ImageJ2: ImageJ for the next generation of scientific image data

ImageJ is an image analysis program extensively used in the biological sciences and beyond. Due to its ease of use, recordable macro language, and extensible plug-in architecture, ImageJ enjoys contributions from non-programmers, amateur programmers, and professional developers alike. Enabling such a diversity of contributors has resulted in a large community that spans the biological and physical sciences. However, a rapidly growing user base, diverging plugin suites, and technical limitations have revealed a clear need for a concerted software engineering effort to support emerging imaging paradigms, to ensure the software's ability to handle the requirements of modern science. Due to these new and emerging challenges in scientific imaging, ImageJ is at a critical development crossroads. We present ImageJ2, a total redesign of ImageJ offering a host of new functionality. It separates concerns, fully decoupling the data model from the user interface. It emphasizes integration with external applications to maximize interoperability. Its robust new plugin framework allows everything from image formats, to scripting languages, to visualization to be extended by the community. The redesigned data model supports arbitrarily large, N-dimensional datasets, which are increasingly common in modern image acquisition. Despite the scope of these changes, backwards compatibility is maintained such that this new functionality can be seamlessly integrated with the classic ImageJ interface, allowing users and developers to migrate to these new methods at their own pace. ImageJ2 provides a framework engineered for flexibility, intended to support these requirements as well as accommodate future needs

Exploring the Use of Virtual Worlds as a Scientific Research Platform: The Meta-Institute for Computational Astrophysics (MICA)

We describe the Meta-Institute for Computational Astrophysics (MICA), the first professional scientific organization based exclusively in virtual worlds (VWs). The goals of MICA are to explore the utility of the emerging VR and VWs technologies for scientific and scholarly work in general, and to facilitate and accelerate their adoption by the scientific research community. MICA itself is an experiment in academic and scientific practices enabled by the immersive VR technologies. We describe the current and planned activities and research directions of MICA, and offer some thoughts as to what the future developments in this arena may be.Comment: 15 pages, to appear in the refereed proceedings of "Facets of Virtual Environments" (FaVE 2009), eds. F. Lehmann-Grube, J. Sablating, et al., ICST Lecture Notes Ser., Berlin: Springer Verlag (2009); version with full resolution color figures is available at http://www.mica-vw.org/wiki/index.php/Publication

Analysis of Visualisation and Interaction Tools Authors

This document provides an in-depth analysis of visualization and interaction tools employed in the context of Virtual Museum. This analysis is required to identify and design the tools and the different components that will be part of the Common Implementation Framework (CIF). The CIF will be the base of the web-based services and tools to support the development of Virtual Museums with particular attention to online Virtual Museum.The main goal is to provide to the stakeholders and developers an useful platform to support and help them in the development of their projects, despite the nature of the project itself. The design of the Common Implementation Framework (CIF) is based on an analysis of the typical workflow ofthe V-MUST partners and their perceived limitations of current technologies. This document is based also on the results of the V-MUST technical questionnaire (presented in the Deliverable 4.1). Based on these two source of information, we have selected some important tools (mainly visualization tools) and services and we elaborate some first guidelines and ideas for the design and development of the CIF, that shall provide a technological foundation for the V-MUST Platform, together with the V-MUST repository/repositories and the additional services defined in the WP4. Two state of the art reports, one about user interface design and another one about visualization technologies have been also provided in this document

Big Data Analytics for Earth Sciences: the EarthServer approach

Big Data Analytics is an emerging field since massive storage and computing capabilities have been made available by advanced e-infrastructures. Earth and Environmental sciences are likely to benefit from Big Data Analytics techniques supporting the processing of the large number of Earth Observation datasets currently acquired and generated through observations and simulations. However, Earth Science data and applications present specificities in terms of relevance of the geospatial information, wide heterogeneity of data models and formats, and complexity of processing. Therefore, Big Earth Data Analytics requires specifically tailored techniques and tools. The EarthServer Big Earth Data Analytics engine offers a solution for coverage-type datasets, built around a high performance array database technology, and the adoption and enhancement of standards for service interaction (OGC WCS and WCPS). The EarthServer solution, led by the collection of requirements from scientific communities and international initiatives, provides a holistic approach that ranges from query languages and scalability up to mobile access and visualization. The result is demonstrated and validated through the development of lighthouse applications in the Marine, Geology, Atmospheric, Planetary and Cryospheric science domains

Declarative modeling based on knowledge

Les nouvelles technologies de l'image 3D permettent la création de mondes virtuels et des créatures qui les peuplent avec un tel niveau de détails, que pour les effets spéciaux de cinéma, il est difficile de distinguer les éléments sont générés par ordinateur. Cependant, cette technologie est dans les mains habiles de designers, artistes et programmeurs, pour lesquels il faut des semaines à plusieurs années pour se former aux outils et obtenir ces résultats. La Modélisation Déclarative est une méthode qui permet de créer des modèles en fournissant les propriétés donnant la description des composants du modèle. Appliquée à l’infographie, la modélisation déclarative est utilisée pour générer le monde virtuel, en déterminant le contexte nécessaire à l'animation et à la conception de la scène, en calculant la position de chaque objet relativement aux relations spatiales, et en générant le rendu de la scène, utilisé par une système d'animation et de visualisation. Ce mémoire présente les travaux de recherche consacrés à l'utilisation de la modélisation déclarative pour créer des environnements virtuels, en tirant partie des connaissances sur le contexte de la scène. Les connaissances sont utilisées afin de faciliter la tâche de description, en automatisant ce qui peut être déduit, comme les usages et les fonctionnalités habituelles. Elles sont également fondamentales pour que le résultat produit corresponde le mieux possible à ce qui est attendu par le concepteur à partir de la description fournie. Les connaissances sont enfin nécessaires pour faciliter la transition entre le modèle de données et l'architecture qui aura la charge d'animer et de faire évoluer la scène.Modern technology has allowed the creation and presentation or VirtualWorlds and creatures with such a high level of detail, that when used in movies, sometimes it is difficult to tell which elements arecomputer-generated and which not. Also, video-games had reached a level close to photographicrealism. However, such technology is at the hands of skillful designer, artists, and programmers, for whom ittakes from weeks to years to complete these results.Declarative modeling is a method which allows to create models specifying just a few properties for the model’s components. Applied to VW creation, declarative modeling can be used to construct theVW, establishing the layout for the objects, generating the necessary context to provide animation and scene design, and generate the outputs used by a visualization/animation system.This document present a research devoted to explore the use of declarative modeling to create VirtualEnvironments, using knowledge exploitation to support the process and ease the transition from the data model to an underlaying architecture which take the task of animating and evolving the scene