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Instruments / Technical Area	Publication Details	Published
B16-Test Beamline I12-JEEP: Joint Engineering, Environmental and Processing	Practical implementations of speckle-based phase-retrieval methods in Python and GPU for tomography Nghia T. Vo , Hongchang Wang , Lingfei Hu , Tunhe Zhou , Marie-~christine Zdora , Hans Deyhle , Robert C. Atwood , Michael Drakopoulos SPIE Optical Engineering + Applications (2022) DOI: 10.1117/12.2636834 Diamond Proposal Number(s): [27987, 20763, 27144, 31131] Show Abstract ▼ Abstract: X-ray phase-contrast tomography (X-PCT) techniques are capable of imaging samples with small differences in densities. They enable scientists to study biological or medical samples using high energy X-rays, which means less X-ray absorption and less sample damage, with high contrast quality. One branch of these techniques known as speckle-based methods have been well developed and demonstrated on real applications by different groups of developers using their own codes. However, there is lack of collective effort to package these methods into an open-source software which is easy-to-install, easy-to-use, well-documented, and optimized for speed. Such software is crucial to make the X-PCT techniques accessible to generic users and become regular tools. This report demonstrates the effort which implements speckle-based phase-retrieval methods in Python and GPU.	Oct 2022
DIAD-Dual Imaging and Diffraction Beamline	Flexible positioning of a large area detector using an industrial robot Christina Reinhard , Michael Drakopoulos , Christopher M. Charlesworth , Andrew James , Hiten Patel , Paul Tutthill , Davide Crivelli , Hans Deyhle , Sharif I. Ahmed Journal Of Synchrotron Radiation 29, 1004 - 1013 DOI: 10.1107/S1600577522006300 Diamond Proposal Number(s): [30995] Open Access Show Abstract ▼ Abstract: The DIAD beamline for Dual Imaging and Diffraction at Diamond Light Source has opted to use an industrial robot to position its Dectris Pilatus 2M CdTe diffraction detector. This setup was chosen to enable flexible positioning of the detector in a quarter-sphere around the sample position whilst reliably holding the large weight of 139 kg of detector, detector mount and cabling in a stable position. Metrology measurements showed that the detector can be positioned with a linear repeatability of <19.7 µm and a rotational repeatability of <16.3 µrad. The detector position stays stable for a 12 h period with <10.1 µm of movement for linear displacement and <3.8 µrad for rotational displacement. X-ray diffraction from calibration samples confirmed that the robot is sufficiently stable to resolve lattice d-spacings within the instrumental broadening given by detector position and beam divergence.	Jul 2022
Metrology	Effects of fast X-Ray cone-beam tomographic measurement on dimensional metrology Charalambos Rossides , Hossein Towsyfyan , Ander Biguri , Hans Deyhle , Reuben Lindroos , Mark Mavrogordato , Richard Boardman , Wenjuan Sun , Thomas Blumensath Metrologia DOI: 10.1088/1681-7575/ac7926 Open Access Show Abstract ▼ Abstract: X-ray computed tomography (XCT) is increasingly used for dimensional metrology, where it can offer accurate measurements of internal features that are not accessible with other techniques. However, XCT scanning can be relatively slow, which often prevents routine uptake for many applications. This paper explores the feasibility of improving the speed of XCT measurements whilst maintaining the quality of the dimensional measurements derived from reconstructed volumes. In particular, we compare two approaches to fast XCT acquisition, the use of fewer XCT projections as well as the use of shortened x-ray exposure times for each projection. The study shows that the additional Poisson noise produced by reducing the exposure for each projection has significantly less impact on dimensional measurements compared to the artefacts associated with strategies that take fewer projection images, leading to about half the measurement error variability. Advanced reconstruction algorithms such as the conjugate gradient least squares method or total variation constrained approaches, are shown to allow further improvements in measurement speed, though this can come at the cost of increased measurement bias (e.g. 2.8 % increase in relative error in one example) and variance (e.g. 25 % in the same example).	Jun 2022
