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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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Lee JY, Mack AF, Mattheus U, Donato S, Longo R, Tromba G, Shiozawa T, Scheffler K, Hagberg GE. Distribution of corpora amylacea in the human midbrain: using synchrotron radiation phase-contrast microtomography, high-field magnetic resonance imaging, and histology. Front Neurosci 2023; 17:1236876. [PMID: 37869518 PMCID: PMC10586329 DOI: 10.3389/fnins.2023.1236876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 09/06/2023] [Indexed: 10/24/2023] Open
Abstract
Corpora amylacea (CA) are polyglucosan aggregated granules that accumulate in the human body throughout aging. In the cerebrum, CA have been found in proximity to ventricular walls, pial surfaces, and blood vessels. However, studies showing their three-dimensional spatial distribution are sparse. In this study, volumetric images of four human brain stems were obtained with MRI and phase-contrast X-ray microtomography, followed up by Periodic acid Schiff stain for validation. CA appeared as hyperintense spheroid structures with diameters up to 30 μm. An automatic pipeline was developed to segment the CA, and the spatial distribution of over 200,000 individual corpora amylacea could be investigated. A threefold-or higher-density of CA was detected in the dorsomedial column of the periaqueductal gray (860-4,200 CA count/mm3) than in the superior colliculus (150-340 CA count/mm3). We estimated that about 2% of the CA were located in the immediate vicinity of the vessels or in the peri-vascular space. While CA in the ependymal lining of the cerebral aqueduct was rare, the sub-pial tissue of the anterior and posterior midbrain contained several CA. In the sample with the highest CA density, quantitative maps obtained with MRI revealed high R2* values and a diamagnetic shift in a region which spatially coincided with the CA dense region.
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Affiliation(s)
- Ju Young Lee
- Graduate Training Centre of Neuroscience, Eberhard Karl's University of Tübingen, Tübingen, Germany
- High Field Magnetic Resonance, Max Planck Institute for Biological Cybernetics, Tübingen, Germany
| | - Andreas F. Mack
- Institute of Clinical Anatomy and Cell Analysis, Eberhard Karl's University of Tübingen, Tübingen, Germany
| | - Ulrich Mattheus
- Institute of Clinical Anatomy and Cell Analysis, Eberhard Karl's University of Tübingen, Tübingen, Germany
| | - Sandro Donato
- Department of Physics and STAR-LAB, University of Calabria, Rende, Italy
- Division of Frascati, Istituto Nazionale di Fisica Nucleare (INFN), Frascati, Italy
| | - Renata Longo
- Department of Physics, University of Trieste, Trieste, Italy
- Division of Trieste, Istituto Nazionale di Fisica Nucleare (INFN), Trieste, Italy
| | | | - Thomas Shiozawa
- Institute of Clinical Anatomy and Cell Analysis, Eberhard Karl's University of Tübingen, Tübingen, Germany
| | - Klaus Scheffler
- High Field Magnetic Resonance, Max Planck Institute for Biological Cybernetics, Tübingen, Germany
- Department of Biomedical Magnetic Resonance, University Hospital Tübingen, Tübingen, Germany
| | - Gisela E. Hagberg
- High Field Magnetic Resonance, Max Planck Institute for Biological Cybernetics, Tübingen, Germany
- Department of Biomedical Magnetic Resonance, University Hospital Tübingen, Tübingen, Germany
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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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Das A, Ding S, Liu R, Huang C. Quantifying the Growth of Glioblastoma Tumors Using Multimodal MRI Brain Images. Cancers (Basel) 2023; 15:3614. [PMID: 37509277 PMCID: PMC10377296 DOI: 10.3390/cancers15143614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/11/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Predicting the eventual volume of tumor cells, that might proliferate from a given tumor, can help in cancer early detection and medical procedure planning to prevent their migration to other organs. In this work, a new statistical framework is proposed using Bayesian techniques for detecting the eventual volume of cells expected to proliferate from a glioblastoma (GBM) tumor. Specifically, the tumor region was first extracted using a parallel image segmentation algorithm. Once the tumor region was determined, we were interested in the number of cells that could proliferate from this tumor until its survival time. For this, we constructed the posterior distribution of the tumor cell numbers based on the proposed likelihood function and a certain prior volume. Furthermore, we extended the detection model and conducted a Bayesian regression analysis by incorporating radiomic features to discover those non-tumor cells that remained undetected. The main focus of the study was to develop a time-independent prediction model that could reliably predict the ultimate volume a malignant tumor of the fourth-grade severity could attain and which could also determine if the incorporation of the radiomic properties of the tumor enhanced the chances of no malignant cells remaining undetected.
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Affiliation(s)
- Anisha Das
- Department of Statistics, Florida State University, Tallahassee, FL 32306, USA
| | - Shengxian Ding
- Department of Statistics, Florida State University, Tallahassee, FL 32306, USA
| | - Rongjie Liu
- Department of Statistics, Florida State University, Tallahassee, FL 32306, USA
| | - Chao Huang
- Department of Statistics, Florida State University, Tallahassee, FL 32306, USA
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Lee JY, Mack AF, Shiozawa T, Longo R, Tromba G, Scheffler K, Hagberg GE. Microvascular imaging of the unstained human superior colliculus using synchrotron-radiation phase-contrast microtomography. Sci Rep 2022; 12:9238. [PMID: 35655082 PMCID: PMC9163179 DOI: 10.1038/s41598-022-13282-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 05/23/2022] [Indexed: 12/05/2022] Open
Abstract
Characterizing the microvasculature of the human brain is critical to advance understanding of brain vascular function. Most methods rely on tissue staining and microscopy in two-dimensions, which pose several challenges to visualize the three-dimensional structure of microvessels. In this study, we used an edge-based segmentation method to extract the 3D vasculature from synchrotron radiation phase-contrast microtomography (PC-μCT) of two unstained, paraffin-embedded midbrain region of the human brain stem. Vascular structures identified in PC-μCT were validated with histology of the same specimen. Using the Deriche-Canny edge detector that was sensitive to the boundary between tissue and vascular space, we could segment the vessels independent of signal variations in PC-μCT images. From the segmented volumetric vasculature, we calculated vessel diameter, vessel length and volume fraction of the vasculature in the superior colliculi. From high resolution images, we found the most frequent vessel diameter to be between 8.6-10.2 µm. Our findings are consistent with the known anatomy showing two types of vessels with distinctive morphology: peripheral collicular vessels and central collicular vessels. The proposed method opens up new possibilities for vascular research of the central nervous system using synchrotron radiation PC-μCT of unstained human tissue.
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Affiliation(s)
- Ju Young Lee
- High Field Magnetic Resonance, Max Planck Institute for Biological Cybernetics, Tübingen, Germany.
