ORCID Profile
0000-0002-0606-4094
Current Organisation
Australian National University
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Synchrotrons; Accelerators; Instruments and Techniques | Other Physical Sciences | Petroleum and Reservoir Engineering | Condensed Matter Imaging | Classical and Physical Optics | Manufacturing Engineering | Condensed Matter Physics | Manufacturing Processes and Technologies (excl. Textiles) | Computational Fluid Dynamics | Timber, Pulp and Paper | Fluid Physics | Complex Physical Systems | Condensed Matter Characterisation Technique Development |
ANZSRC Socio-Economic Objective (SEO)
Oil and Gas Exploration | Oil and Gas Extraction | Scientific Instruments | Soils not elsewhere classified | Management of Greenhouse Gas Emissions from Electricity Generation | Information Processing Services (incl. Data Entry and Capture) | Wood, Wood Products and Paper not elsewhere classified | Industrial Instruments | Medical Instruments | Fabricated Metal Products not elsewhere classified
Related Links
Publications
Spectral information from photon statistics in x-ray radiography and computed tomography
Publisher: American Physical Society (APS)
Date: 14-07-2022
Lossless Image Compression and Selective Encryption using a Discrete Radon Transform
Publisher: IEEE
Date: 2007
The discrete Radon transform: a more efficient approach to image reconstruction?
Publisher: SPIE
Date: 28-08-2008
DOI: 10.1117/12.795779
First detection of a novel ‘unknown host’ flavivirus in a Malaysian rodent
Publisher: Microbiology Society
Date: 15-04-2021
Abstract: Current phylogenetic analysis of the flavivirus genus has identified a group of mosquito-borne viruses for which the vertebrate hosts are currently unknown. Here we report the identification of a novel member of this group from a peridomestic rodent species ( Sundamys muelleri ) collected in Sarawak, Malaysia in 2016. We propose to name this novel flavivirus Batu Kawa virus after the location in which it was identified, with the abbreviation BKWV. Characterization of the BKWV genome allowed identification of putative mature peptides, potential enzyme motifs and conserved structural elements. Phylogenetic analysis found BKWV to be most closely related to Nhumirim virus (from Brazil) and Barkedji virus (from Senegal and Israel). Both of these viruses have been identified in Culex mosquitoes and belong to a group of viruses with unknown vertebrate hosts. This is the first known report of a member of this group of viruses from a potential mammalian host.
Association of rodent-borne Leptospira spp. with urban environments in Malaysian Borneo
Publisher: Public Library of Science (PLoS)
Date: 27-02-2019
3D X-Ray Source Deblurring in High Cone-Angle Micro-CT
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
Date: 10-2015
Geometric Shape Effects in Redundant Keys used to Encrypt Data Transformed by Finite Discrete Radon Projections
Publisher: IEEE
Date: 2005
The effects of manufacturing parameters on geometrical and mechanical properties of copper foams produced by space holder technique
Publisher: Elsevier BV
Date: 2014
Least-squares and maximum-likelihood in computed tomography
Publisher: SPIE-Intl Soc Optical Eng
Date: 06-05-2022
Neutron ghost imaging
Publisher: American Physical Society (APS)
Date: 18-05-2020
Erasure Coding with the Finite Radon Transform
Publisher: IEEE
Date: 04-2010
Direct inversion of Mojette projections
Publisher: IEEE
Date: 09-2013
Genomic Characterization of Yogue, Kasokero, Issyk-Kul, Keterah, Gossas, and Thiafora Viruses: Nairoviruses Naturally Infecting Bats, Shrews, and Ticks
Publisher: American Society of Tropical Medicine and Hygiene
Date: 04-11-2015
Robust Digital Image Reconstruction via the Discrete Fourier Slice Theorem
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
Date: 06-2014
High-resolution helical cone-beam micro-CT with theoretically-exact reconstruction from experimental data
Publisher: Wiley
Date: 19-09-2011
DOI: 10.1118/1.3633900
Abstract: 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. 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. 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. 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.
