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

PROVIDING INFORMATION SYSTEMS WITH FULL HYPERMEDIA FUNCTIONALITY

The goal of this research is to provide hypermedia functionality to all information systems. In this paper I present the architecture of a system-level hypermedia engine, designed both to manage fill hypermedia functionality for an information system and to bind interface-oriented âfront-end" systems with separate computation-oriented "back-end "systems. The engine dynamically superimposes a hypermedia representation over a back-end application's knowledge components and processes. I then describe a set of minimal requirements for integrating the hypermedia engine. The more sophisticated and cooperative the information system, the higher the level of hypermedia support the engine will provide.Information Systems Working Papers Serie

Web and Semantic Web Query Languages

A number of techniques have been developed to facilitate powerful data retrieval on the Web and Semantic Web. Three categories of Web query languages can be distinguished, according to the format of the data they can retrieve: XML, RDF and Topic Maps. This article introduces the spectrum of languages falling into these categories and summarises their salient aspects. The languages are introduced using common sample data and query types. Key aspects of the query languages considered are stressed in a conclusion

On integrating hypermedia into decision support and other information systems

The goal of this research is to provide hypermedia functionality to all information systems that interact with people. Hypermedia is a concept involving access to information, embodying the notions of context-sensitive navigation, annotation and tailored presentation. This paper presents the architecture of a system-level hypermedia engine, designed both to manage full hypermedia functionality for an information system and to bind interface-oriented front-end systems with separate computation-oriented back-end systems. The engine dynamically superimposes a hypermedia representation over a back-end application's knowledge components and processes. The hypermedia engine generates this representation using bridge laws, which capture the internal structure of client systems. Users access the application through its hypermedia representation. The paper also describes a set of minimal requirements for integrating the hypermedia engine with an information system. These guidelines apply to all integration efforts, not just that described here. Information systems will require some supplementary routines for the engine to manage hypermedia functionality for them. The more sophisticated and cooperative the information system, the higher the level of hypermedia support the engine will provide.Information Systems Working Papers Serie

