research-article

Multi-component heart reconstruction from volumetric imaging

Authors:

Chandrajit Bajaj,

Samrat GoswamiAuthors Info & Claims

SPM '08: Proceedings of the 2008 ACM symposium on Solid and physical modeling

Pages 193 - 202

https://doi.org/10.1145/1364901.1364928

Published: 02 June 2008 Publication History

Abstract

Computer Tomography (CT) and in particular super fast, 64 and 256 detector CT has rapidly advanced over recent years, such that high resolution cardiac imaging has become a reality. In this paper, we briefly introduce a framework that we have built to construct three dimensional (3D) finite-element and boundary element mesh models of the human heart directly from high resolution CT imaging data. Although, the overall IMAGING-MODELING framework consists of image processing, geometry processing and meshing algorithms, our main focus in this paper will revolve around three key geometry processing steps which are parts of the so-called IMAGING-MODELING framework. These three steps are geometry cleanup or CURATION, anatomy guided annotation or SEGMENTATION and construction of GENERALIZED OFFSET SURFACE. These three algorithms, due to the very nature of the computation involved, can also be thought as parts of a more generalized modeling technique, namely geometric modeling with distance function. As part of the results presented in the paper, we will show that our algorithms are robust enough to effectively deal with the challenges posed by the real-world patient CT data collected from our radiologist collaborators.

References

[1]

Allouche, C. F., Makam, S., Ayache, N., and Delingette, H. 2001. A new kinetic modeling scheme for the human left ventricle wall motion with mr-tagging imaging. In Functional Imaging and Modeling of Heart, T. Katila, I. E. Magnin, P. Clarysse, J. Montagnat, and J. Nenonen, Eds., LNCS, 61--68.

Digital Library

[2]

Bajaj, C., and Goswami, S. 2006. Automatic fold and structural motif elucidation from 3d em maps of macromolecules. In ICVGIP 2006, 264--275.

Digital Library

[3]

Bajaj, C., and Xu, G. 2001. Smooth shell construction with mixed prism fat surfaces. Brunett, G., Bieri, H., Farin, G. (eds.), Geometric Modeling Computing Supplement 14, 19--35.

Digital Library

[4]

Bajaj, C., and Xu, G. 2003. Anisotropic diffusion of surfaces and functions on surfaces. ACM Transactions on Graphics 22, 1, 4--32.

Digital Library

[5]

Bajaj, C., Goswami, S., Yu, Z., Zhang, Y., Bazilevs, Y., and Hughes, T. 2006. Patient specific heart models from high resolution ct. In Proceedings of Computational Modelling of Objects Represented in Images, CompIMAGE, 157--165.

[6]

Bajaj, C., Gillette, A., and Goswami, S. 2007. Topology based selection and curation of level sets. In Topology-in-Visualization, A. Wiebel, H. Hege, K. Polthier, and G. Scheuer-mann, Eds.

[7]

Biswas, A., Shapiro, V., and Tsukanov, I. 2004. Heterogeneous material modeling with distance fields. Computer Aided Geometric Design 21, 3, 215--242.

Digital Library

[8]

Braess, D. 1995. Towards algebraic multigrid for elliptic problems of second order. Computing 55, 379--393.

Digital Library

[9]

Brown, P., Byrne, G., and Hindmarsh, A. 1989. VODE: A variable-coefficient ode solver. SIAM Journal on Scientific Computation 10, 1038--1057.

Digital Library

[10]

Cgal Consortium. 2007. CGAL (3.3.1): Computational Geometry Algorithms Library. http://www.cgal.org.

[11]

Chazal, F., and Lieutier, A. 2004. Stability and homotopy of a subset of the medial axis. In Proc. 9th ACM Sympos. Solid Modeling and Applications, 243--248.

Digital Library

[12]

Chazal, F., and Lieutier, A. 2006. Topology guaranteeing manifold reconstruction using distance function to noisy data. In Sympos. on Comput. Geom., 112--118.

Digital Library

[13]

Chen, Y. J., and Ravani, B. 1987. Offset surface generation and contouring in computer-aided design. Journal of Mech. Trans. Autom. Design 109, 1, 133--142.

