Optimal Multiresolution 3D Level-Set Method for Liver Segmentation incorporating Local Curvature Constraints

Advanced liver surgery requires a precise pre-operative planning, where liver segmentation and remnant liver volume are key elements to avoid post-operative liver failure. In that context, level-set algorithms have achieved better results than others, especially with altered liver parenchyma or in cases with previous surgery. In order to improve functional liver parenchyma volume measurements, in this work we propose two strategies to enhance previous level-set algorithms: an optimal multi-resolution strategy with fine details correction and adaptive curvature, as well as an additional semiautomatic step imposing local curvature constraints. Results show more accurate segmentations, especially in elongated structures, detecting internal lesions and avoiding leakages to close structures

An Automatic Quantification and Registration Strategy to Create a Gene Expression Atlas of Zebrafish Embryogenesis

In order to properly understand and model the gene regulatory networks in animals development, it is crucial to obtain detailed measurements, both in time and space, about their gene expression domains. In this paper, we propose a complete computational framework to fulfill this task and create a 3D Atlas of the early zebrafish embryogenesis annotated with both the cellular localizations and the level of expression of different genes at different developmental stages. The strategy to construct such an Atlas is described here with the expression pattern of 5 different genes at 6 hours of development post fertilization.

Multimodal non-rigid image registration methods for therapy and surgery planning

La planificación pre-operatoria se ha convertido en una tarea esencial en cirugías y terapias de marcada complejidad, especialmente aquellas relacionadas con órgano blando. Un ejemplo donde la planificación preoperatoria tiene gran interés es la cirugía hepática. Dicha planificación comprende la detección e identificación precisa de las lesiones individuales y vasos así como la correcta segmentación y estimación volumétrica del hígado funcional. Este proceso es muy importante porque determina tanto si el paciente es un candidato adecuado para terapia quirúrgica como la definición del abordaje a seguir en el procedimiento. La radioterapia de órgano blando es un segundo ejemplo donde la planificación se requiere tanto para la radioterapia externa convencional como para la radioterapia intraoperatoria. La planificación comprende la segmentación de tumor y órganos vulnerables y la estimación de la dosimetría. La segmentación de hígado funcional y la estimación volumétrica para planificación de la cirugía se estiman habitualmente a partir de imágenes de tomografía computarizada (TC). De igual modo, en la planificación de radioterapia, los objetivos de la radiación se delinean normalmente sobre TC. Sin embargo, los avances en las tecnologías de imagen de resonancia magnética (RM) están ofreciendo progresivamente ventajas adicionales. Por ejemplo, se ha visto que el ratio de detección de metástasis hepáticas es significativamente superior en RM con contraste Gd–EOB–DTPA que en TC. Por tanto, recientes estudios han destacado la importancia de combinar la información de TC y RM para conseguir el mayor nivel posible de precisión en radioterapia y para facilitar una descripción precisa de las lesiones del hígado. Con el objetivo de mejorar la planificación preoperatoria en ambos escenarios se precisa claramente de un algoritmo de registro no rígido de imagen. Sin embargo, la gran mayoría de sistemas comerciales solo proporcionan métodos de registro rígido. Las medidas de intensidad de voxel han demostrado ser criterios de similitud de imágenes robustos, y, entre ellas, la Información Mutua (IM) es siempre la primera elegida en registros multimodales. Sin embargo, uno de los principales problemas de la IM es la ausencia de información espacial y la asunción de que las relaciones estadísticas entre las imágenes son homogéneas a lo largo de su domino completo. La hipótesis de esta tesis es que la incorporación de información espacial de órganos al proceso de registro puede mejorar la robustez y calidad del mismo, beneficiándose de la disponibilidad de las segmentaciones clínicas. En este trabajo, se propone y valida un esquema de registro multimodal no rígido 3D usando una nueva métrica llamada Información Mutua Centrada en el Órgano (Organ-Focused Mutual Information metric (OF-MI)) y se compara con la formulación clásica de la Información Mutua. Esto permite mejorar los resultados del registro en áreas problemáticas incorporando información regional al criterio de similitud, beneficiándose de la disponibilidad real de segmentaciones en protocolos estándares clínicos, y permitiendo que la dependencia estadística entre las dos modalidades de imagen difiera entre órganos o regiones. El método propuesto se ha aplicado al registro de TC y RM con contraste Gd–EOB–DTPA así como al registro de imágenes de TC y MR para planificación de radioterapia intraoperatoria rectal. Adicionalmente, se ha desarrollado un algoritmo de apoyo de segmentación 3D basado en Level-Sets para la incorporación de la información de