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Maldanis L, Fernandez-Remolar D, Lemelle L, Knoll AH, Guizar-Sicairos M, Holler M, da Silva FMC, Magnin V, Mermoux M, Simionovici A. Unveiling Challenging Microbial Fossil Biosignatures from Rio Tinto with Micro-to-Nanoscale Chemical and Ultrastructural Imaging. ASTROBIOLOGY 2024; 24:721-733. [PMID: 38985734 DOI: 10.1089/ast.2023.0127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
Understanding the nature and preservation of microbial traces in extreme environments is crucial for reconstructing Earth's early biosphere and for the search for life on other planets or moons. At Rio Tinto, southwestern Spain, ferric oxide and sulfate deposits similar to those discovered at Meridiani Planum, Mars, entomb a diversity of fossilized organisms, despite chemical conditions commonly thought to be challenging for life and fossil preservation. Investigating this unique fossil microbiota can elucidate ancient extremophile communities and the preservation of biosignatures in acidic environments on Earth and, potentially, Mars. In this study, we use an innovative multiscale approach that combines the state-of-the-art synchrotron X-ray nanoimaging methods of ptychographic X-ray computed laminography and nano-X-ray fluorescence to reveal Rio Tinto's microfossils at subcellular resolution. The unprecedented nanoscale views of several different specimens within their geological and geochemical contexts reveal novel intricacies of preserved microbial communities. Different morphotypes, ecological interactions, and possible taxonomic affinities were inferred based on qualitative and quantitative 3D ultrastructural information, whereas diagenetic processes and metabolic affinities were inferred from complementary chemical information. Our integrated nano-to-microscale analytical approach revealed previously invisible microbial and mineral interactions, which complemented and filled a gap of spatial resolution in conventional methods. Ultimately, this study contributes to the challenge of deciphering the faint chemical and morphological biosignatures that can indicate life's presence on the early Earth and on distant worlds.
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Affiliation(s)
- Lara Maldanis
- ISTerre, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, IRD, IFSTTAR, Grenoble, France
| | - David Fernandez-Remolar
- SKL Lunar and Planetary Sciences, Macau University of Science and Technology, Macau, China
- CNSA Macau Center for Space Exploration and Science, Macau, China
| | | | - Andrew H Knoll
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge Massachusetts, USA
| | - Manuel Guizar-Sicairos
- Paul Scherrer Institute, Villigen PSI, Switzerland
- Institute of Physics, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Mirko Holler
- Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Francisco Mateus Cirilo da Silva
- Brazilian Synchrotron Light Laboratory, LNLS, Brazilian Center for Research in Energy and Materials, CNPEM, Campinas, Brazil
- Institute of Physics, IFGW, Campinas University, UNICAMP, Campinas, Brazil
| | - Valérie Magnin
- ISTerre, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, IRD, IFSTTAR, Grenoble, France
| | - Michel Mermoux
- LEPMI, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, Grenoble INP, 38000 Grenoble, France
| | - Alexandre Simionovici
- ISTerre, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, IRD, IFSTTAR, Grenoble, France
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Nikitin V, Wildenberg G, Mittone A, Shevchenko P, Deriy A, De Carlo F. Laminography as a tool for imaging large-size samples with high resolution. JOURNAL OF SYNCHROTRON RADIATION 2024; 31:851-866. [PMID: 38771775 PMCID: PMC11226144 DOI: 10.1107/s1600577524002923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/03/2024] [Indexed: 05/23/2024]
Abstract
Despite the increased brilliance of the new generation synchrotron sources, there is still a challenge with high-resolution scanning of very thick and absorbing samples, such as a whole mouse brain stained with heavy elements, and, extending further, brains of primates. Samples are typically cut into smaller parts, to ensure a sufficient X-ray transmission, and scanned separately. Compared with the standard tomography setup where the sample would be cut into many pillars, the laminographic geometry operates with slab-shaped sections significantly reducing the number of sample parts to be prepared, the cutting damage and data stitching problems. In this work, a laminography pipeline for imaging large samples (>1 cm) at micrometre resolution is presented. The implementation includes a low-cost instrument setup installed at the 2-BM micro-CT beamline of the Advanced Photon Source. Additionally, sample mounting, scanning techniques, data stitching procedures, a fast reconstruction algorithm with low computational complexity, and accelerated reconstruction on multi-GPU systems for processing large-scale datasets are presented. The applicability of the whole laminography pipeline was demonstrated by imaging four sequential slabs throughout an entire mouse brain sample stained with osmium, in total generating approximately 12 TB of raw data for reconstruction.
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Affiliation(s)
- Viktor Nikitin
- Advanced Photon SourceArgonne National LaboratoryLemontIL60439USA
| | | | - Alberto Mittone
- Advanced Photon SourceArgonne National LaboratoryLemontIL60439USA
| | - Pavel Shevchenko
- Advanced Photon SourceArgonne National LaboratoryLemontIL60439USA
| | - Alex Deriy
- Advanced Photon SourceArgonne National LaboratoryLemontIL60439USA
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Hierarchically guided in situ nanolaminography for the visualisation of damage nucleation in alloy sheets. Sci Rep 2023; 13:1055. [PMID: 36658141 PMCID: PMC9852562 DOI: 10.1038/s41598-022-27035-8] [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: 09/30/2022] [Accepted: 12/23/2022] [Indexed: 01/20/2023] Open
Abstract
Hierarchical guidance is developed for three-dimensional (3D) nanoscale X-ray imaging, enabling identification, refinement, and tracking of regions of interest (ROIs) within specimens considerably exceeding the field of view. This opens up new possibilities for in situ investigations. Experimentally, the approach takes advantage of rapid multiscale measurements based on magnified projection microscopy featuring continuous zoom capabilities. Immediate and continuous feedback on the subsequent experimental progress is enabled by suitable on-the-fly data processing. For this, by theoretical justification and experimental validation, so-called quasi-particle phase-retrieval is generalised to conical-beam conditions, being key for sufficiently fast computation without significant loss of imaging quality and resolution compared to common approaches for holographic microscopy. Exploiting 3D laminography, particularly suited for imaging of ROIs in laterally extended plate-like samples, the potential of hierarchical guidance is demonstrated by the in situ investigation of damage nucleation inside alloy sheets under engineering-relevant boundary conditions, providing novel insight into the nanoscale morphological development of void and particle clusters under mechanical load. Combined with digital volume correlation, we study deformation kinematics with unprecedented spatial resolution. Correlation of mesoscale (i.e. strain fields) and nanoscale (i.e. particle cracking) evolution opens new routes for the understanding of damage nucleation within sheet materials with application-relevant dimensions.
