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Yoshikawa AL, Omura T, Takahashi-Kanemitsu A, Susaki EA. Blueprints from plane to space: outlook of next-generation three-dimensional histopathology. Cancer Sci 2024; 115:1029-1038. [PMID: 38316137 PMCID: PMC11006986 DOI: 10.1111/cas.16095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 01/02/2024] [Accepted: 01/16/2024] [Indexed: 02/07/2024] Open
Abstract
Here, we summarize the literature relevant to recent advances in three-dimensional (3D) histopathology in relation to clinical oncology, highlighting serial sectioning, tissue clearing, light-sheet microscopy, and digital image analysis with artificial intelligence. We look forward to a future where 3D histopathology expands our understanding of human pathophysiology and improves patient care through cross-disciplinary collaboration and innovation.
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Affiliation(s)
- Akira Leon Yoshikawa
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Department of Pathology Informatics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
- Department of Pathology, Kameda Medical Center, Chiba, Japan
| | - Takaki Omura
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Atsushi Takahashi-Kanemitsu
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Etsuo A Susaki
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
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2
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Fulton KA, Watkins PV, Briggman KL. GAUSS-EM, guided accumulation of ultrathin serial sections with a static magnetic field for volume electron microscopy. Cell Rep Methods 2024; 4:100720. [PMID: 38452770 PMCID: PMC10985227 DOI: 10.1016/j.crmeth.2024.100720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/30/2023] [Accepted: 02/09/2024] [Indexed: 03/09/2024]
Abstract
Serial sectioning electron microscopy (EM) of millimeter-scale three-dimensional (3D) anatomical volumes requires the collection of thousands of ultrathin sections. Here, we report a high-throughput automated approach, GAUSS-EM (guided accumulation of ultrathin serial sections-EM), utilizing a static magnetic field to collect and densely pack thousands of sections onto individual silicon wafers. The method is capable of sectioning hundreds of microns of tissue per day at section thicknesses down to 35 nm. Relative to other automated volume EM approaches, GAUSS-EM democratizes the ability to collect large 3D EM volumes because it is simple and inexpensive to implement. We present two exemplar EM volumes of a zebrafish eye and mouse olfactory bulb collected with the method.
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Affiliation(s)
- Kara A Fulton
- Department of Computational Neuroethology, Max Planck Institute for Neurobiology of Behavior - caesar, 53175 Bonn, NRW, Germany
| | - Paul V Watkins
- Department of Computational Neuroethology, Max Planck Institute for Neurobiology of Behavior - caesar, 53175 Bonn, NRW, Germany
| | - Kevin L Briggman
- Department of Computational Neuroethology, Max Planck Institute for Neurobiology of Behavior - caesar, 53175 Bonn, NRW, Germany.
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3
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Andrews AJ, Orton D, Onar V, Addis P, Tinti F, Alexander M. Isotopic life-history signatures are retained in modern and ancient Atlantic bluefin tuna vertebrae. J Fish Biol 2023. [PMID: 37185985 DOI: 10.1111/jfb.15417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 04/23/2023] [Indexed: 05/17/2023]
Abstract
Isotopic, tagging and diet studies of modern-day teleosts lack the ability to contextualise life-histories and trophic dynamics with a historical perspective, when exploitation rates were lower and climatic conditions differed. Isotopic analysis of vertebrae, the most plentiful hard-part in archaeological and museum collections, can potentially fill this data-gap. Chemical signatures of habitat and diet use during growth are retained by vertebrae during bone formation. However, to fulfil their potential to reveal life-history and trophic dynamics, we need a better understanding of the time-frame recorded by vertebrae, currently lacking due to a poor understanding of fish bone remodelling. To address this issue, we serially-sectioned four vertebral centra of the highly migratory Atlantic bluefin tuna (Thunnus thynnus; BFT) captured off Sardinia (Italy) and analysed their isotopic composition. We show how carbon (δ13 C), nitrogen (δ15 N) and sulfur (δ34 S) isotope values can vary significantly across BFT vertebrae growth-axes, revealing patterning in dietary life-histories. Further, we find similar patterns are revealed through incremental isotopic analysis of inner and outer vertebrae centra samples from thirteen archaeological BFT vertebrae dating between the 9th -13th century CE. Our results indicate that multi-year foraging signatures are retained in vertebrae and allow for the study of life-histories in both modern and paleo-environments. These novel methods can be extended across teleost taxa owing to their potential to inform management and conservation on how teleost trophic dynamics change over time and what their long-term environmental, ecological, and anthropological drivers are.
