Challenges in imaging and predictive modeling of rhizosphere processes

Background Plant-soil interaction is central to human food production and ecosystem function. Thus, it is essential to not only understand, but also to develop predictive mathematical models which can be used to assess how climate and soil management practices will affect these interactions. Scope In this paper we review the current developments in structural and chemical imaging of rhizosphere processes within the context of multiscale mathematical image based modeling. We outline areas that need more research and areas which would benefit from more detailed understanding. Conclusions We conclude that the combination of structural and chemical imaging with modeling is an incredibly powerful tool which is fundamental for understanding how plant roots interact with soil. We emphasize the need for more researchers to be attracted to this area that is so fertile for future discoveries. Finally, model building must go hand in hand with experiments. In particular, there is a real need to integrate rhizosphere structural and chemical imaging with modeling for better understanding of the rhizosphere processes leading to models which explicitly account for pore scale processes

Micro-computed tomography pore-scale study of flow in porous media: Effect of voxel resolution

A fundamental understanding of flow in porous media at the pore-scale is necessary to be able to upscale average displacement processes from core to reservoir scale. The study of fluid flow in porous media at the pore-scale consists of two key procedures: Imaging - reconstruction of three-dimensional (3D) pore space images; and modelling such as with single and two-phase flow simulations with Lattice-Boltzmann (LB) or Pore-Network (PN) Modelling. Here we analyse pore-scale results to predict petrophysical properties such as porosity, single-phase permeability and multi-phase properties at different length scales. The fundamental issue is to understand the image resolution dependency of transport properties, in order to up-scale the flow physics from pore to core scale. In this work, we use a high resolution micro-computed tomography (micro-CT) scanner to image and reconstruct three dimensional pore-scale images of five sandstones (Bentheimer, Berea, Clashach, Doddington and Stainton) and five complex carbonates (Ketton, Estaillades, Middle Eastern sample 3, Middle Eastern sample 5 and Indiana Limestone 1) at four different voxel resolutions (4.4 µm, 6.2 µm, 8.3 µm and 10.2 µm), scanning the same physical field of view. Implementing three phase segmentation (macro-pore phase, intermediate phase and grain phase) on pore-scale images helps to understand the importance of connected macro-porosity in the fluid flow for the samples studied. We then compute the petrophysical properties for all the samples using PN and LB simulations in order to study the influence of voxel resolution on petrophysical properties. We then introduce a numerical coarsening scheme which is used to coarsen a high voxel resolution image (4.4 µm) to lower resolutions (6.2 µm, 8.3 µm and 10.2 µm) and study the impact of coarsening data on macroscopic and multi-phase properties. Numerical coarsening of high resolution data is found to be superior to using a lower resolution scan because it avoids the problem of partial volume effects and reduces the scaling effect by preserving the pore-space properties influencing the transport properties. This is evidently compared in this study by predicting several pore network properties such as number of pores and throats, average pore and throat radius and coordination number for both scan based analysis and numerical coarsened data

Quantification of sub-resolution porosity in carbonate rocks by applying high-salinity contrast brine using X-ray microtomography differential imaging

Characterisation of the pore space in carbonate reservoirs and aquifers is of utmost importance in a number of applications such as enhanced oil recovery, geological carbon storage and contaminant transport. We present a new experimental methodology that uses high-salinity contrast brine and differential imaging acquired by X-ray tomography to non-invasively obtain three-dimensional spatially resolved information on porosity and connectivity of two rock samples, Portland and Estaillades limestones, including sub-resolution micro-porosity. We demonstrate that by injecting 30 wt% KI brine solution, a sufficiently high phase contrast can be achieved allowing accurate three-phase segmentation based on differential imaging. This results in spatially resolved maps of the solid grain phase, sub-resolution micro-pores within the grains, and macro-pores. The total porosity values from the three-phase segmentation for two carbonate rock samples are shown to be in good agreement with Helium porosity measurements. Furthermore, our flow-based method allows for an accurate estimate of pore connectivity and a distribution of porosity within the sub-resolution pores

Noise Robustness of a Combined Phase Retrieval and Reconstruction Method for Phase-Contrast Tomography

Classical reconstruction methods for phase-contrast tomography consist of two stages: phase retrieval and tomographic reconstruction. A novel algebraic method combining the two was suggested by Kostenko et al. (Opt. Express, 21, 12185, 2013) and preliminary results demonstrating improved reconstruction compared to a two-stage method given. Using simulated free-space propagation experiments with a single sample-detector distance, we thoroughly compare the novel method with the two-stage method to address limitations of the preliminary results. We demonstrate that the novel method is substantially more robust towards noise; our simulations point to a possible reduction in counting times by an order of magnitude

ToScA North America (6 – 8 June 2017, The University of Texas, Austin, TX) Program

ToScA North America will address key areas of science, including Multi-modal Imaging, Geosciences, Forensics, Increasing Contrast, Educational Outreach, Data, Materials Science and Medical and Biological Science.University of Texas High-Resolution X-ray CT Facility (UTCT); Jackson School of Geosciences, The University of Texas at Austin; Natural History Museum (London); Royal Microscopical Society (Oxford, UK)Geological Science

Quantitative characterization of pore structure of several biochars with 3D imaging

Pore space characteristics of biochars may vary depending on the used raw material and processing technology. Pore structure has significant effects on the water retention properties of biochar amended soils. In this work, several biochars were characterized with three-dimensional imaging and image analysis. X-ray computed microtomography was used to image biochars at resolution of 1.14 $\mu$m and the obtained images were analysed for porosity, pore-size distribution, specific surface area and structural anisotropy. In addition, random walk simulations were used to relate structural anisotropy to diffusive transport. Image analysis showed that considerable part of the biochar volume consist of pores in size range relevant to hydrological processes and storage of plant available water. Porosity and pore-size distribution were found to depend on the biochar type and the structural anisotopy analysis showed that used raw material considerably affects the pore characteristics at micrometre scale. Therefore attention should be paid to raw material selection and quality in applications requiring optimized pore structure.Comment: 16 pages, 4 figures. The final publication is available at Springer via http://dx.doi.org/10.1007/s11356-017-8823-