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 Pierret
  • Santimaitree Gonkhamdee
  • Christophe Jourdan
  • Jean-Luc Maeght
Regular Article

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.

Keywords

Root length Root washing Image analysis Open-source Winrhizo 

Supplementary material

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

References

  1. 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
  2. Bouma TJ, Nielsen KL, Koutstaal B (2000) Sample preparation and scanning protocol for computerised analysis of root length and diameter. Plant Soil 218:185–196CrossRefGoogle Scholar
  3. 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
  4. Clothier BE, Green SR (1997) Roots: the big movers of water and chemical in soil. Soil Sci 162:534–543CrossRefGoogle Scholar
  5. Dowdy RH, Smucker AMJ, Dolan MS, Fergusson JC (1998) Automated image analyses for separating plant roots from soil debris elutrated from soil cores. Plant Soil 200:91–94CrossRefGoogle Scholar
  6. Edwards EJ, Benham DG, Marland LA, Fitter AH (2004) Root production is determined by radiation flux in a temperate grassland community. Global Change Biol 10:209–227CrossRefGoogle Scholar
  7. Esser G, Kattge J, Sakalli A (2011) Feedback of carbon and nitrogen cycles enhances carbon sequestration in the terrestrial biosphere. Global Change Biol 17:819–842CrossRefGoogle Scholar
  8. Ewing RP, Kaspar TC (1995) Accurate perimeter and length measurement using an edge chord algorithm. J Computer-assisted Microsc 7:91–100Google Scholar
  9. Feddes RA, Hoff H, Bruen M, Dawson TE, de Rosnay P, Dirmeyer P, Jackson RB, Kabat P, Kleidon A, Lilly A, Pitman AJ (2001) Modeling root water uptake in hydrological and climate models. Bull Am Meteorol Soc 82:2797–2809CrossRefGoogle Scholar
  10. 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
  11. Gyssels G, Poesen J, Liu G, van Dessel W, Knapen A, de Baets S (2006) Effects of cereal roots on detachment rates of single- and double-drilled topsoils during concentrated flow. Eur J Soil Soc 57:381–391CrossRefGoogle Scholar
  12. Himmelbauer ML, Loiskandl W, Kastanek F (2004) Estimating length, average diameter and surface area of roots using two different image analysis systems. Plant Soil 260:111–120CrossRefGoogle Scholar
  13. Kaspar TC, Ewing RP (1997) ROOTEDGE: software for measuring root length from desktop scanner images. Agron J 89:932–940CrossRefGoogle Scholar
  14. Kell DB (2011) Breeding crop plants with deep roots: their role in sustainable carbon, nutrient and water sequestration. Ann Bot 108:407–418CrossRefPubMedGoogle Scholar
  15. Kimura K, Kikuchi S, Yamasaki S (1999) Accurate root length measurement by image analysis. Plant Soil 216:117–127CrossRefGoogle Scholar
  16. Kimura K, Yamasaki S (2003) Accurate root length and diameter measurement using NIH Image: use of Pythagorean distance for diameter estimation. Plant Soil 254:305–315CrossRefGoogle Scholar
  17. Kleidon A, Heimann M (1998) Optimised rooting depth and its impacts on the simulated climate of an atmospheric general circulation model. Geophys Res Lett 25(3):345–348CrossRefGoogle Scholar
  18. Le Bot J, Serra V, Fabre J, Draye X, Adamowicz S, Pagès L (2010) DART: a software to analyze root system architec-ture and development from captured images. Plant Soil 326:261–273CrossRefGoogle Scholar
  19. Lobet G, Pagès L, Draye X (2011) A novel image-analysis toolbox enabling quantitative analysis of root system architecture. Plant Physiol 157:29–39CrossRefPubMedGoogle Scholar
  20. 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
  21. Meng-Ben W, Qiang Z (2009) Issues in using the WinRHIZO system to determine physical characteristics of plant fine roots. Acta Ecologica Sinica 29:136–138CrossRefGoogle Scholar
  22. Mickovski SB, Bransby M, Bengough AG, Davies MCR, Hallett PD (2010) Resistance of simple plant root systems to uplift loads. Revue canadienne de géotechnique 47:78–95CrossRefGoogle Scholar
