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IJ_Rhizo: an open-source software to measure scanned images of root samples

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Abstract

Background and aims

This paper provides an overview of the measuring capabilities of IJ_Rhizo, an ImageJ macro that measures scanned images of washed root samples. IJ_Rhizo is open-source, platform-independent and offers a simple graphic user interface (GUI) for a main audience of non-programmer scientists. Being open-source based, it is also fully modifiable to accommodate the specific needs of the more computer-literate users. A comparison of IJ_Rhizo’s performance with that of the widely used commercial package WinRHIZO™ is discussed.

Methods

We compared IJ_Rhizo’s performance with that of the commercial package WinRHIZO™ using two sets of images, one comprising test-line images, the second consisting of images of root samples collected in the field. IJ_Rhizo and WinRHIZO™ estimates were compared by means of correlation and regression analysis.

Results

IJ_Rhizo “Kimura” and WinRHIZO™ “Tennant” were the length estimates that were best linearly correlated with each other. Correlation between average root diameter estimates was weaker, due to the sensitivity of this parameter to thresholding and filtering of image background noise.

Conclusions

Overall, IJ_Rhizo offers new opportunities for researchers who cannot afford the cost of commercial software packages to carry out automated measurement of scanned images of root samples, without sacrificing accuracy.

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Acknowledgements

The authors would like to thank the French Institute for Rubber (IFC), and Michelin ⁄ Socfinco ⁄ SIPH Rubber Tree Plantations Companies and the French Agence Nationale de la Recherche (project Ecosfix, ANR-2010-STRA-003), the French Institute for Research for Development (IRD) and International Centre for Agricultural Research for Development (CIRAD) for providing the enabling environment and financial resources that, over the years, allowed us to develop IJ_Rhizo. We also are deeply grateful to the National Agriculture and Forestry Research Institute (NAFRI) of Laos, and Khon Kaen University (KKU), Thailand for their continued logistical support, and to all the owners/farmers who kindly granted us access to their fields for sampling purposes. We are also grateful to Dr. Boris Rewald, BOKU, Austria, for making constructive comments about this manuscript.

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Authors and Affiliations

  1. UMR Bioemco, Institut de Recherche pour le Développement (IRD) c/o National Agriculture and Forestry Research Institute (NAFRI), P.O. Box 4199, Ban Nongviengkham, Xaythany District, Vientiane, Lao P.D.R.

    Alain Pierret

  2. Department of Plant Science & Agricultural Resources, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand

    Santimaitree Gonkhamdee

  3. UMR Eco&Sols, CIRAD, 2 place Viala, 34060, Montpellier, France

    Christophe Jourdan

  4. UMR Bioemco, Institut de Recherche pour le Développement (IRD) c/o UMR AMAP, CIRAD TA A51/PS2, 34398, Montpellier cedex 5, France

    Jean-Luc Maeght

Authors
  1. Alain Pierret
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  2. Santimaitree Gonkhamdee
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  3. Christophe Jourdan
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  4. Jean-Luc Maeght
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Correspondence to Alain Pierret.

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Responsible Editor: Timothy Cavagnaro.

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Pierret, A., Gonkhamdee, S., Jourdan, C. et al. IJ_Rhizo: an open-source software to measure scanned images of root samples. Plant Soil 373, 531–539 (2013). https://doi.org/10.1007/s11104-013-1795-9

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