- Graduate Training Centre of Neuroscience, Eberhard Karl's University of Tübingen, Tübingen, Germany.
| | - Andreas F Mack
- Institute of Clinical Anatomy and Cell Analysis, Eberhard Karl's University of Tübingen, Tübingen, Germany
| | - Thomas Shiozawa
- Institute of Clinical Anatomy and Cell Analysis, Eberhard Karl's University of Tübingen, Tübingen, Germany
| | - Renata Longo
- University of Trieste, Trieste, Italy
- Istituto Nazionale di Fisica Nucleare (INFN), Trieste, Italy
| | | | - Klaus Scheffler
- High Field Magnetic Resonance, Max Planck Institute for Biological Cybernetics, Tübingen, Germany
- Department of Biomedical Magnetic Resonance, University Hospital Tübingen, Tübingen, Germany
| | - Gisela E Hagberg
- High Field Magnetic Resonance, Max Planck Institute for Biological Cybernetics, Tübingen, Germany
- Department of Biomedical Magnetic Resonance, University Hospital Tübingen, Tübingen, Germany
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Non contrast enhanced volumetric histology of blood clots through high resolution propagation-based X-ray microtomography. Sci Rep 2022; 12:2778. [PMID: 35177767 PMCID: PMC8854637 DOI: 10.1038/s41598-022-06623-8] [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: 10/03/2021] [Accepted: 01/31/2022] [Indexed: 11/23/2022] Open
Abstract
We have demonstrated the capability of laboratory propagation-based microtomography (miroCT) in non-destructive 3D virtual histopathology of human blood clots without any contrast agent. The volumetric information are valuable to understand the mechanical properties of clots which are crucial in selecting the most efficient mechanical thrombectomy method for clot extraction. Different clot types retrieved by mechanical thrombectomy from patient victims of acute ischemic stroke were evaluated through propagation-based microCT. The results were correlated with high-resolution scanning electron microscopy (SEM) images, confirming detected cellular and fibrillary structures. Calcifications appeared as glassy opacity areas with relatively intense signal on microCT images, also proved by energy-dispersive spectroscopy and X-ray diffraction. Hyperintense regions on the microCT corresponded to individual or compact aggregates of red blood cells, whereas fibrin dominated volumes appeared at consistently moderate to low normalized microCT values. Red blood cell shapes and sizes are consistent with the SEM observations. Together with other potential parameters, 3D porosity distribution and volume fraction of structures can be easily measured by microCT data. Further development of automated post-processing techniques for X-ray propagation-based micro/nanoCT, also based on machine learning algorithms, can enable high throughput analysis of blood clot composition and their 3D histological features on large sample cohorts.
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Rodgers G, Tanner C, Schulz G, Migga A, Kuo W, Bikis C, Scheel M, Kurtcuoglu V, Weitkamp T, Müller B. Virtual histology of an entire mouse brain from formalin fixation to paraffin embedding. Part 2: Volumetric strain fields and local contrast changes. J Neurosci Methods 2022; 365:109385. [PMID: 34637810 DOI: 10.1016/j.jneumeth.2021.109385] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/07/2021] [Indexed: 01/14/2023]
Abstract
BACKGROUND Fixation and embedding of post mortem brain tissue is a pre-requisite for both gold-standard conventional histology and X-ray virtual histology. This process alters the morphology and density of the brain microanatomy. NEW METHOD To quantify these changes, we employed synchrotron radiation-based hard X-ray tomography with 3 μm voxel length to visualize the same mouse brain after fixation in 4% formalin, immersion in ethanol solutions (50%, 70%, 80%, 90%, and 100%), xylene, and finally after embedding in a paraffin block. The volumetric data were non-rigidly registered to the initial formalin-fixed state to align the microanatomy within the entire mouse brain. RESULTS Volumetric strain fields were used to characterize local shrinkage, which was found to depend on the anatomical region and distance to external surface. X-ray contrast was altered and enhanced by preparation-induced inter-tissue density changes. The preparation step can be selected to highlight specific anatomical features. For example, fiber tract contrast is amplified in 100% ethanol. COMPARISON WITH EXISTING METHODS Our method provides volumetric strain fields, unlike approaches based on feature-to-feature or volume measurements. Volumetric strain fields are produced by non-rigid registration, which is less labor-intensive and observer-dependent than volume change measurements based on manual segmentations. X-ray microtomography provides spatial resolution at least an order of magnitude higher than magnetic resonance microscopy, allowing for analysis of morphology and density changes within the brain's microanatomy. CONCLUSION Our approach belongs to three-dimensional virtual histology with isotropic micrometer spatial resolution and therefore complements atlases based on a combination of magnetic resonance microscopy and optical micrographs of serial histological sections.
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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
| | - 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
| | - Alexandra Migga
- 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
| | - Willy Kuo
- The Interface Group, Institute of Physiology, University of Zurich, 8057 Zurich, Switzerland; National Centre of Competence in Research, Kidney.CH, 8057 Zurich, Switzerland
| | - Christos Bikis
- 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; Integrierte Psychiatrie Winterthur - Zürcher Unterland, 8408 Winterthur, Switzerland
| | - Mario Scheel
- Synchrotron Soleil, 91192 Gif-sur-Yvette, France
| | - Vartan Kurtcuoglu
- The Interface Group, Institute of Physiology, University of Zurich, 8057 Zurich, Switzerland; National Centre of Competence in Research, Kidney.CH, 8057 Zurich, Switzerland
| | | | - 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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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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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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Simultaneous 3D Visualization of the Microvascular and Neural Network in Mouse Spinal Cord Using Synchrotron Radiation Micro-Computed Tomography. Neurosci Bull 2021; 37:1469-1480. [PMID: 34146232 PMCID: PMC8490558 DOI: 10.1007/s12264-021-00715-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 02/06/2021] [Indexed: 11/01/2022] Open
Abstract
Effective methods for visualizing neurovascular morphology are essential for understanding the normal spinal cord and the morphological alterations associated with diseases. However, ideal techniques for simultaneously imaging neurovascular structure in a broad region of a specimen are still lacking. In this study, we combined Golgi staining with angiography and synchrotron radiation micro-computed tomography (SRμCT) to visualize the 3D neurovascular network in the mouse spinal cord. Using our method, the 3D neurons, nerve fibers, and vasculature in a broad region could be visualized in the same image at cellular resolution without destructive sectioning. Besides, we found that the 3D morphology of neurons, nerve fiber tracts, and vasculature visualized by SRμCT were highly consistent with that visualized using the histological method. Moreover, the 3D neurovascular structure could be quantitatively evaluated by the combined methodology. The method shown here will be useful in fundamental neuroscience studies.
