BioMediTech Research Infrastructure

Flow Cytometry

The Flow Cytometry facility offers modern instruments for a variety of experiments, ranging from simple analyses to complex multicolor panels and sorting. The facility personnel can provide assistance in every step of your experiment design and implementation.


Flow cytometry is a laser-based method in which fluorescent-stained cells are suspended in a stream of sheath fluid and excited with a laser. The fluorescent intensity of the emission is measured by the flow cytometer optics. Up to thousands of cells per second are analyzed and classified based on their fluorescence emission and forward and side scattered light. This yields information on surface and intracellular molecules and cell size and structure. Typical application of flow cytometry include cell counting and sorting and analysis of biomarkers, cell cycle and apoptosis. Flow cytometry is routinely utilized in diagnostics and basic research. The cell-sorting cytometer is able to separate and purify cell populations of interest, based on their fluorescent markers.

The flow cytometry facility has three flow cytometers to serve the different requirements of the researchers. The researchers can operate the instrument by themselves, or alternatively, they can purchase the services they need from the facility personnel. We offer a wide and flexible variety of research services, ranging from panel design to sample run assistance and post-acquisition data analysis. For details and inquiries, please contact the facility manager.


All the users of the Flow Cytometry facility services are obligated to acknowledge the facility in publications:

“The authors acknowledge the Tampere facility of Flow Cytometry for their service.”


Usage of the three cytometers is allowed only after comprehensive tutorials, supervised by the persons responsible for the instruments (Laura Kummola for FACSCanto II and FACSAria Fusion, Laura Vesala for Accuri). Tutorials can be tailored according to the individual needs and previous experience of the researchers; see pricing for suggestions for each instrument.

All solutions except your sample suspension buffer are provided by the facility. Basic 5 ml 12×75 mm tubes suitable for sorting and analysis are included in the user fees. Billing for instrument usage is based on Agendo bookings. Minimum reservation time is 2 hours for FACSCanto II and FACSAria Fusion, and 30 minutes for Accuri.


Combining accuracy, reproducibility and performance to ease of use, the FACSCanto II is a powerful tool for demanding and complex flow cytometric analyses with multicolor panels and large sample quantities. The fixed-alignment flow cell enables minimal startup times while the optical system provides outstanding signal detection, resolution and sensitivity.

Equipped with a 488-nm blue laser and a 633-nm red laser, the instrument is capable of detecting six compensated fluorescence parameters and two scatter parameters at a rate of 10,000 events/second. For example, simultaneous measurement of FITC, PE, PerCP-Cy5.5, PE-Cy7, APC and APC-Cy7 in one sample is possible. PMT voltage is completely adjustable by the user.

The High Throughput Sampler (HTS) supports standard plates of 96 and 384 wells and offers fully automated data acquisition from a well plate as fast as in 15 minutes.

Automated fluidics startup, shutdown and cleaning procedures simplify workflows and shorten the time consumed at the instrument.

BD FACSDiva™ software controls all the steps of flow cytometric analysis, managing experiment templates, application settings and automated calculations of compensation matrices as well as post-acquisition data analysis. Daily quality control of the cytometer performance is a fundamental feature of the software. Data files can be exported as FCS 3.0 files into third party analysis  programs

BD FACSAria Fusion

FACSAria Fusion offers a very wide repertoire of multicolor analysis possibilities with a state-of-the-art cell sorting capability and bioprotection. The fiber-launched lasers and patented, next-generation quartz cuvette flow cell with fixed alignment ensure experiment reproducibility and data collection efficiency with optimized resolution.

Equipped with four lasers – a 405-nm violet laser, a 488-nm blue laser, 561-nm yellow-green laser and a 640-nm red laser – FACSAria Fusion can provide the most versatile analysis options of the core instruments, reaching up to 15 fluorescent and two scatter parameters. Samples can be processed at a maximum rate of 70,000 events/second.

