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Flenner S, Hagemann J, Wittwer F, Longo E, Kubec A, Rothkirch A, David C, Müller M, Greving I. Hard X-ray full-field nanoimaging using a direct photon-counting detector. JOURNAL OF SYNCHROTRON RADIATION 2023; 30:390-399. [PMID: 36891852 PMCID: PMC10000802 DOI: 10.1107/s1600577522012103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 12/22/2022] [Indexed: 06/18/2023]
Abstract
Full-field X-ray nanoimaging is a widely used tool in a broad range of scientific areas. In particular, for low-absorbing biological or medical samples, phase contrast methods have to be considered. Three well established phase contrast methods at the nanoscale are transmission X-ray microscopy with Zernike phase contrast, near-field holography and near-field ptychography. The high spatial resolution, however, often comes with the drawback of a lower signal-to-noise ratio and significantly longer scan times, compared with microimaging. In order to tackle these challenges a single-photon-counting detector has been implemented at the nanoimaging endstation of the beamline P05 at PETRA III (DESY, Hamburg) operated by Helmholtz-Zentrum Hereon. Thanks to the long sample-to-detector distance available, spatial resolutions of below 100 nm were reached in all three presented nanoimaging techniques. This work shows that a single-photon-counting detector in combination with a long sample-to-detector distance allows one to increase the time resolution for in situ nanoimaging, while keeping a high signal-to-noise level.
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Affiliation(s)
- Silja Flenner
- Helmholtz-Zentrum Hereon, Max-Planck-Strasse 1, 21502 Geesthacht, Germany
| | - Johannes Hagemann
- Center for X-ray and Nano Science – CXNS, Deutsches Elektronen-Synchrotron – DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Felix Wittwer
- Center for X-ray and Nano Science – CXNS, Deutsches Elektronen-Synchrotron – DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Elena Longo
- Helmholtz-Zentrum Hereon, Max-Planck-Strasse 1, 21502 Geesthacht, Germany
| | - Adam Kubec
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - André Rothkirch
- Center for X-ray and Nano Science – CXNS, Deutsches Elektronen-Synchrotron – DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Christian David
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen, Switzerland
| | - Martin Müller
- Helmholtz-Zentrum Hereon, Max-Planck-Strasse 1, 21502 Geesthacht, Germany
| | - Imke Greving
- Helmholtz-Zentrum Hereon, Max-Planck-Strasse 1, 21502 Geesthacht, Germany
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Flenner S, Bruns S, Longo E, Parnell AJ, Stockhausen KE, Müller M, Greving I. Machine learning denoising of high-resolution X-ray nanotomography data. JOURNAL OF SYNCHROTRON RADIATION 2022; 29:230-238. [PMID: 34985440 PMCID: PMC8733986 DOI: 10.1107/s1600577521011139] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 10/23/2021] [Indexed: 05/13/2023]
Abstract
High-resolution X-ray nanotomography is a quantitative tool for investigating specimens from a wide range of research areas. However, the quality of the reconstructed tomogram is often obscured by noise and therefore not suitable for automatic segmentation. Filtering methods are often required for a detailed quantitative analysis. However, most filters induce blurring in the reconstructed tomograms. Here, machine learning (ML) techniques offer a powerful alternative to conventional filtering methods. In this article, we verify that a self-supervised denoising ML technique can be used in a very efficient way for eliminating noise from nanotomography data. The technique presented is applied to high-resolution nanotomography data and compared to conventional filters, such as a median filter and a nonlocal means filter, optimized for tomographic data sets. The ML approach proves to be a very powerful tool that outperforms conventional filters by eliminating noise without blurring relevant structural features, thus enabling efficient quantitative analysis in different scientific fields.
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Affiliation(s)
- Silja Flenner
- Helmholtz-Zentrum Hereon, Max-Planck-Strasse 1, 21502 Geesthacht, Germany
| | - Stefan Bruns
- Helmholtz-Zentrum Hereon, Max-Planck-Strasse 1, 21502 Geesthacht, Germany
| | - Elena Longo
- Helmholtz-Zentrum Hereon, Max-Planck-Strasse 1, 21502 Geesthacht, Germany
| | - Andrew J. Parnell
- Department of Physics and Astronomy, University of Sheffield, Western Bank, Sheffield S3 7RH, United Kingdom
| | - Kilian E. Stockhausen
- Department of Osteology and Biomechanics, University Medical Center, Lottestrasse 55a, 22529 Hamburg, Germany
| | - Martin Müller
- Helmholtz-Zentrum Hereon, Max-Planck-Strasse 1, 21502 Geesthacht, Germany
| | - Imke Greving
- Helmholtz-Zentrum Hereon, Max-Planck-Strasse 1, 21502 Geesthacht, Germany
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Takeuchi A, Suzuki Y. Recent progress in synchrotron radiation 3D-4D nano-imaging based on X-ray full-field microscopy. ACTA ACUST UNITED AC 2020; 69:259-279. [PMID: 32373929 DOI: 10.1093/jmicro/dfaa022] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 04/09/2020] [Accepted: 04/24/2020] [Indexed: 11/14/2022]
Abstract
The advent of high-flux, high-brilliance synchrotron radiation (SR) has prompted the development of high-resolution X-ray imaging techniques such as full-field microscopy, holography, coherent diffraction imaging and ptychography. These techniques have strong potential to establish non-destructive three- and four-dimensional nano-imaging when combined with computed tomography (CT), called nano-tomography (nano-CT). X-ray nano-CTs based on full-field microscopy are now routinely available and widely used. Here we discuss the current status and some applications of nano-CT using a Fresnel zone plate as an objective. Optical properties of full-field microscopy, such as spatial resolution and off-axis aberration, which determine the effective field of view, are also discussed, especially in relation to 3D tomographic imaging.