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Du M, Di Z(W, 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] [Grants] [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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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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Johnson EC, Wilt M, Rodriguez LM, Norman-Tenazas R, Rivera C, Drenkow N, Kleissas D, LaGrow TJ, Cowley HP, Downs J, K. Matelsky J, J. Hughes M, P. Reilly E, A. Wester B, L. Dyer E, P. Kording K, R. Gray-Roncal W. Toward a scalable framework for reproducible processing of volumetric, nanoscale neuroimaging datasets. Gigascience 2020; 9:giaa147. [PMID: 33347572 PMCID: PMC7751400 DOI: 10.1093/gigascience/giaa147] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 08/19/2020] [Accepted: 12/18/2020] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Emerging neuroimaging datasets (collected with imaging techniques such as electron microscopy, optical microscopy, or X-ray microtomography) describe the location and properties of neurons and their connections at unprecedented scale, promising new ways of understanding the brain. These modern imaging techniques used to interrogate the brain can quickly accumulate gigabytes to petabytes of structural brain imaging data. Unfortunately, many neuroscience laboratories lack the computational resources to work with datasets of this size: computer vision tools are often not portable or scalable, and there is considerable difficulty in reproducing results or extending methods. RESULTS We developed an ecosystem of neuroimaging data analysis pipelines that use open-source algorithms to create standardized modules and end-to-end optimized approaches. As exemplars we apply our tools to estimate synapse-level connectomes from electron microscopy data and cell distributions from X-ray microtomography data. To facilitate scientific discovery, we propose a generalized processing framework, which connects and extends existing open-source projects to provide large-scale data storage, reproducible algorithms, and workflow execution engines. CONCLUSIONS Our accessible methods and pipelines demonstrate that approaches across multiple neuroimaging experiments can be standardized and applied to diverse datasets. The techniques developed are demonstrated on neuroimaging datasets but may be applied to similar problems in other domains.
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Affiliation(s)
- Erik C Johnson
- Research And Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd., Laurel, MD, 20723 USA
| | - Miller Wilt
- Research And Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd., Laurel, MD, 20723 USA
| | - Luis M Rodriguez
- Research And Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd., Laurel, MD, 20723 USA
| | - Raphael Norman-Tenazas
- Research And Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd., Laurel, MD, 20723 USA
| | - Corban Rivera
- Research And Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd., Laurel, MD, 20723 USA
| | - Nathan Drenkow
- Research And Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd., Laurel, MD, 20723 USA
| | - Dean Kleissas
- Research And Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd., Laurel, MD, 20723 USA
| | - Theodore J LaGrow
- School of Electrical & Computer Engineering, Georgia Institute of Technology, 777 Atlantic Dr. NW, Atlanta, GA, 30332 USA
| | - Hannah P Cowley
- Research And Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd., Laurel, MD, 20723 USA
| | - Joseph Downs
- Research And Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd., Laurel, MD, 20723 USA
| | - Jordan K. Matelsky
- Research And Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd., Laurel, MD, 20723 USA
| | - Marisa J. Hughes
- Research And Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd., Laurel, MD, 20723 USA
| | - Elizabeth P. Reilly
- Research And Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd., Laurel, MD, 20723 USA
| | - Brock A. Wester
- Research And Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd., Laurel, MD, 20723 USA
| | - Eva L. Dyer
- School of Electrical & Computer Engineering, Georgia Institute of Technology, 777 Atlantic Dr. NW, Atlanta, GA, 30332 USA
- Coulter Department of Biomedical Engineering, Georgia Institute of Technology, 313 Ferst Dr., Atlanta, GA, 30332 USA
| | - Konrad P. Kording
- Department of Biomedical Engineering, University of Pennsylvania, 210 South 33rd St., Philadelphia, PA, 19104 USA
| | - William R. Gray-Roncal
- Research And Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd., Laurel, MD, 20723 USA
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14
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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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15
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Massimi L, Pieroni N, Maugeri L, Fratini M, Brun F, Bukreeva I, Santamaria G, Medici V, Poloni TE, Balducci C, Cedola A. Assessment of plaque morphology in Alzheimer's mouse cerebellum using three-dimensional X-ray phase-based virtual histology. Sci Rep 2020; 10:11233. [PMID: 32641715 PMCID: PMC7343834 DOI: 10.1038/s41598-020-68045-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 06/18/2020] [Indexed: 02/03/2023] Open
Abstract
Visualization and characterization of \documentclass[12pt]{minimal}
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\begin{document}$$\beta$$\end{document}β-amyloid deposits is a fundamental task in pre-clinical study of Alzheimer’s disease (AD) to assess its evolution and monitor the efficiency of new therapeutic strategies. While the cerebellum is one of the brain areas most underestimated in the context of AD, renewed interest in cerebellar lesions has recently arisen as they may link to motor and cognitive alterations. Thus, we quantitatively investigated three-dimensional plaque morphology in the cerebellum in APP/PS1 transgenic mouse, as a model of AD. In order to obtain a complete high-resolution three-dimensional view of the investigated tissue, we exploited synchrotron X-ray phase contrast tomography (XPCT), providing virtual slices with histology-matching resolution. We found the formation of plaques elongated in shape, and with a specific orientation in space depending on the investigated region of the cerebellar cortex. Remarkably, a similar shape is observed in human cerebellum from demented patients. Our findings demonstrate the capability of XPCT in volumetric quantification, supporting the current knowledge about plaque morphology in the cerebellum and the fundamental role of the surrounding tissue in driving their evolution. A good correlation with the human neuropathology is also reported.
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Affiliation(s)
- Lorenzo Massimi
- Department of Medical Physics and Biomedical Engineering, University College London, London, UK. .,Institute of Nanotechnology - CNR, Rome Unit, Rome, Italy.
| | - Nicola Pieroni
- Institute of Nanotechnology - CNR, Rome Unit, Rome, Italy.,Department of Anatomical Sciences, Histological, Legal Medical and Locomotor, University of Rome "Sapienza", Rome, Italy
| | - Laura Maugeri
- Institute of Nanotechnology - CNR, Rome Unit, Rome, Italy.,IRCCS Santa Lucia Foundation, Rome, Italy
| | - Michela Fratini
- Institute of Nanotechnology - CNR, Rome Unit, Rome, Italy.,Department of Engineering and Architecture, University of Trieste, Trieste, Italy
| | - Francesco Brun
- Institute of Nanotechnology - CNR, Rome Unit, Rome, Italy.,Department of Engineering and Architecture, University of Trieste, Trieste, Italy
| | - Inna Bukreeva
- Institute of Nanotechnology - CNR, Rome Unit, Rome, Italy
| | - Giulia Santamaria
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Valentina Medici
- Department of Neuropathology and Neurology, Golgi-Cenci Foundation, 20081, Abbiategrasso, Italy
| | - Tino Emanuele Poloni
- Department of Neuropathology and Neurology, Golgi-Cenci Foundation, 20081, Abbiategrasso, Italy
| | - Claudia Balducci
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Alessia Cedola
- Institute of Nanotechnology - CNR, Rome Unit, Rome, Italy
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16
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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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17
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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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18
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Buscema M, Hieber SE, Schulz G, Deyhle H, Hipp A, Beckmann F, Lobrinus JA, Saxer T, Müller B. Ex vivo evaluation of an atherosclerotic human coronary artery via histology and high-resolution hard X-ray tomography. Sci Rep 2019; 9:14348. [PMID: 31586080 PMCID: PMC6778097 DOI: 10.1038/s41598-019-50711-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 09/16/2019] [Indexed: 12/12/2022] Open
Abstract
Atherosclerotic arteries exhibit characteristic constrictions and substantial deviations from cylindrical shape. Therefore, determining the artery's cross-section along the centerline is challenging, although high-resolution isotropic three-dimensional data are available. Herein, we apply high-resolution computed tomography in absorption and phase to a plaque-containing human artery post-mortem, through the course of the preparation stages for histology. We identify the impact of paraffin embedding and decalcification on the artery lumen. For automatic extraction of lumen's cross-section along centerline we present a dedicated pipeline. Comparing fixated tissue before and after paraffin embedding gives rise to shape changes with lumen reduction to 50-80%. The histological slicing induces further deformations with respect to tomography. Data acquired after decalcification show debris unintentionally distributed within the vessel preventing the reliable automatic lumen segmentation. Comparing tomography of laboratory- and synchrotron-radiation-based X rays by means of joint histogram analysis leads us to conclude that advanced desktop tomography is capable of quantifying the artery's lumen as an essential input for blood flow simulations. The results indicate that the most reliable lumen quantification is achieved by imaging the non-decalcified specimen fixed in formalin, using phase contrast modality and a dedicated processing pipeline. This study focusses on a methodology to quantitatively evaluate diseased artery segments post-mortem and provides unique structural parameters on the treatment-induced local shrinkage, which will be the basis of future studies on the flow in vessels affected by constrictions.