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Affiliation(s)
- Adam J Andrews
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Campus of Ravenna, Ravenna, Italy
| | - David Orton
- BioArCh, Department of Archaeology, University of York, York, U.K
| | - Vedat Onar
- Osteoarchaeology Practice and Research Centre and Faculty of Veterinary Medicine, Istanbul University-Cerrahpaşa, Istanbul, Turkey
| | - Piero Addis
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Sardinia, Italy
| | - Fausto Tinti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Campus of Ravenna, Ravenna, Italy
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4
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Yang J, Chang S, Chen IA, Kura S, Rosen GA, Saltiel NA, Huber BR, Varadarajan D, Balbastre Y, Magnain C, Chen SC, Fischl B, McKee AC, Boas DA, Wang H. Volumetric Characterization of Microvasculature in Ex Vivo Human Brain Samples By Serial Sectioning Optical Coherence Tomography. IEEE Trans Biomed Eng 2022; 69:3645-3656. [PMID: 35560084 PMCID: PMC9888394 DOI: 10.1109/tbme.2022.3175072] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
OBJECTIVE Serial sectioning optical coherence tomography (OCT) enables accurate volumetric reconstruction of several cubic centimeters of human brain samples. We aimed to identify anatomical features of the ex vivo human brain, such as intraparenchymal blood vessels and axonal fiber bundles, from the OCT data in 3D, using intrinsic optical contrast. METHODS We developed an automatic processing pipeline to enable characterization of the intraparenchymal microvascular network in human brain samples. RESULTS We demonstrated the automatic extraction of the vessels down to a 20 μm in diameter using a filtering strategy followed by a graphing representation and characterization of the geometrical properties of microvascular network in 3D. We also showed the ability to extend this processing strategy to extract axonal fiber bundles from the volumetric OCT image. CONCLUSION This method provides a viable tool for quantitative characterization of volumetric microvascular network as well as the axonal bundle properties in normal and pathological tissues of the ex vivo human brain.
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5
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Mehra A, Howes B, Manzuk R, Spatzier A, Samuels BM, Maloof AC. A Novel Technique for Producing Three-Dimensional Data Using Serial Sectioning and Semi-Automatic Image Classification. Microsc Microanal 2022; 28:1-16. [PMID: 36268627 DOI: 10.1017/s1431927622012442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The three-dimensional characterization of internal features, via metrics such as orientation, porosity, and connectivity, is important to a wide variety of scientific questions. Many spatial and morphological metrics only can be measured accurately through direct in situ three-dimensional observations of large (i.e., big enough to be statistically representative) volumes. For samples that lack material contrast between phases, serial grinding and imaging—which relies solely on color and textural characteristics to differentiate features—is a viable option for extracting such information. Here, we present the Grinding, Imaging, Reconstruction Instrument (GIRI), which automatically serially grinds and photographs centimeter-scale samples at micron resolution. Although the technique is destructive, GIRI produces an archival digital image stack. This digital image stack is run through a supervised machine-learning-based image processing technique that quickly and accurately segments data into predefined classes. These classified data then can be loaded into three-dimensional visualization software for measurement. We share three case studies to illustrate how GIRI can address questions with a significant morphological component for which two-dimensional or small-volume three-dimensional measurements are inadequate. The analyzed metrics include: the morphologies of objects and pores in a granular material, the bulk mineralogy of polyminerallic solids, and measurements of the internal angles and symmetry of crystals.
