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. Pipeline Image Acq. & Processing Segmentation & Structure Identification Geometric Modeling & Fitting Structures Meshing Volume Modeling Simulation/Estimation Verification/Validation Discrete points e.g., sensors Boundar y conditio ns Measure d Data Visualization Seg3D BioMesh3D Shapeworks SCIRun ImageVis3D map3D SCIRun

5. Meshing CAD-based Meshing

6. CAD- based Meshing

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

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

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 BioMesh3DTarantula

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) SICR= 3*I/C SICR Flat Regular C I

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

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

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