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Affiliation(s)
- Marzia Buscema
- 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.
| | - Georg Schulz
- 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
| | - Alexander Hipp
- Institute of Materials Research, Helmholtz-Zentrum Geesthacht, Geesthacht, Germany
| | - Felix Beckmann
- Institute of Materials Research, Helmholtz-Zentrum Geesthacht, Geesthacht, Germany
| | | | - Till Saxer
- Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Bert Müller
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, Allschwil, Switzerland.
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19
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Imaging of post-mortem human brain tissue using electron and X-ray microscopy. Curr Opin Struct Biol 2019; 58:138-148. [PMID: 31349127 DOI: 10.1016/j.sbi.2019.06.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/26/2019] [Accepted: 06/10/2019] [Indexed: 12/12/2022]
Abstract
Electron microscopy imaging of post-mortem human brain (PMHB) comes with a unique set of challenges due to numerous parameters beyond the researcher's control. Nevertheless, the wealth of information provided by the ultrastructural analysis of PMHB is proving crucial in our understanding of neurodegenerative diseases. This review highlights the importance of such studies and covers challenges, limitations and recent developments in the application of current EM imaging, including cryo-ET and correlative hybrid techniques, on PMHB.
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20
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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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21
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Böhm T, Joseph K, Kirsch M, Moroni R, Hilger A, Osenberg M, Manke I, Johnston M, Stieglitz T, Hofmann UG, Haas CA, Thiele S. Quantitative synchrotron X-ray tomography of the material-tissue interface in rat cortex implanted with neural probes. Sci Rep 2019; 9:7646. [PMID: 31113972 PMCID: PMC6529414 DOI: 10.1038/s41598-019-42544-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 04/01/2019] [Indexed: 01/13/2023] Open
Abstract
Neural probes provide many options for neuroscientific research and medical purposes. However, these implantable micro devices are not functionally stable over time due to host-probe interactions. Thus, reliable high-resolution characterization methods are required to understand local tissue changes upon implantation. In this work, synchrotron X-ray tomography is employed for the first time to image the interface between brain tissue and an implanted neural probe, showing that this 3D imaging method is capable of resolving probe and surrounding tissue at a resolution of about 1 micrometer. Unstained tissue provides sufficient contrast to identify electrode sites on the probe, cells, and blood vessels within tomograms. Exemplarily, we show that it is possible to quantify characteristics of the interaction region between probe and tissue, like the blood supply system. Our first-time study demonstrates a way for simultaneous 3D investigation of brain tissue with implanted probe, providing information beyond what was hitherto possible.
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Affiliation(s)
- Thomas Böhm
- Laboratory for MEMS Applications, IMTEK Department of Microsystems Engineering, University of Freiburg, Georges-Köhler-Allee 103, 79110, Freiburg, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, 79110, Freiburg, Germany
- BrainLinks-BrainTools, University of Freiburg, Georges-Köhler-Allee 80, 79110, Freiburg, Germany
| | - Kevin Joseph
- BrainLinks-BrainTools, University of Freiburg, Georges-Köhler-Allee 80, 79110, Freiburg, Germany
- Neuroelectronic Systems, Dept. of Neurosurgery, Faculty of Medicine, University Medical Center, Engesserstraße 4, 79108, Freiburg, Germany
| | - Matthias Kirsch
- BrainLinks-BrainTools, University of Freiburg, Georges-Köhler-Allee 80, 79110, Freiburg, Germany
- Department of Neuroanatomy, Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, Albertstraße 23, 79104, Freiburg, Germany
| | - Riko Moroni
- Laboratory for MEMS Applications, IMTEK Department of Microsystems Engineering, University of Freiburg, Georges-Köhler-Allee 103, 79110, Freiburg, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, 79110, Freiburg, Germany
| | - André Hilger
- Helmholtz Center Berlin for Materials and Energy, Hahn-Meitner-Platz 1, 14109, Berlin, Germany
| | - Markus Osenberg
- Helmholtz Center Berlin for Materials and Energy, Hahn-Meitner-Platz 1, 14109, Berlin, Germany
- Institute of Materials Science and Technology, Technical University Berlin, Hardenbergstraße 36, 10623, Berlin, Germany
| | - Ingo Manke
- Helmholtz Center Berlin for Materials and Energy, Hahn-Meitner-Platz 1, 14109, Berlin, Germany
| | - Midori Johnston
- BrainLinks-BrainTools, University of Freiburg, Georges-Köhler-Allee 80, 79110, Freiburg, Germany
- Experimental Epilepsy Research, Dept. of Neurosurgery, University Medical Center, Breisacher Straße 64, 79106, Freiburg, Germany
| | - Thomas Stieglitz
- BrainLinks-BrainTools, University of Freiburg, Georges-Köhler-Allee 80, 79110, Freiburg, Germany
- Laboratory for Biomedical Microtechnology, IMTEK Department of Microsystems Engineering, University of Freiburg, Georges-Köhler-Allee 102, 79110, Freiburg, Germany
- Bernstein Center Freiburg, Hansastraße 9a, 79104, Freiburg, Germany
| | - Ulrich G Hofmann
- BrainLinks-BrainTools, University of Freiburg, Georges-Köhler-Allee 80, 79110, Freiburg, Germany
- Neuroelectronic Systems, Dept. of Neurosurgery, Faculty of Medicine, University Medical Center, Engesserstraße 4, 79108, Freiburg, Germany
| | - Carola A Haas
- BrainLinks-BrainTools, University of Freiburg, Georges-Köhler-Allee 80, 79110, Freiburg, Germany
- Experimental Epilepsy Research, Dept. of Neurosurgery, University Medical Center, Breisacher Straße 64, 79106, Freiburg, Germany
- Bernstein Center Freiburg, Hansastraße 9a, 79104, Freiburg, Germany
| | - Simon Thiele
- Laboratory for MEMS Applications, IMTEK Department of Microsystems Engineering, University of Freiburg, Georges-Köhler-Allee 103, 79110, Freiburg, Germany.
