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Savatović S, Zdora MC, De Marco F, Bikis C, Olbinado M, Rack A, Müller B, Thibault P, Zanette I. Multi-resolution X-ray phase-contrast and dark-field tomography of human cerebellum with near-field speckles. BIOMEDICAL OPTICS EXPRESS 2024; 15:142-161. [PMID: 38223169 PMCID: PMC10783905 DOI: 10.1364/boe.502664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/30/2023] [Accepted: 11/09/2023] [Indexed: 01/16/2024]
Abstract
In this study, we use synchrotron-based multi-modal X-ray tomography to examine human cerebellar tissue in three dimensions at two levels of spatial resolution (2.3 µm and 11.9 µm). We show that speckle-based imaging (SBI) produces results that are comparable to propagation-based imaging (PBI), a well-established phase-sensitive imaging method. The different SBI signals provide complementary information, which improves tissue differentiation. In particular, the dark-field signal aids in distinguishing tissues with similar average electron density but different microstructural variations. The setup's high resolution and the imaging technique's excellent phase sensitivity enabled the identification of different cellular layers and additionally, different cell types within these layers. We also correlated this high-resolution phase-contrast information with measured dark-field signal levels. These findings demonstrate the viability of SBI and the potential benefit of the dark-field modality for virtual histology of brain tissue.
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Affiliation(s)
- Sara Savatović
- Department of Physics, University of Trieste, Via Valerio 2, 34127 Trieste, Italy
- Elettra-Sincrotrone Trieste, Strada Statale 14 – km 163.5, 34149 Basovizza, Italy
| | - Marie-Christine Zdora
- Department of Biomedical Engineering, ETH Zürich, Gloriastrasse 35, 8092 Zürich, Switzerland
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Fabio De Marco
- Department of Physics, University of Trieste, Via Valerio 2, 34127 Trieste, Italy
- Elettra-Sincrotrone Trieste, Strada Statale 14 – km 163.5, 34149 Basovizza, Italy
| | - Christos Bikis
- Psychiatric Hospital in Winterthur, Wieshofstrasse 102, 8408 Winterthur, Switzerland
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, Hegenheimermattweg 167 B/C, 4123 Allschwil, Switzerland
| | - Margie Olbinado
- Paul Scherrer Institut, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Alexander Rack
- ESRF – The European Synchrotron, CS40220, CEDEX 09, 38043 Grenoble, France
| | - Bert Müller
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, Hegenheimermattweg 167 B/C, 4123 Allschwil, Switzerland
| | - Pierre Thibault
- Department of Physics, University of Trieste, Via Valerio 2, 34127 Trieste, Italy
- Elettra-Sincrotrone Trieste, Strada Statale 14 – km 163.5, 34149 Basovizza, Italy
| | - Irene Zanette
- Elettra-Sincrotrone Trieste, Strada Statale 14 – km 163.5, 34149 Basovizza, Italy
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Rodgers G, Bikis C, Janz P, Tanner C, Schulz G, Thalmann P, Haas CA, Müller B. 3D X-ray Histology for the Investigation of Temporal Lobe Epilepsy in a Mouse Model. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:1730-1745. [PMID: 37584515 DOI: 10.1093/micmic/ozad082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/29/2023] [Accepted: 07/28/2023] [Indexed: 08/17/2023]
Abstract
The most common form of epilepsy among adults is mesial temporal lobe epilepsy (mTLE), with seizures often originating in the hippocampus due to abnormal electrical activity. The gold standard for the histopathological analysis of mTLE is histology, which is a two-dimensional technique. To fill this gap, we propose complementary three-dimensional (3D) X-ray histology. Herein, we used synchrotron radiation-based phase-contrast microtomography with 1.6 μm-wide voxels for the post mortem visualization of tissue microstructure in an intrahippocampal-kainate mouse model for mTLE. We demonstrated that the 3D X-ray histology of unstained, unsectioned, paraffin-embedded brain hemispheres can identify hippocampal sclerosis through the loss of pyramidal neurons in the first and third regions of the Cornu ammonis as well as granule cell dispersion within the dentate gyrus. Morphology and density changes during epileptogenesis were quantified by segmentations from a deep convolutional neural network. Compared to control mice, the total dentate gyrus volume doubled and the granular layer volume quadrupled 21 days after injecting kainate. Subsequent sectioning of the same mouse brains allowed for benchmarking 3D X-ray histology against well-established histochemical and immunofluorescence stainings. Thus, 3D X-ray histology is a complementary neuroimaging tool to unlock the third dimension for the cellular-resolution histopathological analysis of mTLE.
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Affiliation(s)
- Griffin Rodgers
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland
- Biomaterials Science Center, Department of Clinical Research, University Hospital Basel, 4031 Basel, Switzerland
| | - Christos Bikis
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland
- Integrierte Psychiatrie Winterthur-Zürcher Unterland, 8408 Winterthur, Switzerland
| | - Philipp Janz
- Faculty of Medicine, Experimental Epilepsy Research, Department of Neurosurgery, Medical Center-University of Freiburg, 79106 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79106 Freiburg, Germany
- BrainLinks-BrainTools Center, University of Freiburg, 79106 Freiburg, Germany
| | - Christine Tanner
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland
- Biomaterials Science Center, Department of Clinical Research, University Hospital Basel, 4031 Basel, Switzerland
| | - Georg Schulz
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland
- Biomaterials Science Center, Department of Clinical Research, University Hospital Basel, 4031 Basel, Switzerland
- Core Facility Micro- and Nanotomography, Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland
| | - Peter Thalmann
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland
| | - Carola A Haas
- Faculty of Medicine, Experimental Epilepsy Research, Department of Neurosurgery, Medical Center-University of Freiburg, 79106 Freiburg, Germany
- BrainLinks-BrainTools Center, University of Freiburg, 79106 Freiburg, Germany
- Center of Basics in NeuroModulation, Faculty of Medicine, University of Freiburg, 79114 Freiburg, Germany
| | - Bert Müller
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland
- Biomaterials Science Center, Department of Clinical Research, University Hospital Basel, 4031 Basel, Switzerland
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Frost J, Schmitzer B, Töpperwien M, Eckermann M, Franz J, Stadelmann C, Salditt T. 3d virtual histology reveals pathological alterations of cerebellar granule cells in multiple sclerosis. Neuroscience 2023; 520:18-38. [PMID: 37061161 DOI: 10.1016/j.neuroscience.2023.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 03/10/2023] [Accepted: 04/03/2023] [Indexed: 04/17/2023]
Abstract
We investigate structural properties of neurons in the granular layer of human cerebellum with respect to their involvement in multiple sclerosis (MS). To this end we analyze data recorded by X-ray phase contrast tomography from tissue samples collected post mortem from a MS and a healthy control group. Using automated segmentation and histogram analysis based on optimal transport theory (OT) we find that the distributions representing nuclear structure in the granular layer move to a more compact nuclear state, i.e. smaller, denser and more heterogeneous nuclei in MS. We have previously made a similar observation for neurons of the dentate gyrus in Alzheimer's disease, suggesting that more compact structure of neuronal nuclei which we attributed to increased levels of heterochromatin, may possibly represent a more general phenomenon of cellular senescence associated with neurodegeneration.