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Affiliation(s)
- Akshay Mehra
- Department of Geosciences, Princeton University, Princeton, NJ 08544, USA
- Department of Earth Sciences, Dartmouth College, 225 Fairchild Hall, Hanover, NH 03755, USA
| | - Bolton Howes
- Department of Geosciences, Princeton University, Princeton, NJ 08544, USA
| | - Ryan Manzuk
- Department of Geosciences, Princeton University, Princeton, NJ 08544, USA
| | - Alex Spatzier
- Department of Geosciences, Princeton University, Princeton, NJ 08544, USA
- Alex Spatzier Architects, Oakland, CA 94608, USA
| | | | - Adam C Maloof
- Department of Geosciences, Princeton University, Princeton, NJ 08544, USA
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6
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Turegano-Lopez M, Santuy A, Kastanauskaite A, Rodriguez JR, DeFelipe J, Merchan-Perez A. Single-Neuron Labeling in Fixed Tissue and Targeted Volume Electron Microscopy. Front Neuroanat 2022; 16:852057. [PMID: 35528948 PMCID: PMC9070053 DOI: 10.3389/fnana.2022.852057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/15/2022] [Indexed: 11/16/2022] Open
Abstract
The structural complexity of nervous tissue makes it very difficult to unravel the connectivity between neural elements at different scales. Numerous methods are available to trace long-range projections at the light microscopic level, and to identify the actual synaptic connections at the electron microscopic level. However, correlating mesoscopic and nanoscopic scales in the same cell, cell population or brain region is a problematic, laborious and technically demanding task. Here we present an effective method for the 3D reconstruction of labeled subcellular structures at the ultrastructural level, after single-neuron labeling in fixed tissue. The brain is fixed by intracardial perfusion of aldehydes and thick vibratome sections (250 μm) are obtained. Single cells in these vibratome sections are intracellularly injected with horseradish peroxidase (HRP), so that the cell body and its processes can be identified. The thick sections are later flat-embedded in epoxy resin and re-sectioned into a series of thinner (7 μm) sections. The sections containing the regions of interest of the labeled cells are then imaged with automated focused ion beam milling and scanning electron microscopy (FIB-SEM), acquiring long series of high-resolution images that can be reconstructed, visualized, and analyzed in 3D. With this methodology, we can accurately select any cellular segment at the light microscopic level (e.g., proximal, intermediate or distal dendrites, collateral branches, axonal segments, etc.) and analyze its synaptic connections at the electron microscopic level, along with other ultrastructural features. Thus, this method not only facilitates the mapping of the synaptic connectivity of single-labeled neurons, but also the analysis of the surrounding neuropil. Since the labeled processes can be located at different layers or subregions, this method can also be used to obtain data on the differences in local synaptic organization that may exist at different portions of the labeled neurons.
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Affiliation(s)
- Marta Turegano-Lopez
- Laboratorio Cajal de Circuitos Corticales, Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Spain
- Ph.D. Program in Neuroscience, Universidad Autónoma de Madrid – Instituto Cajal, Madrid, Spain
| | - Andrea Santuy
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Asta Kastanauskaite
- Laboratorio Cajal de Circuitos Corticales, Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Spain
| | - Jose-Rodrigo Rodriguez
- Laboratorio Cajal de Circuitos Corticales, Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Spain
- Instituto Cajal, Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), ISCIII, Madrid, Spain
| | - Javier DeFelipe
- Laboratorio Cajal de Circuitos Corticales, Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Spain
- Instituto Cajal, Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), ISCIII, Madrid, Spain
| | - Angel Merchan-Perez
- Laboratorio Cajal de Circuitos Corticales, Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), ISCIII, Madrid, Spain
- Departamento de Arquitectura y Tecnología de Sistemas Informáticos, Universidad Politécnica de Madrid, Madrid, Spain
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7