An auto-focus method for generating sharp 3D tomographic images
Publisher: SPIE
Date: 19-08-2010
DOI: 10.1117/12.860285
Improving dynamic tomography, through maximum a posteriori estimation
Publisher: SPIE
Date: 11-09-2014
DOI: 10.1117/12.2061604
Optimizing nonconfigurable, transversely displaced masks for illumination patterns in classical ghost imaging
Publisher: American Physical Society (APS)
Date: 27-02-2023
Geometric Alignment Of Cone-Beam Helical-Trajectory Micro-Tomography Data Using a PI-Line Difference Metric
Publisher: Oxford University Press (OUP)
Date: 08-2018
PI-Line Difference for Alignment and Motion-Correction of Cone-Beam Helical-Trajectory Micro-Tomography Data
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
Date: 2020
Improving spatial-resolution in high cone-angle micro-CT by source deblurring
Publisher: SPIE
Date: 11-09-2014
DOI: 10.1117/12.2062415
Rats in the city: implications for zoonotic disease risk in an urbanizing world
Publisher: Cold Spring Harbor Laboratory
Date: 19-03-2021
DOI: 10.1101/2021.03.18.436089
Abstract: Urbanization is rapidly transforming much of Southeast Asia, altering the structure and function of the landscape, as well as the frequency and intensity of the interactions between people, animals, and the environment. In this study, we began to explore the impact of urbanization on zoonotic disease risk by simultaneously characterizing changes in the abundance and ersity of reservoir hosts (rodents), ectoparasite vectors (ticks), and microbial pathogens across a gradient of urbanization in Malaysian Borneo. We found that although rodent species ersity decreased with increasing urbanization, two species appeared to thrive in anthropogenic environments: the invasive urban exploiter, Rattus rattus and the native urban adapter, Sundamys muelleri . R. rattus was strongly associated with the presence of built infrastructure across the gradient and dominated the urban rodent community where it was associated with high microbial ersity and multi-host zoonoses capable of environmental transmission, including Leptospira spp., and Toxoplasma gondii . In contrast, S. muelleri was restricted to sites with a significant vegetative component where it was found at high densities in the urban location. This species was strongly associated with the presence of ticks, including the medically important genera Ambylomma , Haemaphysalis , and Ixodes . Overall, our results demonstrate that the response to urbanization varies by species at all levels: host, ectoparasite, and microbe. This may lead to increased zoonotic disease risk in a subset of environments across urban and urbanizing landscapes that can be reduced through improved pest management and public health messaging.
Practical X-ray Ghost Imaging
Publisher: Oxford University Press (OUP)
Date: 08-2018
Redundant image representation via multi-scale digital Radon projections
Publisher: IEEE
Date: 10-2008
Live Virus Neutralisation of the 501Y.V1 and 501Y.V2 SARS-CoV-2 Variants following INO-4800 Vaccination of Ferrets
Publisher: Frontiers Media SA
Date: 25-06-2021
DOI: 10.3389/FIMMU.2021.694857
Abstract: The ongoing COVID-19 pandemic has resulted in significant global morbidity and mortality on a scale similar to the influenza pandemic of 1918. Over the course of the last few months, a number of SARS-CoV-2 variants have been identified against which vaccine-induced immune responses may be less effective. These “variants-of-concern” have garnered significant attention in the media, with discussion around their impact on the future of the pandemic and the ability of leading COVID-19 vaccines to protect against them effectively. To address concerns about emerging SARS-CoV-2 variants affecting vaccine-induced immunity, we investigated the neutralisation of representative ‘G614’, ‘501Y.V1’ and ‘501Y.V2’ virus isolates using sera from ferrets that had received prime-boost doses of the DNA vaccine, INO-4800. Neutralisation titres against G614 and 501Y.V1 were comparable, but titres against the 501Y.V2 variant were approximately 4-fold lower, similar to results reported with other nucleic acid vaccines and supported by in silico biomolecular modelling. The results confirm that the vaccine-induced neutralising antibodies generated by INO-4800 remain effective against current variants-of-concern, albeit with lower neutralisation titres against 501Y.V2 similar to other leading nucleic acid-based vaccines.
Mask design, fabrication, and experimental ghost imaging applications for patterned X-ray illumination
Publisher: Optica Publishing Group
Date: 10-07-2023
DOI: 10.1364/OE.495024
Abstract: A set of non-configurable transversely-displaced masks has been designed and fabricated to generate high-quality X-ray illumination patterns for use in imaging techniques such as ghost imaging (GI), ghost projection, and speckle tracking. The designs include a range of random binary and orthogonal patterns, fabricated through a combination of photolithography and gold electroplating techniques. We experimentally demonstrated that a single wafer can be used as an illumination mask for GI, employing in idual illumination patterns and also a mixture of patterns, using a laboratory X-ray source. The quality of the reconstructed X-ray ghost images has been characterized and evaluated through a range of metrics.
