Plant and Soil

, Volume 373, Issue 1–2, pp 531–539 | Cite as

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

  • Alain PierretEmail author
  • Santimaitree Gonkhamdee
  • Christophe Jourdan
  • Jean-Luc Maeght
Regular Article


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.


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.


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.


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.


Root length Root washing Image analysis Open-source Winrhizo 



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.

Supplementary material

11104_2013_1795_MOESM1_ESM.doc (338 kb)
ESM 1 (DOC 338 kb)


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Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Alain Pierret
    • 1
    Email author
  • Santimaitree Gonkhamdee
    • 2
  • Christophe Jourdan
    • 3
  • Jean-Luc Maeght
    • 4
  1. 1.UMR Bioemco, Institut de Recherche pour le Développement (IRD) c/o National Agriculture and Forestry Research Institute (NAFRI)VientianeLao P.D.R.
  2. 2.Department of Plant Science & Agricultural ResourcesFaculty of Agriculture, Khon Kaen UniversityKhon KaenThailand
  3. 3.UMR Eco&SolsMontpellierFrance
  4. 4.UMR Bioemco, Institut de Recherche pour le Développement (IRD) c/o UMR AMAPMontpellier cedex 5France

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