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

Numerical simulation of the stress-strain state of the dental system

We present mathematical models, computational algorithms and software, which can be used for prediction of results of prosthetic treatment. More interest issue is biomechanics of the periodontal complex because any prosthesis is accompanied by a risk of overloading the supporting elements. Such risk can be avoided by the proper load distribution and prediction of stresses that occur during the use of dentures. We developed the mathematical model of the periodontal complex and its software implementation. This model is based on linear elasticity theory and allows to calculate the stress and strain fields in periodontal ligament and jawbone. The input parameters for the developed model can be divided into two groups. The first group of parameters describes the mechanical properties of periodontal ligament, teeth and jawbone (for example, elasticity of periodontal ligament etc.). The second group characterized the geometric properties of objects: the size of the teeth, their spatial coordinates, the size of periodontal ligament etc. The mechanical properties are the same for almost all, but the input of geometrical data is complicated because of their individual characteristics. In this connection, we develop algorithms and software for processing of images obtained by computed tomography (CT) scanner and for constructing individual digital model of the tooth-periodontal ligament-jawbone system of the patient. Integration of models and algorithms described allows to carry out biomechanical analysis on three-dimensional digital model and to select prosthesis design.Comment: 19 pages, 9 figure

Spatial development of transport structures in apple (Malus x domestica Borkh.) fruit

The void network and vascular system are important pathways for the transport of gases, water and solutes in apple fruit (Malus x domestica Borkh). Here we used X-ray micro-tomography at various spatial resolutions to investigate the growth of these transport structures in 3D during fruit development of ‘Jonagold’ apple. The size of the void space and porosity in the cortex tissue increased considerably. In the core tissue, the porosity was consistently lower, and seemed to decrease towards the end of the maturation period. The voids in the core were more narrow and fragmented than the voids in the cortex. Both the void network in the core and in the cortex changed significantly in terms of void morphology. An automated segmentation protocol underestimated the total vasculature length by 9 to 12% in comparison to manually processed images. Vascular networks increased in length from a total of 5 meter at 9 weeks after full bloom, to more than 20 meter corresponding to 5 cm of vascular tissue per cubic centimeter of apple tissue. A high degree of branching in both the void network and vascular system and a complex three-dimensional pattern was observed across the whole fruit. The 3D visualisations of the transport structures may be useful for numerical modeling of organ growth and transport processes in fruit

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

Capturing natural-colour 3D models of insects for species discovery

Collections of biological specimens are fundamental to scientific understanding and characterization of natural diversity. This paper presents a system for liberating useful information from physical collections by bringing specimens into the digital domain so they can be more readily shared, analyzed, annotated and compared. It focuses on insects and is strongly motivated by the desire to accelerate and augment current practices in insect taxonomy which predominantly use text, 2D diagrams and images to describe and characterize species. While these traditional kinds of descriptions are informative and useful, they cannot cover insect specimens "from all angles" and precious specimens are still exchanged between researchers and collections for this reason. Furthermore, insects can be complex in structure and pose many challenges to computer vision systems. We present a new prototype for a practical, cost-effective system of off-the-shelf components to acquire natural-colour 3D models of insects from around 3mm to 30mm in length. Colour images are captured from different angles and focal depths using a digital single lens reflex (DSLR) camera rig and two-axis turntable. These 2D images are processed into 3D reconstructions using software based on a visual hull algorithm. The resulting models are compact (around 10 megabytes), afford excellent optical resolution, and can be readily embedded into documents and web pages, as well as viewed on mobile devices. The system is portable, safe, relatively affordable, and complements the sort of volumetric data that can be acquired by computed tomography. This system provides a new way to augment the description and documentation of insect species holotypes, reducing the need to handle or ship specimens. It opens up new opportunities to collect data for research, education, art, entertainment, biodiversity assessment and biosecurity control.Comment: 24 pages, 17 figures, PLOS ONE journa