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Virtual histology of an entire mouse brain from formalin fixation to paraffin embedding. Part 1: Data acquisition, anatomical feature segmentation, tracking global volume and density changes. J Neurosci Methods 2021; 364:109354. [PMID: 34529981 DOI: 10.1016/j.jneumeth.2021.109354] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/01/2021] [Accepted: 09/04/2021] [Indexed: 01/14/2023]
Abstract
BACKGROUND Micrometer-resolution neuroimaging with gold-standard conventional histology requires tissue fixation and embedding. The exchange of solvents for the creation of sectionable paraffin blocks modifies tissue density and generates non-uniform brain shrinkage. NEW METHOD We employed synchrotron radiation-based X-ray microtomography for slicing- and label-free virtual histology of the mouse brain at different stages of the standard preparation protocol from formalin fixation via ascending ethanol solutions and xylene to paraffin embedding. Segmentation of anatomical regions allowed us to quantify non-uniform tissue shrinkage. Global and local changes in X-ray absorption gave insight into contrast enhancement for virtual histology. RESULTS The volume of the entire mouse brain was 60%, 56%, and 40% of that in formalin for, respectively, 100% ethanol, xylene, and paraffin. The volume changes of anatomical regions such as the hippocampus, anterior commissure, and ventricles differ from the global volume change. X-ray absorption of the full brain decreased, while local absorption differences increased, resulting in enhanced contrast for virtual histology. These trends were also observed with laboratory microtomography measurements. COMPARISON WITH EXISTING METHODS Microtomography provided sub-10 μm spatial resolution with sufficient density resolution to resolve anatomical structures at each step of the embedding protocol. The spatial resolution of conventional computed tomography and magnetic resonance microscopy is an order of magnitude lower and both do not match the contrast of microtomography over the entire embedding protocol. Unlike feature-to-feature or total volume measurements, our approach allows for calculation of volume change based on segmentation. CONCLUSION We present isotropic micrometer-resolution imaging to quantify morphology and composition changes in a mouse brain during the standard histological preparation. The proposed method can be employed to identify the most appropriate embedding medium for anatomical feature visualization, to reveal the basis for the dramatic X-ray contrast enhancement observed in numerous embedded tissues, and to quantify morphological changes during tissue fixation and embedding.
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Chicherova N, Hieber SE, Khimchenko A, Bikis C, Müller B, Cattin P. Automatic deformable registration of histological slides to μCT volume data. J Microsc 2018. [PMID: 29533457 DOI: 10.1111/jmi.12692] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Localizing a histological section in the three-dimensional dataset of a different imaging modality is a challenging 2D-3D registration problem. In the literature, several approaches have been proposed to solve this problem; however, they cannot be considered as fully automatic. Recently, we developed an automatic algorithm that could successfully find the position of a histological section in a micro computed tomography (μCT) volume. For the majority of the datasets, the result of localization corresponded to the manual results. However, for some datasets, the matching μCT slice was off the ground-truth position. Furthermore, elastic distortions, due to histological preparation, could not be accounted for in this framework. In the current study, we introduce two optimization frameworks based on normalized mutual information, which enabled us to accurately register histology slides to volume data. The rigid approach allocated 81 % of histological sections with a median position error of 8.4 μm in jaw bone datasets, and the deformable approach improved registration by 33 μm with respect to the median distance error for four histological slides in the cerebellum dataset.
