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Munck S, De Bo C, Cawthorne C, Colombelli J. Innovating in a bioimaging core through instrument development. J Microsc 2024; 294:319-337. [PMID: 38683038 DOI: 10.1111/jmi.13312] [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: 03/01/2024] [Revised: 04/18/2024] [Accepted: 04/18/2024] [Indexed: 05/01/2024]
Abstract
Developing devices and instrumentation in a bioimaging core facility is an important part of the innovation mandate inherent in the core facility model but is a complex area due to the required skills and investments, and the impossibility of a universally applicable model. Here, we seek to define technological innovation in microscopy and situate it within the wider core facility innovation portfolio, highlighting how strategic development can accelerate access to innovative imaging modalities and increase service range, and thus maintain the cutting edge needed for sustainability. We consider technology development from the perspective of core facility staff and their stakeholders as well as their research environment and aim to present a practical guide to the 'Why, When, and How' of developing and integrating innovative technology in the core facility portfolio. Core facilities need to innovate to stay up to date. However, how to carry out the innovation is not very obvious. One area of innovation in imaging core facilities is the building of optical setups. However, the creation of optical setups requires specific skill sets, time, and investments. Consequently, the topic of whether a core facility should develop optical devices is discussed as controversial. Here, we provide resources that should help get into this topic, and we discuss different options when and how it makes sense to build optical devices in core facilities. We discuss various aspects, including consequences for staff and the relation of the core to the institute, and also broaden the scope toward other areas of innovation.
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Affiliation(s)
- Sebastian Munck
- Neuroscience Department, KU Leuven, Leuven, Belgium
- VIB BioImaging Core, VIB, Leuven, Belgium
| | | | - Christopher Cawthorne
- Department of Imaging and Pathology, Nuclear Medicine and Molecular Imaging, KU Leuven, Leuven, Belgium
| | - Julien Colombelli
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
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2
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Meechan K, Guan W, Riedinger A, Stankova V, Yoshimura A, Pipitone R, Milberger A, Schaar H, Romero-Brey I, Templin R, Peddie CJ, Schieber NL, Jones ML, Collinson L, Schwab Y. Crosshair, semi-automated targeting for electron microscopy with a motorised ultramicrotome. eLife 2022; 11:80899. [PMCID: PMC9665851 DOI: 10.7554/elife.80899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 10/23/2022] [Indexed: 11/16/2022] Open
Abstract
Volume electron microscopy (EM) is a time-consuming process – often requiring weeks or months of continuous acquisition for large samples. In order to compare the ultrastructure of a number of individuals or conditions, acquisition times must therefore be reduced. For resin-embedded samples, one solution is to selectively target smaller regions of interest by trimming with an ultramicrotome. This is a difficult and labour-intensive process, requiring manual positioning of the diamond knife and sample, and much time and training to master. Here, we have developed a semi-automated workflow for targeting with a modified ultramicrotome. We adapted two recent commercial systems to add motors for each rotational axis (and also each translational axis for one system), allowing precise and automated movement. We also developed a user-friendly software to convert X-ray images of resin-embedded samples into angles and cutting depths for the ultramicrotome. This is provided as an open-source Fiji plugin called Crosshair. This workflow is demonstrated by targeting regions of interest in a series of Platynereis dumerilii samples.