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Lindow N, Brünig FN, Dercksen VJ, Fabig G, Kiewisz R, Redemann S, Müller-Reichert T, Prohaska S, Baum D. Semi-automatic stitching of filamentous structures in image stacks from serial-section electron tomography. J Microsc 2021; 284:25-44. [PMID: 34110027 DOI: 10.1111/jmi.13039] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/11/2021] [Accepted: 06/02/2021] [Indexed: 11/30/2022]
Abstract
We present a software-assisted workflow for the alignment and matching of filamentous structures across a three-dimensional (3D) stack of serial images. This is achieved by combining automatic methods, visual validation, and interactive correction. After the computation of an initial automatic matching, the user can continuously improve the result by interactively correcting landmarks or matches of filaments. Supported by a visual quality assessment of regions that have been already inspected, this allows a trade-off between quality and manual labour. The software tool was developed in an interdisciplinary collaboration between computer scientists and cell biologists to investigate cell division by quantitative 3D analysis of microtubules (MTs) in both mitotic and meiotic spindles. For this, each spindle is cut into a series of semi-thick physical sections, of which electron tomograms are acquired. The serial tomograms are then stitched and non-rigidly aligned to allow tracing and connecting of MTs across tomogram boundaries. In practice, automatic stitching alone provides only an incomplete solution, because large physical distortions and a low signal-to-noise ratio often cause experimental difficulties. To derive 3D models of spindles despite dealing with imperfect data related to sample preparation and subsequent data collection, semi-automatic validation and correction is required to remove stitching mistakes. However, due to the large number of MTs in spindles (up to 30k) and their resulting dense spatial arrangement, a naive inspection of each MT is too time-consuming. Furthermore, an interactive visualisation of the full image stack is hampered by the size of the data (up to 100 GB). Here, we present a specialised, interactive, semi-automatic solution that considers all requirements for large-scale stitching of filamentous structures in serial-section image stacks. To the best of our knowledge, it is the only currently available tool which is able to process data of the type and size presented here. The key to our solution is a careful design of the visualisation and interaction tools for each processing step to guarantee real-time response, and an optimised workflow that efficiently guides the user through datasets. The final solution presented here is the result of an iterative process with tight feedback loops between the involved computer scientists and cell biologists. LAY DESCRIPTION: Electron tomography of biological samples is used for a three-dimensional (3D) reconstruction of filamentous structures, such as microtubules (MTs) in mitotic and meiotic spindles. Large-scale electron tomography can be applied to increase the reconstructed volume for the visualisation of full spindles. For this, each spindle is cut into a series of semi-thick physical sections, from which electron tomograms are acquired. The serial tomograms are then stitched and non-rigidly aligned to allow tracing and connecting of MTs across tomogram boundaries. Previously, we presented fully automatic approaches for this 3D reconstruction pipeline. However, large volumes often suffer from imperfections (ie physical distortions) caused by the image acquisition process, making it difficult to apply fully automatic approaches for matching and stitching of numerous tomograms. Therefore, we developed an interactive, semi-automatic solution that considers all requirements for large-scale stitching of microtubules in image stacks of consecutive sections. We achieved this by combining automatic methods, visual validation and interactive error correction, thus allowing the user to continuously improve the result by interactively correcting landmarks or matches of filaments. We present large-scale reconstructions of spindles in which the automatic workflow failed and where different steps of manual corrections were needed. Our approach is also applicable to other biological samples showing 3D distributions of MTs in a number of different cellular contexts.
