Tools for constraint visualization: The VIFID/TRIFID tool

Visualization of program executions has been used in applications which include education and debugging. However, traditional visualization techniques often fall short of expectations or are altogether inadequate for new programming paradigms, such as Constraint Logic Programming (CLP), whose declarative and operational semantics differ in some crucial ways from those of other paradigms. In particular, traditional ideas regarding the behavior of data often cannot be lifted in a straightforward way to (C)LP from other families of programming languages. In this chapter we discuss techniques for visualizing data evolution in CLP. We briefly review some previously proposed visualization paradigms, and also propose a number of (to our knowledge) novel ones. The graphical representations have been chosen based on the perceived needs of a programmer trying to analyze the behavior and characteristics of an execution. In particular, we concéntrate on the representation of the run-time valúes of the variables, and the constraints among them. Given our interest in visualizing large executions, we also pay attention to abstraction techniques, i.e., techniques which are intended to help in reducing the complexity of the visual information.

Some design issues in the visualization of constraint logic program execution

Visualization of program executions has been found useful in applications which include education and debugging. However, traditional visualization techniques often fall short of expectations or are altogether inadequate for new programming paradigms, such as Constraint Logic Programming (CLP), whose declarative and operational semantics differ in some crucial ways from those of other paradigms. In particular, traditional ideas regarding flow control and the behavior of data often cannot be lifted in a straightforward way to (C)LP from other families of programming languages. In this paper we discuss techniques for visualizing program execution and data evolution in CLP. We briefly review some previously proposed visualization paradigms, and also propose a number of (to our knowledge) novel ones. The graphical representations have been chosen based on the perceived needs of a programmer trying to analyze the behavior and characteristics of an execution. In particular, we concéntrate on the representation of the program execution behavior (control), the runtime valúes of the variables, and the runtime constraints. Given our interest in visualizing large executions, we also pay attention to abstraction techniques, Le., techniques which are intended to help in reducing the complexity of the visual information.

MEDVIR: 3D visual interface applied to gene profile analisys.

The origins for this work arise in response to the increasing need for biologists and doctors to obtain tools for visual analysis of data. When dealing with multidimensional data, such as medical data, the traditional data mining techniques can be a tedious and complex task, even to some medical experts. Therefore, it is necessary to develop useful visualization techniques that can complement the expert’s criterion, and at the same time visually stimulate and make easier the process of obtaining knowledge from a dataset. Thus, the process of interpretation and understanding of the data can be greatly enriched. Multidimensionality is inherent to any medical data, requiring a time-consuming effort to get a clinical useful outcome. Unfortunately, both clinicians and biologists are not trained in managing more than four dimensions. Specifically, we were aimed to design a 3D visual interface for gene profile analysis easy in order to be used both by medical and biologist experts. In this way, a new analysis method is proposed: MedVir. This is a simple and intuitive analysis mechanism based on the visualization of any multidimensional medical data in a three dimensional space that allows interaction with experts in order to collaborate and enrich this representation. In other words, MedVir makes a powerful reduction in data dimensionality in order to represent the original information into a three dimensional environment. The experts can interact with the data and draw conclusions in a visual and quickly way.

A visual framework to accelerate knowledge discovery based on dimensionality reduction minimizing degradation of quality

