The NIH/NIGMS
Center for Integrative Biomedical Computing

 

January 4, 2014

The goal of this tutorial is to introduce participants to a suite of software tools for image-based modeling, simulation, and visualization developed by the NIH/NIGMS Center for Integrative Biomedical Computing (CIBC). This portable flexible collection of interactive tools was designed in particular to support the development of subject specific, image based geometric models for simulation of bioelectric fields, but suite as well as its individual components have been applied to a wider set of problems. The tools in the suite are: ImageVis3D, for visualization of large scale data; Seg3D, for general purpose user-guided image segmentation; Shapeworks, statistical shape analysis software; Cleaver, software for creating surface and volume meshes from segmented image data; SCIRun, a comprehensive problem solving environment that integrates many of the capabilities of an entire image based modeling pipeline.

The tutorial will be a mix of didactic presentations on the component steps of image based modeling, simulation, and visualization; hands on practice with the software, and cases studies on real world applications.

We will provide participants with the software and test data sets. Participants are required to bring their laptop computers, and if relevant their own data as well. See the list of software requirements before arriving.  CIBC staff and developers will be on hand to help participants learn the programs, port their data, and generate useful results. We especially encourage participation by students, post docs, and technical users and software developers.

The tools in the suite include:

• Seg3D, for general purpose user-guided image segmentation;
• ImageVis3D, for visualization of large scale data;
• Shapeworks, statistical shape analysis toolkit;
• Cleaver, software for creating surface and volume meshes from segmented image data;
• SCIRun, a comprehensive problem solving environment that integrates many of the capabilities of an entire image based modeling pipeline.

The tutorial will be a mix of didactic presentations on the components of image based modeling, simulation, and visualization; hands on practice with the software; and cases studies of real world applications. We will provide participants with the software and test data sets and encourage participants to bring their laptop computers, and, if relevant, their own data. CIBC members and developers will be on hand to help participants learn the programs, port their data, and generate useful results. We especially encourage participation by students, post docs, and technical users and software developers. 

Intended audience

Scientists and engineers with an interest in applications of image processing, modeling, simulation, and visualization to their biomedical research.

The goal of this tutorial is to introduce participants to a suite of software tools for image-based modeling, simulation, and visualization developed by the Center for Integrative Biomedical Computing (CIBC), an NIH-supported Biomedical Technology Research Center.

This portable flexible collection of interactive tools was designed to support the development of subject-specific, image-based geometric models for simulation of bioelectric fields. The tools, individually or as a suite, have also been applied to a wider set of problems.

Attendees will:

• learn about the major features of these software packages through presentations and case studies
• have an opportunity for hands-on instruction in our software, in laboratory sessions built into the workshop schedule
• interact with other users and technical personnel from our Center
• be able to try the tools on their own data with help from CIBC members

We will provide participants with the software and test data sets. We encourage participants to bring their laptop computers, and if relevant, their own data as well. CIBC members and developers will be on hand to help participants learn the programs, port their data, and generate useful results. We especially encourage participation by students, post docs, and technical users and software developers, as well as principal investigators.