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  • 1
    Language: English
    In: Ecological Modelling, 2008, Vol.216(3), pp.291-302
    Description: During the past 10 years, soil scientists have started to use 3D Computed Tomography in order to gain a clearer understanding of the geometry of soil structure and its relationships with soil properties. We propose a geometric model for the 3D representation of pore space and a practical method for its computation. Our basic idea consists in representing pore space using a minimal set of maximal balls (Delaunay spheres) recovering the shape skeleton. In this representation, each ball could be considered as a maximal local cavity corresponding to the “intuitive” notion of a pore as described in the literature. The space segmentation induced by the network of balls (pores) was then used to spatialize biological dynamics. Organic matter and microbial decomposers were distributed within the balls (pores). A valuated graph representing the pore network, organic matter and distribution of micro-organisms was then defined. Microbial soil organic matter decomposition was simulated by updating this valuated graph. The method was implemented and tested using real CT images. The model produced realistic simulated results when compared with data in the literature in terms of the water retention curve and carbon mineralization. A decrease in water pressure decreased carbon mineralization, which is also in accordance with findings in the literature. From our results we showed that the influence of water pressure on decomposition is a function of organic matter distribution in the pore space. As far as we know, this is the approach to have linked pore space geometry and biological dynamics in a formal way. Our next goal will be to compare the model with experimental data of decomposition using different soil structures, and to define geometric typologies of pore space shape that can be attached to specific biological and dynamic properties.
    Keywords: Computational Geometry ; Soil Science ; Pore Space Modelling ; Microbial Decomposition Simulation ; 3d Computer Vision ; Environmental Sciences ; Ecology
    ISSN: 0304-3800
    E-ISSN: 1872-7026
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  • 2
    Language: English
    In: Geoderma, 2011, Vol.163(1), pp.127-134
    Description: 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 ( 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 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. ► A sophisticated model based on Delaunay triangulation method was presented. ► It extracts soil pores with maximal balls or connected ball chains. ► The model was applied to two 3D contrasting soil images. ► Pore space characteristics of the two soils were very different. ► The results of the model were close to those obtained with a more standard approach.
    Keywords: Model ; Soil Structure ; Pore Space ; Tomography ; Delaunay Tessellation ; Synchrotron ; Agriculture
    ISSN: 0016-7061
    E-ISSN: 1872-6259
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  • 3
    Language: English
    In: Computers and Geosciences, Feb, 2012, Vol.39, p.50(14)
    Description: To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.cageo.2011.06.010 Byline: Ndeye Fatou Ngom (a), Olivier Monga (b), Mohamed Mahmoud Ould Mohamed (c), Patricia Garnier (d) Abstract: This paper focuses on the modeling of soil microstructures using generalized cylinders, with a specific application to pore space. The geometric modeling of these microstructures is a recent area of study, made possible by the improved performance of computed tomography techniques. X-scanners provide very-high-resolution 3D volume images (3-5[mu]m) of soil samples in which pore spaces can be extracted by thresholding. However, in most cases, the pore space defines a complex volume shape that cannot be approximated using simple analytical functions. We propose representing this shape using a compact, stable, and robust piecewise approximation by means of generalized cylinders. This intrinsic shape representation conserves its topological and geometric properties. Our algorithm includes three main processing stages. The first stage consists in describing the volume shape using a minimum number of balls included within the shape, such that their union recovers the shape skeleton. The second stage involves the optimum extraction of simply connected chains of balls. The final stage copes with the approximation of each simply optimal chain using generalized cylinders: circular generalized cylinders, tori, cylinders, and truncated cones. This technique was applied to several data sets formed by real volume computed tomography soil samples. It was possible to demonstrate that our geometric representation supplied a good approximation of the pore space. We also stress the compactness and robustness of this method with respect to any changes affecting the initial data, as well as its coherence with the intuitive notion of pores. During future studies, this geometric pore space representation will be used to simulate biological dynamics. Author Affiliation: (a) UCAD, UMI 209 UMMISCO, BP 1386, CP 18524, Dakar, Senegal (b) IRD, UMI 209 UMMISCO, BP 1386, CP 18524, Dakar, Senegal (c) Universite Pierre et Marie Curie, UMMISCO, France (d) INRA, UMR 1091 EGC, BP 01, F-78850 Thiverval-Grignon, France Article History: Received 30 August 2010; Revised 31 May 2011; Accepted 15 June 2011
    Keywords: Algorithms -- Analysis
    ISSN: 0098-3004
    Source: Cengage Learning, Inc.
