About


About GIBBON

Summary

GIBBON (The Geometry and Image-Based Bioengineering add-On) is an open-source MATLAB toolbox for segmentation, image-based modeling, visualization, meshing, and finite element analysis. GIBBON includes an array of image and geometry visualization and processing tools and is interfaced with free open source software such as TetGen, for robust tetrahedral meshing, and FEBio for finite element analysis. The combination provides a highly flexible image-based modelling environment and enables advanced inverse finite element analysis.
Overview of GIBBON

Application highlights

Segmentation

The imx.m function provides a graphical user interface for segmenting 3D image data. The demo below stems from: HELP_imx.
Segmentation

Meshing

Multi-material tetrahedral meshing is enabled using TetGen. The TetGen interface is based on the runTetGen.m function. The demo below comes from the help file HELP_runTetGen. Tetrahedral meshing

Finite Element Analysis

Finite element analysis is enabled through the FEBio interface (see also the runMonitorFEBio function. The image below is for large strain analysis of a twisting bar and stems from the demo DEMO_FEBio_bar_twist. Other DEMO_FEBio_... files cover uni-axial tension/compression, bending, indentation, viscoelastic analysis, contact and indentation problems, multi-generational materials for pre-load analysis.
Large strain analysis

Geometric tools

Models, geoSphere
Mesh conversions hex2tet
Refinement, resampling subTri, triSurfaceRemesh
Lattice structures element2lattice
CAD (computer aided design) tools polyExtrude, polyLoftLinear, sweepLoft

Visualization

cFigure vcw im2patch gpatch quiver3DPatch fourthOrderTensorView

Setting up GIBBON

Installation

The GIBBON website (and the readme.md file) contains detailed installation instructions. For basic use only the GIBBON folder and sub-directories need to be added to the MATLAB path. For use with FEBio for finite element analysis FEBio needs to be installed and the patch to FEBio needs to be provided. If exporting of figures to images and animations is of interest the export_fig library needs to be downloaded and added to the MATLAB path also.

Third party packages

  • FEBio [@Maas2012], a finite element solver, which enables finite element analysis with GIBBON. FEBio is available through FEBio website.
  • TetGen, an open source tetrahedral meshing package [@Si2015]. TetGen is utilized in GIBBON for tetrahedral meshing, see also the runTetGen.m function. TetGen is included with GIBBON but alternative versions may be available through the TetGen website.
  • export_fig, a MATLAB library for exporting publication quality figures. export_fig is used in GIBBON with the efw.m (export figure widget) to export figures, and with anim8.m (animation function) to export animated .gif files. export_fig can be obtained via the export_fig GitHub repository.

Use of GIBBON in research