Image Segmentation Using Active Contours Driven by the Bhattacharyya Gradient Flow

©2007 IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or distribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE. This material is presented to ensure timely dissemination of scholarly and technical work. Copyright and all rights therein are retained by authors or by other copyright holders. All persons copying this information are expected to adhere to the terms and constraints invoked by each author's copyright. In most cases, these works may not be reposted without the explicit permission of the copyright holder.DOI: 10.1109/TIP.2007.908073This paper addresses the problem of image segmentation by means of active contours, whose evolution is driven by the gradient flow derived froman energy functional that is based on the Bhattacharyya distance. In particular, given the values of a photometric variable (or of a set thereof), which is to be used for classifying the image pixels, the active contours are designed to converge to the shape that results in maximal discrepancy between the empirical distributions of the photometric variable inside and outside of the contours. The above discrepancy is measured by means of the Bhattacharyya distance that proves to be an extremely useful tool for solving the problem at hand. The proposed methodology can be viewed as a generalization of the segmentation methods, in which active contours maximize the difference between a finite number of empirical moments of the "inside" and "outside" distributions. Furthermore, it is shown that the proposed methodology is very versatile and flexible in the sense that it allows one to easily accommodate a diversity of the image features based on which the segmentation should be performed. As an additional contribution, a method for automatically adjusting the smoothness properties of the empirical distributions is proposed. Such a procedure is crucial in situations when the number of data samples (supporting a certain segmentation class) varies considerably in the course of the evolution of the active contour. In this case, the smoothness properties of the empirical distributions have to be properly adjusted to avoid either over- or underestimation artifacts. Finally, a number of relevant segmentation results are demonstrated and some further research directions are discussed

Towards label-free biosensing in compact disk technologies f or point-of-need analysis

