The Atlas of Zebrafish Development

One of the projects of the Imaging and Bioinformatics  Group at the LIACS is the production of a 3D digital atlas of zebrafish development. Starting point of the 3D reconstructions are sets of serial sections, that consist of microscope images. To acquire these images a computerised microscope set-up is being used.
All known tissues/organs are manually and semi-automaticcally delineated and annotated based on these images. These images and annotations form the material for the production of 3D reference models and 3D visualisation.
All these data are stored in an object relational database, that enables the representation of temporal relationships. The intention is to produce complete annotations of all tissues in the relevant embryonic stages in the zebrafish.
The atlas data are accessible and available for review through internet by means of Java applets. In order to run these applets on your (local) computer some standard software needs to be installed on your system. Please follow the instructions given.
You also might want to consult these helpfull references. Reprints of these references are avaialable on request.

Browse the Atlas

Examples at low at normal video resolution are made available through the Atlas Browser Application. [Zebrafish Atlas Browser]

Animations from the Atlas

Examples obtained from the Atlas Browser are made available in standard animation File Formats and Application. [Zebrafish Animation Browser]


Key Publications
Verbeek, F.J., den Broeder,M.J., Boon, P.J., Buitendijk, B., van Raaij, E.J., Doerry, E., Zivkovic, D. (2000) A Standard 3D digital Atlas of Zebrafish Embryonic Development for Projection of Experimental Data. Proceedings SPIE 3964, Internet Imaging I, 242-252.

Verbeek, F.J., Boon, P.J., Sloetjes, H., van der Velde, R., de Vos, N. (2002) Visualization of complex data sets over Internet: 2D and 3D visualization of the 3D digital atlas of zebrafish development. Proceedings SPIE 4672, Internet Imaging III, 20-29

Verbeek, F.J., Lawson, K.A., and Bard, J.B.L. (1999). Developmental BioInformatics: linking genetic data to virtual embryos. Int.J.Dev.Biol. 43, 761-771.

Additional references
Kimmel, C.B., Ballard, W.W., Kimmel, S.R., Ullman, B., and Schilling,T.F.(1995). Stages of embryonic development of the zebrafish.  Developmental Dynamics 203, 253-310.

Verbeek, F.J. (1999) Theory & Practice of 3D-reconstructions from serial sections. IN: Image Processing, A Practical Approach. (eds. Baldock, Graham), Oxford: Oxford University Press, 153-195.

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