This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The initial focus of the CIBC software group was on the Biomedical Problem Solving Environment, BioPSE. This environment provides a rich a diverse set of modules and capabilities designed to make the design and implementation of modeling, simulation and visualization very flexible and powerful. The idea behind this environment is to provide an infrastructure that liberates the scientist from the user-intensive, mundane tasks associated with most existing software tools. By commanding a modular, extensible, interactive set of software tools, scientists are free to apply their expertise to the science at hand. Traditional Methods Traditional methods for investigating biomedical applications often use multiple, non-integrated computer programs. For example, a scientist using a computer simulation to examine the effect of electrode patch placement on transcardiac current density in defibrillation would require geometric modeling, numerical simulation, and scientific visualization tools to complete the task. One program might be used to define the thoracic surfaces from medical images, another to create a discrete mesh of the volume contained within the surfaces. Another application would be necessary to run a finite element simulation of the electric current distribution from the electrodes through the thoracic volume. Each program is such a scenario is often independent and perhaps comes from a different source and is written in a different language. It will almost certainly have different user interface layout and structure. Such separations and differences form a barrier to integration and rapid development and evaluation of simulations. BioPSE is one approach to integrating the steps of a simulation and thus simplifying both the development and execution of the model. Such simplification, in turn, facilitates the rapid iterations necessary to evaluate the model and the results it generates and explore the behavior of the underlying system. Workflow based program organization Over the past years the CIBC has extended the approach to software environments to developing smaller applications that, while integrated through common formats and interfaces, are actually standalone programs. Initially, we built such applications as instances of BioPSE with a customized interface but found the data flow paradigm intrinsic to BioPSE to be somewhat limiting. As a result, we now organize these applications to share code and algorithms with BioPSE (and the underlying SCIRun architecture) but combine them into workflows that match the assumed use of these programs. We have selected tasks that are relatively discrete and used frequently enough so that users can complete a major piece of the workflow within one program. For example, we have developed a segmentation application called Seg3D that contains support for all the steps typically required to carry out the identification of tissues regions in anatomical volumetric data sets, e.g., from MRI, CT, or confocal microscopy. Segmentation is an essential step in many settings and may even represent almost the entire workflow for particular types of analysis. Other examples of such workflow based programs that we have implemented include map3d (for rendering and analysis of surface based measurements or simulations of multiple time signals), BioMesh3D (for constructing polygonal meshes from segmented volumes), ImageVis3D (for interactive visualization of very large volume data sets), and ShapeWorks (for the statistical shape analysis of surfaces). Each of the programs is now a piece in our software suite, freely available for download and supported with documentation, mailing lists, and regular maintenance and updates.
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