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  1. Article ; Online: In focus: data management and data analysis in microscopy.

    Giepmans, Ben N G / Taatjes, Douglas J / Wolstencroft, Katherine J

    Histochemistry and cell biology

    2023  Volume 160, Issue 3, Page(s) 165–167

    MeSH term(s) Data Management ; Microscopy ; Data Analysis
    Language English
    Publishing date 2023-08-30
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 1222930-1
    ISSN 1432-119X ; 0301-5564 ; 0948-6143
    ISSN (online) 1432-119X
    ISSN 0301-5564 ; 0948-6143
    DOI 10.1007/s00418-023-02226-0
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  2. Article ; Online: Correction to: Neodymium as an alternative contrast for uranium in electron microscopy.

    Kuipers, Jeroen / Giepmans, Ben N G

    Histochemistry and cell biology

    2020  Volume 154, Issue 6, Page(s) 683

    Abstract: After publication of our article, it has come to our attention that the legend. ...

    Abstract After publication of our article, it has come to our attention that the legend.
    Language English
    Publishing date 2020-09-02
    Publishing country Germany
    Document type Published Erratum
    ZDB-ID 1222930-1
    ISSN 1432-119X ; 0301-5564 ; 0948-6143
    ISSN (online) 1432-119X
    ISSN 0301-5564 ; 0948-6143
    DOI 10.1007/s00418-020-01922-5
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  3. Article ; Online: Segmentation in large-scale cellular electron microscopy with deep learning: A literature survey.

    Aswath, Anusha / Alsahaf, Ahmad / Giepmans, Ben N G / Azzopardi, George

    Medical image analysis

    2023  Volume 89, Page(s) 102920

    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 ... ...

    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.
    MeSH term(s) Humans ; Deep Learning ; Image Processing, Computer-Assisted/methods ; Microscopy, Electron ; Algorithms ; Imaging, Three-Dimensional/methods
    Language English
    Publishing date 2023-08-06
    Publishing country Netherlands
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 1356436-5
    ISSN 1361-8423 ; 1361-8431 ; 1361-8415
    ISSN (online) 1361-8423 ; 1361-8431
    ISSN 1361-8415
    DOI 10.1016/j.media.2023.102920
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    Jg. 1995 - 2021: Lesesall (2.OG)
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  4. Article ; Online: Need for Speed: Imaging Biological Ultrastructure with the 64-beams FAST-EM.

    Kievits, Arent J / Peter Duinkerken, B H / Giepmans, Ben N G / Hoogenboom, Jacob P

    Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada

    2023  Volume 29, Issue 29 Suppl 1, Page(s) 2105–2106

    Language English
    Publishing date 2023-08-23
    Publishing country England
    Document type Journal Article
    ZDB-ID 1385710-1
    ISSN 1435-8115 ; 1431-9276
    ISSN (online) 1435-8115
    ISSN 1431-9276
    DOI 10.1093/micmic/ozad067.1091
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  5. Article ; Online: Neodymium as an alternative contrast for uranium in electron microscopy.

    Kuipers, Jeroen / Giepmans, Ben N G

    Histochemistry and cell biology

    2020  Volume 153, Issue 4, Page(s) 271–277

    Abstract: Uranyl acetate is the standard contrasting agent in electron microscopy (EM), but it is toxic and radioactive. We reasoned neodymium acetate might substitute uranyl acetate as a contrasting agent, and we find that neodymium acetate indeed can replace ... ...

    Abstract Uranyl acetate is the standard contrasting agent in electron microscopy (EM), but it is toxic and radioactive. We reasoned neodymium acetate might substitute uranyl acetate as a contrasting agent, and we find that neodymium acetate indeed can replace uranyl acetate in several routine applications. Since neodymium acetate is not toxic, not radioactive and easy to use, we foresee neodymium will replace uranyl in many EM sample preparation applications worldwide.
    MeSH term(s) Cell Line, Tumor ; Contrast Media/chemistry ; Humans ; Microscopy, Electron/methods ; Neodymium/chemistry ; Organometallic Compounds/analysis
    Chemical Substances Contrast Media ; Organometallic Compounds ; uranyl acetate (285PN2K1AO) ; Neodymium (2I87U3734A)
    Language English
    Publishing date 2020-02-01
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 1222930-1
    ISSN 1432-119X ; 0301-5564 ; 0948-6143
    ISSN (online) 1432-119X
    ISSN 0301-5564 ; 0948-6143
    DOI 10.1007/s00418-020-01846-0
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    In stock of ZB MED Cologne/Königswinter

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  6. Book ; Thesis: Towards a molecular understanding of connexin43 gap junctions

    Giepmans, Benjamin Nicolaas Gijsbertus

    2001  

    Author's details door Giepmans, Benjamin Nicolaas Gijsbertus Giepmans
    Language English ; Dutch
    Size 119 S. : Ill., graph.Darst.
    Publishing country Netherlands
    Document type Book ; Thesis
    Thesis / German Habilitation thesis Leiden, Univ., Diss., 2001
    Note Zsfassung in niederländ. Sprache
    HBZ-ID HT013422963
    Database Catalogue ZB MED Medicine, Health

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    Shelf markLoan statusLocation
    2002 E 3258 order for loan Magazin

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  7. Article ; Online: Microscopic modulation and analysis of islets of Langerhans in living zebrafish larvae.

    Faraj, Noura / Duinkerken, B H Peter / Carroll, Elizabeth C / Giepmans, Ben N G

    FEBS letters

    2022  Volume 596, Issue 19, Page(s) 2497–2512

    Abstract: Microscopic analysis of molecules and physiology in living cells and systems is a powerful tool in life sciences. While in vivo subcellular microscopic analysis of healthy and diseased human organs remains impossible, zebrafish larvae allow studying ... ...

