Browsing by Author "Abbey, B"
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- ItemApplication and validity of the Radon transform applied to axisymmetric neutron strain imaging(Elsevier B. V., 2019-12-15) Kirkwood, HJ; Wensrich, CM; Paradowska, AM; Abbey, BNext generation pulsed neutron sources and wavelength dispersive imaging detectors are creating new opportunities for strain analysis. One such technique is Bragg edge transmission analysis in which projected measurements of the crystallographic properties of bulk polycrystalline samples are recorded on a time-of-flight area detector. The ability to measure the elastic strain field poses the question of whether it is possible to reconstruct a three-dimensional map of the elastic strain tensor from a set of lower order projection data. Here we present a fundamental exploration of the validity of axisymmetric strain reconstruction algorithms available for inverting Bragg edge data. The results demonstrate that the compatibility of the elastic strain field under investigation is critical in determining which algorithm may be successfully applied. Finally, a more robust approach to Radon transform strain tomography is presented based on the condition of zero total strain. ©2019 Elsevier Ltd.
- ItemEnergy-resolved neutron imaging options at a small angle neutron scattering instrument at the Australian Center for Neutron Scattering(AIP Publishing, 2019-03-26) Tremsin, AS; Sokolova, AV; Salvemini, F; Luzin, V; Paradowska, AM; Muránsky, O; Kirkwood, HJ; Abbey, B; Wensrich, CM; Kisi, EHEnergy-resolved neutron imaging experiments conducted on the Small Angle Neutron Scattering (SANS) instrument, Bilby, demonstrate how the capabilities of this instrument can be enhanced by a relatively simple addition of a compact neutron counting detector. Together with possible SANS sample surveying and location of the region of interest, this instrument is attractive for many imaging applications. In particular, the combination of the cold spectrum of the neutron beam and its pulsed nature enables unique non-destructive studies of the internal structure for samples that are opaque to other more traditional techniques. In addition to conventional white beam neutron radiography, we conducted energy-resolved imaging experiments capable of resolving features related to microstructure in crystalline materials with a spatial resolution down to ∼0.1 mm. The optimized settings for the beamline configuration were determined for the imaging modality, where the compromise between the beam intensity and the achievable spatial resolution is of key concern. © 2020 AIP Publishing LLC
- ItemPolycrystalline materials analysis using the Maia pixelated energy-dispersive x-ray area detector(Cambridge University Press, 2017-09-26) Kirkwood, HJ; De Jonge, MD; Howard, DL; Ryan, CG; van Riessen, GA; Hofmann, F; Rowles, MR; Paradowska, AM; Abbey, BElemental, chemical, and structural analysis of polycrystalline materials at the micron scale is frequently carried out using microfocused synchrotron X-ray beams, sometimes on multiple instruments. The Maia pixelated energy-dispersive X-ray area detector enables the simultaneous collection of X-ray fluorescence (XRF) and diffraction because of the relatively large solid angle and number of pixels when compared with other systems. The large solid angle also permits extraction of surface topography because of changes in self-absorption. This work demonstrates the capability of the Maia detector for simultaneous measurement of XRF and diffraction for mapping the short- and long-range order across the grain structure in a Ni polycrystalline foil. Copyright © International Centre for Diffraction Data 2017
- ItemPropagation-based x-ray phase-contrast tomography of mastectomy samples using synchrotron radiation(American Association of Physicists in Medicine, 2019-10-01) Gureyev, TE; Nesterets, YI; Baran, PM; Taba, ST; Mayo, SC; Thompson, D; Arhatari, BD; Mihocic, A; Abbey, B; Lockie, D; Fox, J; Kumar, B; Prodanovic, Z; Häusermann, D; Maksimenko, A; Hall, CJ; Peele, AG; Dimmock, MR; Pavlov, KM; Cholewa, M; Lewis, SJ; Tromba, G; Quiney, HM; Brennan, PCPurpose Propagation-based phase-contrast computed tomography (PB-CT) is a method for three-dimensional x-ray imaging that utilizes refraction, as well as absorption, of x rays in the tissues to increase the signal-to-noise ratio (SNR) in the resultant images, in comparison with equivalent conventional absorption-only x-ray tomography (CT). Importantly, the higher SNR is achieved without sacrificing spatial resolution or increasing the radiation dose delivered to the imaged tissues. The present work has been carried out in the context of the current development of a breast CT imaging facility at the Australian Synchrotron. Methods Seven unfixed complete mastectomy samples with and without breast cancer lesions have been imaged using absorption-only CT and PB-CT techniques under controlled experimental conditions. The radiation doses delivered to the mastectomy samples during the scans were comparable to those approved for mammographic screening. Physical characteristics of the reconstructed images, such as spatial resolution and SNR, have been measured and compared with the results of the radiological quality assessment of the complete absorption CT and PB-CT image stacks. Results Despite the presence of some image artefacts, the PB-CT images have outperformed comparable absorption CT images collected at the same radiation dose, in terms of both the measured objective image characteristics and the radiological image scores. The outcomes of these experiments are shown to be consistent with predictions of the theory of PB-CT imaging and previous reported experimental studies of this imaging modality. Conclusions The results presented in this paper demonstrate that PB-CT holds a high potential for improving on the quality and diagnostic value of images obtained using existing medical x-ray technologies, such as mammography and digital breast tomosynthesis (DBT). If implemented at suitable synchrotron imaging facilities, PB-CT can be used to complement existing imaging modalities, leading to more accurate breast cancer diagnosis. © 2023 American Association of Physicists in Medicine
