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  • Article  (10)
  • Image Analysis
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  • Article  (10)
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  • 1
    Language: English
    In: PloS one, 2016, Vol.11(7), pp.e0159948
    Description: Matter turnover in soil is tightly linked to soil structure which governs the heterogeneous distribution of habitats, reaction sites and pathways in soil. Thereby, the temporal dynamics of soil structure alteration is deemed to be important for essential ecosystem functions of soil but very little is known about it. A major reason for this knowledge gap is the lack of methods to study soil structure turnover directly at microscopic scales. Here we devise a conceptual approach and an image processing workflow to study soil structure turnover by labeling some initial state of soil structure with small garnet particles and tracking their fate with X-ray microtomography. The particles adhere to aggregate boundaries at the beginning of the experiment but gradually change their position relative to the nearest pore as structure formation progresses and pores are destructed or newly formed. A new metric based on the contact distances between particles and pores is proposed that allows for a direct quantification of soil structure turnover rates. The methodology is tested for a case study about soil compaction of a silty loam soil during stepwise increase of bulk density (ρ = {1.1, 1.3, 1.5} g/cm3). We demonstrate that the analysis of mean contact distances provides genuinely new insights about changing diffusion pathways that cannot be inferred neither from conventional pore space attributes (porosity, mean pore size, pore connectivity) nor from deformation analysis with digital image correlation. This structure labeling approach to quantify soil structure turnover provides a direct analogy to stable isotope labeling for the analysis of matter turnover and can be readily combined with each other.
    Keywords: X-Ray Microtomography ; Soil -- Chemistry
    E-ISSN: 1932-6203
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  • 2
    Language: English
    In: Vadose Zone Journal, 2011, Vol.10(3), p.1082
    Description: Predicting solute transport through structured soil based on observable structural properties of the material has not been accomplished to date. We evaluated a new approach to predicting breakthrough curves (BTCs) of dissolved chemicals in intact structured soil columns based on attributes of the pore structure at hierarchical spatial scales. The methodology centers on x-ray computed microtomography of a hierarchic suite of undisturbed soil samples (diameters 1, 4.6, 7.5, and 16 cm) to identify the network of pores 〉10 mu m in diameter. The pore structure was quantified in terms of pore size distribution, interface area density, and connectivity. The pore size distribution and pore connectivity were used to set up an equivalent pore network model (PNM) for predicting the BTCs of Br (super -) and Brilliant Blue FCF (BB) at unsaturated, steady-state flux. For a structured silt loam soil column, the predictions of Br (super -) tracer breakthrough were within the variation observed in the column experiments. A similarly good prediction was obtained for Br (super -) breakthrough in a sandy soil column. The BB breakthrough observed in the silt loam was dominated by a large variation in sorption (retardation factors between R = 2.9 and 24.2). The BB sorption distribution coefficient, k (sub d) , was measured in batch tests. Using the average k (sub d) in the PNM resulted in an overestimated retardation (R = 28). By contrast, breakthrough of BB in the sandy soil (experimental R = 3.3) could be roughly predicted using the batch test k (sub d) (PNM simulation R = 5.3). The prediction improved when applying a sorption correction function accounting for the deviation between measured interface area density distribution and its realization in the network model (R = 4.1). Overall, the results support the hypothesis that solute transport can be estimated based on a limited number of characteristics describing pore structure: the pore size distribution, pore topology, and pore-solid interfacial density.
