Flow Cytometry

The Department of Medicine, Huddinge (MedH) Flow Cytometry Facility at Karolinska Institutet

About us

Flow cytometry is a central technology in biomedical research allowing multiparametric analysis and isolation (by cell sorting) of rare cell populations down to a single cell from complex cell mixtures.

The Department of Medicine Huddinge (MedH) flow cytometry facility is a service facility located at the 4th floor of the Novum research building within the Center for Hematology and Regenerative Medicine (HERM) at the Karolinska Huddinge Campus (see visiting address).

The MedH FACS facility provides open access to all interested researchers at KI and Karolinska regardless of their affiliation and strives to provide each user with skilled services, education and training to achieve high quality research.

The Facility was established in August 2011 with an initial support from the Wallenberg Institute for Regenerative Medicine (WIRM) (http://wirmki.se), a research institute financed by Knut och Alice Wallenbergs Stiftelse. To cover most of its running costs, the facility charges fees for its services (see user Fees for detailed information).

The facility currently houses two analysis instruments and two high-speed cell sorters, including a contained instrument capable of Enhanced Biosafety Level 2 (BSL-2+) cell sorting (see technology for detailed information).

The facility offers a broad range of high quality services including assistance with experimental design, training for independent users, and operator-assisted services cell sorting. Independent access to instrumentation is available to users following completed specific trainings in instrument operation and biosafety.

The facility is also involved in flow cytometry education and organizes user meetings, workshops as well as a doctoral course in flow cytometry all with the aim to promote exchange of technical know-how and knowledge in the field of flow cytometry.


The MedH flow cytometry facility currently houses two cell analyzers and two cell sorters  offering possibilities for advanced multicolor cell analysis combined with high-speed cell sorting based on up to 16 fluorescent parameters and at up to enhanced Biosafety Level 2 standards.

16 parameters, 4 Lasers: 405 nm, 640 nm, 488 nm and 561 nm
Cell Analysis and sorting:  Biosafety Level 2
Download “Config FACSAria™ III”
SORP BD FACSAria™ Fusion
16 parameters, 4 Lasers: 405 nm, 640 nm, 488 nm and 561 nm
Cell Analysis and sorting:  Enhanced Biosafety Level 2
Download “Config FACSAria Fusion”
SORP BD LSRFortessa™ 
16 parameters, 4 Lasers: 405 nm, 640 nm, 488 nm and 561 nm and an integrated 96 well plate module for High-Throughput analysis
Cell Analysis Biosafety Level 1
Download “Config LSRFortessa”
BD FACSCalibur™ 
4 parameters, 2 lasers: 488nm and 635nm
Cell Analysis: Biosafety Level 1
Download “Config FACSCalibur”
CytoFLEX S (Beckman Coulter)
13 parameters, 4 Lasers: 405 nm, 638 nm, 488 nm and 561 nm and an integrated 96 well plate module for High-Throughput analysis
Cell Analysis: Biosafety Level 1
Download “Config CytoFlexS” 

Registration and booking

To register as a new user of the facility please visit: https://next.cirklo.org/karolinska/ and select new user.

To book an instrument please visit: https://next.cirklo.org/karolinska/ and login.
Download detailed instructions for registration and booking

For cell sorting please fill in the sort request form below and send it by email to: Iyadh.douagi@ki.se
Download the sort request form

Booking Rules: Analysers (Fortessa, Calibur, CytoFlex)

  • Booking max 3 weeks in advance
  • Reminder about booking sent 1 week in advance and 2 days before analysis
  • Booking can be cancelled or modified up till 24 hrs before analysis (locked and charged as is after 24hr cutoff)
  • Block bookings can be made for max 3 hrs between 08.00 -16.00 and 5 hrs otherwise
  • Minimum booking time 30 min
  • Override possible with justification and interaction with facility manager
  • Possibility to highlight bookings that are uncertain and/or reserve back-up slots for already reserved bookings before the 24 hr cut-off (in case person cancel, the person who is on the reserve will automatically be the one who gets the slot)

Booking Rules: Sorters (ARIA and Fusion)

  • Booking max 3 weeks in advance
  • Booking can be cancelled or modified up till 24hrs before analysis (locked and charged as is after 24hr cutoff)
  • Block bookings can be made for max 8 hrs
  • Minimum booking time 1 hr
  • Override possible with justification and interaction with facility manager


In order to document usage of the MedH FCF, which is important when securing core funding, the users are encouraged to acknowledge the MedH FCF in publications in which data generated in the facility are included. As a core facility, there are no expectations with regard to co-authorships for the staff operating the facility (unless the users think this is scientifically warranted).

Please use the following statement for acknowledging the MedH FACS facility:

“We would like to acknowledge the MedH Core Flow Cytometry facility (Karolinska Institutet), supported by KI/SLL, for providing cell sorting services**/cell analysis services**/technical expertise**/scientific input**”.

