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A framework for the extraction of quantitative traits from 2D images of mature Arabidopsis thaliana

Machine Vision and Applications volume 27, pages 647–661 (2016)Cite this article

Abstract

In this work, we propose an image-based phenotyping framework for the determination of quantitative traits from mature Arabidopsis thaliana plants. Two-dimensional (2D) images taken from the dried and flattened plants are analyzed regarding their geometry as well as their branching topology. The realistic branching architecture is hereby reconstructed from a single 2D image using a tracing approach with a semi-circular search window. The centerline segments of the tracing procedure are subsequently merged and labeled based on a hierarchical approach combining continuity properties with geometrical and topological information determined during tracing. This paper covers a detailed description of the proposed plant phenotyping pipeline from the image acquisition process until the extraction of the quantitative traits. The framework is evaluated using a set of 106 images and compared to a manual phenotyping approach as well as a semi-automatic image-based approach. The most relevant results of this evaluation are presented.

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Notes

  1. http://www.mathworks.com/products/matlab/.

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Acknowledgments

We want to thank Svante Holm (Mid Sweden University, SE) and Alison Anastasio (University of Chicago, US) for planting and harvesting the plants, Man Yu and Andrew Davis for taking the photos and Benjamin Brachi (Bergelson Lab, University of Chicago, US) for his valuable inputs and support along the stages of development.

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Authors and Affiliations

  1. Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria

    Marco Augustin

  2. Center for Medical Statistics, Informatics and Intelligent Systems, Medical University of Vienna, Vienna, Austria

    Yll Haxhimusa

  3. Faculty of Electrical and Computer Engineering, University of Prishtina, Prishtina, Kosovo

    Yll Haxhimusa

  4. Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria

    Wolfgang Busch

  5. Pattern Recognition and Image Processing Group, Vienna University of Technology, Vienna, Austria

    Marco Augustin, Yll Haxhimusa & Walter G. Kropatsch

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  1. Marco Augustin
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  2. Yll Haxhimusa
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  4. Walter G. Kropatsch
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Correspondence to Marco Augustin or Yll Haxhimusa.

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Augustin, M., Haxhimusa, Y., Busch, W. et al. A framework for the extraction of quantitative traits from 2D images of mature Arabidopsis thaliana . Machine Vision and Applications 27, 647–661 (2016). https://doi.org/10.1007/s00138-015-0720-z

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  • DOI: https://doi.org/10.1007/s00138-015-0720-z

Keywords

  • Image-based phenotyping
  • Geometrical traits
  • Topological traits
  • Tracing
  • Hierarchical reconstruction
  • Network of curvilinear structures