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An Iterative Mesh Optimization Method for 3D Meristem Reconstruction at Cell Level

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Biomedical Engineering Systems and Technologies (BIOSTEC 2015)

Part of the book series: Communications in Computer and Information Science ((CCIS,volume 574))

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Abstract

This paper focuses on the reconstruction of 3-dimensional multi-lay-ered triangular mesh representations of plant cell tissues, based on segmented images obtained from confocal microscopy of shoot apical meristems of model plant Arabidopsis thaliana. Obtaining good-quality meshes of cell interfaces in plant tissues is currently a missing step in the existing image analysis pipelines. We propose a method for optimizing the quality of such a mesh representation of the tissue simultaneously along several different citeria, starting from a low-quality mesh. An iterative process minimizes an energy functional defined over this discrete structure, by deforming its geometry and updating its connectivity at fixed complexity. This optimization results in a light discrete representation of the cell surfaces that enables fast visualization, and quantitative analysis, and gives way to in silico physical and mechanical simulations on real-world data. We also propose a complete quantitative evaluation scheme to measure the quality of the cell tissue reconstruction, that demonstrates the capacity of our method to fit multiple optimization criteria.

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Authors and Affiliations

  1. Virtual Plants INRIA Team, INRIA, Montpellier, France

    Guillaume Cerutti & Christophe Godin

Authors
  1. Guillaume Cerutti
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  2. Christophe Godin
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Correspondence to Guillaume Cerutti .

Editor information

Editors and Affiliations

  1. Instituto de Telecomunicações, Lisboa, Portugal

    Ana Fred

  2. New University of Lisbon, Lisboa, Portugal

    Hugo Gamboa

  3. FhP-AICOS, Porto, Portugal

    Dirk Elias

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Cerutti, G., Godin, C. (2015). An Iterative Mesh Optimization Method for 3D Meristem Reconstruction at Cell Level. In: Fred, A., Gamboa, H., Elias, D. (eds) Biomedical Engineering Systems and Technologies. BIOSTEC 2015. Communications in Computer and Information Science, vol 574. Springer, Cham. https://doi.org/10.1007/978-3-319-27707-3_10

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  • DOI: https://doi.org/10.1007/978-3-319-27707-3_10

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-27706-6

  • Online ISBN: 978-3-319-27707-3

  • eBook Packages: Computer ScienceComputer Science (R0)

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