1
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Habermann S, Gerken LRH, Kociak M, Monachon C, Kissling VM, Gogos A, Herrmann IK. Cathodoluminescent and Characteristic X-Ray-Emissive Rare-Earth-Doped Core/Shell Protein Labels for Spectromicroscopic Analysis of Cell Surface Receptors. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2404309. [PMID: 39246186 DOI: 10.1002/smll.202404309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 08/20/2024] [Indexed: 09/10/2024]
Abstract
Understanding the localization and the interactions of biomolecules at the nanoscale and in the cellular context remains challenging. Electron microscopy (EM), unlike light-based microscopy, gives access to the cellular ultrastructure yet results in grey-scale images and averts unambiguous (co-)localization of biomolecules. Multimodal nanoparticle-based protein labels for correlative cathodoluminescence electron microscopy (CCLEM) and energy-dispersive X-ray spectromicroscopy (EDX-SM) are presented. The single-particle STEM-cathodoluminescence (CL) and characteristic X-ray emissivity of sub-20 nm lanthanide-doped nanoparticles are exploited as unique spectral fingerprints for precise label localization and identification. To maximize the nanoparticle brightness, lanthanides are incorporated in a low-phonon host lattice and separated from the environment using a passivating shell. The core/shell nanoparticles are then functionalized with either folic (terbium-doped) or caffeic acid (europium-doped). Their potential for (protein-)labeling is successfully demonstrated using HeLa cells expressing different surface receptors that bind to folic or caffeic acid, respectively. Both particle populations show single-particle CL emission along with a distinctive energy-dispersive X-ray signal, with the latter enabling color-based localization of receptors within swift imaging times well below 2 min perμ m $\umu\text{m}$ 2 while offering high resolution with a pixel size of 2.78 nm. Taken together, these results open a route to multi-color labeling based on electron spectromicroscopy.
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Affiliation(s)
- Sebastian Habermann
- Nanoparticle Systems Engineering Laboratory, Institute of Energy and Process Engineering, Department of Mechanical and Process Engineering, ETH Zurich, Sonneggstrasse 3, 8092, Zurich, Switzerland
- Laboratory for Particles Biology Interactions, Department Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, 9014, St. Gallen, Switzerland
| | - Lukas R H Gerken
- Nanoparticle Systems Engineering Laboratory, Institute of Energy and Process Engineering, Department of Mechanical and Process Engineering, ETH Zurich, Sonneggstrasse 3, 8092, Zurich, Switzerland
- Laboratory for Particles Biology Interactions, Department Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, 9014, St. Gallen, Switzerland
| | - Mathieu Kociak
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, Orsay, 91405, France
| | | | - Vera M Kissling
- Laboratory for Particles Biology Interactions, Department Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, 9014, St. Gallen, Switzerland
| | - Alexander Gogos
- Nanoparticle Systems Engineering Laboratory, Institute of Energy and Process Engineering, Department of Mechanical and Process Engineering, ETH Zurich, Sonneggstrasse 3, 8092, Zurich, Switzerland
- Laboratory for Particles Biology Interactions, Department Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, 9014, St. Gallen, Switzerland
| | - Inge K Herrmann
- Nanoparticle Systems Engineering Laboratory, Institute of Energy and Process Engineering, Department of Mechanical and Process Engineering, ETH Zurich, Sonneggstrasse 3, 8092, Zurich, Switzerland
- Laboratory for Particles Biology Interactions, Department Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, 9014, St. Gallen, Switzerland
- The Ingenuity Lab, University Hospital Balgrist, Balgrist Campus, Forchstrasse 340, 8008, Zurich, Switzerland
- Faculty of Medicine, University of Zurich, Rämistrasse 74, 8006, Zurich, Switzerland
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2
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Son R, Yamazawa K, Oguchi A, Suga M, Tamura M, Yanagita M, Murakawa Y, Kume S. Morphomics via next-generation electron microscopy. J Mol Cell Biol 2024; 15:mjad081. [PMID: 38148118 PMCID: PMC11167312 DOI: 10.1093/jmcb/mjad081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 10/02/2022] [Accepted: 12/23/2023] [Indexed: 12/28/2023] Open
Abstract
The living body is composed of innumerable fine and complex structures. Although these structures have been studied in the past, a vast amount of information pertaining to them still remains unknown. When attempting to observe these ultra-structures, the use of electron microscopy (EM) has become indispensable. However, conventional EM settings are limited to a narrow tissue area, which can bias observations. Recently, new trends in EM research have emerged, enabling coverage of far broader, nano-scale fields of view for two-dimensional wide areas and three-dimensional large volumes. Moreover, cutting-edge bioimage informatics conducted via deep learning has accelerated the quantification of complex morphological bioimages. Taken together, these technological and analytical advances have led to the comprehensive acquisition and quantification of cellular morphology, which now arises as a new omics science termed 'morphomics'.
