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Savatović S, Zdora MC, De Marco F, Bikis C, Olbinado M, Rack A, Müller B, Thibault P, Zanette I. Multi-resolution X-ray phase-contrast and dark-field tomography of human cerebellum with near-field speckles. BIOMEDICAL OPTICS EXPRESS 2024; 15:142-161. [PMID: 38223169 PMCID: PMC10783905 DOI: 10.1364/boe.502664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/30/2023] [Accepted: 11/09/2023] [Indexed: 01/16/2024]
Abstract
In this study, we use synchrotron-based multi-modal X-ray tomography to examine human cerebellar tissue in three dimensions at two levels of spatial resolution (2.3 µm and 11.9 µm). We show that speckle-based imaging (SBI) produces results that are comparable to propagation-based imaging (PBI), a well-established phase-sensitive imaging method. The different SBI signals provide complementary information, which improves tissue differentiation. In particular, the dark-field signal aids in distinguishing tissues with similar average electron density but different microstructural variations. The setup's high resolution and the imaging technique's excellent phase sensitivity enabled the identification of different cellular layers and additionally, different cell types within these layers. We also correlated this high-resolution phase-contrast information with measured dark-field signal levels. These findings demonstrate the viability of SBI and the potential benefit of the dark-field modality for virtual histology of brain tissue.
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Affiliation(s)
- Sara Savatović
- Department of Physics, University of Trieste, Via Valerio 2, 34127 Trieste, Italy
- Elettra-Sincrotrone Trieste, Strada Statale 14 – km 163.5, 34149 Basovizza, Italy
| | - Marie-Christine Zdora
- Department of Biomedical Engineering, ETH Zürich, Gloriastrasse 35, 8092 Zürich, Switzerland
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Fabio De Marco
- Department of Physics, University of Trieste, Via Valerio 2, 34127 Trieste, Italy
- Elettra-Sincrotrone Trieste, Strada Statale 14 – km 163.5, 34149 Basovizza, Italy
| | - Christos Bikis
- Psychiatric Hospital in Winterthur, Wieshofstrasse 102, 8408 Winterthur, Switzerland
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, Hegenheimermattweg 167 B/C, 4123 Allschwil, Switzerland
| | - Margie Olbinado
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Alexander Rack
- ESRF – The European Synchrotron, CS40220, CEDEX 09, 38043 Grenoble, France
| | - Bert Müller
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, Hegenheimermattweg 167 B/C, 4123 Allschwil, Switzerland
| | - Pierre Thibault
- Department of Physics, University of Trieste, Via Valerio 2, 34127 Trieste, Italy
- Elettra-Sincrotrone Trieste, Strada Statale 14 – km 163.5, 34149 Basovizza, Italy
| | - Irene Zanette
- Elettra-Sincrotrone Trieste, Strada Statale 14 – km 163.5, 34149 Basovizza, Italy
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Rodgers G, Bikis C, Janz P, Tanner C, Schulz G, Thalmann P, Haas CA, Müller B. 3D X-ray Histology for the Investigation of Temporal Lobe Epilepsy in a Mouse Model. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:1730-1745. [PMID: 37584515 DOI: 10.1093/micmic/ozad082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/29/2023] [Accepted: 07/28/2023] [Indexed: 08/17/2023]
Abstract
The most common form of epilepsy among adults is mesial temporal lobe epilepsy (mTLE), with seizures often originating in the hippocampus due to abnormal electrical activity. The gold standard for the histopathological analysis of mTLE is histology, which is a two-dimensional technique. To fill this gap, we propose complementary three-dimensional (3D) X-ray histology. Herein, we used synchrotron radiation-based phase-contrast microtomography with 1.6 μm-wide voxels for the post mortem visualization of tissue microstructure in an intrahippocampal-kainate mouse model for mTLE. We demonstrated that the 3D X-ray histology of unstained, unsectioned, paraffin-embedded brain hemispheres can identify hippocampal sclerosis through the loss of pyramidal neurons in the first and third regions of the Cornu ammonis as well as granule cell dispersion within the dentate gyrus. Morphology and density changes during epileptogenesis were quantified by segmentations from a deep convolutional neural network. Compared to control mice, the total dentate gyrus volume doubled and the granular layer volume quadrupled 21 days after injecting kainate. Subsequent sectioning of the same mouse brains allowed for benchmarking 3D X-ray histology against well-established histochemical and immunofluorescence stainings. Thus, 3D X-ray histology is a complementary neuroimaging tool to unlock the third dimension for the cellular-resolution histopathological analysis of mTLE.
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Affiliation(s)
- Griffin Rodgers
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland
- Biomaterials Science Center, Department of Clinical Research, University Hospital Basel, 4031 Basel, Switzerland
| | - Christos Bikis
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland
- Integrierte Psychiatrie Winterthur-Zürcher Unterland, 8408 Winterthur, Switzerland
| | - Philipp Janz
- Faculty of Medicine, Experimental Epilepsy Research, Department of Neurosurgery, Medical Center-University of Freiburg, 79106 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79106 Freiburg, Germany
- BrainLinks-BrainTools Center, University of Freiburg, 79106 Freiburg, Germany
| | - Christine Tanner
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland
- Biomaterials Science Center, Department of Clinical Research, University Hospital Basel, 4031 Basel, Switzerland
| | - Georg Schulz
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland
- Biomaterials Science Center, Department of Clinical Research, University Hospital Basel, 4031 Basel, Switzerland
- Core Facility Micro- and Nanotomography, Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland
| | - Peter Thalmann
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland
| | - Carola A Haas
- Faculty of Medicine, Experimental Epilepsy Research, Department of Neurosurgery, Medical Center-University of Freiburg, 79106 Freiburg, Germany
- BrainLinks-BrainTools Center, University of Freiburg, 79106 Freiburg, Germany
- Center of Basics in NeuroModulation, Faculty of Medicine, University of Freiburg, 79114 Freiburg, Germany
| | - Bert Müller
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland
- Biomaterials Science Center, Department of Clinical Research, University Hospital Basel, 4031 Basel, Switzerland
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3
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Liu Z, Zhu Y, Zhang L, Jiang W, Liu Y, Tang Q, Cai X, Li J, Wang L, Tao C, Yin X, Li X, Hou S, Jiang D, Liu K, Zhou X, Zhang H, Liu M, Fan C, Tian Y. Structural and functional imaging of brains. Sci China Chem 2022; 66:324-366. [PMID: 36536633 PMCID: PMC9753096 DOI: 10.1007/s11426-022-1408-5] [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: 07/27/2022] [Accepted: 09/28/2022] [Indexed: 12/23/2022]
Abstract
Analyzing the complex structures and functions of brain is the key issue to understanding the physiological and pathological processes. Although neuronal morphology and local distribution of neurons/blood vessels in the brain have been known, the subcellular structures of cells remain challenging, especially in the live brain. In addition, the complicated brain functions involve numerous functional molecules, but the concentrations, distributions and interactions of these molecules in the brain are still poorly understood. In this review, frontier techniques available for multiscale structure imaging from organelles to the whole brain are first overviewed, including magnetic resonance imaging (MRI), computed tomography (CT), positron emission tomography (PET), serial-section electron microscopy (ssEM), light microscopy (LM) and synchrotron-based X-ray microscopy (XRM). Specially, XRM for three-dimensional (3D) imaging of large-scale brain tissue with high resolution and fast imaging speed is highlighted. Additionally, the development of elegant methods for acquisition of brain functions from electrical/chemical signals in the brain is outlined. In particular, the new electrophysiology technologies for neural recordings at the single-neuron level and in the brain are also summarized. We also focus on the construction of electrochemical probes based on dual-recognition strategy and surface/interface chemistry for determination of chemical species in the brain with high selectivity and long-term stability, as well as electrochemophysiological microarray for simultaneously recording of electrochemical and electrophysiological signals in the brain. Moreover, the recent development of brain MRI probes with high contrast-to-noise ratio (CNR) and sensitivity based on hyperpolarized techniques and multi-nuclear chemistry is introduced. Furthermore, multiple optical probes and instruments, especially the optophysiological Raman probes and fiber Raman photometry, for imaging and biosensing in live brain are emphasized. Finally, a brief perspective on existing challenges and further research development is provided.
