JPIP proxy server with prefetching strategies based on user-navigation model and semantic map

The efficient transmission of large resolution images and, in particular, the interactive transmission of images in a client-server scenario, is an important aspect for many applications. Among the current image compression standards, JPEG2000 excels for its interactive transmission capabilities. In general, three mechanisms are employed to optimize the transmission of images when using the JPEG2000 Interactive Protocol (JPIP): 1) packet re-sequencing at the server; 2) prefetching at the client; and 3) proxy servers along the network infrastructure. To avoid the congestion of the network, prefetching mechanisms are not commonly employed when many clients within a local area network (LAN) browse images from a remote server. Aimed to maximize the responsiveness of all the clients within a LAN, this work proposes the use of prefetching strategies at the proxy server -rather than at the clients. The main insight behind the proposed prefetching strategies is a user-navigation model and a semantic map that predict the future requests of the clients. Experimental results indicate that the introduction of these strategies into a JPIP proxy server enhances the browsing experience of the end-users notably

Sistemas de microscopía virtual: análisis y perspectivas

Microscopy has been constantly evolving since the end of the Twentieth Century, with the introduction of new resources which have improved its practice. For example, the use of the virtual microscope has reached a high level of maturity; it is a synergy among disciplines such as pathology, histology, medical informatics and image analysis. This technology has moved forward many paradigms in research, diagnosis, education and medical training. The virtual microscopy systems require the digitalization of a physical slide, using motorized microscopes, pre and post image processing, compression, transmission and visualization. This article provides an extensive analysis of each of these processes. The main characteristics of virtual microscopy are presented as well as the impact of these systems in image interpretation and in diagnostic activities.Desde finales del siglo XX la microscopía se ha venido transformando, incluyendo nuevos recursos que mejoran y perfeccionan su práctica. Entre ellos se destaca el microscopio virtual, la sinergia entre disciplinas como la patología, la histología, la informática médica y el análisis de imágenes. Esta tecnología ha cambiado muchos paradigmas en la investigación, el diagnóstico, la educación y el entrenamiento médico. Los sistemas de microscopía virtual requieren de la digitalización de una placa con el uso de microscopios robotizados, antes del procesamiento de la imagen y después de él, compresión, transmisión por la red y visualización. En este artículo se hace un análisis extenso de cada uno de estos procesos, y se presentan las principales características de los microscopios virtuales, junto con el impacto de estos sistemas en actividades de interpretación y diagnóstico

Optimized mobile thin clients through a MPEG-4 BiFS semantic remote display framework

According to the thin client computing principle, the user interface is physically separated from the application logic. In practice only a viewer component is executed on the client device, rendering the display updates received from the distant application server and capturing the user interaction. Existing remote display frameworks are not optimized to encode the complex scenes of modern applications, which are composed of objects with very diverse graphical characteristics. In order to tackle this challenge, we propose to transfer to the client, in addition to the binary encoded objects, semantic information about the characteristics of each object. Through this semantic knowledge, the client is enabled to react autonomously on user input and does not have to wait for the display update from the server. Resulting in a reduction of the interaction latency and a mitigation of the bursty remote display traffic pattern, the presented framework is of particular interest in a wireless context, where the bandwidth is limited and expensive. In this paper, we describe a generic architecture of a semantic remote display framework. Furthermore, we have developed a prototype using the MPEG-4 Binary Format for Scenes to convey the semantic information to the client. We experimentally compare the bandwidth consumption of MPEG-4 BiFS with existing, non-semantic, remote display frameworks. In a text editing scenario, we realize an average reduction of 23% of the data peaks that are observed in remote display protocol traffic

Multi-resolution graph-based representation for analysis of large histo-pathological images

