Skip to main content
Log in

Quantifying the effect of soil moisture content on segmenting root system architecture in X-ray computed tomography images

  • Regular Article
  • Published:
Plant and Soil Aims and scope Submit manuscript

Abstract

Aims

A commonly accepted challenge when visualising plant roots in X-ray micro Computed Tomography (μCT) images is the similar X-ray attenuation of plant roots and soil phases. Soil moisture content remains a recognised, yet currently uncharacterised source of segmentation error. This work sought to quantify the effect of soil moisture content on the ability to segment roots from soil in μCT images.

Methods

Rice (Oryza sativa) plants grown in contrasting soils (loamy sand and clay loam) were μCT scanned daily for nine days whilst drying from saturation. Root volumes were segmented from μCT images and compared with volumes derived by root washing.

Results

At saturation the overlapping attenuation values of root material, water-filled soil pores and soil organic matter significantly hindered segmentation. However, in dry soil (ca. six days of drying post-saturation) the air-filled pores increased image noise adjacent to roots and impeded accurate visualisation of root material. The root volume was most accurately segmented at field capacity.

Conclusions

Root volumes can be accurately segmented from μCT images of undisturbed soil without compromising the growth requirements of the plant providing soil moisture content is kept at field capacity. We propose all future studies in this area should consider the error associated with scanning at different soil moisture contents.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9

Similar content being viewed by others

Abbreviations

μCT:

X-ray micro computed tomography

DAG:

Days after germination

DI:

Deionised water

ROI:

Region of interest

RSA:

Root system architecture

References

  • Carminati A, Vetterlein D, Weller U, Vogel HJ, Oswald SE (2009) When roots lose contact. Vadose Zone J 8:805–809. doi:10.2136%2Fvzj2008.0147

    Article  Google Scholar 

  • Clark R, MacCurdy R, Jung J, Shaff J, McCouch S, Aneshansley D, Kochian L (2011) Three-Dimensional root phenotyping with a novel imaging and software platform. Plant Physiol 156:455–465. doi:10.1104/pp.110.169102

    Article  PubMed  CAS  Google Scholar 

  • Dhondt S, Vanhaeren H, Van Loo D, Cnudde V, Inzé D (2010) Plant structure visualization by high resolution X-ray computed tomography. Trends Plant Sci 15:419–422. doi:10.1016/j.tplants.2010.05.002

    Article  PubMed  CAS  Google Scholar 

  • Ferreira S, Senning M, Sonnewald S, KeBling P, Goldstein R, Sonnewald U (2010) Comparative transcriptome analysis coupled to X-ray CT reveals sucrose supply and growth velocity as major determinants of potato tuber starch biosynthesis. Genomics 11:93. doi:10.1186%2F1471-2164-11-93

    Article  PubMed  Google Scholar 

  • Flavel R, Guppy C, Tighe M, Watt M, McNeil A, Young I (2012) Non-destructive quantification of cereal roots in soil using high-resolution X-ray tomography. J Exp Bot. doi:10.1093/jxb/err421

  • Gregory P (2006) Plant roots: Growth, activity and interaction with soils. Blackwell Publishing, Oxford

    Google Scholar 

  • Hamza MA, Anderson SH, Aylmore LAG (2007) Computed tomographic evaluation of osmotica on shrinkage and recovery of lupin (Lupinus angustifolius L.) and radish (Raphanus sativus L.) roots. Environ Exp Bot 59:334–339. doi:10.1016%2Fj.envexpbot.2006.04.004

    Article  Google Scholar 

  • Heeraman DA, Hopmans JW, Clausnitzer V (1997) Three dimensional imaging of plant roots in situ with X-ray computed tomography. Plant Soil 189:167–179. doi:10.1023%2FB%3APLSO.0000009694.64377.6f

    CAS  Google Scholar 

  • Himmelbauer ML, Loiskandl W, Kastanek F (2004) Estimating length, average diameter and surface area of roots using two different image analyses systems. Plant Soil 260:111–120. doi:10.1023%2FB%3APLSO.0000030171.28821.55

    Article  CAS  Google Scholar 

  • Mairhofer S, Zappala S, Tracy S, Mooney SJ, Pridmore P (2012) RooTrak: automated recovery of 3D plant root architecture in soil from X-ray micro computed tomography using visual tracking. Plant Physiol. doi:10.1104/pp.111.186221

