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.


General guidelines

  • New users should discuss their projects with the EMCF staff to identify the best strategies in answering their biological question. If the work is to be carried out autonomously by the user, a thorough introduction of the machines will be given to the user.
  • Before you start working in the EMCF, an introduction to the machines being used and how waste is disposed is compulsory. If you cannot remember how to operate a machine you were already introduced to, please ask the EMCF staff for advice. Please note: if you have not used the machine for six months after your initial training, the training session will be repeated by an EMCF staff member before further use of the machine.
  • The working environment in the EMCF is S1 (bio safety level 1). In case, you need to work with S2 organisms, please contact us well in advance.
  • We charge an hourly usage fee as a contribution to our maintenance and consumables costs. The usage fee is 45 EUR per hour for external academic visitors. Industry are charged full costs at 135 EUR per hour. Click here for information on the internal usage fee.
  • If you publish work supported by the EMCF (e.g. by using one or more of the machines in the EMCF or by the staff’s support) it is obligatory to include this sentence in the acknowledgement:

We thank the Electron Microscopy Core Facility (EMCF) at the European Molecular Biology Laboratory (EMBL) for their support.

Moreover, if the EMCF staff members contributed significantly to the published work, and it’s in accordance with EMBL IP rule #63, staff members shall be included in the author lists.


  • Booking of the instruments before use is obligatory.
  • You are responsible for the system while you are booked.
  • Delete your booking, if you do not use your slot. If you delete the last booking on the day, ensure that the system is switched off (the previous user might finish before you delete your booking). If it is a microscope, please start the cryo cycle.
  • Check with the facility staff if you expect to run a microscope over an extended period of time (>5h). There are special protocols for automated data collection that might be useful in this case.


  • We strongly advise to save your data immediately on your group server.
  • In case of local storage shortage, the EMCF staff will delete any data files older than 2 days. Any other user of the instrument is entitled to do the same in case more local disk space is needed.Be aware that there is no backup of the local hard disk drives of all EMCF PCs.
  • If you are an external visitor staying for a long period of time, it can be useful to bring an external hard drive to transfer your data before leaving.

Instruments and common spaces

  • Please treat the equipment with extreme care.
  • Check the equipment for any obvious damage or problems and tell an EMCF staff member. Please also fill the incident report in PPMS accordingly.
  • We work with very dangerous and toxic chemicals in the EMCF, therefore all chemicals should be used under the fume hoods. It is compulsory to clean up after yourself when finished, throw waste into proper waste containers and store chemicals in their proper containers. If you are not sure, ask an EMCF staff member.
  • All microtome rooms should be kept clean at all times. When you are finished, clean up after yourself.