Usage Policy: Cytometry


All guidelines described  for ‘microscopy’ also apply for the use of our flow cytometry equipment:

  • All users need a training by the BioImaging Facility staff before they can book a specific system
  • All systems need to be booked before use: see booking system
  • It is strictly forbidden to use any of the setups without booking or training
  • It is strictly forbidden to use any of the setups in the name or booking of another user
  • Bookings can not be made longer than 14 days in advance


Please only make use of our centralized communication channels and avoid direct communication as we can not guarantee staff availability.

The following additional rules apply to the BD FACS Aria III

  1. Startup and shutdown of the machines is performed by BioImaging Facility staff only: we cannot make exceptions, as they result in down-times and additional costs.
  2. FACS Aria III service can only be provided within the following times: 9 am till 5:00 pm Monday-Thursday, 9 am till 15:30 pm Friday.
  3. To ensure availability of the FACS service, your reservation needs to be made at least two working days in advance of your experiment (i.e., Monday for Wednesday etc.). Only when the Aria is booked on time, can we guarantee that the service will be provided – personnel has to be scheduled for the startup/reconfiguration/shutdown times. (Weekend days count as one day- i.e. , you have to book on Friday to ensure service on Monday.)
  4. If FACS service is requested on a shorter term (via email to, we TRY to match your needs, but cannot guarantee it. The reason is, that our FACS experts are also providing other services and have to plan their time in advance.
  5. Cancelling FACS bookings within 24 hours prior to slot start is only possible via email to
    Since the device has to be prepared well in advance, failure to cancel at least 2 hours before the start of your session will result in startup and shutdown charges.
  6. In case late sorts (past 6 p.m.) or weekend sorts are required: we cannot guarantee them. In case there is a SERIOUS experimental demand on this, we can discuss it on a case-by-case basis and look for a solution. Please contact us about such requests several weeks in advance.
  7. If your configuration (nozzle size, temperature or sample collection rack) differs from that of the previous user or if you are the first user at the time of booking, please make sure you always select the ‘Set sorting configurations by BIF’ checkbox in your booking. This is needed to ensure enough time before your slot to allow us to reconfiguration the sorter for your experiment– otherwise we’ll have to do it in your session!

The following additional rules apply to the Sony SH800SFP

Cytometry service hours for assistance and for novice users

  • Monday – Thursday: 8:30 – 17:30
  • Friday: 8:30 – 15:30

Usage policy

  • Novice: All users start with ‘novice usage rights’: Bookings can only be made during the above mentioned cytometry service hours, and need to be confirmed (see guidelines) → Startup, shutdown and sample line exchange must be completed within this timeframe.
  • Autonomous: to book devices outside of core hours “autonomous usage rights” are required. To obtain autonomous user rights on the Sony SH800, one needs to complete 5 independent sessions without need of experimental assistance → incidents due to incorrect use, startup, or shut down procedure might result in a prolongation of the novice period.
  • Contaminating samples: all experiments with potentially contaminating samples (e.g. bacteria) MUST be done with a separate (user owned) sample line. Own sample lines can be used when desired.
  • Sample line exchange: by default, the sample line exchange needs to be requested (see above) and is performed by BIF staff (during core facility hours). Autonomous users can request an additional training (see communication channels) that allows sample line exchange by experienced users.

Assistance & Requests (help, sample line exchange, etc.)

  • To ensure availability of FACS service (novice assistance), your reservation needs to be made minimal two working days in advance of your experiment (i.e., Monday for Wednesday etc.). Only when service is booked in timely in advance, the BioImaging Facility can guarantees that service will be provided. (Weekend days count as one day- i.e. , you have to book on Friday to ensure service on Monday.). Make sure to book assistance using the correct form in PPMS: Request assistance by BIF staff for Flow Cytometry
  • Assistance/session is guaranteed upon confirmation of your request or booking (PPMS – novices).

End of a session / shutdown Sony SH800SFP

  • Cleaning and shutdown protocol must be followed strictly and completely → Tab 4 in the manual
  • Clean the sample chamber and sorting chamber with 70% EtOH → ensure that any sample remains and salt crystals are removed, especially from the deflection plates
  • Refill DI water reservoir after every session
  • Empty waste tank after every session
  • Shut down the main device, PC and compressor completely, unless you are directly approached by the next user → Tab 4 in the manual
  • The last user of the day must refill the sheath tank with PBS to the level indicated on the tank (yellow label) → add the amount of used PBS and MilliQ water bottles to the consumables log-book (located in the pouch inside the cover of manual)