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

Polycontinuous geometries for inverse lipid phases with more than two aqueous network domains

Inverse bicontinuous cubic phases with two aqueous network domains separated by a smooth bilayer are firmly established as equilibrium phases in lipid/water systems. The purpose of this article is to highlight the generalisations of these bicontinuous geometries to polycontinuous geometries, which could be realised as lipid mesophases with three or more network-like aqueous domains separated by a branched bilayer. An analysis of structural homogeneity in terms of bilayer width variations reveals that ordered polycontinuous geometries are likely candidates for lipid mesophase structures, with similar chain packing characteristics to the inverse micellar phases (that once were believed not to exist due to high packing frustration). The average molecular shape required by global geometry to form these multi-network phases is quantified by the surfactant shape parameter, v/(al); we find that it adopts values close to those of the known lipid phases. We specifically analyse the 3etc(187 193) structure of hexagonal symmetry P63 /mcm with three aqueous domains, the 3dia(24 220) structure of cubic symmetry I 3d composed of three distorted diamond networks, the cubic chiral 4srs(24 208) with cubic symmetry P4232 and the achiral 4srs(5 133) structure of symmetry P42/nbc, each consisting of four intergrown undistorted copies of the srs net (the same net as in the QGII gyroid phase). Structural homogeneity is analysed by a medial surface approach assuming that the head-group interfaces are constant mean curvature surfaces. To facilitate future experimental identification, we provide simulated SAXS scattering patterns that, for the 4srs(24 208) and 3dia(24 220) structures, bear remarkable similarity to those of bicontinuous QGII-gyroid and QDII-diamond phases, with comparable lattice parameters and only a single peak that cannot be indexed to the well-established structures. While polycontinuous lipid phases have, to date, not been reported, the likelihood of their formation is further indicated by the reported observation of a solid tricontinuous mesoporous silicate structure, termed IBN-9, which formed in the presence of surfactants [Han et al., Nat. Chem., 2009, 1, 123]

Wavefront aberration correction in medical ultrasound imaging

Medisinsk ultralydavbildning er et relativt rimelig verktøy som er i utstrakte bruk på dagens sykehus og tildels også legekontor. En underliggende antakelse ved dagens avbildningsteknikker er at vevet som skal avbildes i grove trekk er homogent. Det vil i praksis si at de akustiske egenskapene varierer lite. I tilfeller der denne forutsetningen ikke holder vil resultatet bli betraktlig reduksjon av bildekvaliteten. Prosjektet har fokusert på hvordan man best mulig kan korrigere for denne kvalitetsforringelsen. Arbeidet har resultert i et styrket teoretisk rammeverk for modellering, programvare for numerisk simulering. Rammeverket gir en felles forankring for tidligere publiserte metoder som "time-reversal mirror", "beamsum-correlation" og "speckle brightness", og gir derfor en utvidet forståelse av disse metodene. Videre har en ny metode blitt utviklet basert på egenfunksjonsanalyse av et stokastisk tilbakespredt lydfelt. Denne metoden vil potensielt kunne håndtere sterk spredning fra områder utenfor hovedaksen til ultralydstrålen på en bedre måte enn tidligere metoder. Arbeidet er utført ved Institutt for matematiske fag, NTNU, med professor Harald Krogstad, Institutt for matematiske fag, som hovedveileder og professor Bjørn Angelsen, Institutt for sirkulasjon og bildediagnostikk, som medveileder

Forward propagation of acoustic pressure pulses in 3d soft biological tissue

A simulation method for forward propagation of acoustic pressure pulses in a medium with three-dimensional (3D) spatially-variable acoustic properties is presented. The intended application is to study aspects of ultrasound imaging of soft biological tissue. The forward wave propagation is modelled by a one-way wave equation. The equation describes tissue exhibiting nonlinear elasticity and arbitrary frequency-dependent attenuation. A numerical solution to the equation is found by means of first-order accurate operator splitting and propagation along the spatial depth coordinate. Thus diffraction, nonlinearity and attenuation are solved independently at each propagation step, rendering their relative importance easy to monitor. The method is seen to yield an accurate simulation of the wave propagation when compared to numerical solutions of the full wave equation and experiments in a water tank. By this approach it is possible to simulate wave propagation over relatively large distances – typically several hundred wavelengths – at a modest computational complexity compared to solution of the full wave equation. It furthermore facilitates a high degree of parallelism, thus enabling efficient distribution of the required computations over multiple processors.

X-ray beam hardening correction by minimizing reprojection distance

We address the problem of tomographic image quality degradation due to the effects of beam hardening when using a polychromatic X-ray source. Beam hardening refers to the preferential attenuation of low-energy (or soft) X-rays resulting in a beam with a higher average energy (i.e., harder). In projection images, thin or low-Z materials appear more dense relative to thick or higher-Z materials. This misrepresentaion produces artifacts in the reconstructed image such as cupping and streaking. Our method involves a post-acquisition software correction that applies a beam-hardening correction curve to remap the linearised projection intensities. The curve is modelled by an eighth-order polynomial and assumes an average material for the object. The process to determine the best correction curve requires precisely 8 reconstructions and re-projections of the experiment data. The best correction curve is defined as that which generates a projection set p that minimises the reprojection distance. Reprojection distance is defined as the L2 norm of the difference between p, a set of projections, and RRyp, the result after p is reconstructed and then reprojected, i.e., jjRRyp pjj2. Here R denotes the projection operator and Ry is its Moore-Penrose pseudoinverse, i.e., the reconstruction operator. This technique was designed for single-material objects and in this case the calculated curve matches that determined experimentally. However, this technique works very well for multiple-material objects where the resulting curve is a kind of average of all materials present. We show that this technique corrects for both cupping and streaking in tomographic images by including several experimental examples. Note that this correction method requires no knowledge of the X-ray spectrum or materials present and can therefore be applied to old data sets

Synthetic-aperture radar imaging through dispersive media

In this paper we develop a method for synthetic-aperture radar (SAR) imaging through a dispersive medium. We consider the case when the sensor and scatterers are embedded in a known homogeneous dispersive material, the scene to be imaged lies on a known