Creating and Maintaining Consistent Documents with Elucidative Development

Software systems usually consist of multiple artefacts, such as requirements, class diagrams, or source code. Documents, such as specifications and documentation, can also be viewed as artefacts. In practice, however, writing and updating documents is often neglected because it is expensive and brings no immediate benefit. Consequently, documents are often outdated and communicate wrong information about the software. The price is paid later when a software system must be maintained and much implicit knowledge that existed at the time of the original development has been lost. A simple way to keep documents up to date is generation. However, not all documents can be fully generated. Usually, at least some content must be written by a human author. This handwritten content is lost if the documents must be regenerated. In this thesis, Elucidative Development is introduced. It is an approach to create documents by partial generation. Partial generation means that some parts of the document are generated whereas others are handwritten. Elucidative Development retains manually written content when the document is regenerated. An integral part of Elucidative Development is a guidance system, which informs the author about changes in the generated content and helps him update the handwritten content.:1 Introduction 1.1 Contributions 1.2 Scope of the Thesis 1.3 Organisation 2 Problem Analysis and Solution Outline 2.1 Redundancy and Inconsistency 2.2 Improving Consistency with Partial Generation 2.3 Conclusion 3 Background 3.1 Grammar-Based Modularisation 3.2 Model-Driven Software Development 3.3 Round-Trip Engineering 3.4 Conclusion 4 Elucidative Development 4.1 General Idea and Running Example 4.2 Requirements of Elucidative Development 4.3 Structure and Basic Concepts of Elucidative Documents 4.4 Presentation Layer 4.5 Guidance 4.6 Conclusion 5 Model-Driven Elucidative Development 5.1 General Idea and Running Example 5.2 Requirements of Model-Driven Elucidative Development 5.3 Structure and Basic Concepts of Elucidative Documents in Model-Driven Elucidative Development 5.4 Guidance 5.5 Conclusion 6 Extensions of Elucidative Development 6.1 Validating XML-based Elucidative Documents 6.2 Backpropagation-Based Round-Trip Engineering for Computed Text Document Fragments 6.3 Conclusion 7 Tool Support for an Elucidative Development Environment 7.1 Managing Active References 7.2 Inserting Computed Document Fragments 7.3 Caching the Computed Document Fragments 7.4 Elucidative Document Validation with Schemas 7.5 Conclusion 8 Related Work 8.1 Related Documentation Approaches 8.2 Consistency Approaches 8.3 Compound Documents 8.4 Conclusion 9 Evaluation 9.1 Creating and Maintaining the Cool Component Specification 9.2 Creating and Maintaining the UML Specification 9.3 Feasibility Studies 9.4 Conclusion 10 ConclusionSoftwaresysteme setzen sich üblicherweise aus vielen verschiedenen Artefakten zusammen, zum Beispiel Anforderungen, Klassendiagrammen oder Quellcode. Dokumente, wie zum Beispiel Spezifikationen oder Dokumentation, können auch als Artefakte betrachtet werden. In der Praxis wird aber das Schreiben und Aktualisieren von Dokumenten oft vernachlässigt, weil es zum einen teuer ist und zum anderen keinen unmittelbaren Vorteil bringt. Dokumente sind darum häufig veraltet und vermitteln falsche Informationen über die Software. Den Preis muss man später zahlen, wenn die Software gepflegt wird, weil viel von dem impliziten Wissen, das zur Zeit der Entwicklung existierte, verloren ist. Eine einfache Möglichkeit, Dokumente aktuell zu halten, ist Generierung. Allerdings können nicht alle Dokumente generiert werden. Meist muss wenigstens ein Teil von einem Menschen geschrieben werden. Dieser handgeschriebene Inhalt geht verloren, wenn das Dokument neu generiert werden muss. In dieser Arbeit wird das Elucidative Development vorgestellt. Dabei handelt es sich um einen Ansatz zur Dokumenterzeugung mittels partieller Generierung. Das bedeutet, dass Teile eines Dokuments generiert werden und der Rest von Hand ergänzt wird. Beim Elucidative Development bleibt der handgeschriebene Inhalt bestehen, wenn das restliche Dokument neu generiert wird. Ein integraler Bestandteil von Elucidative Development ist darüber hinaus ein Hilfesystem, das den Autor über Änderungen an generiertem Inhalt informiert und ihm hilft, den handgeschriebenen Inhalt zu aktualisieren.:1 Introduction 1.1 Contributions 1.2 Scope of the Thesis 1.3 Organisation 2 Problem Analysis and Solution Outline 2.1 Redundancy and Inconsistency 2.2 Improving Consistency with Partial Generation 2.3 Conclusion 3 Background 3.1 Grammar-Based Modularisation 3.2 Model-Driven Software Development 3.3 Round-Trip Engineering 3.4 Conclusion 4 Elucidative Development 4.1 General Idea and Running Example 4.2 Requirements of Elucidative Development 4.3 Structure and Basic Concepts of Elucidative Documents 4.4 Presentation Layer 4.5 Guidance 4.6 Conclusion 5 Model-Driven Elucidative Development 5.1 General Idea and Running Example 5.2 Requirements of Model-Driven Elucidative Development 5.3 Structure and Basic Concepts of Elucidative Documents in Model-Driven Elucidative Development 5.4 Guidance 5.5 Conclusion 6 Extensions of Elucidative Development 6.1 Validating XML-based Elucidative Documents 6.2 Backpropagation-Based Round-Trip Engineering for Computed Text Document Fragments 6.3 Conclusion 7 Tool Support for an Elucidative Development Environment 7.1 Managing Active References 7.2 Inserting Computed Document Fragments 7.3 Caching the Computed Document Fragments 7.4 Elucidative Document Validation with Schemas 7.5 Conclusion 8 Related Work 8.1 Related Documentation Approaches 8.2 Consistency Approaches 8.3 Compound Documents 8.4 Conclusion 9 Evaluation 9.1 Creating and Maintaining the Cool Component Specification 9.2 Creating and Maintaining the UML Specification 9.3 Feasibility Studies 9.4 Conclusion 10 Conclusio