Tradicionalmente, el uso de técnicas de análisis de datos ha sido una de las principales vías para el descubrimiento de conocimiento oculto en grandes cantidades de datos, recopilados por expertos en diferentes dominios. Por otra parte, las técnicas de visualización también se han usado para mejorar y facilitar este proceso. Sin embargo, existen limitaciones serias en la obtención de conocimiento, ya que suele ser un proceso lento, tedioso y en muchas ocasiones infructífero, debido a la dificultad de las personas para comprender conjuntos de datos de grandes dimensiones. Otro gran inconveniente, pocas veces tenido en cuenta por los expertos que analizan grandes conjuntos de datos, es la degradación involuntaria a la que someten a los datos durante las tareas de análisis, previas a la obtención final de conclusiones. Por degradación quiere decirse que los datos pueden perder sus propiedades originales, y suele producirse por una reducción inapropiada de los datos, alterando así su naturaleza original y llevando en muchos casos a interpretaciones y conclusiones erróneas que podrían tener serias implicaciones. Además, este hecho adquiere una importancia trascendental cuando los datos pertenecen al dominio médico o biológico, y la vida de diferentes personas depende de esta toma final de decisiones, en algunas ocasiones llevada a cabo de forma inapropiada. Ésta es la motivación de la presente tesis, la cual propone un nuevo framework visual, llamado MedVir, que combina la potencia de técnicas avanzadas de visualización y minería de datos para tratar de dar solución a estos grandes inconvenientes existentes en el proceso de descubrimiento de información válida. El objetivo principal es hacer más fácil, comprensible, intuitivo y rápido el proceso de adquisición de conocimiento al que se enfrentan los expertos cuando trabajan con grandes conjuntos de datos en diferentes dominios. Para ello, en primer lugar, se lleva a cabo una fuerte disminución en el tamaño de los datos con el objetivo de facilitar al experto su manejo, y a la vez preservando intactas, en la medida de lo posible, sus propiedades originales. Después, se hace uso de efectivas técnicas de visualización para representar los datos obtenidos, permitiendo al experto interactuar de forma sencilla e intuitiva con los datos, llevar a cabo diferentes tareas de análisis de datos y así estimular visualmente su capacidad de comprensión. De este modo, el objetivo subyacente se basa en abstraer al experto, en la medida de lo posible, de la complejidad de sus datos originales para presentarle una versión más comprensible, que facilite y acelere la tarea final de descubrimiento de conocimiento. MedVir se ha aplicado satisfactoriamente, entre otros, al campo de la magnetoencefalografía (MEG), que consiste en la predicción en la rehabilitación de lesiones cerebrales traumáticas (Traumatic Brain Injury (TBI) rehabilitation prediction). Los resultados obtenidos demuestran la efectividad del framework a la hora de acelerar y facilitar el proceso de descubrimiento de conocimiento sobre conjuntos de datos reales. ABSTRACT Traditionally, the use of data analysis techniques has been one of the main ways of discovering knowledge hidden in large amounts of data, collected by experts in different domains. Moreover, visualization techniques have also been used to enhance and facilitate this process. However, there are serious limitations in the process of knowledge acquisition, as it is often a slow, tedious and many times fruitless process, due to the difficulty for human beings to understand large datasets. Another major drawback, rarely considered by experts that analyze large datasets, is the involuntary degradation to which they subject the data during analysis tasks, prior to obtaining the final conclusions. Degradation means that data can lose part of their original properties, and it is usually caused by improper data reduction, thereby altering their original nature and often leading to erroneous interpretations and conclusions that could have serious implications. Furthermore, this fact gains a trascendental importance when the data belong to medical or biological domain, and the lives of people depends on the final decision-making, which is sometimes conducted improperly. This is the motivation of this thesis, which proposes a new visual framework, called MedVir, which combines the power of advanced visualization techniques and data mining to try to solve these major problems existing in the process of discovery of valid information. Thus, the main objective is to facilitate and to make more understandable, intuitive and fast the process of knowledge acquisition that experts face when working with large datasets in different domains. To achieve this, first, a strong reduction in the size of the data is carried out in order to make the management of the data easier to the expert, while preserving intact, as far as possible, the original properties of the data. Then, effective visualization techniques are used to represent the obtained data, allowing the expert to interact easily and intuitively with the data, to carry out different data analysis tasks, and so visually stimulating their comprehension capacity. Therefore, the underlying objective is based on abstracting the expert, as far as possible, from the complexity of the original data to present him a more understandable version, thus facilitating and accelerating the task of knowledge discovery. MedVir has been succesfully applied to, among others, the field of magnetoencephalography (MEG), which consists in predicting the rehabilitation of Traumatic Brain Injury (TBI). The results obtained successfully demonstrate the effectiveness of the framework to accelerate and facilitate the process of knowledge discovery on real world datasets.

