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Instruments / Technical Area	Publication Details	Published
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
B22-Multimode InfraRed imaging And Microspectroscopy	Biochemical Characterization of Single Weathering Hyphae of Paxillus involutus Using CLSM and Synchrotron Based µFTIR Achim Schmalenberger , Andrew Bray , Adele Duran , Jonathan Leake , Gianfelice Cinque , Mark Frogley , Jacob Filik , Jacek Pijanka , Steeve Bonneville , Liane G Benning , Maria Romero-González Goldschmidt 2011 Show Abstract ▼ Abstract: ectomycorrhizal fungi; nutrient mobilization; Confocal Laser Scanning Microscopy; synchrotron based micro Fourier Transform Infrared spectroscopy.	Jul 2011
B22-Multimode InfraRed imaging And Microspectroscopy Optics	Broadband near-field infrared spectromicroscopy using photothermal probes and synchrotron radiation Paul M. Donaldson , Chris S. Kelley , Mark D. Frogley , Jacob Filik , Katia Wehbe , Gianfelice Cinque Optics Express 24 (3), 1852-1864 DOI: 10.1364/OE.24.001852 Diamond Proposal Number(s): [8960, 10407] Open Access Show Abstract ▼ Abstract: In this paper, we experimentally demonstrate the use of infrared synchrotron radiation (IR-SR) as a broadband source for photothermal near-field infrared spectroscopy. We assess two methods of signal transduction; cantilever resonant thermal expansion and scanning thermal microscopy. By means of rapid mechanical chopping (50-150 kHz), we modulate the IR-SR at rates matching the contact resonance frequencies of atomic force microscope (AFM) cantilevers, allowing us to record interferograms yielding Fourier transform infrared (FT-IR) photothermal absorption spectra of polystyrene and cyanoacrylate films. Complementary offline measurements using a mechanically chopped CW IR laser confirmed that the resonant thermal expansion IR-SR measurements were below the diffraction limit, with a spatial resolution better than 500 nm achieved at a wavelength of 6 μm, i.e. λ/12 for the samples studied. Despite achieving the highest signal to noise so far for a scanning thermal microscopy measurement under conditions approaching near-field (dictated by thermal diffusion), the IR-SR resonant photothermal expansion FT-IR spectra measured were significantly higher in signal to noise in comparison with the scanning thermal data.	Jan 2016
Optics	Calculating temperature-dependent X-ray structure factors of α-quartz with an extensible Python 3 package John P. Sutter , James Pittard , Jacob Filik , Alfred Q. R. Baron Journal Of Applied Crystallography 55 DOI: 10.1107/S1600576722005945 Open Access Show Abstract ▼ Abstract: The design of X-ray optics based on diffraction from crystals depends on the accurate calculation of the structure factors of their Bragg reflections over a wide range of temperatures. In general, the temperature dependence of the lattice parameters, the atomic positions and the atomic thermal vibrations is both anisotropic and nonlinear. Implemented here is a software package for precise and flexible calculation of structure factors for dynamical diffraction. α-Quartz is used as an example because it presents the challenges mentioned above and because it is being considered for use in high-resolution X-ray spectroscopy. The package is designed to be extended easily to other crystals by adding new material files, which are kept separate from the package's stable core. Python 3 was chosen as the language to allow the easy integration of this code into existing packages. The importance of a correct anisotropic treatment of the atomic thermal vibrations is demonstrated by comparison with an isotropic Debye model. Discrepancies between the two models can be as much as 5% for strong reflections and considerably larger (even to the level of 100%) for weak reflections. A script for finding Bragg reflections that backscatter X-rays of a given energy within a given temperature range is demonstrated. The package and example scripts are available on request. Also discussed, in detail, are the various conventions related to the proper description of chiral quartz.	Aug 2022
