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Navarrete-León C, Doherty A, Savvidis S, Gerli MFM, Piredda G, Astolfo A, Bate D, Cipiccia S, Hagen CK, Olivo A, Endrizzi M. X-ray phase-contrast microtomography of soft tissues using a compact laboratory system with two-directional sensitivity. OPTICA 2023; 10:880-887. [PMID: 37841216 PMCID: PMC10575607 DOI: 10.1364/optica.487270] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 05/18/2023] [Accepted: 06/01/2023] [Indexed: 10/17/2023]
Abstract
X-ray microtomography is a nondestructive, three-dimensional inspection technique applied across a vast range of fields and disciplines, ranging from research to industrial, encompassing engineering, biology, and medical research. Phase-contrast imaging extends the domain of application of x-ray microtomography to classes of samples that exhibit weak attenuation, thus appearing with poor contrast in standard x-ray imaging. Notable examples are low-atomic-number materials, like carbon-fiber composites, soft matter, and biological soft tissues. We report on a compact and cost-effective system for x-ray phase-contrast microtomography. The system features high sensitivity to phase gradients and high resolution, requires a low-power sealed x-ray tube, a single optical element, and fits in a small footprint. It is compatible with standard x-ray detector technologies: in our experiments, we have observed that single-photon counting offered higher angular sensitivity, whereas flat panels provided a larger field of view. The system is benchmarked against known-material phantoms, and its potential for soft-tissue three-dimensional imaging is demonstrated on small-animal organs: a piglet esophagus and a rat heart. We believe that the simplicity of the setup we are proposing, combined with its robustness and sensitivity, will facilitate accessing quantitative x-ray phase-contrast microtomography as a research tool across disciplines, including tissue engineering, materials science, and nondestructive testing in general.
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Affiliation(s)
- Carlos Navarrete-León
- Department of Medical Physics and Biomedical Engineering, University College London, Gower Street, London, WC1E 6BT, UK
| | - Adam Doherty
- Department of Medical Physics and Biomedical Engineering, University College London, Gower Street, London, WC1E 6BT, UK
| | - Savvas Savvidis
- Department of Medical Physics and Biomedical Engineering, University College London, Gower Street, London, WC1E 6BT, UK
| | - Mattia F. M. Gerli
- UCL Division of Surgery and Interventional Science, Royal Free Hospital, Rowland Hill Street, London, NW3 2PF, UK
- Stem Cell and Regenerative Medicine Section, Great Ormond Street Institute of Child Health, University College London, London, WC1N 1EH, UK
| | - Giovanni Piredda
- Research Center for Microtechnology, Vorarlberg University of Applied Sciences, Hochschulstr. 1, 6850, Dornbirn, Austria
| | - Alberto Astolfo
- Department of Medical Physics and Biomedical Engineering, University College London, Gower Street, London, WC1E 6BT, UK
| | - David Bate
- Department of Medical Physics and Biomedical Engineering, University College London, Gower Street, London, WC1E 6BT, UK
- Nikon X-Tek Systems Ltd, Tring, Herts, HP23 4JX, UK
| | - Silvia Cipiccia
- Department of Medical Physics and Biomedical Engineering, University College London, Gower Street, London, WC1E 6BT, UK
| | - Charlotte K. Hagen
- Department of Medical Physics and Biomedical Engineering, University College London, Gower Street, London, WC1E 6BT, UK
| | - Alessandro Olivo
- Department of Medical Physics and Biomedical Engineering, University College London, Gower Street, London, WC1E 6BT, UK
| | - Marco Endrizzi
- Department of Medical Physics and Biomedical Engineering, University College London, Gower Street, London, WC1E 6BT, UK
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2
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Alloo SJ, Morgan KS, Paganin DM, Pavlov KM. Multimodal intrinsic speckle-tracking (MIST) to extract images of rapidly-varying diffuse X-ray dark-field. Sci Rep 2023; 13:5424. [PMID: 37012270 PMCID: PMC10070351 DOI: 10.1038/s41598-023-31574-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/14/2023] [Indexed: 04/05/2023] Open
Abstract
Speckle-based phase-contrast X-ray imaging (SB-PCXI) can reconstruct high-resolution images of weakly-attenuating materials that would otherwise be indistinguishable in conventional attenuation-based X-ray imaging. The experimental setup of SB-PCXI requires only a sufficiently coherent X-ray source and spatially random mask, positioned between the source and detector. The technique can extract sample information at length scales smaller than the imaging system's spatial resolution; this enables multimodal signal reconstruction. "Multimodal Intrinsic Speckle-Tracking" (MIST) is a rapid and deterministic formalism derived from the paraxial-optics form of the Fokker-Planck equation. MIST simultaneously extracts attenuation, refraction, and small-angle scattering (diffusive dark-field) signals from a sample and is more computationally efficient compared to alternative speckle-tracking approaches. Hitherto, variants of MIST have assumed the diffusive dark-field signal to be spatially slowly varying. Although successful, these approaches have been unable to well-describe unresolved sample microstructure whose statistical form is not spatially slowly varying. Here, we extend the MIST formalism such that this restriction is removed, in terms of a sample's rotationally-isotropic diffusive dark-field signal. We reconstruct multimodal signals of two samples, each with distinct X-ray attenuation and scattering properties. The reconstructed diffusive dark-field signals have superior image quality-as measured by the naturalness image quality evaluator, signal-to-noise ratio, and azimuthally averaged power-spectrum-compared to our previous approaches which assume the diffusive dark-field to be a slowly varying function of transverse position. Our generalisation may assist increased adoption of SB-PCXI in applications such as engineering and biomedical disciplines, forestry, and palaeontology, and is anticipated to aid the development of speckle-based diffusive dark-field tensor tomography.
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Affiliation(s)
- Samantha J Alloo
- School of Physical and Chemical Sciences, University of Canterbury, Christchurch, New Zealand.
| | - Kaye S Morgan
- School of Physics and Astronomy, Monash University, Clayton, VIC, Australia
| | - David M Paganin
- School of Physics and Astronomy, Monash University, Clayton, VIC, Australia
| | - Konstantin M Pavlov
- School of Physical and Chemical Sciences, University of Canterbury, Christchurch, New Zealand
- School of Physics and Astronomy, Monash University, Clayton, VIC, Australia
- School of Science and Technology, University of New England, Armidale, NSW, Australia
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3
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Resolving hidden pixels beyond the resolution limit of projection imaging by square aperture. Sci Rep 2023; 13:3449. [PMID: 36859466 PMCID: PMC9977726 DOI: 10.1038/s41598-023-30516-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 02/16/2023] [Indexed: 03/03/2023] Open
Abstract
Projection imaging has been employed widely in many areas, such as x-ray radiography, due to its penetration power and ballistic geometry of their paths. However, its resolution limit remains a major challenge, caused by the conflict of source intensity and source size associated with image blurriness. A simple yet robust scheme has been proposed here to solve the problem. An unconventional square aperture, rather than the usual circular beam, is constructed, which allows for the straightforward deciphering of a blurred spot, to unravel hundreds originally hidden pixels. With numerical verification and experimental demonstration, our proposal is expected to benefit multiple disciplines, not limited to x-ray imaging.
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4
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Quinn PD, Cacho-Nerin F, Gomez-Gonzalez MA, Parker JE, Poon T, Walker JM. Differential phase contrast for quantitative imaging and spectro-microscopy at a nanoprobe beamline. JOURNAL OF SYNCHROTRON RADIATION 2023; 30:200-207. [PMID: 36601938 PMCID: PMC9814065 DOI: 10.1107/s1600577522010633] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 11/04/2022] [Indexed: 06/13/2023]
Abstract
The interaction of a focused X-ray beam with a sample in a scanning probe experiment can provide a variety of information about the interaction volume. In many scanning probe experiments X-ray fluorescence (XRF) is supplemented with measurements of the transmitted or scattered intensity using a pixelated detector. The automated extraction of different signals from an area pixelated detector is described, in particular the methodology for extracting differential phase contrast (DPC) is demonstrated and different processing methods are compared across a range of samples. The phase shift of the transmitted X-ray beam by the sample, extracted from DPC, is also compared with ptychography measurements to provide a qualitative and quantitative comparison. While ptychography produces a superior image, DPC can offer a simple, flexible method for phase contrast imaging which can provide fast results and feedback during an experiment; furthermore, for many science problems, such as registration of XRF in a lighter matrix, DPC can provide sufficient information to meet the experimental aims. As the DPC technique is a quantitative measurement, it can be expanded to spectroscopic studies and a demonstration of DPC for spectro-microscopy measurements is presented. Where ptychography can separate the absorption and phase shifts by the sample, quantitative interpretation of a DPC image or spectro-microscopy signal can only be performed directly when absorption is negligible or where the absorption contribution is known and the contributions can be fitted.
