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Klinik für Innere Medizin IHämatologie, Onkologie und Stammzelltransplantation

Flow Cytometry

Cell Sorting

Booking of Cell Sorters

  • Appointment requests should be sent  via email to facslab@uniklinik-freiburg.de.
  • Experienced users can use our new booking calendar system.
  • Standard sorting times are Monday to Thursday between 9:00 and 16:30 and on Friday between 9:00 and 14:30. 
  • Please specify the following information in your request
  • Desired date / time
  • Duration of sort
  • Desired cell-sorter ( MoFLo, Aria, Fusion)
  • Nozzle Size (70, 85, 100, 130 µm). If not specified, the 70 µm Nozzle is used by default
  • Origin of the cells (human, mouse, cell culture etc.)
  • Cell number / sample size and number of samples
  • Biosafety-Level (S1,2,3**)

Cell Sorting Service Fee

The costs for cell sorting for academic users are 50 €/hour + 25 €/appointment. The billing cycle includes both the actual sort time as well as time required for setting up the experiment. Billing begins with the start of the booked appointment. If appointments are canceled upon short notice and it is not possible to find an alternative appointment to fill the slot, 50% of the originally booked time will be charged. 


Lighthouse operates three high speed cell sorters: a 16-color FACS Aria Fusion and a 17-color FACS Aria III, both from Becton Dickinson, as well as a 14-color MoFlo Astrios cell sorter from Beckman Coulter. Due to their complexity these machines must be operated by members of the Core Facility. Note: Because the sorters are heavily booked (wait times are often 3 weeks), it is best to reserve times on the instruments as early as possible. If you need more information as to which combinations of dyes or fluorescent proteins it is possible to use, please contact us. The best time to do this is when first planning a new experiment.

 Lasers Available - Cell Sorters:

Cell Sorters:
FACS Aria Fusion
MoFlo Astrios
Cell Sorter:

Fluorochrome Examples

Near UV:
375 nm*
*colinear with 405 nm laser
DAPI, Hoechst
(including detection of SP cells)

405 nm


405 nm


DAPI, Alexa 405, CFP,
Brilliant Violet Dyes,
Pacific Blue,
Live/Dead Aqua,
Zombie Aqua, etc.
488 nm488 nm
FITC, Alexa 488,
Brilliant Blue 515,
PerCP, PerCP-CY5.5
561 nm561 nm
PE, PE-Texas Red,
PE-CY5, PE-CY5.5,
dsRed, tdTomato,
mCherry, etc.
640 nm633 nm
APC, Alexa 633/647,
Alexa 680/700, etc.

Other possibilities for the cell sorters are:

  • Cell/well cloning directly onto slides or into i.e. 96- or 384-well tissue culture plates (up to 1536 Wells on the MoFlo Astrios)
  • 4-way/6-way sorting: Up to 4 populations can be sorted simultaneously on the Arias and up to 6 populations on the MoFlo Astrios
  • Index Sorting - the ability to look up the phenotype of a cell after cloning
  • Small particle detector - MoFlo Astrios EQ
  • Biosafety Hood - FACS Aria Fusion

For more information about setting up your samples for sorting and the best buffers to use, with your samples please also see: Sample Preparation

Sample tubes

Because of their differing electrostatic properties, it is recommended that you use polystyrene tubes (clear) as sample tubes, and polypropylene tubes (opaque) for sample collection, Sample tubes should be 12 x 75 mm in size, while collection tubes can be either 12 x 75 mm in size, 15 ml conical tubes for large samples, or 1.5 ml tubes for small samples.

Cloning into Plates

When cloning into plates, be sure to plate out the wells with a large amount of medium, so that they are ~75% full. This makes it easier to sort into the well, with less chance of the droplet landing on the side of the well. For special plates or formats it is helpful to bring by an empty plate to set up the stage positions ahead of time.

How to Select the Correct Nozzle Size

As a general rule of thumb: The cell size should not exceed one-fifth of the nozzle diameter. Using the wrong nozzle size causes fanning of the side streams, poor sort purity and nozzle clogging.

Nozzle Size


70 µm


85 µm


100 µm


130 µm


Pressure (pounds per sq. in.) 60-70 psi 45 psi 20-25 psi 10 psi
Max. Cell Diameter 14 µm 17 µm 20 µm 26 µm
Max. Events/Sec. 22.000 - 30.000 11.000 7.000-10.000 3.000
Max. Events/Hour 7-9x107 3-4x107 2x107 1x107
Starting Cell Conc. of Sample 3-5x107/mL 1-2x107/mL 5-7x106/mL 2-4x106/mL
Approx. Size of Drop 1 nL 2 nL 4 nL 11 nL
Cell Concentration Post-Sort 1x106/mL 0,5x106/mL 2,5x105/mL 1.1x105/mL

If you are unsure which nozzle size you will require, just ask one of the sort operators and they will be happy to advise you. They can also help you to determine what diameter your cells have while in suspension.

For additional help with panel design, the configurations of all Lighthouse sorters and analysers are now listed on the Fluorofinder website. To access information about the cell sorters please follow the links below.

MoFlo Astrios Lasers and Channels

Overview about lasers and suitable fluorochromes of cell sorter ARIA III.


FUSION Lasers & Channels

Overview about lasers and suitable fluorochromes of cell sorter ARIA FUSION.


ARIA III Lasers and Channels

Overview about lasers and suitable fluorochromes of cell sorter ARIA III.


Lighthouse Biosafety Form

Sort experiments of any biosafety level can only be carried out after filling out the proper form.


FACS Analysis

For information about our FACS Analysers please see the FACS Analysis page.

Offline Analysis

The Core Facility also has offline analysis workstations with the flow cytometry software programs FlowJo, Diva, Summit and Kaluza available for general use. 

Further Information


Universitätsklinikum Freiburg
Zentrum für Translationale Zellforschung (ZTZ)
Department of Medicine I
Tumorzentrum Freiburg - CCCF/DKTK
Center for Chronic Immune Deficiency - CCI

Contact | Information


FACS-Sorting Booking:


Online Booking Calendar (registration required)


Head of Facility:

Marie Follo, Ph.D.
Telephone: 0761 270-77697
Telefax: 0761 270-63780
Email: Marie Follo



Universitätsklinikum Freiburg
Lighthouse Core Facility

Zentrum für Translationale Zellforschung (ZTZ)
Breisacher Straße 115
D-79106 Freiburg