B18-Core EXAFS I18-Microfocus Spectroscopy	Chemical imaging of single catalyst particles with scanning μ-XANES-CT and μ-XRF-CT S. W. T. Price , K. Ignatyev , K. Geraki , M. Basham , J. Filik , N. T. Vo , P. T. Witte , A. M. Beale , J. F. W. Mosselmans Physical Chemistry Chemical Physics DOI: 10.1039/C4CP04488F PMID: 25407850 Diamond Proposal Number(s): [4939] Show Abstract ▼ Abstract: The physicochemical state of a catalyst is a key factor in determining both activity and selectivity; however these materials are often not structurally or compositionally homogeneous. Here we report on the 3-dimensional imaging of an industrial catalyst, Mo- promoted colloidal Pt supported on carbon. The distribution of both the active Pt species and Mo promoter have been mapped over a single particle of catalyst using microfocus X-ray Fluorescence computed tomography. X-ray absorption near edge spectroscopy (XANES) and extended X-ray absorption fine structure revealed a mixed local coordination environment, including the presence of both metallic Pt clusters and Pt chloride species, but also no direct interaction between the catalyst and Mo promoter. We also report on the benefits of scanning μ-XANES computed tomography for chemical imaging, allowing for 2- and 3-dimensional mapping of the local electronic and geometric environment, in this instance for both the Pt catalyst and Mo promoter throughout the catalyst particle.	Nov 2014
I06-Nanoscience	Data Analysis WorkbeNch (DAWN) Mark Basham , Jacob Filik , Michael Wharmby , Peter Chang , Baha El Kassaby , Matt Gerring , Jun Aishima , Karl Levik , Bill Pulford , Irakli Sikharulidze , Duncan Sneddon , Matthew Webber , Sarnjeet Dhesi , Francesco Maccherozzi , Olof Svensson , Sandor Brockhauser , Gabor Náray , Alun Ashton Journal Of Synchrotron Radiation 22, 828-838 DOI: 10.1107/S1600577515002283 PMID: 25931106 Open Access Show Abstract ▼ Abstract: Synchrotron light source facilities worldwide generate terabytes of data in numerous incompatible data formats from a wide range of experiment types. The Data Analysis WorkbeNch (DAWN) was developed to address the challenge of providing a single visualization and analysis platform for data from any synchrotron experiment (including single-crystal and powder diffraction, tomography and spectroscopy), whilst also being sufficiently extensible for new specific use case analysis environments to be incorporated (e.g. ARPES, PEEM). In this work, the history and current state of DAWN are presented, with two case studies to demonstrate specific functionality. The first is an example of a data processing and reduction problem using the generic tools, whilst the second shows how these tools can be targeted to a specific scientifc area.	May 2015
B22-Multimode InfraRed imaging And Microspectroscopy	Electric field standing wave artefacts in FTIR micro-spectroscopy of biological materials Jacob Filik , Mark D. Frogley , Jacek K. Pijanka , Katia Wehbe , Gianfelice Cinque Analyst DOI: 10.1039/c2an15995c PMID: 22231204 Show Abstract ▼ Abstract: FTIR absorption micro-spectroscopy is a widely used, powerful technique for analysing biological materials. In principle it is a straightforward linear absorption spectroscopy, but it can be affected by artefacts that complicate the interpretation of the data. In this article, artefacts produced by the electric-field standing-wave (EFSW) in micro-reflection-absorption (transflection) spectroscopy are investigated. An EFSW is present at reflective metallic surfaces due to the interference of incident and reflected light. The period of this standing wave is dependent on the wavelength of the radiation and can produce non-linear changes in absorbance with increasing sample thickness (non-Beer–Lambert like behaviour). A protein micro-structure was produced as a simple experimental model for a biological cell and used to evaluate the differences between FTIR spectra collected in transmission and transflection. By varying the thickness of the protein samples, the relationship between the absorbance and sample thickness in transflection was determined, and shown to be consistent with optical interference due to the EFSW coupled with internal reflection from the sample top surface. FTIR spectral image data from MCF 7 breast adenocarcinoma cells was then analysed to determine the severity of the EFSW artefact in data from a real sample. The results from these measurements confirmed that the EFSW artefact has a profound effect on transflection spectra, and in this case the main spectral variations were related to the sample thickness rather than any biochemical differences.	Jan 2012