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Affiliation(s)
- Jakob Frost
- Institute of X-ray Physics, Georg-August Universität Göttingen, Germany
| | - Bernhard Schmitzer
- Institute of Computer Science, Georg-August Universität Göttingen, Germany
| | - Mareike Töpperwien
- Institute of X-ray Physics, Georg-August Universität Göttingen, Germany; Present address: ESRF, Grenoble, France; Present adress: YXLON GmbH, Hamburg, Germany
| | - Marina Eckermann
- Institute of X-ray Physics, Georg-August Universität Göttingen, Germany; Present address: ESRF, Grenoble, France
| | - Jonas Franz
- Institute of Neuropathology, Universical Medical Center Göttingen, Germany
| | - Christine Stadelmann
- Institute of Neuropathology, Universical Medical Center Göttingen, Germany; Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), Georg-August Universität Göttingen, Germany
| | - Tim Salditt
- Institute of X-ray Physics, Georg-August Universität Göttingen, Germany; Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), Georg-August Universität Göttingen, Germany
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Nolte P, Dullin C, Svetlove A, Brettmacher M, Rußmann C, Schilling AF, Alves F, Stock B. Current Approaches for Image Fusion of Histological Data with Computed Tomography and Magnetic Resonance Imaging. Radiol Res Pract 2022; 2022:6765895. [PMID: 36408297 PMCID: PMC9668453 DOI: 10.1155/2022/6765895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/17/2022] [Indexed: 10/30/2023] Open
Abstract
Classical analysis of biological samples requires the destruction of the tissue's integrity by cutting or grinding it down to thin slices for (Immuno)-histochemical staining and microscopic analysis. Despite high specificity, encoded in the stained 2D section of the whole tissue, the structural information, especially 3D information, is limited. Computed tomography (CT) or magnetic resonance imaging (MRI) scans performed prior to sectioning in combination with image registration algorithms provide an opportunity to regain access to morphological characteristics as well as to relate histological findings to the 3D structure of the local tissue environment. This review provides a summary of prevalent literature addressing the problem of multimodal coregistration of hard- and soft-tissue in microscopy and tomography. Grouped according to the complexity of the dimensions, including image-to-volume (2D ⟶ 3D), image-to-image (2D ⟶ 2D), and volume-to-volume (3D ⟶ 3D), selected currently applied approaches are investigated by comparing the method accuracy with respect to the limiting resolution of the tomography. Correlation of multimodal imaging could position itself as a useful tool allowing for precise histological diagnostic and allow the a priori planning of tissue extraction like biopsies.
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Affiliation(s)
- Philipp Nolte
- Faculty of Engineering and Health, University of Applied Sciences and Arts, Goettingen 37085, Germany
- Institute for Diagnostic and Interventional Radiology, University Medical Center Goettingen, Goettingen 37075, Germany
- Department of Trauma Surgery, Orthopedics and Plastic Surgery, University Medical Center Goettingen, Gottingen 37075, Germany
| | - Christian Dullin
- Institute for Diagnostic and Interventional Radiology, University Medical Center Goettingen, Goettingen 37075, Germany
- Translational Molecular Imaging, Max-Planck Institute for Multidisciplinary Sciences, City Campus, 37075 Goettingen, Germany
- Department for Diagnostic and Interventional Radiology, University Hospital Heidelberg, Heidelberg 69120, Germany
| | - Angelika Svetlove
- Institute for Diagnostic and Interventional Radiology, University Medical Center Goettingen, Goettingen 37075, Germany
- Translational Molecular Imaging, Max-Planck Institute for Multidisciplinary Sciences, City Campus, 37075 Goettingen, Germany
| | - Marcel Brettmacher
- Faculty of Engineering and Health, University of Applied Sciences and Arts, Goettingen 37085, Germany
| | - Christoph Rußmann
- Faculty of Engineering and Health, University of Applied Sciences and Arts, Goettingen 37085, Germany
- Brigham and Women's Hospital, Harvard Medical School, Boston 02155, MA, USA
| | - Arndt F. Schilling
- Department of Trauma Surgery, Orthopedics and Plastic Surgery, University Medical Center Goettingen, Gottingen 37075, Germany
| | - Frauke Alves
- Institute for Diagnostic and Interventional Radiology, University Medical Center Goettingen, Goettingen 37075, Germany
- Translational Molecular Imaging, Max-Planck Institute for Multidisciplinary Sciences, City Campus, 37075 Goettingen, Germany
| | - Bernd Stock
- Faculty of Engineering and Health, University of Applied Sciences and Arts, Goettingen 37085, Germany
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Combining High-Resolution Hard X-ray Tomography and Histology for Stem Cell-Mediated Distraction Osteogenesis. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12126286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Distraction osteogenesis is a clinically established technique for lengthening, molding and shaping bone by new bone formation. The experimental evaluation of this expensive and time-consuming treatment is of high impact for better understanding of tissue engineering but mainly relies on a limited number of histological slices. These tissue slices contain two-dimensional information comprising only about one percent of the volume of interest. In order to analyze the soft and hard tissues of the entire jaw of a single rat in a multimodal assessment, we combined micro computed tomography (µCT) with histology. The µCT data acquired before and after decalcification were registered to determine the impact of decalcification on local tissue shrinkage. Identification of the location of the H&E-stained specimen within the synchrotron radiation-based µCT data collected after decalcification was achieved via non-rigid slice-to-volume registration. The resulting bi- and tri-variate histograms were divided into clusters related to anatomical features from bone and soft tissues, which allowed for a comparison of the approaches and resulted in the hypothesis that the combination of laboratory-based µCT before decalcification, synchrotron radiation-based µCT after decalcification and histology with hematoxylin-and-eosin staining could be used to discriminate between different types of collagen, key components of new bone formation.
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Soltau J, Osterhoff M, Salditt T. Coherent Diffractive Imaging with Diffractive Optics. PHYSICAL REVIEW LETTERS 2022; 128:223901. [PMID: 35714250 DOI: 10.1103/physrevlett.128.223901] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 03/14/2022] [Accepted: 04/15/2022] [Indexed: 06/15/2023]
Abstract
We present a novel approach to x-ray microscopy based on a multilayer zone plate which is positioned behind a sample similar to an objective lens. However, unlike transmission x-ray microscopy, we do not content ourselves with a sharp intensity image; instead, we incorporate the multilayer zone plate transfer function directly in an iterative phase retrieval scheme to exploit the large diffraction angles of the small layers. The presence of multiple diffraction orders, which is conventionally a nuisance, now comes as an advantage for the reconstruction and photon efficiency. In a first experiment, we achieve sub-10-nm resolution and a quantitative phase contrast.
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Affiliation(s)
- Jakob Soltau
- Institut für Röntgenphysik, Georg-August-Universität Göttingen, Friedrich-Hund-Platz 1, Göttingen 37077, Germany
| | - Markus Osterhoff
- Institut für Röntgenphysik, Georg-August-Universität Göttingen, Friedrich-Hund-Platz 1, Göttingen 37077, Germany
- Campus-Institut Data Science, Friedrich-Hund-Platz 1, Göttingen 37077, Germany
| | - Tim Salditt
- Institut für Röntgenphysik, Georg-August-Universität Göttingen, Friedrich-Hund-Platz 1, Göttingen 37077, Germany
- Campus-Institut Data Science, Friedrich-Hund-Platz 1, Göttingen 37077, Germany
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Clear E, Grant RA, Carroll M, Brassey CA. A Review and Case Study of 3D Imaging Modalities for Female Amniote Reproductive Anatomy. Integr Comp Biol 2022; 62:icac027. [PMID: 35536568 PMCID: PMC10570564 DOI: 10.1093/icb/icac027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/20/2022] [Indexed: 11/13/2022] Open
Abstract
Recent advances in non-invasive imaging methods have revitalised the field of comparative anatomy, and reproductive anatomy has been no exception. The reproductive systems of female amniotes present specific challenges, namely their often internal "hidden" anatomy. Quantifying female reproductive systems is crucial to recognising reproductive pathologies, monitoring menstrual cycles, and understanding copulatory mechanics. Here we conduct a review of the application of non-invasive imaging techniques to female amniote reproductive anatomy. We introduce the commonly used imaging modalities of computed tomography (CT) and magnetic resonance imaging (MRI), highlighting their advantages and limitations when applied to female reproductive tissues, and make suggestions for future advances. We also include a case study of micro CT and MRI, along with their associated staining protocols, applied to cadavers of female adult stoats (Mustela erminea). In doing so, we will progress the discussion surrounding the imaging of female reproductive anatomy, whilst also impacting the fields of sexual selection research and comparative anatomy more broadly.