Static and Dynamic Experimental Analysis of the Galloping Stability of Porous H-Section Beams

The phenomenon of self-induced vibrations of prismatic beams in a cross-flow has been studied for decades, but it is still of great interest due to their important effects in many different industrial applications. This paper presents the experimental study developed on a prismatic beam with H-section.The aim of this analysis is to add some additional insight into the behaviour of the flow around this type of bodies, in order to reduce galloping and even to avoid it. The influence of some relevant geometrical parameters that define the H-section on the translational galloping behaviour of these beams has been analysed. Wind loads coefficients have been measured through static wind tunnel tests and the Den Hartog criterion applied to elucidate the influence of geometrical parameters on the galloping properties of the bodies under consideration.These results have been completed with surface pressure distribution measurements and, besides, dynamic tests have been also performed to verify the static criterion. Finally, the morphology of the flow past the tested bodies has been visualised by using smoke visualization techniques. Since the rectangular section beam is a limiting case of the H-section configuration, the results here obtained are compared with the ones published in the literature concerning rectangular configurations; the agreement is satisfactory.

Estudio y validación experimental del efecto de aire interno en un perfil aerodinámico hueco

La presente investigación se llevó a cabo en la Universidad Politécnica de Madrid (España) conjuntamente con la Universidad Nacional Experimental del Táchira (Venezuela). El estudio consistió en diseñar una cavidad interna dentro del perfil aerodinámico 2415-3s, el cual fue desarrollado en la Universidad Técnica Checa (Praga, República Checa). Se realizó un estudio computacional, mediante la técnica del CFD, de diferentes modelos de cavidades internas en este perfil, para seleccionar el diseño más adecuado, fabricando un prototipo en 3D; logrando de esta manera validar la simulación computacional con los datos experimentales obtenidos con los ensayos en el túnel de viento AF6109 de la Universidad Nacional Experimental del Táchira. También se aplicaron técnicas de visualización en el túnel de viento, como líneas de corriente de humo y películas de aceite sobre el perfil aerodinámico. Dicho procedimiento permitió corroborar la validación de la simulación computacional. El perfil aerodinámico seleccionado se denominó 2415-3s-TC, cuya característica principal consiste en tres canales independientes entre sí, alojados dentro de la cavidad interna, permitiendo que el flujo de aire forzado a través de la cavidad, cambiara de dirección, para desembocar lo más tangencialmente, así como, lo más perpendicularmente posible al escalón del perfil aerodinámico 2415-3s. Esta configuración de diseñó permitió elevar el coeficiente de sustentación para ángulos de ataque mayores a 8º, así como para ángulos cercanos al ángulo crítico. ABSTRACT This research was conducted at the Polytechnic University of Madrid (Spain) together with the National Experimental University of Táchira (Venezuela). The study was to design an internal cavity within the airfoil 2415-3s, which was developed in the Czech Technical University (Prague, Czech Republic). A computational study was performed using CFD technique, different models of internal cavities in the profile to select the most appropriate design, manufacturing a prototype 3D; thus achieving validate the computer simulation with experimental data obtained from the tests in the wind tunnel AF6109 of the National Experimental University of Táchira. Visualization techniques were also applied in the wind tunnel, as streamlines smoke and oil films on the airfoil. This procedure corroborated validation of computational simulation. The airfoil selected denominated 2415-3s-TC, whose main characteristic consists of three independent channels each other, housed within the inner cavity, allowing the forced air flow through the cavity, change direction, to lead as more tangentially and, as perpendicular as possible to the step 2415-3s aerofoil. This configuration designed allowed increasing the lift coefficient for higher angles of attack to 8º, and for angles near the critical angle.

Offshore stereo measurements of gravity waves: classical epipolar and novel variational techniques

Stereo video techniques are effective for estimating the space-time wave dynamics over an area of the ocean. Indeed, a stereo camera view allows retrieval of both spatial and temporal data whose statistical content is richer than that of time series data retrieved from point wave probes. Classical epipolar techniques and modern variational methods are reviewed to reconstruct the sea surface from the stereo pairs sequentially in time. Current improvements of the variational methods are presented.

