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EPFL Flow Cytometry Core Facility (Lausanne, Switzerland)

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Our Services

The École Polytechnique Fédéral de Lausanne (EPFL) Flow Cytometry Core Facility (FCCF) provides services for cell sorting, designing experiments and analysing data. The facility also has a number of multi-colour analysers available.

Staff of the FCCF have a vast amount of experience in flow cytometry. If you have a question, you can find someone in the facility who can provide help.

To request a sort or help please email

Links and Forms


The benchtop analysers are available for scientists to do the experiments by themselves once they have completed the necessary training. The analysers are maintained and cared for by the FCCF staff. There are two CyAn's, one BD LSR II and one Accuri C6 available on the platform.

All instruments are located in room AI 0247.

First time user

If you have never performed flow cytometry experiments at EPFL and you would like to start, please download the form 'Flow Cytometry Training FCCF EPFL'. Fill it in and then email it to to schedule a training time. The aim of the training is to familiarise you with the operating protocols used in the core facility, to demonstrate how to use the machines correctly and to advise on how to set up and operate the instruments for successful experiments.

Once the training has been completed, access to the intranet booking system is granted and bookings can be made at the convenience of users.


The SVINTRANET web site contains the booking system.

Analyse Data

Please do not book the instruments do analyse your data. There is one PC and one Mac computer available in room AI 0357 to analyse your data.

The available software on the PC are:

  • FlowJo
  • Diva
  • Summit
  • Accuri

The Mac only contains FlowJo.

The FCCF team is available to help you analyse your data, send an email to if you require assistance.


Cell Sorting by Flow Cytometry

A solution of particles with light and fluorescent properties measurable by flow cytometry can also be sorted using cell sorter flow cytometers.

 A gate is drawn on a computer graph to identify the cells or particles that are going to be sorted. A small part of the sample is used to make an 'analysis' file and the gates are set up using this data.

 The sample to be sorted is run through the machine and the stream containing the cells is broken into thousands of droplets. Each droplet containing one copy of the cell to be sorted is given an electric charge. These droplets are attracted to the electrically charged plates and are thus 'pulled out' of the stream and collected.



Two instruments are available to sort cells, the FACSVantage SE DIVA and the FACSAria II.

 Specialist Operators

Both sorters are set up and run by FCCF staff on behalf of scientists to get the most out of the instruments and to ensure that they are maintained to the highest standards.

 New Project

When beginning a new project using cell sorting, you are invited to make an appointment to meet with a staff member from the flow cytometry core facility to discuss what you are trying to achieve and plan how to get the most out of your cell sorting reservations. Email to make an appointment.


Please fill in the Sort Booking Form and email the form to to request a sort. The FCCF staff will do the reservation given availability. You will receive a calendar invitation, please check and accept the invitation for the sort. The booking can also be checked on the SV booking and billing system website if you have an SV user account.    

The availability for the FACSVantage SE Diva and the ARIA II can be checked on the SV Intranet booking calendar. Note: at present we do not have a way to display operator availability. We aim to book your sort as soon as possible, however keep in mind that there are many other tasks that take our time in running the flow cytometry facility. We therefore may not be always available to carry out a sort.

 SV Intranet

Log on to the SV booking and billing system with your EPFL account and click on the ‘switch to day view’ button to view the bookings for both sorters.