[14]

Costa, K. D., Hunter, P. J., Wayne, J. S., Waldmann, L. K., Guccione, J. M., and Mcculloch, A. D. 1996. A three-dimensional finite element method for large elastic deformations of ventricular myocardium: Ii - prolate spheroidal coordinates. J. Biomedical Engineering 118, 4 (November), 464--472.

[15]

Cvc, UT Austin. 2005. Volrover. http://cvcweb.ices.utexas.edu/software/guides.php.

[16]

De Munck, J. 1992. A linear discretization of the volume conductor boundary integral equation using analytically integrated elements. IEEE Trans Biomed. Eng. 39, 9 (September), 986--990.

[17]

Dey, T. K., and Goswami, S. 2003. Tight cocone: A water-tight surface reconstructor. In Proc. 8th ACM Sympos. Solid Modeling and Applications, 127--134.

Digital Library

[18]

Dey, T. K., and Goswami, S. 2004. Provable surface reconstruction from noisy samples. In Proc. 20th ACM-SIAM Sympos. Comput. Geom., 330--339.

Digital Library

[19]

Dey, T. K., Giesen, J., and Goswami, S. 2003. Shape segmentation and matching with flow discretization. In Proc. Workshop Algorithms Data Strucutres (WADS 03), F. Dehne, J.-R. Sack, and M. Smid, Eds., LNCS 2748, 25--36.

[20]

Dey, T. K., Giesen, J., Ramos, E., and Sadri, B. 2005. Critical points of the distance to an epsilon-sampling of a surface and flow-complex-based surface reconstruction. In Proc. 21st ACM-SIAM Sympos. Comput. Geom., 218--227.

Digital Library

[21]

Edelsbrunner, H., Facello, M. A., and Liang, J. 1998. On the definition and the construction of pockets in macromolecules. Discrete Apl. Math. 88, 83--102.

Digital Library

[22]

Edelsbrunner, H. 2002. Surface reconstruction by wrapping finite point sets in space. In Ricky Pollack and Eli Goodman Festschrift, B. Aronov, S. Basu, J. Pach, and M. Sharir, Eds. Springer-Verlag, 379--404.

[23]

Geometry Center, University of Minnesota. 1996. Geomview. http://www.geomview.org/.

[24]

Giesen, J., and John, M. 2003. The flow complex: a data structure for geometric modeling. In Proc. 14th ACM-SIAM Sympos. Discrete Algorithms, 285--294.

Digital Library

[25]

Goerres, G. W., Kamel, E., Seifert, B., Burger, C., Buck, A., Hany, T. F., and Schulthess, G. K. V. 2002. Accuracy of image coregistration of pulmonary lesions in patients with non-small cell lung cancer using an integrated pet/ct system. Journal Nucl. Med. 43, 1469--1475.

[26]

Goswami, S., Dey, T. K., and Bajaj, C. L. 2006. Identifying flat and tubular regions of a shape by unstable manifolds. In Proc. 11th Sympos. Solid and Physical Modeling, 27--37.

Digital Library

[27]

Goswami, S., Gillette, A., and Bajaj, C. 2007. Efficient Delaunay mesh generation from sampled scalar function. In Proc. 16th Int. Meshing Roundtable, 495--511.

[28]

Hackbusch, W. 1985. Multi-Grid Methods and Applications. Springer Verlag, Berlin, Heidelberg, New York, Tokyo.

[29]

Hille, B. 1992. Ionic Channels of Excitable Membranes., Second ed. Sinauer Associates, Inc., Sunderland, MA.

[30]

Hodgkin, A. L., and Huxley, A. F. 1952. A quantitative description of membrane current and its application to conduction and excitation in nerve. Journal of Physiology 117, 500--544.

[31]

Hunter, P., McCulloch, A., Nielsen, P., and Smaill, B. 1988. A finite element model of passive ventricular mechanics. ASMS BED 9, 387--397.

[32]

Ju, T., Losasso, F., Schaefer, S., and Warren, J. 2002. Dual contouring of hermite data. In SIGGRAPH 2002, Computer Graphics Proceedings, ACM Press / ACM SIGGRAPH, 339--346.

