Estudio y desarrollo de un preproceso basado en la difusión no lineal para la segmentación en imágenes

En esta Tesis Doctoral se aborda la utilización de filtros de difusión no lineal para obtener imágenes constantes a trozos como paso previo al proceso de segmentación. En una primera parte se propone un formulación intrínseca para la ecuación de difusión no lineal que proporcione las condiciones de diseño necesarias sobre los filtros de difusión. A partir del marco teórico propuesto, se proporciona una nueva familia de difusividades; éstas son obtenidas a partir de técnicas de difusión no lineal relacionadas con los procesos de difusión regresivos. El objetivo es descomponer la imagen en regiones cerradas que sean homogéneas en sus niveles de grises sin contornos difusos. Asimismo, se prueba que la función de difusividad propuesta satisface las condiciones de un correcto planteamiento semi-discreto. Esto muestra que mediante el esquema semi-implícito habitualmente utilizado, realmente se hace un proceso de difusión no lineal directa, en lugar de difusión inversa, conectando con proceso de preservación de bordes. Bajo estas condiciones establecidas, se plantea un criterio de parada para el proceso de difusión, para obtener imágenes constantes a trozos con un bajo coste computacional. Una vez aplicado todo el proceso al caso unidimensional, se extienden los resultados teóricos, al caso de imágenes en 2D y 3D. Para el caso en 3D, se detalla el esquema numérico para el problema evolutivo no lineal, con condiciones de contorno Neumann homogéneas. Finalmente, se prueba el filtro propuesto para imágenes reales en 2D y 3D y se ilustran los resultados de la difusividad propuesta como método para obtener imágenes constantes a trozos. En el caso de imágenes 3D, se aborda la problemática del proceso previo a la segmentación del hígado, mediante imágenes reales provenientes de Tomografías Axiales Computarizadas (TAC). En ese caso, se obtienen resultados sobre la estimación de los parámetros de la función de difusividad propuesta. This Ph.D. Thesis deals with the case of using nonlinear diffusion filters to obtain piecewise constant images as a previous process for segmentation techniques. I have first shown an intrinsic formulation for the nonlinear diffusion equation to provide some design conditions on the diffusion filters. According to this theoretical framework, I have proposed a new family of diffusivities; they are obtained from nonlinear diffusion techniques and are related with backward diffusion. Their goal is to split the image in closed contours with a homogenized grey intensity inside and with no blurred edges. It has also proved that the proposed filters satisfy the well-posedness semi-discrete and full discrete scale-space requirements. This shows that by using semi-implicit schemes, a forward nonlinear diffusion equation is solved, instead of a backward nonlinear diffusion equation, connecting with an edgepreserving process. Under the conditions established for the diffusivity and using a stopping criterion I for the diffusion time, I have obtained piecewise constant images with a low computational effort. The whole process in the one-dimensional case is extended to the case where 2D and 3D theoretical results are applied to real images. For 3D, develops in detail the numerical scheme for nonlinear evolutionary problem with homogeneous Neumann boundary conditions. Finally, I have tested the proposed filter with real images for 2D and 3D and I have illustrated the effects of the proposed diffusivity function as a method to get piecewise constant images. For 3D I have developed a preprocess for liver segmentation with real images from CT (Computerized Tomography). In this case, I have obtained results on the estimation of the parameters of the given diffusivity function.

Low-resource synchronous coincidence processor for positron emission tomography

We developed a new FPGA-based method for coincidence detection in positronemissiontomography. The method requires low device resources and no specific peripherals in order to resolve coincident digital pulses within a time window of a few nanoseconds. This method has been validated with a low-end Xilinx Spartan-3E and provided coincidence resolutions lower than 6 ns. This resolution depends directly on the signal propagation properties of the target device and the maximum available clock frequency, therefore it is expected to improve considerably on higher-end FPGAs.

Computerized Three-Dimmensional Craniofacial Reconstruction from Skulls Based on Landmarks.

