IJ_Rhizo: an open-source software to measure scanned images of root samples
- 2.5k Downloads
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.
KeywordsRoot 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.
- Arsenault J-L, Pouleur S, Messier C, Guay R (1995) WinRHIZO™, a root-measuring system with a unique overlap correction method. HortSci 30:906Google Scholar
- Christina M, Laclau J-P, Gonçalves JLM, Jourdan C, Nouvellon Y, Bouillet J-P (2011) Almost symmetrical vertical growth rates above and below ground in one of the world’s most productive forests. Ecosphere 2:art27Google Scholar
- Ewing RP, Kaspar TC (1995) Accurate perimeter and length measurement using an edge chord algorithm. J Computer-assisted Microsc 7:91–100Google Scholar
- Gonkhamdee S (2010) Analysis of the interplay between crop and inter-crop roots in young rubber tree plantations of NE Thailand. PhD of the “Université d’Avignon et des pays de Vaucluse” (UAPV). France and Khon Kaen University, ThailandGoogle Scholar
- Magalhaes PC, de Souza TC, Cantao FRO (2011) Early evaluation of root morphology of maize genotypes under phosphorus deficiency. Plant Soil and Environment 57:135–138Google Scholar
- Nelson BD, Phan N (2006) Evaluation of partial resistance in soybean to Phytophthora sojae using WinRhizo root analysis software. Phytopathology 96:S83Google Scholar
- Pierret A, Moran CJ (2011) Plant roots and soil structure. In: Glinski J, Horabik J, Lipiec J (eds) Encyclopedia of agrophysics. Springer, Dordrecht, pp 628–632Google Scholar
- R Core Team (2012) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org/