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Case Study IV: Geometrical Modeling
- f the heart and the
head
Moritz Dannhauer
Motivation
- Geometrical modeling for simulation
Case Study IV: Geometrical Modeling of the heart and the head - - PowerPoint PPT Presentation
Case Study IV: Geometrical Modeling of the heart and the head - - PowerPoint PPT Presentation
Case Study IV: Geometrical Modeling of the heart and the head Moritz Dannhauer Motivation Geometrical modeling for simulation Mesh Content Meshing BioMesh3D new Meshing Approach: Cleaver Pipeline Seg3D Shapeworks Image
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Content
- Meshing
- BioMesh3D
- new Meshing Approach: Cleaver
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Pipeline
Image ¡Acq. ¡& Processing SegmentaAon ¡& ¡ Structure ¡IdenAficaAon Geometric ¡Modeling & ¡Fi;ng ¡Structures Meshing Volume ¡Modeling SimulaAon/EsAmaAon VerificaAon/ValidaAon
Discrete ¡points e.g., ¡sensors Boundary ¡ condiAons Measured ¡ Data
V i s u a l i z a A
- n
Seg3D BioMesh3D Shapeworks SCIRun ImageVis3D map3D S C I R u n
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Meshing
CAD-based Meshing
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Meshing
CAD- based Meshing
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Three Scenarios
- Low detail models
- High detail models
- Medium detail models
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Challenges of Meshing
irregular features multi-material small meshes adaptive mesh run time etc.
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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
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Meshing in Biology
Non-manifold Interfaces
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Conformal Meshing
A B
Non-Conformal Mesh Conformal Mesh
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Conformal Meshes better?
A B
Non-Conformal Mesh Conformal Mesh Still an open question!
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Meshing packages
and many more ...
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Example - Heart
- Oxford Rabbit Heart (BioMesh3D)
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Cross Section of Heart
BioMesh3D Tarantula
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Comparison - Run Time
7.5 15 22.5 30
0.5 24
BioMesh3D Tarantula
Time in [hours]
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Comparison - Complexity
1.5 3 4.5 6
4.4 5.9
BioMesh3D Tarantula
Mesh nodes in [xMillion]
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Comparison - Adaptivity
50000 100000 150000 200000
39171 175028
BioMesh3D Tarantula
Size variability
- f FE -
- Stddev. of
Volumes in [uM^3]
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Comparison - Element Quality
0.25 0.5 0.75 1
1 0.71 0.65
BioMesh3D Tarantula
- ptimal Elements
scaled inscribed (I) to circumscribed ratio (C) (SICR) SICR= 3*I/C SICR Flat Regular C I
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BioMesh3D-Pros/Cons
- Pro: Local refinement
Single Time Point
- Con: Reaction/Diffusion
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BioMesh3D - Properties
Pros: + Conforming + Highly Adaptive + Preserve smooth/ small features
- Robustness
- Usability
- Run time
- Sufficient node density
- Element Quality
Cons:
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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)
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Element quality
- Dihedral Angle
- Condition number
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Comparison - Torso
Cleaver Mesh Result
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Comparison - Torso
Condition number min(Dihedral Angle)
1E+01 1E+02 1E+03 1E+04 1E+05 1E+06 1E+07 1E+08 1E+09 1E+10
2.42E+07 2.94E+09 5.42E+06
2 4 6 8
0.4 7.4
Cleaver BioMesh3D CGAL
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Comparison - Head
8 Materials
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Comparison - Head
2.25 4.5 6.75 9
8.6 6.4
BioMesh3D Cleaver
Mesh nodes in [xMillion]
50 100 150 200
0.7 168
Time in [hours]
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Cleaver in Action
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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