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Using a structural root system model for an in-depth assessment of root image analysis pipeline

View ORCID ProfileGuillaume Lobet, View ORCID ProfileIko Koevoets, View ORCID ProfilePierre Tocquin, Loïc Pagès, View ORCID ProfilePérilleux Claire
doi: https://doi.org/10.1101/074922
Guillaume Lobet
1InBioS-PhytoSYSTEMS, University of Liège, 4000 Liège, Belgium
2Institut fur Bio-und Geowissenschaften: Agrosphare, Forschungszentrum Jülich, D52425 Jülich, Germany
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  • For correspondence: g.lobet@fz-juelich.de
Iko Koevoets
3Plant Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
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Pierre Tocquin
1InBioS-PhytoSYSTEMS, University of Liège, 4000 Liège, Belgium
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Loïc Pagès
4INRA, Centre d’ Avignon, UR 1115 PSH, Site Agroparc, 84914 Avignon cedex 9, France
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Périlleux Claire
1InBioS-PhytoSYSTEMS, University of Liège, 4000 Liège, Belgium
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Abstract

Root system analysis is a complex task, often performed using fully automated image analysis pipelines. However, these pipelines are usually evaluated with a limited number of ground-truthed root images, most likely of limited size and complexity.

We have used a root model, ArchiSimple to create a large and diverse library of ground-truthed root system images (10.000). This library was used to evaluate the accuracy and usefulness of several image descriptors classicaly used in root image analysis pipelines.

Our analysis highlighted that the accuracy of the different metrics is strongly linked to the type of root system analysed (e.g. dicot or monocot) as well as their size and complexity. Metrics that have been shown to be accurate for small dicot root systems might fail for large dicots root systems or small monocot root systems. Our study also demonstrated that the usefulness of the different metrics when trying to discriminate genotypes or experimental conditions may vary.

Overall, our analysis is a call to caution when automatically analysing root images. If a thorough calibration is not performed on the dataset of interest, unexpected errors might arise, especially for large and complex root images. To facilitate such calibration, both the image library and the different codes used in the study have been made available to the community.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted September 14, 2016.
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Using a structural root system model for an in-depth assessment of root image analysis pipeline
Guillaume Lobet, Iko Koevoets, Pierre Tocquin, Loïc Pagès, Périlleux Claire
bioRxiv 074922; doi: https://doi.org/10.1101/074922
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Using a structural root system model for an in-depth assessment of root image analysis pipeline
Guillaume Lobet, Iko Koevoets, Pierre Tocquin, Loïc Pagès, Périlleux Claire
bioRxiv 074922; doi: https://doi.org/10.1101/074922

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