Machine Vision and Applications

, Volume 27, Issue 4, pp 585–606

Leaf segmentation in plant phenotyping: a collation study

  • Hanno Scharr
  • Massimo Minervini
  • Andrew P. French
  • Christian Klukas
  • David M. Kramer
  • Xiaoming Liu
  • Imanol Luengo
  • Jean-Michel Pape
  • Gerrit Polder
  • Danijela Vukadinovic
  • Xi Yin
  • Sotirios A. Tsaftaris
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Abstract

Image-based plant phenotyping is a growing application area of computer vision in agriculture. A key task is the segmentation of all individual leaves in images. Here we focus on the most common rosette model plants, Arabidopsis and young tobacco. Although leaves do share appearance and shape characteristics, the presence of occlusions and variability in leaf shape and pose, as well as imaging conditions, render this problem challenging. The aim of this paper is to compare several leaf segmentation solutions on a unique and first-of-its-kind dataset containing images from typical phenotyping experiments. In particular, we report and discuss methods and findings of a collection of submissions for the first Leaf Segmentation Challenge of the Computer Vision Problems in Plant Phenotyping workshop in 2014. Four methods are presented: three segment leaves by processing the distance transform in an unsupervised fashion, and the other via optimal template selection and Chamfer matching. Overall, we find that although separating plant from background can be accomplished with satisfactory accuracy (\(>\)90 % Dice score), individual leaf segmentation and counting remain challenging when leaves overlap. Additionally, accuracy is lower for younger leaves. We find also that variability in datasets does affect outcomes. Our findings motivate further investigations and development of specialized algorithms for this particular application, and that challenges of this form are ideally suited for advancing the state of the art. Data are publicly available (online at http://www.plant-phenotyping.org/datasets) to support future challenges beyond segmentation within this application domain.

Keywords

Plant phenotyping Leaf Multi-instance segmentation Machine learning 

Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Hanno Scharr
    • 1
  • Massimo Minervini
    • 2
  • Andrew P. French
    • 3
  • Christian Klukas
    • 9
  • David M. Kramer
    • 5
  • Xiaoming Liu
    • 6
  • Imanol Luengo
    • 3
  • Jean-Michel Pape
    • 4
  • Gerrit Polder
    • 7
  • Danijela Vukadinovic
    • 7
  • Xi Yin
    • 6
  • Sotirios A. Tsaftaris
    • 2
    • 8
  1. 1.Institute of Bio- and Geosciences: Plant Sciences (IBG-2) Forschungszentrum Jülich GmbHJülichGermany
  2. 2.IMT Institute for Advanced StudiesLuccaItaly
  3. 3.Schools of Biosciences and Computer Science, Centre for Plant Integrative BiologyUniversity of NottinghamNottinghamUK
  4. 4.Department of Molecular GeneticsLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)GaterslebenGermany
  5. 5.Departments of Energy Plant Research Lab, and Biochemistry and Molecular BiologyMichigan State UniversityEast LansingUSA
  6. 6.Department of Computer Science and EngineeringMichigan State UniversityEast LansingUSA
  7. 7.Greenhouse HorticultureWageningen University and Research CentreWageningenNetherlands
  8. 8.School of EngineeringUniversity of EdinburghEdinburghUK
  9. 9.LemnaTec GmbHAachenGermany

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