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

An open source virtual globe rendering engine for 3D applications: NASA World Wind

Background NASA World Wind is an open source application-programming interface for developing geographic information systems based on a virtual globe rendering engine representing a planet. NASA World Wind provides the ideal environment for scientific data, their analysis, visual representation and interaction with users, in a single platform, which can be deployed both as a Java desktop application (NASA World Wind) or a JavaScript web application (ESA-NASA Web World Wind). Results We give here an overview of the project, reporting details regarding current development direction, with state of the art examples. The European Space Agency is now partnering with NASA on development of the "ESA-NASA Web World Wind"; this high degree of interest from other agencies will boost future project productivity. Conclusions With this contribution, we want to increase awareness of NASA World Wind as a unique opportunity to foster collaboration between scientists, developers and other stakeholders, enriching knowledge of our Earth’s complexity

Configurable nD-visualization for complex Building Information Models

With the ongoing development of building information modelling (BIM) towards a comprehensive coverage of all construction project information in a semantically explicit way, visual representations became decoupled from the building information models. While traditional construction drawings implicitly contained the visual representation besides the information, nowadays they are generated on the fly, hard-coded in software applications dedicated to other tasks such as analysis, simulation, structural design or communication. Due to the abstract nature of information models and the increasing amount of digital information captured during construction projects, visual representations are essential for humans in order to access the information, to understand it, and to engage with it. At the same time digital media open up the new field of interactive visualizations. The full potential of BIM can only be unlocked with customized task-specific visualizations, with engineers and architects actively involved in the design and development process of these visualizations. The visualizations must be reusable and reliably reproducible during communication processes. Further, to support creative problem solving, it must be possible to modify and refine them. This thesis aims at reconnecting building information models and their visual representations: on a theoretic level, on the level of methods and in terms of tool support. First, the research seeks to improve the knowledge about visualization generation in conjunction with current BIM developments such as the multimodel. The approach is based on the reference model of the visualization pipeline and addresses structural as well as quantitative aspects of the visualization generation. Second, based on the theoretic foundation, a method is derived to construct visual representations from given visualization specifications. To this end, the idea of a domain-specific language (DSL) is employed. Finally, a software prototype proofs the concept. Using the visualization framework, visual representations can be generated from a specific building information model and a specific visualization description.Mit der fortschreitenden Entwicklung des Building Information Modelling (BIM) hin zu einer umfassenden Erfassung aller Bauprojektinformationen in einer semantisch expliziten Weise werden Visualisierungen von den Gebäudeinformationen entkoppelt. Während traditionelle Architektur- und Bauzeichnungen die visuellen Reprä̈sentationen implizit als Träger der Informationen enthalten, werden sie heute on-the-fly generiert. Die Details ihrer Generierung sind festgeschrieben in Softwareanwendungen, welche eigentlich für andere Aufgaben wie Analyse, Simulation, Entwurf oder Kommunikation ausgelegt sind. Angesichts der abstrakten Natur von Informationsmodellen und der steigenden Menge digitaler Informationen, die im Verlauf von Bauprojekten erfasst werden, sind visuelle Repräsentationen essentiell, um sich die Information erschließen, sie verstehen, durchdringen und mit ihnen arbeiten zu können. Gleichzeitig entwickelt sich durch die digitalen Medien eine neues Feld der interaktiven Visualisierungen. Das volle Potential von BIM kann nur mit angepassten aufgabenspezifischen Visualisierungen erschlossen werden, bei denen Ingenieur*innen und Architekt*innen aktiv in den Entwurf und die Entwicklung dieser Visualisierungen einbezogen werden. Die Visualisierungen müssen wiederverwendbar sein und in Kommunikationsprozessen zuverlässig reproduziert werden können. Außerdem muss es möglich sein, Visualisierungen zu modifizieren und neu zu definieren, um das kreative Problemlösen zu unterstützen. Die vorliegende Arbeit zielt darauf ab, Gebäudemodelle und ihre visuellen Repräsentationen wieder zu verbinden: auf der theoretischen Ebene, auf der Ebene der Methoden und hinsichtlich der unterstützenden Werkzeuge. Auf der theoretischen Ebene trägt die Arbeit zunächst dazu bei, das Wissen um die Erstellung von Visualisierungen im Kontext von Bauprojekten zu erweitern. Der verfolgte Ansatz basiert auf dem Referenzmodell der Visualisierungspipeline und geht dabei sowohl auf strukturelle als auch auf quantitative Aspekte des Visualisierungsprozesses ein. Zweitens wird eine Methode entwickelt, die visuelle Repräsentationen auf Basis gegebener Visualisierungsspezifikationen generieren kann. Schließlich belegt ein Softwareprototyp die Realisierbarkeit des Konzepts. Mit dem entwickelten Framework können visuelle Repräsentationen aus jeweils einem spezifischen Gebäudemodell und einer spezifischen Visualisierungsbeschreibung generiert werden

The INCF Digital Atlasing Program: Report on Digital Atlasing Standards in the Rodent Brain

The goal of the INCF Digital Atlasing Program is to provide the vision and direction necessary to make the rapidly growing collection of multidimensional data of the rodent brain (images, gene expression, etc.) widely accessible and usable to the international research community. This Digital Brain Atlasing Standards Task Force was formed in May 2008 to investigate the state of rodent brain digital atlasing, and formulate standards, guidelines, and policy recommendations.