Tesis por compendioThis thesis explores new analytical advances using compact disk biosensing technologies, and comprises six scientific publications distributed along four chapters. Special attention is herein payed to Thermochromic Etching Disks (TED) technology (Chapter 1), rational design of disk-based biorecognition assays (Chapter 2), and label-free detection systems for point-of-need analysis (Chapters 3 and 4). First, insights into a novel light-mediated signal developing system for biorecognition assays (based on TED disks and drives) are provided together with an overview of the state-of-the art and future trends in photo- and thermochromic biosensing. This signal developing approach exploits photo- and thermochromism for biosensing in an original manner and represents a potential strategy to simplify signaling processes in bioanalytical systems. Then, how to transform TED technology into lab-on-a-disk systems is addressed. TED has proven to be a very versatile tool to perform sensitive analysis of biorecognition assays, using platforms and scanners easily obtained from regular disks and drives, respectively. Biologically relevant assays of different nature (microarray, cell culture, immunofiltration, turbidimetry, etc.) have been arrayed in a single disk and sensitively analyzed by imaging. Regarding rational design, a theoretical-experimental method (INSEL) based on kinetics and mass-transport modelling for optimizing biorecognition assays and exploring their behavior is presented. INSEL has been implemented as an in silico tool that enables to characterize biointeractions with minimal experimentation, to perform optimizations directed towards custom objectives defined by the user, and to easily compute the effect of critical variables without further experiments. In another study included in this thesis, polycarbonate grooved structures obtained from standard recordable disks (CD-R and DVD-R) were coated with silver and tailored to become SERS-active. This strategy represents a cost-effective and industrially scalable alternative to the SERS substrates typically used for bioanalysis. These disk-based materials have presented tunable plasmonic responses, significant Raman enhancement, and have allowed complex biological targets (such as proteins and exosomes) to be analyzed by SERS without using labeled reagents as tracers. In addition to introduce inexpensive and large-scale SERS substrates for biosensing, this study also suggests the development of prospective Raman scanners based on disk drives. Another approach herein presented addresses the implementation of diffraction-based sensing (DBS) in TED technology in order to conceive disk-based label-free biosensors based on standard disks and drives. At first, a comprehensive experimental assessment of the analytical possibilities offered by DBS is presented. Then, the fabrication of arrays of diffractive protein networks on TED disks is investigated, with which sensitive analysis of antibodies in label-free conditions has been demonstrated, using adapted drives as scanners. This investigation provides important insights into cost-effective and industrially scalable functional materials and detection setups that exploit consumer electronics for label-free biosensing.Esta tesis explora nuevos avances en química analítica usando tecnologías de biosensado basadas en sistemas de disco compacto y comprende seis publicaciones científicas distribuidas a lo largo de cuatro capítulos. Los estudios se han centrado en la tecnología Thermochromic Etching Disks (TED) (Capítulo 1), el diseño racional de ensayos de bioreconocimiento en discos compactos (Capítulo 2), y la detección sin marcaje para realizar análisis in situ (Capítulos 3 y 4). Primero, enmarcado en una discusión del estado del arte y futuras tendencias en biosensado foto y termocrómico, se presenta un nuevo sistema (basado en discos y lectores TED) mediado por luz para el desarrollo de señales en ensayos de bioreconocimiento. Ésta constituye una estrategia novedosa para aprovechar el foto y termocromismo en biosensado, y presenta un gran potencial para simplificar los procesos de desarrollo de señal en sistemas bioanalíticos. A continuación, se aborda cómo transformar la tecnología TED en sistemas analíticos integrados basados en discos compactos. TED ha demostrado ser una herramienta muy versátil para analizar, de forma sensible, ensayos de bioreconocimiento usando plataformas y escáneres fácilmente obtenidos a partir de discos y lectores convencionales, respectivamente. Un único disco ha mostrado poder albergar varios ensayos biológicos importantes y de distinta naturaleza (micromatriz, cultivos celulares, inmunofiltración, turbidimetría, etc.), para ser analizados de forma sensible a través de imágenes En cuanto al diseño racional, se presenta un método teórico-experimental (INSEL), basado en modelos cinéticos y de transporte de masa, para optimizar ensayos de bioreconocimiento y explorar su comportamiento. INSEL se ha implementado como una herramienta in silico que permite caracterizar biointeracciones mediante mínima experimentación, realizar optimizaciones dirigidas a objetivos particulares definidos por el usuario, y computar el efecto de variables críticas de forma sencilla y sin experimentos adicionales. En otro