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Affiliation(s)
- Paul D. Quinn
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Fernando Cacho-Nerin
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Miguel A. Gomez-Gonzalez
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Julia E. Parker
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Timothy Poon
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Jessica M. Walker
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
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5
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Mawson T, Taplin DJ, Brown HG, Clark L, Ishikawa R, Seki T, Ikuhara Y, Shibata N, Paganin DM, Morgan MJ, Weyland M, Petersen TC, Findlay SD. Factors limiting quantitative phase retrieval in atomic-resolution differential phase contrast scanning transmission electron microscopy using a segmented detector. Ultramicroscopy 2022; 233:113457. [PMID: 35016130 DOI: 10.1016/j.ultramic.2021.113457] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 11/30/2021] [Accepted: 12/05/2021] [Indexed: 11/17/2022]
Abstract
Quantitative differential phase contrast imaging of materials in atomic-resolution scanning transmission electron microscopy using segmented detectors is limited by various factors, including coherent and incoherent aberrations, detector positioning and uniformity, and scan-distortion. By comparing experimental case studies of monolayer and few-layer graphene with image simulations, we explore which parameters require the most precise characterisation for reliable and quantitative interpretation of the reconstructed phases. Coherent and incoherent lens aberrations are found to have the most significant impact. For images over a large field of view, the impact of noise and non-periodic boundary conditions are appreciable, but in this case study have less of an impact than artefacts introduced by beam deflections coupling to beam scanning (imperfect tilt-shift purity).
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Affiliation(s)
- T Mawson
- School of Physics and Astronomy, Monash University, Clayton, Victoria 3800, Australia
| | - D J Taplin
- School of Physics and Astronomy, Monash University, Clayton, Victoria 3800, Australia
| | - H G Brown
- Ian Holmes Imaging Center, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
| | - L Clark
- School of Chemical and Process Engineering, University of Leeds, Leeds LS2 9JT, UK
| | - R Ishikawa
- Institute of Engineering Innovation, University of Tokyo, Tokyo 113-8656, Japan; PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 3320012, Japan
| | - T Seki
- Institute of Engineering Innovation, University of Tokyo, Tokyo 113-8656, Japan; PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 3320012, Japan
| | - Y Ikuhara
- Institute of Engineering Innovation, University of Tokyo, Tokyo 113-8656, Japan
| | - N Shibata
- Institute of Engineering Innovation, University of Tokyo, Tokyo 113-8656, Japan
| | - D M Paganin
- School of Physics and Astronomy, Monash University, Clayton, Victoria 3800, Australia
| | - M J Morgan
- School of Physics and Astronomy, Monash University, Clayton, Victoria 3800, Australia
| | - M Weyland
- Monash Centre for Electron Microscopy, Monash University, Clayton, Victoria 3800, Australia; Department of Materials Science and Engineering, Monash University, Clayton, Victoria 3800, Australia
| | - T C Petersen
- School of Physics and Astronomy, Monash University, Clayton, Victoria 3800, Australia; Monash Centre for Electron Microscopy, Monash University, Clayton, Victoria 3800, Australia
| | - S D Findlay
- School of Physics and Astronomy, Monash University, Clayton, Victoria 3800, Australia.
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6
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Xia T, Cheng S, Tao S, Yu W. Colourful imaging and self-reconstruction properties of modified single-focus fractal zone plates. OPTICS EXPRESS 2020; 28:37827-37843. [PMID: 33379610 DOI: 10.1364/oe.409680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 11/05/2020] [Indexed: 06/12/2023]
Abstract
A modified single-focus fractal zone plate (MSFFZP) is proposed to generate a single main focus with many subsidiary foci or two equal-intensity main foci with many subsidiary foci. Widths of high-transmission zones, which have influence on the number of the high-order diffraction foci, such as the second-order focus and the fourth-order focus, can adjust first-order fractal focal intensities, but have no influence on first-order focal positions. Moreover, the MSFFZPs have the first-order foci or the first and second order foci only along the optic axis. It is proved numerically and experimentally that the MSFFZP can generate one or two colourful images with the low chromatic aberrations at the focal planes, and the MSFFZP beam has the self-reconstruction property. In addition, the MSFFZP produces a series of foci at the different focal planes along the optic axis in the simulations and experiments. The method of constructing the MSFFZP is illustrated. The proposed zone plate can be used to produce the multiple clear images, trap particles at the multiple planes simultaneously, and generate the images with the low chromatic aberration.
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7
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Howard DL, de Jonge MD, Afshar N, Ryan CG, Kirkham R, Reinhardt J, Kewish CM, McKinlay J, Walsh A, Divitcos J, Basten N, Adamson L, Fiala T, Sammut L, Paterson DJ. The XFM beamline at the Australian Synchrotron. JOURNAL OF SYNCHROTRON RADIATION 2020; 27:1447-1458. [PMID: 32876622 DOI: 10.1107/s1600577520010152] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 07/22/2020] [Indexed: 06/11/2023]
Abstract
The X-ray fluorescence microscopy (XFM) beamline is an in-vacuum undulator-based X-ray fluorescence (XRF) microprobe beamline at the 3 GeV Australian Synchrotron. The beamline delivers hard X-rays in the 4-27 keV energy range, permitting K emission to Cd and L and M emission for all other heavier elements. With a practical low-energy detection cut-off of approximately 1.5 keV, low-Z detection is constrained to Si, with Al detectable under favourable circumstances. The beamline has two scanning stations: a Kirkpatrick-Baez mirror microprobe, which produces a focal spot of 2 µm × 2 µm FWHM, and a large-area scanning `milliprobe', which has the beam size defined by slits. Energy-dispersive detector systems include the Maia 384, Vortex-EM and Vortex-ME3 for XRF measurement, and the EIGER2 X 1 Mpixel array detector for scanning X-ray diffraction microscopy measurements. The beamline uses event-mode data acquisition that eliminates detector system time overheads, and motion control overheads are significantly reduced through the application of an efficient raster scanning algorithm. The minimal overheads, in conjunction with short dwell times per pixel, have allowed XFM to establish techniques such as full spectroscopic XANES fluorescence imaging, XRF tomography, fly scanning ptychography and high-definition XRF imaging over large areas. XFM provides diverse analysis capabilities in the fields of medicine, biology, geology, materials science and cultural heritage. This paper discusses the beamline status, scientific showcases and future upgrades.
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Affiliation(s)
- Daryl L Howard
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Martin D de Jonge
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Nader Afshar
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Chris G Ryan
- Commonwealth Scientific and Industrial Research Organisation, Normanby Road, Clayton, Victoria, Australia
| | - Robin Kirkham
- Commonwealth Scientific and Industrial Research Organisation, Normanby Road, Clayton, Victoria, Australia
| | - Juliane Reinhardt
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Cameron M Kewish
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Jonathan McKinlay
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Adam Walsh
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Jim Divitcos
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Noel Basten
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Luke Adamson
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Tom Fiala
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Letizia Sammut
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - David J Paterson
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton, Victoria 3168, Australia
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8
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Bagschik K, Wagner J, Buß R, Riepp M, Philippi-Kobs A, Müller L, Buck J, Trinter F, Scholz F, Seltmann J, Hoesch M, Viefhaus J, Grübel G, Oepen HP, Frömter R. Direct 2D spatial-coherence determination using the Fourier-analysis method: multi-parameter characterization of the P04 beamline at PETRA III. OPTICS EXPRESS 2020; 28:7282-7300. [PMID: 32225960 DOI: 10.1364/oe.382608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 01/27/2020] [Indexed: 06/10/2023]
Abstract
We present a systematic 2D spatial-coherence analysis of the soft-X-ray beamline P04 at PETRA III for various beamline configurations. The influence of two different beam-defining apertures on the spatial coherence properties of the beam is discussed and optimal conditions for coherence-based experiments are found. A significant degradation of the spatial coherence in the vertical direction has been measured and sources of this degradation are identified and discussed. The Fourier-analysis method, which gives fast and simple access to the 2D spatial coherence function of the X-ray beam, is used for the experiment. Here, we exploit the charge scattering of a disordered nanodot sample allowing the use of arbitrary X-ray photon energies with this method.