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Affiliation(s)
- Norbert Lindow
- Department of Visual and Data-Centric Computing, Zuse Institute Berlin, Berlin, Germany
| | - Florian N Brünig
- Department of Visual and Data-Centric Computing, Zuse Institute Berlin, Berlin, Germany
| | - Vincent J Dercksen
- Department of Visual and Data-Centric Computing, Zuse Institute Berlin, Berlin, Germany
| | - Gunar Fabig
- Experimental Center, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Robert Kiewisz
- Experimental Center, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Stefanie Redemann
- School of Medicine, Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia.,School of Medicine, Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia.,School of Medicine, Department of Cell Biology, University of Virginia, Charlottesville, Virginia
| | - Thomas Müller-Reichert
- Experimental Center, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Steffen Prohaska
- Department of Visual and Data-Centric Computing, Zuse Institute Berlin, Berlin, Germany
| | - Daniel Baum
- Department of Visual and Data-Centric Computing, Zuse Institute Berlin, Berlin, Germany
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8
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Gbur JL, Kelley R, Lewandowski JJ. Plasma Focused Ion Beam Serial Sectioning as a Technique to Characterize Nonmetallic Inclusions in Superelastic Nitinol Fine Wires. Microsc Microanal 2020; 26:1088-1099. [PMID: 33289465 DOI: 10.1017/s1431927620024617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Nonmetallic inclusion (NMI) populations in superelastic (SE) Nitinol fine wires (<140 μm in diameter) were investigated by combining plasma focused ion beam (PFIB) serial sectioning with scanning electron microscopy (SEM). High purity (HP)—lower oxygen content and standard purity (SP)—higher oxygen content Nitinol wires were sectioned and imaged. The three-dimensional (3D) reconstructions provided more complete connectivity of NMIs and pores as well as information about the distribution of the features within the wire volume that is not possible with traditional two-dimensional (2D) imaging techniques. NMIs were present alone and with pores in the leading and/or trailing edges of the inclusions, in addition to stringers (i.e., fractured, elongated NMI, and intermixed with pores adjacent to each other), all of which were parallel to the wire drawing axis. The area percentages for the NMIs were 0.01% (HP Nitinol) and 0.04% (SP Nitinol), while the volume percentages measured 0.09% (HP Nitinol) and 0.47% (SP Nitinol). The combined PFIB-SEM serial sectioning approach provided the requisite resolution necessary to distinguish between NMIs and pores at micron and submicron sizes. Information gathered from this technique can be used to better inform models and predictions for fatigue lifetimes based on statistical analyses of these feature populations.
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Affiliation(s)
- Janet L Gbur
- Department of Materials Science and Engineering, Case Western Reserve University, Cleveland, OH44106, USA
| | - Ronald Kelley
- Materials & Structural Analysis, Thermo Fisher Scientific, Hillsboro, OR97124, USA
| | - John J Lewandowski
- Department of Materials Science and Engineering, Case Western Reserve University, Cleveland, OH44106, USA
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9
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Lee TJ, Yip MC, Kumar A, Lewallen CF, Bumbarger DJ, Reid RC, Forest CR. Capillary-Based and Stokes-Based Trapping of Serial Sections for Scalable 3D-EM Connectomics. eNeuro 2020; 7:ENEURO. [PMID: 32094293 DOI: 10.1523/ENEURO.0328-19.2019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 12/17/2019] [Accepted: 12/18/2019] [Indexed: 11/23/2022] Open
Abstract
Serial section electron microscopy (ssEM), a technique where volumes of tissue can be anatomically reconstructed by imaging consecutive tissue slices, has proven to be a powerful tool for the investigation of brain anatomy. Between the process of cutting the slices, or “sections,” and imaging them, however, handling 10°−106 delicate sections remains a bottleneck in ssEM, especially for batches in the “mesoscale” regime, i.e., 102–103 sections. We present a tissue section handling device that transports and positions sections, accurately and repeatability, for automated, robotic section pick-up and placement onto an imaging substrate. The device interfaces with a conventional ultramicrotomy diamond knife, accomplishing in-line, exact-constraint trapping of sections with 100-μm repeatability. An associated mathematical model includes capillary-based and Stokes-based forces, accurately describing observed behavior and fundamentally extends the modeling of water-air interface forces. Using the device, we demonstrate and describe the limits of reliable handling of hundreds of slices onto a variety of electron and light microscopy substrates without significant defects (n = 8 datasets composed of 126 serial sections in an automated fashion with an average loss rate and throughput of 0.50% and 63 s/section, respectively. In total, this work represents an automated mesoscale serial sectioning system for scalable 3D-EM connectomics.
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10
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Abstract
This article is a Commentary on https://doi.org/10.1111/nph.16219 .
