Trond Varslot

Digital rock physics: 3D imaging of core material and correlations to acoustic and flow properties

3D X-ray microtomographic imaging and visualization of core material at the pore scale and subsequent analysis of petrophysical properties can give important insight to understanding properties of reservoir core material. 3D images allow one to map in detail the pore and grain structure and interconnectivity of core material. Numerical calculations on image data are in agreement with experimental data for flow and elastic properties on simple core material. This development forms the basis for developing more meaningful structure-property correlations in rock.

Computer simulation of forward wave propagation in soft tissue

A method for simulating forward wavefront propagation in heterogeneous tissue is discussed. The intended application of this method is for the study of aberration produced when performing ultrasound imaging through a layer of soft tissue. A one-way wave equation that permits smooth variation in all acoustically important variables is derived. This equation also describes tissue exhibiting nonlinear elasticity and arbitrary frequency-dependent relaxation. A numerical solution to this equation is found by means of operator splitting and propagation along the spatial depth coordinate. The numerical solution is accurate when compared to analytical solutions for special cases, and when compared to numerical solutions of the full wave equation by other methods. The presented implementation provides a fast numerical method for studying the impact of aberration in medical ultrasound imaging through soft tissue - both on the transmitted beam and the nonlinearly generated harmonic beam.

High-resolution helical cone-beam micro-CT with theoretically-exact reconstruction from experimental data

PURPOSE In this paper we show that optimization-based autofocus may be used to overcome the instabilities that have, until now, made high-resolution theoretically-exact tomographic reconstruction impractical. To our knowledge, this represents the first successful use of theoretically-exact reconstruction in helical micro computed tomography (micro-CT) imaging. We show that autofocus-corrected, theoretically-exact helical CT is a viable option for high-resolution micro-CT imaging at high cone-angles (∼50°). The elevated cone-angle enables better utilization of the available X-ray flux and therefore shorter image acquisition time than conventional micro-CT systems. METHODS By using the theoretically-exact Katsevich 1PI inversion formula, we are not restricted to a low-cone-angle regime; we can in theory obtain artefact-free reconstructions from projection data acquired at arbitrary high cone-angles. However, this reconstruction method is sensitive to misalignments in the tomographic data, which result in geometric distortion and streaking artefacts. We use a parametric model to quantify the deviation between the actual acquisition trajectory and an ideal helix, and use an autofocus method to estimate the relevant parameters. We define optimal units for each parameter, and use these to ensure consistent alignment accuracy across different cone-angles and different magnification factors. The tomographic image is obtained from a set of virtual projections in which software correction for hardware misalignment has been applied. RESULTS We make significant modifications to the autofocus method that allow this method to be used in helical micro-CT reconstruction, and show that these developments enable theoretically-exact reconstruction from experimental data using the Katsevich 1PI (K1PI) inversion formula. We further demonstrate how autofocus-corrected, theoretically-exact helical CT reduces the image acquisition time by an order of magnitude compared to conventional circular scan micro-CT. CONCLUSIONS Autofocus-corrected, theoretically-exact cone-beam reconstruction is a viable option for reducing acquisition time in high-resolution micro-CT imaging. It also opens up the possibility of efficiently imaging long objects.

Automatic sound speed selection in photoacoustic image reconstruction using an autofocus approach

The reconstruction of images in photoacoustic tomography is reliant on specifying the speed of sound within the propagation medium. However, for in vivo imaging, this value is not normally accurately known. Here, an autofocus approach for automatically selecting the sound speed is proposed. This is based on maximizing the sharpness of the reconstructed image as quantified by a focus function. Several focus functions are investigated, and their performance is discussed. The method is demonstrated using phantom measurements made in a medium with a known sound speed and in vivo measurements of the vasculature in the flank of an adult mouse.

Reliable automatic alignment of tomographic projection data by passive auto-focus.

PURPOSE The authors present a robust algorithm that removes the blurring and double-edge artifacts in high-resolution computed tomography (CT) images that are caused by misaligned scanner components. This alleviates the time-consuming process of physically aligning hardware, which is of particular benefit if components are moved or swapped frequently. METHODS The proposed method uses the experimental data itself for calibration. A parameterized model of the scanner geometry is constructed and the parameters are varied until the sharpest 3D reconstruction is found. The concept is similar to passive auto-focus algorithms of digital optical instruments. The parameters are used to remap the projection data from the physical detector to a virtual aligned detector. This is followed by a standard reconstruction algorithm, namely the Feldkamp algorithm. Feldkamp et al. [J. Opt. Soc. Am. A 1, 612-619 (1984)]. RESULTS An example implementation is given for a rabbit liver specimen that was collected with a circular trajectory. The optimal parameters were determined in less computation time than that for a full reconstruction. The example serves to demonstrate that (a) sharpness is an appropriate measure for projection alignment, (b) our parameterization is sufficient to characterize misalignments for cone-beam CT, and (c) the procedure determines parameter values with sufficient precision to remove the associated artifacts. CONCLUSIONS The algorithm is fully tested and implemented for regular use at The Australian National University micro-CT facility for both circular and helical trajectories. It can in principle be applied to more general imaging geometries and modalities. It is as robust as manual alignment but more precise since we have quantified the effect of misalignment.