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Affiliation(s)
- N Chicherova
- Center for medical Image Analysis & Navigation, Department of Biomedical Engineering, University of Basel, Allschwil, Switzerland.,Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, Allschwil, Switzerland
| | - S E Hieber
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, Allschwil, Switzerland
| | - A Khimchenko
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, Allschwil, Switzerland
| | - C Bikis
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, Allschwil, Switzerland
| | - B Müller
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, Allschwil, Switzerland
| | - P Cattin
- Center for medical Image Analysis & Navigation, Department of Biomedical Engineering, University of Basel, Allschwil, Switzerland
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Newton VL, Bradley RS, Seroul P, Cherel M, Griffiths CEM, Rawlings AV, Voegeli R, Watson REB, Sherratt MJ. Novel approaches to characterize age-related remodelling of the dermal-epidermal junction in 2D, 3D andin vivo. Skin Res Technol 2016; 23:131-148. [DOI: 10.1111/srt.12312] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2016] [Indexed: 12/21/2022]
Affiliation(s)
- V. L. Newton
- Centre for Dermatology Research; Institute of Inflammation & Repair; Manchester Academic Health Science Centre; University of Manchester; Manchester UK
- The Dermatology Centre; Salford Royal NHS Foundation Trust; Salford UK
| | - R. S. Bradley
- School of Materials; The University of Manchester; Manchester UK
| | | | | | - C. E. M. Griffiths
- Centre for Dermatology Research; Institute of Inflammation & Repair; Manchester Academic Health Science Centre; University of Manchester; Manchester UK
- The Dermatology Centre; Salford Royal NHS Foundation Trust; Salford UK
| | | | - R. Voegeli
- DSM Nutritional Products Ltd; Kaiseraugst Switzerland
| | - R. E. B. Watson
- Centre for Dermatology Research; Institute of Inflammation & Repair; Manchester Academic Health Science Centre; University of Manchester; Manchester UK
- The Dermatology Centre; Salford Royal NHS Foundation Trust; Salford UK
| | - M. J. Sherratt
- Centre for Tissue Injury and Repair; Institute of Inflammation & Repair; Manchester Academic Health Science Centre; The University of Manchester; Manchester UK
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Khimchenko A, Deyhle H, Schulz G, Schweighauser G, Hench J, Chicherova N, Bikis C, Hieber SE, Müller B. Extending two-dimensional histology into the third dimension through conventional micro computed tomography. Neuroimage 2016; 139:26-36. [PMID: 27321044 DOI: 10.1016/j.neuroimage.2016.06.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 05/11/2016] [Accepted: 06/04/2016] [Indexed: 11/28/2022] Open
Abstract
Histological examination achieves sub-micrometer resolution laterally. In the third dimension, however, resolution is limited to section thickness. In addition, histological sectioning and mounting sections on glass slides introduce tissue-dependent stress and strain. In contrast, state-of-the-art hard X-ray micro computed tomography (μCT) systems provide isotropic sub-micrometer resolution and avoid sectioning artefacts. The drawback of μCT in the absorption contrast mode for visualising physically soft tissue is a low attenuation difference between anatomical features. In this communication, we demonstrate that formalin-fixed paraffin-embedded human cerebellum yields appropriate absorption contrast in laboratory-based μCT data, comparable to conventional histological sections. Purkinje cells, for example, are readily visible. In order to investigate the pros and cons of complementary approaches, two- and three-dimensional data were manually and automatically registered. The joint histogram of histology and the related μCT slice allows for a detailed discussion on how to integrate two-dimensional information from histology into a three-dimensional tomography dataset. This methodology is not only rewarding for the analysis of the human cerebellum, but it also has relevance for investigations of tissue biopsies and post-mortem applications. Our data indicate that laboratory-based μCT as a modality can fill the gap between synchrotron radiation-based μCT and histology for a variety of tissues. As the information from haematoxylin and eosin (H&E) stained sections and μCT data is related, one can colourise local X-ray absorption values according to the H&E stain. Hence, μCT data can correlate and virtually extend two-dimensional (2D) histology data into the third dimension.
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Affiliation(s)
- Anna Khimchenko
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, Allschwil, Switzerland
| | - Hans Deyhle
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, Allschwil, Switzerland
| | - Georg Schulz
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, Allschwil, Switzerland
| | - Gabriel Schweighauser
- Institute of Pathology, Department of Neuropathology, Basel University Hospital, Basel, Switzerland
| | - Jürgen Hench
- Institute of Pathology, Department of Neuropathology, Basel University Hospital, Basel, Switzerland
| | - Natalia Chicherova
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, Allschwil, Switzerland; Medical Image Analysis Center, Department of Biomedical Engineering, University of Basel, Allschwil, Switzerland
| | - Christos Bikis
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, Allschwil, Switzerland
| | - Simone E Hieber
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, Allschwil, Switzerland
| | - Bert Müller
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, Allschwil, Switzerland.