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Affiliation(s)
- Raku Son
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Kenji Yamazawa
- Advanced Manufacturing Support Team, RIKEN Center for Advanced Photonics, Wako 351-0198, Japan
| | - Akiko Oguchi
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Mitsuo Suga
- Multimodal Microstructure Analysis Unit, RIKEN–JEOL Collaboration Center, Kobe 650-0047, Japan
| | - Masaru Tamura
- Technology and Development Team for Mouse Phenotype Analysis, RIKEN BioResource Research Center, Tsukuba 305-0074, Japan
| | - Motoko Yanagita
- Department of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto 606-8501, Japan
| | - Yasuhiro Murakawa
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto 606-8501, Japan
- IFOM—The FIRC Institute of Molecular Oncology, Milan 20139, Italy
| | - Satoshi Kume
- Laboratory for Pathophysiological and Health Science, RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
- Center for Health Science Innovation, Osaka City University, Osaka 530-0011, Japan
- Osaka Electro-Communication University, Neyagawa 572-8530, Japan
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3
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Aswath A, Alsahaf A, Giepmans BNG, Azzopardi G. Segmentation in large-scale cellular electron microscopy with deep learning: A literature survey. Med Image Anal 2023; 89:102920. [PMID: 37572414 DOI: 10.1016/j.media.2023.102920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 07/05/2023] [Accepted: 07/31/2023] [Indexed: 08/14/2023]
Abstract
Electron microscopy (EM) enables high-resolution imaging of tissues and cells based on 2D and 3D imaging techniques. Due to the laborious and time-consuming nature of manual segmentation of large-scale EM datasets, automated segmentation approaches are crucial. This review focuses on the progress of deep learning-based segmentation techniques in large-scale cellular EM throughout the last six years, during which significant progress has been made in both semantic and instance segmentation. A detailed account is given for the key datasets that contributed to the proliferation of deep learning in 2D and 3D EM segmentation. The review covers supervised, unsupervised, and self-supervised learning methods and examines how these algorithms were adapted to the task of segmenting cellular and sub-cellular structures in EM images. The special challenges posed by such images, like heterogeneity and spatial complexity, and the network architectures that overcame some of them are described. Moreover, an overview of the evaluation measures used to benchmark EM datasets in various segmentation tasks is provided. Finally, an outlook of current trends and future prospects of EM segmentation is given, especially with large-scale models and unlabeled images to learn generic features across EM datasets.
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Affiliation(s)
- Anusha Aswath
- Bernoulli Institute of Mathematics, Computer Science and Artificial Intelligence, University Groningen, Groningen, The Netherlands; Department of Biomedical Sciences of Cells and Systems, University Groningen, University Medical Center Groningen, Groningen, The Netherlands.
| | - Ahmad Alsahaf
- Department of Biomedical Sciences of Cells and Systems, University Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ben N G Giepmans
- Department of Biomedical Sciences of Cells and Systems, University Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - George Azzopardi
- Bernoulli Institute of Mathematics, Computer Science and Artificial Intelligence, University Groningen, Groningen, The Netherlands
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4
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Schaible GA, Kohtz AJ, Cliff J, Hatzenpichler R. Correlative SIP-FISH-Raman-SEM-NanoSIMS links identity, morphology, biochemistry, and physiology of environmental microbes. ISME COMMUNICATIONS 2022; 2:52. [PMID: 37938730 PMCID: PMC9723565 DOI: 10.1038/s43705-022-00134-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/23/2022] [Accepted: 06/09/2022] [Indexed: 05/08/2023]
Abstract
Microscopic and spectroscopic techniques are commonly applied to study microbial cells but are typically used on separate samples, resulting in population-level datasets that are integrated across different cells with little spatial resolution. To address this shortcoming, we developed a workflow that correlates several microscopic and spectroscopic techniques to generate an in-depth analysis of individual cells. By combining stable isotope probing (SIP), fluorescence in situ hybridization (FISH), scanning electron microscopy (SEM), confocal Raman microspectroscopy (Raman), and nano-scale secondary ion mass spectrometry (NanoSIMS), we illustrate how individual cells can be thoroughly interrogated to obtain information about their taxonomic identity, structure, physiology, and metabolic activity. Analysis of an artificial microbial community demonstrated that our correlative approach was able to resolve the activity of single cells using heavy water SIP in conjunction with Raman and/or NanoSIMS and establish their taxonomy and morphology using FISH and SEM. This workflow was then applied to a sample of yet uncultured multicellular magnetotactic bacteria (MMB). In addition to establishing their identity and activity, backscatter electron microscopy (BSE), NanoSIMS, and energy-dispersive X-ray spectroscopy (EDS) were employed to characterize the magnetosomes within the cells. By integrating these techniques, we demonstrate a cohesive approach to thoroughly study environmental microbes on a single-cell level.