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Affiliation(s)
- Emma Clear
- Department of Natural Sciences, Manchester Metropolitan University, Chester St, Manchester M1 5GD, UK
- Williamson Park Zoo, Quernmore Road, Lancaster, Lancashire LA1 1UX, UK
| | - Robyn A Grant
- Department of Natural Sciences, Manchester Metropolitan University, Chester St, Manchester M1 5GD, UK
| | - Michael Carroll
- Department of Life Sciences, Manchester Metropolitan University, Chester St, Manchester M1 5GD, UK
| | - Charlotte A Brassey
- Department of Natural Sciences, Manchester Metropolitan University, Chester St, Manchester M1 5GD, UK
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Migga A, Schulz G, Rodgers G, Osterwalder M, Tanner C, Blank H, Jerjen I, Salmon P, Twengström W, Scheel M, Weitkamp T, Schlepütz CM, Bolten JS, Huwyler J, Hotz G, Madduri S, Müller B. Comparative hard x-ray tomography for virtual histology of zebrafish larva, human tooth cementum, and porcine nerve. J Med Imaging (Bellingham) 2022; 9:031507. [PMID: 35372637 PMCID: PMC8968075 DOI: 10.1117/1.jmi.9.3.031507] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 03/08/2022] [Indexed: 07/26/2023] Open
Abstract
Purpose: Synchrotron radiation-based tomography yields microanatomical features in human and animal tissues without physical slicing. Recent advances in instrumentation have made laboratory-based phase tomography feasible. We compared the performance of three cutting-edge laboratory systems benchmarked by synchrotron radiation-based tomography for three specimens. As an additional criterion, the user-friendliness of the three microtomography systems was considered. Approach: The three tomography systems-SkyScan 2214 (Bruker-microCT, Kontich, Belgium), Exciscope prototype (Stockholm, Sweden), and Xradia 620 Versa (Zeiss, Oberkochen, Germany)-were given 36 h to measure three medically relevant specimens, namely, zebrafish larva, archaeological human tooth, and porcine nerve. The obtained datasets were registered to the benchmark synchrotron radiation-based tomography from the same specimens and selected ones to the SkyScan 1275 and phoenix nanotom m® laboratory systems to characterize development over the last decade. Results: Next-generation laboratory-based microtomography almost reached the quality achieved by synchrotron-radiation facilities with respect to spatial and density resolution, as indicated by the visualization of the medically relevant microanatomical features. The SkyScan 2214 system and the Exciscope prototype demonstrated the complementarity of phase information by imaging the eyes of the zebrafish larva. The 3 - μ m thin annual layers in the tooth cementum were identified using Xradia 620 Versa. Conclusions: SkyScan 2214 was the simplest system and was well-suited to visualizing the wealth of anatomical features in the zebrafish larva. Data from the Exciscope prototype with the high photon flux from the liquid metal source showed the spiral nature of the myelin sheaths in the porcine nerve. Xradia 620 Versa, with detector optics as typically installed for synchrotron tomography beamlines, enabled the three-dimensional visualization of the zebrafish larva with comparable quality to the synchrotron data and the annual layers in the tooth cementum.
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Affiliation(s)
- Alexandra Migga
- University of Basel, Biomaterials Science Center, Department of Biomedical Engineering, Allschwil, Switzerland
- University of Basel, Biomaterials Science Center, Department of Clinical Research, Basel, Switzerland
| | - Georg Schulz
- University of Basel, Biomaterials Science Center, Department of Biomedical Engineering, Allschwil, Switzerland
- University of Basel, Core Facility Micro- and Nanotomography, Department of Biomedical Engineering, Allschwil, Switzerland
| | - Griffin Rodgers
- University of Basel, Biomaterials Science Center, Department of Biomedical Engineering, Allschwil, Switzerland
- University of Basel, Biomaterials Science Center, Department of Clinical Research, Basel, Switzerland
| | - Melissa Osterwalder
- University of Basel, Biomaterials Science Center, Department of Biomedical Engineering, Allschwil, Switzerland
- University of Basel, Biomaterials Science Center, Department of Clinical Research, Basel, Switzerland
| | - Christine Tanner
- University of Basel, Biomaterials Science Center, Department of Biomedical Engineering, Allschwil, Switzerland
- University of Basel, Biomaterials Science Center, Department of Clinical Research, Basel, Switzerland
| | | | | | | | | | | | | | | | - Jan S. Bolten
- University of Basel, Pharmaceutical Technology, Department of Pharmaceutical Sciences, Basel, Switzerland
| | - Jörg Huwyler
- University of Basel, Pharmaceutical Technology, Department of Pharmaceutical Sciences, Basel, Switzerland
| | - Gerhard Hotz
- Natural History Museum of Basel, Anthropological Collection, Basel, Switzerland
- University of Basel, Integrative Prehistory and Archaeological Science, Basel, Switzerland
| | - Srinivas Madduri
- University of Basel, Biomaterials Science Center, Department of Biomedical Engineering, Allschwil, Switzerland
- University of Geneva, Department of Surgery, Geneva, Switzerland
- University Hospital Basel, Department of Plastic, Reconstructive, Aesthetic and Hand Surgery, Basel, Switzerland
| | - Bert Müller
- University of Basel, Biomaterials Science Center, Department of Biomedical Engineering, Allschwil, Switzerland
- University of Basel, Biomaterials Science Center, Department of Clinical Research, Basel, Switzerland
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Zeng C, Chen Z, Yang H, Fan Y, Fei L, Chen X, Zhang M. Advanced high resolution three-dimensional imaging to visualize the cerebral neurovascular network in stroke. Int J Biol Sci 2022; 18:552-571. [PMID: 35002509 PMCID: PMC8741851 DOI: 10.7150/ijbs.64373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/28/2021] [Indexed: 11/05/2022] Open
Abstract
As an important method to accurately and timely diagnose stroke and study physiological characteristics and pathological mechanism in it, imaging technology has gone through more than a century of iteration. The interaction of cells densely packed in the brain is three-dimensional (3D), but the flat images brought by traditional visualization methods show only a few cells and ignore connections outside the slices. The increased resolution allows for a more microscopic and underlying view. Today's intuitive 3D imagings of micron or even nanometer scale are showing its essentiality in stroke. In recent years, 3D imaging technology has gained rapid development. With the overhaul of imaging mediums and the innovation of imaging mode, the resolution has been significantly improved, endowing researchers with the capability of holistic observation of a large volume, real-time monitoring of tiny voxels, and quantitative measurement of spatial parameters. In this review, we will summarize the current methods of high-resolution 3D imaging applied in stroke.
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Affiliation(s)
- Chudai Zeng
- Department of Neurology, Xiangya Hospital of Central South University, Changsha, Hunan, China, 410008.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China, 410008
| | - Zhuohui Chen
- Department of Neurology, Xiangya Hospital of Central South University, Changsha, Hunan, China, 410008.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China, 410008
| | - Haojun Yang
- Department of Neurology, Xiangya Hospital of Central South University, Changsha, Hunan, China, 410008.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China, 410008
| | - Yishu Fan
- Department of Neurology, Xiangya Hospital of Central South University, Changsha, Hunan, China, 410008.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China, 410008
| | - Lujing Fei
- Department of Neurology, Xiangya Hospital of Central South University, Changsha, Hunan, China, 410008.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China, 410008
| | - Xinghang Chen
- Department of Neurology, Xiangya Hospital of Central South University, Changsha, Hunan, China, 410008.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China, 410008
| | - Mengqi Zhang
- Department of Neurology, Xiangya Hospital of Central South University, Changsha, Hunan, China, 410008.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China, 410008
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10
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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: 1] [Impact Index Per Article: 0.5] [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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11
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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: 8] [Impact Index Per Article: 2.7] [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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12
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Lawson MJ, Katsamenis OL, Chatelet D, Alzetani A, Larkin O, Haig I, Lackie P, Warner J, Schneider P. Immunofluorescence-guided segmentation of three-dimensional features in micro-computed tomography datasets of human lung tissue. ROYAL SOCIETY OPEN SCIENCE 2021; 8:211067. [PMID: 34737879 PMCID: PMC8564621 DOI: 10.1098/rsos.211067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
Micro-computed tomography (µCT) provides non-destructive three-dimensional (3D) imaging of soft tissue microstructures. Specific features in µCT images can be identified using correlated two-dimensional (2D) histology images allowing manual segmentation. However, this is very time-consuming and requires specialist knowledge of the tissue and imaging modalities involved. Using a custom-designed µCT system optimized for imaging unstained formalin-fixed paraffin-embedded soft tissues, we imaged human lung tissue at isotropic voxel sizes less than 10 µm. Tissue sections were stained with haematoxylin and eosin or cytokeratin 18 in columnar airway epithelial cells using immunofluorescence (IF), as an exemplar of this workflow. Novel utilization of tissue autofluorescence allowed automatic alignment of 2D microscopy images to the 3D µCT data using scripted co-registration and automated image warping algorithms. Warped IF images, which were accurately aligned with the µCT datasets, allowed 3D segmentation of immunoreactive tissue microstructures in the human lung. Blood vessels were segmented semi-automatically using the co-registered µCT datasets. Correlating 2D IF and 3D µCT data enables accurate identification, localization and segmentation of features in fixed soft lung tissue. Our novel correlative imaging workflow provides faster and more automated 3D segmentation of µCT datasets. This is applicable to the huge range of formalin-fixed paraffin-embedded tissues held in biobanks and archives.