Metadata Visualization of Cultural Heritage Information within a Collaborative Environment

Cultural content on the Web is available in various domains (cultural objects, datasets, geospatial data, moving images, scholarly texts and visual resources), concerns various topics, is written in different languages, targeted to both laymen and experts, and provided by different communities (libraries, archives museums and information industry) and individuals (Figure 1). The integration of information technologies and cultural heritage content on the Web is expected to have an impact on everyday life from the point of view of institutions, communities and individuals. In particular, collaborative environment scan recreate 3D navigable worlds that can offer new insights into our cultural heritage (Chan 2007). However, the main barrier is to find and relate cultural heritage information by end-users of cultural contents, as well as by organisations and communities managing and producing them. In this paper, we explore several visualisation techniques for supporting cultural interfaces, where the role of metadata is essential for supporting the search and communication among end-users (Figure 2). A conceptual framework was developed to integrate the data, purpose, technology, impact, and form components of a collaborative environment, Our preliminary results show that collaborative environments can help with cultural heritage information sharing and communication tasks because of the way in which they provide a visual context to end-users. They can be regarded as distributed virtual reality systems that offer graphically realised, potentially infinite, digital information landscapes. Moreover, collaborative environments also provide a new way of interaction between an end-user and a cultural heritage data set. Finally, the visualisation of metadata of a dataset plays an important role in helping end-users in their search for heritage contents on the Web.

Técnica de Inversión Temporal para la Mejora del Enfocado de Imágenes SAR en Entornos Urbanos

Conventional SAR (Synthetic Aperture Radar) techniques only consider a single reflection of transmitted waveforms from targets. Nevertheless, today?s new applications force SAR systems to work in much more complex scenes such as urban environments. As a result, multiple-bounce returns are additionally superposed to direct echoes. We refer to these as ghost images, since they obscure true target image and lead to poor resolution. By applying Time Reversal concept to SAR imaging (TR-SAR), it is possible to reduce considerably ?or almost mitigate? ghosting artifacts, recovering the lost resolution due to multipath effects. Furthermore, some focusing indicators such as entropy (E), contrast (C) and Rényi entropy (RE) provide us a good focusing criterion when using TR-SAR.

Modelización del cálculo de Indicadores Ambientales, a partir de sensores ópticos de alta resolución temporal a bordo de satélite

La presente tesis doctoral tiene por objeto el estudio y análisis de técnicas y modelos de obtención de parámetros biofísicos e indicadores ambientales, de manera automatizada a partir de imágenes procedentes de satélite de alta resolución temporal. En primer lugar se revisan los diferentes programas espaciales de observación del territorio, con especial atención a los que proporcionan dicha resolución. También se han revisado las metodologías y procesos que permiten la obtención de diferentes parámetros cuantitativos y documentos cualitativos, relacionados con diversos aspectos de las cubiertas terrestres, atendiendo a su adaptabilidad a las particularidades de los datos. En segundo lugar se propone un modelo de obtención de parámetros ambientales, que integra información proveniente de sensores espaciales y de otras fuentes auxiliares utilizando, en cierta medida, las metodologías presentadas en apartados anteriores y optimizando algunas de las referidas o proponiendo otras nuevas, de manera que se permita dicha obtención de manera eficiente, a partir de los datos disponibles y de forma sistemática. Tras