Digital Library

[33]

Labelle, F., and Shewchuk, J. R. 2007. Isosurface stuffing: fast tetrahedral meshes with good dihedral angles. ACM Transactions on Graphics 26, 3.

Digital Library

[34]

Lorensen, W., and Cline, H. 1987. Marching Cubes: A High Resolution 3D Surface Construction Algorithm. In SIGGRAPH, 163--169.

Digital Library

[35]

Luo, C., and Rudy, Y. 1991. A model of the ventricular cardiac action potential: Depolarization, repolarization and their interaction. Circulation Research 68, 6, 1501--1526.

[36]

Luo, C., and Rudy, Y. 1994. A dynamic model of the cardiac ventricular action potential: I. simulations of ionic currents and concentration changes. Circulation Research 74, 6, 1071--1096.

[37]

Maekawa, T. 1999. An overview of offset curves and surfaces. Computer-Aided Design 31, 3, 165--173.

[38]

Mari, J.-L., Astart, L., and Sequeira, J. 2001. Geometrical modeling of the heart and its main vessels. In Functional Imaging and Modeling of Heart, T. Katila, I. E. Magnin, P. Clarysse, J. Montagnat, and J. Nenonen, Eds., LNCS, 10--16.

Digital Library

[39]

McVeigh, E., Faris, O., Ennis, D., Helm, P., and Evans, F. 2001. Measurement of ventricular wall motion, epicardial electrical mapping, and myocardial fiber angles in the same heart. In Functional Imaging and Modeling of Heart, T. Katila, I. E. Magnin, P. Clarysse, J. Montagnat, and J. Nenonen, Eds., LNCS, 76--82.

Digital Library

[40]

Muller, C., Rombaut, M., and Janier, M. 2001. Dempster shafer approach for high level data fusion applied to the assessment of myocardial viability. In Functional Imaging and Modeling of Heart, T. Katila, I. E. Magnin, P. Clarysse, J. Montagnat, and J. Nenonen, Eds., LNCS, 104--112.

Digital Library

[41]

Pinsky, H., Dyda, S., Pinsky, R., Misch, K., and Sarment, D. 2006. Accuracy of three-dimensional measurements using cone-beam ct. Dentomaxillofac. Radiol. 35, 6, 410--416.

[42]

Pottmann, H. 1995. Rational curves and surfaces with rational offsets. Computer Aided Geometric Design 12, 2, 175--192.

Digital Library

[43]

Pottmann, H. 1997. General offset surfaces. Neural, Parallel & Scientific Computationsi 5, 1--2, 55--80.

Digital Library

[44]

Rogers, J. M., and McCulloch, A. D. 1994. A collocation-galerkin finite element model of cardiac action potential propagation. IEEE Trans Biomed. Eng. 41, 743--757.

[45]

Rudy, Y., and Plonsey, R. 1980. A comparison of volume conductor and source geometry effects on body surface and epicardial potentials. Circ. Res. 46, 283--291.

[46]

Sachse, F. B. 2004. Computational Cardiology: Modeling of Anatomy, Electrophysiology, and Mechanics. LNCS 2966. Springer, Berlin, Heidelberg, New York.

Digital Library

[47]

Sahni, O., Mueller, J., Jansen, K. E., Shephard, M. S., and Taylor, C. A. 2005. Efficient anisotropic adaptive discretization of the cardiovascular system. Tech. rep., RPI.

[48]

Sahni, O. 2005. Adaptive procedure for efficient blood-flow simulations. PhD thesis, RPI.

[49]

Siersma, D. 1999. Voronoi diagrams and morse theory of the distance function. In Geometry in Present Day Science, O. E. Barndorff and E. B. V. Jensen, Eds. 187--208.

[50]

Simelius, K., Nenonen, J., and Horacek, B. M. 2001. Simulation of anisotropic propagation in the myocardium with a hybrid bidomain model. In Functional Imaging and Modeling of Heart, T. Katila, I. E. Magnin, P. Clarysse, J. Montagnat, and J. Nenonen, Eds., LNCS, 140--147.

Digital Library

[51]

Taylor, C., Hughes, T., and Zarins, C. 1998. Finite element modeling of 3-dimensional pulsatile flow in the abdominal aorta: Relevance to atherosclerosis. Annals of Biomedical Engineering 26, 6, 1--13.

