Observer-dependent variability of the thresholding step in the quantitative analysis of soil images and X-ray microtomography data

Baveye, Philippe C.; Laba, Magdeline; Otten, Wilfred; Bouckaert, Liesbeth; Sterpaio, Patricia Dello; Goswami, Rohit; Grinev, D. V.; Houston, Alasdair N.; Hu, Yining; Liu, Jianli; Mooney, Sacha J.; Pajor, R; Sleutel, Steven; Tarquis, Ana M.; Wang, Wei; Wang, Qiao; Sezgin, Mehmet

doi:10.1016/j.geoderma.2010.03.015

Cited by 161 publications

(117 citation statements)

References 56 publications

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“…As was also found by Tippkötter et al [47] and generally unlike in the case of images obtained with table-top, polychromatic X-ray computed tomography scanners [5,23,24,25], the histograms of the 3D SR-µCT images of the soil samples display three distinct peaks (Fig. 1).…”

Section: Sr-µct Scanssupporting

confidence: 66%

Three-dimensional distribution of water and air in soil pores: Comparison of two-phase two-relaxation-times lattice-Boltzmann and morphological model outputs with synchrotron X-ray computed tomography data

Pot

Peth

Monga

et al. 2015

Advances in Water Resources

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Section: Sr-µct Scanssupporting

confidence: 66%

Three-dimensional distribution of water and air in soil pores: Comparison of two-phase two-relaxation-times lattice-Boltzmann and morphological model outputs with synchrotron X-ray computed tomography data

Pot

Peth

Monga

et al. 2015

Advances in Water Resources

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“…The choice of threshold value was based on the histogram region corresponding with the pore-solid interface, taking into account variation of grey scale values in pores of different shapes and sizes, and averaging over 5 randomly selected slices per sample using Image J (Image J, http://rsb.info.nih.gov/ij/). In a study comparing different thresholding methods it was shown that this methodology predicted porosity close to the mean value of all tested methods and agreed well with the overall porosity of the bulk soil sample (Baveye et al, 2010). To allow for analysis of the effect of pore geometry on fungal growth, the thresholded (binary) datasets were further divided in a consistent way into eight subsamples (pseudo replicates) with dimensions of 128×128×128 voxels (see Fig.…”

Section: Quantification Of Soil Structurementioning

confidence: 75%

Modelling and quantifying the effect of heterogeneity in soil physical conditions on fungal growth

et al. 2010

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Abstract. Despite the importance of fungi in soil ecosystem services, a theoretical framework that links soil management strategies with fungal ecology is still lacking. One of the key challenges is to understand how the complex geometrical shape of pores in soil affects fungal spread and species interaction. Progress in this area has long been hampered by a lack of experimental techniques for quantification. In this paper we use X-ray computed tomography to quantify and characterize the pore geometry at microscopic scales (30 µm) that are relevant for fungal spread in soil. We analysed the pore geometry for replicated samples with bulk-densities ranging from 1.2-1.6 g/cm 3 . The bulk-density of soils significantly affected the total volume, mean pore diameter and connectivity of the pore volume. A previously described fungal growth model comprising a minimal set of physiological processes required to produce a range of phenotypic responses was used to analyse the effect of these geometric descriptors on fungal invasion, and we showed that the degree and rate of fungal invasion was affected mainly by pore volume and pore connectivity. The presented experimental and theoretical framework is a significant first step towards understanding how environmental change and soil management impact on fungal diversity in soils.

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“…The most critical operation in this analysis is the segmentation of the volume, which is usually based on grey value thresholding. Due to effects such as partial volume and image noise, this step is extremely operator dependant (Baveye et al, 2010). Nevertheless, when analysing reconstructed volumes of similar objects, this error is a constant making comparison of these similar objects possible.…”

Section: Operator Dependencymentioning

confidence: 99%

High-resolution X-ray computed tomography in geosciences: A review of the current technology and applications

Cnudde

Boone

2013

Earth-Science Reviews

1,226

700

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Please cite this article as: Cnudde, V., Boone, M.N., "High-resolution X-ray computed tomography in geosciences: a review of the current technology and applications", Earth Science Reviews (2013Reviews ( ), doi: 10.1016Reviews ( /j.earscirev.2013 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.A C C E P T E D M A N U S C R I P T AbstractHigh-resolution X-ray Computed Tomography (HRXCT) or micro-CT (µCT) is a frequently used non-destructive 3D imaging and analysis technique for the investigation of internal structures of a large variety of objects, including geomaterials. Although the possibilities of X-ray micro-CT are becoming better appreciated in earth science research, the demands on this technique are also approaching certain physical limitations. As such, there remains a lot of research to be done in order to solve all the technical problems that occur when higher demands are put on the technique. In this paper, a review of the principle, the advantages and limitations of X-ray CT itself are presented, together with an overview of some current applications of micro-CT in geosciences. One of the main advantages of this technique is the fact that it is a non-destructive characterization technique which allows 4D monitoring of internal structural changes at resolutions down to a few hundred nanometers. Limitations of this technique are the operator dependency for the 3D image analysis from the reconstructed data, the discretations effects and possible imaging artefacts. Driven by the technological and computational progress, the technique is continuously growing as an analysis tool in geosciences and is becoming one of the standard techniques, as is shown by the large and still increasing number of publications in this research area. It is foreseen that this number will continue to rise, and micro-CT will become an indispensable technique in the field of geosciences.

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Observer-dependent variability of the thresholding step in the quantitative analysis of soil images and X-ray microtomography data

Cited by 161 publications

References 56 publications

Three-dimensional distribution of water and air in soil pores: Comparison of two-phase two-relaxation-times lattice-Boltzmann and morphological model outputs with synchrotron X-ray computed tomography data

Three-dimensional distribution of water and air in soil pores: Comparison of two-phase two-relaxation-times lattice-Boltzmann and morphological model outputs with synchrotron X-ray computed tomography data

Modelling and quantifying the effect of heterogeneity in soil physical conditions on fungal growth

High-resolution X-ray computed tomography in geosciences: A review of the current technology and applications

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