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Affiliation(s)
- Zhichao Liu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241 China
| | - Ying Zhu
- Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201210 China
| | - Liming Zhang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241 China
| | - Weiping Jiang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan, 430071 China
| | - Yawei Liu
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022 China
| | - Qiaowei Tang
- Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201210 China
| | - Xiaoqing Cai
- Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201210 China
| | - Jiang Li
- Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201210 China
| | - Lihua Wang
- Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201210 China
| | - Changlu Tao
- Interdisciplinary Center for Brain Information, Brain Cognition and Brain Disease Institute, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Faculty of Life and Health Sciences, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China
| | | | - Xiaowei Li
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Shangguo Hou
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 518055 China
| | - Dawei Jiang
- Department of Nuclear Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Kai Liu
- Department of Chemistry, Tsinghua University, Beijing, 100084 China
| | - Xin Zhou
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan, 430071 China
| | - Hongjie Zhang
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022 China
- Department of Chemistry, Tsinghua University, Beijing, 100084 China
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan, 430071 China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Yang Tian
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241 China
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Barbone GE, Bravin A, Mittone A, Pacureanu A, Mascio G, Di Pietro P, Kraiger MJ, Eckermann M, Romano M, Hrabě de Angelis M, Cloetens P, Bruno V, Battaglia G, Coan P. X-ray multiscale 3D neuroimaging to quantify cellular aging and neurodegeneration postmortem in a model of Alzheimer’s disease. Eur J Nucl Med Mol Imaging 2022; 49:4338-4357. [PMID: 35852558 PMCID: PMC9606093 DOI: 10.1007/s00259-022-05896-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 06/25/2022] [Indexed: 01/19/2023]
Abstract
Abstract
Purpose
Modern neuroimaging lacks the tools necessary for whole-brain, anatomically dense neuronal damage screening. An ideal approach would include unbiased histopathologic identification of aging and neurodegenerative disease.
Methods
We report the postmortem application of multiscale X-ray phase-contrast computed tomography (X-PCI-CT) for the label-free and dissection-free organ-level to intracellular-level 3D visualization of distinct single neurons and glia. In deep neuronal populations in the brain of aged wild-type and of 3xTgAD mice (a triply-transgenic model of Alzheimer’s disease), we quantified intracellular hyperdensity, a manifestation of aging or neurodegeneration.
Results
In 3xTgAD mice, the observed hyperdensity was identified as amyloid-β and hyper-phosphorylated tau protein deposits with calcium and iron involvement, by correlating the X-PCI-CT data to immunohistochemistry, X-ray fluorescence microscopy, high-field MRI, and TEM. As a proof-of-concept, X-PCI-CT was used to analyze hippocampal and cortical brain regions of 3xTgAD mice treated with LY379268, selective agonist of group II metabotropic glutamate receptors (mGlu2/3 receptors). Chronic pharmacologic activation of mGlu2/3 receptors significantly reduced the hyperdensity particle load in the ventral cortical regions of 3xTgAD mice, suggesting a neuroprotective effect with locoregional efficacy.
Conclusions
This multiscale micro-to-nano 3D imaging method based on X-PCI-CT enabled identification and quantification of cellular and sub-cellular aging and neurodegeneration in deep neuronal and glial cell populations in a transgenic model of Alzheimer’s disease. This approach quantified the localized and intracellular neuroprotective effects of pharmacological activation of mGlu2/3 receptors.
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Migga A, Schulz G, Rodgers G, Osterwalder M, Tanner C, Blank H, Jerjen I, Salmon P, Twengström W, Scheel M, Weitkamp T, Schlepütz CM, Bolten JS, Huwyler J, Hotz G, Madduri S, Müller B. Comparative hard x-ray tomography for virtual histology of zebrafish larva, human tooth cementum, and porcine nerve. J Med Imaging (Bellingham) 2022; 9:031507. [PMID: 35372637 PMCID: PMC8968075 DOI: 10.1117/1.jmi.9.3.031507] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 03/08/2022] [Indexed: 07/26/2023] Open
Abstract
Purpose: Synchrotron radiation-based tomography yields microanatomical features in human and animal tissues without physical slicing. Recent advances in instrumentation have made laboratory-based phase tomography feasible. We compared the performance of three cutting-edge laboratory systems benchmarked by synchrotron radiation-based tomography for three specimens. As an additional criterion, the user-friendliness of the three microtomography systems was considered. Approach: The three tomography systems-SkyScan 2214 (Bruker-microCT, Kontich, Belgium), Exciscope prototype (Stockholm, Sweden), and Xradia 620 Versa (Zeiss, Oberkochen, Germany)-were given 36 h to measure three medically relevant specimens, namely, zebrafish larva, archaeological human tooth, and porcine nerve. The obtained datasets were registered to the benchmark synchrotron radiation-based tomography from the same specimens and selected ones to the SkyScan 1275 and phoenix nanotom m® laboratory systems to characterize development over the last decade. Results: Next-generation laboratory-based microtomography almost reached the quality achieved by synchrotron-radiation facilities with respect to spatial and density resolution, as indicated by the visualization of the medically relevant microanatomical features. The SkyScan 2214 system and the Exciscope prototype demonstrated the complementarity of phase information by imaging the eyes of the zebrafish larva. The 3 - μ m thin annual layers in the tooth cementum were identified using Xradia 620 Versa. Conclusions: SkyScan 2214 was the simplest system and was well-suited to visualizing the wealth of anatomical features in the zebrafish larva. Data from the Exciscope prototype with the high photon flux from the liquid metal source showed the spiral nature of the myelin sheaths in the porcine nerve. Xradia 620 Versa, with detector optics as typically installed for synchrotron tomography beamlines, enabled the three-dimensional visualization of the zebrafish larva with comparable quality to the synchrotron data and the annual layers in the tooth cementum.
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Affiliation(s)
- Alexandra Migga
- University of Basel, Biomaterials Science Center, Department of Biomedical Engineering, Allschwil, Switzerland
- University of Basel, Biomaterials Science Center, Department of Clinical Research, Basel, Switzerland
| | - Georg Schulz
- University of Basel, Biomaterials Science Center, Department of Biomedical Engineering, Allschwil, Switzerland
- University of Basel, Core Facility Micro- and Nanotomography, Department of Biomedical Engineering, Allschwil, Switzerland
| | - Griffin Rodgers
- University of Basel, Biomaterials Science Center, Department of Biomedical Engineering, Allschwil, Switzerland
- University of Basel, Biomaterials Science Center, Department of Clinical Research, Basel, Switzerland
| | - Melissa Osterwalder
- University of Basel, Biomaterials Science Center, Department of Biomedical Engineering, Allschwil, Switzerland
- University of Basel, Biomaterials Science Center, Department of Clinical Research, Basel, Switzerland
| | - Christine Tanner
- University of Basel, Biomaterials Science Center, Department of Biomedical Engineering, Allschwil, Switzerland
- University of Basel, Biomaterials Science Center, Department of Clinical Research, Basel, Switzerland
| | | | | | | | | | | | | | | | - Jan S. Bolten
- University of Basel, Pharmaceutical Technology, Department of Pharmaceutical Sciences, Basel, Switzerland
| | - Jörg Huwyler
- University of Basel, Pharmaceutical Technology, Department of Pharmaceutical Sciences, Basel, Switzerland
| | - Gerhard Hotz
- Natural History Museum of Basel, Anthropological Collection, Basel, Switzerland
- University of Basel, Integrative Prehistory and Archaeological Science, Basel, Switzerland
| | - Srinivas Madduri
- University of Basel, Biomaterials Science Center, Department of Biomedical Engineering, Allschwil, Switzerland
- University of Geneva, Department of Surgery, Geneva, Switzerland
- University Hospital Basel, Department of Plastic, Reconstructive, Aesthetic and Hand Surgery, Basel, Switzerland
| | - Bert Müller
- University of Basel, Biomaterials Science Center, Department of Biomedical Engineering, Allschwil, Switzerland
- University of Basel, Biomaterials Science Center, Department of Clinical Research, Basel, Switzerland
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6
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Zeng C, Chen Z, Yang H, Fan Y, Fei L, Chen X, Zhang M. Advanced high resolution three-dimensional imaging to visualize the cerebral neurovascular network in stroke. Int J Biol Sci 2022; 18:552-571. [PMID: 35002509 PMCID: PMC8741851 DOI: 10.7150/ijbs.64373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/28/2021] [Indexed: 11/05/2022] Open
Abstract
As an important method to accurately and timely diagnose stroke and study physiological characteristics and pathological mechanism in it, imaging technology has gone through more than a century of iteration. The interaction of cells densely packed in the brain is three-dimensional (3D), but the flat images brought by traditional visualization methods show only a few cells and ignore connections outside the slices. The increased resolution allows for a more microscopic and underlying view. Today's intuitive 3D imagings of micron or even nanometer scale are showing its essentiality in stroke. In recent years, 3D imaging technology has gained rapid development. With the overhaul of imaging mediums and the innovation of imaging mode, the resolution has been significantly improved, endowing researchers with the capability of holistic observation of a large volume, real-time monitoring of tiny voxels, and quantitative measurement of spatial parameters. In this review, we will summarize the current methods of high-resolution 3D imaging applied in stroke.