estudio incluido en esta tesis, nanoestructuras en forma de surco obtenidas a partir de discos regrabables convencionales (CD-R y DVD-R) fueron recubiertas con plata y adaptadas para ser activas en SERS. Esta estrategia supone una alternativa, económicamente efectiva e industrialmente escalable, a los sustratos SERS típicamente usados en bioanálisis. Estos materiales han mostrado respuestas plasmónicas sintonizables, una amplificación Raman significativa, y han permitido analizar muestras biológicas complejas (como proteínas y exosomas) mediante SERS sin usar marcadores. Además de introducir sustratos SERS grandes y baratos, este trabajo también sugiere el desarrollo de escáneres Raman basados en lectores de disco. Otra aproximación presentada en esta tesis aborda la implementación de DBS (diffraction-based sensing) en tecnologías TED, con el fin de desarrollar biosensores para detección sin marcaje basados en discos y lectores convencionales. Primero, se presenta una amplia evaluación experimental de las posibilidades analíticas ofrecidas por DBS. A continuación, se investiga la fabricación de multitud de redes difractivas de proteínas sobre discos TED, con las que se ha demostrado la determinación sensible y sin marcaje de anticuerpos, usando lectores adaptados como escáneres analíticos. Esta investigación introduce avances importantes que apuntan al desarrollo de materiales funcionales y sistemas de detección, baratos e industrialmente escalables, que aprovechen las tecnologías de consumo para realizar biosensado sin marcaje.Aquesta tesi explora nous avanços en la química analítica usant tecnologies de biosensat basades en sistemes de disc compacte, i comprèn sis publicacions científiques distribuïdes en quatre capítols. Els estudis s'han centrat en la tecnologia Thermochromic Etching Disks (TED) (Capítol 1), el disseny racional d'assajos de bioreconeixement en discos compactes (Capítol 2), i la detecció sense marcatge per realitzar anàlisi in situ (Capítols 3 i 4). Primer, dins del marc d'una discussió de l'estat de l'art i tendències futures en biosensat foto i termocròmic, es presenta un nou sistema (basat en discos i lectors TED) per al desenvolupament de senyals mitjançant llum, en assajos de bioreconeixement. Aquesta constitueix una nova estratègia per aprofitar el foto i termocromisme en biosensat, mentre que també presenta una gran potencial per simplificar els processos de desenvolupament de senyal en sistemes bioanalítics. Tot seguit, s'aborda com transformar la tecnologia TED en sistemes analítics integrats basats en discos compactes. TED ha demostrat ser una eina molt versàtil per analitzar, de forma sensible, assajos de bioreconeixement usant plataformes i escàners fàcilment obtinguts a partir de discos i lectors convencionals, respectivament. Un únic disc ha mostrat poder albergar diversos assajos biològicament importants i de distinta naturalesa (micromatrius, cultius cel·lulars, immunofiltració, turbidimetria, etc.), per a ser analitzats de forma sensible a través d'imatges. Pel que fa al disseny racional, es presenta un mètode teòric-experimental (INSEL), basat en models cinètics i de transport de massa, per optimitzar assajos de bioreconeixement i explorar el seu comportament. INSEL s'ha implementat com a una eina in silico que permet caracteritzar biointeraccions amb mínima experimentació, realitzar optimitzacions dirigides cap a objectius particulars definits per l'usuari, i computar l'efecte de variables crítiques de forma senzilla i sense experiments addicionals. En un altre estudi inclòs en aquesta tesi, nanoestructures en forma de solc obtingudes a partir de discos compactes regravables convencionals (CD-R i DVD-R) van ser recobertes amb plata i adaptades per a ser actives en SERS. Aquesta estratègia suposa una alternativa, econòmicament efectiva i industrialment escalable, als substrats SERS típicament usats en bioanàlisi. Aquests materials han mostrat respostes plasmòniques sintonitzables, una amplificació Raman significativa, i han permès analitzar mostres biològiques complexes (com proteïnes i exosomes) mitjançant SERS sense usar marcadors. A més d'introduir substrats SERS grans i barats, aquest treball també suggereix el desenvolupament d'escàners Raman basats en lectors de disc. Una altra aproximació presentada en aquesta tesi aborda la implementació de DBS (diffraction-based sensing) en tecnologies TED, per tal de desenvolupar biosensors basats en discos i lectors convencionals que permeten detecció sense marcatge. Primer, es presenta una amplia avaluació experimental de les possibilitats analítiques que ofereix aquesta tècnica. A continuació, s'investiga la fabricació de multitud de xarxes difractives de proteïnes sobre discos TED, amb les quals s'ha demostrat la determinació sensible i sense marcatge d'anticossos, usant lectors adaptats com a escàners analítics. Aquesta investigació introdueix avanços importants que apunten cap al desenvolupament de materials funcionals i sistemes de detecció, barats i industrialment escalables, que aprofiten les tecnologies de consum per dur a terme bioanàlisi sense marcatge.Avellà Oliver, JM. (2017). Towards label-free biosensing in compact disk technologies f or point-of-need analysis [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/86128TESISCompendi