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Affiliation(s)
- George A Schaible
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA
- Thermal Biology Institute, Montana State University, Bozeman, MT, 59717, USA
| | - Anthony J Kohtz
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA
- Thermal Biology Institute, Montana State University, Bozeman, MT, 59717, USA
| | - John Cliff
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA.
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA.
- Thermal Biology Institute, Montana State University, Bozeman, MT, 59717, USA.
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, 59717, USA.
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5
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Abstract
This review focuses on the human pancreatic islet-including its structure, cell composition, development, function, and dysfunction. After providing a historical timeline of key discoveries about human islets over the past century, we describe new research approaches and technologies that are being used to study human islets and how these are providing insight into human islet physiology and pathophysiology. We also describe changes or adaptations in human islets in response to physiologic challenges such as pregnancy, aging, and insulin resistance and discuss islet changes in human diabetes of many forms. We outline current and future interventions being developed to protect, restore, or replace human islets. The review also highlights unresolved questions about human islets and proposes areas where additional research on human islets is needed.
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Affiliation(s)
- John T Walker
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Diane C Saunders
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Marcela Brissova
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Alvin C Powers
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- VA Tennessee Valley Healthcare System, Nashville, Tennessee, USA
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6
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Lange F, Agüi-Gonzalez P, Riedel D, Phan NTN, Jakobs S, Rizzoli SO. Correlative fluorescence microscopy, transmission electron microscopy and secondary ion mass spectrometry (CLEM-SIMS) for cellular imaging. PLoS One 2021; 16:e0240768. [PMID: 33970908 PMCID: PMC8109779 DOI: 10.1371/journal.pone.0240768] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 04/13/2021] [Indexed: 11/24/2022] Open
Abstract
Electron microscopy (EM) has been employed for decades to analyze cell structure. To also analyze the positions and functions of specific proteins, one typically relies on immuno-EM or on a correlation with fluorescence microscopy, in the form of correlated light and electron microscopy (CLEM). Nevertheless, neither of these procedures is able to also address the isotopic composition of cells. To solve this, a correlation with secondary ion mass spectrometry (SIMS) would be necessary. SIMS has been correlated in the past to EM or to fluorescence microscopy in biological samples, but not to CLEM. We achieved this here, using a protocol based on transmission EM, conventional epifluorescence microscopy and nanoSIMS. The protocol is easily applied, and enables the use of all three technologies at high performance parameters. We suggest that CLEM-SIMS will provide substantial information that is currently beyond the scope of conventional correlative approaches.
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Affiliation(s)
- Felix Lange
- Research Group Mitochondrial Structure and Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
- Clinic for Neurology, University Medical Center Göttingen, Göttingen, Germany
| | - Paola Agüi-Gonzalez
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany
| | - Dietmar Riedel
- Laboratory of Electron Microscopy, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Nhu T. N. Phan
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany
| | - Stefan Jakobs
- Research Group Mitochondrial Structure and Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
- Clinic for Neurology, University Medical Center Göttingen, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany
- * E-mail: (SJ); (SOR)
| | - Silvio O. Rizzoli
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany
- * E-mail: (SJ); (SOR)
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7
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de Boer P, Giepmans BN. State-of-the-art microscopy to understand islets of Langerhans: what to expect next? Immunol Cell Biol 2021; 99:509-520. [PMID: 33667022 PMCID: PMC8252556 DOI: 10.1111/imcb.12450] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 03/03/2021] [Accepted: 03/04/2021] [Indexed: 12/12/2022]
Abstract
The discovery of Langerhans and microscopic description of islets in the pancreas were crucial steps in the discovery of insulin. Over the past 150 years, many discoveries in islet biology and type 1 diabetes have been made using powerful microscopic techniques. In the past decade, combination of new probes, animal and tissue models, application of new biosensors and automation of light and electron microscopic methods and other (sub)cellular imaging modalities have proven their potential in understanding the beta cell under (patho)physiological conditions. The imaging evolution, from fluorescent jellyfish to real‐time intravital functional imaging, the revolution in automation and data handling and the increased resolving power of analytical imaging techniques are now converging. Here, we review innovative approaches that address islet biology from new angles by studying cells and molecules at high spatiotemporal resolution and in live models. Broad implementation of these cellular imaging techniques will shed new light on cause/consequence of (mal)function in islets of Langerhans in the years to come.