[52]

Taylor, C., Hughes, T., and Zarins, C. 1998. Finite element modeling of blood flow in arteries. Computer Methods in Applied Mechanics and Engineering 158, 1--2, 155--196.

[53]

Taylor, C., Hughes, T., and Zarins, C. 1999. Effect of exercise on hemodynamic conditions in the abdominal aorta. Journal of Vascular Surgery 29, 1077--89.

[54]

Tilg, B., Modre, R., Fischer, G., Hanser, F., Messnarz, B., and Roithinger, F. X. 2001. Imaging of electrical function within the human atrium and ventricle from paced ecg mapping data. In Functional Imaging and Modeling of Heart, T. Katila, I. E. Magnin, P. Clarysse, J. Montagnat, and J. Nenonen, Eds., LNCS, 148--156.

Digital Library

[55]

Toshiba Medical Systems - 64 Slice CT. 2006. Clinical advancement in volumetric CT.

[56]

Veistera, H., and Lotjonen, J. 2001. Reconstructing 3d boundary element heart models from 2d biplane fluoroscopy. In Functional Imaging and Modeling of Heart, T. Katila, I. E. Magnin, P. Clarysse, J. Montagnat, and J. Nenonen, Eds., LNCS, 17--23.

Digital Library

[57]

Vetter, F., McCulloch, A., and Rogers, J. 1998. A finite element model of passive mechanics and electrical propagation in the rabbit ventricles. Computers in Cardiology, 705--708.

[58]

Winslow, R. L., Scollan, D. F., Holmes, A., Yung, C. K., Zhang, J., and Jafri, M. S. 2000. Electrophysiological modeling of cardiac ventricular function: From cell to organ. Annual Reviews in Biomedical Engineering 2, 119--155.

[59]

Yin, L., Luo, X., and Shephard, M. S. 2005. Identifying and meshing thin sections of 3-d curved domains. Tech. rep., RPI.

[60]

Yu, Z., and Bajaj, C. 2002. Normalized gradient vector diffusion and image segmentation. In Proceedings of European Conference on Computer Vision, 517--530.

Digital Library

[61]

Yu, Z., and Bajaj, C. 2004. A fast and adaptive algorithm for image contrast enhancement. In Proc of IEEE International Conference on Image Processing, 1001--1004.

[62]

Zhang, Y., Bajaj, C. L., and Xu, G. 2008. Surface smoothing and quality improvement of quadrilateral/hexahedral meshes with geometric flow. Communications in Numerical Methods in Engineering, To appear.

Cited By

Mukai NAbe YChang YNiki KTakanashi S(2015)Visualization of Pressure and Stress Distributions in Aortic Valve Simulation by Considering Heart's Pulsation and Axial FlowThe Journal of the Society for Art and Science10.3756/artsci.14.114:1(1-8)Online publication date: 25-Mar-2015
https://doi.org/10.3756/artsci.14.1
Kochová PCimrman RŠtengl MOšťádal BTonar Z(2015)A mathematical model of the carp heart ventricle during the cardiac cycleJournal of Theoretical Biology10.1016/j.jtbi.2015.03.014373(12-25)Online publication date: May-2015
https://doi.org/10.1016/j.jtbi.2015.03.014
Wang CManocha D(2013)GPU-based offset surface computation using point samplesComputer-Aided Design10.1016/j.cad.2012.10.01545:2(321-330)Online publication date: Feb-2013
https://doi.org/10.1016/j.cad.2012.10.015
Show More Cited By

Index Terms

Multi-component heart reconstruction from volumetric imaging
1. Computing methodologies
  1. Computer graphics
    1. Shape modeling
2. Theory of computation
  1. Design and analysis of algorithms
  2. Randomness, geometry and discrete structures
    1. Computational geometry

Recommendations

A New Combinatorial Approach to Surface Reconstruction with Sharp Features

This paper presents a new combinatorial approach to surface reconstruction with sharp features. Different from other postprocessing methods, the proposed method provides a systematic way to identify and reconstruct sharp features from unorganized sample ...
Sampling and meshing a surface with guaranteed topology and geometry
SCG '04: Proceedings of the twentieth annual symposium on Computational geometry