Nouveaux schémas de commande et d'observation basés sur les modèles de Takagi-Sugeno

This thesis addresses the estimation and controller design for continuous-time nonlinear systems. The methodologies developed are based on the Takagi-Sugeno (TS) representation of the nonlinear model via the sector nonlinearity approach. All strategies intend to get more relaxed conditions.The results presented for controller design are split in two parts. The first part is about standard TS models under control schemes based on: 1) a quadratic Lyapunov function (QLF); 2) a fuzzy Lyapunov function (FLF); 3) a line-integral Lyapunov functions (LILF); 4) a novel non-quadratic Lyapunov functional (NQLF). The second part concerns to TS descriptor models. Two strategies are proposed: 1) within the quadratic framework, conditions based on a general control law and some matrix transformations; 2) an extension to the nonquadratic approach based on a line-integral Lyapunov function (LILF) using non-PDC control law schemes and the Finsler’s Lemma; this strategy offers parameter-dependent linear matrix inequality (LMI) conditions instead of bilinear matrix inequality (BMI) constraints for second-order systems. On the other hand, the problem of the state estimation for nonlinear systems via TS models is also addressed considering: a) the particular case where premise vectors are based on measured variables and b) the general case where premise vectors can be based on unmeasured variables. Several examples have been included to illustrate the applicability of the obtained results.Cette thèse aborde l'estimation et la conception de commande de systèmes non linéaires à temps continu. Les méthodologies développées sont basées sur la représentation Takagi-Sugeno (TS) du modèle non linéaire par l'approche du secteur non-linéarité. Toutes les stratégies ont l'intention d'obtenir des conditions plus détendu. Les résultats présentés pour la conception de commande sont divisés en deux parties. La première partie est environ sur les modèles TS standard au titre des schémas de commande basés sur: 1) une fonction de Lyapunov quadratique (QLF); 2) une fonction de Lyapunov floue (FLF); 3) une fonction de Lyapunov intégrale de ligne (LILF); 4) un nouveau fonctionnelle de Lyapunov non-quadratique (NQLF). La deuxième partie concerne des modèles TS descripteurs. Deux stratégies sont proposées: 1) dans le cadre quadratique, des conditions basées sur une loi de commande général et quelques transformations de matrices; 2) une extension de l'approche non quadratique basée sur LILF utilisant un schéma de commande non-PDC et le lemme du Finsler; cette stratégie offre conditions sur la forme d’inégalité matricielles linéaires (LMI) dépendant des paramètres au lieu des contraintes sur la forme d’inégalité matricielles bilinéaires (BMI) pour les systèmes de second ordre. D'autre part, le problème de l'estimation de l'état pour les systèmes non linéaires via modèles TS est également abordé considérant: a) le cas particulier où les vecteurs prémisses sont basées sur les variables mesurées et b) le cas général où les vecteurs prémisse peuvent être basés sur des variables non mesurées. Plusieurs exemples ont été inclus pour illustrer l'applicabilité des résultats obtenus

A review of silicon subwavelength gratings: building break-through devices with anisotropic metamaterials

Abstract Silicon photonics is playing a key role in areas as diverse as high-speed optical communications, neural networks, supercomputing, quantum photonics, and sensing, which demand the development of highly efficient and compact light-processing devices. The lithographic segmentation of silicon waveguides at the subwavelength scale enables the synthesis of artificial materials that significantly expand the design space in silicon photonics. The optical properties of these metamaterials can be controlled by a judicious design of the subwavelength grating geometry, enhancing the performance of nanostructured devices without jeopardizing ease of fabrication and dense integration. Recently, the anisotropic nature of subwavelength gratings has begun to be exploited, yielding unprecedented capabilities and performance such as ultrabroadband behavior, engineered modal confinement, and sophisticated polarization management. Here we provide a comprehensive review of the field of subwavelength metamaterials and their applications in silicon photonics. We first provide an in-depth analysis of how the subwavelength geometry synthesizes the metamaterial and give insight into how properties like refractive index or anisotropy can be tailored. The latest applications are then reviewed in detail, with a clear focus on how subwavelength structures improve device performance. Finally, we illustrate the design of two ground-breaking devices in more detail and discuss the prospects of subwavelength gratings as a tool for the advancement of silicon photonics

Improving Model-Based Software Synthesis: A Focus on Mathematical Structures

Computer hardware keeps increasing in complexity. Software design needs to keep up with this. The right models and abstractions empower developers to leverage the novelties of modern hardware. This thesis deals primarily with Models of Computation, as a basis for software design, in a family of methods called software synthesis. We focus on Kahn Process Networks and dataflow applications as abstractions, both for programming and for deriving an efficient execution on heterogeneous multicores. The latter we accomplish by exploring the design space of possible mappings of computation and data to hardware resources. Mapping algorithms are not at the center of this thesis, however. Instead, we examine the mathematical structure of the mapping space, leveraging its inherent symmetries or geometric properties to improve mapping methods in general. This thesis thoroughly explores the process of model-based design, aiming to go beyond the more established software synthesis on dataflow applications. We starting with the problem of assessing these methods through benchmarking, and go on to formally examine the general goals of benchmarks. In this context, we also consider the role modern machine learning methods play in benchmarking. We explore different established semantics, stretching the limits of Kahn Process Networks. We also discuss novel models, like Reactors, which are designed to be a deterministic, adaptive model with time as a first-class citizen. By investigating abstractions and transformations in the Ohua language for implicit dataflow programming, we also focus on programmability. The focus of the thesis is in the models and methods, but we evaluate them in diverse use-cases, generally centered around Cyber-Physical Systems. These include the 5G telecommunication standard, automotive and signal processing domains. We even go beyond embedded systems and discuss use-cases in GPU programming and microservice-based architectures