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

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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.

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Abbreviations

μCT:

X-ray micro computed tomography

DAG:

Days after germination

DI:

Deionised water

ROI:

Region of interest

RSA:

Root system architecture

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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.

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Authors and Affiliations

  1. School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire, LE12 5RD, UK

    Susan Zappala, Stefan Mairhofer, Saoirse Tracy, Craig J. Sturrock, Malcolm Bennett & Sacha J. Mooney

  2. School of Computer Science, University of Nottingham, Jubilee Campus, Wollaton Road, Nottingham, NG8 1BB, UK

    Tony Pridmore

Authors
  1. Susan Zappala
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  2. Stefan Mairhofer
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  3. Saoirse Tracy
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  4. Craig J. Sturrock
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  5. Malcolm Bennett
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  6. Tony Pridmore
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  7. Sacha J. Mooney
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Corresponding author

Correspondence to Susan Zappala.

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Responsible Editor: Alain Pierret.

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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

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