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9
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Single-Shot X-ray Phase Retrieval through Hierarchical Data Analysis and a Multi-Aperture Analyser. J Imaging 2018. [DOI: 10.3390/jimaging4060076] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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10
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Yücelen E, Lazić I, Bosch EGT. Phase contrast scanning transmission electron microscopy imaging of light and heavy atoms at the limit of contrast and resolution. Sci Rep 2018; 8:2676. [PMID: 29422551 PMCID: PMC5805791 DOI: 10.1038/s41598-018-20377-2] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 01/17/2018] [Indexed: 12/04/2022] Open
Abstract
Using state of the art scanning transmission electron microscopy (STEM) it is nowadays possible to directly image single atomic columns at sub-Å resolution. In standard (high angle) annular dark field STEM ((HA)ADF-STEM), however, light elements are usually invisible when imaged together with heavier elements in one image. Here we demonstrate the capability of the recently introduced Integrated Differential Phase Contrast STEM (iDPC-STEM) technique to image both light and heavy atoms in a thin sample at sub-Å resolution. We use the technique to resolve both the Gallium and Nitrogen dumbbells in a GaN crystal in [\documentclass[12pt]{minimal}
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\begin{document}$${\bf{10}}\bar{{\bf{1}}}{\bf{1}}$$\end{document}101¯1] orientation, which each have a separation of only 63 pm. Reaching this ultimate resolution even for light elements is possible due to the fact that iDPC-STEM is a direct phase imaging technique that allows fine-tuning the microscope while imaging. Apart from this qualitative imaging result, we also demonstrate a quantitative match of ratios of the measured intensities with theoretical predictions based on simulations.
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Affiliation(s)
- Emrah Yücelen
- Thermo Fisher Scientific (formerly FEI), Achtseweg Noord 5, 5600KA, Eindhoven, The Netherlands.
| | - Ivan Lazić
- Thermo Fisher Scientific (formerly FEI), Achtseweg Noord 5, 5600KA, Eindhoven, The Netherlands
| | - Eric G T Bosch
- Thermo Fisher Scientific (formerly FEI), Achtseweg Noord 5, 5600KA, Eindhoven, The Netherlands
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11
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Measuring nanometre-scale electric fields in scanning transmission electron microscopy using segmented detectors. Ultramicroscopy 2017; 182:169-178. [DOI: 10.1016/j.ultramic.2017.07.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 06/28/2017] [Accepted: 07/02/2017] [Indexed: 11/18/2022]
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12
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Endrizzi M, Vittoria FA, Rigon L, Dreossi D, Iacoviello F, Shearing PR, Olivo A. X-ray Phase-Contrast Radiography and Tomography with a Multiaperture Analyzer. PHYSICAL REVIEW LETTERS 2017; 118:243902. [PMID: 28665636 DOI: 10.1103/physrevlett.118.243902] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Indexed: 05/23/2023]
Abstract
We present a multiaperture analyzer setup for performing x-ray phase contrast imaging in planar and three-dimensional modalities. The method is based on strongly structuring the x-ray beam with an amplitude modulator, before it reaches the sample, and on a multiaperture analyzing element before detection. A multislice representation of the sample is used to establish a quantitative relation between projection images and the corresponding three-dimensional distributions, leading to successful tomographic reconstruction. Sample absorption, phase, and scattering are retrieved from the measurement of five intensity projections. The method is tested on custom-built phantoms with synchrotron radiation: sample absorption and phase can be reliably retrieved also in combination with strong scatterers, simultaneously attaining high sensitivity and dynamic range.
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Affiliation(s)
- M Endrizzi
- Department of Medical Physics and Biomedical Engineering, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - F A Vittoria
- Department of Medical Physics and Biomedical Engineering, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - L Rigon
- Physics Department, University of Trieste, Via Valerio 2, 34127 Trieste, Italy
- Istituto Nazionale di Fisica Nulceare, Sezione di Trieste, Via Valerio 2, 34127 Trieste, Italy
| | - D Dreossi
- Sincrotrone Trieste SCpA, S.S. 14 km 163.5, 34012 Basovizza Trieste, Italy
| | - F Iacoviello
- Electrochemical Innovation Lab, Department of Chemical Engineering, University College London, WC1E 7JE, United Kingdom
| | - P R Shearing
- Electrochemical Innovation Lab, Department of Chemical Engineering, University College London, WC1E 7JE, United Kingdom
| | - A Olivo
- Department of Medical Physics and Biomedical Engineering, University College London, Gower Street, London WC1E 6BT, United Kingdom
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13
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Korecki P, Sowa KM, Jany BR, Krok F. Defect-Assisted Hard-X-Ray Microscopy with Capillary Optics. PHYSICAL REVIEW LETTERS 2016; 116:233902. [PMID: 27341235 DOI: 10.1103/physrevlett.116.233902] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Indexed: 06/06/2023]
Abstract
Polycapillary x-ray focusing devices are built from hundreds of thousands of bent microcapillaries that are stacked into hexagonal arrays. We show that intrinsic point defects of the optics (e.g., missing or larger capillaries) lead to the formation of multiple x-ray images of an object positioned in the focal plane. These images can be recorded in parallel, and can provide spatial resolution that is limited by the defect size and not by the focal spot size. In a proof-of-principle experiment, we demonstrate submicron resolution, which has not yet been achieved with polycapillary focusing optics. Tailored optics with a controlled distribution of "defects" could be used for multimodal nanoscale x-ray imaging with laboratory setups.
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Affiliation(s)
- Paweł Korecki
- Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków, Poland
| | - Katarzyna M Sowa
- Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków, Poland
| | - Benedykt R Jany
- Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków, Poland
| | - Franciszek Krok
- Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków, Poland
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14
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Bergamaschi A, Medjoubi K, Messaoudi C, Marco S, Somogyi A. MMX-I: data-processing software for multimodal X-ray imaging and tomography. JOURNAL OF SYNCHROTRON RADIATION 2016; 23:783-794. [PMID: 27140159 PMCID: PMC4853872 DOI: 10.1107/s1600577516003052] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 02/20/2016] [Indexed: 05/29/2023]
Abstract
A new multi-platform freeware has been developed for the processing and reconstruction of scanning multi-technique X-ray imaging and tomography datasets. The software platform aims to treat different scanning imaging techniques: X-ray fluorescence, phase, absorption and dark field and any of their combinations, thus providing an easy-to-use data processing tool for the X-ray imaging user community. A dedicated data input stream copes with the input and management of large datasets (several hundred GB) collected during a typical multi-technique fast scan at the Nanoscopium beamline and even on a standard PC. To the authors' knowledge, this is the first software tool that aims at treating all of the modalities of scanning multi-technique imaging and tomography experiments.