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Affiliation(s)
- Pascal de Boer
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ben Ng Giepmans
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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8
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Ramachandra R, Mackey MR, Hu J, Peltier ST, Xuong NH, Ellisman MH, Adams SR. Elemental mapping of labelled biological specimens at intermediate energy loss in an energy-filtered TEM acquired using a direct detection device. J Microsc 2021; 283:127-144. [PMID: 33844293 PMCID: PMC8316382 DOI: 10.1111/jmi.13014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/11/2021] [Accepted: 04/04/2021] [Indexed: 12/30/2022]
Abstract
The technique of colour EM that was recently developed enabled localisation of specific macromolecules/proteins of interest by the targeted deposition of diaminobenzidine (DAB) conjugated to lanthanide chelates. By acquiring lanthanide elemental maps by energy‐filtered transmission electron microscopy (EFTEM) and overlaying them in pseudo‐colour over the conventional greyscale TEM image, a colour EM image is generated. This provides a powerful tool for visualising subcellular component/s, by the ability to clearly distinguish them from the general staining of the endogenous cellular material. Previously, the lanthanide elemental maps were acquired at the high‐loss M4,5 edge (excitation of 3d electrons), where the characteristic signal is extremely low and required considerably long exposures. In this paper, we explore the possibility of acquiring the elemental maps of lanthanides at their N4,5 edge (excitation of 4d electrons), which occurring at a much lower energy‐loss regime, thereby contains significantly greater total characteristic signal owing to the higher inelastic scattering cross‐sections at the N4,5 edge. Acquiring EFTEM lanthanide elemental maps at the N4,5 edge instead of the M4,5 edge, provides ∼4× increase in signal‐to‐noise and ∼2× increase in resolution. However, the interpretation of the lanthanide maps acquired at the N4,5 edge by the traditional 3‐window method, is complicated due to the broad shape of the edge profile and the lower signal‐above‐background ratio. Most of these problems can be circumvented by the acquisition of elemental maps with the more sophisticated technique of EFTEM Spectrum Imaging (EFTEM SI). Here, we also report the chemical synthesis of novel second‐generation DAB lanthanide metal chelate conjugates that contain 2 lanthanide ions per DAB molecule in comparison with 0.5 lanthanide ion per DAB in the first generation. Thereby, fourfold more Ln3+ per oxidised DAB would be deposited providing significant amplification of signal. This paper applies the colour EM technique at the intermediate‐loss energy‐loss regime to three different cellular targets, namely using mitochondrial matrix‐directed APEX2, histone H2B‐Nucleosome and EdU‐DNA. All the examples shown in the paper are single colour EM images only.
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Affiliation(s)
- Ranjan Ramachandra
- Department of Neurosciences, University of California, San Diego, La Jolla, California, USA.,Center for Research in Biological Systems, National Center for Microscopy and, Imaging Research, University of California, San Diego, La Jolla, California, USA
| | - Mason R Mackey
- Department of Neurosciences, University of California, San Diego, La Jolla, California, USA.,Center for Research in Biological Systems, National Center for Microscopy and, Imaging Research, University of California, San Diego, La Jolla, California, USA
| | - Junru Hu
- Department of Neurosciences, University of California, San Diego, La Jolla, California, USA.,Center for Research in Biological Systems, National Center for Microscopy and, Imaging Research, University of California, San Diego, La Jolla, California, USA
| | - Steven T Peltier
- Department of Neurosciences, University of California, San Diego, La Jolla, California, USA.,Center for Research in Biological Systems, National Center for Microscopy and, Imaging Research, University of California, San Diego, La Jolla, California, USA
| | - Nguyen-Huu Xuong
- Center for Research in Biological Systems, National Center for Microscopy and, Imaging Research, University of California, San Diego, La Jolla, California, USA
| | - Mark H Ellisman
- Department of Neurosciences, University of California, San Diego, La Jolla, California, USA.,Center for Research in Biological Systems, National Center for Microscopy and, Imaging Research, University of California, San Diego, La Jolla, California, USA
| | - Stephen R Adams
- Department of Pharmacology, University of California, San Diego, La Jolla, California, USA
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9
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Taskin MB, Ahmad T, Wistlich L, Meinel L, Schmitz M, Rossi A, Groll J. Bioactive Electrospun Fibers: Fabrication Strategies and a Critical Review of Surface-Sensitive Characterization and Quantification. Chem Rev 2021; 121:11194-11237. [DOI: 10.1021/acs.chemrev.0c00816] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Mehmet Berat Taskin
- Department of Functional Materials in Medicine and Dentistry and Bavarian Polymer Institute, University of Würzburg, 97070 Würzburg, Germany
