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 core facility is a service facility located at the 7th floor of the NEO research building at the Karolinska Huddinge Campus (see visiting address). The MedH FACS facility provides open access to all interested researchers at KI and Karolinska Hospital regardless of their affiliation and strives to provide each user with skilled services, education and training to achieve high quality research.

Established in 2011 with an initial support from the Wallenberg Institute for Regenerative Medicine (WIRM), a research institute financed by Knut och Alice Wallenbergs Stiftelse, the facility is currently supported by core facility funding from KI/SLL and Stratregen grant from Karolinska Institutet. To cover most of its running costs, the facility charges fees for its services (see user Fees for detailed information). 

The facility currently houses three 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 with the aim to promote exchange of technical know-how and knowledge in the field of flow cytometry.


The facility currently houses three cell analyzers and two cell sorters  offering possibilities for advanced multicolor cell analysis combined with high-speed cell sorting up to enhanced Biosafety Level 2 standards.

18 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
18 parameters, 5 Lasers: 405 nm, 640 nm, 488 nm, 355 nm and 561 nm
Cell Analysis and sorting:  Enhanced Biosafety Level 2
Download “Config FACSAria Fusion”
SORP BD LSRFortessa™ 
20 parameters, 4 Lasers: 405 nm, 640 nm, 488 nm, 355 nm and 561 nm and an integrated 96 well plate module for High-Throughput analysis
Cell Analysis Biosafety Level 1
Download “Config LSRFortessa”
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” 
SORP BD Symphony™ A5 
30 parameters, 5 Lasers: 405 nm, 637 nm, 488 nm, 355 nm and 561 nm and an integrated 96 well plate module for High-Throughput analysis
Cell Analysis Biosafety Level 1
Download “Config BD Symphony A5”  More information about BD Symphony™ A5 

Biosafety and Risk assessment

A risk assessment shall be carried out in order that everyone shall have a safe work environment, and to raise risk awareness. Prior to cell sorting, the facility requires individual risk assessment for each new project. Download the sort request form.

In addition, the Biosafety Committee at KI has created a risk assessment form for microorganisms, BARA (Biological Agents Risk Assessment). The form can be used to assess the risk of handling micro-organisms (including cell cultures). For risk assessment of blood and other human sample material, the Biosafety Committee has created a form HUMRA (Human Sample Material Risk Assessment).

  • Note that the BARA form should not be used for microorganisms that have been genetically modified, refer instead to ’GMM-applications’.
  • Notification/permit is required for all microorganisms in risk group 2 and higher. Also refer to 'Applications to handle microorganisms'.
  • When relevant assessing the risk of chemicals, refer instead to ’Risk assessment – Chemicals’
  • All forms are available

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 (including risk assessment) 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 Flow Cytometry core 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 (to update using attached doc)

Note: For Cell sorting please fill in the sort request form below (including risk assessment).

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


User group for the MedH Flow cytometry facility

Andreas Lennartsson, BioNut

Peter Swoboda, BioNut

Jurga Laurencikiene, Lipid laboratory

Jakob Michaelsson, CIM

Petter Woll, HERM

Yenan Bryceson, HERM

Hong Qian, HERM

Sidinh Luc, HERM

Petter Höglund, HERM

Visiting Address

The MedH Flow Cytometry Core Facility is situated at the 7th flour, elevator N of the NEO research park in Huddinge, adjacent to Karolinska University Hospital in Huddinge.
(See map below) 

Visiting address:
Blickagången 16 (by train)
Medicinaren 25/Neo (by car)

Find Neo Building 

From the commuter train ”pendeltåg” (arrow B): Go to Flemingsberg’s station with commuter train number 40 towards Södertälje centrum or commuter train number 41X towards Tumba, choose the south exit (facing Södertälje/Tumba), and go to the right. Follow a path towards the hospital, walk past Södertörns University/Högskola to Huddinge hospital, along Blickagången. After Novum (number 6 in picture above) but before the main entrance to the hospital (number 11), you find the entrance to Neo (number 20 in picture below). It is a big entrance hall between Stockholm Food and Espresso House. The address is Blickagången 16, arrow A.

From the bus-stop Huddinge hospital main entrance or From the shuttle ”Pendelbussen” between Karolinska Campus Solna and campus Flemingsberg (arrow C): Walk to the hospital main entrance (number 11 in picture below), take to the left on Blickagången walk by pharmacy/ Apotek, you will find the entrance to Neo (number 20 in picture below). It is a big entrance hall between Stockholm Food and Espresso House. The address is Blickagången 16, arrow A

Postal address:
MedH Flow cytometry facility
Hälsovägen 7, Novum plan, 4 hiss G
SE-14157 Huddinge
Phone: +46 8-524 83458

User Fees

Instrument KI Other Academic Commercial
FACSymphony 420 SEK/hr 520 SEK/hr 1040 SEK/hr

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.

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.

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                11.00-12.00

NEO Gene 5108 (80)

16/02/18 11.00-12.00 NEO Gene 5108 (80)
23/02/18     11.0012.00

NEO Gene 5108 (80)


11:00-12.00    NEO Gene 5108 (80)
11/05/18                11.00-12.00 NEO Gene 5108 (80)
01/06/18                11.00-12.00 NEO Gene 5108 (80)
15/06/18                11.00-12.00 NEO Gene 5108 (80)


A more detailed introduction to flow cytometry:


Training for using DiVa software:


FlowJo Tutorials:



Flow Cytometry Links







NEO Gene 5108 (80)