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Center for Integrative Biomedical Computing (CIBC)

Chris R. Johnson, Ph.D.
P41GM103545
Active

Center Overview

The Center for Integrative Biomedical Computing is dedicated to producing opensource software tools for biomedical image-based modeling, biomedical simulation and estimation, and the visualization of biomedical data. The Center works closely with software users and collaborators in a range of scientific domains to produce user-optimized tools and provides advice, technical support, workshops, and education to enhance user success. Biological projects and collaborations drive our development efforts, all with a single unifying vision: to develop the role of image-based modeling, simulation, and visualization in biomedical science and clinical practice.

Image processing and geometric modeling tools: The center is developing powerful and novel tools for scientists to manage, analyze, segment, and visualize large image datasets and to then use the results to generate surface and volumetric geometric models. These tools are based largely on the Insight Toolkit (ITK) functions and image processing techniques developed by the center's investigators. The latest software provides an application-specific interface to the underlying ITK functionality while hiding many of the details that hinder easy utility. The center is developing specific applications from collaborations with bioscientists that will server as prototypes for the larger biomedical image processing and analysis community.

Simulation tools: Current software supports general scientific computing techniques, such as finite element, finite difference, and boundary element techniques for the numeric solution of bioelectric field problems. The center has also developed novel techniques for regularization techniques to constrain the effects produced by the ill-posed nature of electrocardiogram and electroencephalogram inverse problems. Recently developed simulation tools predict electrical changes in the heart due to ischemia. A current focus is developing interfaces between our integrated software environment and programs created by collaborators; the goal is to minimize the overhead of integrating existing software systems.

Visualization tools: The center builds strongly on the outstanding visualization capabilities of the Scientific Computing and Imaging Institute and seeks to make the most advanced visualization algorithms easily available to biomedical researchers. Specific techniques that the center has implemented include interactive scalar field display, isocontour and isosurface extraction, volume and surface rendering, and vector and tensor field visualization. Current initiatives include quantitative spatio-temporal visualization and methods for the characterization, representation, and presentation of error and uncertainty due to modeling, simulation, and visualization.

Impact on Human Health

The focus of research within the CIBC is to develop new approaches to solving problems in image processing; visualization of scalar, vector, and tensor fields; and simulation of electrophysiology and bioelectric fields from the heart and brain.

Resources

ResourceDescriptionSupported PlatformsSupported FormatsData TypeData Size (compressed)
BioMesh3D
Center for Integrative Biomedical Computing (CIBC)
NIGMS

A tetrahedral mesh generator, capable of generating multi-material quality meshes out of segmented biomedical image data. Integrated with SCIRun to visualize the intermediate results.

Linux, Mac OSX, Windows NRRD (.nhdr), NRRD (.nrrd) N/A N/A
FluoRender
Center for Integrative Biomedical Computing (CIBC)
NIGMS

Interactive rendering tool for confocal microscopy data visualization. Designed for neurobiologists, to help them better visualize fluorescent-stained confocal samples.

Windows Confocal Data N/A N/A
ImageVis3D
Center for Integrative Biomedical Computing (CIBC)
NIGMS

Highly scalable volume rendering program.

Linux, Mac OSX, Windows Analyze (.hdr), Analyze (.img.gz),...(more) N/A N/A
map3d
Center for Integrative Biomedical Computing (CIBC)
NIGMS

A scientific visualization application to display and edit complex, three-dimensional geometric models and scalar, time-based data associated with those models.

Linux, Mac OSX, Windows ascii, Binary, Matlab N/A N/A
SCIRun
Center for Integrative Biomedical Computing (CIBC)
NIGMS

A PSE for modeling, simulation and visualization of scientific problems.

Linux, Mac OSX, Windows Analyze (.hdr), Analyze (.img.gz),...(more) N/A N/A
Seg3D
Center for Integrative Biomedical Computing (CIBC)
NIGMS

Volume segmentation and processing tool, combining a flexible manual segmentation interface with powerful higher-dimensional image processing and segmentation algorithms from the Insight Toolkit.

Linux, Mac OSX, Windows Analyze (.hdr), Analyze (.img.gz),...(more) N/A N/A
ShapeWorks
Center for Integrative Biomedical Computing (CIBC)
NIGMS

Method for constructing compact statistical point-based models of ensembles of similar shapes that does not rely on any specific surface parameterization.

Linux, Mac OSX, Windows Analyze (.hdr), Analyze (.img.gz),...(more) N/A N/A
Aneurysm
Center for Integrative Biomedical Computing (CIBC)
NIGMS

Magnetic resonance angiogram of the vasculature of a patient's head

SCIRun MRA 0 - 500MB
Brain DMW
Center for Integrative Biomedical Computing (CIBC)
NIGMS

MRI scan of a head

Linux, Mac OSX, Windows SCIRun MRI 0 - 500MB
Brain DT
Center for Integrative Biomedical Computing (CIBC)
NIGMS

Twelve diffusion weighted volumes and one non-diffusion-weighted (B=0) reference volume.