La exploración de muestras histopatológicas es potencialmente una importante fuente de información para el diagnóstico de enfermedades, educación y entrenamiento médico. Convencionalmente, este tipo de muestras se observan a través de un microscopio óptico, sin embargo, recientes avances tecnológicos en el área de imagino logia han favorecido el desarrollo de la microscopía virtual, un conjunto de herramientas que permiten la navegación de versiones digitales de placas histopatológicas, también llamadas Placas Virtuales (PV). Ya que las PV son un conjunto de imágenes de campos visuales microscópicos, estas son imágenes de alta resolución. El gran tamaño de las PV representa un cuello de botella para cualquier estrategia de navegación, introduciendo considerables retardos en la presentación de la información al usuario y produciendo en consecuencia, navegaciones poco fluidas. Por esto, el desarrollo de métodos para acelerar la interacción en este tipo de aplicaciones impulsara su uso en áreas como la tele patología. Una de las aproximaciones más aceptadas respecto a este problema son las estrategias de predicción, en las cuales solo las regiones de interés son enviadas al usuario. Por tanto el reto en este tipo de aproximaciones es identificar las regiones relevantes para el patólogo, es decir aquellas que contienen significado semántico para el diagnostico. Los modelos de atención visual intentan emular la percepción visual humana, permitiendo identificar las pocas regiones de una escena que contienen la mayor cantidad de información. Sin embargo, la complejidad de las imágenes histopatológicas hace que este tipo de modelos sea insuficiente para identificar estructuras relevantes dentro de la muestra y se hace necesario utilizar nuevas fuentes de información. En este trabajo se presenta una novedosa aproximación estadística que permite construir un mapa de información relevante de la PV con el fin de permitir navegaciones fluidas en un microscopio virtual. Este trabajo utiliza como una primera aproximación a las regiones relevantes un mapa de saliencia obtenido a partir de un modelo de atención visual \bottom-up", el cual es modificado por conocimiento \top-down. Obtenido a partir de navegaciones de patólogos expertos sobre PVs. Las regiones de la PV son estructuradas en un grafo tipo árbol, de acuerdo a su nivel de relevancia, en esta estructura los nodos representan regiones espaciales de la PV y los arcos representan relaciones de inclusión entre ellas. El método presentado alcanza en promedio, una capacidad de predicción del 67 % de regiones de interés que fueron visitadas en una nueva navegación, asumiendo un caché de solo el 20 % del tamaño total de la placa virtual. Adicionalmente, con respecto a un método más simple, i. e. sin la representación del grafo, el método propuesto mejora en un 3 % la capacidad de identificación de regiones relevantes, lo cual es significativo en este contexto, ya que un porcentaje como este puede representar regiones de mega pixeles en una PV.Exploration of complete histological samples is a very important source of information for diagnosis, learning and medical training. These samples have been conventionally observed through an optical microscope, but recent advances in imaging technology have enabled the development of virtual microscopy, a set of tools that allows navigation of digitized versions of tissue samples (virtual slides or VS). Since VS are the set of several microscopic visual �elds they are high resolution images with huge storage spaces. The size of these images repre- sents a bottle-neck for any navigation strategy, introducing considerable delays in displaying information to the user, which results in non- uid navigations. Development of methodo- logies for accelerate interaction with such volume of data, represents a reinforcement of its use in real applications as telepathology. One of the most accepted methodologies regarding this problem are based on prediction policies, in which only the regions of current interest are provided to the user. Then, the challenge in these approaches is to identify relevant regions, which for VS exploration enclose semantic meaning for diagnosis. Classical visual attention models emulates the human visual perception allowing to identify relevant regions with highest quantity of information. However, complexity of histo-pathological images make insu�cient these models to identify all relevant structures in the sample, furthermore new information sources that lies the identi�cation of salient features is required. In this work is presented a novel statistical hybrid approach which enable to build up relevant informa- tion VS maps to achieve uent virtual navigation. This approach, uses as �rst relevance approximation, a saliency map obtained from a bottom-up visual attention model, which is modi�ed by a top-down relevance information obtained from actual VS explorations of expert pathologists. Image regions are organized in a graph structure according it's levels of relevance, in this structure nodes are related to spatial regions and edges represent belonging relationships between them. The method herein introduced achieve in average, a prediction capacity of 67 % of RoIs that were visited in a new navigation, assuming a cache of only 20 % of total size of VS. Additionally, with respect to a simpler method, i.e. without graph representation, graph-based method outperforms RoIs identi�cation capacity in about 3 % which is signi�cant in this context since such a percentage could represent regions of mega- pixels of a VS.Maestrí