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Affiliation(s)
- Kimberly Meechan
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL)
- Collaboration for Joint PhD Degree Between EMBL and Heidelberg University, Faculty of Biosciences
| | | | - Alfons Riedinger
- Electronic Workshop, European Molecular Biology Laboratory (EMBL)
| | - Vera Stankova
- Electronic Workshop, European Molecular Biology Laboratory (EMBL)
| | | | - Rosa Pipitone
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL)
| | - Arthur Milberger
- Mechanical Workshop, European Molecular Biology Laboratory (EMBL)
| | - Helmuth Schaar
- Mechanical Workshop, European Molecular Biology Laboratory (EMBL)
| | - Inés Romero-Brey
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL)
| | - Rachel Templin
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL)
| | | | - Nicole L Schieber
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL)
| | | | | | - Yannick Schwab
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL)
- Electron Microscopy Core Facility, European Molecular Biology Laboratory (EMBL)
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3
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Heiligenstein X, Lucas MS. One for All, All for One: A Close Look at In-Resin Fluorescence Protocols for CLEM. Front Cell Dev Biol 2022; 10:866472. [PMID: 35846358 PMCID: PMC9280628 DOI: 10.3389/fcell.2022.866472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/13/2022] [Indexed: 11/13/2022] Open
Abstract
Sample preparation is the novel bottleneck for high throughput correlative light and electron microscopy (CLEM). Protocols suitable for both imaging methods must therefore balance the requirements of each technique. For fluorescence light microscopy, a structure of interest can be targeted using: 1) staining, which is often structure or tissue specific rather than protein specific, 2) dye-coupled proteins or antibodies, or 3) genetically encoded fluorescent proteins. Each of these three methods has its own advantages. For ultrastructural investigation by electron microscopy (EM) resin embedding remains a significant sample preparation approach, as it stabilizes the sample such that it withstands the vacuum conditions of the EM, and enables long-term storage. Traditionally, samples are treated with heavy metal salts prior to resin embedding, in order to increase imaging contrast for EM. This is particularly important for volume EM (vEM) techniques. Yet, commonly used contrasting agents (e.g., osmium tetroxide, uranyl acetate) tend to impair fluorescence. The discovery that fluorescence can be preserved in resin-embedded specimens after mild heavy metal staining was a game changer for CLEM. These so-called in-resin fluorescence protocols present a significant leap forward for CLEM approaches towards high precision localization of a fluorescent signal in (volume) EM data. Integrated microscopy approaches, combining LM and EM detection into a single instrument certainly require such an “all in one” sample preparation. Preserving, or adding, dedicated fluorescence prior to resin embedding requires a compromise, which often comes at the expense of EM imaging contrast and membrane visibility. Especially vEM can be strongly hampered by a lack of heavy metal contrasting. This review critically reflects upon the fundamental aspects of resin embedding with regard to 1) specimen fixation and the physics and chemistry underlying the preservation of protein structure with respect to fluorescence and antigenicity, 2) optimization of EM contrast for transmission or scanning EM, and 3) the choice of embedding resin. On this basis, various existing workflows employing in-resin fluorescence are described, highlighting their common features, discussing advantages and disadvantages of the respective approach, and finally concluding with promising future developments for in-resin CLEM.
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Affiliation(s)
| | - Miriam S. Lucas
- Scientific Center for Light and Electron Microscopy (ScopeM), ETH Zurich, Zurich, Switzerland
- *Correspondence: Miriam S. Lucas,
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4
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Loginov SV, Fermie J, Fokkema J, Agronskaia AV, De Heus C, Blab GA, Klumperman J, Gerritsen HC, Liv N. Correlative Organelle Microscopy: Fluorescence Guided Volume Electron Microscopy of Intracellular Processes. Front Cell Dev Biol 2022; 10:829545. [PMID: 35478966 PMCID: PMC9035751 DOI: 10.3389/fcell.2022.829545] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/04/2022] [Indexed: 01/19/2023] Open
Abstract
Intracellular processes depend on a strict spatial and temporal organization of proteins and organelles. Therefore, directly linking molecular to nanoscale ultrastructural information is crucial in understanding cellular physiology. Volume or three-dimensional (3D) correlative light and electron microscopy (volume-CLEM) holds unique potential to explore cellular physiology at high-resolution ultrastructural detail across cell volumes. However, the application of volume-CLEM is hampered by limitations in throughput and 3D correlation efficiency. In order to address these limitations, we describe a novel pipeline for volume-CLEM that provides high-precision (<100 nm) registration between 3D fluorescence microscopy (FM) and 3D electron microscopy (EM) datasets with significantly increased throughput. Using multi-modal fiducial nanoparticles that remain fluorescent in epoxy resins and a 3D confocal fluorescence microscope integrated into a Focused Ion Beam Scanning Electron Microscope (FIB.SEM), our approach uses FM to target extremely small volumes of even single organelles for imaging in volume EM and obviates the need for post-correlation of big 3D datasets. We extend our targeted volume-CLEM approach to include live-cell imaging, adding information on the motility of intracellular membranes selected for volume-CLEM. We demonstrate the power of our approach by targeted imaging of rare and transient contact sites between the endoplasmic reticulum (ER) and lysosomes within hours rather than days. Our data suggest that extensive ER-lysosome and mitochondria-lysosome interactions restrict lysosome motility, highlighting the unique capabilities of our integrated CLEM pipeline for linking molecular dynamic data to high-resolution ultrastructural detail in 3D.
