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.


Our Mission

The Electron Microscopy Core Facility provides advanced expertise in cellular electron microscopy ─ from sample preparation to image analysis ─ and for a large variety of biological samples ranging from macromolecular complexes to tissues. The services we provide consist of: performing the experiments, assisting the users in their use of facility resources and providing advanced teaching and training. The imaging techniques that we can provide bridge analysis at an atomic resolution with microscopy techniques on living specimens.

Advanced Equipment

The EMCF offers access to cutting edge electron microscopes and machines for advanced specimen preparation. We are equipped with a high-pressure freezing machine, which is routinely used for vitrifying biological samples. Specimens can then be dehydrated, stabilised and embedded in resins using our advanced freeze substitution units. Strong expertise has been developed for many different specimens such as yeast cells, adherent cultured cells, Drosophila embryos, nematodes, zebrafish embryos, marine organisms, and tissues. In addition, chemical fixation can be performed in a microwave-assisted sample processor, which greatly reduces the time spent preparing the samples (from days to hours).

We are equipped with three transmission electron microscopes: a FEI Tecnai F30 300kV microscope used for electron tomography on plastic sections, a JEOL JEM 2100Plus 200kV microscope for 2D screening, large-area montaging and electron tomography, and a JEOL JEM1400Flash 120kV microscope used for 2D screening.

For 3D volume techniques we currently have two Zeiss Crossbeam Focused Ion Beam (FIBSEM) systems (Crossbeam 540 and Crossbeam 550) and a Zeiss Gemini/3View Serial Block Face Electron Microscope (SBEM).

EMCF services include access to EMBL IT’s central storage and computing facilities for 3D reconstruction and cellular modelling.

Techniques offered in the EMCF:

Sample preparation for electron microscopy

  • Negative staining
  • Chemical fixation

Ultramicrotomy (including serial sectioning).

Cryo-ultramicrotomy (Tokuyasu technique).


Volume EM and 3D imaging

Correlative light and electron microscopy 

  • on section CLEM
  • cryo-CLEM (Tokuyasu CLEM)
  • 3D CLEM

Image analysis and 3D cellular modelling.


We charge an hourly usage fee as a contribution to our maintenance and consumables costs.

As of 1.3.2023 these fees are as follows:

• Academic visitors: 45€ per hour

• Industry visitors: full cost (135€ per hour)

Internal usage fees

• Access to the virtual workstations for data analysis and exploration is charged with 1.50€ per hour.