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Affiliation(s)
- Matthew J. Lawson
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Orestis L. Katsamenis
- μ-VIS X-ray Imaging Centre, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, UK
| | - David Chatelet
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Aiman Alzetani
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Oliver Larkin
- Bioengineering Research Group, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, UK
| | - Ian Haig
- Nikon X-Tek Systems Ltd, Tring, UK
| | - Peter Lackie
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Jane Warner
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Philipp Schneider
- Bioengineering Research Group, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, UK
- High-Performance Vision Systems, Center for Vision, Automation and Control, AIT Austrian Institute of Technology, Vienna, Austria
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13
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Automatic Quantification of Atherosclerosis in Contrast-Enhanced MicroCT Scans of Mouse Aortas Ex Vivo. Int J Biomed Imaging 2021; 2021:4998786. [PMID: 34594369 PMCID: PMC8478544 DOI: 10.1155/2021/4998786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/24/2021] [Accepted: 08/30/2021] [Indexed: 12/12/2022] Open
Abstract
Objective While microCT evaluation of atherosclerotic lesions in mice has been formally validated, existing image processing methods remain undisclosed. We aimed to develop and validate a reproducible image processing workflow based on phosphotungstic acid-enhanced microCT scans for the volumetric quantification of atherosclerotic lesions in entire mouse aortas. Approach and Results. 42 WT and 42 apolipoprotein E knockout mouse aortas were scanned. The walls, lumen, and plaque objects were segmented using dual-threshold algorithms. Aortic and plaque volumes were computed by voxel counting and lesion surface by triangulation. The results were validated against manual and histological evaluations. Knockout mice had a significant increase in plaque volume compared to wild types with a plaque to aorta volume ratio of 0.3%, 2.8%, and 9.8% at weeks 13, 18, and 26, respectively. Automatic segmentation correlated with manual (r 2 ≥ 0.89; p < .001) and histological evaluations (r 2 > 0.96; p < .001). Conclusions The semiautomatic workflow enabled rapid quantification of atherosclerotic plaques in mice with minimal manual work.
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14
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Three-Dimensional X-ray Imaging of β-Galactosidase Reporter Activity by Micro-CT: Implication for Quantitative Analysis of Gene Expression. Brain Sci 2021; 11:brainsci11060746. [PMID: 34199780 PMCID: PMC8230009 DOI: 10.3390/brainsci11060746] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/24/2021] [Accepted: 05/27/2021] [Indexed: 02/07/2023] Open
Abstract
Acquisition of detailed anatomical and molecular knowledge from intact biological samples while preserving their native three-dimensional structure is still a challenging issue for imaging studies aiming to unravel a system's functions. Three-dimensional micro-CT X-ray imaging with a high spatial resolution in minimally perturbed naive non-transparent samples has recently gained increased popularity and broad application in biomedical research. Here, we describe a novel X-ray-based methodology for analysis of β-galactosidase (lacZ) reporter-driven gene expression in an intact murine brain ex vivo by micro-CT. The method relies on detection of bromine molecules in the product of the enzymatic β-galactosidase reaction. Enhancement of the X-ray signal is observed specifically in the regions of the murine brain where expression of the lacZ reporter gene is also detected histologically. We performed quantitative analysis of the expression levels of lacZ reporter activity by relative radiodensity estimation of the β-galactosidase/X-gal precipitate in situ. To demonstrate the feasibility of the method, we performed expression analysis of the Tsen54-lacZ reporter gene in the murine brain in a semi-quantitative manner. Human mutations in the Tsen54 gene cause pontocerebellar hypoplasia (PCH), a group of severe neurodegenerative disorders with both mental and motor deficits. Comparing relative levels of Tsen54 gene expression, we demonstrate that the highest Tsen54 expression is observed in anatomical brain substructures important for the normal motor and memory functions in mice.
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15
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El Maanaoui H, Egelkamp C, Meier J. Influence of the tensile static preload dependency on the dynamic lifetime prediction for an HNBR elastomer. J Mech Behav Biomed Mater 2021; 119:104502. [PMID: 33839537 DOI: 10.1016/j.jmbbm.2021.104502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 03/22/2021] [Accepted: 03/29/2021] [Indexed: 10/21/2022]
Abstract
A correlated lifetime prediction concept for load cases without static preload, which argues with crack growth and particle size distribution from 3D computer tomography, has been shown by Ludwig et al. (2015). This method is extended to non-relaxing load cases i.e. with a static preload dependency. A force controlled dynamic fatigue test for a dumbbell specimen is performed to investigate the service life. In addition, a crack growth investigation is carried out using single edge notched tensile (SENT) specimens in displacement control mode to characterize the tearing energy and crack growth rate. The study with carbon black reinforced HNBR rubber shows a correlation between the Wöhler curve and the Paris-Erdogan plot. An extension of the empirical Paris-Erdogan equation considering static preload dependency allows the prediction of uniaxial lifetime statistics by means of particle size distribution. The calculated lifetime values are in reasonable concordance with the experimental findings.
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Affiliation(s)
- H El Maanaoui
- German Institute of Rubber Technology, Eupener Str. 33, 30519, Hanover, Germany.
| | - C Egelkamp
- German Institute of Rubber Technology, Eupener Str. 33, 30519, Hanover, Germany
| | - J Meier
- German Institute of Rubber Technology, Eupener Str. 33, 30519, Hanover, Germany.
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16
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Du M, Di ZW, Gürsoy D, Xian RP, Kozorovitskiy Y, Jacobsen C. Upscaling X-ray nanoimaging to macroscopic specimens. J Appl Crystallogr 2021; 54:386-401. [PMID: 33953650 PMCID: PMC8056767 DOI: 10.1107/s1600576721000194] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 01/06/2021] [Indexed: 11/10/2022] Open
Abstract
Upscaling X-ray nanoimaging to macroscopic specimens has the potential for providing insights across multiple length scales, but its feasibility has long been an open question. By combining the imaging requirements and existing proof-of-principle examples in large-specimen preparation, data acquisition and reconstruction algorithms, the authors provide imaging time estimates for howX-ray nanoimaging can be scaled to macroscopic specimens. To arrive at this estimate, a phase contrast imaging model that includes plural scattering effects is used to calculate the required exposure and corresponding radiation dose. The coherent X-ray flux anticipated from upcoming diffraction-limited light sources is then considered. This imaging time estimation is in particular applied to the case of the connectomes of whole mouse brains. To image the connectome of the whole mouse brain, electron microscopy connectomics might require years, whereas optimized X-ray microscopy connectomics could reduce this to one week. Furthermore, this analysis points to challenges that need to be overcome (such as increased X-ray detector frame rate) and opportunities that advances in artificial-intelligence-based 'smart' scanning might provide. While the technical advances required are daunting, it is shown that X-ray microscopy is indeed potentially applicable to nanoimaging of millimetre- or even centimetre-size specimens.
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Affiliation(s)
- Ming Du
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Zichao Wendy Di
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA.,Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Doǧa Gürsoy
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA.,Department of Electrical Engineering and Computer Science, Northwestern University, Evanston, IL 60208, USA
| | - R Patrick Xian
- Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA
| | - Yevgenia Kozorovitskiy
- Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA.,Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Chris Jacobsen
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA.,Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA.,Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, USA
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17
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Farrag M, Pukale DD, Leipzig ND. Micro-computed tomography utility for estimation of intraparenchymal spinal cord cystic lesions in small animals. Neural Regen Res 2021; 16:2293-2298. [PMID: 33818515 PMCID: PMC8354136 DOI: 10.4103/1673-5374.310690] [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] [Indexed: 11/21/2022] Open
Abstract
Precise assessment of spinal cord cystic lesions is crucial to formulate effective therapeutic strategies, yet histological assessment of the lesion remains the primary method despite numerous studies showing inconsistent results regarding estimation of lesion size via histology. On the other hand, despite numerous advances in micro-computed tomography (micro-CT) imaging and analysis that have allowed precise measurements of lesion size, there is not enough published data on its application to estimate intraspinal lesion size in laboratory animal models. This work attempts to show that micro-CT can be valuable for spinal cord injury research by demonstrating accurate estimation of syrinx size and compares between micro-CT and traditional histological analysis. We used a post-traumatic syringomyelia rat model to compare micro-CT analysis to conventional histological analysis. The study showed that micro-CT can detect lesions within the spinal cord very similar to histology. Importantly, micro-CT appears to provide more accurate estimates of the lesions with more measures (e.g., surface area), can detect compounds within the cord, and can be done with the tissue of interest (spinal cord) intact. In summary, the experimental work presented here provides one of the first investigations of the use of micro-CT for estimating the size of intraparenchymal cysts and detecting materials within the spinal cord. All animal procedures were approved by the University of Akron Institutional Animal Care and Use Committee (IACUC) (protocol # LRE 16-05-09 approved on May 14, 2016).