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Affiliation(s)
- Sergey V. Loginov
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
| | - Job Fermie
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
- Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Jantina Fokkema
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
| | - Alexandra V. Agronskaia
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
| | - Cilia De Heus
- Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Gerhard A. Blab
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
| | - Judith Klumperman
- Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Hans C. Gerritsen
- Molecular Biophysics, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
| | - Nalan Liv
- Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- *Correspondence: Nalan Liv,
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5
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Gabarre S, Vernaillen F, Baatsen P, Vints K, Cawthorne C, Boeynaems S, Michiels E, Vandael D, Gounko NV, Munck S. A workflow for streamlined acquisition and correlation of serial regions of interest in array tomography. BMC Biol 2021; 19:152. [PMID: 34330271 PMCID: PMC8323292 DOI: 10.1186/s12915-021-01072-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 06/14/2021] [Indexed: 11/20/2022] Open
Abstract
Background Array tomography (AT) is a high-resolution imaging method to resolve fine details at the organelle level and has the advantage that it can provide 3D volumes to show the tissue context. AT can be carried out in a correlative way, combing light and electron microscopy (LM, EM) techniques. However, the correlation between modalities can be a challenge and delineating specific regions of interest in consecutive sections can be time-consuming. Integrated light and electron microscopes (iLEMs) offer the possibility to provide well-correlated images and may pose an ideal solution for correlative AT. Here, we report a workflow to automate navigation between regions of interest. Results We use a targeted approach that allows imaging specific tissue features, like organelles, cell processes, and nuclei at different scales to enable fast, directly correlated in situ AT using an integrated light and electron microscope (iLEM-AT). Our workflow is based on the detection of section boundaries on an initial transmitted light acquisition that serves as a reference space to compensate for changes in shape between sections, and we apply a stepwise refinement of localizations as the magnification increases from LM to EM. With minimal user interaction, this enables autonomous and speedy acquisition of regions containing cells and cellular organelles of interest correlated across different magnifications for LM and EM modalities, providing a more efficient way to obtain 3D images. We provide a proof of concept of our approach and the developed software tools using both Golgi neuronal impregnation staining and fluorescently labeled protein condensates in cells. Conclusions Our method facilitates tracing and reconstructing cellular structures over multiple sections, is targeted at high resolution ILEMs, and can be integrated into existing devices, both commercial and custom-built systems. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01072-7.
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Affiliation(s)
- Sergio Gabarre
- VIB-KU Leuven Center for Brain & Disease Research, Electron Microscopy Platform & VIB BioImaging Core, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium.,KU Leuven Department of Neurosciences, Leuven Brain Institute, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium.,VIB-KU Leuven Center for Brain & Disease Research, Light Microscopy Expertise Unit & VIB BioImaging Core, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium
| | - Frank Vernaillen
- VIB BioInformatics Core, Technologiepark 75, 9052, Ghent, Belgium
| | - Pieter Baatsen
- VIB-KU Leuven Center for Brain & Disease Research, Electron Microscopy Platform & VIB BioImaging Core, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium.,KU Leuven Department of Neurosciences, Leuven Brain Institute, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium
| | - Katlijn Vints
- VIB-KU Leuven Center for Brain & Disease Research, Electron Microscopy Platform & VIB BioImaging Core, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium.,KU Leuven Department of Neurosciences, Leuven Brain Institute, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium
| | | | - Steven Boeynaems
- Department of Genetics, Stanford University School of Medicine, Stanford, California, 94305, USA
| | - Emiel Michiels
- VIB Center for Brain and Disease Research, 3000, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, 3000, Leuven, Belgium
| | - Dorien Vandael
- VIB-KU Leuven Center for Brain & Disease Research, Electron Microscopy Platform & VIB BioImaging Core, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium.,KU Leuven Department of Neurosciences, Leuven Brain Institute, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium
| | - Natalia V Gounko
- VIB-KU Leuven Center for Brain & Disease Research, Electron Microscopy Platform & VIB BioImaging Core, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium. .,KU Leuven Department of Neurosciences, Leuven Brain Institute, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium.
| | - Sebastian Munck
- KU Leuven Department of Neurosciences, Leuven Brain Institute, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium. .,VIB-KU Leuven Center for Brain & Disease Research, Light Microscopy Expertise Unit & VIB BioImaging Core, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium.
