Standard 3D digital atlas of zebrafish embryonic development for projection of experimental data

Fons J. Verbeek; M. J. den Broeder; Paul J. Boon; B. Buitendijk; E. Doerry; E. J. van Raaij; D. Zivkovic

doi:10.1117/12.373465

20 December 1999 Standard 3D digital atlas of zebrafish embryonic development for projection of experimental data

Fons J. Verbeek, M. J. den Broeder, Paul J. Boon, B. Buitendijk, E. Doerry, E. J. van Raaij, D. Zivkovic

Proceedings Volume 3964, Internet Imaging; (1999) https://doi.org/10.1117/12.373465
Event: Electronic Imaging, 2000, San Jose, CA, United States

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.

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Fons J. Verbeek, M. J. den Broeder, Paul J. Boon, B. Buitendijk, E. Doerry, E. J. van Raaij, and D. Zivkovic "Standard 3D digital atlas of zebrafish embryonic development for projection of experimental data", Proc. SPIE 3964, Internet Imaging, (20 December 1999); https://doi.org/10.1117/12.373465

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