Plant and Soil

, Volume 370, Issue 1–2, pp 35–45 | Cite as

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

  • Susan ZappalaEmail author
  • Stefan Mairhofer
  • Saoirse Tracy
  • Craig J. Sturrock
  • Malcolm Bennett
  • Tony Pridmore
  • Sacha J. Mooney
Regular Article



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.


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.


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.


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.


Plant root Soil moisture Rhizosphere Root architecture Segmentation X-ray micro computed tomography (CT) 



X-ray micro computed tomography


Days after germination


Deionised water


Region of interest


Root system architecture



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.


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Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Susan Zappala
    • 1
    Email author
  • Stefan Mairhofer
    • 1
  • Saoirse Tracy
    • 1
  • Craig J. Sturrock
    • 1
  • Malcolm Bennett
    • 1
  • Tony Pridmore
    • 2
  • Sacha J. Mooney
    • 1
  1. 1.School of BiosciencesUniversity of Nottingham, Sutton Bonington CampusLeicestershireUK
  2. 2.School of Computer ScienceUniversity of Nottingham, Jubilee CampusNottinghamUK

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