Flow Cytometry


Experiments involving flow cytometry should be planned and discussed ahead with the BioOptics Facility staff. Before using any of the analytical machines (FACS Fortessa, Cytek Aurora, IQue Screener, Penteon) and the Sony SH800 & MA900 sorter, a training by the BioOptics Facility staff is compulsory prior to usage. This is also applicable for additional parts of a system e.g. plate loader.

Users do not train other users!

If you cannot remember how to operate a system you were already introduced to, please do not hesitate to ask the BioOptics team for advice.

The training for the independent use of Flow Cytometers consists of 2 parts - a theoretical lecture (available once a month) and a practical individually scheduled Hands-on session. Because the machines differ in software and features, separate hands-on training is necessary for each machine.

For the Sony MA900, situated in a S2 lab, an additional BioSafety Training is necessary.

Please only request a Hands-on Training when you will use the machine within 3 weeks.

Introductions can be requested via the PPMS booking system

Fur further questions and information please contact the FACS Team via facs(at)imp.ac.at.



Sign-Up Instruments

The analytical machines (FACS Fortessa, Cytek Aurora, IQue Plus, Penteon) and the Sony Sorter SH800 & MA900 can be reserved through the Online Booking system PPMS - https://booking.vbc.ac.at. Sign-Up is on a first come, first serve basis.

If the user does not show up within 30 minutes after the start of the booking-time the whole reservation is cancelled and the equipment is available to everybody.

In PPMS you can also sign up to receive an e-mail, if a booking on a chosen analyser is deleted or shortened and therefore additional instrument-time is available. A quick guide on how to use PPMS can be found here.

To allow proper planning for everybody, we would strongly ask you to well plan your experiments, only book the time you actually need and cancel or shorten your bookings as soon as you find out that plans have changed!

Cell sorters (Aria) may be booked via the BioOptics Service Desk

Please note: For sorting experiments that can be done on the self-operated Sony SH800, Arias must not be used. Please contact facs(at)imp.ac.at for further information.

For S2 sorting needs the sorter Sony MA900 is available in a S2 lab, please request a training via PPMS or contact facs(at)imp.ac.at for further information.

Clean-Up and Shut-Down

Users are responsible to clean up after completion of their measurements. Please follow the respective shutdown and cleaning procedures of the instrument in our protocols section.
The last user is asked to power-down the system at the end of the day (check the booking system!).

Working with Lentivirus

Cells treated with Lentivirus (except for Lentivirus with ecotropic envelope protein), must pass 10 times media exchange and 2 weeks’ time since the treatment, before they are allowed to be processed within rooms of the BioOptics Facility (FACSroom ; Microscopy rooms). In case of doubts about the other viral transfections used, please get in touch with the Biosafety officers and BioOptics staff.

Working with Trizol/β-Mercaptoethanol

Working with Trizol and/or β-Mercaptoethanol is not allowed at the Facility. It is also not allowed in collection tubes for FACS sorting.

Data Storage

All data should be stored on server space! Data stored on local hard disks can be deleted at any time without notice.


If you publish work supported by the BioOptics Facility, e.g. by using one or more analysers or support in cell sorting as well as in data analysis, please do not forget to acknowledge the facility in your paper.


If you encounter any problems with the equipment, please inform BioOptics staff as soon as possible even if the problem has been resolved.
If you have any questions concerning the operation of the machines or the planning and execution of experiments do not hesitate to ask the BioOptics staff for assistance.