Human identification from a skull is a critical process in legal and forensic medicine, specially when no other means are available. Traditional clay-based methods attempt to generate the human face, in order to identify the corresponding person. However, these reconstructions lack of objectivity and consistence, since they depend on the practitioner. Current computerized techniques are based on facial models, which introduce undesired facial features when the final reconstruction is built. This paper presents an objective 3D craniofacial reconstruction technique, implemented in a graphic application, without using any facial template. The only information required by the software tool is the 3D image of the target skull and three parameters: age, gender and Body Mass Index (BMI) of the individual. Complexity is minimized, since the application database only consists of the anthropological information provided by soft tissue depth values in a set of points of the skull.

Technical developments for computed tomography on the CENBG nanobeam line

The use of ion microbeams as probes for computedtomography has proven to be a powerful tool for the three-dimensional characterization of specimens a few tens of micrometers in size. Compared to other types of probes, the main advantage is that quantitative information about mass density and composition can be obtained directly, using specific reconstruction codes. At the Centre d’Etudes Nucléaires de Bordeaux Gradignan (CENBG), this technique was initially developed for applications in cellular biology. However, the observation of the cell ultrastructure requires a sub-micron resolution. The construction of the nanobeamline at the Applications Interdisciplinaires des Faisceaux d’Ions en Region Aquitaine (AIFIRA) irradiation facility has opened new perspectives for such applications. The implementation of computedtomography on the nanobeamline of CENBG has required a careful design of the analysis chamber, especially microscopes for precise sample visualization, and detectors for scanning transmission ion microscopy (STIM) and for particle induced X-ray emission (PIXE). The sample can be precisely positioned in the three directions X, Y, Z and a stepper motor coupled to a goniometer ensures the rotational motion. First images of 3D tomography were obtained on a reference sample containing microspheres of certified diameter, showing the good stability of the beam and the sample stage, and the precision of the motion.

Hybrid topological derivative and gradient-based methods for electrical impedance tomography

We present a technique to reconstruct the electromagnetic properties of a medium or a set of objects buried inside it from boundary measurements when applying electric currents through a set of electrodes. The electromagnetic parameters may be recovered by means of a gradient method without a priori information on the background. The shape, location and size of objects, when present, are determined by a topological derivative-based iterative procedure. The combination of both strategies allows improved reconstructions of the objects and their properties, assuming a known background.

Super-Resolution in Respiratory Synchronized Positron Emission Tomography

Respiratory motion is a major source of reduced quality in positron emission tomography (PET). In order to minimize its effects, the use of respiratory synchronized acquisitions, leading to gated frames, has been suggested. Such frames, however, are of low signal-to-noise ratio (SNR) as they contain reduced statistics. Super-resolution (SR) techniques make use of the motion in a sequence of images in order to improve their quality. They aim at enhancing a low-resolution image belonging to a sequence of images representing different views of the same scene. In this work, a maximum a posteriori (MAP) super-resolution algorithm has been implemented and applied to respiratory gated PET images for motion compensation. An edge preserving Huber regularization term was used to ensure convergence. Motion fields were recovered using a B-spline based elastic registration algorithm. The performance of the SR algorithm was evaluated through the use of both simulated and clinical datasets by assessing image SNR, as well as the contrast, position and extent of the different lesions. Results were compared to summing the registered synchronized frames on both simulated and clinical datasets. The super-resolution image had higher SNR (by a factor of over 4 on average) and lesion contrast (by a factor of 2) than the single respiratory synchronized frame using the same reconstruction matrix size. In comparison to the motion corrected or the motion free images a similar SNR was obtained, while improvements of up to 20% in the recovered lesion size and contrast were measured. Finally, the recovered lesion locations on the SR images were systematically closer to the true simulated lesion positions. These observations concerning the SNR, lesion contrast and size were confirmed on two clinical datasets included in the study. In conclusion, the use of SR techniques applied to respiratory motion synchronized images lead to motion compensation combined with improved image SNR and contrast, without any increase in the overall acquisition times.

