Two approaches are proposed in this dissertation: the divide-and-conquer approach and the convex shape analysis approach. The divide-and-conquer approach solves each task separately, taking less than one minute to complete the required analysis, even for the largest-sized micrograph. However, its separating capability of particle overlaps is limited, meaning that it is able to split only touching particles. The convex shape analysis approach solves shape inference and classification simultaneously for better accuracy, but it requires more computation time, ten minutes for the biggest-sized electron micrograph. However, with a little sacrifice of time efficiency, the second approach achieves far superior separation than the divide-and-conquer approach, and it handles the chain-linked structure of particle overlaps well. The capabilities of the two proposed methods cannot be substituted by generic image processing and bio-imaging methods. This is due to the unique features that the electron microscopic pictures of nanoparticles have, including special particle overlap structures, and large number of particles to be processed. The application of the proposed methods to real electron microscopic pictures showed that the two proposed methods were more capable of extracting the morphology information than the state-of-the-art methods. When nanoparticles do not have many overlaps, the divide-and-conquer approach performed adequately. When nanoparticles have many overlaps, forming chain-linked clusters, the convex shape analysis approach performed much better than the state-of-the-art alternatives in bio-imaging. The author believes that the capabilities of the proposed methods expedite the morphology characterization process of nanoparticles. The author further conjectures that the technical generality of the proposed methods could even be a competent alternative to the current methods analyzing general overlapping convex-shaped objects other than nanoparticles

Direction Selective Contour Detection for Salient Objects

The active contour model is a widely used technique for automatic object contour extraction. Existing methods based on this model can perform with high accuracy even in case of complex contours, but challenging issues remain, like the need for precise contour initialization for high curvature boundary segments or the handling of cluttered backgrounds. To deal with such issues, this paper presents a salient object extraction method, the first step of which is the introduction of an improved edge map that incorporates edge direction as a feature. The direction information in the small neighborhoods of image feature points are extracted, and the images’ prominent orientations are defined for direction-selective edge extraction. Using such improved edge information, we provide a highly accurate shape contour representation, which we also combine with texture features. The principle of the paper is to interpret an object as the fusion of its components: its extracted contour and its inner texture. Our goal in fusing textural and structural information is twofold: it is applied for automatic contour initialization, and it is also used to establish an improved external force field. This fusion then produces highly accurate salient object extractions. We performed extensive evaluations which confirm that the presented object extraction method outperforms parametric active contour models and achieves higher efficiency than the majority of the evaluated automatic saliency methods

Safe Driving using Vision-based Hand Gesture Recognition System in Non-uniform Illumination Conditions

Nowadays, there is tremendous growth in in-car interfaces for driver safety and comfort, but controlling these devices while driving requires the driver's attention. One of the solutions to reduce the number of glances at these interfaces is to design an advanced driver assistance system (ADAS). A vision-based touch-less hand gesture recognition system is proposed here for in-car human-machine interfaces (HMI). The performance of such systems is unreliable under ambient illumination conditions, which change during the course of the day. Thus, the main focus of this work was to design a system that is robust towards changing lighting conditions. For this purpose, a homomorphic filter with adaptive thresholding binarization is used. Also, gray-level edge-based segmentation ensures that it is generalized for users of different skin tones and background colors. This work was validated on selected gestures from the Cambridge Hand Gesture Database captured in five sets of non-uniform illumination conditions that closely resemble in-car illumination conditions, yielding an overall system accuracy of 91%, an average frame-by-frame accuracy of 81.38%, and a latency of 3.78 milliseconds. A prototype of the proposed system was implemented on a Raspberry Pi 3 interface together with an Android application, which demonstrated its suitability for non-critical in-car interfaces like infotainment systems

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