Sorting of up to four populations is possible to different tube formats. Automatic Cell Deposition Unit sorts onto slides and well plates and sorting can be performed at a precision of one cell per well. The facility provides nozzles of 70, 85 and 100 µm for cells of varying sizes and sensitivity.

Biosafety is taken into consideration by the biosafety cabinet that houses the FACSAria Fusion. It protects the user and the environment as well as the samples from contamination. An additional and independent aerosol management system evacuates any aerosols from the sort chamber.

Automation in startup, shutdown and cleaning add user-friendliness and speed to instrument use.

BD FACSDiva™ software in FACSAria Fusion is nearly identical to the software in FACSCanto II, with same features. Having the same software in both cytometers helps users master both instruments. As with the other instruments, FACSAria Fusion data files can be exported as FCS 3.0 files.

Accuri C6 Flow Cytometer

An industry-standard, sheath-focused core facilitates high performance while enabling event rates of up to 10,000 events/second and sample concentrations over 5×107 cells/ml. The device measures the volume pulled from your sample so that you can calculate cell concentration. It has a fully digital data collection system, allowing complete flexibility to display and analyze data post-collection, without permanent alteration of your original data file.

Equipped with a blue and a red laser, two scatter detectors, and four fluorescence detectors with interference filters optimized for the detection of FITC, PE, PerCP-Cy5.5 and APC.

Works with the same reagents you currently use on the market- leading flow cytometers.

C6 fluidics system is non-pressurized enabling any brand of sample tube that is 12×75 mm or smaller to be used. This includes microcentrifuge tubes and tubes made of polypropylene or polystyrene.

CFlow® files can be exported in FCS 3.0 format for seamless importation of your data into most 3rd party flow cytometry software programs including FCS Express and FlowJo.


All the users of Tampere Facility of Electrophysiological Measurements services are obligated to acknowledge the facility in publications:

“The authors acknowledge Tampere Facility of Electrophysiological Measurements for their service.”

External Links

BD Introduction to Flow Cytometry (video course):

Bio-Rad Introduction to Flow Cytometry – Basics Guide:

Excyte – Expert Flow Cytometry Blog:

BD Fluorescence Spectrum Viewer:

BD FACSAria Fusion Filter Guide:

Optimizing a Multi-colour Immunophenotyping Assay (useful for non-immunologists too!):

The importance of area scaling with FACS DIVA software:


Analysis 13 €/h
Tutorial 1 h, scheduled beforehand (Laura Vesala) 45 €
Tube mode 15 €/h
Plate mode 13 €/h
Tutorial(1 360 €
Analysis only 16 €/h
Sorting 18 €/h
Tutorial(2 610 €
Sorting service 10 h(3 610 €
Assistance, scheduled beforehand (Laura Kummola)(4 45 €/h

1FACSCanto II Tutorial includes three runs (2+2+2 hours) and reagents. For additional hours, extra costs will be charged
2FACSAria Fusion Tutorial includes three runs (4+4+2 hours) and reagents. For additional hours, extra costs will be charged
3FACSAria Fusion Sorting service includes planning, sorting and reagents (total 10 hours). For additional hours, extra costs will be charged
4Scheduled assistance includes e.g. shorter tutorials for old users and aid in data analysis.

Pricing is valid for user groups from the Tampere University. Other academic or non-academic users are asked to inquire specific pricing.

The Flow Cytometry Facility reserves the right to price adjustments.


Facility Manager
FACSCanto II and FACSAria Fusion

Laura Kummola
Tel: +358 50 437 7412
Room: ARVO F354

Accuri C6

Laura Vesala
Tel: +358 50 318 2294
Room: ARVO F324

Facility Technician

Paula Kosonen
Tel: +358 50 406 9410
Room: ARVO D232


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Heinimäki S, Malm M, Vesikari T, Blazevic V. Intradermal and intranasal immunizations with oligomeric middle layer rotavirus VP6 induce Th1, Th2 and Th17 cell subsets and CD4+ T lymphocytes with cytotoxic potential. Antiviral Res. 2018 Sep;157:1-8. doi: 10.1016/j.antiviral.2018.06.012.

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