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Hoshino M, Uesugi K, Tsukube T, Yagi N. Quantitative and dynamic measurements of biological fresh samples with X-ray phase contrast tomography. JOURNAL OF SYNCHROTRON RADIATION 2014; 21:1347-57. [PMID: 25343804 PMCID: PMC4421879 DOI: 10.1107/s1600577514018128] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 08/07/2014] [Indexed: 05/24/2023]
Abstract
X-ray phase contrast tomography using a Talbot grating interferometer was applied to biological fresh samples which were not fixed by any fixatives. To achieve a high-throughput measurement for the fresh samples the X-ray phase contrast tomography measurement procedure was improved. The three-dimensional structure of a fresh mouse fetus was clearly depicted as a mass density map using X-ray phase contrast tomography. The mouse fetus measured in the fresh state was then fixed by formalin and measured in the fixed state. The influence of the formalin fixation on soft tissue was quantitatively evaluated by comparing the fresh and fixed samples. X-ray phase contrast tomography was also applied to the dynamic measurement of a biological fresh sample. Morphological changes of a ring-shaped fresh pig aorta were measured tomographically under different degrees of stretching.
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Affiliation(s)
- Masato Hoshino
- Research and Utilization Division, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Kentaro Uesugi
- Research and Utilization Division, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Takuro Tsukube
- Japanese Red Cross Kobe Hospital, 1-3-1 Wakinohamakaigandori, Chuo-ku, Kobe, Hyogo 651-0073, Japan
| | - Naoto Yagi
- Research and Utilization Division, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
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Holme MN, Schulz G, Deyhle H, Weitkamp T, Beckmann F, Lobrinus JA, Rikhtegar F, Kurtcuoglu V, Zanette I, Saxer T, Müller B. Complementary X-ray tomography techniques for histology-validated 3D imaging of soft and hard tissues using plaque-containing blood vessels as examples. Nat Protoc 2014; 9:1401-15. [PMID: 24853926 DOI: 10.1038/nprot.2014.091] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A key problem in X-ray computed tomography is choosing photon energies for postmortem specimens containing both soft and hard tissues. Increasing X-ray energy reduces image artifacts from highly absorbing hard tissues including plaque, but it simultaneously decreases contrast in soft tissues including the endothelium. Therefore, identifying the lumen within plaque-containing vessels is challenging. Destructive histology, the gold standard for tissue evaluation, reaches submicron resolution in two dimensions, whereas slice thickness limits spatial resolution in the third. We present a protocol to systematically analyze heterogeneous tissues containing weakly and highly absorbing components in the original wet state, postmortem. Taking the example of atherosclerotic human coronary arteries, the successively acquired 3D data of benchtop and synchrotron radiation-based tomography are validated by histology. The entire protocol requires ∼20 working days, enables differentiation between plaque, muscle and fat tissues without using contrast agents and permits blood flow simulations in vessels with plaque-induced constrictions.