| | - Taufiq Ahmad
- Department of Functional Materials in Medicine and Dentistry and Bavarian Polymer Institute, University of Würzburg, 97070 Würzburg, Germany
| | - Laura Wistlich
- Department of Functional Materials in Medicine and Dentistry and Bavarian Polymer Institute, University of Würzburg, 97070 Würzburg, Germany
| | - Lorenz Meinel
- Institute of Pharmacy and Food Chemistry and Helmholtz Institute for RNA Based Infection Research, 97074 Würzburg, Germany
| | - Michael Schmitz
- Department of Functional Materials in Medicine and Dentistry and Bavarian Polymer Institute, University of Würzburg, 97070 Würzburg, Germany
| | - Angela Rossi
- Department of Functional Materials in Medicine and Dentistry and Bavarian Polymer Institute, University of Würzburg, 97070 Würzburg, Germany
| | - Jürgen Groll
- Department of Functional Materials in Medicine and Dentistry and Bavarian Polymer Institute, University of Würzburg, 97070 Würzburg, Germany
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10
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Pirozzi NM, Kuipers J, Giepmans BNG. Sample preparation for energy dispersive X-ray imaging of biological tissues. Methods Cell Biol 2020; 162:89-114. [PMID: 33707024 DOI: 10.1016/bs.mcb.2020.10.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Traditional electron microscopy (EM) can be complemented with analytical EM to increase objective sample information enabling feature identification. Energy dispersive X-ray (EDX) imaging provides semi-quantitative elemental composition of the sample with high spatial resolution (~10nm) in ultrathin sections. However, EDX imaging of biological samples is still challenging as a routine method because many elements are at the detection limit for this technique. Moreover, samples undergo extensive preparation before analysis, which can introduce disruptive X-ray cross-talk or artifacts. EDX data can, for instance, be skewed by (i) osmium interference with endogenous phosphorus, (ii) chlorine present in EPON-embedded tissues, (iii) lead interference with endogenous sulfur, and (iv) potential spectral overlaps with grid material, contrast agents, and the in-microscope sample holder. Here, we highlight how to circumvent these potential pitfalls and outline how we approach sample preparation and analysis for detection of different elements of interest. Utilization of well-considered a priori sample preparation techniques will best ensure conclusive EDX experiments.
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Affiliation(s)
- Nicole M Pirozzi
- Department of Biomedical Sciences of Cells and Systems, Groningen, The Netherlands
| | - Jeroen Kuipers
- Department of Biomedical Sciences of Cells and Systems, Groningen, The Netherlands
| | - Ben N G Giepmans
- Department of Biomedical Sciences of Cells and Systems, Groningen, The Netherlands.
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11
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Taatjes DJ, Roth J. In focus in HCB. Histochem Cell Biol 2020; 154:597-607. [PMID: 33277679 DOI: 10.1007/s00418-020-01944-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2020] [Indexed: 11/26/2022]
Affiliation(s)
- Douglas J Taatjes
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, 05405, USA.
| | - Jürgen Roth
- University of Zurich, CH-8091, Zurich, Switzerland
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12
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Keevend K, Krummenacher R, Kungas E, Gerken LRH, Gogos A, Stiefel M, Herrmann IK. Correlative Cathodoluminescence Electron Microscopy: Immunolabeling Using Rare-Earth Element Doped Nanoparticles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2004615. [PMID: 33090693 DOI: 10.1002/smll.202004615] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/10/2020] [Indexed: 06/11/2023]
Abstract
The understanding of living systems and their building blocks relies on the assessment of structure-function relationships at the nanoscale. Although electron microscopy (EM) gives access to ultrastructural imaging with nanometric resolution, the unambiguous localization of specific molecules is challenging. An EM approach capable of localizing biomolecules with respect to the cellular ultrastructure will offer a direct route to the molecular blueprints of biological systems. In an approach departing from conventional correlative imaging, an electron beam may be used as excitation source to generate optical emission with nanometric resolution, that is, cathodoluminescence (CL). Once suitable luminescent labels become available, CL may be harnessed to enable identification of biomolecule labels based on spectral signatures rather than electron density and size. This work presents CL-enabled immunolabeling based on rare-earth element doped nanoparticle-labels allowing specific molecules to be visualized at nanoscale resolution in the context of the cellular ultrastructure. Folic acid decorated nanoparticles exhibiting single particle CL emission are employed to specifically label receptors and identify characteristic receptor clustering on the surface of cancer cells. This demonstration of CL immunotargeting gives access to protein localization in the context of the cellular ultrastructure and paves the way for immunolabeling of multiple proteins in EM.