  • Mees F, Swennen R, Van Geet M, Jacobs P (2003) Applications of X-ray computed tomography in the geosciences. Geol Soc Lond Spec Publ 215:1–6. doi:10.1144%2FGSL.SP.2003.215.01.01

    Article  Google Scholar 

  • Mooney SJ, Pridmore TP, Helliwell J, Bennett MJ (2012) Developing X-ray computed tomography to non-invasively image 3-D root systems architecture in soil. Plant Soil. doi:10.1007/s11104-011-1039-9

  • Moran CJ, Pierret A, Stevenson AW (2000) X-ray absorption and phase contrast imaging to study the interplay between plant roots and soil structure. Plant Soil 223:101–117. doi:10.1023/A:1004835813094

    Article  Google Scholar 

  • Pálsdóttir AM, Alsanius BM, Johannesson V, Ask A (2008) Prospect of non-destructive analysis of root growth and geometry using computerised tomography (CT X-Ray). Proc. IS on Growing Media. Editor Michel, J.C. Acta Hort 779: 155–159

  • Perret JS, Al-Belushi ME, Deadman M (2007) Non-destructive visualisation and quantification of roots using computed tomography. Soil Biol Biochem 39:391–399. doi:10.1016/j.soilbio.2006.07.018

    Article  CAS  Google Scholar 

  • Pires L, Borges J, Bacchy O, Reichardt K (2010) Twenty-five years of computed tomography in soil physics: a literature review of the Brazilian contribution. Soil Tillage Res 110:197–210. doi:10.1016/j.still.2010.07.013

    Article  Google Scholar 

  • Ryser P (2006) The mysterious root length. Plant Soil 286:1–6

    Article  CAS  Google Scholar 

  • Seignez N, Gauthier A, Mess F, Brunel C, Dubios M, Potdevin JL (2010) Development of plant roots network in polluted soils: an X-Ray computed tomography investigation. Water Air Soil Pollut 209:199–207. doi:10.1007/s11270-009-0192-8

    Article  CAS  Google Scholar 

  • Tracy SR, Roberts J, Black CR, McNeill A, Davidson R, Mooney SJ (2010) The X-factor: visualizing undisturbed root architecture in soils using X-ray computed tomography. J Exp Bot 61:311–313. doi:10.1093/jxb/erp386

    Article  PubMed  CAS  Google Scholar 

  • Tracy SR, Black CR, Roberts JR, McNeill A, Davidson R, Tester M, Samec M, Korošak D, Sturrock C, Mooney SJ (2012a) Quantifying the effect of soil compaction on three varieties of wheat (Triticum aestivum L.) with differing root architecture using X-ray micro computed tomography (CT). Plant Soil. doi:10.1007/s11104-011-1022-5

  • Tracy SR, Black CR, Roberts JA, Sturrock C, Mairhofer S, Craigon J, Mooney SJ (2012b) Quantifying the impact of soil compaction on root system architecture in tomato (Solanum lycopersicum) by X-ray micro-computed tomography. Ann Bot London. doi:10.1093/aob/MCS031

  • Wang M, Zhang Q (2009) Issues in using the WinRHIZO system to determine physical characteristics of plant fine roots. Acta Ecol Sin 29:136–138. doi:10.1007/s11104-008-9577-5

    Article  Google Scholar 

  • Whalley WR, Watts CW, Gregory AS, Mooney SJ, Clark LJ, Whitmore AP (2008) The effect of soil strength on the yield of wheat. Plant Soil 306:237–247. doi:10.1007%2Fs11104-008-9577-5

    Article  CAS  Google Scholar 

  • Zobel R (2008) Hardware and software efficacy in assessment of fine root diameter distributions. Comput Electron Agric 60:178–189. doi:10.1016/j.compag.2007.08.002

    Article  Google Scholar 

Download references

Acknowledgments

This work was supported by an Engineering and Physical Sciences Research Council (EPSRC) Doctoral Training Award to SZ. The authors wish to acknowledge the help of Pedro Carvalho for his part in the WinRHIZO volume measurements.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Susan Zappala.

Additional information

Responsible Editor: Alain Pierret.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Zappala, S., Mairhofer, S., Tracy, S. et al. Quantifying the effect of soil moisture content on segmenting root system architecture in X-ray computed tomography images. Plant Soil 370, 35–45 (2013). https://doi.org/10.1007/s11104-013-1596-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11104-013-1596-1

Keywords

Navigation