    Keywords: Soils ; Bad Lauchstadt Germany ; Boundary Conditions ; Breakthrough Curves ; Bromine ; Central Europe ; Central Germany ; Chemical Dispersion ; Chernozems ; Computed Tomography ; Convection ; Density ; Dye Tracers ; Equations ; Europe ; Experimental Studies ; Fuhrberg Germany ; Germany ; Halogens ; Image Analysis ; Laboratory Studies ; Lower Saxony Germany ; Microtomography ; Minckowski Functions ; Morphology ; Networks ; Podzols ; Porosity ; Quantitative Analysis ; Saxony-Anhalt Germany ; Simulation ; Soils ; Solute Transport ; Spectra ; Tomography ; Topology ; Transport ; X-Ray Spectra;
    ISSN: Vadose Zone Journal
    E-ISSN: 1539-1663
    Source: CrossRef
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  • 3
    In: Water Resources Research, November 2018, Vol.54(11), pp.9033-9044
    Description: Structural hierarchy is a fundamental characteristic of natural porous media. Yet it provokes one of the grand challenges for the modeling of fluid flow and transport since pore‐scale structures and continuum‐scale domains often coincide independent of the observation scale. Common approaches to represent structural hierarchy build, for example, on a multidomain continuum for transport or on the coupling of the Stokes equations with Darcy's law for fluid flow. These approaches, however, are computationally expensive or introduce empirical parameters that are difficult to derive with independent observations. We present an efficient model for fluid flow based on Darcy's law and the law of Hagen‐Poiseuille that is parameterized based on the explicit pore space morphology obtained, for example, by X‐ray μ‐CT and inherently permits the coupling of pore‐scale and continuum‐scale domain. We used the resulting flow field to predict the transport of solutes via particle tracking across the different domains. Compared to experimental breakthrough data from laboratory‐scale columns with hierarchically structured porosity built from solid glass beads and microporous glass pellets, an excellent agreement was achieved without any calibration. Furthermore, we present different test scenarios to compare the flow fields resulting from the Stokes‐Brinkman equations and our approach to comprehensively illustrate its advantages and limitations. In this way, we could show a striking efficiency and accuracy of our approach that qualifies as general alternative for the modeling of fluid flow and transport in hierarchical porous media, for example, fractured rock or karstic aquifers. A model for the simulation of pore‐scale and continuum‐scale flow in hierarchically structured porous media is developed Explicit pore space morphology obtained by image analysis of X‐ray micro‐CT images is used for parameterization Predictions of solute breakthrough obtained by particle tracking perfectly match observations
    Keywords: Darcy'S Law ; Particle Tracking ; Column Experiments ; X‐Ray Μ‐Ct ; Pore Space Morphology ; Image Analysis
    ISSN: 0043-1397
    E-ISSN: 1944-7973
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  • 4
    Language: English
    In: Soil & Tillage Research, January 2018, Vol.175, pp.205-216
    Description: In recent years, there has been an increased application of conservation-oriented tillage techniques, where instead of being turned the soil is only loosened or not tilled at all. Strip tillage, a special form of conservation tillage, results in small-scale structural differences, since tillage is performed only within the seed row, while the soil between seed rows is not tilled. However, tillage always impacts upon physical soil properties and processes. A combined application of conventional soil mechanical methods and X-ray computed tomography (X-ray CT) is employed here in order to investigate small-scale structural differences in a chernozem (texture 0–30 cm: silt loam) located in central Germany under strip tillage (within and between seed rows) compared to no tillage and mulch tillage. Apart from recording changes over time (years: 2012, 2014, 2015) to dry bulk density and saturated conductivity at soil depths 2–8 and 12–18 cm, stress-strain tests were conducted to map mechanical behaviour for a load range of 5–550 kPa at a soil depth of 12–18 cm (year 2015). Mechanical precompression stress was determined from the stress-dry bulk density curves. In addition, computed tomography scans were created followed by quantitative image analysis of the morphometric parameters mean macropore diameter, macroporosity, connectivity and anisotropy of the same soil samples. For strip tillage between seed rows and no tillage, a significant increase in dry bulk density was observed over time compared to strip tillage within the seed row and mulch tillage. This was more pronounced at a soil depth of 2–8 cm than at 12–18 cm. Despite higher dry bulk density, strip tillage between the seed row displayed also an increasing saturated conductivity compared to strip tillage within the seed row and mulch tillage. The computed tomography scans showed that the macropores became more compressed and soil aggregates were pushed together as mechanical stress increased, with the aggregate arrangement being transformed down into a coherent soil mass. The soil mechanical and morphometric parameters supported each other in terms of what they revealed about the mechanical properties of the soil structures. For instance, in the strip tillage between seed rows and no tillage treatments, the lack of soil tillage not only resulted in higher dry bulk densities, but also higher aggregate densities, mechanical precompression stress values, mean macropore diameters as well as lower macroporosity and connectivity values compared to mulch tillage and strip tillage within the seed row. The computed tomography parameters are therefore highly suitable for providing Supplementary information about the compaction process. Overall, this study showed that strip tillage combines the advantages of no tillage and a deeper, soil conservation-oriented primary tillage because, on a small scale, it creates two distinct soil structures which are beneficial in terms of optimal plant growth as well as mechanical resistance by driving over the soil.
