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

A general framework for positioning, evaluating and selecting the new generation of development tools.

This paper focuses on the evaluation and positioning of a new generation of development tools containing subtools (report generators, browsers, debuggers, GUI-builders, ...) and programming languages that are designed to work together and have a common graphical user interface and are therefore called environments. Several trends in IT have led to a pluriform range of developments tools that can be classified in numerous categories. Examples are: object-oriented tools, GUI-tools, upper- and lower CASE-tools, client/server tools and 4GL environments. This classification does not sufficiently cover the tools subject in this paper for the simple reason that only one criterion is used to distinguish them. Modern visual development environments often fit in several categories because to a certain extent, several criteria can be applied to evaluate them. In this study, we will offer a broad classification scheme with which tools can be positioned and which can be refined through further research.

Mathematical and computer modeling of electro-optic systems using a generic modeling approach

The conventional approach to modelling electro-optic sensor systems is to develop separate models for individual systems or classes of system, depending on the detector technology employed in the sensor and the application. However, this ignores commonality in design and in components of these systems. A generic approach is presented for modelling a variety of sensor systems operating in the infrared waveband that also allows systems to be modelled with different levels of detail and at different stages of the product lifecycle. The provision of different model types (parametric and image-flow descriptions) within the generic framework can allow valuable insights to be gained

Integration of all FSSIM components within SEAMLESS-IF and a stand alone Graphical User Interface for FSSIM

Agricultural and Food Policy, Environmental Economics and Policy, Farm Management, Land Economics/Use,

Towards using online portfolios in computing courses

The direct experience we had with teaching a summer pre-college computing course in which we adopted an online portfolio approach has led us to consider the use of online portfolios in our regular computer science undergraduate courses. The technical challenges we foresee include: the necessary support from the college\u27s IT department; the use of Microsoft-based web authoring technologies vs. the use of Open Source / freeware counterparts; the need for adequate technical knowledge on the part of our faculty; the need for server-side hardware and software resources