ON INTEGRATING HYPERMEDIA INTO DECISION SUPPORT AND OTHER INFORMATION SYSTEMS

The goal of this research is to provide hypermedia functionality to all information systems that interact with people. Hypermedia is a concept involving access to information, embodying the notions of context-sensitive navigation, annotation and tailored presentation. We present the architecture of a system-level hypermedia engine, designed both to manage full hypermedia functionality for an information system and to bind interface-oriented front-end systems with separate computation-oriented back-end systems. The engine dynamically superimposes a hypermedia representation over a back-end application's knowledge components and processes. The hypermedia engine generates this representation using bridge laws, which capture the internal structure of client systems. Users access the application through its hypermedia representation. We also describe a set of minimal requirements for integrating our hypermedia engine with an information system. We believe these guidelines apply to all integration efforts, not just our own. Information systems will require some supplementary routines for the engine to manage hypermedia functionality for them. The more sophisticated and cooperative the information system, the higher the level of hypermedia support the engine will provide.Information Systems Working Papers Serie

PROVIDING INFORMATION SYSTEMS WITH FULL HYPERMEDIA FUNCTIONALITY

The goal of this research is to provide hypermedia functionality to all information systems. In this paper I present the architecture of a system-level hypermedia engine, designed both to manage fill hypermedia functionality for an information system and to bind interface-oriented âfront-end" systems with separate computation-oriented "back-end "systems. The engine dynamically superimposes a hypermedia representation over a back-end application's knowledge components and processes. I then describe a set of minimal requirements for integrating the hypermedia engine. The more sophisticated and cooperative the information system, the higher the level of hypermedia support the engine will provide.Information Systems Working Papers Serie

Adaptive object management for distributed systems

This thesis describes an architecture supporting the management of pluggable software components and evaluates it against the requirement for an enterprise integration platform for the manufacturing and petrochemical industries. In a distributed environment, we need mechanisms to manage objects and their interactions. At the least, we must be able to create objects in different processes on different nodes; we must be able to link them together so that they can pass messages to each other across the network; and we must deliver their messages in a timely and reliable manner. Object based environments which support these services already exist, for example ANSAware(ANSA, 1989), DEC's Objectbroker(ACA,1992), Iona's Orbix(Orbix,1994)Yet such environments provide limited support for composing applications from pluggable components. Pluggability is the ability to install and configure a component into an environment dynamically when the component is used, without specifying static dependencies between components when they are produced. Pluggability is supported to a degree by dynamic binding. Components may be programmed to import references to other components and to explore their interfaces at runtime, without using static type dependencies. Yet thus overloads the component with the responsibility to explore bindings. What is still generally missing is an efficient general-purpose binding model for managing bindings between independently produced components. In addition, existing environments provide no clear strategy for dealing with fine grained objects. The overhead of runtime binding and remote messaging will severely reduce performance where there are a lot of objects with complex patterns of interaction. We need an adaptive approach to managing configurations of pluggable components according to the needs and constraints of the environment. Management is made difficult by embedding bindings in component implementations and by relying on strong typing as the only means of verifying and validating bindings. To solve these problems we have built a set of configuration tools on top of an existing distributed support environment. Specification tools facilitate the construction of independent pluggable components. Visual composition tools facilitate the configuration of components into applications and the verification of composite behaviours. A configuration model is constructed which maintains the environmental state. Adaptive management is made possible by changing the management policy according to this state. Such policy changes affect the location of objects, their bindings, and the choice of messaging system

On integrating hypermedia into decision support and other information systems

The goal of this research is to provide hypermedia functionality to all information systems that interact with people. Hypermedia is a concept involving access to information, embodying the notions of context-sensitive navigation, annotation and tailored presentation. This paper presents the architecture of a system-level hypermedia engine, designed both to manage full hypermedia functionality for an information system and to bind interface-oriented front-end systems with separate computation-oriented back-end systems. The engine dynamically superimposes a hypermedia representation over a back-end application's knowledge components and processes. The hypermedia engine generates this representation using bridge laws, which capture the internal structure of client systems. Users access the application through its hypermedia representation. The paper also describes a set of minimal requirements for integrating the hypermedia engine with an information system. These guidelines apply to all integration efforts, not just that described here. Information systems will require some supplementary routines for the engine to manage hypermedia functionality for them. The more sophisticated and cooperative the information system, the higher the level of hypermedia support the engine will provide.Information Systems Working Papers Serie