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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
I13-2-Diamond Manchester Imaging	InSegtCone: interactive segmentation of crystalline cones in compound eyes Pierre Tichit , Tunhe Zhou , Hans Martin Kjer , Vedrana Andersen Dahl , Anders Bjorholm Dahl , Emily Baird Bmc Zoology 7 DOI: 10.1186/s40850-021-00101-w Diamond Proposal Number(s): [13848, 16052] Open Access Show Abstract ▼ Abstract: Background: Understanding the diversity of eyes is crucial to unravel how different animals use vision to interact with their respective environments. To date, comparative studies of eye anatomy are scarce because they often involve time-consuming or inefficient methods. X-ray micro-tomography (micro-CT) is a promising high-throughput imaging technique that enables to reconstruct the 3D anatomy of eyes, but powerful tools are needed to perform fast conversions of anatomical reconstructions into functional eye models. Results: We developed a computing method named InSegtCone to automatically segment the crystalline cones in the apposition compound eyes of arthropods. Here, we describe the full auto-segmentation process, showcase its application to three different insect compound eyes and evaluate its performance. The auto-segmentation could successfully label the full individual shapes of 60-80% of the crystalline cones and is about as accurate and 250 times faster than manual labelling of the individual cones. Conclusions: We believe that InSegtCone can be an important tool for peer scientists to measure the orientation, size and dynamics of crystalline cones, leading to the accurate optical modelling of the diversity of arthropod eyes with micro-CT.	Feb 2022
B16-Test Beamline Optics	Hard X-ray ptychography for optics characterization using a partially coherent synchrotron source Thomas E. J. Moxham , Aaron Parsons , Tunhe Zhou , Lucia Alianelli , Hongchang Wang , David Laundy , Vishal Dhamgaye , Oliver J. L. Fox , Kawal Sawhney , Alexander M. Korsunsky Journal Of Synchrotron Radiation 27 DOI: 10.1107/S1600577520012151 Open Access Show Abstract ▼ Abstract: Ptychography is a scanning coherent diffraction imaging technique which provides high resolution imaging and complete spatial information of the complex electric field probe and sample transmission function. Its ability to accurately determine the illumination probe has led to its use at modern synchrotrons and free-electron lasers as a wavefront-sensing technique for optics alignment, monitoring and correction. Recent developments in the ptychography reconstruction process now incorporate a modal decomposition of the illuminating probe and relax the restriction of using sources with high spatial coherence. In this article a practical implementation of hard X-ray ptychography from a partially coherent X-ray source with a large number of modes is demonstrated experimentally. A strongly diffracting Siemens star test sample is imaged using the focused beam produced by either a Fresnel zone plate or beryllium compound refractive lens. The recovered probe from each optic is back propagated in order to plot the beam caustic and determine the precise focal size and position. The power distribution of the reconstructed probe modes also allows the quantification of the beams coherence and is compared with the values predicted by a Gaussian–Schell model and the optics exit intensity.	Nov 2020
Optics	Applications of laboratory-based phase-contrast imaging using speckle tracking technique towards high energy x-rays Tunhe Zhou , Fei Yang , Rolf Kaufmann , Hongchang Wang Journal Of Imaging 4 DOI: 10.3390/jimaging4050069 Open Access Show Abstract ▼ Abstract: The recently developed speckle-based technique is a promising candidate for laboratory-based X-ray phase-contrast imaging due to its compatibility with polychromatic X-rays, multi-modality and flexibility. Previously, successful implementations of the method on laboratory systems have been shown mostly with energies less than 20 keV on samples with materials like soft tissues or polymer. Higher energy X-rays are needed for penetrating materials with a higher atomic number or that are thicker in size. A first demonstration using high energy X-rays was recently given. Here, we present more potential application examples, i.e., a multi-contrast imaging of an IC chip and a phase tomography of a mortar sample, at an average photon energy of 40 keV using a laboratory X-ray tube. We believe the results demonstrate the applicability of this technique in a wide range of fields for non-destructive examination in industry and material science.	May 2018

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