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Faragó T, Gasilov S, Emslie I, Zuber M, Helfen L, Vogelgesang M, Baumbach T. Tofu: a fast, versatile and user-friendly image processing toolkit for computed tomography. JOURNAL OF SYNCHROTRON RADIATION 2022; 29:916-927. [PMID: 35511025 PMCID: PMC9070706 DOI: 10.1107/s160057752200282x] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 03/14/2022] [Indexed: 06/01/2023]
Abstract
Tofu is a toolkit for processing large amounts of images and for tomographic reconstruction. Complex image processing tasks are organized as workflows of individual processing steps. The toolkit is able to reconstruct parallel and cone beam as well as tomographic and laminographic geometries. Many pre- and post-processing algorithms needed for high-quality 3D reconstruction are available, e.g. phase retrieval, ring removal and de-noising. Tofu is optimized for stand-alone GPU workstations on which it achieves reconstruction speed comparable with costly CPU clusters. It automatically utilizes all GPUs in the system and generates 3D reconstruction code with minimal number of instructions given the input geometry (parallel/cone beam, tomography/laminography), hence yielding optimal run-time performance. In order to improve accessibility for researchers with no previous knowledge of programming, tofu contains graphical user interfaces for both optimization of 3D reconstruction parameters and batch processing of data with pre-configured workflows for typical computed tomography reconstruction. The toolkit is open source and extensive documentation is available for both end-users and developers. Thanks to the mentioned features, tofu is suitable for both expert users with specialized image processing needs (e.g. when dealing with data from custom-built computed tomography scanners) and for application-specific end-users who just need to reconstruct their data on off-the-shelf hardware.
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Affiliation(s)
- Tomáš Faragó
- Institute for Photon Science and Synchrotron Radiation, Karlsruhe Institute of Technology (KIT), Herrmann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Sergey Gasilov
- Canadian Light Source, 44 Innovation Blvd, Saskatoon, Canada S7N 2V3
| | - Iain Emslie
- Canadian Light Source, 44 Innovation Blvd, Saskatoon, Canada S7N 2V3
| | - Marcus Zuber
- Institute for Photon Science and Synchrotron Radiation, Karlsruhe Institute of Technology (KIT), Herrmann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Laboratory for Applications of Synchrotron Radiation, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
| | - Lukas Helfen
- Institute for Photon Science and Synchrotron Radiation, Karlsruhe Institute of Technology (KIT), Herrmann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Institut Laue-Langevin, 71 Avenue des Martyrs, CS 20156, 38042 Grenoble Cedex 9, France
| | - Matthias Vogelgesang
- Institute for Data Processing and Electronics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Tilo Baumbach
- Institute for Photon Science and Synchrotron Radiation, Karlsruhe Institute of Technology (KIT), Herrmann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Laboratory for Applications of Synchrotron Radiation, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
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Bossema FG, Domínguez-Delmás M, Palenstijn WJ, Kostenko A, Dorscheid J, Coban SB, Hermens E, Batenburg KJ. A novel method for dendrochronology of large historical wooden objects using line trajectory X-ray tomography. Sci Rep 2021; 11:11024. [PMID: 34040035 PMCID: PMC8154960 DOI: 10.1038/s41598-021-90135-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/04/2021] [Indexed: 02/04/2023] Open
Abstract
Dendrochronology is an essential tool to determine the date and provenance of wood from historical art objects. As standard methods to access the tree rings are invasive, X-ray computed tomography (CT) has been proposed for non-invasive dendrochronological investigation. While traditional CT can provide clear images of the inner structure of wooden objects, it requires their full rotation, imposing strong limitations on the size of the object. These limitations have previously encouraged investigations into alternative acquisition trajectories, including trajectories with only linear movement. In this paper, we use such a line-trajectory (LT) X-ray tomography technique to retrieve tree-ring patterns from large wooden objects. We demonstrate that by moving a wooden artifact sideways between the static X-ray source and the detector during acquisition, sharp reconstruction images of the tree rings can be produced. We validate this technique using computer simulations and two wooden test planks, and demonstrate it on a large iconic chest from the Rijksmuseum collection (Amsterdam, The Netherlands). The LT scanning method can be easily implemented in standard X-ray imaging units available at museum research facilities. Therefore, this scanning technique represents a major step towards the standard implementation of non-invasive dendrochronology on large wooden cultural heritage objects.
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Affiliation(s)
- Francien G Bossema
- Computational Imaging, Centrum Wiskunde & Informatica, Science Park 123, 1098 XG, Amsterdam, The Netherlands.
- Conservation and Science Department, Rijksmuseum, Hobbemastraat 22, 1071 ZC, Amsterdam, The Netherlands.