Forward Error Correction applied to JPEG-XS codestreams

JPEG-XS offers low complexity image compression for applications with constrained but reasonable bit-rate, and low latency. Our paper explores the deployment of JPEG-XS on lossy packet networks. To preserve low latency, Forward Error Correction (FEC) is envisioned as the protection mechanism of interest. Despite the JPEG-XS codestream is not scalable in essence, we observe that the loss of a codestream fraction impacts the decoded image quality differently, depending on whether this codestream fraction corresponds to codestream headers, to coefficients significance information, or to low/high frequency data, respectively. Hence, we propose a rate-distortion optimal unequal error protection scheme that adapts the redundancy level of Reed-Solomon codes according to the rate of channel losses and the type of information protected by the code. Our experiments demonstrate that, at 5% loss rates, it reduces the Mean Squared Error by up to 92% and 65%, compared to a transmission without and with optimal but equal protection, respectively

Verbesserung der Dateiverarbeitungskette in Betriebssystemen durch Nutzung der Skalierbarkeit moderner Kompressionsverfahren

Motivated by the current challenges in the field of computerized processing of multimedia information, this work contributes to the field of research on data processing and file management within computer systems. It presents novel techniques that enhance existing file- and operating systems by utilizing the scalability of modern media formats. For this purpose, the compression formats JPEG 2000 and H.264 SVC will be presented with a focus on how they achieve scalability. An analysis of the limiting hard- and software components in a computer system for the application area is presented. In particular, the restrictions of the utilized storage-devices, data interfaces and file systems are laid out and workarounds to compensate the performance bottlenecks are depicted. According to the observation that compensating the defiles requires extra efforts, new solution statements utilizing scalable media are derived and examined, subsequently. The present work reveals new concepts for managing scalable media files comprising a new rights management as well as a use-case-optimized storage technique. The rights management allows for granting access to certain parts of a file by which the scalability of the media files can be exploited in a way that users get access to various variants depending on their access rights. The use-case-optimized storage technique increases the throughput of hard disk drives when the subsequent access pattern to the media content is known a-priori. In addition, enhancements for existing data workflows are proposed by taking advantage of scalable media. Based on the Substitution Strategy, where missing data from a scalable file is compensated, a real-time capable procedure for reading files is shown. Using this strategy, image-sequences comprising a video can be shown at a given frame rate without interruptions caused by insufficient throughput of the storage device or low-speed interfaces used to connect the storage device. Adapted caching-strategies facilitate an increase of images residing in cache compared to non-scalable-variants. Additionally, a concept called Parameterizable File-Access is introduced which allows users to request a certain variant of a scalable file directly from the file system by adding side-information to a virtual file name.Motiviert durch die aktuellen Herausforderungen im Bereich der computergestützten Bearbeitung vom Multimediadaten, leistet die vorliegende Arbeit einen Beitrag zum Forschungsgebiet der Datenverarbeitung und Dateiverwaltung innerhalb von Computersystemen durch neuartige Verfahren zur Nutzung skalierbarer Medien unter Verwendung vorhandener Datei- und Betriebssysteme. Hierzu werden die Kompressionsformate JPEG 2000 und H.264 SVC vorgestellt und gezeigt, wie die Eigenschaft der Skalierbarkeit innerhalb der verschiedenen Verfahren erreicht wird. Es folgt eine Analyse der limitierenden Hard- und Softwarekomponenten in einem Computersystem für das o.g. Einsatzgebiet. Ausgehend vom hohen Aufwand zur Kompensation der Leistungsengpässe werden anschließend neue Lösungsansätze unter Nutzung skalierbarer Medienformate abgeleitet, die nachfolgend untersucht werden. Die vorliegende Arbeit zeigt hierzu neue Konzepte zur Verwaltung skalierbarer Mediendaten, die durch ein neues Rechtemanagement sowie durch eine speicheradaptive Ablagestrategie abgedeckt werden. Das Rechtemanagement erlaubt die Vergabe von Zugriffsrechten auf verschiedene Abschnitte einer Datei, wodurch die Skalierbarkeit der Medien derart abgebildet werden kann, dass verschiedene Benutzer unterschiedliche Varianten einer Datei angezeigt bekommen. Die speicheradaptive Ablagestrategie erreicht Durchsatzsteigerungen der verwendeten Datenträger, wenn das spätere Zugriffsverhalten auf die gespeicherten Medien vorab bekannt ist. Weiter werden Verbesserungen der Verarbeitungsabläufe unter Ausnutzung skalierbarer Medien gezeigt. Auf Basis der entwickelten Substitutionsmethode zur Kompensation fehlender Daten einer skalierbaren Datei wird eine echtzeitfähige Einlesestrategie vorgestellt, die unzureichende Durchsatzraten von Speichermedien bzw. langsamen Schnittstellen derart kompensieren kann, dass eine unterbrechungsfreie Ausspielung von Bildsequenzen bei einer vorgegebenen Bildwiederholrate gewährleistet werden kann. Angepasste Cache-Strategien ermöglichen eine Steigerung der im Cache vorhaltbaren Einzelbilder im Vergleich zu nicht skalierbaren Varianten. Darüber hinaus wird das Konzept eines parametrisierbaren Dateiaufrufes eingeführt, wodurch mittels Zusatzinformationen im virtuellen Dateinamen eine gewünschte Variante einer skalierbaren Datei vom Datenspeicher angefragt werden kann

