AUTOMATIC SEGMENTATION OF EMBRYONIC HEART IN TIME-LAPSE FLUORESCENCE MICROSCOPY IMAGE SEQUENCES

P. Krämer, F. Boto, D. Wald, F. Bessy, C. Paloc, C. Callol, A. Letamendia, I. Ibarbia, O. Holgado, J. M. Virto

Abstract

Embryos of animal models are becoming widely used to study cardiac development and genetics. However, the analysis of the embryonic heart is still mostly done manually. This is a very laborious and expensive task as each embryo has to be inspected visually by a biologist. We therefore propose to automatically segment the embryonic heart from high-speed fluorescence microscopy image sequences, allowing morphological and functional quantitative features of cardiac activity to be extracted. Several methods are presented and compared within a large range of images, varying in quality, acquisition parameters, and embryos position. Although manual control and visual assessment would still be necessary, the best of our methods has the potential to drastically reduce biologist workload by automating manual segmentation.

References

  1. Bishop, C.M. (2007). Pattern Recognition and Machine Learning. (Information Science and Statistics). Springer.
  2. Cox, T. and Cox, M. (2001). Multidimensional Scaling (2nd ed.). Chapman & Hall/CRC.
  3. Fink, M., Callol-Massot, C., Chu, A., Ruiz-Lozano, P., Belmonte, J. C., Giles, W., Bodmer, R., and Ocorr, K. (2009). A new method for detection and quantification of heartbeat parameters in drosophila, zebrafish, and embryonic mouse hearts. BioTechniques, 46(2), 101- 113.
  4. Ge, F., Wang, S., and Liu, T. (2007). New benchmark for image segmentation evaluation. Journal of Electronic Imaging, 16(3):033011.
  5. Hu, N., Sedmera, D., Yost, H., and Clark, E. (2000). Structure and function of the developing zebrafish heart. The Anatomical Record, 260(2), 148-157.
  6. Imelinska, C., Downes, M., and Yuan, W. (2002). Semiautomated color segmentation of anatomical tissue. Computerized Medical Imaging and Graphics, 24, 173-180.
  7. LaViola Jr., J. (2003). Double exponential smoothing: An alternative to kalman filter-based predictive tracking. In Immersive Projection Technology and Virtual Environments, 199-206.
  8. Li, C., Xu, C., Gui, C., and Fox, M. (2005). Level set evolution without re-initialization: A new variational formulation. CVPR, 1, 430-436. IEEE.
  9. Liebling, M., Forouhar, A., Wolleschensky, R., Zimmermann, B., Ankerhold, R., Fraser, S., Gharib, M., and Dickinson, M. E. (2006). Rapid threedimensional imaging and analysis of the beating embryonic heart reveals functional changes during development. Developmental Dynamics, 235(11), 2940-2948.
  10. Luengo-Oroz, M., Faure, E., Lombardot, B., Sance, R., Bourgine, P., Peyríeras, N., and Santos, A. (2007). Twister segment morphological filtering. A new method for live zebrafish embryos confocal images processing. ICIP, 253-256. IEEE.
  11. Otsu, N. (1979). A threshold selection method from graylevel histograms. IEEE Trans. on Systems, Man and Cybernetics, 1(9), 62-69.
  12. Sezgin, M. and Sankur, B. (2004). Survey over image thresholding techniques and quantitative performance evaluation. Journal of Electronic Imaging, 13(1), 146- 168.
  13. Vermot, J., Fraser, S., and Liebling, M. (2008). Fast fluorescence microscopy for imaging the dynamics of embryonic development. HFSP Journal, 2(3), 143- 155.
  14. Zhang, H., Fritts, J., and Goldman, S. (2008). Image segmentation evaluation: A survey of unsupervised methods. Computer Vision and Image Understanding, 110(2), 260-280.
  15. Zuiderveld, K. (1994). Graphics Gems IV, chapter Contrast Limited Adaptive Histogram Equalization, pages 474-485. Academic Press.
Download


Paper Citation


in Harvard Style

Krämer P., Boto F., Wald D., Bessy F., Paloc C., Callol C., Letamendia A., Ibarbia I., Holgado O. and Virto J. (2010). AUTOMATIC SEGMENTATION OF EMBRYONIC HEART IN TIME-LAPSE FLUORESCENCE MICROSCOPY IMAGE SEQUENCES . In Proceedings of the Third International Conference on Bio-inspired Systems and Signal Processing - Volume 1: BIOSIGNALS, (BIOSTEC 2010) ISBN 978-989-674-018-4, pages 121-126. DOI: 10.5220/0002342501210126


in Bibtex Style

@conference{biosignals10,
author={P. Krämer and F. Boto and D. Wald and F. Bessy and C. Paloc and C. Callol and A. Letamendia and I. Ibarbia and O. Holgado and J. M. Virto},
title={AUTOMATIC SEGMENTATION OF EMBRYONIC HEART IN TIME-LAPSE FLUORESCENCE MICROSCOPY IMAGE SEQUENCES},
booktitle={Proceedings of the Third International Conference on Bio-inspired Systems and Signal Processing - Volume 1: BIOSIGNALS, (BIOSTEC 2010)},
year={2010},
pages={121-126},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0002342501210126},
isbn={978-989-674-018-4},
}


in EndNote Style

TY - CONF
JO - Proceedings of the Third International Conference on Bio-inspired Systems and Signal Processing - Volume 1: BIOSIGNALS, (BIOSTEC 2010)
TI - AUTOMATIC SEGMENTATION OF EMBRYONIC HEART IN TIME-LAPSE FLUORESCENCE MICROSCOPY IMAGE SEQUENCES
SN - 978-989-674-018-4
AU - Krämer P.
AU - Boto F.
AU - Wald D.
AU - Bessy F.
AU - Paloc C.
AU - Callol C.
AU - Letamendia A.
AU - Ibarbia I.
AU - Holgado O.
AU - Virto J.
PY - 2010
SP - 121
EP - 126
DO - 10.5220/0002342501210126