Embryonic Hearts

  • Project Members:

    Dr. Sandra Rugonyi

    Dr. Charless Fowlkes

    Dr. Cindy Grimm

    Project Description:

    During embryonic development, the heart transforms from a tubular to a four-chamber structure. These changes depend on pre-programmed genetic processes, but are also modulated by environmental factors such as blood flow. Blood flow provides biomechanical stimuli to cardiac cells. These stimuli modulate cell responses and cellular adaptations to hemodynamic conditions, which lead to morphological remodeling of the heart. As a result of cellular adaptations, altered blood flow conditions during early embryonic development lead to cardiac defects, which are deviations in the shape of the heart with respect to its normal shape. Changes in heart morphology also affect heart function. Cardiac walls contract to pump blood, and in doing so they interact with blood flow and affect flowing patterns. Heart morphology and the motion of the heart during the cardiac cycle are therefore linked to cardiac function. Difficulties in reliably quantifying cardiac morphology and motion have prevented researchers from fully understanding the extent to which alterations in hemodynamic conditions, as well as other environmental factors and genetic alterations, affect heart development.

    The goal of this collaborative effort was to develop tools for mathematically describing biological shape, as well as methods for extracting meaningful information on biological variation. We used data from chicken embryonic hearts, and in particular the heart OFT, to guide development of tools and algorithms. As part of this project, we developed: i) an algorithm to semi-automatically segment the motion of the developing embryonic heart OFT from 3D OCT images 1; ii) a consistent parameterization for the OFT surfaces together with a procedure to improve mesh registration over time based on the minimization of strains 2; iii) visualization techniques to analyze cardiac motion and shape changes; iv) procedures to measure and mathematically model blood flow dynamics in the developing heart OFT 3,4. We applied these methods and procedures to the description of cardiac motion during early stages of embryonic development 2, and we also employed the methodologies to the description of abdominal aortic aneurysm progression 5 - broadening the impact of the developed algorithms and procedures.