Iterative reconstruction optimisations for high angle cone-beam micro-CT
Publisher: SPIE
Date: 11-09-2014
DOI: 10.1117/12.2062450
High Prevalence of Rodent-borne Bartonella spp. in Urbanizing Environments in Sarawak, Malaysian Borneo
Publisher: American Society of Tropical Medicine and Hygiene
Date: 06-03-2018
Orthogonal discrete Radon transform over images
Publisher: Elsevier BV
Date: 08-2006
X-ray beam hardening correction by minimizing reprojection distance
Publisher: SPIE
Date: 17-10-2012
DOI: 10.1117/12.928883
Ground-truth verification of dynamic x-ray micro-tomography images of fluid displacement
Publisher: SPIE
Date: 17-10-2012
DOI: 10.1117/12.929410
Bayesian approach to time-resolved tomography
Publisher: The Optical Society
Date: 24-07-2015
DOI: 10.1364/OE.23.020062
Ghost projection. II. Beam shaping using realistic spatially random masks
Publisher: American Physical Society (APS)
Date: 20-09-2022
Dynamics of Lead Bioavailability and Speciation in Indoor Dust and X-ray Spectroscopic Investigation of the Link between Ingestion and Inhalation Pathways
Publisher: American Chemical Society (ACS)
Date: 28-08-2019
Adaptive Discrete Radon Transforms for Greyscale Images
Publisher: Elsevier BV
Date: 03-2003
Tomographic image analysis and processing to simulate micro-petrophysical experiments
Publisher: SPIE
Date: 19-08-2010
DOI: 10.1117/12.860293
Fast high-resolution micro-CT with exact reconstruction methods
Publisher: SPIE
Date: 19-08-2010
DOI: 10.1117/12.860298
Dynamic tomography with a priori information
Publisher: The Optical Society
Date: 08-07-2011
DOI: 10.1364/AO.50.003685
Towards a practical implementation of X-ray ghost imaging with synchrotron light
Publisher: International Union of Crystallography (IUCr)
Date: 07-06-2018
DOI: 10.1107/S205225251800711X
Abstract: An experimental procedure for transmission X-ray ghost imaging using synchrotron light is presented. Hard X-rays from an undulator were ided by a beamsplitter to produce two copies of a speckled incident beam. Both beams were simultaneously measured on an indirect pixellated detector and the intensity correlation between the two copies was used to retrieve the ghost image of s les placed in one of the two beams, without measuring the s les directly. Aiming at future practical uses of X-ray ghost imaging, the authors discuss details regarding data acquisition, image reconstruction strategies and measure the point-spread function of the ghost-imaging system. This approach may become relevant for applications of ghost imaging with X-ray sources such as undulators in storage rings, free-electron lasers and lower-coherence laboratory facilities.
The index of dispersion as a metric of quanta – unravelling the Fano factor
Publisher: International Union of Crystallography (IUCr)
Date: 28-07-2017
DOI: 10.1107/S2052520617009222
Abstract: In statistics, the index of dispersion (or variance-to-mean ratio) is unity (σ 2 /〈 x 〉 = 1) for a Poisson-distributed process with variance σ 2 for a variable x that manifests as unit increments. Where x is a measure of some phenomenon, the index takes on a value proportional to the quanta that constitute the phenomenon. That outcome might thus be anticipated to apply for an enormously wide variety of applied measurements of quantum phenomena. However, in a photon-energy proportional radiation detector, a set of M witnessed Poisson-distributed measurements { W 1 , W 2 ,… W M } scaled so that the ideal expectation value of the quantum is unity, is generally observed to give σ 2 /〈 W 〉 1 because of detector losses as broadly indicated by Fano [ Phys. Rev. (1947), 72 , 26]. In other cases where there is spectral dispersion, σ 2 /〈 W 〉 1. Here these situations are examined analytically, in Monte Carlo simulations, and experimentally. The efforts reveal a powerful metric of quanta broadly associated with such measurements, where the extension has been made to polychromatic and lossy situations. In doing so, the index of dispersion's variously established yet curiously overlooked role as a metric of underlying quanta is indicated. The work's X-ray aspects have very erse utility and have begun to find applications in radiography and tomography, where the ability to extract spectral information from conventional intensity detectors enables a superior level of material and source characterization.
Farey Sequences and Discrete Radon Transform Projection Angles
Publisher: Elsevier BV
Date: 03-2003
Applications of Multi-Scale Imaging Techniques to Unconventional Reservoirs
Publisher: SPE
Date: 09-11-2015
DOI: 10.2118/176948-MS
Abstract: Understanding and prediction of hydrocarbon transport within the matrix of unconventional tight reservoirs demands an integrated imaging strategy spanning from the smallest nanoscale pores to plug scale and beyond. Recent developments in multi-scale imaging are presented for Barnett shale s les to illustrate this approach to upscaling. The utility of micro-CT imaging for shales can be extended by X-ray contrast enhancement techniques coupled with tomogram registration. In particular, saturation of a shale plug with a highly attenuating liquid and subtraction of this tomogram from the registered dry-state tomogram yields a 3D voxel map of connected porosity over the plug. The same procedure can be applied to sub-plugs s led from the parent plug to capture micron-scale variations in porosity. This approach does not directly provide the size, shape and connectivity of in idual pores, since the vast majority of shale pores remain below tomogram resolution even for small sub-plugs. Two approaches to access this higher-order information are addressed. The first uses the state of the shale sub-plug saturated with X-ray dense liquid as the starting point for dynamic micro-CT imaging of the diffusion of a second, miscible, X-ray transparent liquid into the sub-plug. This can reveal the presence of faster pathways of transport through pores of larger size or lower tortuosity. The second approach involves broad beam ion-milling of the sub-plug for acquisition of 2D BSEM image mosaics and mineral maps, and their registration into the corresponding section of the 3D tomograms. This provides a registered basis for upscaling of transport properties, e.g. simulated from small FIB-SEM cubes, to sub-plug and in turn to plug via their micro-CT porosity maps. Very high resolution SEM imaging of broken surfaces can provide useful complementary information as to the finest scale of organic-hosted nanopores. The Barnett shale s les exhibited fairly homogeneous distributions of porosity on the plug and sub-plug scales, and also displayed relatively uniform diffusion across the sub-plug, suggesting that they are amenable to characterization and upscaling using only a limited set of parameters. This homogeneity is thought to be due in significant part to the predominance of organic-hosted porosity and to the structural uniformity of these nano-scale organic pore networks.