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Affiliation(s)
| | - Klara Voggeneder
- Institute of BotanyUniversity of Natural Resources and Life SciencesVienna1180Austria
| | - Danny Tholen
- Institute of BotanyUniversity of Natural Resources and Life SciencesVienna1180Austria
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11
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Mavlyutov TA, Yang H, Epstein ML, Ruoho AE, Yang J, Guo LW. APEX2-enhanced electron microscopy distinguishes sigma-1 receptor localization in the nucleoplasmic reticulum. Oncotarget 2017; 8:51317-51330. [PMID: 28881650 PMCID: PMC5584251 DOI: 10.18632/oncotarget.17906] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 05/04/2017] [Indexed: 12/03/2022] Open
Abstract
The sigma-1 receptor (Sig1R) is an endoplasmic reticulum chaperonin that is attracting tremendous interest as a potential anti-neurodegenerative target. While this membrane protein is known to reside in the inner nuclear envelope (NE) and influences transcription, apparent Sig1R presence in the nucleoplasm is often observed, seemingly contradicting its NE localization. We addressed this confounding issue by applying an antibody-free approach of electron microscopy (EM) to define Sig1R nuclear localization. We expressed APEX2 peroxidase fused to Sig1R-GFP in a Sig1R-null NSC34 neuronal cell line generated with CRISPR-Cas9. APEX2-catalyzed gold/silver precipitation markedly improved EM clarity and confirmed an apparent intra-nuclear presence of Sig1R. However, serial sectioning combined with APEX2-enhanced EM revealed that Sig1R actually resided in the nucleoplasmic reticulum (NR), a specialized nuclear compartment formed via NE invagination into the nucleoplasm. NR cross-sections also indicated Sig1R in ring-shaped NR membranes. Thus, this study distinguishes Sig1R in the NR which could otherwise appear localized in the nucleoplasm if detected with low-resolution methods. Our finding is important for uncovering potential Sig1R regulations in the nucleus.
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Affiliation(s)
- Timur A Mavlyutov
- Department of Surgery, Wisconsin Institute for Medical Research, University of Wisconsin, Madison, WI 53705, USA
| | - Huan Yang
- Department of Surgery, Wisconsin Institute for Medical Research, University of Wisconsin, Madison, WI 53705, USA
| | - Miles L Epstein
- Department of Neuroscience, University of Wisconsin, Madison, WI 53706, USA
| | - Arnold E Ruoho
- Department of Neuroscience, University of Wisconsin, Madison, WI 53706, USA
| | - Jay Yang
- Department of Anesthesiology, Wisconsin Institute for Medical Research, University of Wisconsin, Madison, WI 53705, USA
| | - Lian-Wang Guo
- Department of Surgery, Wisconsin Institute for Medical Research, University of Wisconsin, Madison, WI 53705, USA.,McPherson Eye Research Institute, University of Wisconsin, Madison, WI 53705, USA.,Department of Surgery, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA.,Department of Physiology and Cell Biology, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA
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12
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Ramani P, Krithika C, Ananthalakshmi R, Singaram M, Jagdish P, Janardhanan S, Jeevakarunyam S. Verrucoid Variant of Invasive Squamous Cell Carcinoma in Oral Submucous Fibrosis: A Clinicopathological Challenge. Cureus 2016; 8:e862. [PMID: 28361010 PMCID: PMC5362275 DOI: 10.7759/cureus.862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Verrucous carcinoma (VC) is an exophytic, low-grade, well-differentiated variant of squamous cell carcinoma. It is described as a lesion appearing in the sixth or seventh decade of life that has minimal aggressive potential and, in long-standing cases, has been shown to transform into squamous cell carcinoma. Oral submucous fibrosis (OSMF) is a potentially malignant disorder, and about one-third of the affected population develop oral squamous cell carcinoma. The histopathological diagnosis of verrucous carcinoma is challenging, and the interpretation of early squamous cell carcinoma requires immense experience. Here we present a rare case of a 24-year-old male with OSMF transforming to verrucous carcinoma with invasive squamous cell carcinoma. Even though the case had a straightforward clinical diagnosis, the serial sectioning done for pathological diagnosis disclosed the squamous cell carcinoma.
