42 research outputs found

    New algorithms for the analysis of live-cell images acquired in phase contrast microscopy

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    La détection et la caractérisation automatisée des cellules constituent un enjeu important dans de nombreux domaines de recherche tels que la cicatrisation, le développement de l'embryon et des cellules souches, l’immunologie, l’oncologie, l'ingénierie tissulaire et la découverte de nouveaux médicaments. Étudier le comportement cellulaire in vitro par imagerie des cellules vivantes et par le criblage à haut débit implique des milliers d'images et de vastes quantités de données. Des outils d'analyse automatisés reposant sur la vision numérique et les méthodes non-intrusives telles que la microscopie à contraste de phase (PCM) sont nécessaires. Comme les images PCM sont difficiles à analyser en raison du halo lumineux entourant les cellules et de la difficulté à distinguer les cellules individuelles, le but de ce projet était de développer des algorithmes de traitement d'image PCM dans Matlab® afin d’en tirer de l’information reliée à la morphologie cellulaire de manière automatisée. Pour développer ces algorithmes, des séries d’images de myoblastes acquises en PCM ont été générées, en faisant croître les cellules dans un milieu avec sérum bovin (SSM) ou dans un milieu sans sérum (SFM) sur plusieurs passages. La surface recouverte par les cellules a été estimée en utilisant un filtre de plage de valeurs, un seuil et une taille minimale de coupe afin d'examiner la cinétique de croissance cellulaire. Les résultats ont montré que les cellules avaient des taux de croissance similaires pour les deux milieux de culture, mais que celui-ci diminue de façon linéaire avec le nombre de passages. La méthode de transformée par ondelette continue combinée à l’analyse d'image multivariée (UWT-MIA) a été élaborée afin d’estimer la distribution de caractéristiques morphologiques des cellules (axe majeur, axe mineur, orientation et rondeur). Une analyse multivariée réalisée sur l’ensemble de la base de données (environ 1 million d’images PCM) a montré d'une manière quantitative que les myoblastes cultivés dans le milieu SFM étaient plus allongés et plus petits que ceux cultivés dans le milieu SSM. Les algorithmes développés grâce à ce projet pourraient être utilisés sur d'autres phénotypes cellulaires pour des applications de criblage à haut débit et de contrôle de cultures cellulaires.Automated cell detection and characterization is important in many research fields such as wound healing, embryo development, immune system studies, cancer research, parasite spreading, tissue engineering, stem cell research and drug research and testing. Studying in vitro cellular behavior via live-cell imaging and high-throughput screening involves thousands of images and vast amounts of data, and automated analysis tools relying on machine vision methods and non-intrusive methods such as phase contrast microscopy (PCM) are a necessity. However, there are still some challenges to overcome, since PCM images are difficult to analyze because of the bright halo surrounding the cells and blurry cell-cell boundaries when they are touching. The goal of this project was to develop image processing algorithms to analyze PCM images in an automated fashion, capable of processing large datasets of images to extract information related to cellular viability and morphology. To develop these algorithms, a large dataset of myoblasts images acquired in live-cell imaging (in PCM) was created, growing the cells in either a serum-supplemented (SSM) or a serum-free (SFM) medium over several passages. As a result, algorithms capable of computing the cell-covered surface and cellular morphological features were programmed in Matlab®. The cell-covered surface was estimated using a range filter, a threshold and a minimum cut size in order to look at the cellular growth kinetics. Results showed that the cells were growing at similar paces for both media, but their growth rate was decreasing linearly with passage number. The undecimated wavelet transform multivariate image analysis (UWT-MIA) method was developed, and was used to estimate cellular morphological features distributions (major axis, minor axis, orientation and roundness distributions) on a very large PCM image dataset using the Gabor continuous wavelet transform. Multivariate data analysis performed on the whole database (around 1 million PCM images) showed in a quantitative manner that myoblasts grown in SFM were more elongated and smaller than cells grown in SSM. The algorithms developed through this project could be used in the future on other cellular phenotypes for high-throughput screening and cell culture control applications

    COSPO/CENDI Industry Day Conference

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    The conference's objective was to provide a forum where government information managers and industry information technology experts could have an open exchange and discuss their respective needs and compare them to the available, or soon to be available, solutions. Technical summaries and points of contact are provided for the following sessions: secure products, protocols, and encryption; information providers; electronic document management and publishing; information indexing, discovery, and retrieval (IIDR); automated language translators; IIDR - natural language capabilities; IIDR - advanced technologies; IIDR - distributed heterogeneous and large database support; and communications - speed, bandwidth, and wireless