esta revisión de metodologías y propuesta del modelo, se ha procedido a la realización de experimentos, con la finalidad de comprobar su comportamiento en diferentes casos prácticos, depurar los flujos de datos y procesos, así como establecer las situaciones que pueden afectar a los resultados. De todo ello se deducirá la evaluación del referido modelo. Los sensores considerados en este trabajo han sido MODIS, de alta resolución temporal y Thematic Mapper (TM), de media resolución espacial, por tratarse de instrumentos de referencia en la realización de estudios ambientales. También por la duración de sus correspondientes misiones de registro de datos, lo que permite realizar estudios de evolución temporal de ciertos parámetros biofísicos, durante amplios periodos de tiempo. Así mismo. es de destacar que la continuidad de los correspondientes programas parece estar asegurada. Entre los experimentos realizados, se ha ensayado una metodología para la integración de datos procedentes de ambos sensores. También se ha analizado un método de interpolación temporal que permite obtener imágenes sintéticas con la resolución espacial de TM (30 m) y la temporal de MODIS (1 día), ampliando el rango de aplicación de este último sensor. Asimismo, se han analizado algunos de los factores que afectan a los datos registrados, tal como la geometría de la toma de los mismos y los episodios de precipitación, los cuales alteran los resultados obtenidos. Por otro lado, se ha comprobado la validez del modelo propuesto en el estudio de fenómenos ambientales dinámicos, en concreto la contaminación orgánica de aguas embalsadas. Finalmente, se ha demostrado un buen comportamiento del modelo en todos los casos ensayados, así como su flexibilidad, lo que le permite adaptarse a nuevos orígenes de datos, o nuevas metodologías de cálculo. Abstract This thesis aims to the study and analysis of techniques and models, in order to obtain biophysical parameters and environmental indicators in an automated way, using high temporal resolution satellite data. Firstly we have reviewed the main Earth Observation Programs, paying attention to those that provide high temporal resolution. Also have reviewed the methodologies and process flow diagrams in order to obtain quantitative parameters and qualitative documents, relating to various aspects of land cover, according to their adaptability to the peculiarities of the data. In the next stage, a model which allows obtaining environmental parameters, has been proposed. This structure integrates information from space sensors and ancillary data sources, using the methodologies presented in previous sections that permits the parameters calculation in an efficient and automated way. After this review of methodologies and the proposal of the model, we proceeded to carry out experiments, in order to check the behavior of the structure in real situations. From this, we derive the accuracy of the model. The sensors used in this work have been MODIS, which is a high temporal resolution sensor, and Thematic Mapper (TM), which is a medium spatial resolution instrument. This choice was motivated because they are reference sensors in environmental studies, as well as for the duration of their corresponding missions of data logging, and whose continuity seems assured. Among the experiments, we tested a methodology that allows the integration of data from cited sensors, we discussed a proposal for a temporal interpolation method for obtaining synthetic images with spatial resolution of TM (30 m) and temporal of MODIS (1 day), extending the application range of this one. Furthermore, we have analyzed some of the factors that affect the recorded data, such as the relative position of the satellite with the ground point, and the rainfall events, which alter the obtained results. On the other hand, we have proven the validity of the proposed model in the study of the organic contamination in inland water bodies. Finally, we have demonstrated a good performance of the proposed model in all cases tested, as well as its flexibility and adaptability.