  23. Nelson BD, Phan N (2006) Evaluation of partial resistance in soybean to Phytophthora sojae using WinRhizo root analysis software. Phytopathology 96:S83Google Scholar
  24. Nepstad DC, de Carvalho CR, Davidson EA, Jipp PH, Lefebvre PA, Negreiros GH, da Silva ED, Stone TA, Trumbore SE, Vieira S (1994) The role of deep roots in the hydrological and carbon cycles of Amazonian forests and pastures. Nature 372:666–669CrossRefGoogle Scholar
  25. Newman EI (1966) A method of estimating the total length of root in a sample. J Appl Ecol 3:139–145CrossRefGoogle Scholar
  26. Pierret A, Moran CJ, Doussan C (2005) Conventional detection methodology is limiting our ability to better under- stand the roles and functions of fine roots. New Phytol 66:967–980CrossRefGoogle Scholar
  27. Pierret A, Latchackak K, Chathanvongsa P, Sengtaheuanghoung O, Valentin C (2007) Interactions between root growth, slope and soil detachment depending on land use: a case study in a small mountain catchment of Northern Laos. Plant Soil 301:51–64CrossRefGoogle Scholar
  28. 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
  29. 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/
  30. Rasse DP, Rumpel C, Dignac M-F (2005) Is soil carbon mostly root carbon? Mechanisms for a specific stabilisation. Plant Soil 269:341–356CrossRefGoogle Scholar
  31. Roumet C, Urcelay C, Díaz S (2006) Suites of root traits differ between annual and perennial species growing in the field. New Phytol 170:357–368CrossRefPubMedGoogle Scholar
  32. Ryser (2006) The mysterious root length. Plant Soil 286:1–6CrossRefGoogle Scholar
  33. Schmidt MW, Torn MS, Abiven S, Dittmar T, Guggenberger G, Janssens IA, Kleber M, Kögel-Knabner I, Lehmann J, Manning DA, Nannipieri P, Rasse DP, Weiner S, Trumbore SE (2011) Persistence of soil organic matter as an ecosystem property. Nature 478:49–56CrossRefPubMedGoogle Scholar
  34. Stokes A, Atger C, Bengough AG, Fourcaud T, Sidle RC (2009) Desirable plant root traits for protecting natural and engineered slopes against landslides. Plant Soil 324:1–30CrossRefGoogle Scholar
  35. Tajimaa R, Kato Y (2011) Comparison of threshold algorithms for automatic image processing of rice roots using freeware image. J Field Crops Res 121:460–463CrossRefGoogle Scholar
  36. Tennant D (1975) A test of a modified line intersect method of estimating root length. J Ecology 63:995–1001CrossRefGoogle Scholar
  37. Vegapareddy M, Richter GM, Goulding KWT (2010) Using digital image analysis to quantify the architectural parameters of roots grown in thin rhizotrons. Plant Biosystems 144:499–506CrossRefGoogle Scholar
  38. Zeng G, Birchfield ST, Wells CE (2006) Detecting and measuring fine roots in minirhizotron images using matched filtering and local entropy thresholding. Mach Vis Appl 17:265–278CrossRefGoogle Scholar
  39. Zeng G, Birchfield ST, Wells CE (2008) Automatic discrimination of fine roots in minirhizotron images. New Phytol 177:549–557PubMedGoogle Scholar
  40. Zeng X, Dai Y-J, Dickinson RE, Shaikh M (1998) The role of root distribution for climate simulation over land. Geophys Res Letters 25:4533–4536CrossRefGoogle Scholar
  41. Zobel RW (2003) Sensitivity analysis of computer-based diameter measurement from digital images. Crop Sci 43:583–591CrossRefGoogle Scholar
  42. Zobel RW, Alloush GA, Belesky DP (2006) Differential root morphology response to no versus high phosphorus, in three hydroponically grown forage chicory cultivars. Environ Experimental Botany 57:201–208CrossRefGoogle Scholar
  43. Zobel RW (2008) Hardware and software efficacy in assessment of fine root diameter distributions. Comput Electron Agric 60:178–189CrossRefGoogle Scholar
  44. Zoon FC, van Tienderen PH (1990) A rapid quantitative measurement of root length and root branching by microcomputer image analysis. Plant Soil 126:301–308CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Alain Pierret
    • 1
  • 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

Personalised recommendations