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Affiliation(s)
- Chudai Zeng
- Department of Neurology, Xiangya Hospital of Central South University, Changsha, Hunan, China, 410008.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China, 410008
| | - Zhuohui Chen
- Department of Neurology, Xiangya Hospital of Central South University, Changsha, Hunan, China, 410008.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China, 410008
| | - Haojun Yang
- Department of Neurology, Xiangya Hospital of Central South University, Changsha, Hunan, China, 410008.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China, 410008
| | - Yishu Fan
- Department of Neurology, Xiangya Hospital of Central South University, Changsha, Hunan, China, 410008.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China, 410008
| | - Lujing Fei
- Department of Neurology, Xiangya Hospital of Central South University, Changsha, Hunan, China, 410008.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China, 410008
| | - Xinghang Chen
- Department of Neurology, Xiangya Hospital of Central South University, Changsha, Hunan, China, 410008.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China, 410008
| | - Mengqi Zhang
- Department of Neurology, Xiangya Hospital of Central South University, Changsha, Hunan, China, 410008.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China, 410008
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7
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Eckermann M, van der Meer F, Cloetens P, Ruhwedel T, Möbius W, Stadelmann C, Salditt T. Three-dimensional virtual histology of the cerebral cortex based on phase-contrast X-ray tomography. BIOMEDICAL OPTICS EXPRESS 2021; 12:7582-7598. [PMID: 35003854 PMCID: PMC8713656 DOI: 10.1364/boe.434885] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 05/09/2023]
Abstract
In this work, we optimize the setups and experimental parameters of X-ray phase-contrast computed-tomography for the three-dimensional imaging of the cyto- and myeloarchitecture of cerebral cortex, including both human and murine tissue. We present examples for different optical configurations using state-of-the art synchrotron instruments for holographic tomography, as well as compact laboratory setups for phase-contrast tomography in the direct contrast (edge-enhancement) regime. Apart from unstained and paraffin-embedded tissue, we tested hydrated tissue, as well as heavy metal stained and resin-embedded tissue using two different protocols. Further, we show that the image quality achieved allows to assess the neuropathology of multiple sclerosis in a biopsy sample collected during surgery.
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Affiliation(s)
- Marina Eckermann
- Institut für Röntgenphysik, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany
| | | | - Peter Cloetens
- ESRF, the European Synchrotron, 71, avenue des Martyrs, 38043 Grenoble Cedex 9, France
| | - Torben Ruhwedel
- Max-Planck-Institut für experimentelle Medizin, Hermann-Rein-Straße 3, 37075 Göttingen, Germany
| | - Wiebke Möbius
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany
- Max-Planck-Institut für experimentelle Medizin, Hermann-Rein-Straße 3, 37075 Göttingen, Germany
| | - Christine Stadelmann
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany
- Institut für Neuropathologie, Robert-Koch-Straße 40, 37075 Göttingen, Germany
| | - Tim Salditt
- Institut für Röntgenphysik, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany
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8
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Three-dimensional virtual histology of the human hippocampus based on phase-contrast computed tomography. Proc Natl Acad Sci U S A 2021; 118:2113835118. [PMID: 34819378 PMCID: PMC8640721 DOI: 10.1073/pnas.2113835118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2021] [Indexed: 12/17/2022] Open
Abstract
We demonstrate multiscale phase-contrast X-ray computed tomography (CT) of postmortem human brain tissue. Large tissue volumes can be covered by parallel-beam CT and combined with subcellular detail for selected regions scanned at high magnification. This has been repeated identically for a larger number of individuals, including both Alzheimer’s-diseased patients and a control group. Optimized phase retrieval, followed by automated segmentation based on machine learning, as well as feature identification and classification based on optimal transport theory, indicates a pathway from healthy to pathological structure without prior hypothesis. This study provides a blueprint for studying the cytoarchitecture of the human brain and its alterations associated with neurodegenerative diseases. We have studied the three-dimensional (3D) cytoarchitecture of the human hippocampus in neuropathologically healthy and Alzheimer’s disease (AD) individuals, based on phase-contrast X-ray computed tomography of postmortem human tissue punch biopsies. In view of recent findings suggesting a nuclear origin of AD, we target in particular the nuclear structure of the dentate gyrus (DG) granule cells. Tissue samples of 20 individuals were scanned and evaluated using a highly automated approach of measurement and analysis, combining multiscale recordings, optimized phase retrieval, segmentation by machine learning, representation of structural properties in a feature space, and classification based on the theory of optimal transport. Accordingly, we find that the prototypical transformation between a structure representing healthy granule cells and the pathological state involves a decrease in the volume of granule cell nuclei, as well as an increase in the electron density and its spatial heterogeneity. The latter can be explained by a higher ratio of heterochromatin to euchromatin. Similarly, many other structural properties can be derived from the data, reflecting both the natural polydispersity of the hippocampal cytoarchitecture between different individuals in the physiological context and the structural effects associated with AD pathology.
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9
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Romano M, Bravin A, Mittone A, Eckhardt A, Barbone GE, Sancey L, Dinkel J, Bartzsch S, Ricke J, Alunni-Fabbroni M, Hirner-Eppeneder H, Karpov D, Giannini C, Bunk O, Bouchet A, Ruf V, Giese A, Coan P. A Multi-Scale and Multi-Technique Approach for the Characterization of the Effects of Spatially Fractionated X-ray Radiation Therapies in a Preclinical Model. Cancers (Basel) 2021; 13:cancers13194953. [PMID: 34638437 PMCID: PMC8507698 DOI: 10.3390/cancers13194953] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/23/2021] [Accepted: 09/27/2021] [Indexed: 12/15/2022] Open
Abstract
The purpose of this study is to use a multi-technique approach to detect the effects of spatially fractionated X-ray Microbeam (MRT) and Minibeam Radiation Therapy (MB) and to compare them to seamless Broad Beam (BB) irradiation. Healthy- and Glioblastoma (GBM)-bearing male Fischer rats were irradiated in-vivo on the right brain hemisphere with MRT, MB and BB delivering three different doses for each irradiation geometry. Brains were analyzed post mortem by multi-scale X-ray Phase Contrast Imaging-Computed Tomography (XPCI-CT), histology, immunohistochemistry, X-ray Fluorescence (XRF), Small- and Wide-Angle X-ray Scattering (SAXS/WAXS). XPCI-CT discriminates with high sensitivity the effects of MRT, MB and BB irradiations on both healthy and GBM-bearing brains producing a first-time 3D visualization and morphological analysis of the radio-induced lesions, MRT and MB induced tissue ablations, the presence of hyperdense deposits within specific areas of the brain and tumor evolution or regression with respect to the evaluation made few days post-irradiation with an in-vivo magnetic resonance imaging session. Histology, immunohistochemistry, SAXS/WAXS and XRF allowed identification and classification of these deposits as hydroxyapatite crystals with the coexistence of Ca, P and Fe mineralization, and the multi-technique approach enabled the realization, for the first time, of the map of the differential radiosensitivity of the different brain areas treated with MRT and MB. 3D XPCI-CT datasets enabled also the quantification of tumor volumes and Ca/Fe deposits and their full-organ visualization. The multi-scale and multi-technique approach enabled a detailed visualization and classification in 3D of the radio-induced effects on brain tissues bringing new essential information towards the clinical implementation of the MRT and MB radiation therapy techniques.
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Affiliation(s)
- Mariele Romano
- Department of Medical Physics, Faculty of Physics, Ludwig-Maximilians-Universität, Am Coulombwall 1, München, 85748 Garching, Germany; (M.R.); (A.E.); (G.E.B.)
| | - Alberto Bravin
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France; (A.B.); (A.M.); (D.K.)
- Department of Physics, Faculty of Physics, University of Milano-Bicocca, 20126 Milan, Italy
| | - Alberto Mittone
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France; (A.B.); (A.M.); (D.K.)
- CELLS-ALBA Synchrotron, 08290 Cerdanyola del Valles, Spain
| | - Alicia Eckhardt
- Department of Medical Physics, Faculty of Physics, Ludwig-Maximilians-Universität, Am Coulombwall 1, München, 85748 Garching, Germany; (M.R.); (A.E.); (G.E.B.)
| | - Giacomo E. Barbone
- Department of Medical Physics, Faculty of Physics, Ludwig-Maximilians-Universität, Am Coulombwall 1, München, 85748 Garching, Germany; (M.R.); (A.E.); (G.E.B.)