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Affiliation(s)
| | - Kadda Medjoubi
- Synchrotron SOLEIL, BP 48, Saint-Aubin, 91192 Gif sur Yvette, France
| | - Cédric Messaoudi
- UMR 9187, Université Paris-Saclay, CNRS, Université Paris-Saclay, F-91405 Orsay, France
- U1196, Institut Curie, INSERM, PSL Reseach University, F-91405 Orsay, France
| | - Sergio Marco
- UMR 9187, Université Paris-Saclay, CNRS, Université Paris-Saclay, F-91405 Orsay, France
- U1196, Institut Curie, INSERM, PSL Reseach University, F-91405 Orsay, France
| | - Andrea Somogyi
- Synchrotron SOLEIL, BP 48, Saint-Aubin, 91192 Gif sur Yvette, France
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15
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Towards quantitative, atomic-resolution reconstruction of the electrostatic potential via differential phase contrast using electrons. Ultramicroscopy 2015; 159 Pt 1:124-37. [DOI: 10.1016/j.ultramic.2015.09.002] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 07/14/2015] [Accepted: 09/03/2015] [Indexed: 11/23/2022]
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16
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Lazić I, Bosch EGT, Lazar S. Phase contrast STEM for thin samples: Integrated differential phase contrast. Ultramicroscopy 2015; 160:265-280. [PMID: 26590505 DOI: 10.1016/j.ultramic.2015.10.011] [Citation(s) in RCA: 197] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 10/08/2015] [Accepted: 10/11/2015] [Indexed: 10/22/2022]
Abstract
It has been known since the 1970s that the movement of the center of mass (COM) of a convergent beam electron diffraction (CBED) pattern is linearly related to the (projected) electrical field in the sample. We re-derive a contrast transfer function (CTF) for a scanning transmission electron microscopy (STEM) imaging technique based on this movement from the point of view of image formation and continue by performing a two-dimensional integration on the two images based on the two components of the COM movement. The resulting integrated COM (iCOM) STEM technique yields a scalar image that is linear in the phase shift caused by the sample and therefore also in the local (projected) electrostatic potential field of a thin sample. We confirm that the differential phase contrast (DPC) STEM technique using a segmented detector with 4 quadrants (4Q) yields a good approximation for the COM movement. Performing a two-dimensional integration, just as for the COM, we obtain an integrated DPC (iDPC) image which is approximately linear in the phase of the sample. Beside deriving the CTFs of iCOM and iDPC, we clearly point out the objects of the two corresponding imaging techniques, and highlight the differences to objects corresponding to COM-, DPC-, and (HA) ADF-STEM. The theory is validated with simulations and we present first experimental results of the iDPC-STEM technique showing its capability for imaging both light and heavy elements with atomic resolution and a good signal to noise ratio (SNR).
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Affiliation(s)
- Ivan Lazić
- FEI Company, Achtseweg Noord 5, PO Box 80066, 5600 KA Eindhoven, The Netherlands.
| | - Eric G T Bosch
- FEI Company, Achtseweg Noord 5, PO Box 80066, 5600 KA Eindhoven, The Netherlands
| | - Sorin Lazar
- FEI Company, Achtseweg Noord 5, PO Box 80066, 5600 KA Eindhoven, The Netherlands
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17
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Sharif A. Review on advances in nanoscale microscopy in cement research. Micron 2015; 80:45-58. [PMID: 26447783 DOI: 10.1016/j.micron.2015.09.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 08/28/2015] [Accepted: 09/19/2015] [Indexed: 12/19/2022]
Abstract
With the rapid advancement of nanotechnology, manipulation and characterization of materials in nano scale have become an obvious part of construction related technology. This review will focus on some of the nanoscopy techniques that are most frequently used in current research of cement based nanostructured materials. In particular scanning electron microscopy, transmission electron microscopy, atomic force microscopy, scanning tunneling microscopy, tomography, scanning transmission X-ray microscopy and laser scanning confocal microscopy are addressed. A number of case studies related to microscopic characterization of nano materials utilizing the aforementioned techniques from the published literature are discussed. While these approaches are beginning to yield promising insight, continued progress will definitely provide a potential sustainable solution for the design, development and promotion towards nanoscale engineering of cementitious materials.
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Affiliation(s)
- Ahmed Sharif
- Department of Materials & Metallurgical Engineering, Bangladesh University of Engineering and Technology, Dhaka 1000, Bangladesh.
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18
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Hong YP, Chen S, Jacobsen C. A New Workflow for x-ray fluorescence tomography: MAPSToTomoPy. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2015; 9592. [PMID: 27103755 DOI: 10.1117/12.2194162] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
X-ray fluorescence tomography involves the acquisition of a series of 2D x-ray fluorescence datasets between which a specimen is rotated. At the Advanced Photon Source at Argonne National Laboratory, the workflow at beamlines 2-ID-E and 21-ID-D (the Bionanoprobe, a cryogenic microscope system) has included the use of the program MAPS for obtaining elemental concentrations from 2D images, and the program TomoPy which was developed to include several tomographic reconstruction methods for x-ray transmission data. In the past, fluorescence projection images from an individual chemical element were hand-assembled into a 3D dataset for reconstruction using interactive tools such as ImageJ. We describe here the program MAPSToTomoPy, which provides a graphical user interface (GUI) to control a workflow between MAPS and TomoPy, with tools for visualizing the sinograms of projection image sequences from particular elements and to use these to help correct misalignments of the rotation axis. The program also provides an integrated output of the 3D distribution of the detected elements for subsequent 3D visualization packages.
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Affiliation(s)
- Young Pyo Hong
- Department of Physics and Astronomy, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Si Chen
- Advanced Photon Source, Argonne National Laboratory, 9700 S. Cass Ave., Argonne IL 60439-4837 USA
| | - Chris Jacobsen
- Advanced Photon Source, Argonne National Laboratory, 9700 S. Cass Ave., Argonne IL 60439-4837 USA; Department of Physics and Astronomy, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
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19
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Aloisio IA, Paganin DM, Wright CA, Morgan KS. Exploring experimental parameter choice for rapid speckle-tracking phase-contrast X-ray imaging with a paper analyzer. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:1279-1288. [PMID: 26289280 DOI: 10.1107/s1600577515011406] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 06/12/2015] [Indexed: 06/04/2023]
Abstract
Phase-contrast X-ray imaging using a paper analyzer enables the visualization of X-ray transparent biological structures using the refractive properties of the sample. The technique measures the sample-induced distortions of a spatially random reference pattern to retrieve quantitative sample information. This phase-contrast method is promising for biomedical application due to both a simple experimental set-up and a capability for real-time imaging. The authors explore the experimental configuration required to achieve robustness and accuracy in terms of (i) the paper analyzer feature size, (ii) the sample-to-detector distance, and (iii) the exposure time. Results using a synchrotron source confirm that the technique achieves accurate phase retrieval with a range of paper analyzers and at exposures as short as 0.5 ms. These exposure times are sufficiently short relative to characteristic physiological timescales to enable real-time dynamic imaging of living samples. A theoretical guide to the choice of sample-to-detector distance is also derived. While the measurements are specific to the set-up, these guidelines, the example speckle images, the strategies for analysis in the presence of noise and the experimental considerations and discussion will be of value to those who wish to use the speckle-tracking paper analyzer technique.
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Affiliation(s)
- Isobel A Aloisio
- Central Medical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3800, Australia
| | - David M Paganin
- School of Physics and Astronomy, Monash University, Clayton, VIC 3800, Australia
| | - Christopher A Wright
- Central Medical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Kaye S Morgan
- School of Physics and Astronomy, Monash University, Clayton, VIC 3800, Australia
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20
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Osterhoff M, Eberl C, Döring F, Wilke RN, Wallentin J, Krebs HU, Sprung M, Salditt T. Towards multi-order hard X-ray imaging with multilayer zone plates. J Appl Crystallogr 2015; 48:116-124. [PMID: 26089748 PMCID: PMC4453173 DOI: 10.1107/s1600576714026016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 11/27/2014] [Indexed: 11/29/2022] Open
Abstract
This article describes holographic imaging experiments using a hard X-ray multilayer zone plate (MZP) with an outermost zone width of 10 nm at a photon energy of 18 keV. An order-sorting aperture (OSA) is omitted and emulated during data analysis by a 'software OSA'. Scanning transmission X-ray microscopy usually carried out in the focal plane is generalized to the holographic regime. The MZP focus is characterized by a three-plane phase-retrieval algorithm to an FWHM of 10 nm.