Detailed damage mechanisms assessment in composite materials by means of X-ray tomography

This research focused on the evaluation of damage formation on ±45º carbon fiber laminates subjected to tensile tests. The damage was evaluated by means of X-ray tomography. A high density of cracks developed during the plateau of the stress-strain curve and were qualitatively analyzed, showing that the inner plies eventually developed a higher crack concentration than the outer plies. Delamination started to occur in the outermost ply interface when the slope after the plateau of the stress-strain curve began to increase.

Dental Implants Success Prediction: Tomography Based and Data Mining Based Approach.

There are a number of factors that contribute to the success of dental implant operations. Among others, is the choice of location in which the prosthetic tooth is to be implanted. This project offers a new approach to analyse jaw tissue for the purpose of selecting suitable locations for teeth implant operations. The application developed takes as input jaw computed tomography stack of slices and trims data outside the jaw area, which is the point of interest. It then reconstructs a three dimensional model of the jaw highlighting points of interest on the reconstructed model. On another hand, data mining techniques have been utilised in order to construct a prediction model based on an information dataset of previous dental implant operations with observed stability values. The goal is to find patterns within the dataset that would help predicting the success likelihood of an implant.

Desarrollo y caracterización de un material celular de alta porosidad con base cementicia activada mediante agentes inorgánicos

