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

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

Research output: Chapter in Book/Report/Conference proceedingConference contribution

9 Citations (Scopus)

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, imaging 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 all 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.

Original languageEnglish (US)
Title of host publicationProceedings of SPIE - The International Society for Optical Engineering
PublisherSociety of Photo-Optical Instrumentation Engineers
Pages242-252
Number of pages11
Volume3964
StatePublished - 2000
Externally publishedYes
EventProceedings of the 2000 Internet Imaging - San Jose, CA, USA
Duration: Jan 26 2000Jan 28 2000

Other

OtherProceedings of the 2000 Internet Imaging
CitySan Jose, CA, USA
Period1/26/001/28/00

Fingerprint

Gene expression
projection
embryos
XML
Information management
annotations
Genes
gene expression
Internet
biology
Imaging techniques
data management
anatomy
genes
layouts
Developmental Biology
cascades
platforms
anomalies
computer programs

ASJC Scopus subject areas

  • Electrical and Electronic Engineering
  • Condensed Matter Physics

Cite this

Verbeek, F. J., den Broeder, M. J., Boon, P. J., Buitendijk, B., Doerry, E., van Raaij, E. J., & Zivkovic, D. (2000). Standard 3D digital atlas of zebrafish embryonic development for projection of experimental data. In Proceedings of SPIE - The International Society for Optical Engineering (Vol. 3964, pp. 242-252). Society of Photo-Optical Instrumentation Engineers.

Standard 3D digital atlas of zebrafish embryonic development for projection of experimental data. / Verbeek, Fons J.; den Broeder, M. J.; Boon, P. J.; Buitendijk, B.; Doerry, Eckehard; van Raaij, E. J.; Zivkovic, D.

Proceedings of SPIE - The International Society for Optical Engineering. Vol. 3964 Society of Photo-Optical Instrumentation Engineers, 2000. p. 242-252.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Verbeek, FJ, den Broeder, MJ, Boon, PJ, Buitendijk, B, Doerry, E, van Raaij, EJ & Zivkovic, D 2000, Standard 3D digital atlas of zebrafish embryonic development for projection of experimental data. in Proceedings of SPIE - The International Society for Optical Engineering. vol. 3964, Society of Photo-Optical Instrumentation Engineers, pp. 242-252, Proceedings of the 2000 Internet Imaging, San Jose, CA, USA, 1/26/00.
Verbeek FJ, den Broeder MJ, Boon PJ, Buitendijk B, Doerry E, van Raaij EJ et al. Standard 3D digital atlas of zebrafish embryonic development for projection of experimental data. In Proceedings of SPIE - The International Society for Optical Engineering. Vol. 3964. Society of Photo-Optical Instrumentation Engineers. 2000. p. 242-252
Verbeek, Fons J. ; den Broeder, M. J. ; Boon, P. J. ; Buitendijk, B. ; Doerry, Eckehard ; van Raaij, E. J. ; Zivkovic, D. / Standard 3D digital atlas of zebrafish embryonic development for projection of experimental data. Proceedings of SPIE - The International Society for Optical Engineering. Vol. 3964 Society of Photo-Optical Instrumentation Engineers, 2000. pp. 242-252
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