- Department of Radiology, University Hospital, Ludwig-Maximilians-Universität, 81377 Munich, Germany; (J.D.); (J.R.); (M.A.-F.); (H.H.-E.)
| | - Lucie Sancey
- Centre de Recherche UGA/INSERM U1209/CNRS UMR5309, Institute for Advanced Biosciences, 38700 La Tronche, France;
| | - Julien Dinkel
- Department of Radiology, University Hospital, Ludwig-Maximilians-Universität, 81377 Munich, Germany; (J.D.); (J.R.); (M.A.-F.); (H.H.-E.)
| | - Stefan Bartzsch
- Department of Radiation Oncology, School of Medicine, Technical University of Munich, Klinikum Rechts der Isar, 81675 Munich, Germany;
- Department of Radiation Sciences (DRS), Institute of Radiation Medicine (IRM), Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Jens Ricke
- Department of Radiology, University Hospital, Ludwig-Maximilians-Universität, 81377 Munich, Germany; (J.D.); (J.R.); (M.A.-F.); (H.H.-E.)
| | - Marianna Alunni-Fabbroni
- Department of Radiology, University Hospital, Ludwig-Maximilians-Universität, 81377 Munich, Germany; (J.D.); (J.R.); (M.A.-F.); (H.H.-E.)
| | - Heidrun Hirner-Eppeneder
- Department of Radiology, University Hospital, Ludwig-Maximilians-Universität, 81377 Munich, Germany; (J.D.); (J.R.); (M.A.-F.); (H.H.-E.)
| | - Dmitry Karpov
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France; (A.B.); (A.M.); (D.K.)
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen, Switzerland;
| | - Cinzia Giannini
- Institute of Crystallography, National Research Council, 70126 Bari, Italy;
| | - Oliver Bunk
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen, Switzerland;
| | - Audrey Bouchet
- Inserm U1296 Unit “Radiation: Defense, Health Environment”, 69008 Lyon, France;
| | - Viktoria Ruf
- Center for Neuropathology and Prion Research, Ludwig-Maximilians-Universität, 81377 Munich, Germany; (V.R.); (A.G.)
| | - Armin Giese
- Center for Neuropathology and Prion Research, Ludwig-Maximilians-Universität, 81377 Munich, Germany; (V.R.); (A.G.)
| | - Paola Coan
- Department of Medical Physics, Faculty of Physics, Ludwig-Maximilians-Universität, Am Coulombwall 1, München, 85748 Garching, Germany; (M.R.); (A.E.); (G.E.B.)
- Department of Radiology, University Hospital, Ludwig-Maximilians-Universität, 81377 Munich, Germany; (J.D.); (J.R.); (M.A.-F.); (H.H.-E.)
- Correspondence:
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10
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Asbestos bodies count and morphometry in bulk lung tissue samples by non-invasive X-ray micro-tomography. Sci Rep 2021; 11:10608. [PMID: 34012032 PMCID: PMC8136473 DOI: 10.1038/s41598-021-90057-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/06/2021] [Indexed: 02/03/2023] Open
Abstract
The number of the Asbestos Bodies (AB), i.e. asbestos that developed an iron-protein coating during its permanence in biological tissues, is one of the most accessible markers of asbestos exposure in individuals. The approaches developed to perform AB count in biological tissues are based on the manual examination of tissue digests or histological sections by means of light or electron microscopies. Although these approaches are well established and relatively accessible, manual examination is time-consuming and can be reader-dependent. Besides, approximations are applied because of the limitations of 2D readings and to speed up manual counts. In addition, sample preparation using tissue digests require an amount of tissue that can only be obtained by invasive surgery or post-mortem sampling. In this paper, we propose a new approach to AB counting based on non-destructive 3D imaging, which has the potential to overcome most of the limitations of conventional approaches. This method allows automating the AB count and determining their morphometry distribution in bulk tissue samples (ideally non-invasive needle biopsies), with minimal sample preparation and avoiding approximations. Although the results are promising, additional testing on a larger number of AB-containing biological samples would be required to fully validate the method.
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11
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Abstract
The cochlea of our auditory system is an intricate structure deeply embedded in the temporal bone. Compared with other sensory organs such as the eye, the cochlea has remained poorly accessible for investigation, for example, by imaging. This limitation also concerns the further development of technology for restoring hearing in the case of cochlear dysfunction, which requires quantitative information on spatial dimensions and the sensorineural status of the cochlea. Here, we employed X-ray phase-contrast tomography and light-sheet fluorescence microscopy and their combination for multiscale and multimodal imaging of cochlear morphology in species that serve as established animal models for auditory research. We provide a systematic reference for morphological parameters relevant for cochlear implant development for rodent and nonhuman primate models. We simulate the spread of light from the emitters of the optical implants within the reconstructed nonhuman primate cochlea, which indicates a spatially narrow optogenetic excitation of spiral ganglion neurons.
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12
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Rodrigues PV, Tostes K, Bosque BP, de Godoy JVP, Amorim Neto DP, Dias CSB, Fonseca MDC. Illuminating the Brain With X-Rays: Contributions and Future Perspectives of High-Resolution Microtomography to Neuroscience. Front Neurosci 2021; 15:627994. [PMID: 33815039 PMCID: PMC8010130 DOI: 10.3389/fnins.2021.627994] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 02/26/2021] [Indexed: 12/27/2022] Open
Abstract
The assessment of three-dimensional (3D) brain cytoarchitecture at a cellular resolution remains a great challenge in the field of neuroscience and constant development of imaging techniques has become crucial, particularly when it comes to offering direct and clear obtention of data from macro to nano scales. Magnetic resonance imaging (MRI) and electron or optical microscopy, although valuable, still face some issues such as the lack of contrast and extensive sample preparation protocols. In this context, x-ray microtomography (μCT) has become a promising non-destructive tool for imaging a broad range of samples, from dense materials to soft biological specimens. It is a new supplemental method to be explored for deciphering the cytoarchitecture and connectivity of the brain. This review aims to bring together published works using x-ray μCT in neurobiology in order to discuss the achievements made so far and the future of this technique for neuroscience.
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Affiliation(s)
- Paulla Vieira Rodrigues
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Department of Structural and Functional Biology, State University of Campinas, Campinas, Brazil
| | - Katiane Tostes
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Beatriz Pelegrini Bosque
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Department of Structural and Functional Biology, State University of Campinas, Campinas, Brazil
| | - João Vitor Pereira de Godoy
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Department of Structural and Functional Biology, State University of Campinas, Campinas, Brazil
| | - Dionisio Pedro Amorim Neto
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Department of Structural and Functional Biology, State University of Campinas, Campinas, Brazil
| | - Carlos Sato Baraldi Dias
- Brazilian Synchrotron Light National Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Matheus de Castro Fonseca
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
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13
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Du M, Di ZW, Gürsoy D, Xian RP, Kozorovitskiy Y, Jacobsen C. Upscaling X-ray nanoimaging to macroscopic specimens. J Appl Crystallogr 2021; 54:386-401. [PMID: 33953650 PMCID: PMC8056767 DOI: 10.1107/s1600576721000194] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 01/06/2021] [Indexed: 11/10/2022] Open
Abstract
Upscaling X-ray nanoimaging to macroscopic specimens has the potential for providing insights across multiple length scales, but its feasibility has long been an open question. By combining the imaging requirements and existing proof-of-principle examples in large-specimen preparation, data acquisition and reconstruction algorithms, the authors provide imaging time estimates for howX-ray nanoimaging can be scaled to macroscopic specimens. To arrive at this estimate, a phase contrast imaging model that includes plural scattering effects is used to calculate the required exposure and corresponding radiation dose. The coherent X-ray flux anticipated from upcoming diffraction-limited light sources is then considered. This imaging time estimation is in particular applied to the case of the connectomes of whole mouse brains. To image the connectome of the whole mouse brain, electron microscopy connectomics might require years, whereas optimized X-ray microscopy connectomics could reduce this to one week. Furthermore, this analysis points to challenges that need to be overcome (such as increased X-ray detector frame rate) and opportunities that advances in artificial-intelligence-based 'smart' scanning might provide. While the technical advances required are daunting, it is shown that X-ray microscopy is indeed potentially applicable to nanoimaging of millimetre- or even centimetre-size specimens.
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Affiliation(s)
- Ming Du
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Zichao Wendy Di
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA.,Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Doǧa Gürsoy
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA.,Department of Electrical Engineering and Computer Science, Northwestern University, Evanston, IL 60208, USA
| | - R Patrick Xian
- Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA
| | - Yevgenia Kozorovitskiy
- Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA.,Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Chris Jacobsen
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA.,Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA.,Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, USA
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14
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Barbone GE, Bravin A, Mittone A, Grosu S, Ricke J, Cavaletti G, Djonov V, Coan P. High-Spatial-Resolution Three-dimensional Imaging of Human Spinal Cord and Column Anatomy with Postmortem X-ray Phase-Contrast Micro-CT. Radiology 2021; 298:135-146. [DOI: 10.1148/radiol.2020201622] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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15
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Kuan AT, Phelps JS, Thomas LA, Nguyen TM, Han J, Chen CL, Azevedo AW, Tuthill JC, Funke J, Cloetens P, Pacureanu A, Lee WCA. Dense neuronal reconstruction through X-ray holographic nano-tomography. Nat Neurosci 2020; 23:1637-1643. [PMID: 32929244 PMCID: PMC8354006 DOI: 10.1038/s41593-020-0704-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 08/05/2020] [Indexed: 12/21/2022]
Abstract
Imaging neuronal networks provides a foundation for understanding the nervous system, but resolving dense nanometer-scale structures over large volumes remains challenging for light microscopy (LM) and electron microscopy (EM). Here we show that X-ray holographic nano-tomography (XNH) can image millimeter-scale volumes with sub-100-nm resolution, enabling reconstruction of dense wiring in Drosophila melanogaster and mouse nervous tissue. We performed correlative XNH and EM to reconstruct hundreds of cortical pyramidal cells and show that more superficial cells receive stronger synaptic inhibition on their apical dendrites. By combining multiple XNH scans, we imaged an adult Drosophila leg with sufficient resolution to comprehensively catalog mechanosensory neurons and trace individual motor axons from muscles to the central nervous system. To accelerate neuronal reconstructions, we trained a convolutional neural network to automatically segment neurons from XNH volumes. Thus, XNH bridges a key gap between LM and EM, providing a new avenue for neural circuit discovery.