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, 79110, Freiburg, Germany.
- BrainLinks-BrainTools, University of Freiburg, Georges-Köhler-Allee 80, 79110, Freiburg, Germany.
- Forschungszentrum Jülich GmbH, Helmholtz-Institute Erlangen-Nürnberg for Renewable Energy (IEK-11), Egerlandstraße 3, 91058, Erlangen, Germany.
- Department of Chemical and Biological Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg, Egerlandstraße 3, 91058, Erlangen, Germany.
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22
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Tesařová M, Mancini L, Simon A, Adameyko I, Kaucká M, Elewa A, Lanzafame G, Zhang Y, Kalasová D, Szarowská B, Zikmund T, Novotná M, Kaiser J. A quantitative analysis of 3D-cell distribution in regenerating muscle-skeletal system with synchrotron X-ray computed microtomography. Sci Rep 2018; 8:14145. [PMID: 30237460 PMCID: PMC6148031 DOI: 10.1038/s41598-018-32459-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 09/10/2018] [Indexed: 02/07/2023] Open
Abstract
One of the greatest enigmas of modern biology is how the geometry of muscular and skeletal structures are created and how their development is controlled during growth and regeneration. Scaling and shaping of vertebrate muscles and skeletal elements has always been enigmatic and required an advanced technical level in order to analyse the cell distribution in 3D. In this work, synchrotron X-ray computed microtomography (µCT) and chemical contrasting has been exploited for a quantitative analysis of the 3D-cell distribution in tissues of a developing salamander (Pleurodeles waltl) limb – a key model organism for vertebrate regeneration studies. We mapped the limb muscles, their size and shape as well as the number and density of cells within the extracellular matrix of the developing cartilage. By using tomographic approach, we explored the polarity of the cells in 3D, in relation to the structure of developing joints. We found that the polarity of chondrocytes correlates with the planes in joint surfaces and also changes along the length of the cartilaginous elements. Our approach generates data for the precise computer simulations of muscle-skeletal regeneration using cell dynamics models, which is necessary for the understanding how anisotropic growth results in the precise shapes of skeletal structures.
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Affiliation(s)
- Markéta Tesařová
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Lucia Mancini
- Elettra-Sincrotrone Trieste S.C.p.A., Basovizza, Trieste, Italy
| | - Andras Simon
- Department of Cellular and Molecular Biology, Karolinska Institutet, Solna, 171777, Stockholm, Sweden
| | - Igor Adameyko
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, 171777, Stockholm, Sweden.,Department of Molecular Neurosciences, Medical University Vienna, Vienna, Austria
| | - Markéta Kaucká
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, 171777, Stockholm, Sweden.,Department of Molecular Neurosciences, Medical University Vienna, Vienna, Austria
| | - Ahmed Elewa
- Department of Cellular and Molecular Biology, Karolinska Institutet, Solna, 171777, Stockholm, Sweden
| | | | - Yi Zhang
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, 171777, Stockholm, Sweden.,Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Dominika Kalasová
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Bára Szarowská
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, 171777, Stockholm, Sweden
| | - Tomáš Zikmund
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Marie Novotná
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Jozef Kaiser
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic.
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23
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Optimising complementary soft tissue synchrotron X-ray microtomography for reversibly-stained central nervous system samples. Sci Rep 2018; 8:12017. [PMID: 30104610 PMCID: PMC6089931 DOI: 10.1038/s41598-018-30520-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 07/24/2018] [Indexed: 11/08/2022] Open
Abstract
Synchrotron radiation microtomography (SRμCT) is a nominally non-destructive 3D imaging technique which can visualise the internal structures of whole soft tissues. As a multi-stage technique, the cumulative benefits of optimising sample preparation, scanning parameters and signal processing can improve SRμCT imaging efficiency, image quality, accuracy and ultimately, data utility. By evaluating different sample preparations (embedding media, tissue stains), imaging (projection number, propagation distance) and reconstruction (artefact correction, phase retrieval) parameters, a novel methodology (combining reversible iodine stain, wax embedding and inline phase contrast) was optimised for fast (~12 minutes), high-resolution (3.2-4.8 μm diameter capillaries resolved) imaging of the full diameter of a 3.5 mm length of rat spinal cord. White-grey matter macro-features and micro-features such as motoneurons and capillary-level vasculature could then be completely segmented from the imaged volume for analysis through the shallow machine learning SuRVoS Workbench. Imaged spinal cord tissue was preserved for subsequent histology, establishing a complementary SRμCT methodology that can be applied to study spinal cord pathologies or other nervous system tissues such as ganglia, nerves and brain. Further, our 'single-scan iterative downsampling' approach and side-by-side comparisons of mounting options, sample stains and phase contrast parameters should inform efficient, effective future soft tissue SRμCT experiment design.
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24
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Cole JM, Symes DR, Lopes NC, Wood JC, Poder K, Alatabi S, Botchway SW, Foster PS, Gratton S, Johnson S, Kamperidis C, Kononenko O, De Lazzari M, Palmer CAJ, Rusby D, Sanderson J, Sandholzer M, Sarri G, Szoke-Kovacs Z, Teboul L, Thompson JM, Warwick JR, Westerberg H, Hill MA, Norris DP, Mangles SPD, Najmudin Z. High-resolution μCT of a mouse embryo using a compact laser-driven X-ray betatron source. Proc Natl Acad Sci U S A 2018; 115:6335-6340. [PMID: 29871946 PMCID: PMC6016801 DOI: 10.1073/pnas.1802314115] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In the field of X-ray microcomputed tomography (μCT) there is a growing need to reduce acquisition times at high spatial resolution (approximate micrometers) to facilitate in vivo and high-throughput operations. The state of the art represented by synchrotron light sources is not practical for certain applications, and therefore the development of high-brightness laboratory-scale sources is crucial. We present here imaging of a fixed embryonic mouse sample using a compact laser-plasma-based X-ray light source and compare the results to images obtained using a commercial X-ray μCT scanner. The radiation is generated by the betatron motion of electrons inside a dilute and transient plasma, which circumvents the flux limitations imposed by the solid or liquid anodes used in conventional electron-impact X-ray tubes. This X-ray source is pulsed (duration <30 fs), bright (>1010 photons per pulse), small (diameter <1 μm), and has a critical energy >15 keV. Stable X-ray performance enabled tomographic imaging of equivalent quality to that of the μCT scanner, an important confirmation of the suitability of the laser-driven source for applications. The X-ray flux achievable with this approach scales with the laser repetition rate without compromising the source size, which will allow the recording of high-resolution μCT scans in minutes.
