Image-Based Phenotyping of the Mature Arabidopsis Shoot System

  • Marco Augustin
  • Yll HaxhimusaEmail author
  • Wolfgang Busch
  • Walter G. Kropatsch
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 8928)


The image-based phenotyping of mature plants faces several challenges from the image acquisition to the determination of quantitative characteristics describing their appearance. In this work a framework to extract geometrical and topological traits of 2D images of mature Arabidopsis thaliana is proposed. The phenotyping pipeline recovers the realistic branching architecture of dried and flattened plants in two steps. In the first step, a tracing approach is used for the extraction of centerline segments of the plant. In the second step, a hierarchical reconstruction is done to group the segments according to continuity principles. This paper covers an overview of the relevant processing steps along the proposed pipeline and provides an insight into the image acquisition as well as into the most relevant results from the evaluation process.


Image-based phenotyping Geometrical/topological traits Tracing Hierarchical reconstruction Network of curvilinear structures 


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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Marco Augustin
    • 1
  • Yll Haxhimusa
    • 1
    Email author
  • Wolfgang Busch
    • 2
  • Walter G. Kropatsch
    • 1
  1. 1.Pattern Recognition and Image Processing GroupVienna University of TechnologyViennaAustria
  2. 2.Gregor Mendel Institute of Molecular Plant BiologyAustrian Academy of SciencesViennaAustria

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