The Cardiac Atlas Project: Development of a Framework Integrating Cardiac Images and Models

  • Michael Backhaus
  • Randall Britten
  • Jae Do Chung
  • Brett R. Cowan
  • Carissa G. Fonseca
  • Pau Medrano-Gracia
  • Wenchao Tao
  • Alistair A. Young
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6364)


We describe the software design, architecture and infrastructure employed in the Cardiac Atlas Project (CAP), an international collaboration to establish a web-accessible structural and functional atlas of the normal and pathological heart. Cardiac imaging data is de-identified in a HIPAA compliant manner using the LONI Debabeler with customized DICOM mappings. A production database and web-interface were employed based on existing tools developed by LONI. A new open-source database and web interface have been developed for research purposes. After consideration and evaluation of several software frameworks, the research database has been implemented based on a 3-tier architecture utilizing MySQL, JBoss and Dcm4chee. Parts of Dcm4chee have been extended to enable access to MRI specific attributes and arbitrary search parameters. An XML schema has been designed representing the elements associated with the creation and curation of volumetric shape models. The research database is implemented compliant to the DICOM standard, thus providing compatibility with existing clinical networks and devices. A modeling tool, the CAP client, has been developed to enable browsing of 3D image data and creation and modification of volumetric shape models. All software components developed by the CAP are open source and are freely available under the Mozilla license.