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Affiliation(s)
- Aaron T Kuan
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Jasper S Phelps
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
- Program in Neuroscience, Harvard University, Boston, MA, USA
| | - Logan A Thomas
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Tri M Nguyen
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Julie Han
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Chiao-Lin Chen
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Anthony W Azevedo
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - John C Tuthill
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Jan Funke
- HHMI Janelia Research Campus, Ashburn, VA, USA
| | | | - Alexandra Pacureanu
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA.
- ESRF, The European Synchrotron, Grenoble, France.
| | - Wei-Chung Allen Lee
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
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16
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Kastner DB, Kharazia V, Nevers R, Smyth C, Astudillo-Maya DA, Williams GM, Yang Z, Holobetz CM, Santina LD, Parkinson DY, Frank LM. Scalable method for micro-CT analysis enables large scale quantitative characterization of brain lesions and implants. Sci Rep 2020; 10:20851. [PMID: 33257721 PMCID: PMC7705725 DOI: 10.1038/s41598-020-77796-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 11/17/2020] [Indexed: 12/18/2022] Open
Abstract
Anatomic evaluation is an important aspect of many studies in neuroscience; however, it often lacks information about the three-dimensional structure of the brain. Micro-CT imaging provides an excellent, nondestructive, method for the evaluation of brain structure, but current applications to neurophysiological or lesion studies require removal of the skull as well as hazardous chemicals, dehydration, or embedding, limiting their scalability and utility. Here we present a protocol using eosin in combination with bone decalcification to enhance contrast in the tissue and then employ monochromatic and propagation phase-contrast micro-CT imaging to enable the imaging of brain structure with the preservation of the surrounding skull. Instead of relying on descriptive, time-consuming, or subjective methods, we develop simple quantitative analyses to map the locations of recording electrodes and to characterize the presence and extent of hippocampal brain lesions.
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Affiliation(s)
- David B Kastner
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA, 94143, USA. .,Kavli Institute for Fundamental Neuroscience and Department of Physiology, University of California, San Francisco, CA, 94158, USA.
| | - Viktor Kharazia
- Kavli Institute for Fundamental Neuroscience and Department of Physiology, University of California, San Francisco, CA, 94158, USA
| | - Rhino Nevers
- Kavli Institute for Fundamental Neuroscience and Department of Physiology, University of California, San Francisco, CA, 94158, USA
| | - Clay Smyth
- Kavli Institute for Fundamental Neuroscience and Department of Physiology, University of California, San Francisco, CA, 94158, USA
| | - Daniela A Astudillo-Maya
- Kavli Institute for Fundamental Neuroscience and Department of Physiology, University of California, San Francisco, CA, 94158, USA
| | - Greer M Williams
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA, 94143, USA
| | - Zhounan Yang
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA, 94143, USA
| | - Cristofer M Holobetz
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA, 94143, USA
| | - Luca Della Santina
- Deparment of Ophthalmology, University of California, San Francisco, CA, 94143, USA.,Bakar Computational Health Science Unit, University of California, San Francisco, CA, 94158, USA
| | - Dilworth Y Parkinson
- Advanced Light Source, Lawrence Berkeley National Labs, Berkeley, CA, 94720, USA
| | - Loren M Frank
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA, 94143, USA.,Kavli Institute for Fundamental Neuroscience and Department of Physiology, University of California, San Francisco, CA, 94158, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
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17
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Tran HT, Tsai EHR, Lewis AJ, Moors T, Bol JGJM, Rostami I, Diaz A, Jonker AJ, Guizar-Sicairos M, Raabe J, Stahlberg H, van de Berg WDJ, Holler M, Shahmoradian SH. Alterations in Sub-Axonal Architecture Between Normal Aging and Parkinson's Diseased Human Brains Using Label-Free Cryogenic X-ray Nanotomography. Front Neurosci 2020; 14:570019. [PMID: 33324142 PMCID: PMC7724048 DOI: 10.3389/fnins.2020.570019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 10/14/2020] [Indexed: 01/25/2023] Open
Abstract
Gaining insight to pathologically relevant processes in continuous volumes of unstained brain tissue is important for a better understanding of neurological diseases. Many pathological processes in neurodegenerative disorders affect myelinated axons, which are a critical part of the neuronal circuitry. Cryo ptychographic X-ray computed tomography in the multi-keV energy range is an emerging technology providing phase contrast at high sensitivity, allowing label-free and non-destructive three dimensional imaging of large continuous volumes of tissue, currently spanning up to 400,000 μm3. This aspect makes the technique especially attractive for imaging complex biological material, especially neuronal tissues, in combination with downstream optical or electron microscopy techniques. A further advantage is that dehydration, additional contrast staining, and destructive sectioning/milling are not required for imaging. We have developed a pipeline for cryo ptychographic X-ray tomography of relatively large, hydrated and unstained biological tissue volumes beyond what is typical for the X-ray imaging, using human brain tissue and combining the technique with complementary methods. We present four imaged volumes of a Parkinson's diseased human brain and five volumes from a non-diseased control human brain using cryo ptychographic X-ray tomography. In both cases, we distinguish neuromelanin-containing neurons, lipid and melanic pigment, blood vessels and red blood cells, and nuclei of other brain cells. In the diseased sample, we observed several swellings containing dense granular material resembling clustered vesicles between the myelin sheaths arising from the cytoplasm of the parent oligodendrocyte, rather than the axoplasm. We further investigated the pathological relevance of such swollen axons in adjacent tissue sections by immunofluorescence microscopy for phosphorylated alpha-synuclein combined with multispectral imaging. Since cryo ptychographic X-ray tomography is non-destructive, the large dataset volumes were used to guide further investigation of such swollen axons by correlative electron microscopy and immunogold labeling post X-ray imaging, a possibility demonstrated for the first time. Interestingly, we find that protein antigenicity and ultrastructure of the tissue are preserved after the X-ray measurement. As many pathological processes in neurodegeneration affect myelinated axons, our work sets an unprecedented foundation for studies addressing axonal integrity and disease-related changes in unstained brain tissues.
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Affiliation(s)
| | | | - Amanda J. Lewis
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Basel, Switzerland
| | - Tim Moors
- Department of Anatomy and Neurosciences, Section Clinical Neuroanatomy, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - J. G. J. M. Bol
- Department of Anatomy and Neurosciences, Section Clinical Neuroanatomy, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | | | - Ana Diaz
- Paul Scherrer Institut, Villigen, Switzerland
| | - Allert J. Jonker
- Department of Anatomy and Neurosciences, Section Clinical Neuroanatomy, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | | | - Joerg Raabe
- Paul Scherrer Institut, Villigen, Switzerland
| | - Henning Stahlberg
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Basel, Switzerland
| | - Wilma D. J. van de Berg
- Department of Anatomy and Neurosciences, Section Clinical Neuroanatomy, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
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18
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Frohn J, Pinkert-Leetsch D, Missbach-Güntner J, Reichardt M, Osterhoff M, Alves F, Salditt T. 3D virtual histology of human pancreatic tissue by multiscale phase-contrast X-ray tomography. JOURNAL OF SYNCHROTRON RADIATION 2020; 27:1707-1719. [PMID: 33147198 PMCID: PMC7642968 DOI: 10.1107/s1600577520011327] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 08/18/2020] [Indexed: 05/05/2023]
Abstract
A multiscale three-dimensional (3D) virtual histology approach is presented, based on two configurations of propagation phase-contrast X-ray tomography, which have been implemented in close proximity at the GINIX endstation at the beamline P10/PETRA III (DESY, Hamburg, Germany). This enables the 3D reconstruction of characteristic morphological features of human pancreatic normal and tumor tissue, as obtained from cancer surgery, first in the form of a large-scale overview by parallel-beam illumination, followed by a zoom into a region-of-interest based on zoom tomography using a Kirkpatrick-Baez mirror with additional waveguide optics. To this end 1 mm punch biopsies of the tissue were taken. In the parallel tomography, a volumetric throughput on the order of 0.01 mm3 s-1 was achieved, while maintaining the ability to segment isolated cells. With a continuous rotation during the scan, a total acquisition time of less than 2 min was required for a full tomographic scan. Using the combination of both setups, islets of Langerhans, a three-dimensional cluster of cells in the endocrine part of the pancreas, could be located. Cells in such an islet were segmented and visualized in 3D. Further, morphological alterations of tumorous tissue of the pancreas were characterized. To this end, the anisotropy parameter Ω, based on intensity gradients, was used in order to quantify the presence of collagen fibers within the entire biopsy specimen. This proof-of-concept experiment of the multiscale approach on human pancreatic tissue paves the way for future 3D virtual pathology.