| | - Marta Domínguez-Delmás
- Conservation and Science Department, Rijksmuseum, Hobbemastraat 22, 1071 ZC, Amsterdam, The Netherlands
- Department of History of Art, University of Amsterdam, BG2 Turfdraagsterpad 15-17, 1012 XT, Amsterdam, The Netherlands
| | - Willem Jan Palenstijn
- Computational Imaging, Centrum Wiskunde & Informatica, Science Park 123, 1098 XG, Amsterdam, The Netherlands
| | - Alexander Kostenko
- Computational Imaging, Centrum Wiskunde & Informatica, Science Park 123, 1098 XG, Amsterdam, The Netherlands
| | - Jan Dorscheid
- Conservation and Science Department, Rijksmuseum, Hobbemastraat 22, 1071 ZC, Amsterdam, The Netherlands
| | - Sophia Bethany Coban
- Computational Imaging, Centrum Wiskunde & Informatica, Science Park 123, 1098 XG, Amsterdam, The Netherlands
| | - Erma Hermens
- Conservation and Science Department, Rijksmuseum, Hobbemastraat 22, 1071 ZC, Amsterdam, The Netherlands
- Department of History of Art, University of Amsterdam, BG2 Turfdraagsterpad 15-17, 1012 XT, Amsterdam, The Netherlands
| | - K Joost Batenburg
- Computational Imaging, Centrum Wiskunde & Informatica, Science Park 123, 1098 XG, Amsterdam, The Netherlands
- Leiden Institute of Advanced Computer Science, Leiden University, Niels Bohrweg 1, 2333 CA, Leiden, The Netherlands
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Danilewsky AN. X‐Ray Topography—More than Nice Pictures. CRYSTAL RESEARCH AND TECHNOLOGY 2020. [DOI: 10.1002/crat.202000012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Holler M, Odstrčil M, Guizar-Sicairos M, Lebugle M, Frommherz U, Lachat T, Bunk O, Raabe J, Aeppli G. LamNI - an instrument for X-ray scanning microscopy in laminography geometry. JOURNAL OF SYNCHROTRON RADIATION 2020; 27:730-736. [PMID: 32381775 PMCID: PMC7206541 DOI: 10.1107/s1600577520003586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 03/09/2020] [Indexed: 05/02/2023]
Abstract
Across all branches of science, medicine and engineering, high-resolution microscopy is required to understand functionality. Although optical methods have been developed to `defeat' the diffraction limit and produce 3D images, and electrons have proven ever more useful in creating pictures of small objects or thin sections, so far there is no substitute for X-ray microscopy in providing multiscale 3D images of objects with a single instrument and minimal labeling and preparation. A powerful technique proven to continuously access length scales from 10 nm to 10 µm is ptychographic X-ray computed tomography, which, on account of the orthogonality of the tomographic rotation axis to the illuminating beam, still has the limitation of necessitating pillar-shaped samples of small (ca 10 µm) diameter. Large-area planar samples are common in science and engineering, and it is therefore highly desirable to create an X-ray microscope that can examine such samples without the extraction of pillars. Computed laminography, where the axis of rotation is not perpendicular to the illumination direction, solves this problem. This entailed the development of a new instrument, LamNI, dedicated to high-resolution 3D scanning X-ray microscopy via hard X-ray ptychographic laminography. Scanning precision is achieved by a dedicated interferometry scheme and the instrument covers a scan range of 12 mm × 12 mm with a position stability of 2 nm and positioning errors below 5 nm. A new feature of LamNI is a pair of counter-rotating stages carrying the sample and interferometric mirrors, respectively.
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Affiliation(s)
- Mirko Holler
- Photon Science, Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Michal Odstrčil
- Photon Science, Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Manuel Guizar-Sicairos
- Photon Science, Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Maxime Lebugle
- Photon Science, Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Ulrich Frommherz
- Large Research Facilities, Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Thierry Lachat
- EnDes Engineering Partner AG, 4703 Kestenholz, Switzerland
| | - Oliver Bunk
- Photon Science, Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Joerg Raabe
- Photon Science, Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Gabriel Aeppli
- Photon Science, Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
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Witte K, Späth A, Finizio S, Donnelly C, Watts B, Sarafimov B, Odstrcil M, Guizar-Sicairos M, Holler M, Fink RH, Raabe J. From 2D STXM to 3D Imaging: Soft X-ray Laminography of Thin Specimens. NANO LETTERS 2020; 20:1305-1314. [PMID: 31951418 DOI: 10.1021/acs.nanolett.9b04782] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
X-ray tomography has become an indispensable tool for studying complex 3D interior structures with high spatial resolution. Three-dimensional imaging using soft X-rays offers powerful contrast mechanisms but has seen limited success with tomography due to the restrictions imposed by the much lower energy of the probe beam. The generalized geometry of laminography, characterized by a tilted axis of rotation, provides nm-scale 3D resolution for the investigation of extended (mm range) but thin (μm to nm) samples that are well suited to soft X-ray studies. This work reports on the implementation of soft X-ray laminography (SoXL) at the scanning transmission X-ray spectromicroscope of the PolLux beamline at the Swiss Light Source, Paul Scherrer Institut, which enables 3D imaging of extended specimens from 270 to 1500 eV. Soft X-ray imaging provides contrast mechanisms for both chemical sensitivity to molecular bonds and oxidation states and magnetic dichroism due to the much stronger attenuation of X-rays in this energy range. The presented examples of applications range from functionalized nanomaterials to biological photonic crystals and sophisticated nanoscaled magnetic domain patterns, thus illustrating the wide fields of research that can benefit from SoXL.
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Affiliation(s)
- Katharina Witte
- Swiss Light Source , Paul Scherrer Institut , Forschungsstrasse 111 , 5232 Villigen , Switzerland
| | - Andreas Späth
- Department Chemie und Pharmazie, Physikalische Chemie , Friedrich-Alexander-Universität Erlangen-Nürnberg , Egerlandstrasse 3 , 91058 Erlangen , Germany
| | - Simone Finizio
- Swiss Light Source , Paul Scherrer Institut , Forschungsstrasse 111 , 5232 Villigen , Switzerland
| | - Claire Donnelly
- Cavendish Laboratory , University of Cambridge , JJ Thomson Avenue , Cambridge , CB3 0HE , United Kingdom
| | - Benjamin Watts
- Swiss Light Source , Paul Scherrer Institut , Forschungsstrasse 111 , 5232 Villigen , Switzerland
| | - Blagoj Sarafimov
- Swiss Light Source , Paul Scherrer Institut , Forschungsstrasse 111 , 5232 Villigen , Switzerland
| | - Michal Odstrcil
- Swiss Light Source , Paul Scherrer Institut , Forschungsstrasse 111 , 5232 Villigen , Switzerland
| | - Manuel Guizar-Sicairos
- Swiss Light Source , Paul Scherrer Institut , Forschungsstrasse 111 , 5232 Villigen , Switzerland
| | - Mirko Holler
- Swiss Light Source , Paul Scherrer Institut , Forschungsstrasse 111 , 5232 Villigen , Switzerland
| | - Rainer H Fink
- Department Chemie und Pharmazie, Physikalische Chemie , Friedrich-Alexander-Universität Erlangen-Nürnberg , Egerlandstrasse 3 , 91058 Erlangen , Germany
| | - Jörg Raabe
- Swiss Light Source , Paul Scherrer Institut , Forschungsstrasse 111 , 5232 Villigen , Switzerland
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Odstrčil M, Holler M, Raabe J, Guizar-Sicairos M. Alignment methods for nanotomography with deep subpixel accuracy. OPTICS EXPRESS 2019; 27:36637-36652. [PMID: 31873438 DOI: 10.1364/oe.27.036637] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 11/15/2019] [Indexed: 06/10/2023]
Abstract
As the resolution of X-ray tomography improves, the limited long-term stability and accuracy of nanoimaging tools does not allow computing artifact-free three-dimensional (3D) reconstructions without an additional step of numerical alignment of the measured projections. However, the common iterative alignment methods are significantly more computationally demanding than a simple tomographic reconstruction of the acquired volume. Here, we address this issue and present an alignment toolkit, which exploits methods with deep-subpixel accuracy combined with a multi-resolution scheme. This leads to robust and accurate alignment with significantly reduced computational and memory requirements. The performance of the presented methods is demonstrated on simulated and measured datasets for tomography and also laminography acquisition geometries. A GPU accelerated implementation of our alignment framework is publicly available.