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6
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Goggin P, Ho EML, Gnaegi H, Searle S, Oreffo ROC, Schneider P. Development of protocols for the first serial block-face scanning electron microscopy (SBF SEM) studies of bone tissue. Bone 2020; 131:115107. [PMID: 31669251 PMCID: PMC6961117 DOI: 10.1016/j.bone.2019.115107] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/27/2019] [Accepted: 10/09/2019] [Indexed: 11/28/2022]
Abstract
There is an unmet need for a high-resolution three-dimensional (3D) technique to simultaneously image osteocytes and the matrix in which these cells reside. In serial block-face scanning electron microscopy (SBF SEM), an ultramicrotome mounted within the vacuum chamber of a microscope repeatedly sections a resin-embedded block of tissue. Backscattered electron scans of the block face provide a stack of high-resolution two-dimensional images, which can be used to visualise and quantify cells and organelles in 3D. High-resolution 3D images of biological tissues from SBF SEM have been exploited considerably to date in the neuroscience field. However, non-brain samples, in particular hard biological tissues, have appeared more challenging to image by SBF SEM due to the difficulties of sectioning and rendering the samples conductive. We have developed and propose protocols for bone tissue preparation using SBF SEM, for imaging simultaneously soft and hard bone tissue components in 3D. We review the state of the art in high-resolution imaging of osteocytes, provide a historical perspective of SBF SEM, and we present first SBF SEM proof-of-concept studies for murine and human tissue. The application of SBF SEM to hard tissues will facilitate qualitative and quantitative 3D studies of tissue microstructure and ultrastructure in bone development, ageing and pathologies such as osteoporosis and osteoarthritis.
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Affiliation(s)
- Patricia Goggin
- Bioengineering Science Research Group, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, UK
| | - Elaine M L Ho
- Bioengineering Science Research Group, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, UK
| | | | | | - Richard O C Oreffo
- Bone and Joint Research Group, Centre for Human Development, Stem Cells and Regeneration, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Philipp Schneider
- Bioengineering Science Research Group, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, UK.
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7
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Dobson KL, Howe CL, Nishimura Y, Marra V. Dedicated Setup for the Photoconversion of Fluorescent Dyes for Functional Electron Microscopy. Front Cell Neurosci 2019; 13:312. [PMID: 31417358 PMCID: PMC6681119 DOI: 10.3389/fncel.2019.00312] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 06/25/2019] [Indexed: 11/22/2022] Open
Abstract
Here, we describe a cost-effective setup for targeted photoconversion of fluorescent signals into electron dense ones. This approach has offered invaluable insights in the morphology and function of fine neuronal structures. The technique relies on the localized oxidation of diaminobenzidine (DAB) mediated by excited fluorophores. This paper includes a detailed description of how to build a simple photoconversion setup that can increase reliability and throughput of this well-established technique. The system described here, is particularly well-suited for thick neuronal tissue, where light penetration and oxygen diffusion may be limiting DAB oxidation. To demonstrate the system, we use Correlative Light and Electron Microscopy (CLEM) to visualize functionally-labeled individual synaptic vesicles released onto an identified layer 5 neuron in an acute cortical slice. The setup significantly simplifies the photoconversion workflow, increasing the depth of photoillumination, improving the targeting of the region of interest and reducing the time required to process each individual sample. We have tested this setup extensively for the photoconversion of FM 1-43FX and Lucifer Yellow both excited at 473 nm. In principle, the system can be adapted to any dye or nanoparticle able to oxidize DAB when excited by a specific wavelength of light.
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Affiliation(s)
- Katharine L. Dobson
- Department of Neuroscience, Psychology and Behaviour, University of Leicester, Leicester, United Kingdom
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Carmel L. Howe
- Department of Bioengineering, Imperial College London, London, United Kingdom
| | - Yuri Nishimura
- Department of Neuroscience, Psychology and Behaviour, University of Leicester, Leicester, United Kingdom
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Vincenzo Marra
- Department of Neuroscience, Psychology and Behaviour, University of Leicester, Leicester, United Kingdom
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8
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Lippens S, Kremer A, Borghgraef P, Guérin CJ. Serial block face-scanning electron microscopy for volume electron microscopy. Methods Cell Biol 2019; 152:69-85. [PMID: 31326027 DOI: 10.1016/bs.mcb.2019.04.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
There are different technologies that can be used to obtain a 3D image at nanometer resolution. Over the past decade, there has been a growing interest in applying Serial Block Face Scanning Electron Microscopy (SBF-SEM) in different fields of life science research. This technology has the advantage that it can cover a range of volumes, going from monolayers to multiple tissue layers in all three dimensions. SBF-SEM was originally used in neuroscience and then expanded to other research domains. The whole process of sample preparation for SBF-SEM is very long and consists of many steps, which makes adjustment of a given workflow very challenging. Here we describe the SBF-SEM workflow and those steps in the process that can be tweaked for any sample.
