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Instruments / Technical Area	Publication Details	Published
I12-JEEP: Joint Engineering, Environmental and Processing	Preprocessing techniques for removing artifacts in synchrotron-based tomographic images Nghia Vo , Robert C. Atwood , Michael Drakopoulos SPIE Optical Engineering + Applications, 2019 DOI: 10.1117/12.2530324 Open Access Show Abstract ▼ Abstract: X-Ray parallel-beam micro-tomography systems at synchrotron facilities are mainly bespoke designs. Technical problems from a detector system can strongly affect the quality of reconstruction results. Radial lens distortion in the visible light optics causes streak artifacts which get stronger towards the edge of the image. The irregular response of the detector gives rise to a variety of stripe artifacts in the sonogram; full stripes, partial stripes, fluctuating stripes, and unresponsive stripes. These give rise to ring artifacts of different kinds in the reconstructed image. The scattering of the scintillation photons can cause artifacts which are similar to beam hardening artifacts and reduce the resolution of the image. Here we present our practical approaches to tackle each such problem. These approaches are easy to implement and have low computational cost. The algorithms are freely available as open-source software.	Sep 2019
I12-JEEP: Joint Engineering, Environmental and Processing	Quantitative measurement of olivine composition in three dimensions using helical-scan X-ray micro-tomography Matthew J. Pankhurst , Nghia T. Vo , Alan R. Butcher , Haili Long , Hongchang Wang , Sara Nonni , Jason Harvey , Guđmundur Guđfinnsson , Ronald Fowler , Robert Atwood , Richard Walshaw , Peter D. Lee American Mineralogist 103, 1800 - 1811 DOI: 10.2138/am-2018-6419 Diamond Proposal Number(s): [14033] Show Abstract ▼ Abstract: Olivine is a key constituent in the silicate Earth; its composition and texture informs petrogenetic understanding of numerous rock types. Here we develop a quantitative and reproducible method to measure olivine composition in three dimensions without destructive analysis, meaning full textural context is maintained. The olivine solid solution between forsterite and fayalite was measured using a combination of three-dimensional (3D) X-ray imaging techniques, 2D backscattered electron imaging, and spot-analyses using wavelength-dispersive electron probe microanalysis. The linear attenuation coefficient of natural crystals across a range of forsterite content from ∼73–91 mol% were confirmed to scale linearly with composition using 53, 60, and 70 kV monochromatic beams at I12-JEEP beamline, Diamond Light Source utilizing the helical fly-scan acquisition. A polychromatic X-ray source was used to scan the same crystals, which yielded image contrast equivalent to measuring the mol% of forsterite with an accuracy of <1.0%. X-ray tomography can now provide fully integrated textural and chemical analysis of natural samples containing olivine, which will support 3D and 3D+time petrologic modeling. The study has revealed >3 mm domains within a large crystal of San Carlos forsterite that varies by ∼2 Fo mol%. This offers a solution to an outstanding question of inter-laboratory standardization, and also demonstrates the utility of 3D, non-destructive, chemical measurement. To our knowledge, this study is the first to describe the application of XMT to quantitative chemical measurement across a mineral solid solution. Our approach may be expanded to calculate the chemistry of other mineral systems in 3D, depending upon the number, chemistry, and density of end-members.	Nov 2018
I12-JEEP: Joint Engineering, Environmental and Processing	Superior techniques for eliminating ring artifacts in X-ray micro-tomography Nghia T. Vo , Robert. C. Atwood , Michael Drakopoulos Optics Express 26 DOI: 10.1364/OE.26.028396 Open Access Show Abstract ▼ Abstract: Synchrotron-based X-ray micro-tomography systems often suffer severe ring artifacts in reconstructed images. In sinograms the artifacts appear as straight lines or stripe artifacts. These artifacts are caused by the irregular response of a detecting system giving rise to a variety of observed types of stripes: full stripes, partial stripes, fluctuating stripes, and unresponsive stripes. The use of pre-processing techniques such as distortion correction or phase retrieval blurs and enlarges these stripes. It is impossible for a single approach to remove all types of stripe artifacts. Here, we propose three techniques for tackling all of them. The proposed techniques are easy to implement; do not generate extra stripe artifacts and void-center artifacts; and give superior quality on challenging data sets and in comparison with other techniques. Implementations in Python and a challenging data set are available for download.	Oct 2018