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Yoneyama A, Hyodo K, Baba R, Takeya S, Takeda T. Feasibility study of phase-contrast X-ray laminography using X-ray interferometry. JOURNAL OF SYNCHROTRON RADIATION 2018; 25:1841-1846. [PMID: 30407197 DOI: 10.1107/s1600577518013826] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 09/29/2018] [Indexed: 06/08/2023]
Abstract
For fine observation of laminar samples, phase-contrast X-ray laminography using X-ray interferometry was developed. An imaging system fitted with a two-crystal X-ray interferometer was used to perform the observations, and the sectional images were calculated by a three-dimensional iterative reconstruction method. Obtained images of an old flat slab of limestone from the Carnic Alps depicted fusulinids in the Carboniferous period with 3 mg cm-3 density resolution, and those of carbon paper used for a fuel-cell battery displayed the inner fibrous structures clearly.
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Affiliation(s)
- Akio Yoneyama
- SAGA Light Source, 8-7 Yayoigaoka, Tosu, Saga 841-0005, Japan
| | - Kazuyuki Hyodo
- Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Rika Baba
- Research and Development Group, Hitachi Ltd, 1-280 Higashi-koigakubo, Kokubunji, Tokyo 185-8601, Japan
| | - Satoshi Takeya
- Research Institute for Material and Chemical Measurement, National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Tohoru Takeda
- School of Allied Health Sciences, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
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11
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Multi-contrast diffraction enhanced computed laminography at Beijing Synchrotron Radiation Facility. Anal Bioanal Chem 2018; 410:7221-7228. [PMID: 30171283 DOI: 10.1007/s00216-018-1329-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 08/11/2018] [Accepted: 08/15/2018] [Indexed: 11/27/2022]
Abstract
Synchrotron radiation X-ray computed tomography (CT) enables nondestructive visualization of 3D morphological and chemical changes inside a sample and has become a powerful analysis tool to monitor reactive parts and their chemical states. However, synchrotron radiation CT imaging of specimens with lateral extensions much larger than the acceptance window of detectors is rather problematic due to strong absorption of X-rays in the lateral directions. On the other hand, X-ray computed laminography (CL) permits 3D imaging of flat samples while X-ray diffraction enhanced imaging (DEI) can provide high-quality results with different imaging contrasts such as absorption, phase and dark-field for samples with weak absorptions. Combining CL and DEI together, we have developed a multi-contrast DEI-CL system at the 4W1A beamline of the Beijing Synchrotron Radiation Facility for this kind of sample. Here we reported its design, implementation, and preliminary experimental results of carbon fiber reinforced polymer laminates with three kinds of imaging contrasts. The results have demonstrated the validity of this DEI-CL system. It will be helpful to push the applications of the state-of-the-art synchrotron radiation methods and instruments towards cutting-edge research. Graphical abstract ᅟ.
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Electromigration Mechanism of Failure in Flip-Chip Solder Joints Based on Discrete Void Formation. Sci Rep 2017; 7:17950. [PMID: 29263329 PMCID: PMC5738397 DOI: 10.1038/s41598-017-06250-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 06/09/2017] [Indexed: 11/09/2022] Open
Abstract
In this investigation, SnAgCu and SN100C solders were electromigration (EM) tested, and the 3D laminography imaging technique was employed for in-situ observation of the microstructure evolution during testing. We found that discrete voids nucleate, grow and coalesce along the intermetallic compound/solder interface during EM testing. A systematic analysis yields quantitative information on the number, volume, and growth rate of voids, and the EM parameter of DZ*. We observe that fast intrinsic diffusion in SnAgCu solder causes void growth and coalescence, while in the SN100C solder this coalescence was not significant. To deduce the current density distribution, finite-element models were constructed on the basis of the laminography images. The discrete voids do not change the global current density distribution, but they induce the local current crowding around the voids: this local current crowding enhances the lateral void growth and coalescence. The correlation between the current density and the probability of void formation indicates that a threshold current density exists for the activation of void formation. There is a significant increase in the probability of void formation when the current density exceeds half of the maximum value.
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Hänschke D, Danilewsky A, Helfen L, Hamann E, Baumbach T. Correlated Three-Dimensional Imaging of Dislocations: Insights into the Onset of Thermal Slip in Semiconductor Wafers. PHYSICAL REVIEW LETTERS 2017; 119:215504. [PMID: 29219418 DOI: 10.1103/physrevlett.119.215504] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Indexed: 06/07/2023]
Abstract
Correlated x-ray diffraction imaging and light microscopy provide a conclusive picture of three-dimensional dislocation arrangements on the micrometer scale. The characterization includes bulk crystallographic properties like Burgers vectors and determines links to structural features at the surface. Based on this approach, we study here the thermally induced slip-band formation at prior mechanical damage in Si wafers. Mobilization and multiplication of preexisting dislocations are identified as dominating mechanisms, and undisturbed long-range emission from regenerative sources is discovered.