    Keywords: Pre-Compression Stress ; Dry Bulk Density ; Aggregate Density ; Image Analysis ; Soil Compaction ; Agriculture
    ISSN: 0167-1987
    E-ISSN: 1879-3444
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  • 5
    Language: English
    In: Vadose Zone Journal, 2014, Vol.13(8), p.0
    Description: Root system architecture and associated root–soil interactions exhibit large changes over time. Nondestructive methods for the quantification of root systems and their temporal development are needed to improve our understanding of root activity in natural soils. X-ray computed tomography (X-ray CT) was used to visualize and quantify growth of a single Vicia faba L. root system during a drying period. The plant was grown under controlled conditions in a sandy soil mixture and imaged every second day. Minkowski functionals and Euclidean distance transform were used to quantify root architectural traits. We were able to image the root system with water content decreasing from 29.6 to 6.75%. Root length was slightly underestimated compared with destructive measurements. Based on repeated measurements over time it was possible to quantify the dynamics of root growth and the demography of roots along soil depth. Measurement of Euclidean distances from any point within the soil to the nearest root surface yielded a frequency distribution of travel distances for water and nutrients towards roots. Our results demonstrate that a meaningful quantitative characterization of root systems and their temporal dynamics is possible.
    Keywords: Agriculture;
    ISSN: Vadose Zone Journal
    E-ISSN: 1539-1663
    Source: CrossRef
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  • 6
    In: Water Resources Research, April 2009, Vol.45(4), pp.n/a-n/a
    Description: High‐resolution optical bench‐scale experiments were conducted in order to investigate local gas flow pattern and integral flow properties caused by point‐like gas injection into water‐saturated glass beads. The main goal of this study was to test the validity of the continuum approach for two‐fluid flow in macroscopic homogeneous media. Analyzing the steady state experimental gas flow pattern that satisfies the necessary coherence condition by image processing and calibrating the optical gas distribution by the gravimetrical gas saturation, it was found that a pulse‐like function yields the best fit for the lateral gas saturation profile. This strange behavior of a relatively sharp saturation transition is in contradiction to the widely anticipated picture of a smooth Gaussian‐like transition, which is obtained by the continuum approach. This transition is caused by the channelized flow structure, and it turns out that only a narrow range of capillary pressure is realized by the system, whereas the continuum approach assumes that within the representative elementary volume the whole spectrum of capillary pressures can be realized. It was found that the stochastical hypothesis proposed by Selker et al. (2007) that bridges pore scale and continuum scale is supported by the experiments. In order to study channelized gas flow on the pore scale, a variational treatment, which minimizes the free energy of an undulating capillary, was carried out. On the basis of thermodynamical arguments the geometric form of a microcapillary, macrochannel formation and a length‐scale‐dependent transition in gas flow pattern from coherent to incoherent flow are discussed.
    Keywords: Air Sparging ; Continuum Modeling ; Pore‐Scale Modeling ; Gas Flow Pattern ; Instability Analysis ; Image Processing
    ISSN: 0043-1397
    E-ISSN: 1944-7973
    Source: John Wiley & Sons, Inc.