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Affiliation(s)
- Mahmoud Farrag
- Integrated Bioscience Program, The University of Akron, Akron, OH, USA
| | - Dipak D Pukale
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Akron, OH, USA
| | - Nic D Leipzig
- Department of Chemical, Biomolecular, and Corrosion Engineering, Integrated Bioscience Program, The University of Akron, Akron, OH, USA
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18
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New fatigue test sample: Lifetime prediction of carbon black filled elastomers based on the probability distribution of particles. POLYMER 2020. [DOI: 10.1016/j.polymer.2020.122973] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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19
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Frohn J, Pinkert-Leetsch D, Missbach-Güntner J, Reichardt M, Osterhoff M, Alves F, Salditt T. 3D virtual histology of human pancreatic tissue by multiscale phase-contrast X-ray tomography. JOURNAL OF SYNCHROTRON RADIATION 2020; 27:1707-1719. [PMID: 33147198 PMCID: PMC7642968 DOI: 10.1107/s1600577520011327] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 08/18/2020] [Indexed: 05/05/2023]
Abstract
A multiscale three-dimensional (3D) virtual histology approach is presented, based on two configurations of propagation phase-contrast X-ray tomography, which have been implemented in close proximity at the GINIX endstation at the beamline P10/PETRA III (DESY, Hamburg, Germany). This enables the 3D reconstruction of characteristic morphological features of human pancreatic normal and tumor tissue, as obtained from cancer surgery, first in the form of a large-scale overview by parallel-beam illumination, followed by a zoom into a region-of-interest based on zoom tomography using a Kirkpatrick-Baez mirror with additional waveguide optics. To this end 1 mm punch biopsies of the tissue were taken. In the parallel tomography, a volumetric throughput on the order of 0.01 mm3 s-1 was achieved, while maintaining the ability to segment isolated cells. With a continuous rotation during the scan, a total acquisition time of less than 2 min was required for a full tomographic scan. Using the combination of both setups, islets of Langerhans, a three-dimensional cluster of cells in the endocrine part of the pancreas, could be located. Cells in such an islet were segmented and visualized in 3D. Further, morphological alterations of tumorous tissue of the pancreas were characterized. To this end, the anisotropy parameter Ω, based on intensity gradients, was used in order to quantify the presence of collagen fibers within the entire biopsy specimen. This proof-of-concept experiment of the multiscale approach on human pancreatic tissue paves the way for future 3D virtual pathology.
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Affiliation(s)
- Jasper Frohn
- Institute for X-ray Physics, Universität Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Diana Pinkert-Leetsch
- Institute of Diagnostic and Interventional Radiology, University Medical Center Göttingen, Robert Koch Strasse 40, 37075 Göttingen, Germany
- Max Planck Institute for Experimental Medicine, Group of Translational Molecular Imaging, Hermann-Rein-Strasse 3, 37075 Göttingen, Germany
| | - Jeannine Missbach-Güntner
- Institute of Diagnostic and Interventional Radiology, University Medical Center Göttingen, Robert Koch Strasse 40, 37075 Göttingen, Germany
| | - Marius Reichardt
- Institute for X-ray Physics, Universität Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Markus Osterhoff
- Institute for X-ray Physics, Universität Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Frauke Alves
- Institute of Diagnostic and Interventional Radiology, University Medical Center Göttingen, Robert Koch Strasse 40, 37075 Göttingen, Germany
- Max Planck Institute for Experimental Medicine, Group of Translational Molecular Imaging, Hermann-Rein-Strasse 3, 37075 Göttingen, Germany
- Clinic of Hematology and Medical Oncology, University Medical Center Göttingen, Robert Koch Strase 40, 37075 Göttingen, Germany
| | - Tim Salditt
- Institute for X-ray Physics, Universität Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
- Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells (MBExC), University Medical Center Göttingen, Robert Koch Strase 40, 37075 Göttingen, Germany
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20
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Eckermann M, Peruzzi N, Frohn J, Bech M, Englund E, Veress B, Salditt T, Dahlin LB, Ohlsson B. 3d phase-contrast nanotomography of unstained human skin biopsies may identify morphological differences in the dermis and epidermis between subjects. Skin Res Technol 2020; 27:316-323. [PMID: 33022848 PMCID: PMC8246570 DOI: 10.1111/srt.12974] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/07/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND Enteric neuropathy is described in most patients with gastrointestinal dysmotility and may be found together with reduced intraepidermal nerve fiber density (IENFD). The aim of this pilot study was to assess whether three-dimensional (3d) imaging of skin biopsies could be used to examine various tissue components in patients with gastrointestinal dysmotility. MATERIAL AND METHODS Four dysmotility patients of different etiology and two healthy volunteers were included. From each subject, two 3-mm punch skin biopsies were stained with antibodies against protein gene product 9.5 or evaluated as a whole with two X-ray phase-contrast computed tomography (CT) setups, a laboratory µCT setup and a dedicated synchrotron radiation nanoCT end-station. RESULTS Two patients had reduced IENFD, and two normal IENFD, compared with controls. µCT and X-ray phase-contrast holographic nanotomography scanned whole tissue specimens, with optional high-resolution scans revealing delicate structures, without differentiation of various fibers and cells. Irregular architecture of dermal fibers was observed in the patient with Ehlers-Danlos syndrome and the patient with idiopathic dysmotility showed an abundance of mesenchymal ground substance. CONCLUSIONS 3d phase-contrast tomographic imaging may be useful to illustrate traits of connective tissue dysfunction in various organs and to demonstrate whether disorganized dermal fibers could explain organ dysfunction.
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Affiliation(s)
- Marina Eckermann
- Institute for X-Ray Physics, University of Göttingen, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Niccolò Peruzzi
- Medical Radiation Physics, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Jasper Frohn
- Institute for X-Ray Physics, University of Göttingen, Göttingen, Germany
| | - Martin Bech
- Medical Radiation Physics, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Elisabet Englund
- Division of Oncology and Pathology, Skane University Hospital, Lund University, Lund, Sweden
| | - Béla Veress
- Department of Pathology, Skåne University Hospital, Malmö, Sweden
| | - Tim Salditt
- Institute for X-Ray Physics, University of Göttingen, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Lars B Dahlin
- Department of Translational Medicine - Hand Surgery, Lund University, Malmö, Sweden.,Department of Hand Surgery, Skåne University Hospital, Malmö, Sweden
| | - Bodil Ohlsson
- Department of Internal Medicine, Skåne University Hospital, Lund University, Malmö, Sweden
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21
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Eckermann M, Frohn J, Reichardt M, Osterhoff M, Sprung M, Westermeier F, Tzankov A, Werlein C, Kühnel M, Jonigk D, Salditt T. 3D virtual pathohistology of lung tissue from Covid-19 patients based on phase contrast X-ray tomography. eLife 2020; 9:e60408. [PMID: 32815517 PMCID: PMC7473770 DOI: 10.7554/elife.60408] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 08/17/2020] [Indexed: 01/25/2023] Open
Abstract
We present a three-dimensional (3D) approach for virtual histology and histopathology based on multi-scale phase contrast x-ray tomography, and use this to investigate the parenchymal architecture of unstained lung tissue from patients who succumbed to Covid-19. Based on this first proof-of-concept study, we propose multi-scale phase contrast x-ray tomography as a tool to unravel the pathophysiology of Covid-19, extending conventional histology by a third dimension and allowing for full quantification of tissue remodeling. By combining parallel and cone beam geometry, autopsy samples with a maximum cross section of 8 mm are scanned and reconstructed at a resolution and image quality, which allows for the segmentation of individual cells. Using the zoom capability of the cone beam geometry, regions-of-interest are reconstructed with a minimum voxel size of 167 nm. We exemplify the capability of this approach by 3D visualization of diffuse alveolar damage (DAD) with its prominent hyaline membrane formation, by mapping the 3D distribution and density of lymphocytes infiltrating the tissue, and by providing histograms of characteristic distances from tissue interior to the closest air compartment.
