I13-2-Diamond Manchester Imaging
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Diamond Proposal Number(s):
[28557]
Open Access
Abstract: Swelling of shale in response to interaction with water is an important consideration within subsurface energy systems. In the case of waste disposal, swelling can provide important barriers around the waste and enhance the sealing ability of rocks. For shale gas exploration purpose, however, swelling may cause wellbore instability. Therefore, a careful study of shale swelling is critical for subsurface energy related applications. Here, the swelling effects of shale were imaged at nanoscale using an advanced synchrotron Transmission X-ray Microscopy (TXM) imaging technique for the first time, with a spatial resolution down to 40.9 nm. Organic matter and clays within the analysed sample were observed to display large swelling effects which resulted in a 50% reduction in porosity. Strain maps generated using Digital Volume Correlation (DVC) show deformation and significant strain were mostly localized to between the contact boundaries of sharp brittle minerals and softer organic matter and clays. This is the first study, to our knowledge, to directly image the swelling deformation of shale at the tens of nanometer scale and provide local information on the strain evolution.
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Jul 2023
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I13-2-Diamond Manchester Imaging
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Abstract: Accurately estimating developmental age and life history traits in fossils is crucial for identifying
and classifying extinct species and understanding how biological attributes evolved. The
evolution of life history traits such as growth pattern is far from clear in birds, and development
has been studied in only a handful of modern species. The exceptionally rapid growth of
modern birds means ageing methods based on annual incremental growth lines, used in other
vertebrates, are inapplicable to birds and robust alternative methods remain to be established.
Analysis of avian intracortical bone microstructure, which varies both with age and tissue
deposition rate, is a promising approach already used in palaeobiology. However, current thin
section-based histological methods are destructive. Moreover, to date, most microstructural
studies in avian bone are qualitative, 2D, and involve a limited range of extant species. The
objective of this study was to investigate cortical bone microstructure and developmental age
and life history traits in living birds, to identify phenotypes which can then be applied to
examination of the fossil record, using minimally-destructive high-resolution 3D imaging.
First, the necessity of 3D measurement was tested: a combination of idealised, simulated
datasets and real synchrotron-based computed tomography (SR CT) datasets were used to
compare published methods for measuring key microstructural traits based on 2D sections and
3D volumes. Next, SR CT imaging and quantitative measurements were used to characterise
age-related changes in bone microstructure in a range of extant bird species: growth series
ducks and pheasants, and a smaller sample size in starlings, rock doves, partridges, and ostrich.
The methods tested in modern material were applied to fossils as a proof-of concept.
It was found that 3D quantification methods are required for measuring vascular canal
orientation and osteocyte lacunar shape and volume, though 2D sections could be used to
measure traits such as bone volume fraction (BV/TV) and osteocyte lacunar volume. In all
species studied, juvenile, subadult, and adult species could be distinguished by their values of
BV/TV, and further information could be added using measured values of vascular canal
diameter as well as qualitative assessment. Using a synchrotron-based CT system,
high-resolution 3D datasets comparable to modern bone samples were obtained from fossils,
and preliminary estimates of developmental age can be made.
Further work may reveal more changes within juvenile age stages, and better characterise the
variation within extant birds, allowing more accurate interpretation of the fossil record.
Therefore developmental studies in a greater number of extant bird species are required using
larger sample sizes, to support and add to the results presented in this thesis.
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Jan 2023
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I13-2-Diamond Manchester Imaging
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Diamond Proposal Number(s):
[16205]
Open Access
Abstract: Methane (CH4) hydrate dissociation and CH4 release are potential geohazards currently investigated using X-ray computed tomography (XCT). Image segmentation is an important data processing step for this type of research. However, it is often time consuming, computing resource-intensive, operator-dependent, and tailored for each XCT dataset due to differences in greyscale contrast. In this paper, an investigation is carried out using U-Nets, a class of Convolutional Neural Network, to segment synchrotron XCT images of CH4-bearing sand during hydrate formation, and extract porosity and CH4 gas saturation. Three U-Net deployments previously untried for this task are assessed: (1) a bespoke 3D hierarchical method, (2) a 2D multi-label, multi-axis method and (3) RootPainter, a 2D U-Net application with interactive corrections. U-Nets are trained using small, targeted hand-annotated datasets to reduce operator time. It was found that the segmentation accuracy of all three methods surpass mainstream watershed and thresholding techniques. Accuracy slightly reduces in low-contrast data, which affects volume fraction measurements, but errors are small compared with gravimetric methods. Moreover, U-Net models trained on low-contrast images can be used to segment higher-contrast datasets, without further training. This demonstrates model portability, which can expedite the segmentation of large datasets over short timespans.