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Affiliation(s)
- D Hänschke
- Karlsruhe Institute of Technology (KIT), Institute for Photon Science and Synchrotron Radiation (IPS), 76344 Eggenstein-Leopoldshafen, Germany
- Karlsruhe Institute of Technology (KIT), Laboratory for Applications of Synchrotron Radiation (LAS), 76128 Karlsruhe, Germany
| | - A Danilewsky
- Kristallographie, Institut für Geo- und Umweltnaturwissenschaften, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - L Helfen
- Karlsruhe Institute of Technology (KIT), Institute for Photon Science and Synchrotron Radiation (IPS), 76344 Eggenstein-Leopoldshafen, Germany
- European Synchrotron Radiation Facility (ESRF), 38043 Grenoble, France
| | - E Hamann
- Karlsruhe Institute of Technology (KIT), Institute for Photon Science and Synchrotron Radiation (IPS), 76344 Eggenstein-Leopoldshafen, Germany
| | - T Baumbach
- Karlsruhe Institute of Technology (KIT), Institute for Photon Science and Synchrotron Radiation (IPS), 76344 Eggenstein-Leopoldshafen, Germany
- Karlsruhe Institute of Technology (KIT), Laboratory for Applications of Synchrotron Radiation (LAS), 76128 Karlsruhe, Germany
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Wei Z, Yuan L, Liu B, Wei C, Sun C, Yin P, Wei L. A micro-CL system and its applications. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2017; 88:115107. [PMID: 29195415 DOI: 10.1063/1.4989444] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The computed laminography (CL) method is preferable to computed tomography for the non-destructive testing of plate-like objects. A micro-CL system is developed for three-dimensional imaging of plate-like objects. The details of the micro-CL system are described, including the system architecture, scanning modes, and reconstruction algorithm. The experiment results of plate-like fossils, insulated gate bipolar translator module, ball grid array packaging, and printed circuit board are also presented to demonstrate micro-CL's ability for 3D imaging of flat specimens and universal applicability in various fields.
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Affiliation(s)
- Zenghui Wei
- Division of Nuclear Technology and Applications, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Lulu Yuan
- Division of Nuclear Technology and Applications, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Baodong Liu
- Division of Nuclear Technology and Applications, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Cunfeng Wei
- Division of Nuclear Technology and Applications, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Cuili Sun
- Division of Nuclear Technology and Applications, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Pengfei Yin
- Key Laboratory of Vertebrate Evolution and Human Origin of Chinese Academy of Sciences, Beijing 100044, China
| | - Long Wei
- Division of Nuclear Technology and Applications, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
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15
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Zuber M, Laaß M, Hamann E, Kretschmer S, Hauschke N, van de Kamp T, Baumbach T, Koenig T. Augmented laminography, a correlative 3D imaging method for revealing the inner structure of compressed fossils. Sci Rep 2017; 7:41413. [PMID: 28128302 PMCID: PMC5269749 DOI: 10.1038/srep41413] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 12/19/2016] [Indexed: 11/09/2022] Open
Abstract
Non-destructive imaging techniques can be extremely useful tools for the investigation and the assessment of palaeontological objects, as mechanical preparation of rare and valuable fossils is precluded in most cases. However, palaeontologists are often faced with the problem of choosing a method among a wide range of available techniques. In this case study, we employ x-ray computed tomography (CT) and computed laminography (CL) to study the first fossil xiphosuran from the Muschelkalk (Middle Triassic) of the Netherlands. The fossil is embedded in micritic limestone, with the taxonomically important dorsal shield invisible, and only the outline of its ventral part traceable. We demonstrate the complementarity of CT and CL which offers an excellent option to visualize characteristic diagnostic features. We introduce augmented laminography to correlate complementary information of the two methods in Fourier space, allowing to combine their advantages and finally providing increased anatomical information about the fossil. This method of augmented laminography enabled us to identify the xiphosuran as a representative of the genus Limulitella.
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Affiliation(s)
- Marcus Zuber
- Karlsruhe Institute of Technology (KIT), Institute for Photon Science and Synchrotron Radiation (IPS) &Institute for Beam Physics and Technology (IBPT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.,Karlsruhe Institute of Technology (KIT), Laboratory for Applications of Synchrotron Radiation (LAS), Kaiserstr. 12, 76131 Karlsruhe, Germany
| | - Michael Laaß
- University of Duisburg-Essen, Department of General Zoology, Faculty of Biology, Universitätsstr. 5, 45117 Essen, Germany
| | - Elias Hamann
- Karlsruhe Institute of Technology (KIT), Institute for Photon Science and Synchrotron Radiation (IPS) &Institute for Beam Physics and Technology (IBPT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Sophie Kretschmer
- Martin-Luther-University Halle-Wittenberg, Institute of Geosciences and Geography, Von-Seckendorff-Platz 3, 06120 Halle (Saale), Germany
| | - Norbert Hauschke
- Martin-Luther-University Halle-Wittenberg, Institute of Geosciences and Geography, Von-Seckendorff-Platz 3, 06120 Halle (Saale), Germany
| | - Thomas van de Kamp
- Karlsruhe Institute of Technology (KIT), Institute for Photon Science and Synchrotron Radiation (IPS) &Institute for Beam Physics and Technology (IBPT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.,Karlsruhe Institute of Technology (KIT), Laboratory for Applications of Synchrotron Radiation (LAS), Kaiserstr. 12, 76131 Karlsruhe, Germany
| | - Tilo Baumbach
- Karlsruhe Institute of Technology (KIT), Institute for Photon Science and Synchrotron Radiation (IPS) &Institute for Beam Physics and Technology (IBPT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.,Karlsruhe Institute of Technology (KIT), Laboratory for Applications of Synchrotron Radiation (LAS), Kaiserstr. 12, 76131 Karlsruhe, Germany
| | - Thomas Koenig
- Karlsruhe Institute of Technology (KIT), Institute for Photon Science and Synchrotron Radiation (IPS) &Institute for Beam Physics and Technology (IBPT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.,Ziehm Imaging GmbH, Donaustr. 31, 90451 Nuremberg, Germany
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16
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Hirano K, Takahashi Y, Hyodo K, Kimura M. X-ray analyzer-based phase-contrast computed laminography. JOURNAL OF SYNCHROTRON RADIATION 2016; 23:1484-1489. [PMID: 27787254 DOI: 10.1107/s1600577516014831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 09/20/2016] [Indexed: 06/06/2023]
Abstract
X-ray analyzer-based phase-contrast imaging is combined with computed laminography for imaging regions of interest in laterally extended flat specimens of weak absorption contrast. The optics discussed here consist of an asymmetrically cut collimator crystal and a symmetrically cut analyzer crystal arranged in a nondispersive (+, -) diffraction geometry. A generalized algorithm is given for calculating multi-contrast (absorption, refraction and phase contrast) images of a sample. Basic formulae are also presented for laminographic reconstruction. The feasibility of the method discussed was verified at the vertical wiggler beamline BL-14B of the Photon Factory. At a wavelength of 0.0733 nm, phase-contrast sectional images of plastic beads were successfully obtained. Owing to strong circular artifacts caused by a sample holder, the field of view was limited to about 6 mm in diameter.
