X-Ray Computed Tomography for Root Quantification


Soil cores from a field growing barley and barley mutants without root hairs under conventional and minimum tillage were sampled. They were X-ray scanned to produce a 3D image and then the roots were washed out and weight and length were determined by conventional means. Root volume and surface area were then calculated from the 3D images using state of the art software and methodology, and the measured and calculated measures were correlated. The only strong and significant correlation was between measured weight and calculated volume for mutants without root hairs. It is concluded that the software cannot segment out very small roots, but segmentation accuracy also depends on root structure in some unknown way. Any study using X-ray computed tomography to quantify roots as they grow in situ should start with a calibration for the conditions in question.

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Foereid, B. (2015) X-Ray Computed Tomography for Root Quantification. Open Journal of Soil Science, 5, 145-148. doi: 10.4236/ojss.2015.57014.

Conflicts of Interest

The authors declare no conflicts of interest.


[1] Ketcham, R.A. and Carlson, W.D. (2001) Acquisition, Optimization and Interpretation of X-Ray Computed Tomographic Imagery: Applications to the Geosciences. Computers and Geosciences, 27, 381-400.
[2] De Gryze, S., Jassogne, L., Six, J., Bossuyt, H., Wevers, M. and Merckx, R. (2006) Pore Structure Changes during Decomposition of Fresh Residue: X-Ray Tomography Analyses. Geoderma, 134, 82-96.
[3] Nunan, N., Ritz, K., Rivers, M., Feeney, D.S. and Young, I.M. (2006) Investigating Microbial Micro-Habitat Structure Using X-Ray Computed Tomography. Geoderma, 133, 398-407.
[4] Sleutel, S., Cnudde, V., Masschaele, B., Vlassenbroek, J., Dierick, M., Van Hoorebeke, L., Jacobs, P. and De Neve, S. (2008) Comparison of Different Nano- and Micro-Focus X-Ray Computed Tomography Set-Ups for the Visualization of the Soil Microstructure and Soil Organic Matter. Computers and Geosciences, 34, 931-938.
[5] Iassonov, P., Gebrenegus, T. and Tuller, M. (2009) Segmentation of X-Ray Computed Tomography Images of Porous Materials: A Crucial Step for Characterization and Quantitative Analysis of Pore Structures. Water Resources Research, 45, W09415.
[6] Elyeznasni, N., Sellami, F., Pot, V., Benoit, P., Vieublé-Gonod, L., Young, I. and Peth, S. (2012) Exploration of Soil Micromorphology to Identify Coarse-Sized OM Assemblages in X-Ray CT Images of Undisturbed Cultivated Soil Cores. Geoderma, 179-180, 38-45.
[7] Taina, I.A., Heck1, R.J. and Elliot, T.R. (2007) Application of X-Ray Computed Tomography to Soil Science: A Literature Review. Canadian Journal of Soil Science, 88, 1-19.
[8] Mooney, S.J. Pridmore, T.P., Helliwell, J. and Bennett, M.J. (2012) Developing X-Ray Computed Tomography to Non-Invasively Image 3-D Root Systems Architecture in Soil. Plant and Soil, 352, 1-22.
[9] Hapca, S., Houston, A.N., Otten, W. and Baveye. P. (2013) New Objective Segmentation Method Based on Minimizing Locally the Intra-Class Variance of Grayscale Images. Vadoze Zone, 12, 13 p.
[10] Houston, A.N., Otten, W., Baveye, P. and Hapca, S. (2013) Thresholding of Computed Tomography Images of Heterogeneous Porous Media by Adaptive-Window Indicator Kriging. Computers and Geosciences, 54, 239-248.
[11] Houston, A.N., Schmidt, S., Otten, W., Baveye, P. and Hapca, S. (2013) Effect of Scanning and Image Reconstruction Settings in X-Ray Computed Tomography on Soil Image Quality and Segmentation Performance. Geoderma, 207-208, 154-165.
[12] Schmidt, S. Bengough, A.G., Gregory, P.J., Grinev, D.V. and Otten, W. (2012) Estimating Root-Soil Contact from 3-D X-Ray Microtomography. European Journal of Soil Science, 63, 776-786.
[13] Haling, R.E., Tighe, M.K., Flavel, R.J. and Young, I.M. (2013) Application of X-Ray Computed Tomography to Quantify Fresh Root Decomposition in Situ. Plant and Soil, 372, 619-627.
[14] Sun, B., Hallett, P.D., Caul, S., Daniell, T.J. and Hopkins, D.W. (2011) Distribution of Soil Carbon and Microbial Biomass in Arable Soils under Different Tillage Regimes. Plant and Soil, 338, 17-25.
[15] Brown, L.K., George, T.S., Barrett, G.E., Hubbard, S.F. and White, P.J. (2013) Interactions between Root Hair Length and Arbuscular Mycorrhizal Colonization in Phosphorus Deficient Barley (Hordeum vulgare). Plant and Soil, 372, 195-205.
[16] Hirano, Y., Yamamoto, R., Dannoura, M., Aono, K., Igarashi, T., Ishii, M., Yamase, K., Makita, N. and Kanazawa, Y. (2012) Detection Frequency of Pinus thunbergii Roots by Ground-Penetrating Radar Is Related to Root Biomass. Plant and Soil, 360, 363-373.

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