Automated statistical method to align 2D chemical maps with 3D X-ray computed micro-tomographic images of soils

Simona M. Hapca, Zi X. Wang, Wilfred Otten, Clare Wilson, Philippe C. Baveye

Research output: Contribution to journalArticle

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Abstract

Recent 2-dimensional measurements reveal that soils are chemically very heterogeneous at nanometric and micrometric scales. Direct measurement techniques are still lacking to extend these observations to 3 dimensions. Sequential sectioning of soils, followed by 2-dimensional mapping of chemical elements and geometric interpolation to 3D, appears to be the only available alternative. Unfortunately, sectioning of soil samples suffers from geometric distortions that are difficult to avoid in practise. In this regard, the objective of the research described in this article was to develop a procedure enabling one to locate, in a 3D X-ray microtomographic image of a soil sample, a physical surface that is obtained by sectioning and for which a number of chemical maps are available. This procedure involves three steps: (1) the reconstitution of the physical structure of the soil layer surface, (2) the alignment of the chemical maps with the reconstituted soil surface image, and (3) the 3D alignment of the 2D chemical maps with the internal structure of the soil cube. Visual comparison of the C and Si maps and of the reconstituted CT images of the layer surfaces suggests a good correspondence between them, which is supported by Pearson correlation coefficients of − 0.57, − 0.58, 0.45, and 0.43 for the different surfaces and elements considered. Relative to the original 3D X-ray CT image of the soil sample, the planes associated with the C and Si maps, respectively, are nearly superposed, which further confirms the validity of the alignment procedure. Research highlights ► A procedure is developed to locate physical planes in 3D X-ray CT images of soils. ► This procedure allows alignment of 2D chemical maps with the soil structure. ► Measured C and Si maps and reconstituted CT images correspond well with each other. ► Planes associated with the C and Si maps are nearly superposed.
Original languageEnglish
Pages (from-to)146-154
Number of pages9
JournalGeoderma
Volume164
Issue number3-4
DOIs
StatePublished - Sep 2011

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soil
soil sampling
soil structure
surface layer
soil surface layers
statistical analysis
methodology
chemical element
interpolation
soil surface

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Hapca, S. M., Wang, Z. X., Otten, W., Wilson, C., & Baveye, P. C. (2011). Automated statistical method to align 2D chemical maps with 3D X-ray computed micro-tomographic images of soils. Geoderma, 164(3-4), 146-154. DOI: 10.1016/j.geoderma.2011.05.018

Hapca, Simona M.; Wang, Zi X.; Otten, Wilfred; Wilson, Clare; Baveye, Philippe C. / Automated statistical method to align 2D chemical maps with 3D X-ray computed micro-tomographic images of soils.

In: Geoderma, Vol. 164, No. 3-4, 09.2011, p. 146-154.

Research output: Contribution to journalArticle

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title = "Automated statistical method to align 2D chemical maps with 3D X-ray computed micro-tomographic images of soils",
abstract = "Recent 2-dimensional measurements reveal that soils are chemically very heterogeneous at nanometric and micrometric scales. Direct measurement techniques are still lacking to extend these observations to 3 dimensions. Sequential sectioning of soils, followed by 2-dimensional mapping of chemical elements and geometric interpolation to 3D, appears to be the only available alternative. Unfortunately, sectioning of soil samples suffers from geometric distortions that are difficult to avoid in practise. In this regard, the objective of the research described in this article was to develop a procedure enabling one to locate, in a 3D X-ray microtomographic image of a soil sample, a physical surface that is obtained by sectioning and for which a number of chemical maps are available. This procedure involves three steps: (1) the reconstitution of the physical structure of the soil layer surface, (2) the alignment of the chemical maps with the reconstituted soil surface image, and (3) the 3D alignment of the 2D chemical maps with the internal structure of the soil cube. Visual comparison of the C and Si maps and of the reconstituted CT images of the layer surfaces suggests a good correspondence between them, which is supported by Pearson correlation coefficients of − 0.57, − 0.58, 0.45, and 0.43 for the different surfaces and elements considered. Relative to the original 3D X-ray CT image of the soil sample, the planes associated with the C and Si maps, respectively, are nearly superposed, which further confirms the validity of the alignment procedure. Research highlights ► A procedure is developed to locate physical planes in 3D X-ray CT images of soils. ► This procedure allows alignment of 2D chemical maps with the soil structure. ► Measured C and Si maps and reconstituted CT images correspond well with each other. ► Planes associated with the C and Si maps are nearly superposed.",
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Hapca, SM, Wang, ZX, Otten, W, Wilson, C & Baveye, PC 2011, 'Automated statistical method to align 2D chemical maps with 3D X-ray computed micro-tomographic images of soils' Geoderma, vol 164, no. 3-4, pp. 146-154. DOI: 10.1016/j.geoderma.2011.05.018

Automated statistical method to align 2D chemical maps with 3D X-ray computed micro-tomographic images of soils. / Hapca, Simona M.; Wang, Zi X.; Otten, Wilfred; Wilson, Clare; Baveye, Philippe C.

In: Geoderma, Vol. 164, No. 3-4, 09.2011, p. 146-154.

Research output: Contribution to journalArticle

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AU - Hapca,Simona M.

AU - Wang,Zi X.

AU - Otten,Wilfred

AU - Wilson,Clare

AU - Baveye,Philippe C.

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AB - Recent 2-dimensional measurements reveal that soils are chemically very heterogeneous at nanometric and micrometric scales. Direct measurement techniques are still lacking to extend these observations to 3 dimensions. Sequential sectioning of soils, followed by 2-dimensional mapping of chemical elements and geometric interpolation to 3D, appears to be the only available alternative. Unfortunately, sectioning of soil samples suffers from geometric distortions that are difficult to avoid in practise. In this regard, the objective of the research described in this article was to develop a procedure enabling one to locate, in a 3D X-ray microtomographic image of a soil sample, a physical surface that is obtained by sectioning and for which a number of chemical maps are available. This procedure involves three steps: (1) the reconstitution of the physical structure of the soil layer surface, (2) the alignment of the chemical maps with the reconstituted soil surface image, and (3) the 3D alignment of the 2D chemical maps with the internal structure of the soil cube. Visual comparison of the C and Si maps and of the reconstituted CT images of the layer surfaces suggests a good correspondence between them, which is supported by Pearson correlation coefficients of − 0.57, − 0.58, 0.45, and 0.43 for the different surfaces and elements considered. Relative to the original 3D X-ray CT image of the soil sample, the planes associated with the C and Si maps, respectively, are nearly superposed, which further confirms the validity of the alignment procedure. Research highlights ► A procedure is developed to locate physical planes in 3D X-ray CT images of soils. ► This procedure allows alignment of 2D chemical maps with the soil structure. ► Measured C and Si maps and reconstituted CT images correspond well with each other. ► Planes associated with the C and Si maps are nearly superposed.

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DO - 10.1016/j.geoderma.2011.05.018

M3 - Article

VL - 164

SP - 146

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JO - Geoderma

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SN - 0016-7061

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ER -

Hapca SM, Wang ZX, Otten W, Wilson C, Baveye PC. Automated statistical method to align 2D chemical maps with 3D X-ray computed micro-tomographic images of soils. Geoderma. 2011 Sep;164(3-4):146-154. Available from, DOI: 10.1016/j.geoderma.2011.05.018