Techniques in helical scanning, dynamic imaging and image segmentation for improved quantitative analysis with X-ray micro-CT

This paper reports on recent advances at the micro-computed tomography facility at the Australian National University. Since 2000 this facility has been a significant centre for developments in imaging hardware and associated software for image reconstruction, image analysis and image-based modelling. In 2010 a new instrument was constructed that utilises theoretically-exact image reconstruction based on helical scanning trajectories, allowing higher cone angles and thus better utilisation of the available X-ray flux. We discuss the technical hurdles that needed to be overcome to allow imaging with cone angles in excess of 60°. We also present dynamic tomography algorithms that enable the changes between one moment and the next to be reconstructed from a sparse set of projections, allowing higher speed imaging of time-varying samples. Researchers at the facility have also created a sizeable distributed-memory image analysis toolkit with capabilities ranging from tomographic image reconstruction to 3D shape characterisation. We show results from image registration and present some of the new imaging and experimental techniques that it enables. Finally, we discuss the crucial question of image segmentation and evaluate some recently proposed techniques for automated segmentation

An x-ray tomography facility for quantitative prediction of mechanical and transport properties in geological, biological and synthetic systems

A fully integrated X-ray tomography facility with the ability to generate tomograms with 20483 voxels at 2 micron spatial resolution was built to satisfy the requirements of a virtual materials testing laboratory. The instrument comprises of a continuously pumped micro-focus X-ray gun, a milli-degree rotation stage and a high resolution and large field X-ray camera, configured in a cone beam geometry with a circular trajectory. The purpose of this facility is to routinely analyse and investigate real world biological, geological and synthetic materials at a scale in which the traditional domains of physics, chemistry, biology and geology merge. During the first 2 years of operation, approximately 4 Terabytes of data have been collected, processed and analysed, both as static and in some cases as composite dynamic data sets. This incorporates over 300 tomograms with 10243 voxels and 50 tomograms with 20483 voxels for a wide range of research fields. Specimens analysed include sedimentary rocks, soils, bone, soft tissue, ceramics, fibre-reinforced composites, foams, wood, paper, fossils, sphere packs, bio-morphs and small animals. In this paper, the flexibility of the facility is highlighted with some prime examples

X-ray Tomography for Mesoscale Physics Applications

The field of mesoscale physics is concerned with length scales which lie in the sub-micron to millimetre range. As a subject, it covers complexity, disorder, cooperative effects and structure-property relationships. Much of modern material science can b

Nanocompartmentalization of soft materials with three mutually immiscible solvents: synthesis and self-assembly of three-arm star-polyphiles

We report synthesis, thermotropic, and lyotropic mesomorphism of a family of novel “star-polyphiles”: small star-shaped molecules bearing three mutually immiscible arms, hydrophilic (oligoethylene glycol), oleophilic (alkanes), and fluorophilic (perfluorinated alkanes), attached to a central 1,3,5-trihydroxybenzene core. A facile, flexible multistep synthesis giving high-purity yields of 14 distinct members of the family is described, with variable arm lengths, forming crystalline, or various mesostructured gel phases in their neat state at room temperature. Furthermore, we show that specific members of these star-polyphiles can be simultaneously loaded with up to three mutually immiscible solvents, dodecane, perfluoro-nonane, and water, to form liquid crystals and microemulsions with multiple chemically distinct mesoscale compartments. The mesoscale chemical polyfunctionality of these polyphiles, coupled with thermotropic and lyotropic polymorphism, make them promising potential soft materials for a variety of applications, including host matrices for multiple mutually immiscible chemicals and drug deliveryWe acknowledge support from the Australian Research Council’s Discovery grant scheme

Genetic association mapping identifies single nucleotide polymorphisms in genes that affect abscisic acid levels in maize floral tissues during drought

In maize, water stress at flowering causes loss of kernel set and productivity. While changes in the levels of sugars and abscisic acid (ABA) are thought to play a role in this stress response, the mechanistic basis and genes involved are not known. A candidate gene approach was used with association mapping to identify loci involved in accumulation of carbohydrates and ABA metabolites during stress. A panel of single nucleotide polymorphisms (SNPs) in genes from these metabolic pathways and in genes for reproductive development and stress response was used to genotype 350 tropical and subtropical maize inbred lines that were well watered or water stressed at flowering. Pre-pollination ears, silks, and leaves were analysed for sugars, starch, proline, ABA, ABA-glucose ester, and phaseic acid. ABA and sugar levels in silks and ears were negatively correlated with their growth. Association mapping with 1229 SNPs in 540 candidate genes identified an SNP in the maize homologue of the Arabidopsis MADS-box gene, PISTILLATA, which was significantly associated with phaseic acid in ears of well-watered plants, and an SNP in pyruvate dehydrogenase kinase, a key regulator of carbon flux into respiration, that was associated with silk sugar concentration. An SNP in an aldehyde oxidase gene was significantly associated with ABA levels in silks of water-stressed plants. Given the short range over which decay of linkage disequilibrium occurs in maize, the results indicate that allelic variation in these genes affects ABA and carbohydrate metabolism in floral tissues during drought