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Affiliation(s)
- Kerda Keevend
- Laboratory for Particles Biology Interactions, Department Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, St. Gallen, CH-9014, Switzerland
- Nanoparticle Systems Engineering Laboratory, Institute of Process Engineering, Department of Mechanical and Process Engineering, ETH Zürich, Sonneggstrasse 3, Zürich, CH-8092, Switzerland
| | - Roman Krummenacher
- Laboratory for Particles Biology Interactions, Department Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, St. Gallen, CH-9014, Switzerland
| | - Egle Kungas
- Laboratory for Particles Biology Interactions, Department Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, St. Gallen, CH-9014, Switzerland
| | - Lukas R H Gerken
- Laboratory for Particles Biology Interactions, Department Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, St. Gallen, CH-9014, Switzerland
- Nanoparticle Systems Engineering Laboratory, Institute of Process Engineering, Department of Mechanical and Process Engineering, ETH Zürich, Sonneggstrasse 3, Zürich, CH-8092, Switzerland
| | - Alexander Gogos
- Laboratory for Particles Biology Interactions, Department Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, St. Gallen, CH-9014, Switzerland
| | - Michael Stiefel
- Laboratory for Transport at Nanoscale Interfaces, Department Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), Überlandstrasse 129, Dübendorf, CH-8600, Switzerland
| | - Inge K Herrmann
- Laboratory for Particles Biology Interactions, Department Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, St. Gallen, CH-9014, Switzerland
- Nanoparticle Systems Engineering Laboratory, Institute of Process Engineering, Department of Mechanical and Process Engineering, ETH Zürich, Sonneggstrasse 3, Zürich, CH-8092, Switzerland
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13
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Keevend K, Coenen T, Herrmann IK. Correlative cathodoluminescence electron microscopy bioimaging: towards single protein labelling with ultrastructural context. NANOSCALE 2020; 12:15588-15603. [PMID: 32677648 DOI: 10.1039/d0nr02563a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The understanding of living systems and their building blocks relies heavily on the assessment of structure-function relationships at the nanoscale. Ever since the development of the first optical microscope, the reliance of scientists across disciplines on microscopy has increased. The development of the first electron microscope and with it the access to information at the nanoscale has prompted numerous disruptive discoveries. While fluorescence imaging allows identification of specific entities based on the labelling with fluorophores, the unlabelled constituents of the samples remain invisible. In electron microscopy on the other hand, structures can be comprehensively visualized based on their distinct electron density and geometry. Although electron microscopy is a powerful tool, it does not implicitly provide information on the location and activity of specific organic molecules. While correlative light and electron microscopy techniques have attempted to unify the two modalities, the resolution mismatch between the two data sets poses major challenges. Recent developments in optical super resolution microscopy enable high resolution correlative light and electron microscopy, however, with considerable constraints due to sample preparation requirements. Labelling of specific structures directly for electron microscopy using small gold nanoparticles (i.e. immunogold) has been used extensively. However, identification of specific entities solely based on electron contrast, and the differentiation from endogenous dense granules, remains challenging. Recently, the use of correlative cathodoluminescence electron microscopy (CCLEM) imaging based on luminescent inorganic nanocrystals has been proposed. While nanometric resolution can be reached for both the electron and the optical signal, high energy electron beams are potentially damaging to the sample. In this review, we discuss the opportunities of (volumetric) multi-color single protein labelling based on correlative cathodoluminescence electron microscopy, and its prospective impact on biomedical research in general. We elaborate on the potential challenges of correlative cathodoluminescence electron microscopy-based bioimaging and benchmark CCLEM against alternative high-resolution correlative imaging techniques.
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Affiliation(s)
- Kerda Keevend
- Laboratory for Particles Biology Interactions, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, CH-9014, St Gallen, Switzerland.
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14
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de Boer P, Pirozzi NM, Wolters AHG, Kuipers J, Kusmartseva I, Atkinson MA, Campbell-Thompson M, Giepmans BNG. Large-scale electron microscopy database for human type 1 diabetes. Nat Commun 2020; 11:2475. [PMID: 32424134 PMCID: PMC7235089 DOI: 10.1038/s41467-020-16287-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 04/23/2020] [Indexed: 01/13/2023] Open
Abstract
Autoimmune β-cell destruction leads to type 1 diabetes, but the pathophysiological mechanisms remain unclear. To help address this void, we created an open-access online repository, unprecedented in its size, composed of large-scale electron microscopy images ('nanotomy') of human pancreas tissue obtained from the Network for Pancreatic Organ donors with Diabetes (nPOD; www.nanotomy.org). Nanotomy allows analyses of complete donor islets with up to macromolecular resolution. Anomalies we found in type 1 diabetes included (i) an increase of 'intermediate cells' containing granules resembling those of exocrine zymogen and endocrine hormone secreting cells; and (ii) elevated presence of innate immune cells. These are our first results of mining the database and support recent findings that suggest that type 1 diabetes includes abnormalities in the exocrine pancreas that may induce endocrine cellular stress as a trigger for autoimmunity.