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Affiliation(s)
- Jasper Frohn
- Institute for X-ray Physics, Universität Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Diana Pinkert-Leetsch
- Institute of Diagnostic and Interventional Radiology, University Medical Center Göttingen, Robert Koch Strasse 40, 37075 Göttingen, Germany
- Max Planck Institute for Experimental Medicine, Group of Translational Molecular Imaging, Hermann-Rein-Strasse 3, 37075 Göttingen, Germany
| | - Jeannine Missbach-Güntner
- Institute of Diagnostic and Interventional Radiology, University Medical Center Göttingen, Robert Koch Strasse 40, 37075 Göttingen, Germany
| | - Marius Reichardt
- Institute for X-ray Physics, Universität Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Markus Osterhoff
- Institute for X-ray Physics, Universität Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Frauke Alves
- Institute of Diagnostic and Interventional Radiology, University Medical Center Göttingen, Robert Koch Strasse 40, 37075 Göttingen, Germany
- Max Planck Institute for Experimental Medicine, Group of Translational Molecular Imaging, Hermann-Rein-Strasse 3, 37075 Göttingen, Germany
- Clinic of Hematology and Medical Oncology, University Medical Center Göttingen, Robert Koch Strase 40, 37075 Göttingen, Germany
| | - Tim Salditt
- Institute for X-ray Physics, Universität Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
- Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells (MBExC), University Medical Center Göttingen, Robert Koch Strase 40, 37075 Göttingen, Germany
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19
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Bukreeva I, Junemann O, Cedola A, Palermo F, Maugeri L, Begani Provinciali G, Pieroni N, Sanna A, Otlyga DA, Buzmakov A, Krivonosov Y, Zolotov D, Chukalina M, Ivanova A, Saveliev S, Asadchikov V, Fratini M. Investigation of the human pineal gland 3D organization by X-ray phase contrast tomography. J Struct Biol 2020; 212:107659. [PMID: 33152420 DOI: 10.1016/j.jsb.2020.107659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 10/23/2022]
Abstract
Pineal gland (PG) is a part of the human brain epithalamus that plays an important role in sleep, circadian rhythm, immunity, and reproduction. The calcium deposits and lesions in PG interfere with normal function of the organ and can be associated with different health disorders including serious neurological diseases. At the moment, the detailed mechanisms of PG calcifications and PG lesions formation as well as their involvement in pathological processes are not fully understood. The deep and comprehensive study of the structure of the uncut human PG with histological details, poses a stiff challenge to most imaging techniques, due to low spatial resolution, low visibility or to exceedingly aggressive sample preparation. Here, we investigate the whole uncut and unstained human post-mortem PGs by X-ray phase contrast tomography (XPCT). XPCT is an advanced 3D imaging technique, that permits to study of both soft and calcified tissue of a sample at different scales: from the whole organ to cell structure. In our research we simultaneously resolved 3D structure of parenchyma, vascular network and calcifications. Moreover, we distinguished structural details of intact and degenerated PG tissue. We discriminated calcifications with different structure, pinealocytes nuclei and the glial cells processes. All results were validated by histology. Our research clear demonstrated that XPCT is a potential tool for the high resolution 3D imaging of PG morphological features. This technique opens a new perspective to investigate PG dysfunction and understand the mechanisms of onset and progression of diseases involving the pineal gland.
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Affiliation(s)
- Inna Bukreeva
- Institute of Nanotechnology- CNR, Lecce Unit, Campus Ecotekne Via Monteroni, Lecce; Rome Unit, Piazzale Aldo Moro 5, Rome, Italy; P.N. Lebedev Physical Institute, RAS, Leninskiy pr., 53 Moscow, Russian Federation.
| | - Olga Junemann
- FSSI Research Institute of Human Morphology, Tsyurupy Str 3, Moscow, Russian Federation.
| | - Alessia Cedola
- Institute of Nanotechnology- CNR, Lecce Unit, Campus Ecotekne Via Monteroni, Lecce; Rome Unit, Piazzale Aldo Moro 5, Rome, Italy.
| | - Francesca Palermo
- Institute of Nanotechnology- CNR, Lecce Unit, Campus Ecotekne Via Monteroni, Lecce; Rome Unit, Piazzale Aldo Moro 5, Rome, Italy; Department of Physics, University of Calabria, I-87036 Arcavacata di Rende (CS), Italy
| | - Laura Maugeri
- Institute of Nanotechnology- CNR, Lecce Unit, Campus Ecotekne Via Monteroni, Lecce; Rome Unit, Piazzale Aldo Moro 5, Rome, Italy; IRCCS Fondazione Santa Lucia, Via Ardeatina 352, Rome, Italy
| | - Ginevra Begani Provinciali
- Institute of Nanotechnology- CNR, Lecce Unit, Campus Ecotekne Via Monteroni, Lecce; Rome Unit, Piazzale Aldo Moro 5, Rome, Italy; Laboratoire d'Optique appliquée, ENSTA Paris, Institut Polytechnique de Paris, 828 boulevard des Maréchaux, Palaiseau, France
| | - Nicola Pieroni
- Institute of Nanotechnology- CNR, Lecce Unit, Campus Ecotekne Via Monteroni, Lecce; Rome Unit, Piazzale Aldo Moro 5, Rome, Italy; SAIMLAL Department, Sapienza University, via A. Scarpa 14, Rome, Italy
| | - Alessia Sanna
- Institute of Nanotechnology- CNR, Lecce Unit, Campus Ecotekne Via Monteroni, Lecce; Rome Unit, Piazzale Aldo Moro 5, Rome, Italy
| | - Dmitry A Otlyga
- FSSI Research Institute of Human Morphology, Tsyurupy Str 3, Moscow, Russian Federation
| | - Alexey Buzmakov
- FSRC «Crystallography and Photonics» RAS, Leninskiy pr., 59, Moscow, Russian Federation
| | - Yuri Krivonosov
- FSRC «Crystallography and Photonics» RAS, Leninskiy pr., 59, Moscow, Russian Federation
| | - Denis Zolotov
- FSRC «Crystallography and Photonics» RAS, Leninskiy pr., 59, Moscow, Russian Federation
| | - Marina Chukalina
- FSRC «Crystallography and Photonics» RAS, Leninskiy pr., 59, Moscow, Russian Federation; Smart Engines Service LLC, 60-letiya Oktyabrya pr., 9, Moscow, Russian Federation
| | - Anna Ivanova
- FSRC «Crystallography and Photonics» RAS, Leninskiy pr., 59, Moscow, Russian Federation
| | - Sergey Saveliev
- FSSI Research Institute of Human Morphology, Tsyurupy Str 3, Moscow, Russian Federation
| | - Victor Asadchikov
- FSRC «Crystallography and Photonics» RAS, Leninskiy pr., 59, Moscow, Russian Federation
| | - Michela Fratini
- Institute of Nanotechnology- CNR, Lecce Unit, Campus Ecotekne Via Monteroni, Lecce; Rome Unit, Piazzale Aldo Moro 5, Rome, Italy; IRCCS Fondazione Santa Lucia, Via Ardeatina 352, Rome, Italy
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20
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Eckermann M, Peruzzi N, Frohn J, Bech M, Englund E, Veress B, Salditt T, Dahlin LB, Ohlsson B. 3d phase-contrast nanotomography of unstained human skin biopsies may identify morphological differences in the dermis and epidermis between subjects. Skin Res Technol 2020; 27:316-323. [PMID: 33022848 PMCID: PMC8246570 DOI: 10.1111/srt.12974] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/07/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND Enteric neuropathy is described in most patients with gastrointestinal dysmotility and may be found together with reduced intraepidermal nerve fiber density (IENFD). The aim of this pilot study was to assess whether three-dimensional (3d) imaging of skin biopsies could be used to examine various tissue components in patients with gastrointestinal dysmotility. MATERIAL AND METHODS Four dysmotility patients of different etiology and two healthy volunteers were included. From each subject, two 3-mm punch skin biopsies were stained with antibodies against protein gene product 9.5 or evaluated as a whole with two X-ray phase-contrast computed tomography (CT) setups, a laboratory µCT setup and a dedicated synchrotron radiation nanoCT end-station. RESULTS Two patients had reduced IENFD, and two normal IENFD, compared with controls. µCT and X-ray phase-contrast holographic nanotomography scanned whole tissue specimens, with optional high-resolution scans revealing delicate structures, without differentiation of various fibers and cells. Irregular architecture of dermal fibers was observed in the patient with Ehlers-Danlos syndrome and the patient with idiopathic dysmotility showed an abundance of mesenchymal ground substance. CONCLUSIONS 3d phase-contrast tomographic imaging may be useful to illustrate traits of connective tissue dysfunction in various organs and to demonstrate whether disorganized dermal fibers could explain organ dysfunction.