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Affiliation(s)
- Keiichi Hirano
- Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1, Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Yumiko Takahashi
- Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1, Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Kazuyuki Hyodo
- Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1, Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Masao Kimura
- Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1, Oho, Tsukuba, Ibaraki 305-0801, Japan
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17
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O'Brien NS, Boardman RP, Sinclair I, Blumensath T. Recent Advances in X-ray Cone-beam Computed Laminography. JOURNAL OF X-RAY SCIENCE AND TECHNOLOGY 2016; 24:691-707. [PMID: 27341626 DOI: 10.3233/xst-160581] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
X-ray computed tomography is an established volume imaging technique used routinely in medical diagnosis, industrial non-destructive testing, and a wide range of scientific fields. Traditionally, computed tomography uses scanning geometries with a single axis of rotation together with reconstruction algorithms specifically designed for this setup. Recently there has however been increasing interest in more complex scanning geometries. These include so called X-ray computed laminography systems capable of imaging specimens with large lateral dimensions or large aspect ratios, neither of which are well suited to conventional CT scanning procedures. Developments throughout this field have thus been rapid, including the introduction of novel system trajectories, the application and refinement of various reconstruction methods, and the use of recently developed computational hardware and software techniques to accelerate reconstruction times. Here we examine the advances made in the last several years and consider their impact on the state of the art.
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Affiliation(s)
- Neil S O'Brien
- μ-VIS X-ray Imaging Centre, University of Southampton, UK
| | | | - Ian Sinclair
- μ-VIS X-ray Imaging Centre, University of Southampton, UK
| | - Thomas Blumensath
- μ-VIS X-ray Imaging Centre, University of Southampton, UK
- Institute for Sound and Vibration Research, University of Southampton, UK
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18
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Vogelgesang M, Farago T, Morgeneyer TF, Helfen L, Dos Santos Rolo T, Myagotin A, Baumbach T. Real-time image-content-based beamline control for smart 4D X-ray imaging. JOURNAL OF SYNCHROTRON RADIATION 2016; 23:1254-1263. [PMID: 27577784 DOI: 10.1107/s1600577516010195] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 06/21/2016] [Indexed: 06/06/2023]
Abstract
Real-time processing of X-ray image data acquired at synchrotron radiation facilities allows for smart high-speed experiments. This includes workflows covering parameterized and image-based feedback-driven control up to the final storage of raw and processed data. Nevertheless, there is presently no system that supports an efficient construction of such experiment workflows in a scalable way. Thus, here an architecture based on a high-level control system that manages low-level data acquisition, data processing and device changes is described. This system is suitable for routine as well as prototypical experiments, and provides specialized building blocks to conduct four-dimensional in situ, in vivo and operando tomography and laminography.
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Affiliation(s)
- Matthias Vogelgesang
- Institute for Data Processing and Electronics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Tomas Farago
- Institute for Photon Science and Synchrotron Radiation, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Thilo F Morgeneyer
- MINES ParisTech, PSL Research University, MAT - Centre des Materiaux, CNRS UMR 7633, BP 87, 91003 Evry, France
| | - Lukas Helfen
- Institute for Photon Science and Synchrotron Radiation, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Tomy Dos Santos Rolo
- Institute for Accelerator Physics and Technology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Anton Myagotin
- St Petersburg State University of Civil Aviation, St Petersburg, Russia
| | - Tilo Baumbach
- Institute for Photon Science and Synchrotron Radiation, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
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19
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Voropaev A, Myagotin A, Helfen L, Baumbach T. Direct Fourier Inversion Reconstruction Algorithm for Computed Laminography. IEEE TRANSACTIONS ON IMAGE PROCESSING : A PUBLICATION OF THE IEEE SIGNAL PROCESSING SOCIETY 2016; 25:2368-2378. [PMID: 27046874 DOI: 10.1109/tip.2016.2546547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Synchrotron radiation computed laminography (CL) was developed to complement the conventional computed tomography as a non-destructive 3D imaging method for the inspection of flat thin objects. Recent progress in hardware at synchrotron sources allows one to record internal evolution of specimens at the micrometer scale and sub-second range but also requires increased reconstruction speed to follow structural changes online. A 3D image of the sample interior is usually reconstructed by the well-established filtered backprojection (FBP) approach. Despite of a great success in the reduction of reconstruction time via parallel computations, the FBP algorithm still remains a time-consuming procedure. A promising way to significantly shorten computation time is to directly perform backprojection in frequency domain (a direct Fourier inversion approach). The corresponding algorithms are rarely considered in the literature because of a poor performance or inferior reconstruction quality resulted from inaccurate interpolation in Fourier domain. In this paper, we derive a Fourier-based reconstruction equation designed for the CL scanning geometry. Furthermore, we outline the translation of the continuous solution to a discrete version, which utilizes 3D sinc interpolation. A projection resampling technique allowing for the reduction of the expensive interpolation to its 1D version is proposed. A series of numerical experiments confirms that the resulting image quality is well comparable with the FBP approach while reconstruction time is drastically reduced.