3D Wavelet-based Fusion Techniques for Biomedical Imaging

Hoy en día las técnicas de adquisición de imágenes tridimensionales son comunes en diversas áreas, pero cabe destacar la relevancia que han adquirido en el ámbito de la imagen biomédica, dentro del cual encontramos una amplia gama de técnicas como la microscopía confocal, microscopía de dos fotones, microscopía de fluorescencia mediante lámina de luz, resonancia magnética nuclear, tomografía por emisión de positrones, tomografía de coherencia óptica, ecografía 3D y un largo etcétera. Un denominador común de todas esas aplicaciones es la constante necesidad por aumentar la resolución y la calidad de las imágenes adquiridas. En algunas de dichas técnicas de imagen tridimensional se da una interesante situación: aunque que cada volumen adquirido no contiene información suficiente para representar el objeto bajo estudio dentro de los parámetros de calidad requeridos por algunas aplicaciones finales, el esquema de adquisición permite la obtención de varios volúmenes que representan diferentes vistas de dicho objeto, de tal forma que cada una de las vistas proporciona información complementaria acerca del mismo. En este tipo de situación es posible, mediante la combinación de varias de esas vistas, obtener una mejor comprensión del objeto que a partir de cada una de ellas por separado. En el contexto de esta Tesis Doctoral se ha propuesto, desarrollado y validado una nueva metodología de proceso de imágenes basada en la transformada wavelet disc¬reta para la combinación, o fusión, de varias vistas con información complementaria de un mismo objeto. El método de fusión propuesto aprovecha la capacidad de descom¬posición en escalas y orientaciones de la transformada wavelet discreta para integrar en un solo volumen toda la información distribuida entre el conjunto de vistas adquiridas. El trabajo se centra en dos modalidades diferentes de imagen biomédica que per¬miten obtener tales adquisiciones multi-vista. La primera es una variante de la micro¬scopía de fluorescencia, la microscopía de fluorescencia mediante lámina de luz, que se utiliza para el estudio del desarrollo temprano de embriones vivos en diferentes modelos animales, como el pez cebra o el erizo de mar. La segunda modalidad es la resonancia magnética nuclear con realce tardío, que constituye una valiosa herramienta para evaluar la viabilidad del tejido miocárdico en pacientes con diversas miocardiopatías. Como parte de este trabajo, el método propuesto ha sido aplicado y validado en am¬bas modalidades de imagen. En el caso de la aplicación a microscopía de fluorescencia, los resultados de la fusión muestran un mejor contraste y nivel de detalle en comparación con cualquiera de las vistas individuales y el método no requiere de conocimiento previo acerca la función de dispersión puntual del sistema de imagen. Además, los resultados se han comparado con otros métodos existentes. Con respecto a la aplicación a imagen de resonancia magnética con realce tardío, los volúmenes fusionados resultantes pre-sentan una mejora cuantitativa en la nitidez de las estructuras relevantes y permiten una interpretación más sencilla y completa de la compleja estructura tridimensional del tejido miocárdico en pacientes con cardiopatía isquémica. Para ambas aplicaciones los resultados de esta tesis se encuentran actualmente en uso en los centros clínicos y de investigación con los que el autor ha colaborado durante este trabajo. Además se ha puesto a libre disposición de la comunidad científica la implementación del método de fusión propuesto. Por último, se ha tramitado también una solicitud de patente internacional que cubre el método de visualización desarrollado para la aplicación de Resonancia Magnética Nuclear. Abstract Nowadays three dimensional imaging techniques are common in several fields, but es-pecially in biomedical imaging, where we can find a wide range of techniques including: Laser Scanning Confocal Microscopy, Laser Scanning Two Photon Microscopy, Light Sheet Fluorescence Microscopy, Magnetic Resonance Imaging, Positron Emission To-mography, Optical Coherence Tomography, 3D Ultrasound Imaging, etc. A common denominator of all those applications being the constant need for further increasing resolution and quality of the acquired images. Interestingly, in some of the mentioned three-dimensional imaging techniques a remarkable situation arises: while a single volume does not contain enough information to represent the object being imaged within the quality parameters required by the final application, the acquisition scheme allows recording several volumes which represent different views of a given object, with each of the views providing complementary information. In this kind of situation one can get a better understanding of the object by combining several views instead of looking at each of them separately. Within such context, in this PhD Thesis we propose, develop and test new image processing methodologies based on the discrete wavelet transform for the combination, or fusion, of several views containing complementary information of a given object. The proposed fusion method exploits the scale and orientation decomposition capabil¬ities of the discrete wavelet transform to integrate in a single volume all the available information distributed among the set of acquired views. The work focuses in two different biomedical imaging modalities which provide such multi-view datasets. The first one is a particular fluorescence microscopy technique, Light-Sheet Fluorescence Microscopy, used for imaging and gaining understanding of the early development of live embryos from different animal models (like zebrafish or sea urchin). The second is Delayed Enhancement Magnetic Resonance Imaging, which is a valuable tool for assessing the viability of myocardial tissue on patients suffering from different cardiomyopathies. As part of this work, the proposed method was implemented and then validated on both imaging modalities. For the fluorescence microscopy application, the fusion results show improved contrast and detail discrimination when compared to any of the individual views and the method does not rely on prior knowledge of the system’s point spread function (PSF). Moreover, the results have shown improved performance with respect to previous PSF independent methods. With respect to its application to Delayed Enhancement Magnetic Resonance Imaging, the resulting fused volumes show a quantitative sharpness improvement and enable an easier and more complete interpretation of complex three-dimensional scar and heterogeneous tissue information in ischemic cardiomyopathy patients. In both applications, the results of this thesis are currently in use in the clinical and research centers with which the author collaborated during his work. An imple¬mentation of the fusion method has also been made freely available to the scientific community. Finally, an international patent application has been filed covering the visualization method developed for the Magnetic Resonance Imaging application.