Verbesserung der Dateiverarbeitungskette in Betriebssystemen durch Nutzung der Skalierbarkeit moderner Kompressionsverfahren

Motivated by the current challenges in the field of computerized processing of multimedia information, this work contributes to the field of research on data processing and file management within computer systems. It presents novel techniques that enhance existing file- and operating systems by utilizing the scalability of modern media formats. For this purpose, the compression formats JPEG 2000 and H.264 SVC will be presented with a focus on how they achieve scalability. An analysis of the limiting hard- and software components in a computer system for the application area is presented. In particular, the restrictions of the utilized storage-devices, data interfaces and file systems are laid out and workarounds to compensate the performance bottlenecks are depicted. According to the observation that compensating the defiles requires extra efforts, new solution statements utilizing scalable media are derived and examined, subsequently. The present work reveals new concepts for managing scalable media files comprising a new rights management as well as a use-case-optimized storage technique. The rights management allows for granting access to certain parts of a file by which the scalability of the media files can be exploited in a way that users get access to various variants depending on their access rights. The use-case-optimized storage technique increases the throughput of hard disk drives when the subsequent access pattern to the media content is known a-priori. In addition, enhancements for existing data workflows are proposed by taking advantage of scalable media. Based on the Substitution Strategy, where missing data from a scalable file is compensated, a real-time capable procedure for reading files is shown. Using this strategy, image-sequences comprising a video can be shown at a given frame rate without interruptions caused by insufficient throughput of the storage device or low-speed interfaces used to connect the storage device. Adapted caching-strategies facilitate an increase of images residing in cache compared to non-scalable-variants. Additionally, a concept called Parameterizable File-Access is introduced which allows users to request a certain variant of a scalable file directly from the file system by adding side-information to a virtual file name.Motiviert durch die aktuellen Herausforderungen im Bereich der computergestützten Bearbeitung vom Multimediadaten, leistet die vorliegende Arbeit einen Beitrag zum Forschungsgebiet der Datenverarbeitung und Dateiverwaltung innerhalb von Computersystemen durch neuartige Verfahren zur Nutzung skalierbarer Medien unter Verwendung vorhandener Datei- und Betriebssysteme. Hierzu werden die Kompressionsformate JPEG 2000 und H.264 SVC vorgestellt und gezeigt, wie die Eigenschaft der Skalierbarkeit innerhalb der verschiedenen Verfahren erreicht wird. Es folgt eine Analyse der limitierenden Hard- und Softwarekomponenten in einem Computersystem für das o.g. Einsatzgebiet. Ausgehend vom hohen Aufwand zur Kompensation der Leistungsengpässe werden anschließend neue Lösungsansätze unter Nutzung skalierbarer Medienformate abgeleitet, die nachfolgend untersucht werden. Die vorliegende Arbeit zeigt hierzu neue Konzepte zur Verwaltung skalierbarer Mediendaten, die durch ein neues Rechtemanagement sowie durch eine speicheradaptive Ablagestrategie abgedeckt werden. Das Rechtemanagement erlaubt die Vergabe von Zugriffsrechten auf verschiedene Abschnitte einer Datei, wodurch die Skalierbarkeit der Medien derart abgebildet werden kann, dass verschiedene Benutzer unterschiedliche Varianten einer Datei angezeigt bekommen. Die speicheradaptive Ablagestrategie erreicht Durchsatzsteigerungen der verwendeten Datenträger, wenn das spätere Zugriffsverhalten auf die gespeicherten Medien vorab bekannt ist. Weiter werden Verbesserungen der Verarbeitungsabläufe unter Ausnutzung skalierbarer Medien gezeigt. Auf Basis der entwickelten Substitutionsmethode zur Kompensation fehlender Daten einer skalierbaren Datei wird eine echtzeitfähige Einlesestrategie vorgestellt, die unzureichende Durchsatzraten von Speichermedien bzw. langsamen Schnittstellen derart kompensieren kann, dass eine unterbrechungsfreie Ausspielung von Bildsequenzen bei einer vorgegebenen Bildwiederholrate gewährleistet werden kann. Angepasste Cache-Strategien ermöglichen eine Steigerung der im Cache vorhaltbaren Einzelbilder im Vergleich zu nicht skalierbaren Varianten. Darüber hinaus wird das Konzept eines parametrisierbaren Dateiaufrufes eingeführt, wodurch mittels Zusatzinformationen im virtuellen Dateinamen eine gewünschte Variante einer skalierbaren Datei vom Datenspeicher angefragt werden kann

