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

Synchrotron-based visualization and segmentation of elastic lamellae in the mouse carotid artery during quasi-static pressure inflation

This dataset contains images that were obtained during quasi-static pressure inflation of mouse carotid arteries. Images were taken with phase propagation imaging at the X02DA TOMCAT beamline of the Swiss Light Source synchrotron at the Paul Scherrer Institute in Villigen, Switzerland. Scans of n=12 left carotid arteries (n-6 Apoe-deficient mice, n=6 wild-type mice, all on a C57Bl6J background) were taken at pressure levels of 0, 10, 20, 30, 40, 50, 70, 90 and 120 mmHg. For analysis we selected 75 images from the center of each stack (starting at the center of the stack, and skipping 2 of every three images in both cranial and caudal axial directions) for each sample and for each pressure level, resulting in a total of 75 x 12 x 9 = 8100 analyzed images from 108 different scans. Segmentation, 3D visualization and geometric analysis is presented in the corresponding manuscript. Files are uploaded in 16bit .tif format and are named: mouseid_pressurelevel_stacknumber, with mouseid consisting of either Apoe (Apoe-deficient) or Bl (wild-type) and the mouse number, pressurelevel varies from P0 to P120 and stacknumber indicates which image from the stack has been uploaded

Ptychographic X-ray computed tomography of extended colloidal networks in food emulsions

As a main structural level in colloidal food materials, extended colloidal networks are important for texture and rheology. By obtaining the 3D microstructure of the network, macroscopic mechanical properties of the material can be inferred. However, this approach is hampered by the lack of suitable non-destructive 3D imaging techniques with submicron resolution. We present results of quantitative ptychographic X-ray computed tomography applied to a palm kernel oil based oil-in-water emulsion. The measurements were carried out at ambient pressure and temperature. The 3D structure of the extended colloidal network of fat globules was obtained with a resolution of around 300 nm. Through image analysis of the network structure, the fat globule size distribution was computed and compared to previous findings. In further support, the reconstructed electron density values were within 4% of reference values.Comment: 19 pages, 4 figures, to be published in Food Structur

Recent trends, technical concepts and components of computer-assisted orthopedic surgery systems: A comprehensive review

Computer-assisted orthopedic surgery (CAOS) systems have become one of the most important and challenging types of system in clinical orthopedics, as they enable precise treatment of musculoskeletal diseases, employing modern clinical navigation systems and surgical tools. This paper brings a comprehensive review of recent trends and possibilities of CAOS systems. There are three types of the surgical planning systems, including: systems based on the volumetric images (computer tomography (CT), magnetic resonance imaging (MRI) or ultrasound images), further systems utilize either 2D or 3D fluoroscopic images, and the last one utilizes the kinetic information about the joints and morphological information about the target bones. This complex review is focused on three fundamental aspects of CAOS systems: their essential components, types of CAOS systems, and mechanical tools used in CAOS systems. In this review, we also outline the possibilities for using ultrasound computer-assisted orthopedic surgery (UCAOS) systems as an alternative to conventionally used CAOS systems.Web of Science1923art. no. 519

Tomography of atomic number and density of materials using dual-energy imaging and the Alvarez and Macovski attenuation model

Dual-energy computed tomography and the Alvarez and Macovski [Phys. Med. Biol. 21, 733 (1976)] transmitted intensity (AMTI) model were used in this study to estimate the maps of density (ρ) and atomic number (Z) of mineralogical samples. In this method, the attenuation coefficients are represented [Alvarez and Macovski, Phys. Med. Biol. 21, 733 (1976)] in the form of the two most important interactions of X-rays with atoms that is, photoelectric absorption (PE) and Compton scattering (CS). This enables material discrimination as PE and CS are, respectively, dependent on the atomic number (Z) and density (ρ) of materials [Alvarez and Macovski, Phys. Med. Biol. 21, 733 (1976)]. Dual-energy imaging is able to identify sample materials even if the materials have similar attenuation coefficients at single-energy spectrum. We use the full model rather than applying one of several applied simplified forms [Alvarez and Macovski, Phys. Med. Biol. 21, 733 (1976); Siddiqui et al., SPE Annual Technical Conference and Exhibition (Society of Petroleum Engineers, 2004); Derzhi, U.S. patent application 13/527,660 (2012); Heismann et al., J. Appl. Phys. 94, 2073–2079 (2003); Park and Kim, J. Korean Phys. Soc. 59, 2709 (2011); Abudurexiti et al., Radiol. Phys. Technol. 3, 127–135 (2010); and Kaewkhao et al., J. Quant. Spectrosc. Radiat. Transfer 109, 1260–1265 (2008)]. This paper describes the tomographic reconstruction of ρ and Z maps of mineralogical samples using the AMTI model. The full model requires precise knowledge of the X-ray energy spectra and calibration of PE and CS constants and exponents of atomic number and energy that were estimated based on fits to simulations and calibration measurements. The estimated ρ and Z images of the samples used in this paper yield average relative errors of 2.62% and 1.19% and maximum relative errors of 2.64% and 7.85%, respectively. Furthermore, we demonstrate that the method accounts for the beam hardening effect in density (ρ) and atomic number (Z) reconstructions to a significant extent.S.J.L., G.R.M., and A.M.K. acknowledge funding through the DigiCore consortium and the support of a linkage grant (LP150101040) from the Australian Research Council and FEI Company