Dual-energy iterative reconstruction for material characterisation
Publisher: SPIE
Date: 11-09-2014
DOI: 10.1117/12.2062442
Generalised finite radon transform for N×N images
Publisher: Elsevier BV
Date: 10-2007
Structural and mechanical features of the order-disorder transition in experimental hard-sphere packings
Publisher: American Physical Society (APS)
Date: 05-06-2015
Ghost tomography
Publisher: The Optical Society
Date: 29-11-2018
Environmental risk factors associated with the presence of Mycobacterium ulcerans in Victoria, Australia
Publisher: Public Library of Science (PLoS)
Date: 13-09-2022
DOI: 10.1371/JOURNAL.PONE.0274627
Abstract: In recent years reported cases of Buruli ulcer, caused by Mycobacterium ulcerans , have increased substantially in Victoria, Australia, with the epidemic also expanding geographically. To develop an understanding of how M . ulcerans circulates in the environment and transmits to humans we analyzed environmental s les collected from 115 properties of recent Buruli ulcer cases and from 115 postcode-matched control properties, for the presence of M . ulcerans . Environmental factors associated with increased odds of M . ulcerans presence at a property included certain native plant species and native vegetation in general, more alkaline soil, lower altitude, the presence of common ringtail possums ( Pseudocheirus peregrinus ) and overhead powerlines. However, only overhead powerlines and the absence of the native plant Melaleuca lanceolata were associated with Buruli ulcer case properties. S les positive for M . ulcerans were more likely to be found at case properties and were associated with detections of M . ulcerans in ringtail possum feces, supporting the hypothesis that M . ulcerans is zoonotic, with ringtail possums the strongest reservoir host candidate. However, the disparity in environmental risk factors associated with M . ulcerans positive properties versus case properties indicates the involvement of human behavior or the influence of other environmental factors in disease acquisition that requires further study.
Techniques for high-fidelity X-ray micro-tomography of additively manufactured metal components
Publisher: Informa UK Limited
Date: 24-06-2020
Rapidly converging multigrid reconstruction of cone-beam tomographic data
Publisher: SPIE
Date: 03-10-2016
DOI: 10.1117/12.2238267
Micro-CT Analysis of Pores and Organics in Unconventionals Using Novel Contrast Strategies
Publisher: American Association of Petroleum Geologists
Date: 2014
Spiral scanning X-ray fluorescence computed tomography
Publisher: The Optical Society
Date: 15-09-2017
DOI: 10.1364/OE.25.023424
Genomic analysis of bluetongue virus episystems in Australia and Indonesia
Publisher: Springer Science and Business Media LLC
Date: 23-11-2017
Experimental and in silico evidence suggests vaccines are unlikely to be affected by D614G mutation in SARS-CoV-2 spike protein
Publisher: Springer Science and Business Media LLC
Date: 08-10-2020
DOI: 10.1038/S41541-020-00246-8
Abstract: The ‘D614G’ mutation (Aspartate-to-Glycine change at position 614) of the SARS-CoV-2 spike protein has been speculated to adversely affect the efficacy of most vaccines and countermeasures that target this glycoprotein, necessitating frequent vaccine matching. Virus neutralisation assays were performed using sera from ferrets which received two doses of the INO-4800 COVID-19 vaccine, and Australian virus isolates (VIC01, SA01 and VIC31) which either possess or lack this mutation but are otherwise comparable. Through this approach, supported by biomolecular modelling of this mutation and the commonly-associated P314L mutation in the RNA-dependent RNA polymerase, we have shown that there is no experimental evidence to support this speculation. We additionally demonstrate that the putative elastase cleavage site introduced by the D614G mutation is unlikely to be accessible to proteases.