NRRD (.nhdr), NRRD (.nrrd) DWI 0 - 500MB
Brain EG
Center for Integrative Biomedical Computing (CIBC)
NIGMS

Comprehensive dataset of a head. This dataset contains a segmented tetrahedral finite element mesh, high- and low-resolution surface models of the scalp and cortex, a point-cloud of electrodes, and a dipole location for a forward simulation.

Linux, Mac OSX, Windows SCIRun EEG 0 - 500MB
Capecchi Mouse Paw
Center for Integrative Biomedical Computing (CIBC)
NIGMS

Mouse paw dataset used to test the Capecchi use case scenario in Seg3D

NRRD (.nhdr), NRRD (.nrrd) CT 0 - 500MB
Convert Examples
Center for Integrative Biomedical Computing (CIBC)
NIGMS

Examples that demonstrate how to use the SCIRun converters.

Linux, Mac OSX, Windows SCIRun Geometric Model 0 - 500MB
Cylinder (3-shell)
Center for Integrative Biomedical Computing (CIBC)
NIGMS

This is a 3-shell cylinder model. Each shell has a distinct conductivity index.

Linux, Mac OSX, Windows SCIRun Geometric Model 0 - 500MB
FEM Electrodes
Center for Integrative Biomedical Computing (CIBC)
NIGMS

Simple example datasets that can be used as electrodes in finite element simulations.

Linux, Mac OSX, Windows SCIRun Geometric Model 0 - 500MB
Heart DT
Center for Integrative Biomedical Computing (CIBC)
NIGMS

Diffusion weighted images of the heart.

NRRD (.nhdr), NRRD (.nrrd) DWI 0 - 500MB
map3d
Center for Integrative Biomedical Computing (CIBC)
NIGMS

Various datasets for map3d.

Geometric Model 0 - 500MB
Matlab Examples
Center for Integrative Biomedical Computing (CIBC)
NIGMS

Matlab data contains geometry and potentials for a dog heart. The type of time series data is epicardial potentials. The mesh represents the geometry of 490 sock electrodes.

Matlab Geometric Model 0 - 500MB
MicroCT Collection
Center for Integrative Biomedical Computing (CIBC)
NIGMS

Collection of 51 small animal microCT scans.

VFF CT 0 - 500MB
Time-Dependent
Center for Integrative Biomedical Computing (CIBC)
NIGMS

Time-dependent datasets for use with the tikhonov-inversion, show-eeg-data, and torso-tank-bem, BioPSE networks.

Linux, Mac OSX, Windows Matlab, SCIRun EEG 0 - 500MB
Torsotank 10jan01
Center for Integrative Biomedical Computing (CIBC)
NIGMS

Torsotank experiment. Geometry includes the 490 ventricular electrode sock and the CVRTI torso tank (374 leads). Interventions were controlled flow in left anterior descending artery.

Geometric Model 500MB - 2GB
Torsotank 18dec03
Center for Integrative Biomedical Computing (CIBC)
NIGMS

CVRTI torso tank experiment with 490 lead epicardial sock and 374 lead torso tank. Includes aligned geometry. Interventions included limiting coronary flow and inserting a left ventricular balloon to provide mechanical load.

Geometric Model 0 - 500MB
Torsotank 19jun03
Center for Integrative Biomedical Computing (CIBC)
NIGMS

CVRTI torso tank experiment with 490 lead epicardial sock and 374 lead torso tank. Includes aligned geometry. Interventions included limiting coronary flow and inserting a left ventricular balloon to provide mechanical load. This one also has extensive MRI data.

Geometric Model 500MB - 2GB
Utah Torso
Center for Integrative Biomedical Computing (CIBC)
NIGMS

High resolution geometry of the Utah Torso model. The meshes are tetrahedral volumes, with conductivity tensors stored with the elements. There are ten different conductivity values throughout the volume. The surfaces are TriSurfs and correspond to the boundaries of the distinct conductivity regions.

Linux, Mac OSX, Windows SCIRun Geometric Model 0 - 500MB
Utah Torso (low res)
Center for Integrative Biomedical Computing (CIBC)
NIGMS

Low resolution geometry of the Utah Torso model. The meshes are tetrahedral volumes, with conductivity tensors stored with the elements. The surfaces are TriSurfs and correspond to the boundaries of the distinct conductivity regions.

Linux, Mac OSX, Windows SCIRun Geometric Model 0 - 500MB
Utah Torso (text based)
Center for Integrative Biomedical Computing (CIBC)
NIGMS

High resolution geometry of the Utah Torso model. The meshes are tetrahedral volumes, with conductivity tensors stored with the elements. There are ten different conductivity values throughout the volume. The surfaces are TriSurfs and correspond to the boundaries of the distinct conductivity regions.

Text (.txt) Geometric Model 0 - 500MB