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Affiliation(s)
- Markus Osterhoff
- Institut für Röntgenphysik, Georg-August-Universität Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Christian Eberl
- Institut für Materialphysik, Georg-August-Universität Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Florian Döring
- Institut für Materialphysik, Georg-August-Universität Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Robin N. Wilke
- Institut für Röntgenphysik, Georg-August-Universität Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Jesper Wallentin
- Institut für Röntgenphysik, Georg-August-Universität Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Hans-Ulrich Krebs
- Institut für Materialphysik, Georg-August-Universität Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Michael Sprung
- DESY Photon Science, Notkestrasse 85, 22607 Hamburg, Germany
| | - Tim Salditt
- Institut für Röntgenphysik, Georg-August-Universität Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
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21
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de Jonge MD, Ryan CG, Jacobsen CJ. X-ray nanoprobes and diffraction-limited storage rings: opportunities and challenges of fluorescence tomography of biological specimens. JOURNAL OF SYNCHROTRON RADIATION 2014; 21:1031-47. [PMID: 25177992 PMCID: PMC4151681 DOI: 10.1107/s160057751401621x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 07/11/2014] [Indexed: 05/22/2023]
Abstract
X-ray nanoprobes require coherent illumination to achieve optic-limited resolution, and so will benefit directly from diffraction-limited storage rings. Here, the example of high-resolution X-ray fluorescence tomography is focused on as one of the most voracious demanders of coherent photons, since the detected signal is only a small fraction of the incident flux. Alternative schemes are considered for beam delivery, sample scanning and detectors. One must consider as well the steps before and after the X-ray experiment: sample preparation and examination conditions, and analysis complexity due to minimum dose requirements and self-absorption. By understanding the requirements and opportunities for nanoscale fluorescence tomography, one gains insight into the R&D challenges in optics and instrumentation needed to fully exploit the source advances that diffraction-limited storage rings offer.
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Affiliation(s)
- Martin D. de Jonge
- Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Christopher G. Ryan
- CSIRO Earth Science and Research Engineering, Clayton, Victoria 3168, Australia
| | - Chris J. Jacobsen
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
- Department of Physics, Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston, IL 60208, USA
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22
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Sperl JI, Bequé D, Kudielka GP, Mahdi K, Edic PM, Cozzini C. A Fourier-domain algorithm for total-variation regularized phase retrieval in differential X-ray phase contrast imaging. OPTICS EXPRESS 2014; 22:450-462. [PMID: 24515005 DOI: 10.1364/oe.22.000450] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Phase retrieval in differential X-ray phase contrast imaging involves a one dimensional integration step. In the presence of noise, standard integration methods result in image blurring and streak artifacts. This work proposes a regularized integration method which takes the availability of two dimensional data as well as the integration-specific frequency-dependent noise amplification into account. In more detail, a Fourier-domain algorithm is developed comprising a frequency-dependent minimization of the total variation orthogonal to the direction of integration. For both simulated and experimental data, the novel method yielded strong artefact reduction without increased blurring superior to the results obtained by standard integration methods or regularization techniques in the image domain.
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23
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Hong YP, Gleber SC, O’Halloran TV, Que EL, Bleher R, Vogt S, Woodruff TK, Jacobsen C. Alignment of low-dose X-ray fluorescence tomography images using differential phase contrast. JOURNAL OF SYNCHROTRON RADIATION 2014; 21:229-34. [PMID: 24365941 PMCID: PMC3874022 DOI: 10.1107/s1600577513029512] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 10/25/2013] [Indexed: 05/09/2023]
Abstract
X-ray fluorescence nanotomography provides unprecedented sensitivity for studies of trace metal distributions in whole biological cells. Dose fractionation, in which one acquires very low dose individual projections and then obtains high statistics reconstructions as signal from a voxel is brought together (Hegerl & Hoppe, 1976), requires accurate alignment of these individual projections so as to correct for rotation stage runout. It is shown here that differential phase contrast at 10.2 keV beam energy offers the potential for accurate cross-correlation alignment of successive projections, by demonstrating that successive low dose, 3 ms per pixel, images acquired at the same specimen position and rotation angle have a narrower and smoother cross-correlation function (1.5 pixels FWHM at 300 nm pixel size) than that obtained from zinc fluorescence images (25 pixels FWHM). The differential phase contrast alignment resolution is thus well below the 700 nm × 500 nm beam spot size used in this demonstration, so that dose fractionation should be possible for reduced-dose, more rapidly acquired, fluorescence nanotomography experiments.
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Affiliation(s)
- Young Pyo Hong
- Department of Physics and Astronomy, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- Correspondence e-mail:
| | - Sophie-Charlotte Gleber
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Thomas V. O’Halloran
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Emily L. Que
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Reiner Bleher
- Department of Materials Science and Engineering, 2220 Campus Drive, Evanston, IL 60208, USA
| | - Stefan Vogt
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Teresa K. Woodruff
- Department of Obstetrics and Gynecology, Northwestern University, 303 East Superior Street, Chicago, IL 60611, USA
| | - Chris Jacobsen
- Department of Physics and Astronomy, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
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24
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Chen S, Deng J, Yuan Y, Flachenecker C, Mak R, Hornberger B, Jin Q, Shu D, Lai B, Maser J, Roehrig C, Paunesku T, Gleber SC, Vine DJ, Finney L, VonOsinski J, Bolbat M, Spink I, Chen Z, Steele J, Trapp D, Irwin J, Feser M, Snyder E, Brister K, Jacobsen C, Woloschak G, Vogt S. The Bionanoprobe: hard X-ray fluorescence nanoprobe with cryogenic capabilities. JOURNAL OF SYNCHROTRON RADIATION 2014; 21:66-75. [PMID: 24365918 PMCID: PMC3874019 DOI: 10.1107/s1600577513029676] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 10/28/2013] [Indexed: 05/20/2023]
Abstract
Hard X-ray fluorescence microscopy is one of the most sensitive techniques for performing trace elemental analysis of biological samples such as whole cells and tissues. Conventional sample preparation methods usually involve dehydration, which removes cellular water and may consequently cause structural collapse, or invasive processes such as embedding. Radiation-induced artifacts may also become an issue, particularly as the spatial resolution increases beyond the sub-micrometer scale. To allow imaging under hydrated conditions, close to the `natural state', as well as to reduce structural radiation damage, the Bionanoprobe (BNP) has been developed, a hard X-ray fluorescence nanoprobe with cryogenic sample environment and cryo transfer capabilities, dedicated to studying trace elements in frozen-hydrated biological systems. The BNP is installed at an undulator beamline at sector 21 of the Advanced Photon Source. It provides a spatial resolution of 30 nm for two-dimensional fluorescence imaging. In this first demonstration the instrument design and motion control principles are described, the instrument performance is quantified, and the first results obtained with the BNP on frozen-hydrated whole cells are reported.
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Affiliation(s)
- S. Chen
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - J. Deng
- Applied Physics, Northwestern University, Evanston, IL 60208, USA
| | - Y. Yuan
- Department of Radiation Oncology, Northwestern University, Chicago, IL 60611, USA
| | | | - R. Mak
- Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, USA
| | | | - Q. Jin
- Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, USA
| | - D. Shu
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - B. Lai
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - J. Maser
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - C. Roehrig
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - T. Paunesku
- Department of Radiation Oncology, Northwestern University, Chicago, IL 60611, USA
| | - S. C. Gleber
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - D. J. Vine
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - L. Finney
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - J. VonOsinski
- Northwestern Synchrotron Research Center, Argonne, IL 60439, USA
| | - M. Bolbat
- Northwestern Synchrotron Research Center, Argonne, IL 60439, USA
| | - I. Spink
- Xradia Inc., Pleasanton, CA 94588, USA
| | - Z. Chen
- Xradia Inc., Pleasanton, CA 94588, USA
| | - J. Steele
- Xradia Inc., Pleasanton, CA 94588, USA
| | - D. Trapp
- Xradia Inc., Pleasanton, CA 94588, USA
| | - J. Irwin
- Xradia Inc., Pleasanton, CA 94588, USA
| | - M. Feser
- Xradia Inc., Pleasanton, CA 94588, USA
| | - E. Snyder
- Xradia Inc., Pleasanton, CA 94588, USA
| | - K. Brister
- Northwestern Synchrotron Research Center, Argonne, IL 60439, USA
| | - C. Jacobsen
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
- Applied Physics, Northwestern University, Evanston, IL 60208, USA
- Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - G. Woloschak
- Department of Radiation Oncology, Northwestern University, Chicago, IL 60611, USA
| | - S. Vogt
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
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25
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Takeuchi A, Uesugi K, Suzuki Y. Three-dimensional phase-contrast X-ray microtomography with scanning-imaging X-ray microscope optics. JOURNAL OF SYNCHROTRON RADIATION 2013; 20:793-800. [PMID: 23955044 PMCID: PMC4032070 DOI: 10.1107/s0909049513018876] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 07/08/2013] [Indexed: 05/30/2023]
Abstract
A three-dimensional (3D) X-ray tomographic micro-imaging system has been developed. The optical system is based on a scanning-imaging X-ray microscope (SIXM) optics, which is a hybrid system consisting of a scanning microscope optics with a one-dimensional (1D) focusing (line-focusing) device and an imaging microscope optics with a 1D objective. In the SIXM system, each 1D dataset of a two-dimensional (2D) image is recorded independently. An object is illuminated with a line-focused beam. Positional information of the region illuminated by the line-focused beam is recorded with the 1D imaging microscope optics as line-profile data. By scanning the object with the line focus, 2D image data are obtained. In the same manner as for a scanning microscope optics with a multi-pixel detector, imaging modes such as phase contrast and absorption contrast can be arbitrarily configured after the image data acquisition. By combining a tomographic scan method and the SIXM system, quantitative 3D imaging is performed. Results of a feasibility study of the SIXM for 3D imaging are shown.