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    • Hossain, M. Shahriar, Praveen Kumar Reddy Ojili, Cindy Grimm, Rolf Muller, Layne T. Watson, and Naren Ramakrishnan. "Scatter/gather clustering: flexibly incorporating user feedback to steer clustering results." Visualization and Computer Graphics, IEEE Transactions on 18, no. 12 (2012): 2829-2838.
    • Meymand, Sajjad Zeinoddini, Mittu Pannala, and Rolf Muller. "Characterization of the time-variant behavior of a biomimetic beamforming baffle." The Journal of the Acoustical Society of America 133.2 (2013): 1141-1150.
    • Motamedi, Mohammad, and Rolf Muller. "Characterization of the diversity in bat biosonar beampatterns with spherical harmonics power spectra." The Journal of the Acoustical Society of America 135.6 (2014): 3613-3619.
    • Pannala, Mittu, Sajjad Zeinoddini Meymand, and Rolf Muller. "Interplay of static and dynamic features in biomimetic smart ears." Bioinspiration & biomimetics 8.2 (2013): 026008.
    • Caspers, Philip, Alexander Leonessa, and Rolf Mueller. "Eigenbeam analysis of the diversity in bat biosonar beampatterns." The Journal of the Acoustical Society of America 135.4 (2014): 2207-2207.
    • Muller, Rolf, Jianguo Ma, Zhen Yan, Cindy Grimm, and Washington Mio. "Bioinspiration From Biodiversity in Sensor Design." In ASME 2011 International Mechanical Engineering Congress and Exposition, pp. 825-834. American Society of Mechanical Engineers, 2011.
    • Knutsen, Andrew K., Yulin V. Chang, Cindy M. Grimm, Ly Phan, Larry A. Taber, and Philip V. Bayly. "A new method to measure cortical growth in the developing brain." Journal of biomechanical engineering 132, no. 10 (2010): 101004.
    • Heider, Paul, Alain Pierre-Pierre, Ruosi Li, Rolf Mueller, and Cindy Grimm. "Comparing local shape descriptors." The Visual Computer 28, no. 9 (2012): 919-929.
    • Kurtek, Sebastian, Jingyong Su, Cindy Grimm, Michelle Vaughan, Ross Sowell, and Anuj Srivastava. "Statistical analysis of manual segmentations of structures in medical images." Computer Vision and Image Understanding 117, no. 9 (2013): 1036-1050.
    • Ly Phan, Sandra Rugonyi, Cindy Grimm, Visualization techniques for the developing chicken heart. (in preparation to IEEE TRANS. ON VISUALIZATION AND COMPUTER GRAPHICS), 2014
    • Shi, Liang, Sevan Goenezen, Stephen Haller, Monica T. Hinds, Kent L. Thornburg, and Sandra Rugonyi. "Alterations in pulse wave propagation reflect the degree of outflow tract banding in HH18 chicken embryos." American Journal of Physiology-Heart and Circulatory Physiology 305, no. 3 (2013): H386-H396.
    • Yin, Xin, Aiping Liu, Kent L. Thornburg, Ruikang K. Wang, and Sandra Rugonyi. "Extracting cardiac shapes and motion of the chick embryo heart outflow tract from four-dimensional optical coherence tomography images." Journal of biomedical optics 17, no. 9 (2012): 096005-096005.
    • Madeline Midgett, Sevan Goenezen and Sandra Rugonyi, Blood flow dynamics reflect degree of outflow tract banding in Hamburger -Hamilton stage 18 chicken embryos. J. R. Soc. Interface 2014 11, 20140643, published 27 August 2014
    • Li, Peng, Xin Yin, Liang Shi, Sandra Rugonyi, and Ruikang K. Wang. "In vivo functional imaging of blood flow and wall strain rate in outflow tract of embryonic chick heart using ultrafast spectral domain optical coherence tomography." Journal of biomedical optics 17, no. 9 (2012): 0960061-0960068.
    • Yin X, Liu A, Thornburg K, Wang RK, Rugonyi S. Extracting the 3D Cardiac Shape and Motion of the Chick Embryo Heart Outflow Tract from 4D Optical Coherence Tomography Images. Journal of Biomedical Optics 2012;17:096005.
    • Phan L, Knutsen AK, Bayly PV, Rugonyi S, Grimm C. Refining shape correspondence for similar objects using strain. Eurographic Workshop on 3D Retrieval 2011;Sect. 17-24.
    • Shi L, Goenezen S, Haller S, Hinds MT, Thornburg KL, Rugonyi S. Alterations in pulse wave propagation reflect the degree of outflow tract banding in HH18 chicken embryos. American Journal of Physiology - Heart and Circulatory Physiology 2013;305:H386-H96.