**delete as required.


New users please register here

Please fill in the request form and send it by email to: Iyadh.douagi@ki.se

Download the Service request form

Note: For Cell sorting please also fill in a sort Application form

Download the Sort Application form


Iyadh Douagi

Director Flow Cytometry Facility


Phone: +46 8-585 83602


Leadership group for the MedH Flow cytometry facility:

Dr Petter Woll, Scientific Lead


Dr. Yenan Bryceson


Dr. Iyadh Douagi


Visiting Address

The MedH Flow cytometry facility is situated at the 4th flour, elevator G of the NOVUM research park in Huddinge, adjacent to Karolinska University Hospital in Huddinge.
(See map below)

Visiting address:

Blickagången 6 (by train)

Hälsovägen 7 (by car)

Postal address:

MedH Flow cytometry facility

Hälsovägen 7, Novum plan, 4 hiss G

SE-14157 Huddinge


Phone: +46 8-585 83602

User Fees

Instrument KI Other Academic Commercial

320 SEK/hr

420 SEK/hr 840 SEK/hr
Fortessa 380 SEK/hr 480 SEK/hr 960 SEK/hr
CytoFLEXS 350 SEK/hr 450 SEK/hr 900 SEK/hr
Assisted sort

490 SEK/hr

980 SEK/hr 1960 SEK/hr
Non-assisted sort 490 SEK/hr    
Starting Nov1, 2016
Minimum time for analysis is 30 min and for sorting is 60 min.

Annual membership fee

To cover the cost required for mandatory basic practical training allowing new users to operate analysis instruments in the core facility and annual administrative cost, the facility will from January 2017 implement an annual membership fee of 2000 SEK per user.


FACS educational training and user interaction

With the challenges associated with FACS data, the MedH FACS facility would like to offer all users the opportunity to get expert input on their FACS experiments.

We will meet bi-weekly, Fridays between 12.00-13.00. We will have three slots that are described in more detail below:

1) Short presentation of a specific FACS topic (15 min)

2) Lab specific presentation and discussion (15-20 min)

3) Open Forum (15-20 min)

Short presentation of a specific FACS topic

To spread the general FACS competence that is present in the facility, we have already identified several relevant topics but we also welcome users to suggest FACS related topics that you would like to be discussed. Some of these presentations will be held by the facility staff, but to take advantage of the strong scientific expertise among our users we will also ask individual users that we think have established FACS applications relevant for other users to present as well. Topics will include multi parameter flow cytometry for identification of different stem and progenitor subsets, cell cycle analysis, phosphoflow analysis, high-throughput analysis, cell sorting, controls in FACS, sample preparation and many more. 

Lab specific presentation and discussion

This is intended to give every lab that uses the FACS facility an opportunity to get dedicated time to expose and discuss their FACS data with the members of the facility. To make this efficient for both the facility and the respective labs, we will ask each interested group leader to nominate one person from their lab to organise the presentations. This is to help the facility reduce the number of contacts they need to make in order to make the interaction with the different labs more efficient. The contact person does not necessarily have to present, but can delegate this to one or several other members of the lab. We hope all groups actively will take part of this opportunity. PIs that do not nominate a contact person will not get an assigned presentation slot. However, lab members are nonetheless free to present in the Open Forum (see below). Practically, the users should briefly put the experiment(s) in scientific context (max one slide), describe what they want to achieve with FACS experiments and outline what they would like to get input on. The presenter should also show raw data, not processed data as this could hide important issues that could preclude appropriate discussion. What each lab presents is very much up the them, but this could be simple antibody titrations, complex antibody panel design, instrument configurations and data interpretation to name a few.

Open Forum

This is intended to allow any user to bring up urgent FACS issues that they would like to get input on. The format is as indicated for the lab specific presentations, and the presenter should come prepared to show the raw data related to the problem they want to get input on.

We strongly believe the forum format will ensure a higher degree of scientific competence that can provide both valuable technical and scientific insights to all users of our core facility.

Therefore, we highly encourage everyone with interest in flow cytometry and its research application to take advantage of this opportunity to contribute to these sessions!

Date Time Location


12.00-13.00 RED Seminar Room, Novum plan 6
09/02/18                12.00-13.00 RED Seminar Room, Novum plan6
23/02/18                12.00-13.00 NEO
23/03/18                12.00-13.00 NEO
20/04/18                12.00-13.00 NEO
04/05/18                12.00-13.00 NEO
18/05/18                12.00-13.00 NEO
01/06/18                12.00-13.00 NEO
15/06/18                12.00-13.00 NEO


A more detailed introduction to flow cytometry:


Training for using DiVa software:


FlowJo Tutorials:



Flow Cytometry Links