órgano en el registro. El algoritmo de segmentación se ha diseñado específicamente para la estimación volumétrica de hígado sano funcional y ha demostrado un buen funcionamiento en un conjunto de imágenes de TC abdominales. Los resultados muestran una mejora estadísticamente significativa de OF-MI comparada con la Información Mutua clásica en las medidas de calidad de los registros; tanto con datos simulados (p<0.001) como con datos reales en registro hepático de TC y RM con contraste Gd– EOB–DTPA y en registro para planificación de radioterapia rectal usando OF-MI multi-órgano (p<0.05). Adicionalmente, OF-MI presenta resultados más estables con menor dispersión que la Información Mutua y un comportamiento más robusto con respecto a cambios en la relación señal-ruido y a la variación de parámetros. La métrica OF-MI propuesta en esta tesis presenta siempre igual o mayor precisión que la clásica Información Mutua y consecuentemente puede ser una muy buena alternativa en aplicaciones donde la robustez del método y la facilidad en la elección de parámetros sean particularmente importantes. Abstract Pre-operative planning has become an essential task in complex surgeries and therapies, especially for those affecting soft tissue. One example where soft tissue preoperative planning is of high interest is liver surgery. It involves the accurate detection and identification of individual liver lesions and vessels as well as the proper functional liver segmentation and volume estimation. This process is very important because it determines whether the patient is a suitable candidate for surgical therapy and the type of procedure. Soft tissue radiation therapy is a second example where planning is required for both conventional external and intraoperative radiotherapy. It involves the segmentation of the tumor target and vulnerable organs and the estimation of the planned dose. Functional liver segmentations and volume estimations for surgery planning are commonly estimated from computed tomography (CT) images. Similarly, in radiation therapy planning, targets to be irradiated and healthy and vulnerable tissues to be protected from irradiation are commonly delineated on CT scans. However, developments in magnetic resonance imaging (MRI) technology are progressively offering advantages. For instance, the hepatic metastasis detection rate has been found to be significantly higher in Gd–EOB–DTPAenhanced MRI than in CT. Therefore, recent studies highlight the importance of combining the information from CT and MRI to achieve the highest level of accuracy in radiotherapy and to facilitate accurate liver lesion description. In order to improve those two soft tissue pre operative planning scenarios, an accurate nonrigid image registration algorithm is clearly required. However, the vast majority of commercial systems only provide rigid registration. Voxel intensity measures have been shown to be robust measures of image similarity, and among them, Mutual Information (MI) is always the first candidate in multimodal registrations. However, one of the main drawbacks of Mutual Information is the absence of spatial information and the assumption that statistical relationships between images are the same over the whole domain of the image. The hypothesis of the present thesis is that incorporating spatial organ information into the registration process may improve the registration robustness and quality, taking advantage of the clinical segmentations availability. In this work, a multimodal nonrigid 3D registration framework using a new Organ- Focused Mutual Information metric (OF-MI) is proposed, validated and compared to the classical formulation of the Mutual Information (MI). It allows improving registration results in problematic areas by adding regional information into the similitude criterion taking advantage of actual segmentations availability in standard clinical protocols and allowing the statistical dependence between the two modalities differ among organs or regions. The proposed method is applied to CT and T1 weighted delayed Gd–EOB–DTPA-enhanced MRI registration as well as to register CT and MRI images in rectal intraoperative radiotherapy planning. Additionally, a 3D support segmentation algorithm based on Level-Sets has been developed for the incorporation of the organ information into the registration. The segmentation algorithm has been specifically designed for the healthy and functional liver volume estimation demonstrating good performance in a set of abdominal CT studies. Results show a statistical significant improvement of registration quality measures with OF-MI compared to MI with both simulated data (p<0.001) and real data in liver applications registering CT and Gd–EOB–DTPA-enhanced MRI and in registration for rectal radiotherapy planning using multi-organ OF-MI (p<0.05). Additionally, OF-MI presents more stable results with smaller dispersion than MI and a more robust behavior with respect to SNR changes and parameters variation. The proposed OF-MI always presents equal or better accuracy than the classical MI and consequently can be a very convenient alternative within applications where the robustness of the method and the facility to choose the parameters are particularly important.