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Affiliation(s)
- Saskia Lippens
- VIB BioImaging Core, VIB, Ghent, Belgium; VIB Inflammation Research Center, VIB, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
| | - Anna Kremer
- VIB BioImaging Core, VIB, Ghent, Belgium; VIB Inflammation Research Center, VIB, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Peter Borghgraef
- VIB BioImaging Core, VIB, Ghent, Belgium; VIB Inflammation Research Center, VIB, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Christopher J Guérin
- VIB BioImaging Core, VIB, Ghent, Belgium; VIB Inflammation Research Center, VIB, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
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9
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Smith D, Starborg T. Serial block face scanning electron microscopy in cell biology: Applications and technology. Tissue Cell 2019; 57:111-122. [DOI: 10.1016/j.tice.2018.08.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 08/22/2018] [Accepted: 08/26/2018] [Indexed: 10/28/2022]
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10
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Luckner M, Wanner G. From Light Microscopy to Analytical Scanning Electron Microscopy (SEM) and Focused Ion Beam (FIB)/SEM in Biology: Fixed Coordinates, Flat Embedding, Absolute References. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2018; 24:526-544. [PMID: 30246679 PMCID: PMC6378657 DOI: 10.1017/s1431927618015015] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 06/05/2018] [Accepted: 07/16/2018] [Indexed: 05/07/2023]
Abstract
Correlative light and electron microscopy (CLEM) has been in use for several years, however it has remained a costly method with difficult sample preparation. Here, we report a series of technical improvements developed for precise and cost-effective correlative light and scanning electron microscopy (SEM) and focused ion beam (FIB)/SEM microscopy of single cells, as well as large tissue sections. Customized coordinate systems for both slides and coverslips were established for thin and ultra-thin embedding of a wide range of biological specimens. Immobilization of biological samples was examined with a variety of adhesives. For histological sections, a filter system for flat embedding was developed. We validated ultra-thin embedding on laser marked slides for efficient, high-resolution CLEM. Target cells can be re-located within minutes in SEM without protracted searching and correlative investigations were reduced to a minimum of preparation steps, while still reaching highest resolution. The FIB/SEM milling procedure is facilitated and significantly accelerated as: (i) milling a ramp becomes needless, (ii) significant re-deposition of milled material does not occur; and (iii) charging effects are markedly reduced. By optimizing all technical parameters FIB/SEM stacks with 2 nm iso-voxels were achieved over thousands of sections, in a wide range of biological samples.
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Affiliation(s)
- Manja Luckner
- Department Biology I, Ultrastructural Research, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Gerhard Wanner
- Department Biology I, Ultrastructural Research, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
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11
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Webb RI, Schieber NL. Volume Scanning Electron Microscopy: Serial Block-Face Scanning Electron Microscopy Focussed Ion Beam Scanning Electron Microscopy. BIOLOGICAL AND MEDICAL PHYSICS, BIOMEDICAL ENGINEERING 2018. [DOI: 10.1007/978-3-319-68997-5_5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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12
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Lemercier N, Middel V, Hentsch D, Taubert S, Takamiya M, Beil T, Vonesch JL, Baumbach T, Schultz P, Antony C, Strähle U. Microtome-integrated microscope system for high sensitivity tracking of in-resin fluorescence in blocks and ultrathin sections for correlative microscopy. Sci Rep 2017; 7:13583. [PMID: 29051533 PMCID: PMC5648784 DOI: 10.1038/s41598-017-13348-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 09/22/2017] [Indexed: 12/02/2022] Open
Abstract
Many areas of biological research demand the combined use of different imaging modalities to cover a wide range of magnifications and measurements or to place fluorescent patterns into an ultrastructural context. A technically difficult problem is the efficient specimen transfer between different imaging modalities without losing the coordinates of the regions-of-interest (ROI). Here, we report a new and highly sensitive integrated system that combines a custom designed microscope with an ultramicrotome for in-resin-fluorescence detection in blocks, ribbons and sections on EM-grids. Although operating with long-distance lenses, this system achieves a very high light sensitivity. Our instrumental set-up and operating workflow are designed to investigate rare events in large tissue volumes. Applications range from studies of individual immune, stem and cancer cells to the investigation of non-uniform subcellular processes. As a use case, we present the ultrastructure of a single membrane repair patch on a muscle fiber in intact muscle in a whole animal context.
