Advanced Light Microscopy Facility

This facility offers a collection of state-of-the-art light microscopy equipment and image processing tools.


General guidelines

  • Introduction by ALMF staff is compulsory for all ALMF systems.
  • If you cannot remember how to operate a system you were already introduced to, please do not hesitate to ask the ALMF team for advice.
  • The working environment in the ALMF is BSL1 (bio safety level 1). In case, you need to work with S2 organisms, please contact us and the safety office well in advance.
  • We charge an hourly usage fee. For external academic visitors (EMBL member state) the usage fee is a contribution to our maintenance and consumables costs. Industry and academic visitors (non-EMBL member states) are charged full costs. Click here for information on the external or internal usage fee.
  • If you publish work supported by the ALMF, e.g. by using one or more ALMF microscopes or support in image or data analysis, it is obligatory to include this sentence in the acknowledgement (also see the EMBL Publication Policy):

We thank the Advanced Light Microscopy Facility (ALMF) at the European Molecular Biology Laboratory (EMBL) and [COMPANY OF USED EQUIPMENT] for support.


  • Booking of the microscope 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 you plan to use the incubator
    • please select the checkbox Temperature different from room temperature in PPMS and indicate the temperature as comment (warming up time should be included in your booking in this case).
      The booked slot should then appear green and the temperature will be visible.
    • When you use the microscope with the incubator, please check PPMS booking at the end of your session
      • If person after you also using the incubator, please leave it on and adjust the temperature if required.
      • If temperature for the next slot is not indicated (Blue box), the incubator has to be switched off. To cool down system faster, please leave opened incubator doors and condenser arm.
    • When booking a slot in PPMS (regardless whether or not using the incubator), please check the bookings before and after you. If temperature needs to be adjusted between the sessions, please try to select your slot such that there is an hour gap between respective sessions.

ALM specific rules

  • Do not reserve the systems for more than 2 weeks in advance.
  • You can book up to 4 hours per day or long-term experiments between 6:00 p.m and 10:00 a.m. and during the whole weekend. Please don’t forget to switch off devices not needed during long-term experiments like the HBO lamp on confocal systems.

High-throughput specific rules

  • To book the high-throughput equipment, please use our booking system. Please contact us for access rights and introduction.
  • Long-term (>1 week) reservations have to be discussed well in advance.


  • We strongly advise to save your data immediately on your group server.
  • In case you save data locally, store it in a folder with the name “user_phone number”, be aware that there is no backup of the local hard disk drives of all ALMF PCs.
  • In case of local memory shortage ALMF staff will delete data files older than 2 days.

ALM-specific rules

  • We provide disc space \\almf\almf\ to transfer data up to 15 GB (temporary, automatically deleted after 30 days).

High-throughput specific rules

  • We provide disc space \\almfscreen\almfscreen to store data up to 250 GB for 6 weeks. Data are automatically deleted after 6 weeks, with a warning by e-mail one week in advance.
  • We strongly recommend to use our Laboratory Information Management System (LIMS), which enables you to link all your images with treatment information.

Before you start

  • Check the equipment for any obvious damage or spoilage and report technical problems as incident in PPMS or tell ALMF.
  • Wipe off dust and smear from the lens and the sample cover slip using lens tissue (soaked in ethanol if required).

While working

  • Check which immersion media are required for each lens you use, before you add any medium (oil, glycerol, water, air). If you don’t know: ask ALMF.
  • Clean immersion media from lenses with a dry lens tissue every time you change slides. Slides should also be cleaned by a dry tissue.
  • Use moderate amounts (1 drop=50 µl) of immersion media. Immediately remove immersion media spilling over the objective rim.

After you have finished

  • Clean immersion media from every lens you used with a dry lens tissue.
  • Check whether the system is booked later on the same day.
  • If you are second last to use the system, make sure the user after you shows up.
  • If you are last user of the day, switch off all lamps and lasers as described in the operations short-manual for each system provided by ALMF.
  • Report problems of the system by informing ALMF by email or in person or create an incident on the PPMS booking page.