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Dec 2022
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I13-2-Diamond Manchester Imaging
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Diamond Proposal Number(s):
[28574]
Open Access
Abstract: We present a flyscan compatible acquisition scheme for three-modal X-Ray Computed Tomography (CT) with two-dimensional phase sensitivity. Our approach is demonstrated using a “beam tracking” setup, through which a sample’s attenuation, phase (refraction) and scattering properties can be measured from a single frame, providing three complementary contrast channels. Up to now, such setups required the sample to be stepped at each rotation angle to sample signals at an adequate rate, to prevent resolution losses, anisotropic resolution, and under-sampling artefacts. However, the need for stepping necessitated a step-and-shoot implementation, which is affected by motors’ overheads and increases the total scan time. By contrast, our proposed scheme, by which continuous horizontal and vertical translations of the sample are integrated with its rotation (leading to a “cycloidal-spiral” trajectory), is fully compatible with continuous scanning (flyscans). This leads to greatly reduced scan times while largely preserving image quality and isotropic resolution.
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Dec 2022
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I13-1-Coherence
I13-2-Diamond Manchester Imaging
Optics
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Open Access
Abstract: I13 is a 250 m long hard X-ray beamline for imaging and coherence experiments at the Diamond Light Source [1]. The beamline comprises two independent experimental branches: one for imaging in direct space using X-ray microscopy and one for imaging in reciprocal space using coherent imaging techniques. The mechanical stability is very important for implementation of increased capabilities at latest generation of long beamlines [2]. Therefore, the beam stability monitoring is essential part of the day-to-day operation of the beamlines as well as for analysis of mechanical instability sources for the Diamond II upgrade. In this paper we present the setup developed to measure mechanical stability of beamline based on optical autocollimator.
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Dec 2022
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I13-2-Diamond Manchester Imaging
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Diamond Proposal Number(s):
[22575]
Open Access
Abstract: Nature-inspired material design is driven by superior properties found in natural architected materials and enabled by recent developments in additive manufacturing and machine learning. Existing approaches to push design beyond biomimicry typically use supervised deep learning algorithms to predict and optimize properties based on experimental or simulation data. However, these methods constrain generated material designs to abstracted labels and to “black box” outputs that are only indirectly manipulable. Here we report an alternative approach using an unsupervised generative adversarial network (GAN) model. Training the model on unlabeled data constructs a latent space free of human intervention, which can then be explored through seeding, image encoding, and vector arithmetic to control specific parameters of de novo generated material designs and to push them beyond training data distributions for broad applicability. We illustrate this end-to-end with new materials inspired by leaf microstructures, showing how biological 2D structures can be used to develop novel architected materials in 2 and 3 dimensions. We further utilize a genetic algorithm to optimize generated microstructures for mechanical properties, operating directly on the latent space. This approach allows for transfer of information across manifestations using the latent space as mediator, opening new avenues for exploration of nature-inspired materials.
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Nov 2022
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I13-2-Diamond Manchester Imaging
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Diamond Proposal Number(s):
[19322]
Abstract: In-line phase contrast synchrotron tomography combined with in situ mechanical loading enables the characterisation of soft tissue micromechanics via digital volume correlation (DVC) within whole organs. Optimising scan time is important for reducing radiation dose from multiple scans and to limit sample movement during acquisition. Also, although contrasted edges provided by in-line phase contrast tomography of soft tissues are useful for DVC, the effect of phase contrast imaging on its accuracy has yet to be investigated. Due to limited time at synchrotron facilities, scan parameters are often decided during imaging and their effect on DVC accuracy is not fully understood. Here, we used previously published data of intervertebral disc phase contrast tomography to evaluate the influence of i) fibrous image texture, ii) number of projections, iii) tomographic reconstruction method, and iv) phase contrast propagation distance on DVC results. A greater understanding of how image texture influences optimal DVC tracking was obtained by visualising objective function mapping, enabling tracking inaccuracies to be identified. When reducing the number of projections, DVC was minimally affected by image high frequency noise but with a compromise in accuracy. Iterative reconstruction methods improved image signal-to-noise and consequently significantly lowered DVC displacement uncertainty. Propagation distance was shown to affect DVC accuracy. Consistent DVC results were achieved within a propagation distance range which provided contrast to the smallest scale features, where; too short a distance provided insufficient features to track, whereas too long led to edge effect inconsistencies, particularly at greater deformations. Although limited to a single sample type and image setup, this study provides general guidelines for future investigations when optimising image quality and scan times for in situ phase contrast x-ray tomography of fibrous connective tissues.