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Affiliation(s)
- Akihisa Takeuchi
- Research and Utilization Division, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Sayo-gun, Hyogo 679-5198, Japan.
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26
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Yan H, Chu YS, Maser J, Nazaretski E, Kim J, Kang HC, Lombardo JJ, Chiu WKS. Quantitative x-ray phase imaging at the nanoscale by multilayer Laue lenses. Sci Rep 2013; 3:1307. [PMID: 23419650 PMCID: PMC3575587 DOI: 10.1038/srep01307] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 01/22/2013] [Indexed: 11/22/2022] Open
Abstract
For scanning x-ray microscopy, many attempts have been made to image the phase contrast based on a concept of the beam being deflected by a specimen, the so-called differential phase contrast imaging (DPC). Despite the successful demonstration in a number of representative cases at moderate spatial resolutions, these methods suffer from various limitations that preclude applications of DPC for ultra-high spatial resolution imaging, where the emerging wave field from the focusing optic tends to be significantly more complicated. In this work, we propose a highly robust and generic approach based on a Fourier-shift fitting process and demonstrate quantitative phase imaging of a solid oxide fuel cell (SOFC) anode by multilayer Laue lenses (MLLs). The high sensitivity of the phase to structural and compositional variations makes our technique extremely powerful in correlating the electrode performance with its buried nanoscale interfacial structures that may be invisible to the absorption and fluorescence contrasts.
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Affiliation(s)
- Hanfei Yan
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA.
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27
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Dixit G, Slowik JM, Santra R. Proposed imaging of the ultrafast electronic motion in samples using x-ray phase contrast. PHYSICAL REVIEW LETTERS 2013; 110:137403. [PMID: 23581370 DOI: 10.1103/physrevlett.110.137403] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Indexed: 06/02/2023]
Abstract
Tracing the motion of electrons has enormous relevance to understanding ubiquitous phenomena in ultrafast science, such as the dynamical evolution of the electron density during complex chemical and biological processes. Scattering of ultrashort x-ray pulses from an electronic wave packet would appear to be the most obvious approach to image the electronic motion in real time and real space with the notion that such scattering patterns, in the far-field regime, encode the instantaneous electron density of the wave packet. However, recent results by Dixit et al. [Proc. Natl. Acad. Sci. U.S.A. 109, 11636 (2012)] have put this notion into question and have shown that the scattering in the far-field regime probes spatiotemporal density-density correlations. Here, we propose a possible way to image the instantaneous electron density of the wave packet via ultrafast x-ray phase contrast imaging. Moreover, we show that inelastic scattering processes, which plague ultrafast scattering in the far-field regime, do not contribute in ultrafast x-ray phase contrast imaging as a consequence of an interference effect. We illustrate our general findings by means of a wave packet that lies in the time and energy range of the dynamics of valence electrons in complex molecular and biological systems. This present work offers a potential to image not only instantaneous snapshots of nonstationary electron dynamics, but also the laplacian of these snapshots which provide information about the complex bonding and topology of the charge distributions in the systems.
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Affiliation(s)
- Gopal Dixit
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, D-22607 Hamburg, Germany.
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28
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29
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Vogt S, Ralle M. Opportunities in multidimensional trace metal imaging: taking copper-associated disease research to the next level. Anal Bioanal Chem 2013; 405:1809-20. [PMID: 23079951 PMCID: PMC3566297 DOI: 10.1007/s00216-012-6437-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 09/07/2012] [Accepted: 09/18/2012] [Indexed: 01/09/2023]
Abstract
Copper plays an important role in numerous biological processes across all living systems predominantly because of its versatile redox behavior. Cellular copper homeostasis is tightly regulated and disturbances lead to severe disorders such as Wilson disease and Menkes disease. Age-related changes of copper metabolism have been implicated in other neurodegenerative disorders such as Alzheimer disease. The role of copper in these diseases has been a topic of mostly bioinorganic research efforts for more than a decade, metal-protein interactions have been characterized, and cellular copper pathways have been described. Despite these efforts, crucial aspects of how copper is associated with Alzheimer disease, for example, are still only poorly understood. To take metal-related disease research to the next level, emerging multidimensional imaging techniques are now revealing the copper metallome as the basis to better understand disease mechanisms. This review describes how recent advances in X-ray fluorescence microscopy and fluorescent copper probes have started to contribute to this field, specifically in Wilson disease and Alzheimer disease. It furthermore provides an overview of current developments and future applications in X-ray microscopic methods.
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Affiliation(s)
- Stefan Vogt
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, IL 60439
| | - Martina Ralle
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239
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30
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Takeuchi A, Suzuki Y, Uesugi K. Differential phase contrast x-ray microimaging with scanning-imaging x-ray microscope optics. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2012; 83:083701. [PMID: 22938297 DOI: 10.1063/1.4739761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
A novel x-ray microimaging system that consists of a scanning microscope optics with a one-dimensional focusing (line-focusing) device and an imaging microscope optics with a one-dimensional objective is developed. These two optical systems are set normal to each other regarding the optical axis. A two-dimensional image is obtained with one-dimensional translation scan of the line probe. During scans, positional data in the normal to the scanning direction are obtained simultaneously with the imaging microscope optics. Differential phase contrast (DPC) image and absorption contrast (AC) image can be arbitrarily obtained by image processing after data acquisition. Preliminary experiment has been carried out by using a couple of one-dimensional Fresnel zone plate as the linear-focusing device and the one-dimensional objective. Two-dimensional DPC and AC images of test sample have been successfully obtained with 8 keV x-rays.
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31
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Chesnel K, Nelson J, Wilcken B, Kevan SD. Mapping spatial and field dependence of magnetic domain memory by soft X-ray speckle metrology. JOURNAL OF SYNCHROTRON RADIATION 2012; 19:293-306. [PMID: 22514162 DOI: 10.1107/s0909049512008047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Accepted: 02/22/2012] [Indexed: 05/27/2023]
Abstract
The occurrence of magnetic domain memory has been observed in ferromagnets, either induced by structural defects or by exchange couplings. Being able to quantify the amount of memory as a function of length scale, field and temperature is both of fundamental and technological importance. A technique has been refined to statistically quantify the magnetic domain memory in ferromagnetic thin films by using coherent soft-X-ray scattering metrology. This technique, based on cross-correlating magnetic speckle patterns, provides a unique way to map out the behavior of domain memory. Here, the details of our correlation method and the necessary treatment of the X-ray scattering images to extract spatial and field dependences in the memory information are reviewed. The resulting correlation maps, measured on [Co/Pd]IrMn multilayers, show how magnetic domain memory evolves at various spatial scales, as a function of the field magnitude throughout magnetization cycles, but also as a function of field cycling and of temperature. This technique can easily be applied to a wide variety of systems presenting memory effects, in soft and hard matter, and also to dynamical studies.