I12-JEEP: Joint Engineering, Environmental and Processing	The effect of long-term bisphosphonate therapy on trabecular bone strength and microcrack density A. Jin , J. Cobb , U. Hansen , R. Bhattacharya , C. Reinhard , N. Vo , R. Atwood , J. Li , A. Karunaratne , C. Wiles , R. Abel Bone And Joint Research 6, 602 - 609 DOI: 10.1302/2046-3758.610.BJR-2016-0321.R1 Diamond Proposal Number(s): [9811, 852] Open Access Show Abstract ▼ Abstract: Objectives Bisphosphonates (BP) are the first-line treatment for preventing fragility fractures. However, concern regarding their efficacy is growing because bisphosphonate is associated with over-suppression of remodelling and accumulation of microcracks. While dual-energy X-ray absorptiometry (DXA) scanning may show a gain in bone density, the impact of this class of drug on mechanical properties remains unclear. We therefore sought to quantify the mechanical strength of bone treated with BP (oral alendronate), and correlate data with the microarchitecture and density of microcracks in comparison with untreated controls. Methods Trabecular bone from hip fracture patients treated with BP (n = 10) was compared with naïve fractured (n = 14) and non-fractured controls (n = 6). Trabecular cores were synchrotron scanned and micro-CT scanned for microstructural analysis, including quantification of bone volume fraction, microarchitecture and microcracks. The specimens were then mechanically tested in compression. Results BP bone was 28% lower in strength than untreated hip fracture bone, and 48% lower in strength than non-fractured control bone (4.6 MPa vs 6.4 MPa vs 8.9 MPa). BP-treated bone had 24% more microcracks than naïve fractured bone and 51% more than non-fractured control (8.12/cm2 vs 6.55/cm2 vs 5.25/cm2). BP and naïve fracture bone exhibited similar trabecular microarchitecture, with significantly lower bone volume fraction and connectivity than non-fractured controls. Conclusion BP therapy had no detectable mechanical benefit in the specimens examined. Instead, its use was associated with substantially reduced bone strength. This low strength may be due to the greater accumulation of microcracks and a lack of any discernible improvement in bone volume or microarchitecture. This preliminary study suggests that the clinical impact of BP-induced microcrack accumulation may be significant.	Oct 2017
I12-JEEP: Joint Engineering, Environmental and Processing	Effects of Peripapillary Scleral Stiffening on the Deformation of the Lamina Cribrosa Baptiste Coudrillier , Ian C. Campbell , A. Thomas Read , Diogo M. Geraldes , Nghia Vo , Andrew Feola , John Mulvihill , Julie Albon , Richard L. Abel , C. Ross Ethier Investigative Opthalmology & Visual Science 57 DOI: 10.1167/iovs.15-18193 Diamond Proposal Number(s): [8491] Open Access Show Abstract ▼ Abstract: Purpose: Scleral stiffening has been proposed as a treatment for glaucoma to protect the lamina cribrosa (LC) from excessive intraocular pressure–induced deformation. Here we experimentally evaluated the effects of moderate stiffening of the peripapillary sclera on the deformation of the LC. Methods: An annular sponge, saturated with 1.25% glutaraldehyde, was applied to the external surface of the peripapillary sclera for 5 minutes to stiffen the sclera. Tissue deformation was quantified in two groups of porcine eyes, using digital image correlation (DIC) or computed tomography imaging and digital volume correlation (DVC). In group A (n = 14), eyes were subjected to inflation testing before and after scleral stiffening. Digital image correlation was used to measure scleral deformation and quantify the magnitude of scleral stiffening. In group B (n = 5), the optic nerve head region was imaged using synchrotron radiation phase-contrast