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  • Vogel, Hans-Joerg  (11)
  • Tomography
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  • 1
    Language: English
    In: Vadose Zone Journal, 2015, Vol.14(5), p.0
    Description: We used X-ray computed microtomography to study gas trapping in a fluctuating water table. Our results show that capillary forces control trapping and phase distribution in dynamic capillary fringes. In porous media, the nonwetting phase is trapped on water saturation due to capillary forces acting in a heterogeneous porous structure. Within the capillary fringe, the gas phase is trapped and released along with the fluctuation of the water table, creating a highly active zone for biological transformations and mass transport. We conducted column experiments to observe and quantify the magnitude and structure of the trapped gas phase at the pore scale using computed microtomography. Different grain size distributions of glass beads were used to study the effect of the pore structure on trapping at various capillary numbers. Viscous forces were found to have negligible impact on phase trapping compared with capillary and buoyancy forces. Residual gas saturations ranged from 0.5 to 10%, while residual saturation increased with decreasing grain size. The gas phase was trapped by snap-off in single pores but also in pore clusters, while this single-pore trapping was dominant for grains larger than 1 mm in diameter. Gas surface area was found to increase linearly with increasing gas volume and with decreasing grain size.
    Keywords: Grain Size ; Water Table ; Mass Transport ; Buoyancy ; Pores ; Porous Media ; Particle Size ; Water Table ; Saturation ; Vadose Water ; Fluctuations ; Trapping ; Buoyancy ; Methods and Instruments ; General;
    ISSN: Vadose Zone Journal
    E-ISSN: 1539-1663
    Source: CrossRef
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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
    Language: English
    In: Computers and Geosciences, 2010, Vol.36(10), pp.1246-1251
    Description: For many analyses, grey scale images from X-ray tomography and other sources need to be segmented into objects and background which often is a difficult task and afflicted by an arbitrary and subjective choice of threshold values. This is especially true if the volume fraction of objects is small and the histogram becomes unimodal. Bi-level segmentation based on region growing is a promising approach to cope with the fuzzy transition zone between object and background due to the partial volume effect, but until now there is no method to properly determine the required thresholds in case of unimodality. We propose an automatic and robust technique for threshold selection based on edge detection. The method uses gradient masks which are defined as regions of interest for the determination of threshold values. Its robustness is analysed by a systematic performance test and finally demonstrated for the segmentation of pores in different soils using images from X-ray tomography.
    Keywords: Segmentation ; Thresholding ; Edge Detection ; Region Growing ; Tomography ; Geology
    ISSN: 0098-3004
    E-ISSN: 1873-7803
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  • 4
    In: Water Resources Research, June 2017, Vol.53(6), pp.4709-4724
    Description: The relaxation dynamics toward a hydrostatic equilibrium after a change in phase saturation in porous media is governed by fluid reconfiguration at the pore scale. Little is known whether a hydrostatic equilibrium in which all interfaces come to rest is ever reached and which microscopic processes govern the time scales of relaxation. Here we apply fast synchrotron‐based X‐ray tomography (X‐ray CT) to measure the slow relaxation dynamics of fluid interfaces in a glass bead pack after fast drainage of the sample. The relaxation of interfaces triggers internal redistribution of fluids, reduces the surface energy stored in the fluid interfaces, and relaxes the contact angle toward the equilibrium value while the fluid topology remains unchanged. The equilibration of capillary pressures occurs in two stages: (i) a quick relaxation within seconds in which most of the pressure drop that built up during drainage is dissipated, a process that is to fast to be captured with fast X‐ray CT, and (ii) a slow relaxation with characteristic time scales of 1–4 h which manifests itself as a spontaneous imbibition process that is well described by the Washburn equation for capillary rise in porous media. The slow relaxation implies that a hydrostatic equilibrium is hardly ever attained in practice when conducting two‐phase experiments in which a flux boundary condition is changed from flow to no‐flow. Implications for experiments with pressure boundary conditions are discussed. What happens to fluids in a porous medium after pumping is stopped? Fast X‐ray tomography shows that even in a sample smaller than a sugar cube fluid interfaces continue to move for hours until an optimal fluid configuration is reached. The pace is limited by slow relaxation of dynamic contact angles. Therefore hydrostatic equilibrium, which is the state at which all fluid interfaces come to rest, is hardly ever attained in practice when conducting two‐phase flow experiments where the flow is stopped in much larger soil or rock samples. Relaxation dynamics through internal redistribution of fluids after fast drainage occurs in two stages A quick dissipation within seconds is followed by slow relaxation within several hours due to relaxation of dynamic contact angles Fluid configurations during relaxation are very different from those during quasi‐static drainage and imbibition
    Keywords: Two‐Phase Flow ; Dynamic Effects ; Hydraulic Nonequilibrium ; Dynamic Contact Angle ; Fluid Configuration ; Fluid Topology
    ISSN: 0043-1397
    E-ISSN: 1944-7973
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  • 5
    Language: English
    In: Vadose Zone Journal, 2012, Vol.11(3), p.0
    Description: The rhizosphere has a controlling role in the flow of water and nutrients from soil to plant roots; however, its hydraulic properties are not well understood. As roots grow, they change the pore size distribution of the surrounding soil. Roots release polymeric substances such as mucilage into their rhizosphere. Microorganisms living in the rhizosphere feed on these organic materials and release other polymeric substances into the rhizosphere. The presence of these organic materials might affect the water retention properties and the hydraulic conductivity of the rhizosphere soil during drying and rewetting. We used neutron radiography to monitor the dynamics of water distribution in the rhizosphere of lupin (Lupinus albus L.) plants during a period of drying and rewetting. The rhizosphere was shown to have a higher water content than the bulk soil during the drying period but a lower one during the subsequent rewetting. We evaluated the wettability of the bulk soil and the rhizosphere soil by measuring the contact angle of water in the soil. We found significantly higher contact angles for the rhizosphere soil than the bulk soil after drying, which indicates slight water repellency in the rhizosphere. This explains the lower soil water content in the rhizosphere than the bulk soil after rewetting. Our results suggest that the water holding capacity of the rhizosphere is dynamic and might shift toward higher or lower values than those of the surrounding bulk soil, not affected by roots, depending on the history of drying and rewetting cycles.
