Article: Research on segmentation of dorsal diencephalon and ventral midbrain of zebrafish embryo based on active contour model Journal: International Journal of Computational Biology and Drug Design (IJCBDD) 2012 Vol.5 No.1 pp.3 - 15 Abstract: Zebrafish is a valuable vertebrate model in life science research. In the zebrafish research, segmentation of zebrafish embryo images is a prerequisite for subsequent processing and analysis. Specifically, shape analysis of zebrafish's two important organs, the dorsal diencephalon and the ventral midbrain, is significant for studying the mutants caused by gene expression. Nevertheless, due to non-uniform intensity distribution and weak boundaries in dorsal diencephalon and ventral midbrain microscopic images, classical segmentation methods are unable to determine the precise boundaries. In this paper, a novel segmentation technique for zebrafish embryo images is proposed based on active contour model, which includes region based active contour model and geodesic active contour. Finally, the effectiveness of this approach is confirmed by the experimental results that the agreement between the algorithm and manual segmentation is more than 90%. Inderscience Publishers - linking academia, business and industry through research

Title: Research on segmentation of dorsal diencephalon and ventral midbrain of zebrafish embryo based on active contour model

Authors: Tao Wu; Jianfeng Lu; Yanting Lu; Jingyu Yang

Addresses: School of Computer Science, Nanjing University of Science and Technology, Nanjing, Jiangsu, 210094, China. ' School of Computer Science, Nanjing University of Science and Technology, Nanjing, Jiangsu, 210094, China. ' School of Computer Science, Nanjing University of Science and Technology, Nanjing, Jiangsu, 210094, China. ' School of Computer Science, Nanjing University of Science and Technology, Nanjing, Jiangsu, 210094, China

Abstract: Zebrafish is a valuable vertebrate model in life science research. In the zebrafish research, segmentation of zebrafish embryo images is a prerequisite for subsequent processing and analysis. Specifically, shape analysis of zebrafish's two important organs, the dorsal diencephalon and the ventral midbrain, is significant for studying the mutants caused by gene expression. Nevertheless, due to non-uniform intensity distribution and weak boundaries in dorsal diencephalon and ventral midbrain microscopic images, classical segmentation methods are unable to determine the precise boundaries. In this paper, a novel segmentation technique for zebrafish embryo images is proposed based on active contour model, which includes region based active contour model and geodesic active contour. Finally, the effectiveness of this approach is confirmed by the experimental results that the agreement between the algorithm and manual segmentation is more than 90%.

Keywords: zebrafish embryo images; brain segmentation; active contour modelling; level set; image processing; dorsal diencephalon; vertebrate models; ventral midbrain; mutants; gene expression; image segmentation.

DOI: 10.1504/IJCBDD.2012.045948

International Journal of Computational Biology and Drug Design, 2012 Vol.5 No.1, pp.3 - 15

Published online: 05 Dec 2014 *

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Title: Research on segmentation of dorsal diencephalon and ventral midbrain of zebrafish embryo based on active contour model

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