microcomputed tomography (PC μCT) at an isotropic spatial resolution of 3.2 μm. Digital volume correlation was used to compute the full-field three-dimensional deformation within the LC and evaluate the effects of peripapillary scleral cross-linking on LC biomechanics. Results: On average, scleral treatment with glutaraldehyde caused a 34 ± 14% stiffening of the peripapillary sclera measured at 17 mm Hg and a 47 ± 12% decrease in the maximum tensile strain in the LC measured at 15 mm Hg. The reduction in LC strains was not due to cross-linking of the LC. Conclusions: Peripapillary scleral stiffening is effective at reducing the magnitude of biomechanical strains within the LC. Its potential and future utilization in glaucoma axonal neuroprotection requires further investigation.	May 2016
I12-JEEP: Joint Engineering, Environmental and Processing	Long-term effects of bisphosphonate therapy: perforations, microcracks and mechanical properties Shaocheng Ma , En Lin Goh , Andi Jin , Rajarshi Bhattacharya , Oliver R. Boughton , Bhavi Patel , Angelo Karunaratne , Nghia T. Vo , Robert Atwood , Justin P. Cobb , Ulrich Hansen , Richard L. Abel Scientific Reports 7 DOI: 10.1038/srep43399 Diamond Proposal Number(s): [852, 9811, 11204, 13337] Open Access Show Abstract ▼ Abstract: Osteoporosis is characterised by trabecular bone loss resulting from increased osteoclast activation and unbalanced coupling between resorption and formation, which induces a thinning of trabeculae and trabecular perforations. Bisphosphonates are the frontline therapy for osteoporosis, which act by reducing bone remodelling, and are thought to prevent perforations and maintain microstructure. However, bisphosphonates may oversuppress remodelling resulting in accumulation of microcracks. This paper aims to investigate the effect of bisphosphonate treatment on microstructure and mechanical strength. Assessment of microdamage within the trabecular bone core was performed using synchrotron X-ray micro-CT linked to image analysis software. Bone from bisphosphonate-treated fracture patients exhibited fewer perforations but more numerous and larger microcracks than both fracture and non-fracture controls. Furthermore, bisphosphonate-treated bone demonstrated reduced tensile strength and Young’s Modulus. These findings suggest that bisphosphonate therapy is effective at reducing perforations but may also cause microcrack accumulation, leading to a loss of microstructural integrity and consequently, reduced mechanical strength.	Mar 2016
I12-JEEP: Joint Engineering, Environmental and Processing	I12: the Joint Engineering, Environment and Processing (JEEP) beamline at Diamond Light Source Michael Drakopoulos , Thomas Connolley , Christina Reinhard , Robert Atwood , Oxana Magdysyuk , Nghia Vo , Mike Hart , Leigh Connor , Bob Humphreys , George Howell , Steve Davies , Tim Hill , Guy Wilkin , Ulrik Pedersen , Andrew Foster , Nicoletta De Maio , Mark Basham , Fajin Yuan , Kaz Wanelik Journal Of Synchrotron Radiation 22 DOI: 10.1107/S1600577515003513 PMID: 25931103 Open Access Show Abstract ▼ Abstract: I12 is the Joint Engineering, Environmental and Processing (JEEP) beamline, constructed during Phase II of the Diamond Light Source. I12 is located on a short (5 m) straight section of the Diamond storage ring and uses a 4.2 T superconducting wiggler to provide polychromatic and monochromatic X-rays in the energy range 50150 keV. The beam energy enables good penetration through large or dense samples, combined with a large beam size (1 mrad horizontally x 0.3 mrad vertically). The beam characteristics permit the study of materials and processes inside environmental chambers without unacceptable attenuation of the beam and without the need to use sample sizes which are atypically small for the process under study. X-ray techniques available to users are radiography, tomography, energy-dispersive diffraction, monochromatic and white-beam two-dimensional diffraction/scattering and small-angle X-ray scattering. Since commencing operations in November 2009, I12 has established a broad user community in materials science and processing, chemical processing, biomedical engineering, civil engineering, environmental science, palaeontology and physics.	May 2015

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