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  • 4
    Language: English
    In: Soft Computing, 2018, Vol.22(5), pp.1381-1384
    Description: To access, purchase, authenticate, or subscribe to the full-text of this article, please visit this link: http://dx.doi.org/10.1007/s00500-017-2999-3 Byline: Gwanggil Jeon (1), Marco Anisetti (2), Ernesto Damiani (3), Olivier Monga (4) Author Affiliation: (1) 0000 0004 0532 7395, grid.412977.e, Incheon National University, Incheon, Korea (2) 0000 0004 1757 2822, grid.4708.b, Universita degli studi di Milano, Milan, Italy (3) 0000 0004 1762 9729, grid.440568.b, EBTIC, Khalifa University, Abu Dhabi, UAE (4) 0000000122879528, grid.4399.7, Institut de Recherche pour le Developpement, Marseille, France Article History: Registration Date: 28/12/2017 Online Date: 06/01/2018
    Keywords: Image Processing Equipment – Methods ; Image Processing – Methods;
    ISSN: 1432-7643
    E-ISSN: 1433-7479
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  • 5
    Language: English
    In: Computers and Geosciences, 2007, Vol.33(9), pp.1140-1161
    Description: Only in the last decade have geoscientists started to use 3D computed tomography (CT) images of soil for better understanding and modeling of soil properties. In this paper, we propose one of the first approaches to allow the definition and computation of stable (intrinsic) geometric representations of structures in 3D CT soil images. This addresses the open problem set by the description of volume shapes from discrete traces without any information. The basic concept involves representing the volume shape by a piecewise approximation using simple volume primitives (bowls, cylinders, cones, etc.). This typical representation is assumed to optimize a criterion ensuring its stability. This criterion includes the representation scale, which characterizes the trade-off between the fitting error and the number of patches. We also take into account the preservation of topological properties of the initial shape: the number of connected components, adjacency relationships, etc. We propose an efficient computation method for this piecewise approximation using cylinders or bowls. For cylinders, we use optimal region growing in a valuated adjacency graph that represents the primitives and their adjacency relationships. For bowls, we compute a minimal set of Delaunay spheres recovering the skeleton. Our method is applied to modeling of a coarse pore space extracted from 3D CT soil images. The piecewise bowls approximation gives a geometric formalism corresponding to the intuitive notion of pores and also an efficient way to compute it. This geometric and topological representation of coarse pore space can be used, for instance, to simulate biological activity in soil.
    Keywords: 3d Computed Tomography Soil Images ; Functional Minimization ; Soil Properties ; Geometric Modeling ; Computational Geometry ; Region Growing ; Delaunay Triangulation ; Geology
    ISSN: 0098-3004
    E-ISSN: 1873-7803
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  • 6
    Language: English
    In: Acta Biotheoretica, 2018, Vol.66(1), pp.17-60
    Description: Within the last decade, several approaches using quaternion numbers to handle and model multiband images in a holistic manner were introduced. The quaternion Fourier transform can be efficiently used to model texture in multidimensional data such as color images. For practical application, multispectral satellite data appear as a primary source for measuring past trends and monitoring changes in forest carbon stocks. In this work, we propose a texture-color descriptor based on the quaternion Fourier transform to extract relevant information from multiband satellite images. We propose a new multiband image texture model extraction, called FOTO++, in order to address biomass estimation issues. The first stage consists in removing noise from the multispectral data while preserving the edges of canopies. Afterward, color texture descriptors are extracted thanks to a discrete form of the quaternion Fourier transform, and finally the support vector regression method is used to deduce biomass estimation from texture indices. Our texture features are modeled using a vector composed with the radial spectrum coming from the amplitude of the quaternion Fourier transform. We conduct several experiments in order to study the sensitivity of our model to acquisition parameters. We also assess its performance both on synthetic images and on real multispectral images of Cameroonian forest. The results show that our model is more robust to acquisition parameters than the classical Fourier Texture Ordination model (FOTO). Our scheme is also more accurate for aboveground biomass estimation. We stress that a similar methodology could be implemented using quaternion wavelets. These results highlight the potential of the quaternion-based approach to study multispectral satellite images.