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Affiliation(s)
- K Chesnel
- Physics Department, Brigham Young University, UT 84602, USA.
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32
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Liu Y, Meirer F, Williams PA, Wang J, Andrews JC, Pianetta P. TXM-Wizard: a program for advanced data collection and evaluation in full-field transmission X-ray microscopy. JOURNAL OF SYNCHROTRON RADIATION 2012; 19:281-7. [PMID: 22338691 PMCID: PMC3284347 DOI: 10.1107/s0909049511049144] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Accepted: 11/17/2011] [Indexed: 05/04/2023]
Abstract
Transmission X-ray microscopy (TXM) has been well recognized as a powerful tool for non-destructive investigation of the three-dimensional inner structure of a sample with spatial resolution down to a few tens of nanometers, especially when combined with synchrotron radiation sources. Recent developments of this technique have presented a need for new tools for both system control and data analysis. Here a software package developed in MATLAB for script command generation and analysis of TXM data is presented. The first toolkit, the script generator, allows automating complex experimental tasks which involve up to several thousand motor movements. The second package was designed to accomplish computationally intense tasks such as data processing of mosaic and mosaic tomography datasets; dual-energy contrast imaging, where data are recorded above and below a specific X-ray absorption edge; and TXM X-ray absorption near-edge structure imaging datasets. Furthermore, analytical and iterative tomography reconstruction algorithms were implemented. The compiled software package is freely available.
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Affiliation(s)
- Yijin Liu
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Florian Meirer
- MiNALab, CMM-irst, Fondazione Bruno Kessler, Via Sommarive 18, Povo, Trento 38123, Italy
| | - Phillip A. Williams
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Junyue Wang
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Joy C. Andrews
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Correspondence e-mail:
| | - Piero Pianetta
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
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33
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Liu Y, Meirer F, Wang J, Requena G, Williams P, Nelson J, Mehta A, Andrews JC, Pianetta P. 3D elemental sensitive imaging using transmission X-ray microscopy. Anal Bioanal Chem 2012; 404:1297-301. [DOI: 10.1007/s00216-012-5818-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 01/30/2012] [Accepted: 01/31/2012] [Indexed: 10/28/2022]
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34
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Kosior E, Bohic S, Suhonen H, Ortega R, Devès G, Carmona A, Marchi F, Guillet JF, Cloetens P. Combined use of hard X-ray phase contrast imaging and X-ray fluorescence microscopy for sub-cellular metal quantification. J Struct Biol 2012; 177:239-47. [DOI: 10.1016/j.jsb.2011.12.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Revised: 12/02/2011] [Accepted: 12/05/2011] [Indexed: 10/14/2022]
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35
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36
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Bohic S, Cotte M, Salomé M, Fayard B, Kuehbacher M, Cloetens P, Martinez-Criado G, Tucoulou R, Susini J. Biomedical applications of the ESRF synchrotron-based microspectroscopy platform. J Struct Biol 2012; 177:248-58. [DOI: 10.1016/j.jsb.2011.12.006] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Revised: 12/02/2011] [Accepted: 12/05/2011] [Indexed: 01/30/2023]
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37
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Thüring T, Modregger P, Pinzer BR, Wang Z, Stampanoni M. Non-linear regularized phase retrieval for unidirectional X-ray differential phase contrast radiography. OPTICS EXPRESS 2011; 19:25545-25558. [PMID: 22273948 DOI: 10.1364/oe.19.025545] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Phase retrieval from unidirectional radiographic differential phase contrast images requires integration of noisy data. A method is presented, which aims to suppress stripe artifacts arising from direct image integration. It is purely algorithmic and therefore, compared to alternative approaches, neither additional alignment nor an increased scan time is required. We report on the theory of this method and present results using numerical as well as experimental data. The method shows significant improvements on the phase retrieval accuracy and enhances contrast in the phase image. Due to its general applicability, the proposed method provides a valuable tool for various 2D imaging applications using differential data.
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Affiliation(s)
- Thomas Thüring
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, Switzerland
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38
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Morgan KS, Paganin DM, Siu KKW. Quantitative single-exposure x-ray phase contrast imaging using a single attenuation grid. OPTICS EXPRESS 2011; 19:19781-9. [PMID: 21996920 DOI: 10.1364/oe.19.019781] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A single-exposure quantitative method of x-ray phase contrast imaging, suitable for animal in vivo observations, is described and shown experimentally both for a known static sample and an ex vivo biological airway. The ability to acquire the desired information within a single exposure is important for dynamic samples, as is sufficient sensitivity to reveal small variations in the composition or thickness of such a sample. This approach satisfies both these needs by analyzing how a reference grid pattern is deformed by the presence of the sample, similar to a Shack-Hartmann sensor. By resolving the shift of the pattern into horizontal and vertical components, a quantitative phase depth map is recovered, sensitive to both sharp edges as well as low phase gradients.
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Affiliation(s)
- Kaye S Morgan
- School of Physics, Monash University, Clayton, VIC, 3800, Australia.
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39
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Kaulich B, Thibault P, Gianoncelli A, Kiskinova M. Transmission and emission x-ray microscopy: operation modes, contrast mechanisms and applications. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2011; 23:083002. [PMID: 21411893 DOI: 10.1088/0953-8984/23/8/083002] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Advances in microscopy techniques based on x-rays have opened unprecedented opportunities in terms of spatial resolution, combined with chemical and morphology sensitivity, to analyze solid, soft and liquid matter. The advent of ultrabright third and fourth generation photon sources and the continuous development of x-ray optics and detectors has pushed the limits of imaging and spectroscopic analysis to structures as small as a few tens of nanometers. Specific interactions of x-rays with matter provide elemental and chemical sensitivity that have made x-ray spectromicroscopy techniques a very attractive tool, complementary to other microscopies, for characterization in all actual research fields. The x-ray penetration power meets the demand to examine samples too thick for electron microscopes implementing 3D imaging and recently also 4D imaging which adds time resolution as well. Implementation of a variety of phase contrast techniques enhances the structural sensitivity, especially for the hard x-ray regime. Implementation of lensless or diffraction imaging helps to enhance the lateral resolution of x-ray imaging to the wavelength dependent diffraction limit.
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Affiliation(s)
- Burkhard Kaulich
- ELETTRA-Sincrotrone Trieste, Strada Statale 14, km 163.5 in Area Science Park, I-34149 Trieste-Basovizza, Italy.
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40
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Liu Y, Andrews JC, Wang J, Meirer F, Zhu P, Wu Z, Pianetta P. Phase retrieval using polychromatic illumination for transmission X-ray microscopy. OPTICS EXPRESS 2011; 19:540-5. [PMID: 21263593 DOI: 10.1364/oe.19.000540] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
An alternative method for quantitative phase retrieval in a transmission X-ray microscope system at sub-50-nm resolution is presented. As an alternative to moving the sample in the beam direction in order to analyze the propagation-introduced phase effect, we have illuminated the TXM using X-rays of different energy without any motor movement in the TXM system. Both theoretical analysis and experimental studies have confirmed the feasibility and the advantage of our method, because energy tuning can be performed with very high energy resolution using a double crystal monochromator at a synchrotron beam line, and there is zero motor error in TXM system in our approach. High-spatial-resolution phase retrieval is accomplished using the proposed method.
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Affiliation(s)
- Yijin Liu
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA.
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41
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Liu Y, Andrews JC, Wang J, Meirer F, Zhu P, Wu Z, Pianetta P. Phase retrieval using polychromatic illumination for transmission X-ray microscopy. OPTICS EXPRESS 2011. [PMID: 21263593 PMCID: PMC3482903 DOI: 10.1364/oe.19.0540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
An alternative method for quantitative phase retrieval in a transmission X-ray microscope system at sub-50-nm resolution is presented. As an alternative to moving the sample in the beam direction in order to analyze the propagation-introduced phase effect, we have illuminated the TXM using X-rays of different energy without any motor movement in the TXM system. Both theoretical analysis and experimental studies have confirmed the feasibility and the advantage of our method, because energy tuning can be performed with very high energy resolution using a double crystal monochromator at a synchrotron beam line, and there is zero motor error in TXM system in our approach. High-spatial-resolution phase retrieval is accomplished using the proposed method.