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Affiliation(s)
- Nicolas Lemercier
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1, rue Laurent Fries, 67404, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, 1, rue Laurent Fries, 67404, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, 1, rue Laurent Fries, 67404, Illkirch, France.,Université de Strasbourg, 1, rue Laurent Fries, 67404, Illkirch, France
| | - Volker Middel
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Didier Hentsch
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1, rue Laurent Fries, 67404, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, 1, rue Laurent Fries, 67404, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, 1, rue Laurent Fries, 67404, Illkirch, France.,Université de Strasbourg, 1, rue Laurent Fries, 67404, Illkirch, France
| | - Serge Taubert
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1, rue Laurent Fries, 67404, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, 1, rue Laurent Fries, 67404, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, 1, rue Laurent Fries, 67404, Illkirch, France.,Université de Strasbourg, 1, rue Laurent Fries, 67404, Illkirch, France
| | - Masanari Takamiya
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Tanja Beil
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Jean-Luc Vonesch
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1, rue Laurent Fries, 67404, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, 1, rue Laurent Fries, 67404, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, 1, rue Laurent Fries, 67404, Illkirch, France.,Université de Strasbourg, 1, rue Laurent Fries, 67404, Illkirch, France
| | - Tilo Baumbach
- Laboratory for Applications of Synchrotron Radiation, Karlsruhe Institute of Technology, Kaiserstr. 12, 76131, Karlsruhe, Germany
| | - Patrick Schultz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1, rue Laurent Fries, 67404, Illkirch, France. .,Centre National de la Recherche Scientifique, UMR7104, 1, rue Laurent Fries, 67404, Illkirch, France. .,Institut National de la Santé et de la Recherche Médicale, U964, 1, rue Laurent Fries, 67404, Illkirch, France. .,Université de Strasbourg, 1, rue Laurent Fries, 67404, Illkirch, France.
| | - Claude Antony
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1, rue Laurent Fries, 67404, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, 1, rue Laurent Fries, 67404, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, 1, rue Laurent Fries, 67404, Illkirch, France.,Université de Strasbourg, 1, rue Laurent Fries, 67404, Illkirch, France.,Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Uwe Strähle
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.
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Schieber NL, Machado P, Markert SM, Stigloher C, Schwab Y, Steyer AM. Minimal resin embedding of multicellular specimens for targeted FIB-SEM imaging. Methods Cell Biol 2017; 140:69-83. [DOI: 10.1016/bs.mcb.2017.03.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Brama E, Peddie CJ, Wilkes G, Gu Y, Collinson LM, Jones ML. ultraLM and miniLM: Locator tools for smart tracking of fluorescent cells in correlative light and electron microscopy. Wellcome Open Res 2016; 1:26. [PMID: 28090593 PMCID: PMC5234702 DOI: 10.12688/wellcomeopenres.10299.1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In-resin fluorescence (IRF) protocols preserve fluorescent proteins in resin-embedded cells and tissues for correlative light and electron microscopy, aiding interpretation of macromolecular function within the complex cellular landscape. Dual-contrast IRF samples can be imaged in separate fluorescence and electron microscopes, or in dual-modality integrated microscopes for high resolution correlation of fluorophore to organelle. IRF samples also offer a unique opportunity to automate correlative imaging workflows. Here we present two new locator tools for finding and following fluorescent cells in IRF blocks, enabling future automation of correlative imaging. The ultraLM is a fluorescence microscope that integrates with an ultramicrotome, which enables ‘smart collection’ of ultrathin sections containing fluorescent cells or tissues for subsequent transmission electron microscopy or array tomography. The miniLM is a fluorescence microscope that integrates with serial block face scanning electron microscopes, which enables ‘smart tracking’ of fluorescent structures during automated serial electron image acquisition from large cell and tissue volumes.
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Affiliation(s)
- Elisabeth Brama
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
| | - Christopher J Peddie
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
| | - Gary Wilkes
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
| | - Yan Gu
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
| | - Lucy M Collinson
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
| | - Martin L Jones
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
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