This paper presents an algorithm for sampling and triangulatinga smooth surface Σ ⊂ ℝ³ where the triangulation is homeomorphic to Σ. The only assumption we make is that the input surface representation is amenable to certain types of computations, ...
Sampling and Meshing a Surface with Guaranteed Topology and Geometry

This paper presents an algorithm for sampling and triangulating a generic $C^2$-smooth surface $\Sigma\subset \mathbb{R}^3$ that is input with an implicit equation. The output triangulation is guaranteed to be homeomorphic to $\Sigma$. We also prove ...

Comments

Information & Contributors

Information

Published In

cover image ACM Conferences

SPM '08: Proceedings of the 2008 ACM symposium on Solid and physical modeling

June 2008

423 pages

ISBN:9781605581064

DOI:10.1145/1364901

Conference Chairs:
Eric Haines
Autodesk
,
Morgan McGuire
Williams College

Copyright © 2008 ACM.

Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

Sponsors

SIGGRAPH: ACM Special Interest Group on Computer Graphics and Interactive Techniques

Publisher

Association for Computing Machinery

New York, NY, United States

Publication History

Published: 02 June 2008

Permissions

Request permissions for this article.

Request Permissions

Check for updates

Author Tags

Qualifiers

Research-article

Funding Sources

Conference

SPM08

Sponsor:

SIGGRAPH

SPM08: SPM '08 - ACM Solid and Physical Modeling Symposium

June 2 - 4, 2008

New York, Stony Brook

Contributors

Other Metrics

View Article Metrics

Bibliometrics & Citations

Bibliometrics

Article Metrics

6
Total Citations
View Citations
373
Total Downloads

Downloads (Last 12 months)2
Downloads (Last 6 weeks)0

Reflects downloads up to 09 Jan 2025

Other Metrics

View Author Metrics

Citations

Cited By

Mukai NAbe YChang YNiki KTakanashi S(2015)Visualization of Pressure and Stress Distributions in Aortic Valve Simulation by Considering Heart's Pulsation and Axial FlowThe Journal of the Society for Art and Science10.3756/artsci.14.114:1(1-8)Online publication date: 25-Mar-2015
https://doi.org/10.3756/artsci.14.1
Kochová PCimrman RŠtengl MOšťádal BTonar Z(2015)A mathematical model of the carp heart ventricle during the cardiac cycleJournal of Theoretical Biology10.1016/j.jtbi.2015.03.014373(12-25)Online publication date: May-2015
https://doi.org/10.1016/j.jtbi.2015.03.014
Wang CManocha D(2013)GPU-based offset surface computation using point samplesComputer-Aided Design10.1016/j.cad.2012.10.01545:2(321-330)Online publication date: Feb-2013
https://doi.org/10.1016/j.cad.2012.10.015
Rossi SRuiz‐Baier RPavarino LQuarteroni A(2012)Orthotropic active strain models for the numerical simulation of cardiac biomechanicsInternational Journal for Numerical Methods in Biomedical Engineering10.1002/cnm.247328:6-7(761-788)Online publication date: 28-Feb-2012
https://doi.org/10.1002/cnm.2473
Hu PChen HWu WHeng P(2010)Multi-Tissue Tetrahedral Mesh Generation from Medical Images2010 4th International Conference on Bioinformatics and Biomedical Engineering10.1109/ICBBE.2010.5514705(1-4)Online publication date: Jun-2010
https://doi.org/10.1109/ICBBE.2010.5514705
Bajaj CDiCarlo APaoluzzi A(2008)PROTO-PLASM: parallel language for adaptive and scalable modelling of biosystemsPhilosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences10.1098/rsta.2008.0076366:1878(3045-3065)Online publication date: 13-Sep-2008
https://doi.org/10.1098/rsta.2008.0076

View Options

Login options

Check if you have access through your login credentials or your institution to get full access on this article.

Full Access

Get this Publication

View options

PDF

View or Download as a PDF file.

eReader

View online with eReader.

Media

Figures

Other

Tables

View Table of Contents