Considerations for high-magnification high-cone-angle helical micro-CT
Publisher: SPIE
Date: 17-10-2012
DOI: 10.1117/12.929304
Metatranscriptomic profiling reveals diverse tick‐borne bacteria, protozoans and viruses in ticks and wildlife from Australia
Publisher: Hindawi Limited
Date: 16-05-2022
DOI: 10.1111/TBED.14581
Abstract: Tick-borne zoonoses are emerging globally due to changes in climate and land use. While the zoonotic threats associated with ticks are well studied elsewhere, in Australia, the ersity of potentially zoonotic agents carried by ticks and their significance to human and animal health is not sufficiently understood. To this end, we used untargeted metatranscriptomics to audit the prokaryotic, eukaryotic and viral biomes of questing ticks and wildlife blood s les from two urban and rural sites in New South Wales, Australia. Ixodes holocyclus and Haemaphysalis bancrofti were the main tick species collected, and blood s les from Rattus rattus, Rattus fuscipes, Perameles nasuta and Trichosurus vulpecula were also collected and screened for tick-borne microorganisms using metatranscriptomics followed by conventional targeted PCR to identify important microbial taxa to the species level. Our analyses identified 32 unique tick-borne taxa, including 10 novel putative species. Overall, a wide range of tick-borne microorganisms were found in questing ticks including haemoprotozoa such as Babesia, Theileria, Hepatozoon and Trypanosoma spp., bacteria such as Borrelia, Rickettsia, Ehrlichia, Neoehrlichia and Anaplasma spp., and numerous viral taxa including Reoviridiae (including two coltiviruses) and a novel Flaviviridae-like jingmenvirus. Of note, a novel hard tick-borne relapsing fever Borrelia sp. was identified in questing H. bancrofti ticks which is closely related to, but distinct from, cervid-associated Borrelia spp. found throughout Asia. Notably, all tick-borne microorganisms were phylogenetically unique compared to their relatives found outside Australia, and no foreign tick-borne human pathogens such as Borrelia burgdorferi s.l. or Babesia microti were found. This work adds to the growing literature demonstrating that Australian ticks harbour a unique and endemic microbial fauna, including potentially zoonotic agents which should be further studied to determine their relative risk to human and animal health.
In-situ study of mineral liberation at the onset of fragmentation of a copper ore using X-ray micro-computed tomography
Publisher: arXiv
Date: 2022
Building a bone μCT images atlas for micro-architecture recognition
Publisher: SPIE
Date: 17-03-2015
DOI: 10.1117/12.2082807
Chaotic Sensing
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
Date: 12-2018
Space-Filling X-Ray Source Trajectories for Efficient Scanning in Large-Angle Cone-Beam Computed Tomography
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
Date: 09-2018
X-ray ghost-tomography: artefacts, dose distribution and mask considerations
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
Date: 03-2018
Extending reference scan drift correction to high-magnification high-cone-angle tomography
Publisher: The Optical Society
Date: 15-12-2011
DOI: 10.1364/OL.36.004809
Finite Radial Reconstruction for Magnetic Resonance Imaging: A Theoretical Study
Publisher: IEEE
Date: 11-2016
Least-squares and maximum-likelihood in XCT
Publisher: SPIE
Date: 09-09-2021
DOI: 10.1117/12.2595559
Linear iterative near-field phase retrieval (LIPR) for dual-energy x-ray imaging and material discrimination
Publisher: The Optical Society
Date: 26-10-2018
Geometric Shape Effects in Redundant Keys used to Encrypt Data Transformed by Finite Discrete Radon Projections
Publisher: IEEE
Date: 12-2005
3D Multiscale Imaging of the Distribution of Pores, Organic Matter and Oil in Place in Vaca Muerta Shale Samples
Publisher: American Association of Petroleum Geologists
Date: 2016
Correction of beam hardening artefacts in microtomography for samples imaged in containers
Publisher: SPIE
Date: 11-09-2014
DOI: 10.1117/12.2062393
Synchrotron-based X-ray Fluorescence Ghost Imaging
Publisher: Optica Publishing Group
Date: 23-10-2023
DOI: 10.1364/OL.499046
Imaging Mean Energy of X-ray Spectra through Intensity Variation in Radiographs with an Example Application to Beam Hardening Correction.