Refraction corrected transmission ultrasound computed tomography for application in breast imaging.

PURPOSE We present an iterative framework for CT reconstruction from transmission ultrasound data which accurately and efficiently models the strong refraction effects that occur in our target application: Imaging the female breast. METHODS Our refractive ray tracing framework has its foundation in the fast marching method (FNMM) and it allows an accurate as well as efficient modeling of curved rays. We also describe a novel regularization scheme that yields further significant reconstruction quality improvements. A final contribution is the development of a realistic anthropomorphic digital breast phantom based on the NIH Visible Female data set. RESULTS Our system is able to resolve very fine details even in the presence of significant noise, and it reconstructs both sound speed and attenuation data. Excellent correspondence with a traditional, but significantly more computationally expensive wave equation solver is achieved. CONCLUSIONS Apart from the accurate modeling of curved rays, decisive factors have also been our regularization scheme and the high-quality interpolation filter we have used. An added benefit of our framework is that it accelerates well on GPUs where we have shown that clinical 3D reconstruction speeds on the order of minutes are possible.

Aberration in nonlinear acoustic wave propagation

Theory and simulations are presented indicating that imaging at the second-harmonic frequency does not solve the problem of ultrasonic wave aberration. The non-linearity of acoustic wave propagation in biological tissue is routinely exploited in medical imaging because the improved contrast resolution leads to better image quality in many applications. The major sources of acoustic noise in ultrasound images are aberration and multiple reflections between the transducer and tissue structures (reverberations), both of which are the result of spatial variations in the acoustic properties of the tissue. These variations mainly occur close to the body surface, i.e., the body wall. As a result, the nonlinearly generated, second harmonic is believed to alleviate both reverberation and aberration because it is assumed that the second harmonic is mainly generated after the body wall. However, in the case of aberration, the second harmonic is generated by an aberrated source. Thus the second harmonic experiences considerable aberration at all depths, originating from this source. The results in this paper show that the second harmonic experiences similar aberration as its generating source, the first harmonic.

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 P6(3) /mcm with three aqueous domains, the 3dia(24 220) structure of cubic symmetry I43d 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 QII(G) gyroid phase). Structural homogeneity is analysed by a medial surface approach assuming that the headgroup 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 QII(G)-gyroid and QII(D)-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].

A novel lyotropic liquid crystal formed by triphilic star-polyphiles: hydrophilic/oleophilic/fluorophilic rods arranged in a 12.6.4. tiling

Triphilic star-polyphiles are short-chain oligomeric molecules with a radial arrangement of hydrophilic, hydrocarbon and fluorocarbon chains linked to a common centre. They form a number of liquid crystalline structures when mixed with water. In this contribution we focus on a hexagonal liquid crystalline mesophase found in star-polyphiles as compared to the corresponding double-chain surfactant to determine whether the hydrocarbon and fluorocarbon chains are in fact demixed in these star-polyphile systems, or whether both hydrocarbon and fluorocarbon chains are miscible, leading to a single hydrophobic domain, making the star-polyphile effectively amphiphilic. We report SANS contrast variation data that are compatible only with the presence of three distinct immiscible domains within this hexagonal mesophase, confirming that these star-polyphile liquid crystals are indeed hydrophilic/oleophilic/fluorophilic 3-phase systems. Quantitative comparison with scattering simulations shows that the experimental data are in very good agreement with an underlying 2D columnar (12.6.4) tiling. As in a conventional amphiphilic hexagonal mesophase, the hexagonally packed water channels (dodecagonal prismatic domains) are embedded in a hydrophobic matrix, but that matrix is split into oleophilic hexagonal prismatic domains and fluorophilic quadrangular prismatic domains.

Abersim: A simulation program for 3D nonlinear acoustic wave propagation for arbitrary pulses and arbitrary transducer geometries

Abersim, a simulation package for 3D nonlinear acoustic wave propagation of wide-band pulses from arbitrary transducers, is presented. This study validates the 3D diffraction and attenuation produced by Abersim, by comparing them to those obtained using Field II. For the presented test cases, the axial pressure amplitude and the RMS values deviate less than 0.7 dB, both for axis-symmetric and array transducers. Abersim has a MATLAB programming interface, and is freely available under the GPL license.