Our first objective has been the preparation of a detailed document that includes the vision and specific description of an infrastructure, systems and methods capable of serving the scientific goals of the community, as well as practical issues for achieving
the goals. This report builds on the 1st INCF Workshop on Mouse and Rat Brain Digital Atlasing Systems (Boline et al., 2007, _Nature Preceedings_, doi:10.1038/npre.2007.1046.1) and includes a more detailed analysis of both the current state and desired state of digital atlasing along with specific recommendations for achieving these goals

The state of the art of medical imaging technology: from creation to archive and back.

Medical imaging has learnt itself well into modern medicine and revolutionized medical industry in the last 30 years. Stemming from the discovery of X-ray by Nobel laureate Wilhelm Roentgen, radiology was born, leading to the creation of large quantities of digital images as opposed to film-based medium. While this rich supply of images provides immeasurable information that would otherwise not be possible to obtain, medical images pose great challenges in archiving them safe from corrupted, lost and misuse, retrievable from databases of huge sizes with varying forms of metadata, and reusable when new tools for data mining and new media for data storing become available. This paper provides a summative account on the creation of medical imaging tomography, the development of image archiving systems and the innovation from the existing acquired image data pools. The focus of this paper is on content-based image retrieval (CBIR), in particular, for 3D images, which is exemplified by our developed online e-learning system, MIRAGE, home to a repository of medical images with variety of domains and different dimensions. In terms of novelties, the facilities of CBIR for 3D images coupled with image annotation in a fully automatic fashion have been developed and implemented in the system, resonating with future versatile, flexible and sustainable medical image databases that can reap new innovations

The State of the Art of Medical Imaging Technology: from Creation to Archive and Back

Medical imaging has learnt itself well into modern medicine and revolutionized medical industry in the last 30 years. Stemming from the discovery of X-ray by Nobel laureate Wilhelm Roentgen, radiology was born, leading to the creation of large quantities of digital images as opposed to film-based medium. While this rich supply of images provides immeasurable information that would otherwise not be possible to obtain, medical images pose great challenges in archiving them safe from corrupted, lost and misuse, retrievable from databases of huge sizes with varying forms of metadata, and reusable when new tools for data mining and new media for data storing become available. This paper provides a summative account on the creation of medical imaging tomography, the development of image archiving systems and the innovation from the existing acquired image data pools. The focus of this paper is on content-based image retrieval (CBIR), in particular, for 3D images, which is exemplified by our developed online e-learning system, MIRAGE, home to a repository of medical images with variety of domains and different dimensions. In terms of novelties, the facilities of CBIR for 3D images coupled with image annotation in a fully automatic fashion have been developed and implemented in the system, resonating with future versatile, flexible and sustainable medical image databases that can reap new innovations

3D printing for membrane separation, desalination and water treatment

© 2019 Elsevier Ltd Additive manufacturing or commonly known as 3D printing is driving innovation in many industries and academic research including the water resource sector. The capability of 3D printing to fabricate complex objects in a fast and cost-effective manner makes it highly desirable over conventional manufacturing processes. Recent years have seen a rapid increase in research using 3D printing for membrane separation, desalination and water purification applications, potentially revolutionizing this field. This review focuses on recent advancements in 3D-printed materials and methods for water-related applications including developments in module spacers, novel filtration and desalination membranes, adsorbents, water remediation, solar steam generation materials, catalysis, etc. The emergence of new 3D printers with higher printing resolution, better efficiency, faster speed, and wider material applicability has garnered more interest and can potentially reshape research and development in this field. The promising potential, challenges and future prospects of 3D printing, additive manufacturing, and materials for water resource and treatment-related applications are all discussed in this review

A Hitchhiker's guide through the bio-image analysis software universe

Modern research in the life sciences is unthinkable without computational methods for extracting, quantifying and visualising information derived from microscopy imaging data of biological samples. In the past decade, we observed a dramatic increase in available software packages for these purposes. As it is increasingly difficult to keep track of the number of available image analysis platforms, tool collections, components and emerging technologies, we provide a conservative overview of software that we use in daily routine and give insights into emerging new tools. We give guidance on which aspects to consider when choosing the platform that best suits the user's needs, including aspects such as image data type, skills of the team, infrastructure and community at the institute and availability of time and budget.Peer reviewe