Data Analysis WorkbeNch (DAWN) Basham, Mark; Filik, Jacob; Wharmby, Michael T. ...
Journal of synchrotron radiation,
20/May , Volume:
22, Issue:
3
Journal Article
Peer reviewed
Open access
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 scientific area.
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FZAB, GIS, IJS, IZUM, KILJ, NLZOH, NUK, OILJ, PILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK
The technique of drop coating deposition Raman (DCDR) spectroscopy has been shown to be a highly reproducible and sensitive method of obtaining Raman spectra from low concentration protein solutions. ...This study assesses the ability of DCDR to analyse changes in the relative protein concentrations of aqueous tertiary protein mixtures, with protein levels similar to that found in human tear fluid. The three proteins used to make the mixtures were lysozyme, lactoferrin and albumin. The combination of DCDR spectroscopy and principal components analysis is found to be sensitive enough to detect small changes in the relative protein concentrations, from very small sample volumes (1.5 microl). With certain mixtures it was found that the deposition of proteins was not homogeneous across the width of the ring, but averaging spectra taken at different positions could compensate for this. Principal components regression was able to predict the protein concentrations of test solutions with a good degree of accuracy (root-mean-square errors of prediction of 0.083, 0.112, and 0.082 mg ml(-1) or 8.3, 11.2 and 8.2% of the mean concentration value, for lysozyme, lactoferrin and albumin concentrations respectively). The results of this study suggest that DCDR spectroscopy could be a simple, fast, near-patient technique capable of assisting the diagnosis of ocular infection.
The study of individual cells with infrared (IR) microspectroscopy often requires living cells to be cultured directly onto a suitable substrate. The surface effect of the specific substrates on the ...cell growth—viability and associated biochemistry—as well as on the IR analysis—spectral interference and optical artifacts—is all too often ignored. Using the IR beamline, MIRIAM (Diamond Light Source, UK), we show the importance of the substrate used for IR absorption spectroscopy by analyzing two different cell lines cultured on a range of seven optical substrates in both transmission and reflection modes. First, cell viability measurements are made to determine the preferable substrates for normal cell growth. Successively, synchrotron radiation IR microspectroscopy is performed on the two cell lines to determine any genuine biochemically induced changes or optical effect in the spectra due to the different substrates. Multivariate analysis of spectral data is applied on each cell line to visualize the spectral changes. The results confirm the advantage of transmission measurements over reflection due to the absence of a strong optical standing wave artifact which amplifies the absorbance spectrum in the high wavenumber regions with respect to low wavenumbers in the mid-IR range. The transmission spectra reveal interference from a more subtle but significant optical artifact related to the reflection losses of the different substrate materials. This means that, for comparative studies of cell biochemistry by IR microspectroscopy, it is crucial that all samples are measured on the same substrate type.
Figure
Cell separation by PCA due to the refractive index of the substrate used, revealing transmission artifact.
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DOBA, EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, IZUM, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UILJ, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
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-BeerLambert 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.
This article describes the non-linear, wavelength dependent, relationship between absorbance and sample thickness produced by the electric-field standing wave in micro-reflection-absorption (transflection) FTIR spectroscopy.
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.
A Python 3 software package for precise calculation of X‐ray structure factors of α‐quartz over a wide temperature range is presented. α‐Quartz was chosen because of its practical application in high‐resolution X‐ray spectroscopy, but this software package can be easily extended to other crystals.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
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.
This manuscript presents the current status and technical details of the Spectroscopy Village at Diamond Light Source. The Village is formed of four beamlines: I18, B18, I20‐Scanning and I20‐EDE. The ...village provides the UK community with local access to a hard X‐ray microprobe, a quick‐scanning multi‐purpose XAS beamline, a high‐intensity beamline for X‐ray absorption spectroscopy of dilute samples and X‐ray emission spectroscopy, and an energy‐dispersive extended X‐ray absorption fine‐structure beamline. The optics of B18, I20‐scanning and I20‐EDE are detailed; moreover, recent developments on the four beamlines, including new detector hardware and changes in acquisition software, are described.
The current status and technical details of the four instruments dedicated to X‐ray spectroscopy available at Diamond Light Source are presented.
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FZAB, GIS, IJS, IZUM, KILJ, NLZOH, NUK, OILJ, PILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK
Calcite and vaterite crystallisation is strongly influenced by the presence of additives during the reaction process, as demonstrated by organic molecules in biogenic calcium carbonate formation. The ...effect of additives on the lattice parameters of calcite and vaterite in syntheses are frequently reported, but only as discrete studies discussing a single polymorph. The intertwined nature of these polymorphs, due to their shared reaction pathway, is rarely discussed. In this work we report the results of a large scale citizen science project to explore the influence of amino acids and related additives on both polymorphs, highlighting their differences and commonalities in terms of the effect on the lattice parameters and polymorph selectivity.
Crystallisation pathways of calcium carbonate are strongly influenced by the presence of additives. Through X-ray diffraction, samples made by the Project M Scientists reveal the effect of amino acid and related additives on the crystal structures of calcite and vaterite.
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