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Affiliation(s)
- Marina Eckermann
- Institut für Röntgenphysik, Georg-August-UniversitätGöttingenGermany
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of GöttingenGöttingenGermany
| | - Jasper Frohn
- Institut für Röntgenphysik, Georg-August-UniversitätGöttingenGermany
| | - Marius Reichardt
- Institut für Röntgenphysik, Georg-August-UniversitätGöttingenGermany
| | - Markus Osterhoff
- Institut für Röntgenphysik, Georg-August-UniversitätGöttingenGermany
| | | | | | - Alexandar Tzankov
- Institut für Medizinische Genetik und Pathologie, Universitätsspital BaselBaselSwitzerland
| | - Christopher Werlein
- Medizinische Hochschule Hannover (MHH)HannoverGermany
- Deutsches Zentrum für Lungenforschung (DZL)Hannover (BREATH)Germany
| | - Mark Kühnel
- Medizinische Hochschule Hannover (MHH)HannoverGermany
- Deutsches Zentrum für Lungenforschung (DZL)Hannover (BREATH)Germany
| | - Danny Jonigk
- Medizinische Hochschule Hannover (MHH)HannoverGermany
- Deutsches Zentrum für Lungenforschung (DZL)Hannover (BREATH)Germany
| | - Tim Salditt
- Institut für Röntgenphysik, Georg-August-UniversitätGöttingenGermany
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of GöttingenGöttingenGermany
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22
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Lee TB, Lee J, Jun JH. Three-Dimensional Approaches in Histopathological Tissue Clearing System. KOREAN JOURNAL OF CLINICAL LABORATORY SCIENCE 2020. [DOI: 10.15324/kjcls.2020.52.1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Affiliation(s)
- Tae Bok Lee
- Confocal Core Facility, Center for Medical Innovation, Seoul National University Hospital, Seoul, Korea
| | - Jaewang Lee
- Department of Biomedical Laboratory Science, College of Health Science, Eulji University, Seongnam, Korea
| | - Jin Hyun Jun
- Department of Biomedical Laboratory Science, College of Health Science, Eulji University, Seongnam, Korea
- Department of Senior Healthcare, BK21 Plus Program, Graduate School of Eulji University, Seongnam, Korea
- Eulji Medi-Bio Research Institute (EMBRI), Eulji University, Daejeon, Korea
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23
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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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24
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Katsamenis OL, Olding M, Warner JA, Chatelet DS, Jones MG, Sgalla G, Smit B, Larkin OJ, Haig I, Richeldi L, Sinclair I, Lackie PM, Schneider P. X-ray Micro-Computed Tomography for Nondestructive Three-Dimensional (3D) X-ray Histology. THE AMERICAN JOURNAL OF PATHOLOGY 2019; 189:1608-1620. [PMID: 31125553 PMCID: PMC6680277 DOI: 10.1016/j.ajpath.2019.05.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 04/29/2019] [Accepted: 05/02/2019] [Indexed: 12/12/2022]
Abstract
Historically, micro-computed tomography (μCT) has been considered unsuitable for histologic analysis of unstained formalin-fixed, paraffin-embedded soft tissue biopsy specimens because of a lack of image contrast between the tissue and the paraffin. However, we recently demonstrated that μCT can successfully resolve microstructural detail in routinely prepared tissue specimens. Herein, we illustrate how μCT imaging of standard formalin-fixed, paraffin-embedded biopsy specimens can be seamlessly integrated into conventional histology workflows, enabling nondestructive three-dimensional (3D) X-ray histology, the use and benefits of which we showcase for the exemplar of human lung biopsy specimens. This technology advancement was achieved through manufacturing a first-of-kind μCT scanner for X-ray histology and developing optimized imaging protocols, which do not require any additional sample preparation. 3D X-ray histology allows for nondestructive 3D imaging of tissue microstructure, resolving structural connectivity and heterogeneity of complex tissue networks, such as the vascular network or the respiratory tract. We also demonstrate that 3D X-ray histology can yield consistent and reproducible image quality, enabling quantitative assessment of a tissue's 3D microstructures, which is inaccessible to conventional two-dimensional histology. Being nondestructive, the technique does not interfere with histology workflows, permitting subsequent tissue characterization by means of conventional light microscopy-based histology, immunohistochemistry, and immunofluorescence. 3D X-ray histology can be readily applied to a plethora of archival materials, yielding unprecedented opportunities in diagnosis and research of disease.
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Affiliation(s)
- Orestis L Katsamenis
- μ-VIS X-ray Imaging Centre, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, United Kingdom.
| | - Michael Olding
- Biomedical Imaging Unit, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Jane A Warner
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - David S Chatelet
- Biomedical Imaging Unit, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Mark G Jones
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom; National Institute for Health Research Respiratory Biomedical Research Centre, University Hospital Southampton, Southampton, United Kingdom
| | - Giacomo Sgalla
- National Institute for Health Research Respiratory Biomedical Research Centre, University Hospital Southampton, Southampton, United Kingdom
| | - Bennie Smit
- Nikon X-Tek Systems Ltd., Tring, United Kingdom
| | | | - Ian Haig
- Nikon X-Tek Systems Ltd., Tring, United Kingdom
| | - Luca Richeldi
- National Institute for Health Research Respiratory Biomedical Research Centre, University Hospital Southampton, Southampton, United Kingdom
| | - Ian Sinclair
- μ-VIS X-ray Imaging Centre, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, United Kingdom; Engineering Materials Research Group, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, United Kingdom
| | - Peter M Lackie
- Biomedical Imaging Unit, Faculty of Medicine, University of Southampton, Southampton, United Kingdom; School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Philipp Schneider
- μ-VIS X-ray Imaging Centre, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, United Kingdom; Bioengineering Science Research Group, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, United Kingdom.
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25
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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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26
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Albers J, Pacilé S, Markus MA, Wiart M, Vande Velde G, Tromba G, Dullin C. X-ray-Based 3D Virtual Histology-Adding the Next Dimension to Histological Analysis. Mol Imaging Biol 2019; 20:732-741. [PMID: 29968183 DOI: 10.1007/s11307-018-1246-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Histology and immunohistochemistry of thin tissue sections have been the standard diagnostic procedure in many diseases for decades. This method is highly specific for particular tissue regions or cells, but mechanical sectioning of the specimens is required, which destroys the sample in the process and can lead to non-uniform tissue deformations. In addition, regions of interest cannot be located beforehand and the analysis is intrinsically two-dimensional. Micro X-ray computed tomography (μCT) on the other hand can provide 3D images at high resolution and allows for quantification of tissue structures, as well as the localization of small regions of interest. These advantages advocate the use of μCT for virtual histology tool with or without subsequent classical histology. This review summarizes the most recent examples of virtual histology and provides currently known possibilities of improving contrast and resolution of μCT. Following a background in μCT imaging, ex vivo staining procedures for contrast enhancement are presented as well as label-free virtual histology approaches and the technologies, which could rapidly advance it, such as phase-contrast CT. Novel approaches such as zoom tomography and nanoparticulate contrast agents will also be considered. The current evidence suggests that virtual histology may present a valuable addition to the workflow of histological analysis, potentially reducing the workload in pathology, refining tissue classification, and supporting the detection of small malignancies.