B22-Multimode InfraRed imaging And Microspectroscopy	High resolution functional group mapping of fungi on a mineral surface Andrew Bray , Steeve Bonneville , Gianfelice Cinque , Mark Frogley , Katia Wehbe , Jacob Filik , A Duran , Achim Schmalenberger , Maria Romero-González , Liane G Benning GEOCHIMICA ET COSMOCHIMICA ACTA	Aug 2010
B22-Multimode InfraRed imaging And Microspectroscopy	Isolating stem cells in the inter-follicular epidermis employing synchrotron radiation-based Fourier-transform infrared microspectroscopy and focal plane array imaging Imran Patel , Wesley Harrison , Jemma G. Kerns , Jacob Filik , Katia Wehbe , Paul L. Carmichael , Andrew D. Scott , Mike P. Philpott , Mark D. Frogley , Gianfelice Cinque , Francis L. Martin Analytical And Bioanalytical Chemistry 404, 1745 - 1758 DOI: 10.1007/s00216-012-6314-y Show Abstract ▼ Abstract: Normal function and physiology of the epidermis is maintained by the regenerative capacity of this tissue via adult stem cells (SCs). However, definitive identifying markers for SCs remain elusive. Infrared (IR) spectroscopy exploits the ability of cellular biomolecules to absorb in the mid-IR region (λ = 2.5–25 μm), detecting vibrational transitions of chemical bonds. In this study, we exploited the cell’s inherent biochemical composition to discriminate SCs of the inter-follicular skin epidermis based on IR-derived markers. Paraffin-embedded samples of human scalp skin (n = 4) were obtained, and 10-μm thick sections were mounted for IR spectroscopy. Samples were interrogated in transmission mode using synchrotron radiation-based Fourier-transform IR (FTIR) microspectroscopy (15 × 15 μm) and also imaged employing globar-source FTIR focal plane array (FPA) imaging (5.4 × 5.4 μm). Dependent on the location of derived spectra, wavenumber–absorbance/intensity relationships were examined using unsupervised principal component analysis. This approach showed clear separation and spectral differences dependent on cell type. Spectral biomarkers concurrently associated with segregation of SCs, transit-amplifying cells and terminally-differentiated cells of epidermis were primarily PO2− vibrational modes (1,225 and 1,080 cm−1), related to DNA conformational alterations. FPA imaging coupled with hierarchical cluster analysis also indicated the presence of specific basal layer cells potentially originating from the follicular bulge, suggested by co-clustering of spectra. This study highlights PO2− vibrational modes as potential putative SC markers.	Oct 2012
Data acquisition	Mapping developments at Diamond Rob Walton , Alun Ashton , Mark Basham , Peter Chang , Tom Cobb , S Da Graca , Andrew Dent , Jacob Filik , Matt Gerring , Charles Mita , James Mudd , C M Palmer , U Pederson , Paul Quinn , Nick Rees ICALEPCS2015 DOI: 10.18429/JACoW-ICALEPCS2015-THHB3O01 Open Access Show Abstract ▼ Abstract: Many synchrotron beamlines offer some form of continuous scanning for either energy scanning or sample mapping. However, this is normally done on an ad-hoc beamline by beamline basis. Diamond has recently embarked on an ambitious project to define how to implement continuous scanning as the standard way of doing virtually all mapping tasks on beamlines. The project is split into four main areas: 1) User interfaces to describe the mapping process in a scientifically relevant way, generating a scan description that can be used later; 2) The physical process of scanning and coordinating hardware motion and detector data capture across the beamline; 3) Capture of the detector data and all the associated meta-data to disk, deciding and describing the layout of the file (or files) for the main use cases; 4) Display and analysis of live data and display of processed data. In order to achieve this common approach across beamlines, the standard software used throughout the facility (Delta Tau motor controllers, EPICS, GDA and DAWN), has been built on.	Oct 2015

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