Esta tesis ha estudiado los morteros celulares, centrándose en la experimentación con pastas de cemento aireadas (PCA) con polvo de aluminio como agente expansor. El objetivo es el desarrollo de un material cementicio con una baja conductividad térmica que sirva como aislamiento térmico. La naturaleza inorgánica del material lo hace incombustible, en contraste con las espumas poliméricas existentes en el mercado, cuya aplicación en cámaras ventiladas ha sido prohibida por normativas de construcción tanto a nivel nacional como internacional. Las posibles aplicaciones son con proyección neumática o en paneles prefabricados. Se han ensayado dos series de pastas de cemento con polvo de aluminio: - Serie WPC/CAC/CH. Mezcla de referencia con cemento blanco (WPC), cemento de aluminato cálcico (CAC) y cal aérea (CH) en proporción 5:1:4. - Serie OPC/CH. Mezcla de referencia con cemento portland con cenizas volantes (OPC) y cal aérea (CH) en proporción OPC/CH de 4:1 A las mezclas de referencia se le han añadido adiciones de metacaolín (MK) (10 y 20%) o sepiolita (SP) (1 y 2%) para observar el efecto que producen tanto en el mortero fresco como en el mortero endurecido. Se ha estudiado la reología de las pastas en estado fresco, analizando el proceso de expansión de las pastas, registrando los valores de tensión de fluencia, aire ocluido y temperatura durante la expansión. Con los valores obtenidos se ha discutido la influencia de las adiciones utilizadas en la cinética de corrosión del polvo de aluminio que genera la expansión, concluyendo que las adiciones puzolánicas (CV y MK) y la SP reducen mucho el periodo de inducción, lo que provoca poros más grandes y mayor cantidad de aire ocluido. Asimismo se ha analizado la relación entre la tensión de fluencia y el contenido de aire ocluido, deduciendo que a mayor tensión de fluencia en el momento de iniciarse la expansión, menor tamaño de poros y contenido de aire ocluido. Finalmente, se han obtenido las densidades y capacidades de retención de agua de los morteros frescos. Para caracterizar la red porosa de las pastas aireadas endurecidas, se obtuvieron tanto las densidades reales, netas, aparentes y relativas como las porosidades abiertas, cerradas y totales con ensayos hídricos. Finalmente se obtuvieron imágenes de los poros con tomografía axial computerizada para obtener las porosimetrías de las muestras. La caracterización de la red porosa ha servido para terminar de analizar lo observado en la evolución de la expansión del mortero fresco. Se ha analizado la influencia de la red porosa en la conductividad térmica, obtenida con caja caliente, comparándola con la existente en la literatura existente tanto de morteros celulares como de espumas poliméricas. Se concluye que los valores de conductividad térmica conseguida están en el mínimo posible para un material celular de base cementicia. La microestructura se ha estudiado con microscopía electrónica de barrido, difracción de rayos X y ensayos térmicos TG/ATD, observando que los productos de hidratación encontrados coinciden con los que se producen en morteros sin airear. Las imágenes SEM y los resultados de ultrasonidos han servido para analizar la presencia de microfisuras de retracción en las pastas aireadas, observando que en las muestras con adiciones de MK y SP, se reduce la presencia de microfisuras. ABSTRACT This thesis has studied cellular mortars, focusing in testing aerated cement pastes with aluminum powder as expansive agent. The purpose is the development of a cementitious material with low thermal conductivity that can be used as thermal isolation. Inorganic nature of this material makes it non-combustible, in contrast with polymeric foams in market, whose application in ventilated double skin façade systems has been banned by building standards, both domestically and internationally. Possible uses for this material are pneumatically sprayed applications and precast panels. Two series of batches with aluminum powder have been tested: - WPC/CAC/CH series. Reference paste with white portland cement (WPC), calcium aluminate cement (CAC) and lime (CH) with 5:1:4 ratio. - OPC/CH series. Reference paste with portland cement with fly ash (OPC) and lime (CH) with 4:1 ratio. Metakaolin (MK) (10 and 20%) or sepiolite (SP) (1 and 2%) additions were used in reference pastes to characterize the effect in fresh and hardened mortar. Rheology in fresh pastes was studied, expansion process of pastes was analyzed, recording yield stress, entrained air and temperature values during expansion. Recorded values were used to discuss influence of additions on reaction kinetics of aluminum powder corrosion, that produces expansion.. Conclusion is that pozzolanic additions (FA and MK) and SP greatly reduce induction period, producing bigger pores and more entrained air. Relation between yield stress and entrained air has been also analyzed, observing that the bigger yield stress at beginning of expansion, the smaller pores size and the lower entrained air values. Finally density and water retention of fresh mortars were obtained. Pore network in hardened aerated cement pastes was characterized by imbibition methods providing true, bulk and relative density, and providing also open, closed and total porosity. Finally, pore system imaging were obtained with computerized axial tomography to study porosimetry of specimens. Pore network characterization was useful to complete facts analysis observed in expansion of fresh mortars. Influence of pore network in thermal conductivity, checked in hot box, was analyzed comparing with those existing values in cellular mortar and polymeric foams researches. It was concluded that thermal conductivity values achieved are close to minimum possible in a cementitious cellular material. Microstructure was studied with Scanning Electron Microscopy, X-Ray Diffractometry and TG-DTA analysis, observing that hydration phases found, are those produced in non aerated mortar. SEM imaging and ultrasound results were useful to analyze shrinkage microcracks in aerated cement pastes, concluding that microcrack presence in specimens with MK and SP additions were reduced.

Patient-oriented computerized clinical guidelines for mobile decision support in gestational diabetes

The risks associated with gestational diabetes (GD) can be reduced with an active treatment able to improve glycemic control. Advances in mobile health can provide new patient-centric models for GD to create personalized health care services, increase patient independence and improve patients’ self-management capabilities, and potentially improve their treatment compliance. In these models, decision-support functions play an essential role. The telemedicine system MobiGuide provides personalized medical decision support for GD patients that is based on computerized clinical guidelines and adapted to a mobile environment. The patient’s access to the system is supported by a smartphone-based application that enhances the efficiency and ease of use of the system. We formalized the GD guideline into a computer-interpretable guideline (CIG). We identified several workflows that provide decision-support functionalities to patients and 4 types of personalized advice to be delivered through a mobile application at home, which is a preliminary step to providing decision-support tools in a telemedicine system: (1) therapy, to help patients to comply with medical prescriptions; (2) monitoring, to help patients to comply with monitoring instructions; (3) clinical assessment, to inform patients about their health conditions; and (4) upcoming events, to deal with patients’ personal context or special events. The whole process to specify patient-oriented decision support functionalities ensures that it is based on the knowledge contained in the GD clinical guideline and thus follows evidence-based recommendations but at the same time is patient-oriented, which could enhance clinical outcomes and patients’ acceptance of the whole system.