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  • 7
    Language: English
    In: Geoderma, 01 July 2019, Vol.345, pp.63-71
    Description: Soil structure is not static but undergoes continuous changes due to a wide range of biotic and abiotic drivers such as bioturbation and the mechanical disturbance by tillage. This continuous alteration of soil structure beyond the pure swelling and shrinking of some stable structure is what we refer to as soil structure dynamics. It has important consequences for carbon turnover in soil as it controls how quickly soil organic matter gets occluded from or exposed to mineralization. So far there are hardly any direct observations of the rate at which soil pores are formed and destroyed. Here we employ are recently introduced labeling approach for soil structure that measures how quickly the locations of small garnet particles get randomized in soil as a measure for soil structure dynamics. We investigate the effect of desiccation crack dynamics on pore space attributes in general and soils structure turnover in particular using X-ray microtomography for repeated wetting-drying cycles. This is explored for three different soils with a range of soil organic matter content, clay content and different clay mineralogy that were sieved to a certain aggregate size fraction (0.63–2 mm) and repacked at two different bulk density levels. The total magnitude of desiccation crack formation mainly depended on the clay content and clay mineralogy. Higher soil organic matter content led to a denser crack pattern with smaller aperture. Wetting-drying cycles did not only effect visible macroporosity (〉8 μm), but also unresolved mesoporosity. The changes in macroporosity were higher at lower bulk density. Most importantly, repeated wetting-drying cycles did not lead to a randomization of distances between garnet particles and pores. This demonstrates that former failure zones are reactivated during subsequent drying cycles. Hence, wetting-drying resulted in reversible particle displacement and therefore would not have triggered the exposure of occluded carbon that was not already exposed during the previous drying event.
    Keywords: Soil Structure ; Desiccation Cracks ; X-Ray Tomography ; Macropores ; Clay Mineralogy ; Carbon Turnover ; Agriculture
    ISSN: 0016-7061
    E-ISSN: 1872-6259
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  • 8
    Language: English
    In: Vadose Zone Journal, 2009, Vol.8(3), p.805
    Description: It has been speculated that during periods of water deficit, roots may shrink and lose contact with the soil, with a consequent reduction in root water uptake. Due to the opaque nature of soil, however, this process has never been observed in situ for living plants. Through x-ray tomography and image analysis, we have demonstrated the formation and dynamics of air gaps around roots. The high spatial resolution required to image the soil–root gaps was achieved by combining tomography of the entire sample (field of view of 16 by 16 cm, pixel side 0.32 mm) with local tomography of the soil region around the roots (field of view of 5 by 5 cm, pixel side 0.09 mm). For a sandy soil, we found that when the soil dries to a water content of 0.025 m3 m–3, gaps occur around the taproot and the lateral roots of lupin (Lupinus albus L.). Gaps were larger for the taproot than the laterals and were caused primarily by root shrinkage rather than by soil shrinkage. When the soil was irrigated again, the roots swelled, partially refilling the gaps; however, large gaps persisted in the more proximal, older part of the taproot. Gaps are expected to reduce water transfers between soil and roots. Opening and closing of gaps may help plants to prevent water loss when the soil dries, and to restore the soil–root continuity when water becomes available. The persistence of gaps in the more proximal parts is one reason why roots preferentially take up water from their more distal parts. ; Includes references ; p. 805-809.
