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Geometrical Modeling of the Heart and the Head using BioMesh3D and Cleaver

This case study explores the use of BioMesh3D and Cleaver for geometrical modeling of the heart and head, including meshing, segmentation, and structure identification. It discusses the challenges of meshing irregular features and presents different scenarios for modeling at different levels of detail. Comparison of different meshing packages and their pros and cons is also included. The new Cleaver approach is introduced, highlighting its speed, conforming nature, and guaranteed quality. The Case Study provides examples and comparisons for the Oxford Rabbit Heart, Tarantula, and Torso and Head models.

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Geometrical Modeling of the Heart and the Head using BioMesh3D and Cleaver

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  1. Case Study IV: Geometrical Modeling of the heart and the head • Moritz Dannhauer

  2. Motivation • Geometrical modeling for simulation Mesh

  3. Content • Meshing • BioMesh3D • new Meshing Approach: Cleaver

  4. Visualization Pipeline Seg3D Image Acq. &Processing Discrete pointse.g., sensors Shapeworks Segmentation & Structure Identification BioMesh3D Geometric Modeling& Fitting Structures Boundary conditions SCIRun MeshingVolume Modeling Measured Data Simulation/Estimation Verification/Validation SCIRun ImageVis3D map3D

  5. Meshing CAD-based Meshing

  6. Meshing CAD- based Meshing

  7. Three Scenarios • Low detail models • Medium detail models • High detail models

  8. Challenges of Meshing irregular features multi-material adaptive mesh run time etc. small meshes

  9. What is BioMesh3D? • Tetrahedral conforming volume meshing • Adaptive, multi material, subvoxel accuracy • Goal: Determine accurate boundary surfaces • Tetrahedralization (external): TetGen M. Meyer et. al, IEEE, 2008

  10. Meshing in Biology Non-manifold Interfaces

  11. Conformal Meshing Non-Conformal Mesh Conformal Mesh

  12. Conformal Meshes better? Non-Conformal Mesh Conformal Mesh Still an open question!

  13. Meshing packages and many more ...

  14. Example - Heart • Oxford Rabbit Heart (BioMesh3D)

  15. Cross Section of Heart BioMesh3D Tarantula

  16. Comparison - Run Time Time in [hours]

  17. Comparison - Complexity Mesh nodes in [xMillion]

  18. Comparison - Adaptivity Size variability of FE - Stddev. of Volumes in [uM^3]

  19. Comparison - Element Quality scaled inscribed (I) to circumscribed ratio (C) (SICR) Regular SICR= 3*I/C C I SICR Flat

  20. Single Time Point BioMesh3D-Pros/Cons • Pro: Local refinement • Con: Reaction/Diffusion

  21. BioMesh3D - Properties Pros: Cons: - Robustness - Usability - Run time - Sufficient node density - Element Quality + Conforming + Highly Adaptive + Preserve smooth/small features

  22. New meshing Approach:“Cleaver” min(SICR)>=const "Lattice Cleaving: Conforming Tetrahedral Meshes of Multimaterial Domains with Bounded Quality” Bronson, J., Levine, J., and Whitaker, R. To appear in Proceedings of the 21st International Meshing Roundtable (San Jose, CA, Oct 7 - 10, 2012)

  23. Element quality • Dihedral Angle • Condition number

  24. Comparison - Torso Cleaver Mesh Result

  25. Comparison - Torso Condition number min(Dihedral Angle)

  26. Comparison - Head 8 Materials

  27. Comparison - Head Mesh nodes in [xMillion] Time in [hours]

  28. Cleaver in Action

  29. Cleaver • First Release: Fall 2012 • Features: • Incredibly fast • Conforming • Guarantees on Quality • Input support: SCIRun - NRRD • Output supports: • SCIRun pts/elems • TetGen node/eles • MATLAB Binaries

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