Flow Cytometry Core Facility

The Flow Cytometry Core Facility offers a range of flow cytometric techniques.


The Flow Cytometry Core Facility

provides advanced expertise in the entire workflow of a flow cytometry experiment from sample preparation to post-acquisition analysis.  Please contact the facility by writing an email to: diana.ordonez@embl.de to discuss how we could support your scientific project.  

Experimental Design

We offer our users support in sample preparation, labeling strategies, panel design for multi-color flow cytometry, and reagent selection. We also have an extensive collection of protocols for  sample processing and labeling in our external webpage: https://flowcytometry-embl.de/protocols/

Sample Acquisition

Staff members of the facility could acquire samples for users requiring a one-time experiment.  If your project requires the recurrent usage of the analyzers, a training session should be requested. Please refer to the Training section tab 

* We could support the urgent acquisition of samples before the scheduled training session takes place. Write an email to: fccf-team@embl.de

Cell Sorting

Cell sorting is typically performed by the staff members or independent users after following the corresponding training.

To access the sorting service, users should complete and submit a sort request form found in the ppms reservation system under the “Request” tab.  Please fill in the information about your samples as precisely as possible and provide 3 potential dates for your sort. The request form will be processed and the sorting slot confirmed by email after analyzing the needs of your experiment (summarized in the request form) and the availability and configuration of the instruments. 

The schedules of the sorters could be visualized in the ppms reservation system and should be checked before proposing a sorting date to avoid overlapping with slots already granted.  Please note that users could not book sorters in the ppms system even if they have received training. Independent users of the BD FACSAria Fusion should submit a sort request indicating independent usage. 

Samples to be sorted should be prepared as described in the document: Sample Preparation for Cell Sorting.

Once your sorting is done, data will be transfer to the fccfdata server: Sorting_service folder.  For instructions on how to reach the server, please read the document: Retrieving sorting data.

Please take into account:

Sorting request. The information you provide in the request form allows us to determine the appropriate configuration of the sorter (nozzle size, pressure, optical configuration) to get the best resolution out of your samples. For this reason, we ask you to be as precise as possible when filling the form and to avoid modifications of fluorochromes/fluorescent proteins on the day of the sorting without telling us in advance.                                   

Sorts are scheduled on a first-booked-first-served basis. We will attempt to prioritize sorts that are time-dependent or require subsequent processing in another facility (i.e., gene core). We do expect a reciprocal degree of flexibility from our users. If your sort has to be moved or canceled, the facility will let you know as soon as possible and re-schedule it to the nearest available time.  

Let us know if problems occurred after your sorts, such as low viability, poor cell numbers, contamination, or other issues. If we don’t know about them, we can’t do anything about it, and we could potentially affect other people’s sorts. Please take the time to provide feedback on your sorts.  


We offer training in the use of our flow cytometers, cell sorters, and specialized software for data analysis.  Send an email to fccf-team@embl.de to discuss your training needs. 

Flow cytometers/Analyzers:  Once you get a training slot make sure to read the following document explaining the samples that should be brought to your training: Training information

After completing the training, you will gain access to the analyzers’ room (V104), and you will be able to reserve the cytometers using the “Book” tab in the ppms booking system. As we do not expect you to be totally independent after the training session, you could ask for assistance when acquiring your samples. Please ask in advance to make sure someone from the staff is available to help you.  

Cell sorters: 

Training for sorting is preferentially granted to users who require several sorting per week or need to perform sorting after working hours or during the weekends.   

BD FACSAria Fusion: Training in this sorter is addressed to users with previous experience using the DIVA software,  handling S2 samples, or those who require red and UV lasers. After completing a two-day training session, users could operate the instrument independently but do not get the right to book the instrument by themselves. Independent users of the BD FACSAria Fusion should submit a sort request indicating independent usage. 

Data analysis:

We offer support and training in data analysis  using the following software:




External training 

Please visit our external webpage to check our upcoming events. 



We charge an hourly usage fee.

External academic visitor (EMBL member state) and industry: usage fee is calculated to cover the instrument maintenance and related consumables costs, currently 50€/hour.

For information on internal usage fee, please click on the following link:

Internal usage fee