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Affiliation(s)
- Priya Ramani
- Department of Oral Medicine and Radiology, Thai Moogambigai Dental College and Hospital
| | - C Krithika
- Department of Oral Medicine and Radiology, Thai Moogambigai Dental College and Hospital
| | - R Ananthalakshmi
- Department of Oral Pathology, Thai Moogambigai Dental College and Hospital
| | - Mamta Singaram
- Department of Oral Medicine and Radiology, Thai Moogambigai Dental College and Hospital
| | - Praveena Jagdish
- Department of Oral Medicine and Radiology, Thai Moogambigai Dental College and Hospital
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Dhawan I, Sandhu SV, Bhandari R, Sood N, Bhullar RK, Sethi N. Detection of cervical lymph node micrometastasis and isolated tumor cells in oral squamous cell carcinoma using immunohistochemistry and serial sectioning. J Oral Maxillofac Pathol 2016; 20:436-444. [PMID: 27721609 PMCID: PMC5051292 DOI: 10.4103/0973-029x.190946] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Accepted: 08/16/2016] [Indexed: 01/09/2023] Open
Abstract
INTRODUCTION Oral squamous cell carcinoma (OSCC) comprises one of the largest subsets of cancers with a tendency for regional metastasis. Nodal status is a key prognostic indicator in patients with OSCC, particularly with N0 neck. Occult metastasis in the form of micrometastasis (MM) and isolated tumor cells (ITCs), often goes undetected by routine hematoxylin and eosin (H&E) examination using 1-2 sections for analysis. This limitation could be overcome by combining serial sectioning (SS) with immunohistochemistry (IHC) for the detection of MM and ITC. Pan-cytokeratin (pan-CK) (AE1/AE3) is particularly a useful marker to detect these deposits as their presence has resulted in varied interpretations and different applications of the tumor-node-metastasis system. OBJECTIVES The objective of the study was to identify a suitable method for detecting MM and ITC in lymph nodes (LNs) of OSCC by combining SS and IHC and to compare it with conventional H&E staining. MATERIALS AND METHODS This laboratory-based, prospective study was conducted on 133 LNs harnessed from ten patients treated with radical neck dissection for primary OSCC. The LNs were subjected to SS at 100 μm intervals. The sections were stained with routine H&E staining, pan-CK and analyzed for MM and ITC according to criteria laid by Hermanek et al. STATISTICAL ANALYSIS The obtained data were subjected to statistical analysis using Chi-square test. RESULTS The application of combination of SS and IHC using pan-CK (AE1/AE3) in our study revealed the presence of MM and ITC in 2.25% of the LNs diagnosed as negative on routine H&E examination. The detection of these occult metastatic deposits resulted in upstaging of 33.33% of the patients. CONCLUSION In the view of crucial role of occult LN metastasis in prognosis and survival of OSCC patients with N0 neck, diagnostic tools such as IHC staining, particularly with pan-CK (AE1/AE3), combined with SS should be preferred over conventional methods as they result in upstaging, thus sparing the low-risk patients the morbidity of unnecessary treatment.
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Affiliation(s)
- Isha Dhawan
- Department of Oral and Maxillofacial Pathology, Genesis Institute of Dental Sciences and Research, Ferozepur, Punjab, India
| | - Simarpreet V Sandhu
- Department of Oral and Maxillofacial Pathology, Genesis Institute of Dental Sciences and Research, Ferozepur, Punjab, India
| | - Rajat Bhandari
- Department of Oral and Maxillofacial Pathology, Genesis Institute of Dental Sciences and Research, Ferozepur, Punjab, India
| | - Neena Sood
- Department of Pathology, Dayanand Medical College and Hospital, Ludhiana, Punjab, India
| | - Ramanpreet Kaur Bhullar
- Department of Oral and Maxillofacial Pathology, Desh Bhagat Dental College and Hospital, Muktsar, Punjab, India
| | - Neerja Sethi
- Department of Oral and Maxillofacial Pathology, Genesis Institute of Dental Sciences and Research, Ferozepur, Punjab, India
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Romero-Brey I, Bartenschlager R. Viral Infection at High Magnification: 3D Electron Microscopy Methods to Analyze the Architecture of Infected Cells. Viruses 2015; 7:6316-45. [PMID: 26633469 DOI: 10.3390/v7122940] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 10/16/2015] [Accepted: 11/16/2015] [Indexed: 02/06/2023] Open
Abstract
As obligate intracellular parasites, viruses need to hijack their cellular hosts and reprogram their machineries in order to replicate their genomes and produce new virions. For the direct visualization of the different steps of a viral life cycle (attachment, entry, replication, assembly and egress) electron microscopy (EM) methods are extremely helpful. While conventional EM has given important information about virus-host cell interactions, the development of three-dimensional EM (3D-EM) approaches provides unprecedented insights into how viruses remodel the intracellular architecture of the host cell. During the last years several 3D-EM methods have been developed. Here we will provide a description of the main approaches and examples of innovative applications.