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Affiliation(s)
- J Albers
- Institute for Diagnostic and Interventional Radiology, University Medical Center Göttingen, Göttingen, Germany
| | - S Pacilé
- Department of Engineering and Architecture, University of Trieste, Trieste, Italy.,Elettra Sincrotrone Trieste, Trieste, Italy
| | - M A Markus
- Translational Molecular Imaging, Max-Planck-Institute for Experimental Medicine, Göttingen, Germany
| | - M Wiart
- Univ Lyon, CarMeN Laboratory, INSERM, INRA, INSA Lyon, Université Claude Bernard Lyon 1, 69500, Bron, France
| | - G Vande Velde
- Department of Imaging and Pathology, Faculty of Medicine, KU Leuven-University of Leuven, Leuven, Belgium
| | - G Tromba
- Elettra Sincrotrone Trieste, Trieste, Italy
| | - C Dullin
- Institute for Diagnostic and Interventional Radiology, University Medical Center Göttingen, Göttingen, Germany. .,Elettra Sincrotrone Trieste, Trieste, Italy. .,Translational Molecular Imaging, Max-Planck-Institute for Experimental Medicine, Göttingen, Germany.
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27
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Massimi L, Bukreeva I, Santamaria G, Fratini M, Corbelli A, Brun F, Fumagalli S, Maugeri L, Pacureanu A, Cloetens P, Pieroni N, Fiordaliso F, Forloni G, Uccelli A, Kerlero de Rosbo N, Balducci C, Cedola A. Exploring Alzheimer's disease mouse brain through X-ray phase contrast tomography: From the cell to the organ. Neuroimage 2018; 184:490-495. [PMID: 30240904 DOI: 10.1016/j.neuroimage.2018.09.044] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 09/09/2018] [Accepted: 09/17/2018] [Indexed: 12/14/2022] Open
Abstract
Alzheimer's disease (AD), the most common form of dementia, is a progressive neurodegenerative disorder associated with aberrant production of beta-amyloid (Aβ) peptide depositing in brain as amyloid plaques. While animal models allow investigation of disease progression and therapeutic efficacy, technology to fully dissect the pathological mechanisms of this complex disease at cellular and vascular levels is lacking. X-ray phase contrast tomography (XPCT) is an advanced non-destructive 3D multi-scale direct imaging from the cell through to the whole brain, with exceptional spatial and contrast resolution. We exploit XPCT to simultaneously analyse disease-relevant vascular and neuronal networks in AD mouse brain, without sectioning and staining. The findings clearly show the different typologies and internal structures of Aβ plaques, together with their interaction with patho/physiological cellular and neuro-vascular microenvironment. XPCT enables for the first time a detailed visualization of amyloid-angiopathy at capillary level, which is impossible to achieve with other approaches. XPCT emerges as added-value technology to explore AD mouse brain as a whole, preserving tissue chemistry and structure, enabling the comparison of physiological vs. pathological states at the level of crucial disease targets. In-vivo translation will permit to monitor emerging therapeutic approaches and possibly shed new light on pathological mechanisms of neurodegenerative diseases.
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Affiliation(s)
- Lorenzo Massimi
- Istituto di Nanotecnologia, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Inna Bukreeva
- Istituto di Nanotecnologia, Consiglio Nazionale delle Ricerche, Rome, Italy; Dipartimento di Fisica, Università Sapienza, Rome, Italy
| | | | - Michela Fratini
- Istituto di Nanotecnologia, Consiglio Nazionale delle Ricerche, Rome, Italy; IRCCS Fondazione Santa Lucia, Rome, Italy
| | | | - Francesco Brun
- Istituto di Nanotecnologia, Consiglio Nazionale delle Ricerche, Rome, Italy
| | | | - Laura Maugeri
- Istituto di Nanotecnologia, Consiglio Nazionale delle Ricerche, Rome, Italy; IRCCS Fondazione Santa Lucia, Rome, Italy
| | | | - Peter Cloetens
- European Synchrotron Radiation Facility, Grenoble, France
| | - Nicola Pieroni
- Istituto di Nanotecnologia, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Fabio Fiordaliso
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | | | - Antonio Uccelli
- DINOGMI, Università degli Studi di Genova, Genoa, Italy; Ospedale Policlinico San Martino, Genoa, Italy
| | | | - Claudia Balducci
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy.
| | - Alessia Cedola
- Istituto di Nanotecnologia, Consiglio Nazionale delle Ricerche, Rome, Italy; Dipartimento di Fisica, Università Sapienza, Rome, Italy.
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28
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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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29
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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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30
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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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31
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Pichat J, Iglesias JE, Yousry T, Ourselin S, Modat M. A Survey of Methods for 3D Histology Reconstruction. Med Image Anal 2018; 46:73-105. [DOI: 10.1016/j.media.2018.02.004] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 02/02/2018] [Accepted: 02/14/2018] [Indexed: 02/08/2023]
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32
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Schmitz R, Krause J, Krech T, Rösch T. Virtual Endoscopy Based on 3-Dimensional Reconstruction of Histopathology Features of Endoscopic Resection Specimens. Gastroenterology 2018; 154:1234-1236.e4. [PMID: 29425925 DOI: 10.1053/j.gastro.2017.11.291] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 11/22/2017] [Accepted: 11/28/2017] [Indexed: 01/14/2023]
Affiliation(s)
- Rüdiger Schmitz
- Institute of Anatomy and Experimental Morphology, Center for Experimental Medicine, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Jenny Krause
- I. Department of Internal Medicine, Center for Internal Medicine, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Till Krech
- Institute of Pathology, Center for Diagnostics, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Thomas Rösch
- Department of Interdisciplinary Endoscopy, Center for Radiology and Endoscopy, University Hospital Hamburg-Eppendorf, Hamburg, Germany.
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33
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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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34
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Lundin EL, Stauber M, Papageorgiou P, Ehrbar M, Ghayor C, Weber FE, Tanner C, Goksel O. Automatic registration of 2D histological sections to 3D microCT volumes: Trabecular bone. Bone 2017; 105:173-183. [PMID: 28867374 DOI: 10.1016/j.bone.2017.08.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 08/23/2017] [Accepted: 08/23/2017] [Indexed: 11/30/2022]
Abstract
Histomorphometry and microCT are the two dominant imaging techniques to study bone structure and quality to evaluate repair, regeneration, and disease. These two methods are complementary; where histology provides highly resolved tissue properties on a cellular level in 2D, microCT provides spatial information of bone micro-structure in 3D. For this reason, both of these modalities are commonly used in bone studies. As it is not trivial to combine the images of these two modalities, the two methods are typically applied to different specimens within a study. However, we believe that applying both imaging modalities to the same specimen with a suitable fusion strategy may further strengthen the value of each modality. Therefore, we propose a registration method to align 2D histology slices with a 3D microCT volume, without any prior knowledge of the sectioning direction. In a preprocessing step, bone is extracted from both images. Then, we use a strategy for initializing potential locations, and an iterative approach for searching for an ideal fitting plane using Radon-based rigid transforms and feature-based affine alignments. The algorithm was tested and validated with simulated and real data. For the latter, microCT images of trabecular bone with 76 corresponding histological sections acquired from decalcified and calcified specimens were used. The registration resulted in 94.7% acceptable solutions as defined by a registration orientation error of less than 3°. Average registration accuracy of the acceptable results was 0.6°, leading to a target registration error for our method of 106.3μm, computed based on landmarks annotated by an observer. This corresponds roughly to 10pixels in the images; although, the relation to actual visible structures that provide the features to register, is arguably more relevant.
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Affiliation(s)
- Elin L Lundin
- Scanco Medical AG, Brüttisellen, Switzerland; Computer-assisted Applications in Medicine, ETH Zürich, Switzerland
| | | | | | - Martin Ehrbar
- Department of Obstetrics, University Hospital Zurich, Switzerland
| | - Chafik Ghayor
- Oral Biotechnology & Bioengineering, Center of Dentistry, University of Zurich, Switzerland
| | - Franz E Weber
- Oral Biotechnology & Bioengineering, Center of Dentistry, University of Zurich, Switzerland
| | - Christine Tanner
- Computer-assisted Applications in Medicine, ETH Zürich, Switzerland
| | - Orcun Goksel
- Computer-assisted Applications in Medicine, ETH Zürich, Switzerland
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35
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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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36
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Prinz JC. Melanocytes: Target Cells of an HLA-C*06:02-Restricted Autoimmune Response in Psoriasis. J Invest Dermatol 2017; 137:2053-2058. [PMID: 28941475 DOI: 10.1016/j.jid.2017.05.023] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 05/08/2017] [Accepted: 05/26/2017] [Indexed: 12/17/2022]
Abstract
HLA-C*06:02 is the main psoriasis risk allele. By the unbiased analysis of a Vα3S1/Vβ13S1 T-cell receptor from pathogenic psoriatic CD8+ T cells, we had recently proven that HLA-C*06:02 directs an autoimmune response against melanocytes through autoantigen presentation in psoriasis and identified ADAMTSL5 as a melanocyte autoantigen. We concluded that psoriasis is based on a melanocyte-specific immune response and that HLA-C*06:02 may predispose to psoriasis via this newly identified autoimmune pathway. Understanding this pathway, however, requires more detailed explanation. It is based on the fact that an HLA class I-restricted autoreactive CD8+ T-cell response must be directed against a particular target cell type, because HLA class I molecules present peptide antigens generated from cytoplasmic (i.e., intracellular) proteins. This review summarizes the findings on the melanocyte-specific autoimmune response in the context of the immune mechanisms related to HLA function and T-cell receptor-antigen recognition. Identifying melanocytes as target cells of the psoriatic immune response now explains psoriasis as a primary autoimmune skin disease.