    Keywords: Discrete quaternion Fourier transform ; Quaternion-based texture indices ; Multiband satellite images ; Aboveground biomass ; Cameroon
    ISSN: 0001-5342
    E-ISSN: 1572-8358
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  • 7
    Language: English
    In: Computers and Geosciences, 2012, Vol.39, pp.50-63
    Description: This paper focuses on the modeling of soil microstructures using generalized cylinders, with a specific application to pore space. The geometric modeling of these microstructures is a recent area of study, made possible by the improved performance of computed tomography techniques. X-scanners provide very-high-resolution 3D volume images ( ) of soil samples in which pore spaces can be extracted by thresholding. However, in most cases, the pore space defines a complex volume shape that cannot be approximated using simple analytical functions. We propose representing this shape using a compact, stable, and robust piecewise approximation by means of generalized cylinders. This intrinsic shape representation conserves its topological and geometric properties. Our algorithm includes three main processing stages. The first stage consists in describing the volume shape using a minimum number of balls included within the shape, such that their union recovers the shape skeleton. The second stage involves the optimum extraction of simply connected chains of balls. The final stage copes with the approximation of each simply optimal chain using generalized cylinders: circular generalized cylinders, tori, cylinders, and truncated cones. This technique was applied to several data sets formed by real volume computed tomography soil samples. It was possible to demonstrate that our geometric representation supplied a good approximation of the pore space. We also stress the compactness and robustness of this method with respect to any changes affecting the initial data, as well as its coherence with the intuitive notion of pores. During future studies, this geometric pore space representation will be used to simulate biological dynamics. ► 3D computer vision techniques to compute a hierarchical geometrical representation of pore space microstructures. ► Initial data: high resolution 3D volume computed tomography images of soil samples. ► Composite representation of pore space using a set of volume primitives including generalized cylinders. ► Basic geometrical representation: minimum set of balls included within the shape and recovering shape skeleton. ► Implementation and experimental validation on several real data sets.
    Keywords: Soil Microstructures ; Computed Tomography Images ; 3d Geometric Modeling ; Pore Space ; Computational Geometry ; Volume Segmentation ; Geology
    ISSN: 0098-3004
    E-ISSN: 1873-7803
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  • 8
    Language: English
    In: International Journal of Geosciences, 2013, Vol.4(10), pp.15-26
    Description: Partial Differential Equations (PDEs) have been already widely used to simulate various complex phenomena in porous media. This paper is one of the first attempts to apply PDEs for simulating in real 3D structures. We apply this scheme to the specific case study of the microbial decomposition...
    Keywords: Life Sciences ; Partial Differential Equations ; Soil ; Microbial Decomposition ; Pore Space ; 3d Geometry Modelling ; Computed Tomography ; Geology
    ISSN: 2156-8359
    E-ISSN: 2156-8367
    Source: Hyper Article en Ligne (CCSd)
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  • 9
    Language: English
    In: Computers & geosciences, 2012, Vol.39, pp.50-63
    Description: This paper focuses on the modeling of soil microstructures using generalized cylinders, with a specific application to pore space. The geometric modeling of these microstructures is a recent area of study, made possible by the improved performance of computed tomography techniques. X-scanners provide very-high-resolution 3D volume images (3–5μm) of soil samples in which pore spaces can be extracted by thresholding. However, in most cases, the pore space defines a complex volume shape that cannot be approximated using simple analytical functions. We propose representing this shape using a compact, stable, and robust piecewise approximation by means of generalized cylinders. This intrinsic shape representation conserves its topological and geometric properties. Our algorithm includes three main processing stages. The first stage consists in describing the volume shape using a minimum number of balls included within the shape, such that their union recovers the shape skeleton. The second stage involves the optimum extraction of simply connected chains of balls. The final stage copes with the approximation of each simply optimal chain using generalized cylinders: circular generalized cylinders, tori, cylinders, and truncated cones. This technique was applied to several data sets formed by real volume computed tomography soil samples. It was possible to demonstrate that our geometric representation supplied a good approximation of the pore space. We also stress the compactness and robustness of this method with respect to any changes affecting the initial data, as well as its coherence with the intuitive notion of pores. During future studies, this geometric pore space representation will be used to simulate biological dynamics. ; p. 50-63.
    Keywords: Models ; Data Collection ; Computers ; Computed Tomography ; Topology ; Processing Stages ; Algorithms ; Soil Sampling ; Soil
    ISSN: 0098-3004
    Source: AGRIS (Food and Agriculture Organization of the United Nations)
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  • 10
    Language: English
    In: Vietnam Journal of Mathematics, 2015, Vol.43(4), pp.801-817
    Description: The majority of carbon on earth is in the form of soil organic matter. And its degradation by microorganisms leads to the remineralization of carbon as carbon dioxide. The microbial activity causes a reduction of soil carbon and increases atmospheric carbon. However, most models of organic matter do not explicitly take into account this reality. We try to answer these questions by developing and validating a model describing the action of microorganisms on degradation of organic matter. We use simulation domain as the pores in the soil modeled by a network of balls. The model is solved numerically in the balls by the finite element method with the solver of partial differential equations (PDEs) Freefem3d. We compare the numerical results with experimental data on the mineralization of soil carbon.
    Keywords: Model ; Partial differential equations ; Soil ; Organic matter ; 3D computed tomography image ; Validation
    ISSN: 2305-221X
    E-ISSN: 2305-2228
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