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20
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Cheng Y, Laiarinandrasana L, Helfen L, Proudhon H, Klinkova O, Baumbach T, Morgeneyer TF. 3D Damage Micromechanisms in Polyamide 6 Ahead of a Severe Notch Studied byIn SituSynchrotron Laminography. MACROMOL CHEM PHYS 2016. [DOI: 10.1002/macp.201500316] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yin Cheng
- Centre des Matériaux; MINES ParisTech; PSL Research University; CNRS UMR 7633 BP 87 F-91003 Evry Cedex France
- ANKA/Institute for Photon Science and Synchrotron Radiation (IPS); Karlsruhe Institute of Technology (KIT); D-76344 Eggenstein-Leopoldshafen Germany
- Laboratory for Applications of Synchrotron Radiation (LAS); Karlsruhe Institute of Technology (KIT); D-76049 Karlsruhe Germany
| | - Lucien Laiarinandrasana
- Centre des Matériaux; MINES ParisTech; PSL Research University; CNRS UMR 7633 BP 87 F-91003 Evry Cedex France
| | - Lukas Helfen
- ANKA/Institute for Photon Science and Synchrotron Radiation (IPS); Karlsruhe Institute of Technology (KIT); D-76344 Eggenstein-Leopoldshafen Germany
- Laboratory for Applications of Synchrotron Radiation (LAS); Karlsruhe Institute of Technology (KIT); D-76049 Karlsruhe Germany
- European Synchrotron Radiation Facility (ESRF); BP 220 F-38043 Grenoble Cedex France
| | - Henry Proudhon
- Centre des Matériaux; MINES ParisTech; PSL Research University; CNRS UMR 7633 BP 87 F-91003 Evry Cedex France
| | - Olga Klinkova
- Centre des Matériaux; MINES ParisTech; PSL Research University; CNRS UMR 7633 BP 87 F-91003 Evry Cedex France
| | - Tilo Baumbach
- ANKA/Institute for Photon Science and Synchrotron Radiation (IPS); Karlsruhe Institute of Technology (KIT); D-76344 Eggenstein-Leopoldshafen Germany
- Laboratory for Applications of Synchrotron Radiation (LAS); Karlsruhe Institute of Technology (KIT); D-76049 Karlsruhe Germany
| | - Thilo F. Morgeneyer
- Centre des Matériaux; MINES ParisTech; PSL Research University; CNRS UMR 7633 BP 87 F-91003 Evry Cedex France
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21
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Verboven P, Herremans E, Helfen L, Ho QT, Abera M, Baumbach T, Wevers M, Nicolaï BM. Synchrotron X-ray computed laminography of the three-dimensional anatomy of tomato leaves. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 81:169-82. [PMID: 25319143 DOI: 10.1111/tpj.12701] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 10/01/2014] [Accepted: 10/10/2014] [Indexed: 05/23/2023]
Abstract
Synchrotron radiation computed laminography (SR-CL) is presented as an imaging method for analyzing the three-dimensional (3D) anatomy of leaves. The SR-CL method was used to provide 3D images of 1-mm² samples of intact leaves at a pixel resolution of 750 nm. The method allowed visualization and quantitative analysis of palisade and spongy mesophyll cells, and showed local venation patterns, aspects of xylem vascular structure and stomata. The method failed to image subcellular organelles such as chloroplasts. We constructed 3D computer models of leaves that can provide a basis for calculating gas exchange, light penetration and water and solute transport. The leaf anatomy of two different tomato genotypes grown in saturating light conditions was compared by 3D analysis. Differences were found in calculated values of tissue porosity, cell number density, cell area to volume ratio and cell volume and cell shape distributions of palisade and spongy cell layers. In contrast, the exposed cell area to leaf area ratio in mesophyll, a descriptor that correlates to the maximum rate of photosynthesis in saturated light conditions, was no different between spongy and palisade cells or between genotypes. The use of 3D image processing avoids many of the limitations of anatomical analysis with two-dimensional sections.
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Affiliation(s)
- Pieter Verboven
- Division BIOSYST-MeBioS, Katholieke Universiteit Leuven, B-3001, Leuven, Belgium
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22
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Tada M, Uruga T, Iwasawa Y. Key Factors Affecting the Performance and Durability of Cathode Electrocatalysts in Polymer Electrolyte Fuel Cells Characterized by In Situ Real Time and Spatially Resolved XAFS Techniques. Catal Letters 2014. [DOI: 10.1007/s10562-014-1428-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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23
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Myagotin A, Voropaev A, Helfen L, Hänschke D, Baumbach T. Efficient volume reconstruction for parallel-beam computed laminography by filtered backprojection on multi-core clusters. IEEE TRANSACTIONS ON IMAGE PROCESSING : A PUBLICATION OF THE IEEE SIGNAL PROCESSING SOCIETY 2013; 22:5348-5361. [PMID: 24228274 DOI: 10.1109/tip.2013.2285600] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Computed laminography (CL) was developed to use X-rays from synchrotron sources for high-resolution imaging of the internal structure of a flat specimen from a series of 2-D projection images. The projections are acquired by irradiation of the sample under different rotation angles where the object rotation axis is inclined with respect to the beam direction. This yields for laterally extended objects a more uniform average transmitted intensity during sample rotation compared with computed tomography (CT). The reconstruction problem of CL cannot be reduced to a data-efficient 2-D case (as for parallel-beam CT) since each single slice perpendicular to the rotation axis requires a 2-D region on the detector as input data for all projection directions. This paper describes a computationally efficient reconstruction procedure based on filtered backprojection (FBP) adapted to the CL acquisition geometry. From the Fourier slice theorem, we derive a framework for analytic image reconstruction and outline implementation details of the generic FBP algorithm. Different approaches reducing the reconstruction time by means of parallel and distributed computations are considered and evaluated.
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24
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Zápražný Z, Korytár D, Mikulík P, Ač V. Processing of projections containing phase contrast in laboratory micro-computerized tomography imaging. J Appl Crystallogr 2013; 46:933-938. [PMID: 24046501 PMCID: PMC3769065 DOI: 10.1107/s002188981300558x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 02/26/2013] [Indexed: 11/29/2022] Open
Abstract
Processing of phase-contrast images in laboratory conditions is described. Free-space-propagation-based imaging belongs to several techniques for achieving phase contrast in the hard X-ray range. The basic precondition is to use an X-ray beam with a high degree of coherence. Although the best sources of coherent X-rays are synchrotrons, spatially coherent X-rays emitted from a sufficiently small spot of laboratory microfocus or sub-microfocus sources allow the transfer of some of the modern imaging techniques from synchrotrons to laboratories. Spatially coherent X-rays traverse a sample leading to a phase shift. Beam deflection induced by the local change of refractive index may be expressed as a dark–bright contrast on the edges of the object in an X-ray projection. This phenomenon of edge enhancement leads to an increase in spatial resolution of X-ray projections but may also lead to unpleasant artefacts in computerized tomography unless phase and absorption contributions are separated. The possibilities of processing X-ray images of lightweight objects containing phase contrast using phase-retrieval methods in laboratory conditions are tested and the results obtained are presented. For this purpose, simulated and recorded X-ray projections taken from a laboratory imaging system with a microfocus X-ray source and a high-resolution CCD camera were processed and a qualitative comparison of results was made.
