Electron Microscopy Core Facility

The facility provides advanced expertise in electron microscopy, from sample preparation to image analysis, for a wide variety of biological samples.

The EMCF activities cover a large spectrum of EM techniques with a major focus on sample preparation, immuno-localisation of proteins, ultrastructural analysis in 2D and 3D, correlative light and electron microscopy and data processing. 


Major projects

Staff in the facility can help you to define optimal experimental conditions for your project – we have experience spanning virtually the full spectrum of biological specimens, with high-level resources for both research and training.

Advanced equipment

Besides the EM imaging, we offer access to a high-pressure freezing machine. These instruments are routinely used to vitrify biological samples. Specimens can then be dehydrated, stabilised and embedded in resins in specific freeze-substitution units. Strong expertise has been developed for yeast cells, adherent cultured cells, Drosophila embryos, nematodes, zebrafish embryos, and mouse tissues. A microwave-assisted sample processor, used for chemical fixation, dehydration and embedding, greatly reduces time spent preparing the samples (from days to hours). For Tomography, two transmission electron microscopes (a FEI TECNAI F30 300kV and a 200kV JEOL JEM 2100Plus are available. EMCF services include access to EMBL IT’s central storage and compute facilities for 3D reconstruction and cellular modelling.

The Electron microscopist ‘savoir faire’

We are deeply involved in method development and training. A recent example in correlative light and electron microscopy (CLEM) is the implementation of a technique developed by the Briggs and Kaksonen groups, which tracks the signal of fluorescent proteins in resin sections with high precision.

We have just published a detailed step-by-step video tutorial on this method in EMBL’s e-learning channel.

The future in perspective

Since 2014, the facility has started to provide services in automated serial imaging in scanning electron microscopy (ASI-SEM), such as focused ion beam SEM (FIB-SEM)). This technique complements our portfolio of 3D imaging applications (serial section, electron tomography) by providing new opportunities for understanding the cellular fine architecture of multi-cellular specimens. The facility is also offering support for the recently developed cryo-CLEM techniques (see Schorb and Briggs 2014, 2016), which will nicely bridge structural and cell biology.

Figure 1: On section CLEM: the signal from fluorescent proteins is used to target the EM analysis to specific subcellular timepoints during the endocytic process (adapted from Avinoam, et al. 2015).

Figure 2: Live-cell correlative light and FIB-SEM captures specific stages of anaphase in dividing HeLa cells, revealing the formation of new nuclear envelope and the integration of nuclear pores. Adapted with permission from Otsuka et al. 2018

Single-particle and tomography cryo-EM for structural biology projects is offered through the cryo-EM service platform.


Recent achievements

Software tools for automated transmission electron microscopy.
Schorb M, Haberbosch I, Hagen WJH, Schwab Y, Mastronarde DN.
Nature Methods. 2019 Jun. doi: 10.1038/s41592-019-0396-9.

Postmitotic nuclear pore assembly proceeds by radial dilation of small membrane openings.
Otsuka S, Steyer AM, Schorb M, Hériché JK, Hossain MJ, Sethi S, Kueblbeck M, Schwab Y, Beck M, Ellenberg J.
Nat Struct Mol Biol. 2018 Jan;25(1):21-28. doi: 10.1038/s41594-017-0001-9. | Abstract

Pre-assembled Nuclear Pores Insert into the Nuclear Envelope during Early Development.
Hampoelz B, Mackmull MT, Machado P, Ronchi P, Bui KH, Schieber N, Santarella-Mellwig R, Necakov A, Andrés-Pons A, Philippe JM, Lecuit T, Schwab Y, Beck M.
Cell 2016, 166(3):664-78. doi: 10.1016/j.cell.2016.06.015 | Abstract

Visiting the ECMF

We are very happy to welcome visitors in the Electron Microscopy Facility if capacity allows.

Please note that visitors from EMBL’s Member or Associated Member States are our first priority.

If you would like to apply as a visitor in the EMCF, please contact us by email including a short overview of your project. We will discuss the feasibility of your project internally and in case of a positive evaluation we will contact you for a more detailed meeting over the phone, via Zoom or video conference.

The EMCF currently participates in several initiatives supporting visitor access:

  • Euro-BioImaging open access
    The ALMF is part of the EMBL node in Euro-BioImaging. Together with the Electron Microscopy Core Faciility (EMCF) at EMBL Heidelberg and the Mesoscopic Imaging Facility (MIF) at EMBL Barcelona, the EMBL node offers open access to a broad range of state-of-the-art technologies in biological imaging for life scientists.
  • Christian Boulin fellowship
    The Fellowships support travel and accommodation costs of young scientists visiting EMBL Core Facilities at the different EMBL sites.


Electron Microscopy Core Facility
EMBL Heidelberg,
Meyerhofstraße 1,
69117 Heidelberg, Germany
Phone: +49 6221 387-8413
Send an email