- ItemSimultaneous X-ray diffraction, crystallography and fluorescence mapping using the Maia detector(Elsevier, 2018-02-01) Kirkwood, HJ; de Jonge, MD; Muránsky, O; Hofmann, F; Howard, DL; Ryan, CG; van Riessen, GA; Rowles, MR; Paradowska, AM; Abbey, BInteractions between neighboring grains influence the macroscale behavior of polycrystalline materials, particularly their deformation behavior, damage initiation and propagation mechanisms. However, mapping all of the critical material properties normally requires that several independent measurements are performed. Here we report the first grain mapping of a polycrystalline foil using a pixelated energy-dispersive X-ray area detector, simultaneously measuring X-ray fluorescence and diffraction with the Maia detector in order to determine grain orientation and estimate lattice strain. These results demonstrate the potential of the next generation of X-ray area detectors for materials characterization. By scanning the incident X-ray energy we investigate these detectors as a complete solution for simultaneously mapping the crystallographic and chemical properties of the sample. The extension of these techniques to broadband X-ray sources is also discussed. © 2017 Acta Materialia Inc. Published by Elsevier Ltd.
- ItemSimultaneously localising biometals within the high resolution ultrastructure of whole C. elegans(Australian Microscopy and Microanalysis Society, 2016-02-04) Jones, MWM; McColl, G; van Riessen, GA; Phillips, NW; Vine, D; Abbey, B; de Jonge, MDPtychography is a coherent diffraction imaging method where multiple overlapping diffraction frames are combined, providing high resolution images of the electron density of extended objects. Recently, X-ray ptychography has seen many efficiency improvements that allow large areas to be imaged rapidly, making simultaneous X-ray ptychography and fluorescence microscopy experimentally viable. Here we use simultaneous X-ray fluorescence microscopy and ptychography to image entire C. elegans, with sub-micron and sub 100 nm elemental and ultrastructure resolutions respectively. Rapid data collection allowed the entire 1 mm long animal to be imaged in only a few hours. With the information from both techniques, the elemental maps can be viewed in the context of the high resolution ultrastructure, allowing further insights into the localisation of the fluorescent signal.
- ItemTowards real-time analysis of liquid jet alignment in serial femtosecond crystallography(International Union of Crystallography, 2022-06-02) Patel, J; Round, A; Bielecki, J; Doerner, K; Kirkwood, HJ; Letrun, R; Schulz, J; Sikorski, M; Valiki, M; de Wijn, R; Peele, AG; Mancuso, AP; Abbey, BLiquid sample delivery systems are used extensively for serial femtosecond crystallography at X-ray free-electron lasers (XFELs). However, misalignment of the liquid jet and the XFEL beam leads to the X-rays either partially or completely missing the sample, resulting in sample wastage and a loss of experiment time. Implemented here is an algorithm to analyse optical images using machine vision to determine whether there is overlap of the X-ray beam and liquid jet. The long-term goal is to use the output from this algorithm to implement an automated feedback mechanism to maintain constant alignment of the X-ray beam and liquid jet. The key elements of this jet alignment algorithm are discussed and its performance is characterized by comparing the results with a manual analysis of the optical image data. The success rate of the algorithm for correctly identifying hits is quantified via a similarity metric, the Dice coefficient. In total four different nozzle designs were used in this study, yielding an overall Dice coefficient of 0.98. © 2022 The Authors, CC BY 4.0 licence
- ItemTowards real-time analysis of liquid jet alignment in SFX(Australian Nuclear Science and Technology Organisation, 2021-11-25) Patel, J; Peele, AG; Abbey, B; Round, AP; Mancuso, ASerial femtosecond crystallography (SFX) enables atomic scale imaging of protein structures via X-ray diffraction measurements from large numbers of small crystals intersecting intense X-ray Free Electron Laser (XFEL) pulses. Sample injection typically involves continuous delivery of crystals to the pulsed XFEL beam via a liquid jet. Due to movement of the jet, which is often focused to further reduce its diameter using a gas virtual dynamic nozzle (GVDN), jet position is often adjusted multiple times during the experiment. This can result in loss of beamtime and significant manual intervention. Here we present a novel approach to the problem of liquid jet misalignment in SFX based on machine vision. We demonstrate automatic identification and classification of when there is overlap (‘hit’) and when there is not overlap (‘miss’) between the XFEL beam and jet. Our algorithm takes as its input optical images from the ‘side microscope’ located inside the X-ray hutch. This algorithm will be incorporated into the control system at the SFX/SPB beamline at the European XFEL where it will be used for in-situ ‘alignment correction’ via a continuous feedback loop with the stepper motors controlling the location of the nozzle within the chamber. Full automation of this process will result in a larger volume of useful data being collected. By increasing the efficiency and reducing the per experiment operational cost of SFX at the European XFEL a higher volume of experiments can be performed. In addition, via analysis of the feedback metrology we anticipate that optimised nozzle designs and jetting conditions could be achieved further benefitting the end user.
