MITK-ModelFit: A generic open-source framework for model fits and their exploration in medical imaging -- design, implementation and application on the example of DCE-MRI

Many medical imaging techniques utilize fitting approaches for quantitative parameter estimation and analysis. Common examples are pharmacokinetic modeling in DCE MRI/CT, ADC calculations and IVIM modeling in diffusion-weighted MRI and Z-spectra analysis in chemical exchange saturation transfer MRI. Most available software tools are limited to a special purpose and do not allow for own developments and extensions. Furthermore, they are mostly designed as stand-alone solutions using external frameworks and thus cannot be easily incorporated natively in the analysis workflow. We present a framework for medical image fitting tasks that is included in MITK, following a rigorous open-source, well-integrated and operating system independent policy. Software engineering-wise, the local models, the fitting infrastructure and the results representation are abstracted and thus can be easily adapted to any model fitting task on image data, independent of image modality or model. Several ready-to-use libraries for model fitting and use-cases, including fit evaluation and visualization, were implemented. Their embedding into MITK allows for easy data loading, pre- and post-processing and thus a natural inclusion of model fitting into an overarching workflow. As an example, we present a comprehensive set of plug-ins for the analysis of DCE MRI data, which we validated on existing and novel digital phantoms, yielding competitive deviations between fit and ground truth. Providing a very flexible environment, our software mainly addresses developers of medical imaging software that includes model fitting algorithms and tools. Additionally, the framework is of high interest to users in the domain of perfusion MRI, as it offers feature-rich, freely available, validated tools to perform pharmacokinetic analysis on DCE MRI data, with both interactive and automatized batch processing workflows.Comment: 31 pages, 11 figures URL: http://mitk.org/wiki/MITK-ModelFi

The Agent Pattern Driven Business Engineering (APBDE) approach enabled business-based systems

Agent design patterns form a new methodology used to improve the development of software agents. Agent design patterns can help by capturing solutions to common problems in agent design [Lange and Oshima, 1998].Agent design patterns are applied in different systems such as knowledge management systems, real-time systems, and network management systems. Agent design patterns for business-based systems, aim to support different ecommerce paradigms business-to-business (B2B) and business-to-consumer (B2C).In this paper, we developed an approach for extracting agent-based design patterns for B2C e-commerce to improve business-based processes.This approach is called an Agent Pattern Driven Business Engineering (APDBE).Based on this approach, we derived two agent-based commerce design patterns namely, the De-coupler Design Pattern (DecDP), and the Dynamic Design Pattern (DynDP). These design patterns are used to support selling/buying-based processes in e-commerce domain

Semantic web services for simulation component reuse and interoperability: An ontology approach

Commercial-off-the-shelf (COTS) Simulation Packages (CSPs) are widely used in industry primarily due to economic factors associated with developing proprietary software platforms. Regardless of their widespread use, CSPs have yet to operate across organizational boundaries. The limited reuse and interoperability of CSPs are affected by the same semantic issues that restrict the inter-organizational use of software components and web services. The current representations of Web components are predominantly syntactic in nature lacking the fundamental semantic underpinning required to support discovery on the emerging Semantic Web. The authors present new research that partially alleviates the problem of limited semantic reuse and interoperability of simulation components in CSPs. Semantic models, in the form of ontologies, utilized by the authors’ Web service discovery and deployment architecture provide one approach to support simulation model reuse. Semantic interoperation is achieved through a simulation component ontology that is used to identify required components at varying levels of granularity (i.e. including both abstract and specialized components). Selected simulation components are loaded into a CSP, modified according to the requirements of the new model and executed. The research presented here is based on the development of an ontology, connector software, and a Web service discovery architecture. The ontology is extracted from simulation scenarios involving airport, restaurant and kitchen service suppliers. The ontology engineering framework and discovery architecture provide a novel approach to inter-organizational simulation, by adopting a less intrusive interface between participants Although specific to CSPs this work has wider implications for the simulation community. The reason being that the community as a whole stands to benefit through from an increased awareness of the state-of-the-art in Software Engineering (for example, ontology-supported component discovery and reuse, and service-oriented computing), and it is expected that this will eventually lead to the development of a unique Software Engineering-inspired methodology to build simulations in future

Proximal business intelligence on the semantic web

This is the post-print version of this article. The official version can be accessed from the link below - Copyright @ 2010 Springer.Ubiquitous information systems (UBIS) extend current Information System thinking to explicitly differentiate technology between devices and software components with relation to people and process. Adapting business data and management information to support specific user actions in context is an ongoing topic of research. Approaches typically focus on providing mechanisms to improve specific information access and transcoding but not on how the information can be accessed in a mobile, dynamic and ad-hoc manner. Although web ontology has been used to facilitate the loading of data warehouses, less research has been carried out on ontology based mobile reporting. This paper explores how business data can be modeled and accessed using the web ontology language and then re-used to provide the invisibility of pervasive access; uncovering more effective architectural models for adaptive information system strategies of this type. This exploratory work is guided in part by a vision of business intelligence that is highly distributed, mobile and fluid, adapting to sensory understanding of the underlying environment in which it operates. A proof-of concept mobile and ambient data access architecture is developed in order to further test the viability of such an approach. The paper concludes with an ontology engineering framework for systems of this type – named UBIS-ONTO

Interaction protocols for cross-organisational workflows

Workflow technologies are widely used in industry and commerce to assist in the specification, execution and completion of well defined processes within organisations. As industrial and commercial relations have evolved, based on advances on information and communications technologies, cross-organisational workflow integration has become an important issue. Since organisations can have very different workflows, the creation of compatible workflows so that organisations can collaborate and/or carry out mutual transactions automatically in an integrated fashion can be a very complex and time consuming process. As a consequence, the development of technologies to support the creation and execution of compatible workflows is a most relevant issue. In the present article we introduce the JamSession coordination platform as a tool to implement cross-organisational workflow integration. JamSession is declarative and based on algebraic specification methods, and therefore workflow integration implemented using this platform can profit from formal behavioural analysis, based on which desired features and properties can be verified and/or obtained

From i* models to service oriented architecture models

Requirements engineering and architectural design are key activities for successful development of software systems. Specifically in the service-oriented development systems there is a gap between the requirements description and architecture design and assessment. This article presents a systematic process for systematically deriving service-oriented architecture from goal-oriented models. This process allows generate candidate architectures based on i* models and helps architects to select a solution using services oriented patterns for both services and components levels. The process is exemplified by applying it in a synthesis metadata and assembly learning objects system.Peer ReviewedPostprint (author’s final draft