DIAD-Dual Imaging and Diffraction Beamline	Beamline K11 DIAD: a new instrument for dual imaging and diffraction at Diamond Light Source Christina Reinhard , Michael Drakopoulos , Sharif I. Ahmed , Hans Deyhle , Andrew James , Christopher M. Charlesworth , Martin Burt , John Sutter , Steven Alexander , Peter Garland , Thomas Yates , Russell Marshall , Ben Kemp , Edmund Warrick , Armando Pueyos , Ben Bradnick , Maurizio Nagni , A. Douglas Winter , Jacob Filik , Mark Basham , Nicola Wadeson , Oliver N. F. King , Navid Aslani , Andrew J. Dent Journal Of Synchrotron Radiation 28 DOI: 10.1107/S1600577521009875 Open Access Show Abstract ▼ Abstract: The Dual Imaging and Diffraction (DIAD) beamline at Diamond Light Source is a new dual-beam instrument for full-field imaging/tomography and powder diffraction. This instrument provides the user community with the capability to dynamically image 2D and 3D complex structures and perform phase identification and/or strain mapping using micro-diffraction. The aim is to enable in situ and in operando experiments that require spatially correlated results from both techniques, by providing measurements from the same specimen location quasi-simultaneously. Using an unusual optical layout, DIAD has two independent beams originating from one source that operate in the medium energy range (7–38 keV) and are combined at one sample position. Here, either radiography or tomography can be performed using monochromatic or pink beam, with a 1.4 mm × 1.2 mm field of view and a feature resolution of 1.2 µm. Micro-diffraction is possible with a variable beam size between 13 µm × 4 µm and 50 µm × 50 µm. One key functionality of the beamline is image-guided diffraction, a setup in which the micro-diffraction beam can be scanned over the complete area of the imaging field-of-view. This moving beam setup enables the collection of location-specific information about the phase composition and/or strains at any given position within the image/tomography field of view. The dual beam design allows fast switching between imaging and diffraction mode without the need of complicated and time-consuming mode switches. Real-time selection of areas of interest for diffraction measurements as well as the simultaneous collection of both imaging and diffraction data of (irreversible) in situ and in operando experiments are possible.	Nov 2021
	Accuracy of commercial intraoral scanners Mattia Sacher , Georg Schulz , Hans Deyhle , Kurt Jäger , Bert Muller Journal Of Medical Imaging 8 DOI: 10.1117/1.JMI.8.3.035501 Open Access Show Abstract ▼ Abstract: Purpose: In dental offices, there is a trend replacing conventional silicone impressions and plaster cast models by imaging data of intraoral scanners to map the denture and surrounding tissues. The aim of the study is the analysis of the accuracy of selected commercially available scanners. The accuracy is considered as the main drawback in comparison to the conventional approach. Approach: We evaluated the reproduction performance of five optical scanners by a direct comparison with high-resolution hard x-ray computed tomography data, all obtained from a polyetheretherketone model with similarity to a full-arch upper jaw. Results: Using the software GOM Inspect (GOM GmbH, Braunschweig, Germany), we could classify the intraoral scanners into two groups. The more accurate instruments gave rise to the following precision values: 35 μm (TRIOS® 3, 3shape, Copenhagen, Denmark), 43 μm (CS 3600, Carestream, Atlanta, Georgia), and 46 μm (3M™ True Definition Scanner, 3M ESPE, St. Paul, Minnesota). The less precise systems yielded 93 μm (Medit i500, Medit corp., Seongbuk-gu, South Korea) and 97 μm (Emerald™, Planmeca Oy, Helsinki, Finland). Conclusions: The selected scanners are suitable for single crowns, small bridges, and separate quadrants prostheses. Scanners based on triangulation are hardly appropriate for full-arch prostheses. Besides precision, however, the choice of the scanner depends on scanning time, intraoral-camera size, and the user’s learning curve. The developed protocol, which includes three-dimensional (3D) imaging and advanced computational tools for the registration with the design data, will be increasingly used in geometrical metrology by nondestructive procedures to perform dimensional measurements with micrometer precision and is capable for detailed 3D geometrical models reconstruction.	May 2021
I13-2-Diamond Manchester Imaging	Optimizing contrast and spatial resolution in hard x-ray tomography of medically relevant tissues Griffin Rodgers , Georg Schulz , Hans Deyhle , Willy Kuo , Christoph Rau , Timm Weitkamp , Bert Muller Applied Physics Letters 116 DOI: 10.1063/1.5133742 Diamond Proposal Number(s): [19829, 20746] Show Abstract ▼ Abstract: Hard x-ray tomography with Paganin's widespread single-distance phase retrieval filter improves the contrast-to-noise ratio (CNR) while reducing spatial resolution (SR). We demonstrate that a Gaussian filter provided larger CNR at high SR with interpretable density measurements for two medically relevant soft tissue samples. Paganin's filter produced larger CNR at low SR, though a priori assumptions were generally false and image quality gains diminish for CNR > 1. Therefore, simple absorption measurements of low-Z specimens combined with Gaussian filtering can provide improved image quality and model-independent density measurements compared to single-distance phase retrieval.	Jan 2020
