Extraction of three-dimensional soil pore space from microtomography images using a geometrical approach

Abstract This paper presents a geometrical model of soil pore space based on the quantitative analysis of synchrotron X-ray microtomography data. Our model calculated the minimal set of balls that recovered the skeleton of the pore space using Delaunay tessellation, and the simply connected sets of balls that could be considered as potential pore channels. This model (DTM software) was then applied to three-dimensional tomography reconstructions of soil aggregates (~ 5 mm diameter) from two management systems (conventionally tilled soil, namely CTT and grassland soil, namely GL) with a voxel edge length of 3.2 μm and 5.4 μm, respectively. Geometric characteristics such as the frequency distribution of pore radius, length, and tortuosity as well as the retention curve were calculated using our model. The organic matter decomposition was also simulated using DTM approach. The results were compared with pore space statistics obtained during a previously published study on the same data using algorithms based on the medial axis and throat computation ( 3dma software). The same tendency on the geometrical statistic was obtained using both methods, with more pores of smaller length and diameter calculated for the aggregate from the conventionally tilled site compared to the grassland aggregate. However, the 3dma method generated a larger quantity of voxels (385,673 and 189,250 for CTT and GL, respectively) compared to the amount of balls in DTM (170,250 and 64,273 for CTT and GL, respectively) and shorter channels because of the presence of throats.

[1]  R. Falconer,et al.  Biomass recycling: a key to efficient foraging by fungal colonies , 2007 .

[2]  Jerzy Lipiec,et al.  Complete characterization of pore size distribution of tilled and orchard soil using water retention curve, mercury porosimetry, nitrogen adsorption, and water desorption methods , 2006 .

[3]  Olivier Monga,et al.  Representing geometric structures in 3D tomography soil images: Application to pore-space modeling , 2007, Comput. Geosci..

[4]  R. Horn.  Aggregate characterization as compared to soil bulk properties , 1990 .

[5]  Roel Merckx,et al.  Spatial location of carbon decomposition in the soil pore system , 2004 .

[6]  Hans-Jörg Vogel,et al.  Quantitative morphology and network representation of soil pore structure , 2001 .

[7]  Hans-Jörg Vogel,et al.  Comparison of a Lattice‐Boltzmann Model, a Full‐Morphology Model, and a Pore Network Model for Determining Capillary Pressure–Saturation Relationships , 2005 .

[8]  W. Brent Lindquist,et al.  Image Thresholding by Indicator Kriging , 1999, IEEE Trans. Pattern Anal. Mach. Intell..

[9]  Zeyun Yu,et al.  New algorithms in 3D image analysis and their application to the measurement of a spatialized pore size distribution in soils , 1999 .

[10]  Xiaoxian Zhang,et al.  Domain-decomposition method for parallel lattice Boltzmann simulation of incompressible flow in porous media. , 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.

[11]  O. Monga,et al.  3D geometric structures and biological activity: Application to microbial soil organic matter decomposition in pore space , 2008 .

[12]  R. Al-Raoush,et al.  Extraction of physically realistic pore network properties from three-dimensional synchrotron X-ray microtomography images of unconsolidated porous media systems , 2005 .

[13]  D. Malo,et al.  Porosity and Pore-Size Distribution in Cultivated Ustolls and Usterts , 2004 .

[14]  M. Tuller,et al.  Segmentation of X‐ray computed tomography images of porous materials: A crucial step for characterization and quantitative analysis of pore structures , 2009 .

[15]  T. Addiscott,et al.  Mineralization of native soil organic matter is not regulated by the size, activity or composition of the soil microbial biomass-a new perspective , 2008 .

[16]  Rainer Horn,et al.  Three-dimensional quantification of intra-aggregate pore-space features using synchrotron-radiation-based microtomography , 2008 .

[17]  E. Lugato,et al.  Relationship between aggregate pore size distribution and organic–humic carbon in contrasting soils , 2009 .

[18]  Olivier Monga,et al.  Using pore space 3D geometrical modelling to simulate biological activity: Impact of soil structure , 2009, Comput. Geosci..

[19]  W. B. Lindquist,et al.  Medial axis analysis of void structure in three-dimensional tomographic images of porous media , 1996 .

[20]  J. Crawford,et al.  New methods and models for characterising structural heterogeneity of soil , 2001 .

[21]  Stephen H. Anderson,et al.  CT-measured pore characteristics of surface and subsurface soils influenced by agroforestry and grass buffers , 2008 .

[22]  M. R. Carter,et al.  Structure and Organic Matter Storage in Agricultural Soils , 1995 .

[23]  Clinton S. Willson,et al.  Comparison of Network Generation Techniques for Unconsolidated Porous Media , 2003 .

[24]  W. B. Lindquist,et al.  Pore and throat size distributions measured from synchrotron X-ray tomographic images of Fontaineble , 2000 .