3D Determination of Area-at-Risk in Acute Myocardial Infarction

MRI methods for acute myocardial infarction

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.

Detecting unknown attacks in wireless sensor networks that contain mobile nodes

As wireless sensor networks are usually deployed in unattended areas, security policies cannot be updated in a timely fashion upon identification of new attacks. This gives enough time for attackers to cause significant damage. Thus, it is of great importance to provide protection from unknown attacks. However, existing solutions are mostly concentrated on known attacks. On the other hand, mobility can make the sensor network more resilient to failures, reactive to events, and able to support disparate missions with a common set of sensors, yet the problem of security becomes more complicated. In order to address the issue of security in networks with mobile nodes, we propose a machine learning solution for anomaly detection along with the feature extraction process that tries to detect temporal and spatial inconsistencies in the sequences of sensed values and the routing paths used to forward these values to the base station. We also propose a special way to treat mobile nodes, which is the main novelty of this work. The data produced in the presence of an attacker are treated as outliers, and detected using clustering techniques. These techniques are further coupled with a reputation system, in this way isolating compromised nodes in timely fashion. The proposal exhibits good performances at detecting and confining previously unseen attacks, including the cases when mobile nodes are compromised.

Ubiquitous green computing techniques for high demand applications in smart environments

Ubiquitous sensor network deployments, such as the ones found in Smart cities and Ambient intelligence applications, require constantly increasing high computational demands in order to process data and offer services to users. The nature of these applications imply the usage of data centers. Research has paid much attention to the energy consumption of the sensor nodes in WSNs infrastructures. However, supercomputing facilities are the ones presenting a higher economic and environmental impact due to their very high power consumption. The latter problem, however, has been disregarded in the field of smart environment services. This paper proposes an energy-minimization workload assignment technique, based on heterogeneity and application-awareness, that redistributes low-demand computational tasks from high-performance facilities to idle nodes with low and medium resources in the WSN infrastructure. These non-optimal allocation policies reduce the energy consumed by the whole infrastructure and the total execution time.

GreenDisc: a HW/SW energy optimization framework in globally distributed computation

In recent future, wireless sensor networks (WSNs) will experience a broad high-scale deployment (millions of nodes in the national area) with multiple information sources per node, and with very specific requirements for signal processing. In parallel, the broad range deployment of WSNs facilitates the definition and execution of ambitious studies, with a large input data set and high computational complexity. These computation resources, very often heterogeneous and driven on-demand, can only be satisfied by high-performance Data Centers (DCs). The high economical and environmental impact of the energy consumption in DCs requires aggressive energy optimization policies. These policies have been already detected but not successfully proposed. In this context, this paper shows the following on-going research lines and obtained results. In the field of WSNs: energy optimization in the processing nodes from different abstraction levels, including reconfigurable application specific architectures, efficient customization of the memory hierarchy, energy-aware management of the wireless interface, and design automation for signal processing applications. In the field of DCs: energy-optimal workload assignment policies in heterogeneous DCs, resource management policies with energy consciousness, and efficient cooling mechanisms that will cooperate in the minimization of the electricity bill of the DCs that process the data provided by the WSNs.

Comparison of methods for the analysis of Phase Sensitivity Inversion Recovery Images in the Assessment of Myocardial Infarction

Métodos estadísticos para análisis de MRI PSIR

Leveraging heterogeneity for energy minimization in data centers

Energy consumption in data centers is nowadays a critical objective because of its dramatic environmental and economic impact. Over the last years, several approaches have been proposed to tackle the energy/cost optimization problem, but most of them have failed on providing an analytical model to target both the static and dynamic optimization domains for complex heterogeneous data centers. This paper proposes and solves an optimization problem for the energy-driven configuration of a heterogeneous data center. It also advances in the proposition of a new mechanism for task allocation and distribution of workload. The combination of both approaches outperforms previous published results in the field of energy minimization in heterogeneous data centers and scopes a promising area of research.

