High-resolution X-ray Computed Tomography Scanner Research Articles

Soil pore characteristics assessed from X-ray micro-CT derived images and correlations to soil friability

X-ray computed tomography (CT) scanning technology has, in recent decades, been shown to be a very powerful technique to visualize and quantify soil structure. The objective of this project was to quantify soil pore characteristics, on undisturbed field moist soil, using a high resolution X-ray CT scanner and link then these results to soil friability assessed using the drop shatter method. Minimally disturbed soil cores were taken from selected treatments in a long-term rotation and tillage treatment experiment located on a silt loam at the Elora Research Station near Elora, Ontario, Canada. Soil cores varied in porosity and pore characteristics. A drop shatter test was used as a reference procedure to quantify soil friability. The top 40mm of the 80mm high soil samples were scanned using a X-ray micro-CT scanner. The selected region of interest (36×36×36mm) was reconstructed with a voxel size of 60μm. Estimated surface area, produced from the drop-shatter test, varied between 0.2 and 1.62m2kg−1, and an average of 0.79m2kg−1. Total and air-filled porosity was determined on the soil cores using traditional methods. Total porosity ranged from 41 to 60m3100m−3, and an average of 49m3100m−3. The air-filled porosity, at sampling/testing, ranged between 5 and 32m3100m−3, with an average of 15m3100m−3. The porosity determined from CT imagery ranged between 1 and 31m3100m−3, with an average of 4.5m3100m−3. The number of branches, junctions and end points averaged 298, 117 and 198 per cm3, respectively. We found significant and strong correlations between the soil pore characteristics assessed on the whole soil cores and the characteristics of the air-filled pores determined using high-resolution X-ray computer tomography (CT). Our study confirmed a significant correlation between soil friability, expressed by surface area produced by standardized drop-shatter, and soil pore characteristics. The strongest correlations were found with porosity, surface area and number of junctions per cm3.

Assessment of Common Scab-Inducing Pathogen Effects on Potato Underground Organs Via Computed Tomography Scanning

Common scab caused by Streptomyces scabies is a major bacterial disease of potato (Solanum tuberosum). Its best known symptom is superficial lesions on the surface of progeny potato tubers, observed at harvesting. In this study, effects of S. scabies on space occupancy by underground organs and on structural complexity of root systems are investigated during growth via computed tomography (CT) scanning. Two groups of potato plants were grown in a greenhouse in middle-sized plastic pots. Using a high-resolution X-ray CT scanner formerly used for medical applications, their underground organs and surrounding medium (sieved and autoclaved homogeneous sand) were submitted to CT scanning 4, 6, and 8 weeks after planting. For one group, sand was inoculated with the common scab-inducing pathogen (S. scabies EF-35) at potting. Space occupancy by underground organs was estimated via curve fitting applied to histograms of CT scan data, while three-dimensional skeletal images were used for fractal analysis. Root systems of diseased plants were found to be less complex than those of healthy plants 4 weeks after planting, and the relative growth rates derived from space occupancy measures were of different sign between the two groups from week 4 to week 8.

Advances in the acquisition and analysis of CT scan data to isolate a crop root system from the soil medium and quantify root system complexity in 3-D space

Root systems play an important role in soil-based resource acquisition. The ability to quantify the structural complexity of a root system should lead to an improved understanding of its many functions, but first of all, root systems must be visualized in the soil medium. Accordingly, the main objective of the reported study was to bring the novel approach based on computed tomography (CT) scanning to the next stage in root system studies, by upgrading the operational and analytical procedures available and reporting concrete results for a given crop species (i.e. maize) in different soil-moisture combinations. We also wanted to quantify the structural complexity of root systems by fractal analysis. Maize ( Zea mays L.) was sown in standard plastic pots, 100 mm in top diameter. Sieved and homogenized mineral soils with no or very little organic material were used as growth media. A high-resolution X-ray CT scanner, formerly used for medical purposes, produced series of 500 CT images of 0.1-mm thick cross-sections of the root systems of the seedlings in dry and water-saturated soil conditions. Some seedlings were grown in a homogenous sandy soil, and were CT scanned about 5 days after emergence. Others were grown in loamy sand, and were CT scanned 3 days after emergence, because of their faster growth rate. Data analysis was performed on the 512 × 512 matrices of CT numbers used to construct CT images. Each CT number provided an indirect measure of density for one voxel with dimensions 0.12 × 0.12 × 0.1 mm 3. We present the procedures that we used to digitally isolate a root system from the soil medium in 3-D space using CT scan data and to skeletonize the resulting 3-D image. We explain how to estimate the fractal dimension (FD) on such a skeletonized 3-D image of a root system in order to quantify its complexity. For the same root system, once removed from the soil and washed, FD was also estimated from a 2-D photograph. The expected dissimilarities between the FD estimates of the two types are confirmed and discussed. We found that the soil conditions allowing more accurate visualization of maize root systems by CT scanning were dry homogeneous sand and water-saturated loamy sand. The use of sieved and homogenized mineral soils facilitated the presentation of the new methodology here. In future studies, non-homogeneous soils can be used, and the guidelines that we have proposed will then be helpful in analyzing root geometry with respect to soil structure, for example.

