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, E. Doerry, E. J. van Raaij, D. Zivkovic

Research output: Contribution to journalConference articlepeer-review

12 Scopus citations


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)
Pages (from-to)242-252
Number of pages11
JournalProceedings of SPIE - The International Society for Optical Engineering
StatePublished - 2000
EventProceedings of the 2000 Internet Imaging - San Jose, CA, USA
Duration: Jan 26 2000Jan 28 2000

ASJC Scopus subject areas

  • Electronic, Optical and Magnetic Materials
  • Condensed Matter Physics
  • Computer Science Applications
  • Applied Mathematics
  • Electrical and Electronic Engineering


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