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Affiliation(s)
- Jason M Cole
- The John Adams Institute for Accelerator Science, Blackett Laboratory, Imperial College London, London SW7 2AZ, United Kingdom
| | - Daniel R Symes
- Central Laser Facility, Science and Technology Facilities Council (STFC) Rutherford Appleton Laboratory, Chilton, Didcot OX11 0QX, United Kingdom;
| | - Nelson C Lopes
- The John Adams Institute for Accelerator Science, Blackett Laboratory, Imperial College London, London SW7 2AZ, United Kingdom
- Group of Lasers and Plasmas (GoLP)/Instituto de Plasmas e Fusão Nuclear, Instituto Superior Técnico, University of Lisbon, Lisboa 1049-001, Portugal
| | - Jonathan C Wood
- The John Adams Institute for Accelerator Science, Blackett Laboratory, Imperial College London, London SW7 2AZ, United Kingdom
| | - Kristjan Poder
- The John Adams Institute for Accelerator Science, Blackett Laboratory, Imperial College London, London SW7 2AZ, United Kingdom
| | - Saleh Alatabi
- The John Adams Institute for Accelerator Science, Blackett Laboratory, Imperial College London, London SW7 2AZ, United Kingdom
| | - Stanley W Botchway
- Central Laser Facility, Science and Technology Facilities Council (STFC) Rutherford Appleton Laboratory, Chilton, Didcot OX11 0QX, United Kingdom
| | - Peta S Foster
- Central Laser Facility, Science and Technology Facilities Council (STFC) Rutherford Appleton Laboratory, Chilton, Didcot OX11 0QX, United Kingdom
| | - Sarah Gratton
- Central Laser Facility, Science and Technology Facilities Council (STFC) Rutherford Appleton Laboratory, Chilton, Didcot OX11 0QX, United Kingdom
| | - Sara Johnson
- The Mary Lyon Centre, MRC Harwell Institute, Harwell OX11 0RD, United Kingdom
| | - Christos Kamperidis
- The John Adams Institute for Accelerator Science, Blackett Laboratory, Imperial College London, London SW7 2AZ, United Kingdom
- Extreme Light Infrastructure Attosecond Light Pulse Source (ELI-ALPS), ELI-HU Non-profit Ltd., H-6720 Szeged, Hungary
| | - Olena Kononenko
- Linear Accelerator Technologies, Deutsches Elektronen-Synchrotron (DESY), 22607 Hamburg, Germany
| | - Michael De Lazzari
- Cancer Research UK/Medical Research Council (CRUK/MRC) Oxford Institute for Radiation Research, Gray Laboratories, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Charlotte A J Palmer
- Linear Accelerator Technologies, Deutsches Elektronen-Synchrotron (DESY), 22607 Hamburg, Germany
| | - Dean Rusby
- Central Laser Facility, Science and Technology Facilities Council (STFC) Rutherford Appleton Laboratory, Chilton, Didcot OX11 0QX, United Kingdom
| | - Jeremy Sanderson
- Medical Research Council (MRC) Harwell Institute, Harwell OX11 0RD, United Kingdom
| | - Michael Sandholzer
- Medical Research Council (MRC) Harwell Institute, Harwell OX11 0RD, United Kingdom
| | - Gianluca Sarri
- School of Mathematics and Physics, Queen's University, Belfast BT7 1NN, United Kingdom
| | | | - Lydia Teboul
- The Mary Lyon Centre, MRC Harwell Institute, Harwell OX11 0RD, United Kingdom
| | - James M Thompson
- Cancer Research UK/Medical Research Council (CRUK/MRC) Oxford Institute for Radiation Research, Gray Laboratories, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Jonathan R Warwick
- School of Mathematics and Physics, Queen's University, Belfast BT7 1NN, United Kingdom
| | - Henrik Westerberg
- Medical Research Council (MRC) Harwell Institute, Harwell OX11 0RD, United Kingdom
| | - Mark A Hill
- Cancer Research UK/Medical Research Council (CRUK/MRC) Oxford Institute for Radiation Research, Gray Laboratories, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Dominic P Norris
- Medical Research Council (MRC) Harwell Institute, Harwell OX11 0RD, United Kingdom
| | - Stuart P D Mangles
- The John Adams Institute for Accelerator Science, Blackett Laboratory, Imperial College London, London SW7 2AZ, United Kingdom
| | - Zulfikar Najmudin
- The John Adams Institute for Accelerator Science, Blackett Laboratory, Imperial College London, London SW7 2AZ, United Kingdom
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25
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Three-dimensional virtual histology of human cerebellum by X-ray phase-contrast tomography. Proc Natl Acad Sci U S A 2018; 115:6940-6945. [PMID: 29915047 PMCID: PMC6142271 DOI: 10.1073/pnas.1801678115] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The complex cytoarchitecture of human brain tissue is traditionally studied by histology, providing structural information in 2D planes. This can be partly extended to 3D by inspecting many parallel slices, however, at nonisotropic resolution. This work shows that propagation-based X-ray phase-contrast tomography, both at the synchrotron and even at a compact laboratory source, can be used to perform noninvasive 3D virtual histology on unstained paraffin-embedded human cerebellum at isotropic subcellular resolution. The resulting data quality is high enough to visualize and automatically locate ∼106 neurons within the different layers of the cerebellum, providing unprecedented data on its 3D cytoarchitecture and spatial organization. To quantitatively evaluate brain tissue and its corresponding function, knowledge of the 3D cellular distribution is essential. The gold standard to obtain this information is histology, a destructive and labor-intensive technique where the specimen is sliced and examined under a light microscope, providing 3D information at nonisotropic resolution. To overcome the limitations of conventional histology, we use phase-contrast X-ray tomography with optimized optics, reconstruction, and image analysis, both at a dedicated synchrotron radiation endstation, which we have equipped with X-ray waveguide optics for coherence and wavefront filtering, and at a compact laboratory source. As a proof-of-concept demonstration we probe the 3D cytoarchitecture in millimeter-sized punches of unstained human cerebellum embedded in paraffin and show that isotropic subcellular resolution can be reached at both setups throughout the specimen. To enable a quantitative analysis of the reconstructed data, we demonstrate automatic cell segmentation and localization of over 1 million neurons within the cerebellar cortex. This allows for the analysis of the spatial organization and correlation of cells in all dimensions by borrowing concepts from condensed-matter physics, indicating a strong short-range order and local clustering of the cells in the granular layer. By quantification of 3D neuronal “packing,” we can hence shed light on how the human cerebellum accommodates 80% of the total neurons in the brain in only 10% of its volume. In addition, we show that the distribution of neighboring neurons in the granular layer is anisotropic with respect to the Purkinje cell dendrites.