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Affiliation(s)
- Margaret N Holme
- Biomaterials Science Center (BMC), University of Basel, University Hospital Basel, Basel, Switzerland
| | - Georg Schulz
- Biomaterials Science Center (BMC), University of Basel, University Hospital Basel, Basel, Switzerland
| | - Hans Deyhle
- Biomaterials Science Center (BMC), University of Basel, University Hospital Basel, Basel, Switzerland
| | | | - Felix Beckmann
- Institute of Materials Research, Helmholtz-Zentrum Geesthacht, Geesthacht, Germany
| | | | - Farhad Rikhtegar
- Laboratory of Thermodynamics in Emerging Technologies, ETH Zurich, Zurich, Switzerland
| | - Vartan Kurtcuoglu
- The Interface Group, Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - Irene Zanette
- 1] European Synchrotron Radiation Facility, Grenoble, France. [2] Physik-Department, Technische Universität München, Garching, Germany
| | - Till Saxer
- University Hospitals Geneva, Geneva, Switzerland
| | - Bert Müller
- Biomaterials Science Center (BMC), University of Basel, University Hospital Basel, Basel, Switzerland
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Tapfer A, Braren R, Bech M, Willner M, Zanette I, Weitkamp T, Trajkovic-Arsic M, Siveke JT, Settles M, Aichler M, Walch A, Pfeiffer F. X-ray phase-contrast CT of a pancreatic ductal adenocarcinoma mouse model. PLoS One 2013; 8:e58439. [PMID: 23536795 PMCID: PMC3594292 DOI: 10.1371/journal.pone.0058439] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 02/04/2013] [Indexed: 12/20/2022] Open
Abstract
To explore the potential of grating-based x-ray phase-contrast computed tomography (CT) for preclinical research, a genetically engineered mouse model of pancreatic ductal adenocarcinoma (PDAC) was investigated. One ex-vivo mouse specimen was scanned with different grating-based phase-contrast CT imaging setups covering two different settings: i) high-resolution synchrotron radiation (SR) imaging and ii) dose-reduced imaging using either synchrotron radiation or a conventional x-ray tube source. These experimental settings were chosen to assess the potential of phase-contrast imaging for two different types of application: i) high-performance imaging for virtual microscopy applications and ii) biomedical imaging with increased soft-tissue contrast for in-vivo applications. For validation and as a reference, histological slicing and magnetic resonance imaging (MRI) were performed on the same mouse specimen. For each x-ray imaging setup, attenuation and phase-contrast images were compared visually with regard to contrast in general, and specifically concerning the recognizability of lesions and cancerous tissue. To quantitatively assess contrast, the contrast-to-noise ratios (CNR) of selected regions of interest (ROI) in the attenuation images and the phase images were analyzed and compared. It was found that both for virtual microscopy and for in-vivo applications, there is great potential for phase-contrast imaging: in the SR-based benchmarking data, fine details about tissue composition are accessible in the phase images and the visibility of solid tumor tissue under dose-reduced conditions is markedly superior in the phase images. The present study hence demonstrates improved diagnostic value with phase-contrast CT in a mouse model of a complex endogenous cancer, promoting the use and further development of grating-based phase-contrast CT for biomedical imaging applications.
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Affiliation(s)
- Arne Tapfer
- Department of Physics and Institute of Medical Engineering, Technische Universität München, Garching, Germany.
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Zanette I, Weitkamp T, Le Duc G, Pfeiffer F. X-ray grating-based phase tomography for 3D histology. RSC Adv 2013. [DOI: 10.1039/c3ra41372a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
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Schulz G, Waschkies C, Pfeiffer F, Zanette I, Weitkamp T, David C, Müller B. Multimodal imaging of human cerebellum - merging X-ray phase microtomography, magnetic resonance microscopy and histology. Sci Rep 2012; 2:826. [PMID: 23145319 PMCID: PMC3494013 DOI: 10.1038/srep00826] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 10/02/2012] [Indexed: 01/22/2023] Open
Abstract
Imaging modalities including magnetic resonance imaging and X-ray computed tomography are established methods in daily clinical diagnosis of human brain. Clinical equipment does not provide sufficient spatial resolution to obtain morphological information on the cellular level, essential for applying minimally or non-invasive surgical interventions. Therefore, generic data with lateral sub-micrometer resolution have been generated from histological slices post mortem. Sub-cellular spatial resolution, lost in the third dimension as a result of sectioning, is obtained using magnetic resonance microscopy and micro computed tomography. We demonstrate that for human cerebellum grating-based X-ray phase tomography shows complementary contrast to magnetic resonance microscopy and histology. In this study, the contrast-to-noise values of magnetic resonance microscopy and phase tomography were comparable whereas the spatial resolution in phase tomography is an order of magnitude better. The registered data with their complementary information permit the distinct segmentation of tissues within the human cerebellum.