GreenDisc: a HW/SW energy optimization framework in globally distributed computation

In recent future, wireless sensor networks ({WSNs}) will experience a broad high-scale deployment (millions of nodes in the national area) with multiple information sources per node, and with very specific requirements for signal processing. In parallel, the broad range deployment of {WSNs} facilitates the definition and execution of ambitious studies, with a large input data set and high computational complexity. These computation resources, very often heterogeneous and driven on-demand, can only be satisfied by high-performance Data Centers ({DCs}). The high economical and environmental impact of the energy consumption in {DCs} requires aggressive energy optimization policies. These policies have been already detected but not successfully proposed. In this context, this paper shows the following on-going research lines and obtained results. In the field of {WSNs}: energy optimization in the processing nodes from different abstraction levels, including reconfigurable application specific architectures, efficient customization of the memory hierarchy, energy-aware management of the wireless interface, and design automation for signal processing applications. In the field of {DCs}: energy-optimal workload assignment policies in heterogeneous {DCs}, resource management policies with energy consciousness, and efficient cooling mechanisms that will cooperate in the minimization of the electricity bill of the DCs that process the data provided by the WSNs.

Estudio del comportamiento del hormigón de alta resistencia reforzado con fibras de acero frente al impacto de proyectiles

En la presente investigación se buscó estudiar el efecto de la adición de fibras metálicas como refuerzo en hormigones de alta resistencia, y en especial su comportamiento frente al impacto de proyectiles. Se efectuó el estudio sobre un hormigón de alta resistencia (HAR), analizando los aspectos mecánicos, durabilidad y trabajabilidad para su colocación en obra. Las pruebas de laboratorio se llevaron a cabo en el Laboratorio de Materiales de Construcción de la Escuela Técnica Superior de Caminos Canales y Puertos de la UPM y los ensayos balísticos en la galería de tiro cubierta del Polígono de Experiencia de Carabanchel, adscrito a la Dirección General de Infraestructura del Ministerio de la Defensa. La caracterización del HAR empleado en el estudio se centró en los aspectos de resistencias mecánicas a compresión, tracción, flexotracción, tenacidad a flexotracción, punzonamiento, retracción, fluencia, temperatura interna y resistencia al impacto de proyectiles, siempre buscando de manera primordial analizar el efecto de la adición de fibras en el hormigón de alta resistencia. El programa de ensayos balísticos comprendió la fabricación de 47 placas de hormigón de diferentes espesores, desde 5 a 40 cm., 26 de dichas placas eran de HAR con una adición de fibras metálicas de 80 kg/m3, 11 de ellas eran de HAR sin fibras y 10 de un hormigón de resistencia convencional con y sin fibras; sobre dichas placas se efectuaron diversos impactos con proyectiles de los cuatro calibres siguientes: 7.62 AP, 12.70 M8, 20 mm APDS y 25 mm APDS. Las pruebas mostraron que el HAR presenta una mayor resistencia a los impactos de proyectiles, aunque sin la adición de fibras su fragilidad es un serio inconveniente para su utilización como barrera protectora, la adición de fibras reduce considerablemente la fragmentación en la cara posterior “scabbing” y en menor medida en la cara anterior “spalling”. También se incrementa la capacidad del hormigón a la resistencia de múltiples impactos. Se efectuó un estudio de las diferentes formulas y modelos, en especial el modelo desarrollado por Moreno [60], que se vienen utilizando para el diseño de barreras protectoras de hormigón contra impacto de proyectiles, analizando su viabilidad en el caso del hormigón de alta resistencia, hormigón para el cual no fueron desarrolladas y para el que no existen bases de cálculo específicas. In this research we have tried to study the effect of adding metallic fibres as a means of reinforcing high strength concrete, and especially its behaviour when impacted upon by projectiles. The study was carried out using high strength concrete (HSC), analysing its mechanical facets, durability and malleability when used in construction. The laboratory tests took place in the Laboratorio de Materiales de Construcción of the Escuela Técnica Superior de Caminos Canales y Puertos of the Universidad Politécnica de Madrid, and the ballistic tests were carried out in the covered shooting gallery of the Polígono de Experiencias in Carabanchel (Madrid), belongs to the Departamento de Infraestructura of the Ministerio de Defensa. The aspects of the HSC studied are its mechanical strength to compression, traction, flexotraction, resilience to flexo-traction, shear strength, creep, shrinkage, internal temperature and strength to the impact of projectiles, always looking to analyse the effect of adding fibres to HSC. The ballistic testing process required the construction of 47 concrete plates of different thicknesses, from 5 to 40 cm, 26 made which HSC containing of 80 kg/m3 metallic fibres of, 11 made of HSC without fibres, and 10 made with concrete of normal strength with and without fibres. These plates were subjected to a variety of impacts by four projectile, 7.62 AP, 12.70 M8, 20 mm APDS and 25 mm APDS. The results showed that HSC has a greater resistance to the impact of projectiles, although without the addition of fibres, its fragility makes it much less suitable for use as a protective barrier. The addition of fibres reduces considerably frontal fragmentation, known as “scabbing”, and to a lesser extent causes fragmentation of the reverse side, known as “spalling”. In addition, the concrete’s capacity to resist multiple impacts is improved by its letter ductility. A study was carried out on the various formulae and models used to design protective concrete barriers impacted on by projectiles, analysing their viability in the case of HSC for which they were not developed and for which no specific calculations exist.

