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

Pierret Alain, Gonkhamdee Santimaitree, Jourdan Christophe, Maeght Jean-Luc. 2013. IJ_Rhizo: An open-source software to measure scanned images of root samples. Plant and Soil, 371 (1-2) : 531-539.

Quartile : Q1, Sujet : AGRONOMY / Quartile : Q1, Sujet : SOIL SCIENCE / Quartile : Q1, Sujet : PLANT SCIENCES

Résumé : 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.

Classification Agris : F50 - Anatomie et morphologie des plantes
U30 - Méthodes de recherche
000 - Autres thèmes

Champ stratégique Cirad : Axe 1 (2005-2013) - Intensification écologique

Auteurs et affiliations

• Pierret Alain, IRD (LAO)
• Gonkhamdee Santimaitree, Khon Kaen University (THA)
• Jourdan Christophe, CIRAD-PERSYST-UMR Eco&Sols (FRA) ORCID: 0000-0001-9857-3269
• Maeght Jean-Luc, IRD (FRA)

Source : Cirad - Agritrop (https://agritrop.cirad.fr/571907/)

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