Publisher: Oxford University Press (OUP)
Date: 08-2018
Projective Transforms on Periodic Discrete Image Arrays
Publisher: Elsevier
Date: 2006
Environmental risk factors associated with the presence of Mycobacterium ulcerans in Victoria, Australia
Publisher: Cold Spring Harbor Laboratory
Date: 11-01-2022
DOI: 10.1101/2022.01.10.22269030
Abstract: In recent years reported cases of Buruli ulcer (BU), caused by Mycobacterium ulcerans (MU), have increased substantially in Victoria, Australia, with the epidemic also expanding geographically. To develop an understanding of how MU circulates in the environment and transmits to humans we analyzed environmental s les collected from 115 properties of recent BU cases and from 115 postcode-matched control properties, for the presence of MU. Environmental factors associated with increased odds of MU presence at a property included certain native plant species and native vegetation in general, more alkaline soil, lower altitude, the presence of common ringtail possums ( Pseudocheirus peregrinus ) and overhead powerlines. However, only powerlines and the absence of the native plant Melaleuca lanceolata were associated with BU case properties. S les positive for MU were more likely to be found at case properties and were associated with detections of MU in ringtail possum feces, supporting the hypothesis that MU is zoonotic, with ringtail possums the strongest reservoir host candidate. However, the disparity in environmental risk factors associated with MU positive properties versus case properties indicates a strong human behavioral component or the influence of other environmental factors in disease acquisition that requires further study. Possums, powerlines, and native vegetation are associated with the presence of Mycobacterium ulcerans in residential properties in Victoria, Australia.
Recovering Missing Slices of the Discrete Fourier Transform Using Ghosts
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
Date: 10-2012
Multi-resolution radiograph alignment for motion correction in X-ray micro-tomography
Publisher: SPIE
Date: 03-10-2016
DOI: 10.1117/12.2238259
Universal mask for hard x rays
Publisher: Optica Publishing Group
Date: 03-08-2023
Abstract: The penetrating power of x rays underpins important applications such as medical radiography. However, this same attribute makes it challenging to achieve flexible on-demand patterning of x-ray beams. One possible path to this goal is “ghost projection,” a method that may be viewed as a reversed form of classical ghost imaging. This technique employs multiple exposures of a single illuminated non-configurable mask that is transversely displaced to a number of specified positions to create any desired pattern. An experimental proof of concept is given for this idea, using hard x rays. The written pattern is arbitrary, up to a tunable constant offset, and its spatial resolution is limited by both (i) the finest features present in the illuminated mask and (ii) inaccuracies in mask positioning and mask exposure time. In principle, the method could be used to make a universal lithographic mask in the hard-x-ray regime. Ghost projection might also be used as a dynamically configurable beam-shaping element, namely, the hard-x-ray equivalent of a spatial light modulator. The underpinning principle can also be applied to gamma rays, neutrons, electrons, muons, and atomic beams. Our flexible approach to beam shaping gives a potentially useful means to manipulate such fields.
High cone-angle x-ray computed micro-tomography with 186 GigaVoxel datasets
Publisher: SPIE
Date: 04-10-2016
DOI: 10.1117/12.2238258
3D mapping of deformation in an unconsolidated sand: A micro mechanical study
Publisher: Society of Exploration Geophysicists
Date: 09-2012
Rats and the city: Implications of urbanization on zoonotic disease risk in Southeast Asia
Publisher: Proceedings of the National Academy of Sciences
Date: 19-09-2022
Abstract: Urbanization is rapidly transforming much of Southeast Asia, altering the structure and function of the landscape, as well as the frequency and intensity of the interactions between people, animals, and the environment. In this study, we explored the impact of urbanization on zoonotic disease risk by simultaneously characterizing changes in the ecology of animal reservoirs (rodents), ectoparasite vectors (ticks), and pathogens across a gradient of urbanization in Kuching, a city in Malaysian Borneo. We s led 863 rodents across rural, developing, and urban locations and found that rodent species ersity decreased with increasing urbanization—from 10 species in the rural location to 4 in the rural location. Notably, two species appeared to thrive in urban areas, as follows: the invasive urban exploiter Rattus rattus ( n = 375) and the native urban adapter Sundamys muelleri ( n = 331). R. rattus was strongly associated with built infrastructure across the gradient and carried a high ersity of pathogens, including multihost zoonoses capable of environmental transmission (e.g., Leptospira spp.). In contrast, S. muelleri was restricted to green patches where it was found at high densities and was strongly associated with the presence of ticks, including the medically important genera Amblyomma , Haemaphysalis , and Ixodes . Our analyses reveal that zoonotic disease risk is elevated and heterogeneously distributed in urban environments and highlight the potential for targeted risk reduction through pest management and public health messaging.