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Affiliation(s)
- Marina Eckermann
- Institute for X-Ray Physics, University of Göttingen, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Niccolò Peruzzi
- Medical Radiation Physics, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Jasper Frohn
- Institute for X-Ray Physics, University of Göttingen, Göttingen, Germany
| | - Martin Bech
- Medical Radiation Physics, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Elisabet Englund
- Division of Oncology and Pathology, Skane University Hospital, Lund University, Lund, Sweden
| | - Béla Veress
- Department of Pathology, Skåne University Hospital, Malmö, Sweden
| | - Tim Salditt
- Institute for X-Ray Physics, University of Göttingen, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Lars B Dahlin
- Department of Translational Medicine - Hand Surgery, Lund University, Malmö, Sweden.,Department of Hand Surgery, Skåne University Hospital, Malmö, Sweden
| | - Bodil Ohlsson
- Department of Internal Medicine, Skåne University Hospital, Lund University, Malmö, Sweden
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21
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Longo E, Sancey L, Flenner S, Kubec A, Bonnin A, David C, Müller M, Greving I. X-ray Zernike phase contrast tomography: 3D ROI visualization of mm-sized mice organ tissues down to sub-cellular components. BIOMEDICAL OPTICS EXPRESS 2020; 11:5506-5517. [PMID: 33149967 PMCID: PMC7587279 DOI: 10.1364/boe.396695] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/29/2020] [Accepted: 07/13/2020] [Indexed: 05/26/2023]
Abstract
Thanks to its non-invasive nature, X-ray phase contrast tomography is a very versatile imaging tool for biomedical studies. In contrast, histology is a well-established method, though having its limitations: it requires extensive sample preparation and it is quite time consuming. Therefore, the development of nano-imaging techniques for studying anatomic details at the cellular level is gaining more and more importance. In this article, full field transmission X-ray nanotomography is used in combination with Zernike phase contrast to image millimeter sized unstained tissue samples at high spatial resolution. The regions of interest (ROI) scans of different tissues were obtained from mouse kidney, spleen and mammalian carcinoma. Thanks to the relatively large field of view and effective pixel sizes down to 36 nm, this 3D approach enabled the visualization of the specific morphology of each tissue type without staining or complex sample preparation. As a proof of concept technique, we show that the high-quality images even permitted the 3D segmentation of multiple structures down to a sub-cellular level. Using stitching techniques, volumes larger than the field of view are accessible. This method can lead to a deeper understanding of the organs' nano-anatomy, filling the resolution gap between histology and transmission electron microscopy.
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Affiliation(s)
- E. Longo
- Helmholtz-Zentrum Geesthacht, Institute of Material Research, Max-Planck-Strasse 1, 21502 Geesthacht, Germany
| | - L. Sancey
- Institute for Advanced Biosciences U1209 UMR5309 UGA, Allée des Alpes - Site Santé, La Tronche, 38700, France
| | - S. Flenner
- Helmholtz-Zentrum Geesthacht, Institute of Material Research, Max-Planck-Strasse 1, 21502 Geesthacht, Germany
| | - A. Kubec
- Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - A. Bonnin
- Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - C. David
- Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - M. Müller
- Helmholtz-Zentrum Geesthacht, Institute of Material Research, Max-Planck-Strasse 1, 21502 Geesthacht, Germany
| | - I. Greving
- Helmholtz-Zentrum Geesthacht, Institute of Material Research, Max-Planck-Strasse 1, 21502 Geesthacht, Germany
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22
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Eckermann M, Frohn J, Reichardt M, Osterhoff M, Sprung M, Westermeier F, Tzankov A, Werlein C, Kühnel M, Jonigk D, Salditt T. 3D virtual pathohistology of lung tissue from Covid-19 patients based on phase contrast X-ray tomography. eLife 2020; 9:e60408. [PMID: 32815517 PMCID: PMC7473770 DOI: 10.7554/elife.60408] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 08/17/2020] [Indexed: 01/25/2023] Open
Abstract
We present a three-dimensional (3D) approach for virtual histology and histopathology based on multi-scale phase contrast x-ray tomography, and use this to investigate the parenchymal architecture of unstained lung tissue from patients who succumbed to Covid-19. Based on this first proof-of-concept study, we propose multi-scale phase contrast x-ray tomography as a tool to unravel the pathophysiology of Covid-19, extending conventional histology by a third dimension and allowing for full quantification of tissue remodeling. By combining parallel and cone beam geometry, autopsy samples with a maximum cross section of 8 mm are scanned and reconstructed at a resolution and image quality, which allows for the segmentation of individual cells. Using the zoom capability of the cone beam geometry, regions-of-interest are reconstructed with a minimum voxel size of 167 nm. We exemplify the capability of this approach by 3D visualization of diffuse alveolar damage (DAD) with its prominent hyaline membrane formation, by mapping the 3D distribution and density of lymphocytes infiltrating the tissue, and by providing histograms of characteristic distances from tissue interior to the closest air compartment.
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Affiliation(s)
- Marina Eckermann
- Institut für Röntgenphysik, Georg-August-UniversitätGöttingenGermany
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of GöttingenGöttingenGermany
| | - Jasper Frohn
- Institut für Röntgenphysik, Georg-August-UniversitätGöttingenGermany
| | - Marius Reichardt
- Institut für Röntgenphysik, Georg-August-UniversitätGöttingenGermany
| | - Markus Osterhoff
- Institut für Röntgenphysik, Georg-August-UniversitätGöttingenGermany
| | | | | | - Alexandar Tzankov
- Institut für Medizinische Genetik und Pathologie, Universitätsspital BaselBaselSwitzerland
| | - Christopher Werlein
- Medizinische Hochschule Hannover (MHH)HannoverGermany
- Deutsches Zentrum für Lungenforschung (DZL)Hannover (BREATH)Germany
| | - Mark Kühnel
- Medizinische Hochschule Hannover (MHH)HannoverGermany
- Deutsches Zentrum für Lungenforschung (DZL)Hannover (BREATH)Germany
| | - Danny Jonigk
- Medizinische Hochschule Hannover (MHH)HannoverGermany
- Deutsches Zentrum für Lungenforschung (DZL)Hannover (BREATH)Germany
| | - Tim Salditt
- Institut für Röntgenphysik, Georg-August-UniversitätGöttingenGermany
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of GöttingenGöttingenGermany
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23
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Cörek E, Rodgers G, Siegrist S, Einfalt T, Detampel P, Schlepütz CM, Sieber S, Fluder P, Schulz G, Unterweger H, Alexiou C, Müller B, Puchkov M, Huwyler J. Shedding Light on Metal-Based Nanoparticles in Zebrafish by Computed Tomography with Micrometer Resolution. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2000746. [PMID: 32567135 DOI: 10.1002/smll.202000746] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/26/2020] [Indexed: 06/11/2023]
Abstract
Metal-based nanoparticles are clinically used for diagnostic and therapeutic applications. After parenteral administration, they will distribute throughout different organs. Quantification of their distribution within tissues in the 3D space, however, remains a challenge owing to the small particle diameter. In this study, synchrotron radiation-based hard X-ray tomography (SRμCT) in absorption and phase contrast modes is evaluated for the localization of superparamagnetic iron oxide nanoparticles (SPIONs) in soft tissues based on their electron density and X-ray attenuation. Biodistribution of SPIONs is studied using zebrafish embryos as a vertebrate screening model. This label-free approach gives rise to an isotropic, 3D, direct space visualization of the entire 2.5 mm-long animal with a spatial resolution of around 2 µm. High resolution image stacks are available on a dedicated internet page (http://zebrafish.pharma-te.ch). X-ray tomography is combined with physico-chemical characterization and cellular uptake studies to confirm the safety and effectiveness of protective SPION coatings. It is demonstrated that SRμCT provides unprecedented insights into the zebrafish embryo anatomy and tissue distribution of label-free metal oxide nanoparticles.