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26
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Khimchenko A, Bikis C, Pacureanu A, Hieber SE, Thalmann P, Deyhle H, Schweighauser G, Hench J, Frank S, Müller‐Gerbl M, Schulz G, Cloetens P, Müller B. Hard X-Ray Nanoholotomography: Large-Scale, Label-Free, 3D Neuroimaging beyond Optical Limit. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2018; 5:1700694. [PMID: 29938163 PMCID: PMC6010902 DOI: 10.1002/advs.201700694] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 02/17/2018] [Indexed: 05/22/2023]
Abstract
There have been great efforts on the nanoscale 3D probing of brain tissues to image subcellular morphologies. However, limitations in terms of tissue coverage, anisotropic resolution, stain dependence, and complex sample preparation all hinder achieving a better understanding of the human brain functioning in the subcellular context. Herein, X-ray nanoholotomography is introduced as an emerging synchrotron radiation-based technology for large-scale, label-free, direct imaging with isotropic voxel sizes down to 25 nm, exhibiting a spatial resolution down to 88 nm. The procedure is nondestructive as it does not require physical slicing. Hence, it allows subsequent imaging by complementary techniques, including histology. The feasibility of this 3D imaging approach is demonstrated on human cerebellum and neocortex specimens derived from paraffin-embedded tissue blocks. The obtained results are compared to hematoxylin and eosin stained histological sections and showcase the ability for rapid hierarchical neuroimaging and automatic rebuilding of the neuronal architecture at the level of a single cell nucleolus. The findings indicate that nanoholotomography can complement microscopy not only by large isotropic volumetric data but also by morphological details on the sub-100 nm level, addressing many of the present challenges in brain tissue characterization and probably becoming an important tool in nanoanatomy.
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Affiliation(s)
- Anna Khimchenko
- Biomaterials Science Center (BMC)Department of Biomedical EngineeringUniversity of Basel4123AllschwilSwitzerland
| | - Christos Bikis
- Biomaterials Science Center (BMC)Department of Biomedical EngineeringUniversity of Basel4123AllschwilSwitzerland
| | - Alexandra Pacureanu
- ID16A‐NI Nano‐Imaging BeamlineEuropean Synchrotron Radiation Facility (ESRF)38043GrenobleFrance
| | - Simone E. Hieber
- Biomaterials Science Center (BMC)Department of Biomedical EngineeringUniversity of Basel4123AllschwilSwitzerland
| | - Peter Thalmann
- Biomaterials Science Center (BMC)Department of Biomedical EngineeringUniversity of Basel4123AllschwilSwitzerland
| | - Hans Deyhle
- Biomaterials Science Center (BMC)Department of Biomedical EngineeringUniversity of Basel4123AllschwilSwitzerland
| | - Gabriel Schweighauser
- Institute of PathologyDepartment of NeuropathologyBasel University Hospital4056BaselSwitzerland
| | - Jürgen Hench
- Institute of PathologyDepartment of NeuropathologyBasel University Hospital4056BaselSwitzerland
| | - Stephan Frank
- Institute of PathologyDepartment of NeuropathologyBasel University Hospital4056BaselSwitzerland
| | - Magdalena Müller‐Gerbl
- Musculoskeletal Research GroupDepartment of BiomedicineUniversity of Basel4056BaselSwitzerland
| | - Georg Schulz
- Biomaterials Science Center (BMC)Department of Biomedical EngineeringUniversity of Basel4123AllschwilSwitzerland
| | - Peter Cloetens
- ID16A‐NI Nano‐Imaging BeamlineEuropean Synchrotron Radiation Facility (ESRF)38043GrenobleFrance
| | - Bert Müller
- Biomaterials Science Center (BMC)Department of Biomedical EngineeringUniversity of Basel4123AllschwilSwitzerland
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27
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Töpperwien M, Gradl R, Keppeler D, Vassholz M, Meyer A, Hessler R, Achterhold K, Gleich B, Dierolf M, Pfeiffer F, Moser T, Salditt T. Propagation-based phase-contrast x-ray tomography of cochlea using a compact synchrotron source. Sci Rep 2018; 8:4922. [PMID: 29563553 PMCID: PMC5862924 DOI: 10.1038/s41598-018-23144-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 03/06/2018] [Indexed: 11/23/2022] Open
Abstract
We demonstrate that phase retrieval and tomographic imaging at the organ level of small animals can be advantageously carried out using the monochromatic radiation emitted by a compact x-ray light source, without further optical elements apart from source and detector. This approach allows to carry out microtomography experiments which - due to the large performance gap with respect to conventional laboratory instruments - so far were usually limited to synchrotron sources. We demonstrate the potential by mapping the functional soft tissue within the guinea pig and marmoset cochlea, including in the latter case an electrical cochlear implant. We show how 3d microanatomical studies without dissection or microscopic imaging can enhance future research on cochlear implants.
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Affiliation(s)
- Mareike Töpperwien
- Institute for X-Ray Physics, University of Göttingen, Göttingen, Germany.,Center for Nanoscopy and Molecular Physiology of the Brain, Göttingen, Germany
| | - Regine Gradl
- Chair of Biomedical Physics, Department of Physics, Technical University of Munich, Garching, Germany.,Institute for Advanced Study, Technical University of Munich, Garching, Germany.,Munich School of BioEngineering, Technical University of Munich, Garching, Germany
| | - Daniel Keppeler
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany
| | - Malte Vassholz
- Institute for X-Ray Physics, University of Göttingen, Göttingen, Germany
| | - Alexander Meyer
- InnerEarLab, Department of Otolaryngology, University Medical Center Göttingen, Göttingen, Germany
| | | | - Klaus Achterhold
- Chair of Biomedical Physics, Department of Physics, Technical University of Munich, Garching, Germany.,Munich School of BioEngineering, Technical University of Munich, Garching, Germany
| | - Bernhard Gleich
- Munich School of BioEngineering, Technical University of Munich, Garching, Germany
| | - Martin Dierolf
- Chair of Biomedical Physics, Department of Physics, Technical University of Munich, Garching, Germany.,Munich School of BioEngineering, Technical University of Munich, Garching, Germany
| | - Franz Pfeiffer
- Chair of Biomedical Physics, Department of Physics, Technical University of Munich, Garching, Germany.,Institute for Advanced Study, Technical University of Munich, Garching, Germany.,Munich School of BioEngineering, Technical University of Munich, Garching, Germany.,Department of Diagnostic and Interventional Radiology, Klinikum rechts der Isar, Technical University of Munich, München, Germany
| | - Tobias Moser
- Center for Nanoscopy and Molecular Physiology of the Brain, Göttingen, Germany.,Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany.,Bernstein Focus for Neurotechnology, University of Göttingen, Göttingen, Germany
| | - Tim Salditt
- Institute for X-Ray Physics, University of Göttingen, Göttingen, Germany. .,Center for Nanoscopy and Molecular Physiology of the Brain, Göttingen, Germany.