Computational methods to create and analyze a digital gene expression atlas of embryo development from microscopy images

Abstract The creation of atlases, or digital models where information from different subjects can be combined, is a field of increasing interest in biomedical imaging. When a single image does not contain enough information to appropriately describe the organism under study, it is then necessary to acquire images of several individuals, each of them containing complementary data with respect to the rest of the components in the cohort. This approach allows creating digital prototypes, ranging from anatomical atlases of human patients and organs, obtained for instance from Magnetic Resonance Imaging, to gene expression cartographies of embryo development, typically achieved from Light Microscopy. Within such context, in this PhD Thesis we propose, develop and validate new dedicated image processing methodologies that, based on image registration techniques, bring information from multiple individuals into alignment within a single digital atlas model. We also elaborate a dedicated software visualization platform to explore the resulting wealth of multi-dimensional data and novel analysis algo-rithms to automatically mine the generated resource in search of bio¬logical insights. In particular, this work focuses on gene expression data from developing zebrafish embryos imaged at the cellular resolution level with Two-Photon Laser Scanning Microscopy. Disposing of quantitative measurements relating multiple gene expressions to cell position and their evolution in time is a fundamental prerequisite to understand embryogenesis multi-scale processes. However, the number of gene expressions that can be simultaneously stained in one acquisition is limited due to optical and labeling constraints. These limitations motivate the implementation of atlasing strategies that can recreate a virtual gene expression multiplex. The developed computational tools have been tested in two different scenarios. The first one is the early zebrafish embryogenesis where the resulting atlas constitutes a link between the phenotype and the genotype at the cellular level. The second one is the late zebrafish brain where the resulting atlas allows studies relating gene expression to brain regionalization and neurogenesis. The proposed computational frameworks have been adapted to the requirements of both scenarios, such as the integration of partial views of the embryo into a whole embryo model with cellular resolution or the registration of anatom¬ical traits with deformable transformation models non-dependent on any specific labeling. The software implementation of the atlas generation tool (Match-IT) and the visualization platform (Atlas-IT) together with the gene expression atlas resources developed in this Thesis are to be made freely available to the scientific community. Lastly, a novel proof-of-concept experiment integrates for the first time 3D gene expression atlas resources with cell lineages extracted from live embryos, opening up the door to correlate genetic and cellular spatio-temporal dynamics. La creación de atlas, o modelos digitales, donde la información de distintos sujetos puede ser combinada, es un campo de creciente interés en imagen biomédica. Cuando una sola imagen no contiene suficientes datos como para describir apropiadamente el organismo objeto de estudio, se hace necesario adquirir imágenes de varios individuos, cada una de las cuales contiene información complementaria respecto al resto de componentes del grupo. De este modo, es posible crear prototipos digitales, que pueden ir desde atlas anatómicos de órganos y pacientes humanos, adquiridos por ejemplo mediante Resonancia Magnética, hasta cartografías de la expresión genética del desarrollo de embrionario, típicamente adquiridas mediante Microscopía Optica. Dentro de este contexto, en esta Tesis Doctoral se introducen, desarrollan y validan nuevos métodos de procesado de imagen que, basándose en técnicas de registro de imagen, son capaces de alinear imágenes y datos provenientes de múltiples individuos en un solo atlas digital. Además, se ha elaborado una plataforma de visualization específicamente diseñada para explorar la gran cantidad de datos, caracterizados por su multi-dimensionalidad, que resulta de estos métodos. Asimismo, se han propuesto novedosos algoritmos de análisis y minería de datos que permiten inspeccionar automáticamente los atlas generados en busca de conclusiones biológicas significativas. En particular, este trabajo se centra en datos de expresión genética del desarrollo embrionario del pez cebra, adquiridos mediante Microscopía dos fotones con resolución celular. Disponer de medidas cuantitativas que relacionen estas expresiones genéticas con las posiciones celulares y su evolución en el tiempo es un prerrequisito fundamental para comprender los procesos multi-escala característicos de la morfogénesis. Sin embargo, el número de expresiones genéticos que pueden ser simultáneamente etiquetados en una sola adquisición es reducido debido a limitaciones tanto ópticas como del etiquetado. Estas limitaciones requieren la implementación de estrategias de creación de atlas que puedan recrear un multiplexado virtual de expresiones genéticas. Las herramientas computacionales desarrolladas han sido validadas en dos escenarios distintos. El primer escenario es el desarrollo embrionario temprano del pez cebra, donde el atlas resultante permite constituir un vínculo, a nivel celular, entre el fenotipo y el genotipo de este organismo modelo. El segundo escenario corresponde a estadios tardíos del desarrollo del cerebro del pez cebra, donde el atlas resultante permite relacionar expresiones genéticas con la regionalización del cerebro y la formación de neuronas. La plataforma computacional desarrollada ha sido adaptada a los requisitos y retos planteados en ambos escenarios, como la integración, a resolución celular, de vistas parciales dentro de un modelo consistente en un embrión completo, o el alineamiento entre estructuras de referencia anatómica equivalentes, logrado mediante el uso de modelos de transformación deformables que no requieren ningún marcador específico. Está previsto poner a disposición de la comunidad científica tanto la herramienta de generación de atlas (Match-IT), como su plataforma de visualización (Atlas-IT), así como las bases de datos de expresión genética creadas a partir de estas herramientas. Por último, dentro de la presente Tesis Doctoral, se ha incluido una prueba conceptual innovadora que permite integrar los mencionados atlas de expresión genética tridimensionales dentro del linaje celular extraído de una adquisición in vivo de un embrión. Esta prueba conceptual abre la puerta a la posibilidad de correlar, por primera vez, las dinámicas espacio-temporales de genes y células.

