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Proceedings Paper

Standard 3D digital atlas of zebrafish embryonic development for projection of experimental data
Author(s): Fons J. Verbeek; M. J. den Broeder; Paul J. Boon; B. Buitendijk; E. Doerry; E. J. van Raaij; D. Zivkovic
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Paper Abstract

In developmental biology an overwhelming amount of experimental data concerning patterns of gene expression is produced revealing the genetic layout of the embryo and finding evidence for anomalies. Genes are part of complex genetic cascades and consequently their study requires tools for handling combinatorial problems. Gene expression is spatio-temporal and generally, imagin is used to analyze expression in four dimensions. Reporting and retrieving experimental data has become so complex that printed literature is no longer adequate and therefore databases are being implemented. Zebrafish is a popular model system in developmental biology. We are developing a 3D digital atlas of the zebrafish embryo, which is envisaged as standard allowing comparisons of experimentally induced and normally developing embryos. This 3D atlas is based on microscopical anatomy. From serial sections 3D images are reconstructed by capturing section images and registering these images respectively. This is accomplished for al developmental stages. Data management is solved using XML which is platform independent, ASCII-based, interchangeable and allows easy browsing. Applying supervised segmentation accomplishes a completely anatomically annotated 3D image. It divides the image into domains required for comparison and mapping. Experts provided with dedicated software and Internet-access to the images review annotations. Complete annotation and review is stored in a database.

Paper Details

Date Published: 20 December 1999
PDF: 11 pages
Proc. SPIE 3964, Internet Imaging, (20 December 1999); doi: 10.1117/12.373465
Show Author Affiliations
Fons J. Verbeek, Netherlands Institute for Developmental Biology (Netherlands)
M. J. den Broeder, Netherlands Institute for Developmental Biology (Netherlands)
Paul J. Boon, Netherlands Institute for Developmental Biology (Netherlands)
B. Buitendijk, Netherlands Institute for Developmental Biology and Netherlands Inst. for Sci. Information (Netherlands)
E. Doerry, Univ. of Oregon (Netherlands)
E. J. van Raaij, Netherlands Institute for Developmental Biology (Netherlands)
D. Zivkovic, Netherlands Institute for Developmental Biology (Netherlands)

Published in SPIE Proceedings Vol. 3964:
Internet Imaging
Giordano B. Beretta; Raimondo Schettini, Editor(s)

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