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  • Vogel, H.-J.  (10)
  • Tomography
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  • 1
    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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  • 2
    In: New Phytologist, November 2011, Vol.192(3), pp.653-663
    Description: • Despite the importance of rhizosphere properties for water flow from soil to roots, there is limited quantitative information on the distribution of water in the rhizosphere of plants. • Here, we used neutron tomography to quantify and visualize the water content in the rhizosphere of the plant species chickpea (Cicer arietinum), white lupin (Lupinus albus), and maize (Zea mays) 12 d after planting. • We clearly observed increasing soil water contents (θ) towards the root surface for all three plant species, as opposed to the usual assumption of decreasing water content. This was true for tap roots and lateral roots of both upper and lower parts of the root system. Furthermore, water gradients around the lower part of the roots were smaller and extended further into bulk soil compared with the upper part, where the gradients in water content were steeper. • Incorporating the hydraulic conductivity and water retention parameters of the rhizosphere into our model, we could simulate the gradual changes of θ towards the root surface, in agreement with the observations. The modelling result suggests that roots in their rhizosphere may modify the hydraulic properties of soil in a way that improves uptake under dry conditions.
    Keywords: Extent Of Rhizosphere ; Modelling ; Neutron Tomography ; Rhizosphere Hydraulic Properties ; Root Water Uptake ; Soil Moisture Profile ; Water Distribution
    ISSN: 0028-646X
    E-ISSN: 1469-8137
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  • 3
    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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  • 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, 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
    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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  • 7
    Language: English
    In: Journal of Plant Nutrition and Soil Science, February 2010, Vol.173(1), pp.88-99
    Description: Soil, the “Earth's thin skin” serves as the delicate interface between the biosphere, hydrosphere, atmosphere, and lithosphere. It is a dynamic and hierarchically organized system of various organic and inorganic constituents and organisms, the spatial structure of which defines a large, complex, and heterogeneous interface. Biogeochemical processes at soil interfaces are fundamental for the overall soil development, and they are the primary driving force for key ecosystem functions such as plant productivity and water quality. Ultimately, these processes control the fate and transport of contaminants and nutrients into the vadose zone and as such their biogeochemical cycling. The definite objective in biogeochemical‐interface research is to gain a mechanistic understanding of the architecture of these biogeochemical interfaces in soils and of the complex interplay and interdependencies of the physical, chemical, and biological processes acting at and within these dynamic interfaces in soil. The major challenges are (1) to identify the factors controlling the architecture of biogeochemical interfaces, (2) to link the processes operative at the individual molecular and/or organism scale to the phenomena active at the aggregate scale in a mechanistic way, and (3) to explain the behavior of organic chemicals in soil within a general mechanistic framework. To put this in action, integration of soil physical, chemical, and biological disciplines is mandatory. Indispensably, it requires the adaption and development of characterization and probing techniques adapted from the neighboring fields of molecular biology, analytical and computational chemistry as well as materials and nano‐sciences. To shape this field of fundamental soil research, the German Research Foundation (DFG) has granted the Priority Program “Biogeochemical Interfaces in Soil”, in which 22 individual research projects are involved.
    Keywords: Soil Function ; Soil Architecture ; Spectro‐Microscopy ; Tomography ; Som ; Soil Microbial Ecology ; Organic Chemicals
    ISSN: 1436-8730
    E-ISSN: 1522-2624
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  • 8
    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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  • 9
    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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  • 10
    Language: English
    In: Biogeosciences, Sept 27, 2019, Vol.16(18), p.3665
    Description: pSoil denitrification is the most important terrestrial process returning reactive nitrogen to the atmosphere, but remains poorly understood. In upland soils, denitrification occurs in hotspots of enhanced microbial activity, even under well-aerated conditions, and causes harmful emissions of nitric (NO) and nitrous oxide (N.sub.2 O). The timing and magnitude of such emissions are difficult to predict due to the delicate balance of oxygen (O.sub.2) consumption and diffusion in soil. To study how spatial distribution of hotspots affects O.sub.2 exchange and denitrification, we embedded microbial hotspots composed of porous glass beads saturated with growing cultures of either Agrobacterium tumefaciens (a denitrifier lacking N.sub.2 O reductase) or Paracoccus denitrificans (a "complete" denitrifier) in different architectures (random vs. layered) in sterile sand that was adjusted to different water saturations (30thinsp;%, 60thinsp;%, 90thinsp;%). Gas kinetics (O.sub.2, CO.sub.2, NO, N.sub.2 O and N.sub.2) were measured at high temporal resolution in batch mode. Air connectivity, air distance and air tortuosity were determined by X-ray tomography after the experiment. The hotspot architecture exerted strong control on microbial growth and timing of denitrification at low and intermediate saturations, because the separation distance between the microbial hotspots governed local oxygen supply. Electron flow diverted to denitrification in anoxic hotspot centers was low (2thinsp;%-7thinsp;%) but increased markedly (17thinsp;%-27thinsp;%) at high water saturation. X-ray analysis revealed that the air phase around most of the hotspots remained connected to the headspace even at 90thinsp;% saturation, suggesting that the threshold response of denitrification to soil moisture could be ascribed to increasing tortuosity of air-filled pores and the distance from the saturated hotspots to these air-filled pores. Our findings suggest that denitrification and its gaseous product stoichiometry depend not only on the amount of microbial hotspots in aerated soil, but also on their spatial distribution. We demonstrate that combining measurements of microbial activity with quantitative analysis of diffusion lengths using X-ray tomography provides unprecedented insights into physical constraints regulating soil microbial respiration in general and denitrification in particular. This paves the way to using observable soil structural attributes to predict denitrification and to parameterize models. Further experiments with natural soil structure, carbon substrates and microbial communities are required to devise and parametrize denitrification models explicit for microbial hotspots.
    Keywords: Nitrogen Oxides – Analysis ; Soil Microbiology – Analysis ; Denitrification – Analysis ; Soil Carbon – Analysis
    ISSN: 1726-4170
    E-ISSN: 17264189
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