Reprojection Alignment for Trajectory Perturbation Estimation in Microtomography
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
Date: 06-2018
At Least Three Doses of Leading Vaccines Essential for Neutralisation of SARS-CoV-2 Omicron Variant
Publisher: Frontiers Media SA
Date: 17-05-2022
DOI: 10.3389/FIMMU.2022.883612
Abstract: Plasma s les taken at different time points from donors who received either AstraZeneca (Vaxzevria) or Pfizer (Comirnaty) or Moderna (Spikevax) coronavirus disease-19 (COVID-19) vaccine were assessed in virus neutralization assays against Delta and Omicron variants of concern and a reference isolate (VIC31). With the Pfizer vaccine there was 6-8-fold reduction in 50% neutralizing antibody titres (NT 50 ) against Delta and VIC31 at 6 months compared to 2 weeks after the second dose followed by 25-fold increase at 2 weeks after the third dose. Neutralisation of Omicron was only consistently observed 2 weeks after the third dose, with most s les having titres below the limit of detection at earlier timepoints. Moderna results were similar to Pfizer at 2 weeks after the second dose, while the titres for AstraZeneca s les derived from older donors were 7-fold lower against VIC31 and below the limit of detection against Delta and Omicron. Age and gender were not found to significantly impact our results. These findings indicate that vaccine matching may be needed, and that at least a third dose of these vaccines is necessary to generate sufficient neutralising antibodies against emerging variants of concern, especially Omicron, amidst the challenges of ensuring vaccine equity worldwide.
Optimized x-ray source scanning trajectories for iterative reconstruction in high cone-angle tomography
Publisher: SPIE
Date: 04-10-2016
DOI: 10.1117/12.2238297
Highly Thermotolerant SARS-CoV-2 Vaccine Elicits Neutralising Antibodies against Delta and Omicron in Mice
Publisher: MDPI AG
Date: 13-04-2022
DOI: 10.3390/V14040800
Abstract: As existing vaccines fail to completely prevent COVID-19 infections or community transmission, there is an unmet need for vaccines that can better combat SARS-CoV-2 variants of concern (VOC). We previously developed highly thermo-tolerant monomeric and trimeric receptor-binding domain derivatives that can withstand 100 °C for 90 min and 37 °C for four weeks and help eliminate cold-chain requirements. We show that mice immunised with these vaccine formulations elicit high titres of antibodies that neutralise SARS-CoV-2 variants VIC31 (with Spike: D614G mutation), Delta and Omicron (BA.1.1) VOC. Compared to VIC31, there was an average 14.4-fold reduction in neutralisation against BA.1.1 for the three monomeric antigen-adjuvant combinations and a 16.5-fold reduction for the three trimeric antigen-adjuvant combinations the corresponding values against Delta were 2.5 and 3.0. Our findings suggest that monomeric formulations are suitable for upcoming Phase I human clinical trials and that there is potential for increasing the efficacy with vaccine matching to improve the responses against emerging variants. These findings are consistent with in silico modelling and AlphaFold predictions, which show that, while oligomeric presentation can be generally beneficial, it can make important epitopes inaccessible and also carries the risk of eliciting unwanted antibodies against the oligomerisation domain.
Reliable automatic alignment of tomographic projection data by passive auto-focus
Publisher: Wiley
Date: 09-08-2011
DOI: 10.1118/1.3609096
Abstract: 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. 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 Feldk algorithm. Feldk et al. [J. Opt. Soc. Am. A 1, 612-619 (1984)]. An ex le 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 ex le 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. 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.
Ordered subsets convex algorithm for 3D terahertz transmission tomography
Publisher: The Optical Society
Date: 16-09-2014
DOI: 10.1364/OE.22.023299
Density estimation in XCT using the Alvarez-Macovski model
Publisher: SPIE
Date: 09-09-2021
DOI: 10.1117/12.2595473
Henipavirus-induced neuropathogenesis in mice
Publisher: Elsevier BV
Date: 10-2023
Tomography of atomic number and density of materials using dual-energy imaging and the Alvarez and Macovski attenuation model
Publisher: AIP Publishing
Date: 06-2016
DOI: 10.1063/1.4950807
Abstract: Dual-energy computed tomography and the Alvarez and Macovski [Phys. Med. Biol. 21, 733 (1976)] transmitted intensity (AMTI) model were used in this study to estimate the maps of density (ρ) and atomic number (Z) of mineralogical s les. In this method, the attenuation coefficients are represented [Alvarez and Macovski, Phys. Med. Biol. 21, 733 (1976)] in the form of the two most important interactions of X-rays with atoms that is, photoelectric absorption (PE) and Compton scattering (CS). This enables material discrimination as PE and CS are, respectively, dependent on the atomic number (Z) and density (ρ) of materials [Alvarez and Macovski, Phys. Med. Biol. 21, 733 (1976)]. Dual-energy imaging is able to identify s le materials even if the materials have similar attenuation coefficients at single-energy spectrum. We use the full model rather than applying one of several applied simplified forms [Alvarez and Macovski, Phys. Med. Biol. 21, 733 (1976) Siddiqui et al., SPE Annual Technical Conference and Exhibition (Society of Petroleum Engineers, 2004) Derzhi, U.S. patent application 13/527,660 (2012) Heismann et al., J. Appl. Phys. 94, 2073–2079 (2003) Park and Kim, J. Korean Phys. Soc. 59, 2709 (2011) Abudurexiti et al., Radiol. Phys. Technol. 3, 127–135 (2010) and Kaewkhao et al., J. Quant. Spectrosc. Radiat. Transfer 109, 1260–1265 (2008)]. This paper describes the tomographic reconstruction of ρ and Z maps of mineralogical s les using the AMTI model. The full model requires precise knowledge of the X-ray energy spectra and calibration of PE and CS constants and exponents of atomic number and energy that were estimated based on fits to simulations and calibration measurements. The estimated ρ and Z images of the s les used in this paper yield average relative errors of 2.62% and 1.19% and maximum relative errors of 2.64% and 7.85%, respectively. Furthermore, we demonstrate that the method accounts for the beam hardening effect in density (ρ) and atomic number (Z) reconstructions to a significant extent.