    Abstract Microscopic analysis of molecules and physiology in living cells and systems is a powerful tool in life sciences. While in vivo subcellular microscopic analysis of healthy and diseased human organs remains impossible, zebrafish larvae allow studying pathophysiology of many organs using in vivo microscopy. Here, we review the potential of the larval zebrafish pancreas in the context of islets of Langerhans and Type 1 diabetes. We highlight the match of zebrafish larvae with the expanding toolbox of fluorescent probes that monitor cell identity, fate and/or physiology in real time. Moreover, fast and efficient modulation and localization of fluorescence at a subcellular level, through fluorescence microscopy, including confocal and light sheet (single plane illumination) microscopes tailored to in vivo larval research, is addressed. These developments make the zebrafish larvae an extremely powerful research tool for translational research. We foresee that living larval zebrafish models will replace many cell line-based studies in understanding the contribution of molecules, organelles and cells to organ pathophysiology in whole organisms.
    MeSH term(s) Animals ; Fluorescent Dyes ; Humans ; Islets of Langerhans ; Larva ; Microscopy, Fluorescence ; Zebrafish
    Chemical Substances Fluorescent Dyes
    Language English
    Publishing date 2022-06-17
    Publishing country England
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 212746-5
    ISSN 1873-3468 ; 0014-5793
    ISSN (online) 1873-3468
    ISSN 0014-5793
    DOI 10.1002/1873-3468.14411
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  8. Article: Integrated Array Tomography for 3D Correlative Light and Electron Microscopy.

    Lane, Ryan / Wolters, Anouk H G / Giepmans, Ben N G / Hoogenboom, Jacob P

    Frontiers in molecular biosciences

    2022  Volume 8, Page(s) 822232

    Abstract: Volume electron microscopy (EM) of biological systems has grown exponentially in recent years due to innovative large-scale imaging approaches. As a standalone imaging method, however, large-scale EM typically has two major limitations: slow rates of ... ...

    Abstract Volume electron microscopy (EM) of biological systems has grown exponentially in recent years due to innovative large-scale imaging approaches. As a standalone imaging method, however, large-scale EM typically has two major limitations: slow rates of acquisition and the difficulty to provide targeted biological information. We developed a 3D image acquisition and reconstruction pipeline that overcomes both of these limitations by using a widefield fluorescence microscope integrated inside of a scanning electron microscope. The workflow consists of acquiring large field of view fluorescence microscopy (FM) images, which guide to regions of interest for successive EM (integrated correlative light and electron microscopy). High precision EM-FM overlay is achieved using cathodoluminescent markers. We conduct a proof-of-concept of our integrated workflow on immunolabelled serial sections of tissues. Acquisitions are limited to regions containing biological targets, expediting total acquisition times and reducing the burden of excess data by tens or hundreds of GBs.
    Language English
    Publishing date 2022-01-19
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2814330-9
    ISSN 2296-889X
    ISSN 2296-889X
    DOI 10.3389/fmolb.2021.822232
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  9. Article: Sample preparation for energy dispersive X-ray imaging of biological tissues.

    Pirozzi, Nicole M / Kuipers, Jeroen / Giepmans, Ben N G

    Methods in cell biology

    2020  Volume 162, Page(s) 89–114

    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 ... ...

    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.
    MeSH term(s) Microscopy, Electron ; Specimen Handling ; X-Rays
    Language English
    Publishing date 2020-12-15
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 0091-679X
    ISSN 0091-679X
    DOI 10.1016/bs.mcb.2020.10.023
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  10. Article: Nanobody-Based Probes for Subcellular Protein Identification and Visualization.

    de Beer, Marit A / Giepmans, Ben N G

    Frontiers in cellular neuroscience

    2020  Volume 14, Page(s) 573278

    Abstract: ... labeling with antibodies such as immunoglobulin G (IgGs) or use of genetically encoded tags ... g., purification are also easily added. These nanobody-based probes can be applied in cells for live ...

    Abstract Understanding how building blocks of life contribute to physiology is greatly aided by protein identification and cellular localization. The two main labeling approaches developed over the past decades are labeling with antibodies such as immunoglobulin G (IgGs) or use of genetically encoded tags such as fluorescent proteins. However, IgGs are large proteins (150 kDa), which limits penetration depth and uncertainty of target position caused by up to ∼25 nm distance of the label created by the chosen targeting approach. Additionally, IgGs cannot be easily recombinantly modulated and engineered as part of fusion proteins because they consist of multiple independent translated chains. In the last decade single domain antigen binding proteins are being explored in bioscience as a tool in revealing molecular identity and localization to overcome limitations by IgGs. These nanobodies have several potential benefits over routine applications. Because of their small size (15 kDa), nanobodies better penetrate during labeling procedures and improve resolution. Moreover, nanobodies cDNA can easily be fused with other cDNA. Multidomain proteins can thus be easily engineered consisting of domains for targeting (nanobodies) and visualization by fluorescence microscopy (fluorescent proteins) or electron microscopy (based on certain enzymes). Additional modules for e.g., purification are also easily added. These nanobody-based probes can be applied in cells for live-cell endogenous protein detection or may be purified prior to use on molecules, cells or tissues. Here, we present the current state of nanobody-based probes and their implementation in microscopy, including pitfalls and potential future opportunities.
    Language English
    Publishing date 2020-11-02
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2452963-1
    ISSN 1662-5102
    ISSN 1662-5102
    DOI 10.3389/fncel.2020.573278
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