    • Midgett M, Goenezen S, Rugonyi S. Blood flow dynamics reflect degree of outflow tract banding in Hamburger-Hamilton stage 18 chicken embryos. Journal of the Royal Society Interface 2014;11:20140643.
    • Zelaya J, Goenezen S, Dargon P, Azarbal A-F, Rugonyi S. Improving the Efficiency of Abdominal Aortic Aneurysm Wall Stress Computations. PLoS ONE 2014;9:e101353.
    • Liu, Aiping, Xin Yin, Liang Shi, Peng Li, Kent L. Thornburg, Ruikang Wang, and Sandra Rugonyi. "Biomechanics of the chick embryonic heart outflow tract at HH18 using 4D optical coherence tomography imaging and computational modeling." PloS one 7, no. 7 (2012): e40869.
    • Midgett M, Rugonyi S. Congenital heart malformations induced by hemodynamic altering surgical interventions. Frontiers in Physiology 2014;5.
    • Keller BB. Embryonic cardiovascular function, coupling and maturation: a species view. In: Burggren WW, Keller BB, eds. Development of Cardiovascular Systems. Cambridge, MA: University Press; 1998.
    • Clark EB, Rosenquist GC. Spectrum of cardiovascular anomalies following cardiac loop constriction in the chick embryo. Birth Defects: Original Article Series 1978;XIV:431-42.
    • Bergwerff M, DeRuiter MC, Poelmann RE, Gittenberger-de Groot AC. Onset of elastogenesis and downregulation of smooth muscle actin as distinguishing phenomena in artery differentiation in the chick embryo. Anat Embryol (Berl) 1996;194:545?57.
    • B. Kong, C. Fowlkes, "Fast Convolutional Sparse Coding", UCI Technical Report, May 2014 http://www.ics.uci.edu/~fowlkes/papers/kf_fcsc_techreport_2014.pdf
    • A. Chen, E. Lee, R. Tu, K. Santiago, A. Grosberg, C. Fowlkes, M. Khine, "Integrated Platform for Functional Monitoring of Biomimetic Heart Sheets Derived From Human Pluripotent Stem Cells", Biomaterials 35(2):675-683, http://www.ics.uci.edu/~fowlkes/papers/chen_et_al_biomaterials_2013.pdf
    • L. Mander, M. Li, W. Mio, C. Fowlkes, S. Punyasena, "Classification of grass pollen through the quantitative analysis of surface ornamentation and texture", Proc. R. Soc. B. 2013 280 (1770) http://www.ics.uci.edu/~fowlkes/papers/mlmfp_pollen.pdf
    • J. Yarkony, A. Ihler, C. Fowlkes, "Fast Planar Correlation Clustering for Image Segmentation'', Proc. of ECCV, Firenze, Italy (Oct. 2012). arXiv:1208.0378v1 http://www.ics.uci.edu/~fowlkes/papers/yif-eccv12-extended.pdf
    • X. Zhu, C. Vondrick, D. Ramanan, C. Fowlkes, "Do we need more training data or better models for object detection?", Proc. of BMVC, Surrey, UK (Sept. 2012). http://www.ics.uci.edu/~fowlkes/papers/zvrf-bmvc12.pdf
    • C. Fowlkes, K. Eckenrode, M. Bragdon, M. Meyer, Z. Wunderlich, L. Simirenko, C. Hendriks, S. Keranen, C. Henreiquez, M. Biggin, M. Eisen, A. DePace, "A conserved developmental patterning network produces quantitatively different output in multiple species of Drosophila," PLoS Genetics, 7(10): e1002346, 2011. http://www.ics.uci.edu/~fowlkes/papers/FowlkesDePace_PLoSGen2011.pdf
    • J. Hengenius, M. Gribskov, A. Rundell, C. Fowlkes, D. Umulis, "Analysis of Gap Gene Regulation in a 3D Organism-Scale Model of the Drosohpila melanogaster Embryo", PLoS ONE 6(11): e26797. doi:10.1371/journal.pone.0026797, 2011. http://www.ics.uci.edu/~fowlkes/papers/Hengenuius_et_al_PLoSone2011.pdf
    • A. Chen, D. Lieu, L. Freschauf, V. Lew, H. Sharma, J. Wang, D. Nguyen, I. Karakikes, R. Hajjar, A. Gopinathan, E. Botvinick, C. Fowlkes, R. Li, M. Khine, "Shrink-Film Configurable Multiscale Wrinkles for Functional Alignment of Human Embryonic Stem Cells and their Cardiac Derivatives", 10.1002/adma.201103463, Advanced Materials, 2011. http://www.ics.uci.edu/~fowlkes/papers/Chen_et_al_AdvMat2011.pdf
    • J. Luna, J. Ciriza, M. Ojeda-Garcia, M. Kong, A. Herren, D. Lieu, R. Li, C. Fowlkes, M. Khine, K. McCloskey, "Multi-scale Biomimetic Topography for the Alignment of Neonatal and Embryonic Stem Cell-derived Heart Cells", Tissue Engineering: Part C , 17(5), p. 579-588 , 2011 http://www.ics.uci.edu/~fowlkes/papers/Luna_et_al_TEC2011.pdf

    New Projects:

    National Science Foundation, Cindy Grimm (PI), CGV: Medium: Collaborative Research: Developing Conceptual Models for Navigation, Marking, and Inspection in the Context of 3D Image Segmentation