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Affiliation(s)
- Emre Cörek
- Department of Pharmaceutical Technology, University of Basel, Klingelbergstrasse. 50, Basel, 4056, Switzerland
| | - Griffin Rodgers
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, Gewerbestrasse 14, Allschwil, 4123, Switzerland
| | - Stefan Siegrist
- Department of Pharmaceutical Technology, University of Basel, Klingelbergstrasse. 50, Basel, 4056, Switzerland
| | - Tomaz Einfalt
- Department of Pharmaceutical Technology, University of Basel, Klingelbergstrasse. 50, Basel, 4056, Switzerland
| | - Pascal Detampel
- Department of Pharmaceutical Technology, University of Basel, Klingelbergstrasse. 50, Basel, 4056, Switzerland
| | - Christian M Schlepütz
- Swiss Light Source, Paul Scherrer Institute, Forschungsstrasse 111, Villigen, 5232, Switzerland
| | - Sandro Sieber
- Department of Pharmaceutical Technology, University of Basel, Klingelbergstrasse. 50, Basel, 4056, Switzerland
| | - Pascal Fluder
- Department of Pharmaceutical Technology, University of Basel, Klingelbergstrasse. 50, Basel, 4056, Switzerland
| | - Georg Schulz
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, Gewerbestrasse 14, Allschwil, 4123, Switzerland
| | - Harald Unterweger
- Department of Otorhinolaryngology, Head and Neck Surgery, Section for Experimental Oncology and Nanomedicine (SEON), Else Kröner-Fresenius Stiftung Professorship, Erlangen University of Erlangen, Waldstraße 1, Erlangen, 91054, Germany
| | - Christoph Alexiou
- Department of Otorhinolaryngology, Head and Neck Surgery, Section for Experimental Oncology and Nanomedicine (SEON), Else Kröner-Fresenius Stiftung Professorship, Erlangen University of Erlangen, Waldstraße 1, Erlangen, 91054, Germany
| | - Bert Müller
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, Gewerbestrasse 14, Allschwil, 4123, Switzerland
| | - Maxim Puchkov
- Department of Pharmaceutical Technology, University of Basel, Klingelbergstrasse. 50, Basel, 4056, Switzerland
| | - Jörg Huwyler
- Department of Pharmaceutical Technology, University of Basel, Klingelbergstrasse. 50, Basel, 4056, Switzerland
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24
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Correlative x-ray phase-contrast tomography and histology of human brain tissue affected by Alzheimer’s disease. Neuroimage 2020; 210:116523. [DOI: 10.1016/j.neuroimage.2020.116523] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 11/01/2019] [Accepted: 01/05/2020] [Indexed: 12/19/2022] Open
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25
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Eckermann M, Töpperwien M, Robisch AL, van der Meer F, Stadelmann C, Salditt T. Phase-contrast x-ray tomography of neuronal tissue at laboratory sources with submicron resolution. J Med Imaging (Bellingham) 2020; 7:013502. [PMID: 32118088 PMCID: PMC7032481 DOI: 10.1117/1.jmi.7.1.013502] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 01/21/2020] [Indexed: 11/14/2022] Open
Abstract
Purpose: Recently, progress has been achieved in implementing phase-contrast tomography of soft biological tissues at laboratory sources. This opens up opportunities for three-dimensional (3-D) histology based on x-ray computed tomography (μ- and nanoCT) in the direct vicinity of hospitals and biomedical research institutions. Combining advanced x-ray generation and detection techniques with phase reconstruction algorithms, 3-D histology can be obtained even of unstained tissue of the central nervous system, as shown, for example, for biopsies and autopsies of human cerebellum. Depending on the setup, i.e., source, detector, and geometric parameters, laboratory-based tomography can be implemented at very different sizes and length scales. We investigate the extent to which 3-D histology of neuronal tissue can exploit the cone-beam geometry at high magnification M using a nanofocus transmission x-ray tube (nanotube) with a 300 nm minimal spot size (Excillum), combined with a single-photon counting camera. Tightly approaching the source spot with the biopsy punch, we achieve high M≈101−102, high flux density, and exploit the superior efficiency of this detector technology. Approach: Different nanotube configurations such as spot size and flux, M, as well as exposure time, Fresnel number, and coherence are varied and selected in view of resolution, field of view, and/or phase-contrast requirements. Results: The data show that the information content for the cytoarchitecture is enhanced by the phase effect. Comparison of results to those obtained at a microfocus rotating-anode x-ray tomography setup with a high-resolution detector, i.e., in low-M geometry, reveals similar to slightly superior data quality for the nanotube setup. In addition to its compactness, reduced power consumption by a factor of 103, and shorter scan duration, the particular advantage of the nanotube setup also lies in its suitability for pixel detector technology, enabling an increased range of opportunities for applications in laboratory phase-contrast x-ray tomography. Conclusions: The phase retrieval scheme utilized mixes amplitude and phase contrast, with results being robust with respect to reconstruction parameters. Structural information content is comparable to slightly superior to previous results achieved with a microfocus rotating-anode setup but can be obtained in shorter scan time. Beyond advantages as compactness, lowered power consumption, and flexibility, the nanotube setup’s scalability in view of the progress in pixel detector technology is particularly beneficial. Further progress is thus likely to bring 3-D virtual histology to the performance in scan time and throughput required for clinical practice in neuropathology.
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Affiliation(s)
- Marina Eckermann
- University of Göttingen, Institute for X-Ray Physics, Göttingen, Germany.,University of Göttingen, Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells", Göttingen, Germany
| | - Mareike Töpperwien
- University of Göttingen, Institute for X-Ray Physics, Göttingen, Germany
| | - Anna-Lena Robisch
- University of Göttingen, Institute for X-Ray Physics, Göttingen, Germany
| | | | - Christine Stadelmann
- University Medical Center Göttingen, Institute for Neuropathology, Göttingen, Germany
| | - Tim Salditt
- University of Göttingen, Institute for X-Ray Physics, Göttingen, Germany.,University of Göttingen, Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells", Göttingen, Germany
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26
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Töpperwien M, Markus A, Alves F, Salditt T. Contrast enhancement for visualizing neuronal cytoarchitecture by propagation-based x-ray phase-contrast tomography. Neuroimage 2019; 199:70-80. [PMID: 31129306 DOI: 10.1016/j.neuroimage.2019.05.043] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 05/16/2019] [Indexed: 12/11/2022] Open
Abstract
Knowledge of the three-dimensional (3d) neuronal cytoarchitecture is an important factor in order to understand the connection between tissue structure and function or to visualize pathological changes in neurodegenerative diseases or tumor development. The gold standard in neuropathology is histology, a technique which provides insights into the cellular organization based on sectioning of the sample. Conventional histology, however, misses the complete 3d information as only individual two-dimensional slices through the object are available. In this work, we use propagation-based phase-contrast x-ray tomography to perform 3d virtual histology on cerebellar tissue from mice. This technique enables us to non-invasively visualize the entire 3d density distribution of the examined samples at isotropic (sub-)cellular resolution. One central challenge, however, of the technique is the fact that contrast for important structural features can be easily lost due to small electron density differences, notably between the cells and surrounding tissue. Here, we evaluate the influence of different embedding media, which are intermediate steps in sample preparation for classical histology, on contrast formation and examine the applicability of the different sample preparations both at a synchrotron-based holotomography setup as well as a laboratory source.
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Affiliation(s)
- Mareike Töpperwien
- Institute for X-Ray Physics, University of Göttingen, Germany; Center for Nanoscopy and Molecular Physiology of the Brain (CNMPB), Germany.
| | - Andrea Markus
- Department of Haematology and Medical Oncology, University Medical Center Göttingen, Germany
| | - Frauke Alves
- Department of Haematology and Medical Oncology, University Medical Center Göttingen, Germany; Department of Diagnostic and Interventional Radiology, University Medical Center Göttingen, Germany; Department of Molecular Biology of Neuronal Signals, Max-Planck-Institute of Experimental Medicine, Germany
| | - Tim Salditt
- Institute for X-Ray Physics, University of Göttingen, Germany; Center for Nanoscopy and Molecular Physiology of the Brain (CNMPB), Germany.
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27
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Shanblatt ER, Sung Y, Gupta R, Nelson BJ, Leng S, Graves WS, McCollough CH. Forward model for propagation-based x-ray phase contrast imaging in parallel- and cone-beam geometry. OPTICS EXPRESS 2019; 27:4504-4521. [PMID: 30876068 DOI: 10.1364/oe.27.004504] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 01/21/2019] [Indexed: 06/09/2023]
Abstract
We demonstrate a fast, flexible, and accurate paraxial wave propagation model to serve as a forward model for propagation-based X-ray phase contrast imaging (XPCI) in parallel-beam or cone-beam geometry. This model incorporates geometric cone-beam effects into the multi-slice beam propagation method. It enables rapid prototyping and is well suited to serve as a forward model for propagation-based X-ray phase contrast tomographic reconstructions. Furthermore, it is capable of modeling arbitrary objects, including those that are strongly or multi-scattering. Simulation studies were conducted to compare our model to other forward models in the X-ray regime, such as the Mie and full-wave Rytov solutions.
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