Inherent dose-reduction potential of classical ghost imaging
Publisher: American Physical Society (APS)
Date: 05-03-2021
Techniques in helical scanning, dynamic imaging and image segmentation for improved quantitative analysis with X-ray micro-CT
Publisher: Elsevier BV
Date: 04-2014
Dynamic Micro-CT Imaging of Diffusion in Unconventionals
Publisher: Society of Petroleum Engineers
Date: 2015
DOI: 10.2118/178617-MS
X-ray attenuation models to account for beam hardening in computed tomography
Publisher: Optica Publishing Group
Date: 07-10-2020
DOI: 10.1364/AO.402304
Abstract: We introduce a beam-hardening correction method for lab-based X-ray computed tomography (CT) by modifying existing iterative tomographic reconstruction algorithms. Our method simplifies the standard Alvarez–Macovski X-ray attenuation model [ Phys. Med. Biol. 21 , 733 ( 1976 ) ] and is compatible with conventional (i.e., single-spectrum) CT scans. The sole modification involves a polychromatic projection operation, which is equivalent to applying a weighting that more closely matches the attenuation of polychromatic X-rays. Practicality is a priority, so we only require information about the X-ray spectrum and some constants relating to material properties. No other changes to the experimental setup or the iterative algorithms are necessary. Using reconstructions of simulations and several large experimental datasets, we show that this method is able to remove or reduce cupping, streaking, and other artefacts from X-ray beam hardening and improve the self-consistency of projected attenuation in CT. When the assumptions made in the simplifications are valid, the reconstructed tomogram can even be quantitative.
Flow rate impacts on capillary pressure and interface curvature of connected and disconnected fluid phases during multiphase flow in sandstone
Publisher: Elsevier BV
Date: 09-2017
Lossless image compression via predictive coding of discrete Radon projections
Publisher: Elsevier BV
Date: 04-2008
A versatile microtomography system to study in situ the failure and fragmentation in geomaterials
Publisher: AIP Publishing
Date: 08-2022
DOI: 10.1063/5.0093650
Abstract: This article describes a microtomography experimental platform enabling in situ micro-mechanical study of failure and fragmentation in geomaterials. The system is based on an original high-pressure triaxial flow cell, which is fully integrated into a custom built microtomography scanner equipped with a laboratory x-ray source. The design of the high-precision mechanical apparatus was informed by the concurrent development of advanced tomographic reconstruction methods based on helical scanning and of algorithms correcting for hardware inaccuracies. This experimental system produces very high-quality 3D images of microstructural changes occurring in rocks undergoing mechanical failure and substantial fragmentation. We present the results of two experiments as case studies to demonstrate the capabilities and versatility of this instrumental platform. These experiments tackle various questions related to the onset of rock failure, the hydromechanical coupling and relaxation mechanisms in fractured rocks, or the fragmentation process in geomaterials such as copper ores.
Visualizing the Microdistribution of Zinc Borate in Oriented Strand Board Using X-Ray Microcomputed Tomography and SEM-EDX
Publisher: Hindawi Limited
Date: 28-02-2015
DOI: 10.1155/2015/630905
Abstract: Oriented strand board (OSB) is an important wood composite used in situations where fungal decay and termite attack can occur. To counter these threats, powdered zinc borate biocide is commonly added to OSB. The effectiveness of biocides depends on their even distribution within composites and resistance to leaching, but little is known about the distribution of zinc borate in OSB. Zinc is denser than wood and it should be possible to map its distribution in OSB using X-ray micro-CT. We test this hypothesis and chemically register zinc in OSB using SEM-EDX. Zinc borate particles aggregated at the wood-adhesive interface in OSB, creating interrupted lines of zinc oriented in the x - y plane. Zinc borate particles were also found in the lumens of wood cells. Zinc was distributed throughout OSB, although slightly less was present in the core of the composite than in surface layers. A network of zinc remained in OSB after leaching in water. The resistance of zinc to leaching may be due to its incorporation in glue-lines within OSB, in addition to its low water-solubility. We conclude that X-ray micro-CT is a powerful tool for studying the distribution of zinc in OSB and other wood composites containing zinc borate.
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