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Affiliation(s)
- Pascal de Boer
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Nicole M Pirozzi
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Anouk H G Wolters
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jeroen Kuipers
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Irina Kusmartseva
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida Diabetes Institute, Gainesville, FL, USA
| | - Mark A Atkinson
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida Diabetes Institute, Gainesville, FL, USA
- Department of Pediatrics, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Martha Campbell-Thompson
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida Diabetes Institute, Gainesville, FL, USA
| | - Ben N G Giepmans
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
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15
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Stewart TJ. Across the spectrum: integrating multidimensional metal analytics for in situ metallomic imaging. Metallomics 2020; 11:29-49. [PMID: 30499574 PMCID: PMC6350628 DOI: 10.1039/c8mt00235e] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
To know how much of a metal species is in a particular location within a biological context at any given time is essential for understanding the intricate roles of metals in biology and is the fundamental question upon which the field of metallomics was born. Simply put, seeing is powerful. With the combination of spectroscopy and microscopy, we can now see metals within complex biological matrices complemented by information about associated molecules and their structures. With the addition of mass spectrometry and particle beam based techniques, the field of view grows to cover greater sensitivities and spatial resolutions, addressing structural, functional and quantitative metallomic questions from the atomic level to whole body processes. In this perspective, I present a paradigm shift in the way we relate to and integrate current and developing metallomic analytics, highlighting both familiar and perhaps less well-known state of the art techniques for in situ metallomic imaging, specific biological applications, and their use in correlative studies. There is a genuine need to abandon scientific silos and, through the establishment of a metallomic scientific platform for further development of multidimensional analytics for in situ metallomic imaging, we have an incredible opportunity to enhance the field of metallomics and demonstrate how discovery research can be done more effectively.
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Affiliation(s)
- Theodora J Stewart
- King's College London, Mass Spectrometry, London Metallomics Facility, 4th Floor Franklin-Wilkins Building, 150 Stamford St., London SE1 9NH, UK.
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Keevend K, Puust L, Kurvits K, Gerken LRH, Starsich FHL, Li JH, Matter MT, Spyrogianni A, Sotiriou GA, Stiefel M, Herrmann IK. Ultrabright and Stable Luminescent Labels for Correlative Cathodoluminescence Electron Microscopy Bioimaging. NANO LETTERS 2019; 19:6013-6018. [PMID: 31373824 DOI: 10.1021/acs.nanolett.9b01819] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The mechanistic understanding of structure-function relationships in biological systems heavily relies on imaging. While fluorescence microscopy allows the study of specific proteins following their labeling with fluorophores, electron microscopy enables holistic ultrastructural analysis based on differences in electron density. To identify specific proteins in electron microscopy, immunogold labeling has become the method of choice. However, the distinction of immunogold-based protein labels from naturally occurring electron dense granules and the identification of several different proteins in the same sample remain challenging. Correlative cathodoluminescence electron microscopy (CCLEM) bioimaging has recently been suggested to provide an attractive alternative based on labels emitting characteristic light. While luminescence excitation by an electron beam enables subdiffraction imaging, structural damage to the sample by high-energy electrons has been identified as a potential obstacle. Here, we investigate the feasibility of various commonly used luminescent labels for CCLEM bioimaging. We demonstrate that organic fluorophores and semiconductor quantum dots suffer from a considerable loss of emission intensity, even when using moderate beam voltages (2 kV) and currents (0.4 nA). Rare-earth element-doped nanocrystals, in particular Y2O3:Tb3+ and YVO4:Bi3+,Eu3+ nanoparticles with green and orange-red emission, respectively, feature remarkably high brightness and stability in the CCLEM bioimaging setting. We further illustrate how these nanocrystals can be readily differentiated from morphologically similar naturally occurring dense granules based on optical emission, making them attractive nanoparticle core materials for molecular labeling and (multi)color CCLEM.