I13-2-Diamond Manchester Imaging	Correction of phase wrapping artifacts in grating-based hard X-ray tomography Griffin Rodgers , Georg Schulz , Hans Deyhle , Shashidhara Marathe , Christos Bikis , Bert Muller , Timm Weitkamp Developments in X-Ray Tomography XII DOI: 10.1117/12.2530709 Diamond Proposal Number(s): [19829] Show Abstract ▼ Abstract: X-ray grating interferometry (XGI) is a phase-contrast imaging technique that allows for a quantitative measurement of the refractive index with high density resolution in a model-independent manner—i.e. without a priori knowledge of the specimen composition. However, the retrieval of the X-ray wavefront phase shift relies on the accurate measurement of the interference pattern phase shift, making XGI vulnerable to phase wrapping when the interference pattern phase shift, related to the derivative of the wavefront phase shift, is large. Standard procedure for avoiding phase wrapping involves submerging the specimen in a water bath to reduce the mismatch of the index of refraction at the boundaries, but this requires a top-down rotation stage and is susceptible to gas bubble formation inside the water bath. Our team has presented an algorithm to remove phase wrapping artifacts for cylindrically shaped specimens that is applied to the phase-retrieved sinogram. This algorithm models and replaces phase-wrapped data to prevent the spread of “cupping” artifacts due to the integration of the differential phase during reconstruction. We give a criterion for selecting the modeling parameters so that the resulting measurement of the index of refraction matches the results of measurements without phase wrapping. We also apply this technique to cases where phase wrapping occurs at multiple interfaces. This algorithm allows for XGI measurements without a water bath and top-down rotation stage at synchrotron and laboratory facilities, especially as sensitivity increases.	Sep 2019
I13-2-Diamond Manchester Imaging	Sensitivity comparison of absorption and grating-based phase tomography of paraffin-embedded human brain tissue Christos Bikis , Griffin Rodgers , Hans Deyhle , Peter Thalmann , Alexander Hipp , Felix Beckmann , Timm Weitkamp , Stamatios Theocharis , Christoph Rau , Georg Schulz , Bert Muller Applied Physics Letters 114 DOI: 10.1063/1.5085302 Diamond Proposal Number(s): [19829] Open Access Show Abstract ▼ Abstract: Advances in high-resolution hard X-ray computed tomography have led to the field of virtual histology to complement histopathological analyses. Phase-contrast modalities have been favored because, for soft tissues, the real part of the refractive index is orders of magnitude greater than the imaginary part. Nevertheless, absorption-contrast measurements of paraffin-embedded tissues have provided exceptionally high contrast combined with a submicron resolution. In this work, we present a quantitative comparison of phase tomography using synchrotron radiation-based X-ray double grating interferometry and conventional synchrotron radiation-based computed tomography in the context of histopathologically relevant paraffin-embedded human brain tissue. We determine the complex refractive index and compare the contrast-to-noise ratio (CNR) of each modality, accounting for the spatial resolution and optimizing the photon energy for absorption tomography. We demonstrate that the CNR in the phase modality is 1.6 times higher than the photon-energy optimized and spatial resolution-matched absorption measurements. We predict, however, that a further optimized phase tomography will provide a CNR gain of 4. This study seeks to boost the discussion of the relative merits of phase and absorption modalities in the context of paraffin-embedded tissues for virtual histology, highlighting the importance of optimization procedures for the two complementary modes and the trade-off between spatial and density resolution, not to mention the disparity in data acquisition and processing.	Feb 2019
I13-2-Diamond Manchester Imaging	Advanced X-ray phase-contrast and dark-field imaging with the unified modulated pattern analysis (UMPA) Marie-Christine Zdora , Pierre Thibault , Hans Deyhle , Joan Vila-Comamala , Willy Kuo , Christoph Rau , Irene Zanette Microscopy And Microanalysis 24, 22 - 23 14th International Conference on X-ray Microscopy (XRM2018) DOI: 10.1017/S1431927618012539	Aug 2018
I13-2-Diamond Manchester Imaging	Visualization and segmentation of cells in unstained paraffin-embedded cerebral tissue Hans Deyhle , Christos Bikis , Anna Khimchenko , Gabriel Schweighauser , Jiirgen Hench , Georg Schulz , Bert Muller , Simone E. Hieber Microscopy And Microanalysis 24, 408 - 409 Microscopy & Microanalysis 2018 DOI: 10.1017/S1431927618014320	Aug 2018

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