Computed tomography scanning for three-dimensional imaging and complexity analysis of developing root systems

To improve our understanding of the role of root systems in soil-based resource acquisition by plants and eventually model it completely, root system complexity must be quantified, in addition to other morphometric traits. In this note, we introduce a new approach in which computed tomography (CT) scan data are collected on crop root systems in three-dimensional (3-D) space nondestructively and noninvasively, thus allowing for repeated measurements and a relevant complexity analysis of root systems. The experimental crop is maize ( Zea mays L.). Four potted seedlings were CT scanned under wet soil conditions on the day of emergence, and each of the two following days. Specifically, a high-resolution X-ray CT scanner formerly used for medical purposes produced 3 × 500 CT images of 0.1 mm thick cross-sections for each seedling. The fractal dimension of each root system on each day was estimated on a skeletonized 3-D image reconstructed from CT scan data. We found that the mean fractal dimension value was not significantly greater than 1 on day 1 (1.015 ± 0.015), contrary to days 2 and 3 (1.037 ± 0.015, 1.065 ± 0.016). Our results, including original 3-D images, provide support for a novel type of root system studies based on the collection and advanced analysis of CT scan data.

Angular orientation of trabecular bone in the femoral head and its relationship to hip joint loads in leaping primates

The elastic properties and mechanical behavior of trabecular bone are largely determined by its three-dimensional (3D) fabric structure. Recent work demonstrating a correlation between the primary mechanical and material axes in trabecular bone specimens suggests that fabric orientation may be used to infer directional components of the material strength and, by extension, the hypothetical loading regime. Here we quantify the principal orientation of trabecular bone in the femoral head and relate these principal fabric directions to loading patterns during various locomotor behaviors. The proximal femora of a diverse sample of prosimians were scanned using a high-resolution X-ray computed tomography scanner with resolution of better than 50 mum. Spherical volumes of interest were defined within the femoral heads and the 3D fabric anisotropy was calculated using the mean intercept length and star volume distribution methods. In addition to differences in bone volume and anisotropy, significant differences were found in the spatial orientation of the principal trabecular axes depending on locomotor behavior. The principal orientations for leapers (Galago, Tarsius, Avahi) are relatively tightly clustered (alpha(95) confidence limit: 8.2; angular variance s: 18.2 degrees ) and oriented in a superoanterior direction, while those of nonleapers are more variable across a range of directions (alpha(95): 16.8; s: 42.0 degrees ). The mean principal directions are significantly different for leaping vs. nonleaping taxa. These results further suggest a relationship between bone microstructure in the hip joint and locomotor behavior and indicate a similarity of loading across leapers despite differences in kinematics and phylogeny.

Three-dimensional modelling of the middle-ear ossicular chain using a commercial high-resolution X-ray CT scanner.

The quantitative measurement of the three-dimensional (3-D) anatomy of the ear is of great importance in the making of teaching models and the design of mathematical models of parts of the ear, and also for the interpretation and presentation of experimental results. This article describes how we used virtual sections from a commercial high-resolution X-ray computed tomography (CT) scanner to make realistic 3-D anatomical models for various applications in our middle-ear research. The important problem of registration of the 3-D model within the experimental reference frame is discussed. The commercial X-ray CT apparatus is also compared with X-ray CT using synchrotron radiation, with magnetic resonance microscopy, with fluorescence optical sectioning, and with physical (histological) serial sections.

Assessing the accuracy of high-resolution X-ray computed tomography of primate trabecular bone by comparisons with histological sections.

Different lines of evidence suggest that trabecular bone architecture contains a functional signal related to an organism's locomotor behavior. An understanding of the interspecific and intraspecific variation in extant nonhuman primate trabecular structure is needed to evaluate its usefulness as a tool to reconstruct the locomotor habits of extinct primates. High-resolution X-ray computed tomography (HRXCT) is a new imaging approach with a resolution in the tens of microns that allows nondestructive access to the internal structure of bony elements. Previous studies indicate that such resolution is necessary to accurately quantify structural parameters of trabecular bone. The primary goal of this study was to test the accuracy of HRXCT by comparing stereological measurements from HRXCT images and histological thin sections of cancellous bone taken from the proximal femur and humerus of baboons. To this end, 11 bone samples were scanned on an HRXCT scanner and then thin-sectioned to reveal the scanned plane. HRXCT images were thresholded using a modified half-maximum height protocol. The stereological measurements included bone volume fraction (BV/TV), trabecular number (Tb.N), bone surface to volume ratio (BS/BV), trabecular thickness (Tb.Th), and trabecular spacing (Tb.Sp). The measurement errors on the HRXCT images were 10.90% for BV/TV, 6.06% for Tb.N, 14.19% for BS/BV, 14.33% for Tb.Th, and 7.09% for Tb.Sp, but none of these measurements were significantly different from the histological standards (alpha = 0.05). A second goal of this study was to examine the influence of thresholding, a necessary step in any morphometric study using computed tomography, on the accuracy of the quantitative morphometry. Threshold values derived from a modified half-maximum height protocol showed that parameters derived from the region of interest (area in which stereological measurements were later taken) produced better reconstructions of the actual bone structure than threshold values derived from more inclusive areas of bone. We conclude that HRXCT can accurately reconstruct the complex architecture of trabecular bone, and that thresholding is a nontrivial step in trabecular bone studies, with even slight changes in the protocol greatly affecting the morphometric data. HRXCT represents a valuable analytical tool that should be of interest to a great many researchers in physical anthropology because it allows nondestructive access to internal morphology, thereby preserving valuable and limited skeletal collections.