Collaboration Through Dissemination

## Center for Integrative Biomedical Computing (CIBC)

### 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

Resource | Description | Supported Platforms | Supported Formats | Data Type | Data Size (compressed) |
---|---|---|---|---|---|

BioMesh3DCenter 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 |

FluoRenderCenter 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 |

ImageVis3DCenter 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 |

map3dCenter 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 |

SCIRunCenter 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 |

Seg3DCenter 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 |

ShapeWorksCenter 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 |

AneurysmCenter for Integrative Biomedical Computing (CIBC) NIGMS |
Magnetic resonance angiogram of the vasculature of a patient's head |
SCIRun | MRA | 0 - 500MB | |

Brain DMWCenter for Integrative Biomedical Computing (CIBC) NIGMS |
MRI scan of a head |
Linux, Mac OSX, Windows | SCIRun | MRI | 0 - 500MB |

Brain DTCenter 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 EGCenter 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 PawCenter 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 ExamplesCenter 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 ElectrodesCenter 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 DTCenter for Integrative Biomedical Computing (CIBC) NIGMS |
Diffusion weighted images of the heart. |
NRRD (.nhdr), NRRD (.nrrd) | DWI | 0 - 500MB | |

map3dCenter for Integrative Biomedical Computing (CIBC) NIGMS |
Various datasets for |
Geometric Model | 0 - 500MB | ||

Matlab ExamplesCenter 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 CollectionCenter for Integrative Biomedical Computing (CIBC) NIGMS |
Collection of 51 small animal microCT scans. |
VFF | CT | 0 - 500MB | |

Time-DependentCenter 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 10jan01Center 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 18dec03Center 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 19jun03Center 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 TorsoCenter 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 |