Computational Atlas Database Parametric Shape Models 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Neu, S.C., Valentino, D.J., Toga, A.W.: The LONI Debabeler: a mediator for neuroimaging software. NeuroImage 24(4) (2005)Google Scholar
  2. 2.
    Young, A.A., Frangi, A.F.: Computational cardiac atlases: from patient to population and back. Experimental Physiology (2009)Google Scholar
  3. 3.
    Meier, W.: eXist: An Open Source Native XML Database. LNCS, vol. 2593. Springer, Berlin (2009)Google Scholar
  4. 4.
    Philip, M.P.: Building Cyber-Infrastructure for the Biomedical Informatics Research Network. IEEE Computer Society, Los Alamitos (2006)Google Scholar
  5. 5.
    Cimino, J.J., Hayamizu, T.F., Bodenreider, O., Davis, B., Stafford, G.A., Ringwald, M.: The caBIG terminology review process. Journal of Biomedical Informatics 42(3), Auditing of Terminologies (2009)Google Scholar
  6. 6.
    Warnock, M.J., Toland, C., Evans, D., Wallace, B., Nagy, P.: Benefits of Using the DCM4CHE DICOM Archive. Journal of Digital Imaging (2007)Google Scholar
  7. 7.
    Widenius, M., Axmark, D., DuBois, P.: Mysql Reference Manual. O’Reilly & Associates, Inc., Sebastopol (2002)Google Scholar
  8. 8.
    Heffelfinger, D.: Java EE 5 Development using GlassFish Application Server. Packt Pub. Ltd. (2007)Google Scholar
  9. 9.
    Backhaus, M., Chung, J., Cowan, B.R., Fonseca, C.G., Tao, W., Young, A.A.: The Cardiac Atlas Project: Towards a Map of the Heart. In: Kerckhoffs, R. (ed.) Patient-specific modeling of the cardiovascular system. Springer, Heidelberg (in press)Google Scholar
  10. 10.
    Sezov, R.: Liferay Portal Administrator’s Guide, 3rd edn. Liferay Press, Los Angeles (2009)Google Scholar
  11. 11.
    Bellas, F.: Standards for second-generation portals. IEEE Internet Computing (2004)Google Scholar
  12. 12.
    Alur, D., Crupi, J., Malks, D.: Core J2EE patterns. Prentice Hall PTR, Englewood Cliffs (2003)Google Scholar
  13. 13.
    Fleury, M., Lindfors, J.: JMX: Managing J2EE with Java Management Extensions. Sams, USA (2002)Google Scholar
  14. 14.
    Bray, T., Paoli, J., Sperberg-McQueen, C.M., Maler, E., Yergeau, F., Cowan, J.: Extensible markup language (XML) 1.1. W3C Recommendation (2006)Google Scholar
  15. 15.
    Parisot, C.: The DICOM standard: A breakthrough for digital information exchange in cardiology. The International Journal of Cardiac Imaging 11(3) (1995)Google Scholar
  16. 16.
    Gregg, B., DAgostino, H., Toledo, E.G.: Creating an IHE ATNA-Based Audit Repository. Journal of Digital Imaging (2006)Google Scholar
  17. 17.
    Smart, J., Hock, K., Csomor, S.: Cross-Platform GUI Programming with wxWidgets. Prentice Hall PTR, Englewood Cliffs (2005)Google Scholar
  18. 18.
    Rosse, C., Mejino Jr., J.L.V.: A reference ontology for biomedical informatics: the Foundational Model of Anatomy. Journal of Biomedical Informatics (2003)Google Scholar
  19. 19.
    Stearns, M.Q., Price, C., Spackman, K.A., Wang, A.Y.: SNOMED clinical terms: overview of the development process and project status. In: Proc. AMIA Symp. (2001)Google Scholar
  20. 20.
    McGuinness, D.L., van Harmelen, F.: OWL web ontology language overview, W3C recommendation (2004)Google Scholar
  21. 21.
    Gamma, E., Helm, R., Johnson, R., Vlissides, J.: Design patterns: elements of reusable object-oriented software. Lavoisier (1995)Google Scholar
  22. 22.
    Nguyen, D.: Abstract Factory Design Pattern. Connexions (2008)Google Scholar
  23. 23.
    Fonseca, C.G., Backhaus, M., Chung, J.D., Tao, W., Medrano-Gracia, P., Cowan, B.R., Hunter, P.J., Finn, J.P., Shivkumar, K., Lima, J.A.C., Bluemke, D.A., Kadish, A.H., Lee, D.C., Young, A.A.: MICCAI 2010 Workshop on Statistical Atlases and Computational Models of the Heart: Mapping Structure and Function plus a Cardiac Electrophysiological Simulation Challenge (STACOM-CESCÕ 2010), Beijing, China. LNCS. Springer, Heidelberg (2010) (in press)Google Scholar
  24. 24.
    Larrabide, I., Omedas, P., Martelli, Y., Planes, X., Nieber, M., Moya, J.A., Butakoff, C., Sebastian, R., Camara, O., De Craene, M., Bijnens, B.H., Frangi, A.F.: GIMIAS: An Open Source Framework for Efficient Development of Research Tools and Clinical Prototypes. LNCS. Springer, Heidelberg (2009)Google Scholar
  25. 25.
    Toussaint, N.: CardioViz3D: Cardiac Simulation Data Processing and Visualization, User Manual, INRIA Sophia-Antipolis (2008)Google Scholar
  26. 26.
    Digital Imaging and Communications in Medicine (DICOM) (2009)Google Scholar
  27. 27.
    MySQL 5.1 Reference Manual, Functions and Operators, XML Functions,
  28. 28.
    XML Path Language (XPath) 2.0, W3C Recommendation (2007),
  29. 29.
    U.S. Department of Health and Human Services, Privacy Rule, 45 CFR Parts 160, 162, and 164Google Scholar
  30. 30.
    CAP Sourceforge project site,
  31. 31.
  32. 32.
  33. 33.
    Physiome Model Repository,
  34. 34.
    JBoss Application Server, JBoss Inc. (2002)Google Scholar
  35. 35.
  36. 36.
  37. 37.
    Cardiovascular Research Grid,
  38. 38.
    Boost C++ Libraries,
  39. 39.
    World Health Organization, Fact sheet No. 317 (Updated September 2009)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • Michael Backhaus
    • 1
  • Randall Britten
    • 1
  • Jae Do Chung
    • 1
  • Brett R. Cowan
    • 1
  • Carissa G. Fonseca
    • 2
  • Pau Medrano-Gracia
    • 1
  • Wenchao Tao
    • 2
  • Alistair A. Young
    • 1
  1. 1.Auckland Bioengineering InstituteUniversity of AucklandAucklandNew Zealand
  2. 2.Diagnostic CardioVascular Imaging, UCLALos Angeles

Personalised recommendations