Design and implementation of a database and program for 3D reconstruction from serial sections: A data-driven approach

Authors

  • Fons J. Verbeek,

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    1. Pattern Recognition Group, Faculty of Applied Physics, Delft University of Technology, Delft, The Netherlands
    2. Department of Anatomy and Embryology, Faculty of Medicine, University of Amsterdam, 1105 Amsterdam, The Netherlands
    • University of Amsterdam, Academic Medical Centre, Department of Anatomy and Embryology, Meibergdreef 15. 1105 AZ Amsterdam, The Netherlands
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  • D. P. Huijsmans,

    1. Department of Computer Science, Leiden University, Leiden, The Netherlands
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  • R. J. A. M. Baeten,

    1. Department of Anatomy and Embryology, Faculty of Medicine, University of Amsterdam, 1105 Amsterdam, The Netherlands
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  • N. J. C. Schoutsen,

    1. Department of Computer Science, Leiden University, Leiden, The Netherlands
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  • W. H. Lamers

    1. Department of Anatomy and Embryology, Faculty of Medicine, University of Amsterdam, 1105 Amsterdam, The Netherlands
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Abstract

This paper describes a structured approach for a standard setup of a computer program for 3D reconstruction from serial sections. Three-dimensional reconstruction as a technique increases in importance as, along with modern immunohistochemical techniques, it is a tool in the understanding of three-dimensional development patterns. In order to apply 3D reconstruction technique in a standard laboratory setup, an attempt was made to streamline the input and the manipulation of the data such that results are obtained easily. One will find a combination of two approaches in this paper: the first is a strict ordering of the complex data, and the second is an ordering of the processes that one wishes to apply on the data (together, these two approaches constitute an information analysis); because it was observed that developmental biologists tend to work from simple lines to describe their observations, the contour model was chosen as the vehicle to build a reconstruction model from. Consequently, the data is ordered in a database that has to be manipulated to get the data out in the desired format. The most important output format is a display of the reconstructed contour stack on a graphical computer screen. Together with the other data manipulation processes, such as the input, the inspection, the revision (correction), and the reconstruction, all processes are described using the reconstruction of an 11 embryonic days (ED) rat embryo as an example. Finally, the merits of the program are illustrated with an example from the development of the human embryonic heart. © 1995 Wiley-Liss, Inc.

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