M.J. Den Broeder

Publications (3)0 Total impact

• Conference Proceeding: A virtual lab-notebook for multidimensional microscope images

  P.J. Boon, N. Eminovic, A. De Vos, B. Buitendijk, E.J. Van Raaij, M.J. Den Broeder, W.J. Hage, F.J. Verbeck
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  ABSTRACT: The paper discusses the use of XML as an intermediate format for storage of information on microscope images and the different techniques to visualize this information. In this manner we have explored XML and built several applications for image management. The XML-files generated by these applications are defined as the lab-notebook. A crucial feature of such a lab-notebook stored in XML is that it directly relates to the Internet so that a modern Web browser can be used to present the data in a user-friendly manner. We discuss how we used XSL and Java applets to accomplish this
  Information Visualization, 2000. Proceedings. IEEE International Conference on; 02/2000
• Conference Proceeding: A Virtual Lab-Notebook for Multidimensional Microscopic Images.

  P. J. Boon, N. Eminovic, A. de Vos, B. Buitendijk, E. J. van Raaij, M. J. den Broeder, W. J. Hage, F. J. Verbeek
  01/2000
• Article: Electronic Imaging

  Fons J. Verbeek, M. J. den Broeder, Paul J. Boon, B. Buitendijk, E. Doerry, E. J. van Raaij, D. Zivkovic
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  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.© (1999) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.
  12/1999;