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28
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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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29
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Du M, Jacobsen C. Relative merits and limiting factors for x-ray and electron microscopy of thick, hydrated organic materials. Ultramicroscopy 2018; 184:293-309. [PMID: 29073575 PMCID: PMC5696083 DOI: 10.1016/j.ultramic.2017.10.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 10/05/2017] [Indexed: 12/01/2022]
Abstract
Electron and x-ray microscopes allow one to image the entire, unlabeled structure of hydrated materials at a resolution well beyond what visible light microscopes can achieve. However, both approaches involve ionizing radiation, so that radiation damage must be considered as one of the limits to imaging. Drawing upon earlier work, we describe here a unified approach to estimating the image contrast (and thus the required exposure and corresponding radiation dose) in both x-ray and electron microscopy. This approach accounts for factors such as plural and inelastic scattering, and (in electron microscopy) the use of energy filters to obtain so-called "zero loss" images. As expected, it shows that electron microscopy offers lower dose for specimens thinner than about 1 µm (such as for studies of macromolecules, viruses, bacteria and archaebacteria, and thin sectioned material), while x-ray microscopy offers superior characteristics for imaging thicker specimen such as whole eukaryotic cells, thick-sectioned tissues, and organs. The required radiation dose scales strongly as a function of the desired spatial resolution, allowing one to understand the limits of live and frozen hydrated specimen imaging. Finally, we consider the factors limiting x-ray microscopy of thicker materials, suggesting that specimens as thick as a whole mouse brain can be imaged with x-ray microscopes without significant image degradation should appropriate image reconstruction methods be identified.
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Affiliation(s)
- Ming Du
- Department of Materials Science and Engineering, Northwestern University, 2145 Sheridan Road, Evanston IL 60208, USA
| | - Chris Jacobsen
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne IL 60439, USA; Department of Physics & Astronomy, Northwestern University, 2145 Sheridan Road, Evanston IL 60208, USA; Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston IL 60208, USA.
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30
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Bikis C, Thalmann P, Degrugillier L, Schulz G, Müller B, Kalbermatten DF, Madduri S, Hieber SE. Three-dimensional and non-destructive characterization of nerves inside conduits using laboratory-based micro computed tomography. J Neurosci Methods 2017; 294:59-66. [PMID: 29129635 DOI: 10.1016/j.jneumeth.2017.11.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 11/07/2017] [Accepted: 11/07/2017] [Indexed: 12/29/2022]
Abstract
BACKGROUND Histological assessment of peripheral nerve regeneration in animals is tedious, time-consuming and challenging for three-dimensional analysis. NEW METHOD The present study reports on how and to what extent micro computed tomography of paraffin-embedded samples can provide a reliable three-dimensional approach for quantitative analysis of peripheral nerves. RESULTS Rat sciatic nerves were harvested, formalin-fixated, positioned into nerve conduits (NC), paraffin-embedded, and imaged using a laboratory-based X-ray microtomography system with an isotropic voxel length of 4μm. Suitable quantitative measures were identified and automatically evaluated, i.e. nerve length, cross-sectional area and volume, as well as vascular structures, to be used as an assessment and comparison indicator of regeneration quality. COMPARISON WITH EXISTING METHODS Compared to imaging using contrast agents, the investigated specimens can subsequently undergo the conventional histological analysis without requiring additional preparation steps. Contrast and spatial resolution are also increased significantly. CONCLUSIONS We demonstrate the potential of the micro computed tomography for non-destructive monitoring of peripheral nerves inside the conduits.
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Affiliation(s)
- Christos Bikis
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, Switzerland
| | - Peter Thalmann
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, Switzerland
| | - Lucas Degrugillier
- Center for Bioengineering and Regenerative Medicine, Department of Biomedical Engineering, University of Basel, Switzerland
| | - Georg Schulz
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, Switzerland
| | - Bert Müller
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, Switzerland.
| | - Daniel F Kalbermatten
- Department of Plastic, Reconstructive, Aesthetic and Hand Surgery, Basel University Hospital, Switzerland; Department of Pathology, University Hospital, Switzerland
| | - Srinivas Madduri
- Center for Bioengineering and Regenerative Medicine, Department of Biomedical Engineering, University of Basel, Switzerland; Department of Plastic, Reconstructive, Aesthetic and Hand Surgery, Basel University Hospital, Switzerland; Department of Biomedicine, University of Basel, Switzerland.
| | - Simone E Hieber
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, Switzerland.
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31
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Dyer EL, Gray Roncal W, Prasad JA, Fernandes HL, Gürsoy D, De Andrade V, Fezzaa K, Xiao X, Vogelstein JT, Jacobsen C, Körding KP, Kasthuri N. Quantifying Mesoscale Neuroanatomy Using X-Ray Microtomography. eNeuro 2017; 4:ENEURO.0195-17.2017. [PMID: 29085899 PMCID: PMC5659258 DOI: 10.1523/eneuro.0195-17.2017] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 08/02/2017] [Accepted: 08/23/2017] [Indexed: 11/21/2022] Open
Abstract
Methods for resolving the three-dimensional (3D) microstructure of the brain typically start by thinly slicing and staining the brain, followed by imaging numerous individual sections with visible light photons or electrons. In contrast, X-rays can be used to image thick samples, providing a rapid approach for producing large 3D brain maps without sectioning. Here we demonstrate the use of synchrotron X-ray microtomography (µCT) for producing mesoscale (∼1 µm 3 resolution) brain maps from millimeter-scale volumes of mouse brain. We introduce a pipeline for µCT-based brain mapping that develops and integrates methods for sample preparation, imaging, and automated segmentation of cells, blood vessels, and myelinated axons, in addition to statistical analyses of these brain structures. Our results demonstrate that X-ray tomography achieves rapid quantification of large brain volumes, complementing other brain mapping and connectomics efforts.
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Affiliation(s)
- Eva L. Dyer
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332
| | - William Gray Roncal
- The Johns Hopkins University Applied Physics Laboratory, Laurel, MD, 20723
- Dept. of Computer Science, The Johns Hopkins University, Baltimore, MD, 21218
| | - Judy A. Prasad
- Dept. of Neurobiology, University of Chicago, Chicago, IL, 60637
| | - Hugo L. Fernandes
- Dept. of Physical Medicine and Rehabilitation, Northwestern University, Chicago, IL, 60611
- Sensory Motor Performance Program, Rehabilitation Institute of Chicago, Chicago, IL, 60611
| | - Doga Gürsoy
- Advanced Photon Source, Argonne National Laboratory, Lemont, IL, 60439
| | | | - Kamel Fezzaa
- Advanced Photon Source, Argonne National Laboratory, Lemont, IL, 60439
| | - Xianghui Xiao
- Advanced Photon Source, Argonne National Laboratory, Lemont, IL, 60439
| | - Joshua T. Vogelstein
- Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, MD, 21205
- Institute of Computational Medicine, The Johns Hopkins University, Baltimore, MD, 21218
| | - Chris Jacobsen
- Advanced Photon Source, Argonne National Laboratory, Lemont, IL, 60439
- Department of Physics and Astronomy, Northwestern University, Chicago, IL, 60208
| | - Konrad P. Körding
- Department of Biomedical Engineering, University of Pennsylvania, Philadelphia, PA, 19104
| | - Narayanan Kasthuri
- Dept. of Neurobiology, University of Chicago, Chicago, IL, 60637
- Center for Nanoscale Materials, Argonne National Laboratory, Lemont, IL, 60439
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