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Affiliation(s)
- Georg Schulz
- Biomaterials Science Center, University of Basel, Basel, Switzerland
| | - Conny Waschkies
- Animal Imaging Center, Institute for Biomedical Engineering, ETH & University of Zurich, Switzerland
| | - Franz Pfeiffer
- Department of Physics (E17), Technische Universität München, Garching, Germany
| | - Irene Zanette
- Department of Physics (E17), Technische Universität München, Garching, Germany
- European Synchrotron Radiation Facility, Grenoble, France
| | | | - Christian David
- Laboratory for Micro- and Nanotechnology, Paul Scherrer Institut, Villigen, Switzerland
| | - Bert Müller
- Biomaterials Science Center, University of Basel, Basel, Switzerland
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Schulz G, Crooijmans HJA, Germann M, Scheffler K, Müller-Gerbl M, Müller B. Three-dimensional strain fields in human brain resulting from formalin fixation. J Neurosci Methods 2011; 202:17-27. [PMID: 21889536 DOI: 10.1016/j.jneumeth.2011.08.031] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Revised: 08/12/2011] [Accepted: 08/17/2011] [Indexed: 12/25/2022]
Abstract
Before investigating human brains post mortem, the first preparation step is often formalin fixation of the brain. As the brain consists of inhomogeneous tissues, the fixation leads to a three-dimensional strain field within the tissue. During the single case MR-based investigation of the brain, first, the starting point with the brain post mortem but still within the cranium, was examined. Then 13 MR data sets were acquired over a fixation period of 70 days and compared to the initial data set. Based on affine registration of the data sets, the global volume shrinkage was found to be 8.1%. By means of a non-rigid registration additional maximal local volume strains of 32% were determined.
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Affiliation(s)
- Georg Schulz
- Biomaterials Science Center, University of Basel, c/o University Hospital Basel, 4031 Basel, Switzerland.
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Schulz G, Weitkamp T, Zanette I, Pfeiffer F, Beckmann F, David C, Rutishauser S, Reznikova E, Müller B. High-resolution tomographic imaging of a human cerebellum: comparison of absorption and grating-based phase contrast. J R Soc Interface 2010; 7:1665-76. [PMID: 20659930 DOI: 10.1098/rsif.2010.0281] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Human brain tissue belongs to the most impressive and delicate three-dimensional structures in nature. Its outstanding functional importance in the organism implies a strong need for brain imaging modalities. Although magnetic resonance imaging provides deep insights, its spatial resolution is insufficient to study the structure on the level of individual cells. Therefore, our knowledge of brain microstructure currently relies on two-dimensional techniques, optical and electron microscopy, which generally require severe preparation procedures including sectioning and staining. X-ray absorption microtomography yields the necessary spatial resolution, but since the composition of the different types of brain tissue is similar, the images show only marginal contrast. An alternative to absorption could be X-ray phase contrast, which is known for much better discrimination of soft tissues but requires more intricate machinery. In the present communication, we report an evaluation of the recently developed X-ray grating interferometry technique, applied to obtain phase-contrast as well as absorption-contrast synchrotron radiation-based microtomography of human cerebellum. The results are quantitatively compared with synchrotron radiation-based microtomography in optimized absorption-contrast mode. It is demonstrated that grating interferometry allows identifying besides the blood vessels, the stratum moleculare, the stratum granulosum and the white matter. Along the periphery of the stratum granulosum, we have detected microstructures about 40 µm in diameter, which we associate with the Purkinje cells because of their location, size, shape and density. The detection of individual Purkinje cells without the application of any stain or contrast agent is unique in the field of computed tomography and sets new standards in non-destructive three-dimensional imaging.
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Affiliation(s)
- Georg Schulz
- Biomaterials Science Center, University of Basel, Switzerland.
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