    Skill-based reconfiguration of industrial mobile robots

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    Caused by a rising mass customisation and the high variety of equipment versions, the exibility of manufacturing systems in car productions has to be increased. In addition to a exible handling of production load changes or hardware breakdowns that are established research areas in literature, this thesis presents a skill-based recon guration mechanism for industrial mobile robots to enhance functional recon gurability. The proposed holonic multi-agent system is able to react to functional process changes while missing functionalities are created by self-organisation. Applied to a mobile commissioning system that is provided by AUDI AG, the suggested mechanism is validated in a real-world environment including the on-line veri cation of the recon gured robot functionality in a Validity Check. The present thesis includes an original contribution in three aspects: First, a recon - guration mechanism is presented that reacts in a self-organised way to functional process changes. The application layer of a hardware system converts a semantic description into functional requirements for a new robot skill. The result of this mechanism is the on-line integration of a new functionality into the running process. Second, the proposed system allows maintaining the productivity of the running process and exibly changing the robot hardware through provision of a hardware-abstraction layer. An encapsulated Recon guration Holon dynamically includes the actual con guration each time a recon guration is started. This allows reacting to changed environment settings. As the resulting agent that contains the new functionality, is identical in shape and behaviour to the existing skills, its integration into the running process is conducted without a considerable loss of productivity. Third, the suggested mechanism is composed of a novel agent design that allows implementing self-organisation during the encapsulated recon guration and dependability for standard process executions. The selective assignment of behaviour-based and cognitive agents is the basis for the exibility and e ectiveness of the proposed recon guration mechanism

    Coalition based approach for shop floor agility – a multiagent approach

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    Dissertation submitted for a PhD degree in Electrical Engineering, speciality of Robotics and Integrated Manufacturing from the Universidade Nova de Lisboa, Faculdade de Ciências e TecnologiaThis thesis addresses the problem of shop floor agility. In order to cope with the disturbances and uncertainties that characterise the current business scenarios faced by manufacturing companies, the capability of their shop floors needs to be improved quickly, such that these shop floors may be adapted, changed or become easily modifiable (shop floor reengineering). One of the critical elements in any shop floor reengineering process is the way the control/supervision architecture is changed or modified to accommodate for the new processes and equipment. This thesis, therefore, proposes an architecture to support the fast adaptation or changes in the control/supervision architecture. This architecture postulates that manufacturing systems are no more than compositions of modularised manufacturing components whose interactions when aggregated are governed by contractual mechanisms that favour configuration over reprogramming. A multiagent based reference architecture called Coalition Based Approach for Shop floor Agility – CoBASA, was created to support fast adaptation and changes of shop floor control architectures with minimal effort. The coalitions are composed of agentified manufacturing components (modules), whose relationships within the coalitions are governed by contracts that are configured whenever a coalition is established. Creating and changing a coalition do not involve programming effort because it only requires changes to the contract that regulates it

    An agile and adaptive holonic architecture for manufacturing control

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    Tese de doutoramento. Engenharia Electrotécnica e de Computadores. 2004. Faculdade de Engenharia. Universidade do Port