Métodos computacionais para otimização de desempenho em redes de imagem médica

Over the last few years, the medical imaging has consolidated its position as a major mean of clinical diagnosis. The amount of data generated by the medical imaging practice is increasing tremendously. As a result, repositories are turning into rich databanks of semi-structured data related to patients, ailments, equipment and other stakeholders involved in the medical imaging panorama. The exploration of these repositories for secondary uses of data promises to elevate the quality standards and efficiency of the medical practice. However, supporting these advanced usage scenarios in traditional institutional systems raises many technical challenges that are yet to be overcome. Moreover, the reported poor performance of standard protocols opened doors to the general usage of proprietary solutions, compromising the interoperability necessary for supporting these advanced scenarios. This thesis has researched, developed, and now proposes a series of computer methods and architectures intended to maximize the performance of multi-institutional medical imaging environments. The methods are intended to improve the performance of standard protocols for medical imaging content discovery and retrieval. The main goal is to use them to increase the acceptance of vendor-neutral solutions through the improvement of their performance. Moreover, it intends to promote the adoption of such standard technologies in advanced scenarios that are still a mirage nowadays, such as clinical research or data analytics directly on top of live institutional repositories. Finally, these achievements will facilitate the cooperation between healthcare institutions and researchers, resulting in an increment of healthcare quality and institutional efficiency.As diversas modalidades de imagem médica têm vindo a consolidar a sua posição dominante como meio complementar de diagnóstico. O número de procedimentos realizados e o volume de dados gerados aumentou significativamente nos últimos anos, colocando pressão nas redes e sistemas que permitem o arquivo e distribuição destes estudos. Os repositórios de estudos imagiológicos são fontes de dados ricas contendo dados semiestruturados relacionados com pacientes, patologias, procedimentos e equipamentos. A exploração destes repositórios para fins de investigação e inteligência empresarial, tem potencial para melhorar os padrões de qualidade e eficiência da prática clínica. No entanto, estes cenários avançados são difíceis de acomodar na realidade atual dos sistemas e redes institucionais. O pobre desempenho de alguns protocolos standard usados em ambiente de produção, conduziu ao uso de soluções proprietárias nestes nichos aplicacionais, limitando a interoperabilidade de sistemas e a integração de fontes de dados. Este doutoramento investigou, desenvolveu e propõe um conjunto de métodos computacionais cujo objetivo é maximizar o desempenho das atuais redes de imagem médica em serviços de pesquisa e recuperação de conteúdos, promovendo a sua utilização em ambientes de elevados requisitos aplicacionais. As propostas foram instanciadas sobre uma plataforma de código aberto e espera-se que ajudem a promover o seu uso generalizado como solução vendor-neutral. As metodologias foram ainda instanciadas e validadas em cenários de uso avançado. Finalmente, é expectável que o trabalho desenvolvido possa facilitar a investigação em ambiente hospitalar de produção, promovendo, desta forma, um aumento da qualidade e eficiência dos serviços.Programa Doutoral em Engenharia Informátic