- ItemTowards real-time analysis of liquid jet alignment in SFX(International Union of Crystallography, 2021-08-14) Patel, J; Round, A; Peele, AG; Mancuso, A; Abbey, BSerial femtosecond crystallography (SFX) enables the retrieval of the molecular structure of protein molecules at the atomic level through the measurement of large numbers of small crystals intersecting intense X-ray pulses. The method of sample delivery for SFX has a very significant impact on the success (or otherwise) of the experiment since this can impact the signal-to-noise, resolution, and amount of data that can be obtained. In particular, highly efficient sample delivery is critical, since this minimises the amount of X-ray Free Electron Laser (XFEL) beamtime required as well as reducing sample consumption and data volumes. Here we present the results from a series of liquid jet experiments performed at the European XFEL using gas focused liquid injectors, gas virtual dynamic nozzle (GVDN), and double flow focusing nozzles. Although these methods are well-established and used extensively at the European XFEL a major drawback of using these injectors is that over time the jet can become misaligned with the XFEL beam. At present, this requires regular manual monitoring in order to ensure that the relative drift of the jet with respect to the X-ray beam does not become so significant that the beam either ‘clips’ or misses the jet entirely. Manual adjustment of the liquid jet to ensure alignment with the Xray beam costs the beamline staff time, is prone to errors, and ultimately reduces the amount of useable data that is collected. In order to address the issue of jet misalignment we present a novel approach to analysing the liquid stream both with (‘hit’) and without (‘miss’) intersection by the X-ray beam using machine vision. Optical images from the from the side microscope currently used to monitor the jet are fed into our machine vision algorithm and used to classify the images as either a hit or miss. Currently we are testing the efficacy of the algorithm with a variety of nozzles and jetting conditions. The algorithm will then be incorporated into the control system at the SFX/SPB beamline at the European XFEL where it will be used to generate an ‘alignment correction’ to the stepper motors controlling the location of the nozzle within the chamber. Via a continuous feedback loop, fine adjustments will be made to the position of the liquid jet ensuring that maximum X-ray beam/liquid jet overlap is achieved. Since this process is fully automated we anticipate that it will result in a larger volume of useful data being collected without requiring any manual intervention. By increasing the efficiency and reducing the per experiment operational cost of SFX at the European XFEL ultimately more experiments can be performed. In addition, via analysis of the feedback metrology we anticipate that optimised nozzle designs and jetting conditions could be achieved further benefitting the end user. © The Authors
- ItemX-ray phase-contrast computed tomography for soft tissue Imaging at the Imaging and Medical Beamline (IMBL) of the Australian Synchrotron(MDPI, 2021-04-30) Arhatari, BD; Stevenson, AW; Abbey, B; Nesterets, YI; Maksimenko, A; Hall, CJ; Thompson, D; Mayo, SC; Fiala, T; Quiney, HM; Taba, ST; Lewis, SJ; Brennan, PC; Dimmock, MR; Häusermann, D; Gureyev, TEThe Imaging and Medical Beamline (IMBL) is a superconducting multipole wiggler-based beamline at the 3 GeV Australian Synchrotron operated by the Australian Nuclear Science and Technology Organisation (ANSTO). The beamline delivers hard X-rays in the 25–120 keV energy range and offers the potential for a range of biomedical X-ray applications, including radiotherapy and medical imaging experiments. One of the imaging modalities available at IMBL is propagation-based X-ray phase-contrast computed tomography (PCT). PCT produces superior results when imaging low-density materials such as soft tissue (e.g., breast mastectomies) and has the potential to be developed into a valuable medical imaging tool. We anticipate that PCT will be utilized for medical breast imaging in the near future with the advantage that it could provide better contrast than conventional X-ray absorption imaging. The unique properties of synchrotron X-ray sources such as high coherence, energy tunability, and high brightness are particularly well-suited for generating PCT data using very short exposure times on the order of less than 1 min. The coherence of synchrotron radiation allows for phase-contrast imaging with superior sensitivity to small differences in soft-tissue density. Here we also compare the results of PCT using two different detectors, as these unique source characteristics need to be complemented with a highly efficient detector. Moreover, the application of phase retrieval for PCT image reconstruction enables the use of noisier images, potentially significantly reducing the total dose received by patients during acquisition. This work is part of ongoing research into innovative tomographic methods aimed at the introduction of 3D X-ray medical imaging at the IMBL to improve the detection and diagnosis of breast cancer. Major progress in this area at the IMBL includes the characterization of a large number of mastectomy samples, both normal and cancerous, which have been scanned at clinically acceptable radiation dose levels and evaluated by expert radiologists with respect to both image quality and cancer diagnosis. © 2021 The Authors, Licensee MDPI, Basel, Switzerland. Open Access Creative Commons Attribution (CC BY).