Stephan G. le Roux

Laboratory X-ray micro-computed tomography : a user guideline for biological samples

Abstract Laboratory x-ray micro–computed tomography (micro-CT) is a fast-growing method in scientific research applications that allows for non-destructive imaging of morphological structures. This paper provides an easily operated “how to” guide for new potential users and describes the various steps required for successful planning of research projects that involve micro-CT. Background information on micro-CT is provided, followed by relevant setup, scanning, reconstructing, and visualization methods and considerations. Throughout the guide, a Jacksons chameleon specimen, which was scanned at different settings, is used as an interactive example. The ultimate aim of this paper is make new users familiar with the concepts and applications of micro-CT in an attempt to promote its use in future scientific studies.

The quantitative analysis of tungsten ore using X-ray microCT

Volumetric quantification of ore minerals is of interest using non-destructive laboratory X-ray tomography, as it allows high throughput, fast analysis, without any/limited sample preparation. This means traditional chemical analysis can still be performed on the same samples, but good information can be provided in a very short time assisting in exploration, mining and beneficiation decision making as well as sample selection for further chemical analysis. This paper describes a case study in which tungsten WO3/scheelite is quantified in 35mm diameter drill core samples and compared to subsequent traditional chemical analysis for the same samples. The results show a good correlation and indicates that laboratory X-ray CT scanning could replace the more time consuming traditional analytical methods for ore grading purposes in some types of deposits. Different image processing methods are compared for these samples, including an advanced thresholding operation which reduces operator input error. The method should work equally well for other types of ore minerals in which the mineral of interest is the most dense particle in the scan volume, and for which the bulk of the particle sizes are at least 3 times larger than the scan resolution. Performing X-ray microCT scans on drill core samples containing tungsten.Using the microCT data to quantify the grade of tungsten ore non-destructively.Illustrating the advantage of local threshold segmentation over global threshold.Correlating the microCT ore grade results to the industry standard results.

Beauty is more than skin deep: a non‐invasive protocol for in vivo anatomical study using micro‐CT

Micro Computed Tomography (μCT) is a widely used tool in biomedical research, employed to investigate tissues and bone structures of small mammals in vivo. The application of in vivo μCT scanning in non-medical studies greatly lags behind the rapid advancements made in the biomedical field wherein the methodology has evolved to allow for longitudinal studies and eliminate the need to sacrifice the animal. Ecological and evolutionary studies often involve morphological measurements of a large sample of live animals, however, the potential of in vivo μCT imaging as a method for data acquisition has yet to be delineated. Here we describe a protocol for in vivo μCT imaging of the internal anatomy of reptiles and amphibians, commonly used study organisms in ecological and evolutionary research. We consider the skeletal and extra-skeletal (i.e. osteoderms) bones of a lizard as a case study to elucidate the potential of in vivo μCT imaging. Firstly, we explore the effects of various parameter settings on radiation dose, scan time and image quality. Secondly, we develop a protocol to immobilise and restrain study organisms during scanning without need for the administration of anaesthetics and compare the results of the in vivo protocol to images obtained post mortem. To immobilise animals, we replace the use of anaesthetics by cooling, thereby allowing the use of previously unsuitable rotating gantry μCT scanners that are readily available in scientific institutions. The resultant image quality of in vivo μCT scans is similar to that of post-mortem μCT scans, especially in the abdominal region. We discuss the effect of tube voltage, distance to x-ray source and metal filtration on radiation dose, and how these parameters could be altered to reduce the cumulative radiation dose while maintaining optimal image quality. The proposed in vivo μCT protocol offers a new approach to acquire anatomical information for non-biomedical studies. We offer specific suggestions as to how the protocol can be employed to suit a variety of model organisms. This article is protected by copyright. All rights reserved.

Standard method for microCT-based additive manufacturing quality control 1: Porosity analysis

Graphical abstract

Snake fangs: 3D morphological and mechanical analysis by microCT, simulation, and physical compression testing

Abstract This Data Note provides data from an experimental campaign to analyse the detailed internal and external morphology and mechanical properties of venomous snake fangs. The aim of the experimental campaign was to investigate the evolutionary development of 3 fang phenotypes and investigate their mechanical behaviour. The study involved the use of load simulations to compare maximum Von Mises stress values when a load is applied to the tip of the fang. The conclusions of this study have been published elsewhere, but in this data note we extend the analysis, providing morphological comparisons including details such as curvature comparisons, thickness, etc. Physical compression results of individual fangs, though reported in the original paper, were also extended here by calculating the effective elastic modulus of the entire snake fang structure including internal cavities for the first time. This elastic modulus of the entire fang is significantly lower than the locally measured values previously reported from indentation experiments, highlighting the possibility that the elastic modulus is higher on the surface than in the rest of the material. The micro–computed tomography (microCT) data are presented both in image stacks and in the form of STL files, which simplifies the handling of the data and allows its re-use for future morphological studies. These fangs might also serve as bio-inspiration for future hypodermic needles.

Investigating Basal Autophagic Activity in Brain Regions Associated with Neurodegeneration using In Vivo and Ex Vivo Models

Objective: Autophagic maintenance of protein turnover for neuronal homeostasis is of critical importance. Although autophagy dysfunction contributes to neurodegenerative pathology, it remains unclear why certain brain regions are initially targeted compared to others. In Alzheimers disease, the hippocampus appears to be most severely and initially affected compared to regions such as the cerebellum, which seem to be spared initially and are only targeted during later stages of neurodegeneration. Here we hypothesize that brain-region specific variations in basal autophagic activity may underlie sensitivity to proteotoxicity and contribute towards pathology. We investigated the abundance of key autophagic markers in different regions of the mouse brain to determine whether variations in basal autophagic activity may underlie brain-region susceptibility to neurodegeneration. Methods: Autophagic lysosomal degradation was inhibited using chloroquine in vivo and bafilomycin ex vivo. We investigated the accumulation of LC3-II and p62 protein levels in different regions of the mouse brain following inhibition using western blot analysis, immunofluorescence and micro-computed tomography imaging techniques. Results: Results indicate clear and robust variation of autophagic marker abundance between different regions of the mouse brain, both in our in vivo and ex vivo models. Increased protein levels were particularly observed in the cerebellum compared to the hippocampus region, suggesting distinct and region specific changes in autophagic activity. Conclusion: Functional specificity and metabolic demands of different brain regions may translate into differential autophagic activities, which may vary from one region to the next. Here we report regional variations of key autophagic markers between different regions of the mouse brain when autophagosome degradation was inhibited. These findings indicate enhanced basal autophagic activity in the cerebellum compared to the hippocampus. We therefore conclude that enhanced basal autophagic activity may render certain brain regions better equipped to deal with imbalances in protein degradation and that lower levels of basal autophagic activity may underlie regional susceptibility towards pathological decline.

3D X-Ray Inspection of a Radio Controlled Airplane Engine

This paper describes a typical 3D X-ray micro computed tomography (microCT) analysis of light metal parts, from a radio controlled airplane engine. This case study shows the power of 3D X-ray inspection and analysis for this type of material, including information about the size and location of casting defects, the location of turbine blade balancing weights and dimensional measurements indicating the axle was not perfectly centre. Advantages and limitations of the method for light metals are described in general

Standard method for microCT-based additive manufacturing quality control 3: Surface roughness

Graphical abstract

Standard method for microCT-based additive manufacturing quality control 2: Density measurement

Graphical abstract

Standard method for microCT-based additive manufacturing quality control 4: metal powder analysis

Graphical abstract