    Keywords: Soils ; Hydrogeology ; Absorption ; Carbohydrates ; Compactness ; Concentration ; Ecology ; Habitat ; Hydraulic Conductivity ; Hydrologic Cycle ; Hydrology ; Hydrophobic Materials ; Imagery ; Lipids ; Lupinus Albus ; Measurement ; Microorganisms ; Moisture ; Nuclear Magnetic Resonance ; Nutrients ; Organic Compounds ; Physical Properties ; Plantae ; Polymers ; Polysaccharides ; Porosity ; Rhizosphere ; Roots ; Soil Profiles ; Soil-Water Balance ; Soils ; Spectroscopy ; Tomography ; Wettability ; X-Ray Data;
    ISSN: Vadose Zone Journal
    E-ISSN: 1539-1663
    Source: CrossRef
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  • 6
    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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  • 7
    Language: English
    In: Soil Science Society of America Journal, 2013, Vol.77(2), p.403
    Description: The influence of clay content in soil-pore structure development and the relative importance of macroporosity in governing convective fluid flow are two key challenges toward better understanding and quantifying soil ecosystem functions. In this study, soil physical measurements (soil-water retention and air permeability) and x-ray computed tomography (CT) scanning were combined and used from two scales on intact soil columns (100 and 580 cm super(3)). The columns were sampled along a natural clay gradient at six locations (L1, L2, L3, L4, L5 and L6 with 0.11, 0.16, 0.21, 0.32, 0.38 and 0.46 kg kg super(-1) clay content, respectively) at a field site in Lerbjerg, Denmark. The water-holding capacity of soils markedly increased with increasing soil clay content, while significantly higher air permeability was observed for the L1 to L3 soils than for the L4 to L6 soils. Higher air permeability values observed for 580- than 100-cm super(3) soil columns implied a scale effect and relatively greater importance of macropores in convective fluid flow at larger scale. Supporting this, x-ray CT showed that both interaggregate pores and biopores (pores formed by earthworms and plant roots) were present at L1 to L3 in decreasing order, whereas only interaggre- gate pores were observed at L4 to L6. Macroporosity inferred from x-ray CT to quantify pores 1 mm decreased from 2.9 to 0.1 % from L1 to L6. A progressive improvement was observed in the linear relationship (R super(2) increasing 0.50-0.95) of air permeability with total air-filled porosity, CT-inferred macroporosity, and CT-inferred limiting macroporosity (minimum macroporosity for any quarter of soil column). The findings of this study show the immense potential in linking x-ray CT-derived soil-pore parameters with classical soil physical measurements for quantifying soil architecture and functions. [PUBLICATION]
    Keywords: Soil ; Permeability ; Earthworms ; Soil Structure ; Clay ; Porosity ; Computed Tomography ; Denmark ; Air Pollution;
    ISSN: Soil Science Society of America Journal
    E-ISSN: 0361-5995
    E-ISSN: 14350661
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  • 8
    Language: English
    In: Frontiers in Microbiology, 01 August 2018, Vol.9
    Description: Over the last 60 years, soil microbiologists have accumulated a wealth of experimental data showing that the bulk, macroscopic parameters (e.g., granulometry, pH, soil organic matter, and biomass contents) commonly used to characterize soils provide insufficient information to describe quantitatively the activity of soil microorganisms and some of its outcomes, like the emission of greenhouse gasses. Clearly, new, more appropriate macroscopic parameters are needed, which reflect better the spatial heterogeneity of soils at the microscale (i.e., the pore scale) that is commensurate with the habitat of many microorganisms. For a long time, spectroscopic and microscopic tools were lacking to quantify processes at that scale, but major technological advances over the last 15 years have made suitable equipment available to researchers. In this context, the objective of the present article is to review progress achieved to date in the significant research program that has ensued. This program can be rationalized as a sequence of steps, namely the quantification and modeling of the physical-, (bio)chemical-, and microbiological properties of soils, the integration of these different perspectives into a unified theory, its upscaling to the macroscopic scale, and, eventually, the development of new approaches to measure macroscopic soil characteristics. At this stage, significant progress has been achieved on the physical front, and to a lesser extent on the (bio)chemical one as well, both in terms of experiments and modeling. With regard to the microbial aspects, although a lot of work has been devoted to the modeling of bacterial and fungal activity in soils at the pore scale, the appropriateness of model assumptions cannot be readily assessed because of the scarcity of relevant experimental data. For significant progress to be made, it is crucial to make sure that research on the microbial components of soil systems does not keep lagging behind the work on the physical and (bio)chemical characteristics. Concerning the subsequent steps in the program, very little integration of the various disciplinary perspectives has occurred so far, and, as a result, researchers have not yet been able to tackle the scaling up to the macroscopic level. Many challenges, some of them daunting, remain on the path ahead. Fortunately, a number of these challenges may be resolved by brand new measuring equipment that will become commercially available in the very near future.
    Keywords: Soil Microbiology ; Biodiversity ; Upscaling ; Tomography ; X-Ray Computed ; Nanosims Imaging ; Biology
    E-ISSN: 1664-302X
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  • 9
    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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  • 10
    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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