Electron Microscopy Center

RTC Microscopy seminars

Experts and users of the RTC Microscopy present seminars on various microscopy setups and their applications.

For each edition of the RTC Microscopy Seminars, we aim to include one seminar on electron microscopy, one on light microscopy, and one on image analysis. The seminars target a broad audience and besides presenting the results of a microscopy-based research project, the presenters typically also provide a basic overview of the possibilities and pitfalls of the used techniques. The next RTC Microscopy Seminars will be announced soon. The past events can be found below.

• 11 July 2023

  Program

  • Luco Rutten (Medical Biosciences): The power of transmission electron microscopy: from basic to advanced TEM at Radboudumc
  • Malou Zuidscherwoude (Medical Biosciences): Advanced light microscopy approaches to understand the interaction between the calcium channel TRPV5 and calmodulin
  • Gert-Jan Bakker (Medical Biosciences): QUAREP-LiMi, a community-driven initiative for improved reproducibility in microscopy related research

• 4 April 2023

  Program

  • Robin van der Meijden (Medical Biosciences): 3D correlative live-to-cryo imaging: combining Raman, light and electron microscopy on Biological Tissues
  • Mark Gorris (Medical Biosciences): Studying Immune Cells in the Tumor Microenvironment: Multiplex Immunohistochemistry and Multispectral Imaging
  • Sjoerd van Deventer (Medical Biosciences): Combining dSTORM and cluster analysis to investigate the plasma membrane nanoscale organization

• 24 November 2022

  Program

  • Julie Verhoef (Medical Microbiology): (Cryo-)Expansion microscopy to visualize malaria parasites
  • Marcos Eufrásio Cruz (Biochemistry): Understanding the functionality of extracellular matrix vehicles using cryogenic transmission electron microscopy
  • Andrea Frielink-Loing (RTC Data Stewardship): Digital Research Environment for data storage, analysis, and collaboration

• 8 September 2022

  Program

  • Moritz Negwer (Human Genetics/Donders Center): Tissue clearing and light-sheet microscopy: whole-organ imaging at cellular resolution
  • Mariska Kea-te Lindert (Electron Microscopy Center, RTC Microscopy): 3D array tomography: an accessible method for 3D imaging of millimeter volumes at nanoscale resolution
  • Merijn van Erp (RTC Microscopy): Deep learning for the selective segmentation of cellular structures

Published papers

• 2024

  • Giubertoni, Giulia, et al. "Elucidating the role of water in collagen self assembly by isotopically modulating collagen hydration." PNAS (2024): 121 (11) e2313162121 https://www.pnas.org/doi/10.1073/pnas.2313162121
  • Schaart, Judith M., et al. "Cell-induced collagen alignment in a 3D in vitro culture during extracellular matrix production." Journal of Structural Biology (2024): 108096. https://www.sciencedirect.com/science/article/pii/S1047847724000364

• 2023

  • Van der Meijden, Robin HM, et al. "A 3D Cell‐Free Bone Model Shows Collagen Mineralization is Driven and Controlled by the Matrix." Advanced Functional Materials (2023): 2212339. https://onlinelibrary.wiley.com/doi/10.1002/adfm.202212339

  • De Beer, Marit, et al. "Precise targeting for 3D cryo-correlative light and electron microscopy volume imaging of tissues using a FinderTOP." Communications Biology 6.1 (2023): 510. https://www.nature.com/articles/s42003-023-04887-y

  • Carotti, Valentina, et al. "Extracellular vesicles contribute to early cyst development in autosomal dominant polycystic kidney disease by cell‐to‐cell communication." The FASEB Journal 37.7 (2023): e23006. https://faseb.onlinelibrary.wiley.com/doi/10.1096/fj.202300490R

  • Bulthuis, Elianne P., et al. "Stress‐dependent macromolecular crowding in the mitochondrial matrix." The EMBO Journal 42.7 (2023): e108533. https://www.embopress.org/doi/full/10.15252/embj.2021108533

  • Konijnenberg, Lara SF, et al. "Imatinib attenuates reperfusion injury in a rat model of acute myocardial infarction." Basic Research in Cardiology 118.1 (2023): 2. https://link.springer.com/article/10.1007/s00395-022-00974-z

  • Besheli, Negar, et al. "Unraveling the Formation of Gelatin Nanospheres by Means of Desolvation." Nano Letters (2023): 11091 https://pubs.acs.org/doi/full/10.1021/acs.nanolett.3c03459

  • Papadopoulou, Panagiota, et al. "Phase-Separated Lipid-Based Nanoparticles: Selective Behavior at the Nano-Bio Interface." Advanced Materials (2023): 2310872. https://onlinelibrary.wiley.com/doi/full/10.1002/adma.202310872

• 2022

  • Kapteijn, Renée, et al. "Endocytosis-like DNA uptake by cell wall-deficient bacteria." Nature Communications 13.1 (2022): 5524. https://www.nature.com/articles/s41467-022-33054-w
  • Jansen, Jitske, et al. "Human pluripotent stem cell-derived kidney organoids for personalized congenital and idiopathic nephrotic syndrome modeling." Development 149.9 (2022): dev200198. https://journals.biologists.com/dev/article/149/9/dev200198/275303/Human-pluripotent-stem-cell-derived-kidney
  • Jansen, Jitske, et al. "SARS-CoV-2 infects the human kidney and drives fibrosis in kidney organoids." Cell stem cell 29.2 (2022): 217-231. https://www.cell.com/cell-stem-cell/pdf/S1934-5909(21)00520-8.pdf
  • de Wildt, Bregje WM, et al. "Bioinspired Silk Fibroin Mineralization for Advanced In Vitro Bone Remodeling Models." Advanced Functional Materials 32.41 (2022): 2206992 https://onlinelibrary.wiley.com/doi/full/10.1002/adfm.202206992
  • Carotti, Valentina, et al. "Involvement of ceramide biosynthesis in increased extracellular vesicle release in Pkd1 knock out cells." Frontiers in Endocrinology 13 (2022): 1005639. https://www.frontiersin.org/articles/10.3389/fendo.2022.1005639/full

• 2021

  • Visualizing biological tissues: A multiscale workflow from live imaging to 3D Cryo-CLEM (Beer et al., 2021)
  • HPM live MU for a full CLEM workflow (Heiligenstein et al., 2021)
  • Composition and stage dynamics of mitochondrial complexes (Evers et al., 2021)

Examples figures from our papers

• Example 1

  Correlation of FIB/SEM with light microscopy in 3D showing mitochondria (in purple) within cells of a zebrafish scale, under cryo conditions.

  Link to the paper: www.nature.com/articles/s42003-023-04887-y

  

• Example 2

  A cryoFIB/SEM image and subsequent 3D reconstruction of a bacteria reveal both intracellular and protruding out vesicles.

  Link to the paper: www.nature.com/articles/s41467-022-33054-w

  

• Example 3

  3D FIB-SEM segmentation showing viral particles (orange) in a vacuole (magenta) in close proximity to the nucleus (blue) of an infected cell in a kidney organoid.

  Link to the paper: https://doi.org/10.1016/j.stem.2021.12.010

  

• Example 4

  3D volume reconstruction of a kidney organoid, imaged by FIB-SEM, showing podocytes (yellow, magenta) and foot processes.

  Link to the paper: https://doi.org/10.1242/dev.200198

  

• Example 5

  3D reconstruction of cells (green) and their extracellular matrix (magenta) in a 3D cell culture system imaged with FIB/SEM. Link to the paper: https://www.sciencedirect.com/science/article/pii/S1047847724000364.