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International Journal of Biomedical Imaging
Volume 2009 (2009), Article ID 968986, 9 pages
Research Article

Region-Based PDEs for Cells Counting and Segmentation in 3D+Time Images of Vertebrate Early Embryogenesis

1DEIS, University of Bologna, Via Venezia 52, 47521 Cesena, Italy
2DEIS, University of Bologna, Via Risorgimento 2, 40136 Bologna, Italy

Received 20 October 2008; Accepted 16 July 2009

Academic Editor: David Wilson

Copyright © 2009 Barbara Rizzi and Alessandro Sarti. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


This paper is devoted to the segmentation of cell nuclei from time lapse confocal microscopy images, taken throughout early Zebrafish embryogenesis. The segmentation allows to identify and quantify the number of cells in the animal model. This kind of information is relevant to estimate important biological parameters such as the cell proliferation rate in time and space. Our approach is based on the active contour model without edges. We compare two different formulations of the model equation and evaluate their performances in segmenting nuclei of different shapes and sizes. Qualitative and quantitative comparisons are performed on both synthetic and real data, by means of suitable gold standard. The best approach is then applied on a number of time lapses for the segmentation and counting of cells during the development of a zebrafish embryo between the sphere and the shield stage.