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Affiliation(s)
- Jörg Christoph Prinz
- Department of Dermatology, University Clinics, Ludwig Maximilian University of Munich, Munich, Germany.
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37
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Vilar AB, Dos Santos TMP, Machado AS, Oliveira DF, Azeredo SR, Lopes RT. X-ray microtomography system for small and light samples using a flat panel detector. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2017; 88:105112. [PMID: 29092468 DOI: 10.1063/1.4996368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A low-cost system able to perform microtomography of samples such as teeth, insects, or other small materials and low atomic numbers is presented. For this, a small flat panel type sensor was used. The process of characterization of the detector is detailed, as well as its main characteristics. The electromechanical control and the software used are also described. The advantages, some limitations, and comparisons with commercial systems are presented along with some three-dimensional volumetric reconstruction of different materials that served as samples during the development of the system.
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Affiliation(s)
- A B Vilar
- Nuclear Engineering Program, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - T M P Dos Santos
- Nuclear Engineering Program, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - A S Machado
- Federal Institute of Education, Science and Technology of Rio de Janeiro, Nilópolis, Brazil
| | - D F Oliveira
- Nuclear Engineering Program, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - S R Azeredo
- Nuclear Engineering Program, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - R T Lopes
- Nuclear Engineering Program, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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38
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Casero R, Siedlecka U, Jones ES, Gruscheski L, Gibb M, Schneider JE, Kohl P, Grau V. Transformation diffusion reconstruction of three-dimensional histology volumes from two-dimensional image stacks. Med Image Anal 2017; 38:184-204. [PMID: 28411458 PMCID: PMC5408912 DOI: 10.1016/j.media.2017.03.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 03/15/2017] [Accepted: 03/21/2017] [Indexed: 12/05/2022]
Abstract
A method for 3D reconstruction of serial 2D histology image stacks is proposed. Pre-alignment to an external pre-cut reference (blockface) prevents shape artifacts. Formulated as diffusion of transformations from each slice to its neighbors. Registrations replaced by much faster transformation operations.
Traditional histology is the gold standard for tissue studies, but it is intrinsically reliant on two-dimensional (2D) images. Study of volumetric tissue samples such as whole hearts produces a stack of misaligned and distorted 2D images that need to be reconstructed to recover a congruent volume with the original sample's shape. In this paper, we develop a mathematical framework called Transformation Diffusion (TD) for stack alignment refinement as a solution to the heat diffusion equation. This general framework does not require contour segmentation, is independent of the registration method used, and is trivially parallelizable. After the first stack sweep, we also replace registration operations by operations in the space of transformations, several orders of magnitude faster and less memory-consuming. Implementing TD with operations in the space of transformations produces our Transformation Diffusion Reconstruction (TDR) algorithm, applicable to general transformations that are closed under inversion and composition. In particular, we provide formulas for translation and affine transformations. We also propose an Approximated TDR (ATDR) algorithm that extends the same principles to tensor-product B-spline transformations. Using TDR and ATDR, we reconstruct a full mouse heart at pixel size 0.92 µm × 0.92 µm, cut 10 µm thick, spaced 20 µm (84G). Our algorithms employ only local information from transformations between neighboring slices, but the TD framework allows theoretical analysis of the refinement as applying a global Gaussian low-pass filter to the unknown stack misalignments. We also show that reconstruction without an external reference produces large shape artifacts in a cardiac specimen while still optimizing slice-to-slice alignment. To overcome this problem, we use a pre-cutting blockface imaging process previously developed by our group that takes advantage of Brewster's angle and a polarizer to capture the outline of only the topmost layer of wax in the block containing embedded tissue for histological sectioning.
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Affiliation(s)
- Ramón Casero
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford OX3 7DQ, UK.
| | - Urszula Siedlecka
- Heart Science Centre, National Lung and Heart Institute, Imperial College London, Harefield UB9 6JH, UK
| | - Elizabeth S Jones
- Heart Science Centre, National Lung and Heart Institute, Imperial College London, Harefield UB9 6JH, UK
| | - Lena Gruscheski
- Heart Science Centre, National Lung and Heart Institute, Imperial College London, Harefield UB9 6JH, UK
| | - Matthew Gibb
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford OX3 7DQ, UK
| | - Jürgen E Schneider
- BHF Experimental MR Unit, Division of Cardiovascular Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Peter Kohl
- Institute for Experimental Cardiovascular Medicine, University Heart Centre Freiburg - Bad Krozingen, School of Medicine, University of Freiburg, Elsässer Str 2Q, 79110 Freiburg, Germany
| | - Vicente Grau
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford OX3 7DQ, UK
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39
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Bidola P, Morgan K, Willner M, Fehringer A, Allner S, Prade F, Pfeiffer F, Achterhold K. Application of sensitive, high-resolution imaging at a commercial lab-based X-ray micro-CT system using propagation-based phase retrieval. J Microsc 2017; 266:211-220. [PMID: 28181677 DOI: 10.1111/jmi.12530] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 01/09/2017] [Accepted: 01/14/2017] [Indexed: 01/13/2023]
Abstract
Several dedicated commercial lab-based micro-computed tomography (μCT) systems exist, which provide high-resolution images of samples, with the capability to also deliver in-line phase contrast. X-ray phase contrast is particularly beneficial when visualizing very small features and weakly absorbing samples. The raw measured projections will include both phase and absorption effects. Extending our previous work that addressed the optimization of experimental conditions at the commercial ZEISS Xradia 500 Versa system, single-distance phase-contrast imaging is demonstrated on complex biological and material samples. From data captured at this system, we demonstrate extraction of the phase signal or the correction of the mixed image for the phase shift, and show how this procedure increases the contrast and removes artefacts. These high-quality images, measured without the use of a synchrotron X-ray source, demonstrate that highly sensitive, micrometre-resolution imaging of 3D volumes is widely accessible using commercially advanced laboratory devices.
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Affiliation(s)
- P Bidola
- Chair of Biomedical Physics, Department of Physics & Munich School of Bioengineering, Technical University of Munich, Garching, Germany
| | - K Morgan
- Chair of Biomedical Physics, Department of Physics & Munich School of Bioengineering, Technical University of Munich, Garching, Germany.,School of Physics and Astronomy, Monash University, Victoria, Australia
| | - M Willner
- Chair of Biomedical Physics, Department of Physics & Munich School of Bioengineering, Technical University of Munich, Garching, Germany.,MITOS GmbH, Garching, Germany
| | - A Fehringer
- Chair of Biomedical Physics, Department of Physics & Munich School of Bioengineering, Technical University of Munich, Garching, Germany
| | - S Allner
- Chair of Biomedical Physics, Department of Physics & Munich School of Bioengineering, Technical University of Munich, Garching, Germany
| | - F Prade
- Chair of Biomedical Physics, Department of Physics & Munich School of Bioengineering, Technical University of Munich, Garching, Germany
| | - F Pfeiffer
- Chair of Biomedical Physics, Department of Physics & Munich School of Bioengineering, Technical University of Munich, Garching, Germany.,Institute for Advanced Study, Technical University of Munich, Garching, Germany.,Department of Diagnostic and Interventional Radiology, Klinikum rechts der Isar, Technical University of Munich, 81675, München, Germany
| | - K Achterhold
- Chair of Biomedical Physics, Department of Physics & Munich School of Bioengineering, Technical University of Munich, Garching, Germany
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