Organ-focused mutual information for nonrigid multimodal registration of liver CT and Gd–EOB–DTPA-enhanced MRI

Accurate detection of liver lesions is of great importance in hepatic surgery planning. Recent studies have shown that the detection rate of liver lesions is significantly higher in gadoxetic acid-enhanced magnetic resonance imaging (Gd–EOB–DTPA-enhanced MRI) than in contrast-enhanced portal-phase computed tomography (CT); however, the latter remains essential because of its high specificity, good performance in estimating liver volumes and better vessel visibility. To characterize liver lesions using both the above image modalities, we propose a multimodal nonrigid registration framework using organ-focused mutual information (OF-MI). This proposal tries to improve mutual information (MI) based registration by adding spatial information, benefiting from the availability of expert liver segmentation in clinical protocols. The incorporation of an additional information channel containing liver segmentation information was studied. A dataset of real clinical images and simulated images was used in the validation process. A Gd–EOB–DTPA-enhanced MRI simulation framework is presented. To evaluate results, warping index errors were calculated for the simulated data, and landmark-based and surface-based errors were calculated for the real data. An improvement of the registration accuracy for OF-MI as compared with MI was found for both simulated and real datasets. Statistical significance of the difference was tested and confirmed in the simulated dataset (p < 0.01).

Bio-inspired enhancement of reputation systems for intelligent environments

Providing security to the emerging field of ambient intelligence will be difficult if we rely only on existing techniques, given their dynamic and heterogeneous nature. Moreover, security demands of these systems are expected to grow, as many applications will require accurate context modeling. In this work we propose an enhancement to the reputation systems traditionally deployed for securing these systems. Different anomaly detectors are combined using the immunological paradigm to optimize reputation system performance in response to evolving security requirements. As an example, the experiments show how a combination of detectors based on unsupervised techniques (self-organizing maps and genetic algorithms) can help to significantly reduce the global response time of the reputation system. The proposed solution offers many benefits: scalability, fast response to adversarial activities, ability to detect unknown attacks, high adaptability, and high ability in detecting and confining attacks. For these reasons, we believe that our solution is capable of coping with the dynamism of ambient intelligence systems and the growing requirements of security demands.

Detecting false testimonies in reputation systems using self-organizing maps

It has been demonstrated that rating trust and reputation of individual nodes is an effective approach in distributed environments in order to improve security, support decision-making and promote node collaboration. Nevertheless, these systems are vulnerable to deliberate false or unfair testimonies. In one scenario, the attackers collude to give negative feedback on the victim in order to lower or destroy its reputation. This attack is known as bad mouthing attack. In another scenario, a number of entities agree to give positive feedback on an entity (often with adversarial intentions). This attack is known as ballot stuffing. Both attack types can significantly deteriorate the performances of the network. The existing solutions for coping with these attacks are mainly concentrated on prevention techniques. In this work, we propose a solution that detects and isolates the abovementioned attackers, impeding them in this way to further spread their malicious activity. The approach is based on detecting outliers using clustering, in this case self-organizing maps. An important advantage of this approach is that we have no restrictions on training data, and thus there is no need for any data pre-processing. Testing results demonstrate the capability of the approach in detecting both bad mouthing and ballot stuffing attack in various scenarios.