Using clustering techniques for intelligent camera-based user interfaces

The area of Human-Machine Interface is growing fast due to its high importance in all technological systems. The basic idea behind designing human-machine interfaces is to enrich the communication with the technology in a natural and easy way. Gesture interfaces are a good example of transparent interfaces. Such interfaces must identify properly the action the user wants to perform, so the proper gesture recognition is of the highest importance. However, most of the systems based on gesture recognition use complex methods requiring high-resource devices. In this work, we propose to model gestures capturing their temporal properties, which significantly reduce storage requirements, and use clustering techniques, namely self-organizing maps and unsupervised genetic algorithm, for their classification. We further propose to train a certain number of algorithms with different parameters and combine their decision using majority voting in order to decrease the false positive rate. The main advantage of the approach is its simplicity, which enables the implementation using devices with limited resources, and therefore low cost. The testing results demonstrate its high potential.

A silviculture-oriented spatio-temporal model for germination in Pinus pinea L. in the Spanish Northern Plateau based on a direct seeding experiment

Natural regeneration in Pinus pinea stands commonly fails throughout the Spanish Northern Plateau under current intensive regeneration treatments. As a result, extensive direct seeding is commonly conducted to guarantee regeneration occurrence. In a period of rationalization of the resources devoted to forest management, this kind of techniques may become unaffordable. Given that the climatic and stand factors driving germination remain unknown, tools are required to understand the process and temper the use of direct seeding. In this study, the spatio-temporal pattern of germination of P. pinea was modelled with those purposes. The resulting findings will allow us to (1) determine the main ecological variables involved in germination in the species and (2) infer adequate silvicultural alternatives. The modelling approach focuses on covariates which are readily available to forest managers. A two-step nonlinear mixed model was fitted to predict germination occurrence and abundance in P. pinea under varying climatic, environmental and stand conditions, based on a germination data set covering a 5-year period. The results obtained reveal that the process is primarily driven by climate variables. Favourable conditions for germination commonly occur in fall although the optimum window is often narrow and may not occur at all in some years. At spatial level, it would appear that germination is facilitated by high stand densities, suggesting that current felling intensity should be reduced. In accordance with other studies on P. pinea dispersal, it seems that denser stands during the regeneration period will reduce the present dependence on direct seeding.

Characterization of underground cellars in the Duero Basin by GNSS, LIDAR and GPR techniques

The underground cellars of the Duero River basin are part of spread and damaged agricultural landscape which is in danger of disappearing. These architectural complexes are allocated next to small towns. Constructions are mostly dug in the ground with a gallery down or "barrel" strait through which you access the cave or cellar. This wider space is used to make and store wine. Observation and detection of the winery both on the outside and underground is essential to make an inventory of the rural heritage. Geodetection is a non-invasive technique, suitable to determinate with precision buried structures in the ground. The undertaken works include LIDAR survey techniques, GNSS and GPR obtained data. The results are used to identify with centimetric precision construction elements forming the winery. Graphic and cartographic obtained documents allow optimum visualization of the studied field and can be used in the reconstruction of the place.