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

GART: The Gesture and Activity Recognition Toolkit

Presented at the 12th International Conference on Human-Computer Interaction, Beijing, China, July 2007.The original publication is available at www.springerlink.comThe Gesture and Activity Recognition Toolit (GART) is a user interface toolkit designed to enable the development of gesture-based applications. GART provides an abstraction to machine learning algorithms suitable for modeling and recognizing different types of gestures. The toolkit also provides support for the data collection and the training process. In this paper, we present GART and its machine learning abstractions. Furthermore, we detail the components of the toolkit and present two example gesture recognition applications

GraXML - Modular Geometric Modeler

Many entities managed by HEP Software Frameworks represent spatial (3-dimensional) real objects. Effective definition, manipulation and visualization of such objects is an indispensable functionality. GraXML is a modular Geometric Modeling toolkit capable of processing geometric data of various kinds (detector geometry, event geometry) from different sources and delivering them in ways suitable for further use. Geometric data are first modeled in one of the Generic Models. Those Models are then used to populate powerful Geometric Model based on the Java3D technology. While Java3D has been originally created just to provide visualization of 3D objects, its light weight and high functionality allow an effective reuse as a general geometric component. This is possible also thanks to a large overlap between graphical and general geometric functionality and modular design of Java3D itself. Its graphical functionalities also allow a natural visualization of all manipulated elements. All these techniques have been developed primarily (or only) for the Java environment. It is, however, possible to interface them transparently to Frameworks built in other languages, like for example C++. The GraXML toolkit has been tested with data from several sources, as for example ATLAS and ALICE detector description and ATLAS event data. Prototypes for other sources, like Geometry Description Markup Language (GDML) exist too and interface to any other source is easy to add.Comment: Talk from the 2003 Computing in High Energy and Nuclear Physics (CHEP03), La Jolla, Ca, USA, March 2003. PSN THJT00

Slisp: A Flexible Software Toolkit for Hybrid, Embedded and Distributed Applications

We describe Slisp (pronounced ‘Ess-Lisp’), a hybrid Lisp–C programming toolkit for the development of scriptable and distributed applications. Computationally expensive operations implemented as separate C-coded modules are selectively compiled into a small Xlisp interpreter, then called as Lisp functions in a Lisp-coded program. The resulting hybrid program may run in several modes: as a stand-alone executable, embedded in a different C program, as a networked server accessed from another Slisp client, or as a networked server accessed from a C-coded client. Five years of experience with Slisp, as well experience with other scripting languages such as Tcl and Perl, are summarized. These experiences suggest that Slisp will be most useful for mid-sized applications in which the kinds of scripting and embeddability features provided by Tcl and Perl can be extended in an efficient manner to larger applications, while maintaining a well-defined standard (Common Lisp) for these extensions. In addition, the generality of Lisp makes Lisp a good candidate for an application-level communication language in distributed environments

The Repast Simulation/Modelling System for Geospatial Simulation

The use of simulation/modelling systems can simplify the implementation of agent-based models. Repast is one of the few simulation/modelling software systems that supports the integration of geospatial data especially that of vector-based geometries. This paper provides details about Repast specifically an overview, including its different development languages available to develop agent-based models. Before describing Repast’s core functionality and how models can be developed within it, specific emphasis will be placed on its ability to represent dynamics and incorporate geographical information. Once these elements of the system have been covered, a diverse list of Agent-Based Modelling (ABM) applications using Repast will be presented with particular emphasis on spatial applications utilizing Repast, in particular, those that utilize geospatial data

An Extensible Timing Infrastructure for Adaptive Large-scale Applications

Real-time access to accurate and reliable timing information is necessary to profile scientific applications, and crucial as simulations become increasingly complex, adaptive, and large-scale. The Cactus Framework provides flexible and extensible capabilities for timing information through a well designed infrastructure and timing API. Applications built with Cactus automatically gain access to built-in timers, such as gettimeofday and getrusage, system-specific hardware clocks, and high-level interfaces such as PAPI. We describe the Cactus timer interface, its motivation, and its implementation. We then demonstrate how this timing information can be used by an example scientific application to profile itself, and to dynamically adapt itself to a changing environment at run time