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Nov 2022
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I13-2-Diamond Manchester Imaging
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Francesca
Palermo
,
Nicola
Pieroni
,
Alessia
Sanna
,
Benedetta
Parodi
,
Consuelo
Venturi
,
Ginevra
Begani Provinciali
,
Lorenzo
Massimi
,
Laura
Maugeri
,
Gian Paolo
Marra
,
Elena
Longo
,
Lorenzo
D’amico
,
Giulia
Saccomano
,
Jonathan
Perrin
,
Giuliana
Tromba
,
Inna
Bukreeva
,
Michela
Fratini
,
Giuseppe
Gigli
,
Nicole
Kerlero De Rosbo
,
Alessia
Cedola
Diamond Proposal Number(s):
[23997]
Open Access
Abstract: The 3D complexity of biological tissues and intricate structural-functional connections call for state-of-the-art X-ray imaging approaches to overcome limitations of classical imaging. Unlike other imaging techniques, X-ray phase-contrast tomography (XPCT) offers a highly sensitive 3D imaging approach to investigate different disease-relevant networks at levels ranging from single cell through to intact organ. We present here a concomitant study of the evolution of tissue damage and inflammation in different organs affected by the disease in the murine model for multiple sclerosis, a demyelinating autoimmune disorder of the central nervous system. XPCT identifies and monitors structural and cellular alterations throughout the central nervous system, but also in the gut, and eye, of mice induced to develop multiple sclerosis-like disease and sacrificed at pre-symptomatic and symptomatic time points. This study details the sequential evolution of multi-organ damages in the murine multiple sclerosis model showing the disease development and progression which is of relevance for the human case.
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Nov 2022
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I13-2-Diamond Manchester Imaging
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Diamond Proposal Number(s):
[16557]
Open Access
Abstract: Skeletal muscle contractions are critical for normal skeletal growth and morphogenesis but it is unclear how the detrimental effects of absent muscle on the bones and joints change over time. Joint shape and cavitation as well as rudiment length and mineralisation were assessed in multiple rudiments at two developmental stages [Theiler stage (TS)24 and TS27] in the splotch-delayed “muscle-less limb” mouse model and littermate controls. Chondrocyte morphology was quantified in 3D in the distal humerus at the same stages. As development progressed, the effects of absent muscle on all parameters except for cavitation become less severe. All major joints in muscle-less limbs were abnormally shaped at TS24, while, by TS27, most muscle-less limb joint shapes were normal or nearly normal. In contrast, any joints that were fused at TS24 did not cavitate by TS27. At TS24, chondrocytes in the distal humerus were significantly smaller in the muscle-less limbs than in controls, while by TS27, chondrocyte volume was similar between the two groups, offering a cell-level mechanism for the partial recovery in shape of muscle-less limbs. Mineralisation showed the most pronounced changes over gestation. At TS24, all muscle-less rudiments studied had less mineralisation than the controls, while at TS27, muscle-less limb rudiments had mineralisation extents equivalent to controls. In conclusion, the effects of muscle absence on prenatal murine skeletogenesis reduced in severity over gestation. Understanding how mammalian bones and joints continue to develop in an environment with abnormal fetal movements provides insights into conditions including hip dysplasia and arthrogryposis.
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Nov 2022
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I13-2-Diamond Manchester Imaging
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Diamond Proposal Number(s):
[20984]
Open Access
Abstract: X-ray synchrotron radiation allows the investigation of many physical processes in unprecedented ways. One application, important to the fine chemicals industry, is characterizing the early stages of crystallization. To aid chemical engineers working in this area we developed the CrystalGrowthTracker package. It allows crystals to be found in videos and their growth rates measured, see Figure 1. We hope that this work can provide the basis for fully automated and 3D systems.
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Nov 2022
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