Automatic quantification of matrix cracking and fiber rotation by X-ray computed tomography in shear-deformed carbon fiber-reinforced laminates

The deformation and damage mechanisms of carbon fiber-reinforced epoxy laminates deformed in shear were studied by means of X-ray computed tomography. In particular, the evolution of matrix cracking, interply delamination and fiber rotation was ascertained as a function of the applied strain. In order to provide quantitative information, an algorithm was developed to automatically determine the crack density and the fiber orientation from the tomograms. The investigation provided new insights about the complex interaction between the different damage mechanisms (i.e. matrix cracking and interply delamination) as a function of the applied strain, ply thickness and ply location within the laminate as well as quantitative data about the evolution of matrix cracking and fiber rotation during deformation

Geometrical characterization of undisturbed soil samples using X-ray computed tomography image analysis. Effect of soil management on soil structure

El estudio de la estructura del suelo es de vital importancia en diferentes campos de la ciencia y la tecnología. La estructura del suelo controla procesos físicos y biológicos importantes en los sistemas suelo-planta-microorganismos. Estos procesos están dominados por la geometría de la estructura del suelo, y una caracterización cuantitativa de la heterogeneidad de la geometría del espacio poroso es beneficiosa para la predicción de propiedades físicas del suelo. La tecnología de la tomografía computerizada de rayos-X (CT) nos permite obtener imágenes digitales tridimensionales del interior de una muestra de suelo, proporcionando información de la geometría de los poros del suelo y permitiendo el estudio de los poros sin destruir las muestras. Las técnicas de la geometría fractal y de la morfología matemática se han propuesto como una poderosa herramienta para analizar y cuantificar características geométricas. Las dimensiones fractales del espacio poroso, de la interfaz poro-sólido y de la distribución de tamaños de poros son indicadores de la complejidad de la estructura del suelo. Los funcionales de Minkowski y las funciones morfológicas proporcionan medios para medir características geométricas fundamentales de los objetos geométricos tridimensionales. Esto es, volumen, superficie, curvatura media de la superficie y conectividad. Las características del suelo como la distribución de tamaños de poros, el volumen del espacio poroso o la superficie poro-solido pueden ser alteradas por diferentes practicas de manejo de suelo. En este trabajo analizamos imágenes tomográficas de muestras de suelo de dos zonas cercanas con practicas de manejo diferentes. Obtenemos un conjunto de medidas geométricas, para evaluar y cuantificar posibles diferencias que el laboreo pueda haber causado en el suelo. ABSTRACT The study of soil structure is of vital importance in different fields of science and technology. Soil structure controls important physical and biological processes in soil-plant-microbial systems. Those processes are dominated by the geometry of soil pore structure, and a quantitative characterization of the spatial heterogeneity of the pore space geometry is beneficial for prediction of soil physical properties. The technology of X-ray computed tomography (CT) allows us to obtain three-dimensional digital images of the inside of a soil sample providing information on soil pore geometry and enabling the study of the pores without disturbing the samples. Fractal geometry and mathematical morphological techniques have been proposed as powerful tools to analyze and quantify geometrical features. Fractal dimensions of pore space, pore-solid interface and pore size distribution are indicators of soil structure complexity. Minkowski functionals and morphological functions provide means to measure fundamental geometrical features of three-dimensional geometrical objects, that is, volume, boundary surface, mean boundary surface curvature, and connectivity. Soil features such as pore-size distribution, pore space volume or pore-solid surface can be altered by different soil management practices. In this work we analyze CT images of soil samples from two nearby areas with contrasting management practices. We performed a set of geometrical measures, some of them from mathematical morphology, to assess and quantify any possible difference that tillage may have caused on the soil.