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Affiliation(s)
- Kerda Keevend
- Laboratory for Particles Biology Interactions, Department of Materials Meet Life , Swiss Federal Laboratories for Materials Science and Technology (Empa) , Lerchenfeldstrasse 5 , CH-9014 St. Gallen , Switzerland
- Optical Nanomaterial Group, Institute for Quantum Electronics, Department of Physics , ETH Zurich , Auguste-Piccard- Hof 1 , CH-8093 Zurich , Switzerland
- Nanoparticle Systems Engineering Laboratory, Institute of Process Engineering, Department of Mechanical and Process Engineering , ETH Zurich , Sonneggstrasse 3 , CH-8092 Zurich , Switzerland
| | - Laurits Puust
- Laboratory of Laser Spectroscopy, Institute of Physics , University of Tartu , W. Ostwaldi St 1 , 50411 Tartu , Estonia
| | - Karoliine Kurvits
- Laboratory of Laser Spectroscopy, Institute of Physics , University of Tartu , W. Ostwaldi St 1 , 50411 Tartu , Estonia
| | - Lukas R H Gerken
- Laboratory for Particles Biology Interactions, Department of Materials Meet Life , Swiss Federal Laboratories for Materials Science and Technology (Empa) , Lerchenfeldstrasse 5 , CH-9014 St. Gallen , Switzerland
- Nanoparticle Systems Engineering Laboratory, Institute of Process Engineering, Department of Mechanical and Process Engineering , ETH Zurich , Sonneggstrasse 3 , CH-8092 Zurich , Switzerland
| | - Fabian H L Starsich
- Particle Technology Laboratory, Institute of Process Engineering, Department of Mechanical and Process Engineering , ETH Zurich , Sonneggstrasse 3 , CH-8092 Zurich , Switzerland
| | - Jian-Hao Li
- Laboratory for Particles Biology Interactions, Department of Materials Meet Life , Swiss Federal Laboratories for Materials Science and Technology (Empa) , Lerchenfeldstrasse 5 , CH-9014 St. Gallen , Switzerland
- Nanoparticle Systems Engineering Laboratory, Institute of Process Engineering, Department of Mechanical and Process Engineering , ETH Zurich , Sonneggstrasse 3 , CH-8092 Zurich , Switzerland
| | - Martin T Matter
- Laboratory for Particles Biology Interactions, Department of Materials Meet Life , Swiss Federal Laboratories for Materials Science and Technology (Empa) , Lerchenfeldstrasse 5 , CH-9014 St. Gallen , Switzerland
- Nanoparticle Systems Engineering Laboratory, Institute of Process Engineering, Department of Mechanical and Process Engineering , ETH Zurich , Sonneggstrasse 3 , CH-8092 Zurich , Switzerland
- Particle Technology Laboratory, Institute of Process Engineering, Department of Mechanical and Process Engineering , ETH Zurich , Sonneggstrasse 3 , CH-8092 Zurich , Switzerland
| | - Anastasia Spyrogianni
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences , ETH Zurich , Vladimir-Prelog-Weg 1-5 , CH-8093 Zurich , Switzerland
| | - Georgios A Sotiriou
- Department of Microbiology, Tumor and Cell Biology , Karolinska Institutet , SE-17177 Stockholm , Sweden
| | - Michael Stiefel
- Laboratory for Transport at Nanoscale Interfaces, Department Materials Meet Life , Swiss Federal Laboratories for Materials Science and Technology (Empa) , Überlandstrasse 129 , CH-8600 Dübendorf , Switzerland
| | - Inge K Herrmann
- Laboratory for Particles Biology Interactions, Department of Materials Meet Life , Swiss Federal Laboratories for Materials Science and Technology (Empa) , Lerchenfeldstrasse 5 , CH-9014 St. Gallen , Switzerland
- Nanoparticle Systems Engineering Laboratory, Institute of Process Engineering, Department of Mechanical and Process Engineering , ETH Zurich , Sonneggstrasse 3 , CH-8092 Zurich , Switzerland
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Templier T. MagC, magnetic collection of ultrathin sections for volumetric correlative light and electron microscopy. eLife 2019; 8:e45696. [PMID: 31294691 PMCID: PMC6697447 DOI: 10.7554/elife.45696] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 07/02/2019] [Indexed: 01/03/2023] Open
Abstract
The non-destructive collection of ultrathin sections on silicon wafers for post-embedding staining and volumetric correlative light and electron microscopy traditionally requires exquisite manual skills and is tedious and unreliable. In MagC introduced here, sample blocks are augmented with a magnetic resin enabling the remote actuation and collection of hundreds of sections on wafer. MagC allowed the correlative visualization of neuroanatomical tracers within their ultrastructural volumetric electron microscopy context.
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Affiliation(s)
- Thomas Templier
- Institute of NeuroinformaticsUniversity of Zurich and ETH ZurichZurichSwitzerland
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