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Affiliation(s)
- Yijin Liu
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA.
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42
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Vila-Comamala J, Gorelick S, Färm E, Kewish CM, Diaz A, Barrett R, Guzenko VA, Ritala M, David C. Ultra-high resolution zone-doubled diffractive X-ray optics for the multi-keV regime. OPTICS EXPRESS 2011; 19:175-184. [PMID: 21263555 DOI: 10.1364/oe.19.000175] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
X-ray microscopy based on Fresnel zone plates is a powerful technique for sub-100 nm resolution imaging of biological and inorganic materials. Here, we report on the modeling, fabrication and characterization of zone-doubled Fresnel zone plates for the multi-keV regime (4-12 keV). We demonstrate unprecedented spatial resolution by resolving 15 nm lines and spaces in scanning transmission X-ray microscopy, and focusing diffraction efficiencies of 7.5% at 6.2 keV photon energy. These developments represent a significant step towards 10 nm spatial resolution for hard X-ray energies of up to 12 keV.
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43
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Holzner C, Feser M, Vogt S, Hornberger B, Baines SB, Jacobsen C. Zernike phase contrast in scanning microscopy with X-rays. NATURE PHYSICS 2010; 6:883-887. [PMID: 21544232 PMCID: PMC3085486 DOI: 10.1038/nphys1765] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Scanning X-ray microscopy focuses radiation to a small spot and probes the sample by raster scanning. It allows information to be obtained from secondary signals such as X-ray fluorescence, which yields an elemental mapping of the sample not available in full-field imaging. The analysis and interpretation from these secondary signals can be considerably enhanced if these data are coupled with structural information from transmission imaging. However, absorption often is negligible and phase contrast has not been easily available. Originally introduced with visible light, Zernike phase contrast(1) is a well-established technique in full-field X-ray microscopes for visualization of weakly absorbing samples(2-7). On the basis of reciprocity, we demonstrate the implementation of Zernike phase contrast in scanning X-ray microscopy, revealing structural detail simultaneously with hard-X-ray trace-element measurements. The method is straightforward to implement without significant influence on the resolution of the fluorescence images and delivers complementary information. We show images of biological specimens that clearly demonstrate the advantage of correlating morphology with elemental information.
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Affiliation(s)
- Christian Holzner
- Department of Physics and Astronomy, Stony Brook University, Nicolls Road, Stony Brook, New York 11794, USA
- Correspondence and requests for materials should be addressed to C.H.
| | - Michael Feser
- Xradia Inc., 5052 Commercial Circle, Concord, California 94520, USA
| | - Stefan Vogt
- Advanced Photon Source, Argonne National Laboratory, 9700 S Cass Avenue, Argonne, Illinois 60439, USA
| | | | - Stephen B. Baines
- Department of Ecology and Evolution, Stony Brook University, Nicolls Road, Stony Brook, New York 11794, USA
| | - Chris Jacobsen
- Department of Physics and Astronomy, Stony Brook University, Nicolls Road, Stony Brook, New York 11794, USA
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44
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de Jonge MD, Vogt S. Hard X-ray fluorescence tomography--an emerging tool for structural visualization. Curr Opin Struct Biol 2010; 20:606-14. [PMID: 20934872 DOI: 10.1016/j.sbi.2010.09.002] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Revised: 09/02/2010] [Accepted: 09/02/2010] [Indexed: 10/19/2022]
Abstract
Hard X-ray fluorescence microscopy is well-suited to in-situ investigations of trace metal distributions within whole, unstained, biological tissue, with sub-parts-per-million detection achievable in whole cells. The high penetration of X-rays indicates the use of X-ray fluorescence tomography for structural visualization, and recent measurements have realised sub-500-nm tomography on a 10-μm cell. Limitations of present approaches impact the duration of an experiment and imaging fidelity. Developments in X-ray resolution, detector speed, cryogenic environments, and the incorporation of auxiliary signals are being pursued within the synchrotron community. Several complementary approaches to X-ray fluorescence tomography will be routinely available to the biologist in the near future. We discuss these approaches and review applications of biological relevance.
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Affiliation(s)
- Martin D de Jonge
- Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia.
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45
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Menzel A, Kewish C, Kraft P, Henrich B, Jefimovs K, Vila-Comamala J, David C, Dierolf M, Thibault P, Pfeiffer F, Bunk O. Scanning transmission X-ray microscopy with a fast framing pixel detector. Ultramicroscopy 2010; 110:1143-7. [DOI: 10.1016/j.ultramic.2010.04.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2009] [Revised: 04/14/2010] [Accepted: 04/15/2010] [Indexed: 11/16/2022]
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46
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Jonge MDD, Hornberger B, Holzner C, Twining B, Paterson D, McNulty I, Jacobsen C, Vogt S. Quantitative scanning differential phase contrast microscopy. ACTA ACUST UNITED AC 2009. [DOI: 10.1088/1742-6596/186/1/012006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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47
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Menzel A, Kewish CM, Dierolf M, Thibault P, Kraft P, Bunk O, Jefimovs K, David C, Pfeiffer F. Hard X-ray scanning transmission microscopy with a 2Dpixel array detector. ACTA ACUST UNITED AC 2009. [DOI: 10.1088/1742-6596/186/1/012054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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48
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Paunesku T, Vogt S, Irving TC, Lai B, Barrea RA, Maser J, Woloschak GE. Biological applications of X-ray microprobes. Int J Radiat Biol 2009; 85:710-3. [PMID: 19637082 DOI: 10.1080/09553000903009514] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
PURPOSE To present an overview of the workshop on X-ray fluorescence microscopy (XFM). RESULTS Talks presented at the workshop and the associated works are highlighted. CONCLUSIONS Use of XFM in biomedical sciences is growing and may be advanced even further by adding (i) high resolution microprobes, and (ii) high throughput approaches to the XFM toolbox.
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Affiliation(s)
- Tatjana Paunesku
- Department of Radiation Oncology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois 60611, USA
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49
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Guehrs E, Günther CM, Könnecke R, Pfau B, Eisebitt S. Holographic soft X-ray omni-microscopy of biological specimens. OPTICS EXPRESS 2009; 17:6710-6720. [PMID: 19365499 DOI: 10.1364/oe.17.006710] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Mask-based digital soft X-ray Fourier transform holography using coherent synchrotron radiation is applied to image diatoms and freeze-dried 3T3 fibroblast cells. At soft X-ray wavelengths between 4 nm and 8 nm we achieve spatial resolutions down to 450 nm over a 33.5 microm field of view. As holography records amplitude and phase of the scattered wavefield, images with different contrast mechanisms can be generated a posteriori by numerical processing of the holographic data ("omni-microscopy"). We present Zernike phase contrast, Schlieren phase contrast, differential interference and gradient contrast images based on amplitude and phase information. We discuss the potential of this approach for destructive single-shot imaging beyond dose limitations of biological samples at coherent femtosecond-pulsed X-ray sources.
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Affiliation(s)
- Erik Guehrs
- Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin, Germany
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50
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Mukaide T, Takada K, Watanabe M, Noma T, Iida A. Scanning hard x-ray differential phase contrast imaging with a double wedge absorber. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2009; 80:033707. [PMID: 19334927 DOI: 10.1063/1.3095440] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Two-directional differential phase contrast images were measured using an x-ray microbeam and a double wedge absorber. The wedge absorber converts the displacement of an x-ray beam that is refracted by an object into change of x-ray intensity. The double wedge absorber made it possible to detect values of two-directional refraction angle with microrad sensitivity simultaneously. By Fourier integration of two-directional phase gradients calculated from the refraction angle instead of line integration of one-directional phase gradients, we obtained a quantitative phase map without artifacts even when only a part of the boundaries of the object were in the field of view. One of the characteristics of this technique is flexibility in a sensitivity of the phase gradient. By changing of shape or material of the wedge absorber, it is comparatively easy to control the detection limit of the refraction angle.
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Affiliation(s)
- Taihei Mukaide
- Materials Technology Development Center, Canon Inc., 30-2, Shimomaruko 3-chome, Ohta-ku, Tokyo 146-8501, Japan
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