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Yio MHN, Mac MJ, Wong HS, Buenfeld NR. 3D imaging of cement-based materials at submicron resolution by combining laser scanning confocal microscopy with serial sectioning. J Microsc 2015; 258:151-69. [PMID: 25651933 DOI: 10.1111/jmi.12228] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 12/30/2014] [Indexed: 12/01/2022]
Abstract
In this paper, we present a new method to reconstruct large volumes of nontransparent porous materials at submicron resolution. The proposed method combines fluorescence laser scanning confocal microscopy with serial sectioning to produce a series of overlapping confocal z-stacks, which are then aligned and stitched based on phase correlation. The method can be extended in the XY plane to further increase the overall image volume. Resolution of the reconstructed image volume does not degrade with increase in sample size. We have used the method to image cementitious materials, hardened cement paste and concrete and the results obtained show that the method is reliable. Possible applications of the method such as three-dimensional characterization of the pores and microcracks in hardened concrete, three-dimensional particle shape characterization of cementitious materials and three-dimensional characterization of other porous materials such as rocks and bioceramics are discussed.
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Affiliation(s)
- M H N Yio
- Concrete Durability Group, Department of Civil and Environmental Engineering, Imperial College London, UK
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Abstract
Ultrastructural analyses with electron microscopy have provided indispensable information to understand physiology and pathology of the nervous system. Recent advancement in imaging methodology paved the way for complete reconstruction of the neuronal connection map in the central nervous system, which is termed 'connectome' and would provide key insights to understand the functions of the brain. The critical advancement includes serial ultrastructural observation with scanning electron microscopy (SEM) instead of conventional serial sectioning transmission electron microscopy along with specific tissue preparation methods to increase heavy metal deposition for efficient SEM imaging. The advanced imaging methods using SEM have distinct advantages and disadvantages in multiple aspects, such as resolution and imaging speed, and should be selected depending on the observation conditions, such as target tissue sizes, required spatial resolution and necessity for re-observation. Dealing with the huge dataset remained to be a major obstacle, and automation in segmentation and 3D reconstruction would be critical to understand neuronal circuits in a larger volume of the brain. Future improvement in acquisition and analyses of the morphological data obtained with the advanced SEM imaging is awaited to elucidate the significance of whole connectome as the structural basis of the consciousness, intelligence and memory of a subject.
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Affiliation(s)
- Nobuhiko Ohno
- Department of Anatomy and Molecular Histology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 1110 Shimokato, Chuo city, Yamanashi 409-3898, Japan
| | - Mitsuhiko Katoh
- Department of Anatomy and Molecular Histology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 1110 Shimokato, Chuo city, Yamanashi 409-3898, Japan
| | - Yurika Saitoh
- Department of Anatomy and Molecular Histology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 1110 Shimokato, Chuo city, Yamanashi 409-3898, Japan
| | - Sei Saitoh
- Department of Anatomy and Molecular Histology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 1110 Shimokato, Chuo city, Yamanashi 409-3898, Japan
| | - Shinichi Ohno
- Department of Anatomy and Molecular Histology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 1110 Shimokato, Chuo city, Yamanashi 409-3898, Japan
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