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Affiliation(s)
- Zdenko Zápražný
- Institute of Electrical Engineering, Slovak Academy of Sciences, Dúbravská cesta 9, SK-841 04 Bratislava, Slovakia
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25
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Xu F, Helfen L, Suhonen H, Elgrabli D, Bayat S, Reischig P, Baumbach T, Cloetens P. Correlative nanoscale 3D imaging of structure and composition in extended objects. PLoS One 2012. [PMID: 23185554 PMCID: PMC3501479 DOI: 10.1371/journal.pone.0050124] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Structure and composition at the nanoscale determine the behavior of biological systems and engineered materials. The drive to understand and control this behavior has placed strong demands on developing methods for high resolution imaging. In general, the improvement of three-dimensional (3D) resolution is accomplished by tightening constraints: reduced manageable specimen sizes, decreasing analyzable volumes, degrading contrasts, and increasing sample preparation efforts. Aiming to overcome these limitations, we present a non-destructive and multiple-contrast imaging technique, using principles of X-ray laminography, thus generalizing tomography towards laterally extended objects. We retain advantages that are usually restricted to 2D microscopic imaging, such as scanning of large areas and subsequent zooming-in towards a region of interest at the highest possible resolution. Our technique permits correlating the 3D structure and the elemental distribution yielding a high sensitivity to variations of the electron density via coherent imaging and to local trace element quantification through X-ray fluorescence. We demonstrate the method by imaging a lithographic nanostructure and an aluminum alloy. Analyzing a biological system, we visualize in lung tissue the subcellular response to toxic stress after exposure to nanotubes. We show that most of the nanotubes are trapped inside alveolar macrophages, while a small portion of the nanotubes has crossed the barrier to the cellular space of the alveolar wall. In general, our method is non-destructive and can be combined with different sample environmental or loading conditions. We therefore anticipate that correlative X-ray nano-laminography will enable a variety of in situ and in operando 3D studies.
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Affiliation(s)
- Feng Xu
- Institute for Synchrotron Radiation, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany.
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26
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Saida T, Sekizawa O, Ishiguro N, Hoshino M, Uesugi K, Uruga T, Ohkoshi SI, Yokoyama T, Tada M. 4D Visualization of a Cathode Catalyst Layer in a Polymer Electrolyte Fuel Cell by 3D Laminography-XAFS. Angew Chem Int Ed Engl 2012; 51:10311-4. [DOI: 10.1002/anie.201204478] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2012] [Indexed: 11/09/2022]
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27
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Saida T, Sekizawa O, Ishiguro N, Hoshino M, Uesugi K, Uruga T, Ohkoshi SI, Yokoyama T, Tada M. 4D Visualization of a Cathode Catalyst Layer in a Polymer Electrolyte Fuel Cell by 3D Laminography-XAFS. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201204478] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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28
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Altapova V, Helfen L, Myagotin A, Hänschke D, Moosmann J, Gunneweg J, Baumbach T. Phase contrast laminography based on Talbot interferometry. OPTICS EXPRESS 2012; 20:6496-6508. [PMID: 22418532 DOI: 10.1364/oe.20.006496] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Synchrotron laminography is combined with Talbot grating interferometry to address weakly absorbing specimens. Integrating both methods into one set-up provides a powerful x-ray diagnostical technique for multiple contrast screening of macroscopically large flat specimen and a subsequent non-destructive three-dimensional (3-D) inspection of regions of interest. The technique simultaneously yields the reconstruction of the 3-D absorption, phase, and the so-called dark-field contrast maps. We report on the theoretical and instrumental implementation of of this novel technique. Its broad application potential is exemplarily demonstrated for the field of cultural heritage, namely study of the historical Dead Sea parchment.
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Affiliation(s)
- Venera Altapova
- Laboratorium f¨ur Applikationen der Synchrotronstrahlung (LAS), Faculty of Physics, Karlsruher Institut f¨ur Technologie (KIT), Postfach 6980, D-76128 Karlsruhe, Germany.
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29
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Xu F, Helfen L, Baumbach T, Suhonen H. Comparison of image quality in computed laminography and tomography. OPTICS EXPRESS 2012; 20:794-806. [PMID: 22274425 DOI: 10.1364/oe.20.000794] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
In computed tomography (CT), projection images of the sample are acquired over an angular range between 180 to 360 degrees around a rotation axis. A special case of CT is that of limited-angle CT, where some of the rotation angles are inaccessible, leading to artefacts in the reconstrucion because of missing information. The case of flat samples is considered, where the projection angles that are close to the sample surface are either i) completely unavailable or ii) very noisy due to the limited transmission at these angles. Computed laminography (CL) is an imaging technique especially suited for flat samples. CL is a generalization of CT that uses a rotation axis tilted by less than 90 degrees with respect to the incident beam. Thus CL avoids using projections from angles closest to the sample surface. We make a quantitative comparison of the imaging artefacts between CL and limited-angle CT for the case of a parallel-beam geometry. Both experimental and simulated images are used to characterize the effect of the artefacts on the resolution and visible image features. The results indicate that CL has an advantage over CT in cases when the missing angular range is a significant portion of the total angular range. In the case when the quality of the projections is limited by noise, CT allows a better tradeoff between the noise level and the missing angular range.
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Affiliation(s)
- Feng Xu
- Institute for Synchrotron Radiation, Karlsruhe Institute of Technology, Germany
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30
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Harasse S, Yashiro W, Momose A. Iterative reconstruction in x-ray computed laminography from differential phase measurements. OPTICS EXPRESS 2011; 19:16560-16573. [PMID: 21935020 DOI: 10.1364/oe.19.016560] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Phase-contrast X-ray computed laminography is demonstrated for the volume reconstruction of extended flat objects, not suitable to the usual tomographic scan. Using a Talbot interferometer, differential phase measurements are obtained and used to reconstruct the real part of the complex refractive index. The specific geometry of laminography leads to unsampled frequencies in a double cone in the reciprocal space, which degrades the spatial resolution in the direction normal to the object plane. First, the filtered backprojection formula from differential measurements is derived. Then, reconstruction is improved by the use of prior information of compact support and limited range, included in an iterative filtered backprojection algorithm. An implementation on GPU hardware was required to handle the reconstruction of volumes within a reasonable time. A synchrotron radiation experiment on polymer meshes is reported and results of the iterative reconstruction are compared with the simpler filtered backprojection.
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Affiliation(s)
- Sébastien Harasse
- Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan.
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