    Organization based multiagent architecture for distributed environments

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    [EN]Distributed environments represent a complex field in which applied solutions should be flexible and include significant adaptation capabilities. These environments are related to problems where multiple users and devices may interact, and where simple and local solutions could possibly generate good results, but may not be effective with regards to use and interaction. There are many techniques that can be employed to face this kind of problems, from CORBA to multi-agent systems, passing by web-services and SOA, among others. All those methodologies have their advantages and disadvantages that are properly analyzed in this documents, to finally explain the new architecture presented as a solution for distributed environment problems. The new architecture for solving complex solutions in distributed environments presented here is called OBaMADE: Organization Based Multiagent Architecture for Distributed Environments. It is a multiagent architecture based on the organizations of agents paradigm, where the agents in the architecture are structured into organizations to improve their organizational capabilities. The reasoning power of the architecture is based on the Case-Based Reasoning methology, being implemented in a internal organization that uses agents to create services to solve the external request made by the users. The OBaMADE architecture has been successfully applied to two different case studies where its prediction capabilities have been properly checked. Those case studies have showed optimistic results and, being complex systems, have demonstrated the abstraction and generalizations capabilities of the architecture. Nevertheless OBaMADE is intended to be able to solve much other kind of problems in distributed environments scenarios. It should be applied to other varieties of situations and to other knowledge fields to fully develop its potencial.[ES]Los entornos distribuidos representan un campo de conocimiento complejo en el que las soluciones a aplicar deben ser flexibles y deben contar con gran capacidad de adaptación. Este tipo de entornos está normalmente relacionado con problemas donde varios usuarios y dispositivos entran en juego. Para solucionar dichos problemas, pueden utilizarse sistemas locales que, aunque ofrezcan buenos resultados en términos de calidad de los mismos, no son tan efectivos en cuanto a la interacción y posibilidades de uso. Existen múltiples técnicas que pueden ser empleadas para resolver este tipo de problemas, desde CORBA a sistemas multiagente, pasando por servicios web y SOA, entre otros. Todas estas mitologías tienen sus ventajas e inconvenientes, que se analizan en este documento, para explicar, finalmente, la nueva arquitectura presentada como una solución para los problemas generados en entornos distribuidos. La nueva arquitectura aquí se llama OBaMADE, que es el acrónimo del inglés Organization Based Multiagent Architecture for Distributed Environments (Arquitectura Multiagente Basada en Organizaciones para Entornos Distribuidos). Se trata de una arquitectura multiagente basasa en el paradigma de las organizaciones de agente, donde los agentes que forman parte de la arquitectura se estructuran en organizaciones para mejorar sus capacidades organizativas. La capacidad de razonamiento de la arquitectura está basada en la metodología de razonamiento basado en casos, que se ha implementado en una de las organizaciones internas de la arquitectura por medio de agentes que crean servicios que responden a las solicitudes externas de los usuarios. La arquitectura OBaMADE se ha aplicado de forma exitosa a dos casos de estudio diferentes, en los que se han demostrado sus capacidades predictivas. Aplicando OBaMADE a estos casos de estudio se han obtenido resultados esperanzadores y, al ser sistemas complejos, se han demostrado las capacidades tanto de abstracción como de generalización de la arquitectura presentada. Sin embargo, esta arquitectura está diseñada para poder ser aplicada a más tipo de problemas de entornos distribuidos. Debe ser aplicada a más variadas situaciones y a otros campos de conocimiento para desarrollar completamente el potencial de esta arquitectura

    KOLAM : human computer interfaces fro visual analytics in big data imagery

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    In the present day, we are faced with a deluge of disparate and dynamic information from multiple heterogeneous sources. Among these are the big data imagery datasets that are rapidly being generated via mature acquisition methods in the geospatial, surveillance (specifically, Wide Area Motion Imagery or WAMI) and biomedical domains. The need to interactively visualize these imagery datasets by using multiple types of views (as needed) into the data is common to these domains. Furthermore, researchers in each domain have additional needs: users of WAMI datasets also need to interactively track objects of interest using algorithms of their choice, visualize the resulting object trajectories and interactively edit these results as needed. While software tools that fulfill each of these requirements individually are available and well-used at present, there is still a need for tools that can combine the desired aspects of visualization, human computer interaction (HCI), data analysis, data management, and (geo-)spatial and temporal data processing into a single flexible and extensible system. KOLAM is an open, cross-platform, interoperable, scalable and extensible framework for visualization and analysis that we have developed to fulfil the above needs. The novel contributions in this thesis are the following: 1) Spatio-temporal caching for animating both giga-pixel and Full Motion Video (FMV) imagery, 2) Human computer interfaces purposefully designed to accommodate big data visualization, 3) Human-in-the-loop interactive video object tracking - ground-truthing of moving objects in wide area imagery using algorithm assisted human-in-the-loop coupled tracking, 4) Coordinated visualization using stacked layers, side-by-side layers/video sub-windows and embedded imagery, 5) Efficient one-click manual tracking, editing and data management of trajectories, 6) Efficient labeling of image segmentation regions and passing these results to desired modules, 7) Visualization of image processing results generated by non-interactive operators using layers, 8) Extension of interactive imagery and trajectory visualization to multi-monitor wall display environments, 9) Geospatial applications: Providing rapid roam, zoom and hyper-jump spatial operations, interactive blending, colormap and histogram enhancement, spherical projection and terrain maps, 10) Biomedical applications: Visualization and target tracking of cell motility in time-lapse cell imagery, collecting ground-truth from experts on whole-slide imagery (WSI) for developing histopathology analytic algorithms and computer-aided diagnosis for cancer grading, and easy-to-use tissue annotation features.Includes bibliographical reference
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