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Snakes on a Plane: A Perfect Snap for Bioimage Analysis

R. Delgado-Gonzalo, V. Uhlmann, D. Schmitter, M. Unser

IEEE Signal Processing Magazine, vol. 32, no. 1, pp. 41-48, January 2015.



In recent years, there has been an increasing interest in getting a proper quantitative understanding of cellular and molecular processes [1], [2]. One of the major challenges of current biomedical research is to characterize not only the spatial organization of these complex systems but also their spatiotemporal relationships [3], [4]. Microscopy has matured to the point that it enables sensitive time-lapse imaging of cells in vivo and even of single molecules [5], [6]. Making microscopy more quantitative brings important scientific benefits in the form of improved performance and reproducibility. This has been fostered by the development of technological achievements such as high-throughput microscopy. A direct consequence is that the size and complexity of image data are increasing. Time-lapse experiments commonly generate hundreds to thousands of images, each containing hundreds of objects to be analyzed [7]. These data often cannot be analyzed manually because the manpower required would be too extensive, which calls for automated methods for the analysis of biomedical images. Such computerized extraction of quantitative information out of the rapidly expanding amount of acquired data remains a major challenge. The development of the related algorithms is nontrivial and is one of the most active fronts in the new field of bioimage informatics [8, 9, 10, 11]. Segmenting thousands of individual biological objects and tracking them over time is remarkably difficult. A typical algorithm will need to be tuned to the imaging modality and will have to cope with the fact that cells can be tightly packed and may appear in various configurations, making them difficult to segregate.

References

  1. Z.N. Demou, "Time-Lapse Analysis and Microdissection of Living 3D Melanoma Cell Cultures for Genomics and Proteomics," Biotechnology and Bioengineering, vol. 101, no. 2, pp. 307-316, October 2008.

  2. K. Kirkegaard, I.E. Agerholm, H.J. Ingerslev, "Time-Lapse Monitoring as a Tool for Clinical Embryo Assessment," Human Reproduction, vol. 27, no. 5, pp. 1277-1285, May 2012.

  3. C. Zimmer, B. Zhang, A. Dufour, A. Thébaud, S. Berlemont, V. Meas-Yedid, and J.-C.O. Marin, "On the Digital Trail of Mobile Cells," IEEE Signal Processing Magazine, vol. 23, no. 3, pp. 54-62, May 2006.

  4. N. Dénervaud, J. Becker, R. Delgado-Gonzalo, P. Damay, A.S. Rajkumar, M. Unser, D. Shore, F. Naef, S.J. Maerki, "A Chemostat Array Enables the Spatio-Temporal Analysis of the Yeast Proteome," Proceedings of the National Academy of Sciences of the United States of America, vol. 110, no. 39, pp. 15842-15847, September 24, 2013.

  5. A. Miyawaki, "Visualization of the Spatial and Temporal Dynamics of Intracellular Signaling," Developmental Cell, vol. 4, no. 3, pp. 295-305, March 2003.

  6. D. Muzzey, A. van Oudenaarden, "Quantitative Time-Lapse Fluorescence Microscopy in Single Cells," Annual Review of Cell and Developmental Biology, vol. 25, pp. 301-327, November 2009.

  7. M. Oheim, "Advances and Challenges in High-Throughput Microscopy for Live-Cell Subcellular Imaging," Expert Opinion on Drug Discovery, vol. 6, no. 12, pp. 1299-1315, December 2011.

  8. G. Myers, "Why Bioimage Informatics Matters," Nature Methods, vol. 9, no. 7, pp. 659-660, July 2012.

  9. A. Cardona, P. Tomancak, "Current Challenges in Open-Source Bioimage Informatics," Nature Methods, vol. 9, no. 7, pp. 661-665, July 2012.

  10. J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. Rueden, S. Saalfeld, B. Schmid, J.-Y. Tinevez, D.J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, A. Cardona, "Fiji: An Open-Source Platform for Biological-Image Analysis," Nature Methods, vol. 9, no. 7, pp. 676-682, July 2012.

  11. F. de Chaumont, S. Dallongeville, N. Chenouard, N. Hervé, S. Pop, T. Provoost, V. Meas-Yedid, P. Pankajakshan, T. Lecomte, Y. Le Montagner, T. Lagache, A. Dufour, J.-C. Olivo-Marin, "Icy: An Open Bioimage Informatics Platform for Extended Reproducible Research," Nature Methods, vol. 9, no. 7, pp. 690-696, July 2012.


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