    Keywords: Soil Water Content ; Roots ; Soil-Plant Interactions ; Shrinkage ; Plants ; Translocation (Plant Physiology) ; Lupinus Albus ; Forage Legumes ; Spatial Variation ; Drought ; Water Stress ; Sandy Soils ; Water Uptake ; Computed Tomography ; Forage Crops ; Image Analysis ; Taproots;
    ISSN: Vadose Zone Journal
    E-ISSN: 1539-1663
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  • 9
    Language: English
    In: Geoderma, 15 September 2019, Vol.350, pp.61-72
    Description: During soil formation, the interaction of different biota (plants, soil fauna, microbes) with weathered mineral material shapes unique structures depending on the parental material and the site specific climatic conditions. While many of these interactions are known, the relative importance of the different biota is difficult to unravel and therefore difficult to quantify. Biological soil structure formation is often superimposed by soil management and swell-shrink dynamics, making it even more difficult to derive mechanistic understanding. We here explore soil structure formation within a “space-for-time” chronosequence in the Rhenish lignite mining area. Loess material from a depth of 4–10 m has been used for reclamation in a standardized procedure for 24 years. Changes in soil pore system are characterized by properties such as connectivity (Euler number) and pore size distribution using undisturbed soil columns with a diameter of 10 cm. They were taken from two different depths (0–20 cm and 40–60 cm) at different sites ranging in age from 0 to 24 years. X-ray CT is used for scanning the original columns as well as undisturbed subsamples of 3 and 0.7 cm diameter. This hierarchical sampling scheme was developed to overcome the trade-off between sample size and resolution. For the first time also information on the development of biopores could be measured by separating them from other structural pores based on their unique shape. The data were complemented by destructive sampling and determination of root length with WinRHIZO to give an estimate of how many biopores are filled with roots. Furthermore HYPROP measurements of water retention curves were conducted and showed a general agreement with the image-derived pore size distribution merged across three scales. An increase in biopore density throughout year zero to year 12, in particular in 40–60 cm soil depth, was observed. The biopore length densities of approximately 17 cm/cm obtained in year 12 was similar to the one measured in year 24, suggesting that equilibrium was reached. Only about 10% of these biopores were filled with roots. In the topsoil (0–20 cm) the equilibrium value in biopore density is already reached after six years due to a higher root length density. Ploughing lead to higher mean pore size and to lower connectivity compared to the well-connected, very stable pore network in 40–60 cm depth. This study shows how fast plant roots create a stable and connected biopore system and how this is disrupted by soil tillage, which produces completely contrasting pore characteristics.
    Keywords: Biopores ; Structure Formation ; X-Ray CT ; Tilled Soil ; Agriculture
    ISSN: 0016-7061
    E-ISSN: 1872-6259
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  • 10
    Language: English
    In: Geoderma, 15 July 2019, Vol.346, pp.52-62
    Description: Some soil physical properties can easily be measured using classical laboratory methods. However, explicit valuable information on the real morphology of the pore structure as well as soil physical properties cannot be obtained at the same time with classical methods. This requires non-destructive measurements such as X-ray computed tomography (CT). However, explicit valuable information on the real morphology of the pore structure as well as soil physical properties cannot be obtained at the same time with classical methods. This paper combines parameters obtained from CT analysis (mean macropore diameter, macroporosity, pore connectivity, anisotropy) and classical laboratory methods (dry bulk and aggregate density, saturated hydraulic conductivity, mechanical precompression stress) to analyse soil compaction, exemplified on samples from two tillage treatments (cultivator and plough) and at two moisture states (6 and 1000 kPa matric potential) on a Chernozem collected at a soil depth of 16–22 cm (texture 0–30 cm: silty clay loam). The study shows that the matric potential can have a decisive impact on the mechanical stability of soil. In the loose but less stable plough treatment a more negative matric potential was clearly beneficial to the mechanical stability. In already dense soil structures, as in the cultivator treatment, a reduction of water content was less effective in increasing soil stability. The CT parameters were all closely and uniquely related to each other. The shown CT parameters can be used for a standardized characterization of the soil. Ploughing has a positive effect on soil structure which persists only as long as macroporosity and mean macropore diameter remain high. Plough maintains higher pore connectivity when compacted under dry conditions.
    Keywords: X-Ray CT ; Mechanical Soil Analysis ; Conservation Tillage ; Conventional Tillage ; Soil Compaction ; Precompression Stress ; Agriculture
    ISSN: 0016-7061
    E-ISSN: 1872-6259
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