Modeling and acceleration of content delivery in world wide web

Ph.DDOCTOR OF PHILOSOPH

Efficient interaction with large medical imaging databases

Everyday, a wide quantity of hospitals and medical centers around the world are producing large amounts of imaging content to support clinical decisions, medical research, and education. With the current trend towards Evidence-based medicine, there is an increasing need of strategies that allow pathologists to properly interact with the valuable information such imaging repositories host and extract relevant content for supporting decision making. Unfortunately, current systems are very limited at providing access to content and extracting information from it because of different semantic and computational challenges. This thesis presents a whole pipeline, comprising 3 building blocks, that aims to to improve the way pathologists and systems interact. The first building block consists in an adaptable strategy oriented to ease the access and visualization of histopathology imaging content. The second block explores the extraction of relevant information from such imaging content by exploiting low- and mid-level information obtained from from morphology and architecture of cell nuclei. The third block aims to integrate high-level information from the expert in the process of identifying relevant information in the imaging content. This final block not only attempts to deal with the semantic gap but also to present an alternative to manual annotation, a time consuming and prone-to-error task. Different experiments were carried out and demonstrated that the introduced pipeline not only allows pathologist to navigate and visualize images but also to extract diagnostic and prognostic information that potentially could support clinical decisions.Resumen: Diariamente, gran cantidad de hospitales y centros médicos de todo el mundo producen grandes cantidades de imágenes diagnósticas para respaldar decisiones clínicas y apoyar labores de investigación y educación. Con la tendencia actual hacia la medicina basada en evidencia, existe una creciente necesidad de estrategias que permitan a los médicos patólogos interactuar adecuadamente con la información que albergan dichos repositorios de imágenes y extraer contenido relevante que pueda ser empleado para respaldar la toma de decisiones. Desafortunadamente, los sistemas actuales son muy limitados en cuanto al acceso y extracción de contenido de las imágenes debido a diferentes desafíos semánticos y computacionales. Esta tesis presenta un marco de trabajo completo para patología, el cual se compone de 3 bloques y tiene como objetivo mejorar la forma en que interactúan los patólogos y los sistemas. El primer bloque de construcción consiste en una estrategia adaptable orientada a facilitar el acceso y la visualización del contenido de imágenes histopatológicas. El segundo bloque explora la extracción de información relevante de las imágenes mediante la explotación de información de características visuales y estructurales de la morfología y la arquitectura de los núcleos celulares. El tercer bloque apunta a integrar información de alto nivel del experto en el proceso de identificación de información relevante en las imágenes. Este bloque final no solo intenta lidiar con la brecha semántica, sino que también presenta una alternativa a la anotación manual, una tarea que demanda mucho tiempo y es propensa a errores. Se llevaron a cabo diferentes experimentos que demostraron que el marco de trabajo presentado no solo permite que el patólogo navegue y visualice imágenes, sino que también extraiga información de diagnóstico y pronóstico que potencialmente podría respaldar decisiones clínicas.Doctorad