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Affiliation(s)
- Akihisa Takeuchi
- Japan Synchrotron Radiation Research Institute (JASRI), SPring-8, Sayo, Hyogo 679-5198, Japan
| | - Yoshio Suzuki
- Graduate School of Frontier Science, University of Tokyo, Kasiwa, Chiba 277-8561, Japan
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Flenner S, Storm M, Kubec A, Longo E, Döring F, Pelt DM, David C, Müller M, Greving I. Pushing the temporal resolution in absorption and Zernike phase contrast nanotomography: enabling fast in situ experiments. JOURNAL OF SYNCHROTRON RADIATION 2020; 27:1339-1346. [PMID: 32876609 PMCID: PMC7467338 DOI: 10.1107/s1600577520007407] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 06/03/2020] [Indexed: 05/26/2023]
Abstract
Hard X-ray nanotomography enables 3D investigations of a wide range of samples with high resolution (<100 nm) with both synchrotron-based and laboratory-based setups. However, the advantage of synchrotron-based setups is the high flux, enabling time resolution, which cannot be achieved at laboratory sources. Here, the nanotomography setup at the imaging beamline P05 at PETRA III is presented, which offers high time resolution not only in absorption but for the first time also in Zernike phase contrast. Two test samples are used to evaluate the image quality in both contrast modalities based on the quantitative analysis of contrast-to-noise ratio (CNR) and spatial resolution. High-quality scans can be recorded in 15 min and fast scans down to 3 min are also possible without significant loss of image quality. At scan times well below 3 min, the CNR values decrease significantly and classical image-filtering techniques reach their limitation. A machine-learning approach shows promising results, enabling acquisition of a full tomography in only 6 s. Overall, the transmission X-ray microscopy instrument offers high temporal resolution in absorption and Zernike phase contrast, enabling in situ experiments at the beamline.
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Affiliation(s)
- Silja Flenner
- Institute of Materials Research, Helmholtz-Zentrum Geesthacht, Max-Planck-Strasse 1, 21502 Geesthacht, Germany
| | - Malte Storm
- Diamond Light Source Ltd, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Adam Kubec
- Paul Scherrer Institut, Forschnungsstrasse 111, 5232 Villingen, Switzerland
| | - Elena Longo
- Institute of Materials Research, Helmholtz-Zentrum Geesthacht, Max-Planck-Strasse 1, 21502 Geesthacht, Germany
| | - Florian Döring
- Paul Scherrer Institut, Forschnungsstrasse 111, 5232 Villingen, Switzerland
| | - Daniël M. Pelt
- Centrum Wiskunde and Informatica, Science Park 123, 1098 XG Amsterdam, The Netherlands
| | - Christian David
- Paul Scherrer Institut, Forschnungsstrasse 111, 5232 Villingen, Switzerland
| | - Martin Müller
- Institute of Materials Research, Helmholtz-Zentrum Geesthacht, Max-Planck-Strasse 1, 21502 Geesthacht, Germany
| | - Imke Greving
- Institute of Materials Research, Helmholtz-Zentrum Geesthacht, Max-Planck-Strasse 1, 21502 Geesthacht, Germany
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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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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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Andrews JC, Meirer F, Liu Y, Mester Z, Pianetta P. Transmission X-ray microscopy for full-field nano imaging of biomaterials. Microsc Res Tech 2010; 74:671-81. [PMID: 20734414 DOI: 10.1002/jemt.20907] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Accepted: 06/14/2010] [Indexed: 11/09/2022]
Abstract
Imaging of cellular structure and extended tissue in biological materials requires nanometer resolution and good sample penetration, which can be provided by current full-field transmission X-ray microscopic techniques in the soft and hard X-ray regions. The various capabilities of full-field transmission X-ray microscopy (TXM) include 3D tomography, Zernike phase contrast, quantification of absorption, and chemical identification via X-ray fluorescence and X-ray absorption near edge structure imaging. These techniques are discussed and compared in light of results from the imaging of biological materials including microorganisms, bone and mineralized tissue, and plants, with a focus on hard X-ray TXM at ≤ 40-nm resolution.
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Affiliation(s)
- Joy C Andrews
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA.
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Thieme J, Niemeyer J. Fractal characterization of hematite aggregates by X-ray microscopy. ACTA ACUST UNITED AC 1996. [DOI: 10.1007/bf02440115] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Abstract
In this review we propose to address the question: for the life-science researcher, what does X-ray microscopy have to offer that is not otherwise easily available?We will see that the answer depends on a combination of resolution, penetrating power, analytical sensitivity, compatibility with wet specimens, and the ease of image interpretation.
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Affiliation(s)
- J Kirz
- Physics Department, State University of New York, Stony Brook 11794-3800, USA
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