Research Cores

The overall organization of the Center is based on three technical cores supported and integrated by means of the BioPSE software system.

Image and geometry processing: The technical goals of this core are to carry out research and development in all areas involving the manipulation of image-based data, the extraction of structure from these data, and the construction of geometric models from either images or other sources of structural information (e.g., point clouds from a three-dimensional digitizer). This core represents the typical starting point for an analysis, simulation, or visualization of spatially distributed data.

Simulation and mathematical modeling: Mathematical modeling and simulation naturally follow imaging and geometry processing in the kinds of workflow the Center seeks to facilitate. The goal is to associate physiological behavior to the elements captured in the structural models and to simulate the outcome of that behavior, often comparing it to measurements that mimic the simulations. The goals of this technical core are thus to carry out research and development leading to a complete set of software tools for modeling and simulating the function of biomedical systems within the scientific scope of the Center and its collaborators.

Visualization: Visualization is not just the natural end point of the processing pipeline but must be a ubiquitous component of every step within that pipeline; the user must see the data from raw images to finished simulation and then be able to visualize the errors and uncertainties that arise from the measurements and computations applied to those data. The goals of this core are to develop and implement advanced, efficient, high-performance algorithms and software for visualizing large, spatially distributed and/or time varying data sets.

Problem solving environment: The most tangible product of the Center will continue to be the software that encapsulates all the techniques that flow from the technical cores. This software provides the researcher with enormous capabilities and infrastructure, a comprehensive set of building blocks from which to create specific software pipelines for almost any imaginable task. The Center will continue to place all software in the public domain with an unrestricted open-source license. In addition, it will continue to provide different levels of access to the functionality of the software to match the computational expertise of the user. The goals of the problem solving environment will include adapting a new architecture that will enable researchers to easily link their software to other software systems, separating the computational and user interface elements to offer more flexibility and customization of the interface, and improving performance and throughput for the large data sets that arise in realistic biomedical research projects.