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Service Unit

Group photo of the Microscopy Service Unit team

Our group provides services and support in field of advanced microscopy for employees of the IEM as well as for the external users. We secure access to the devices, routine service, training, booking system and consultations. Users can access variety of devices from basic fluorescent microscope to the cutting-edge two-photon system for in vivo studies.

Štěpán Kortus

Head of the Department
Štěpán Kortus, Ph.D.

Linkedin profil Štěpán Kortus
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Barbora Hyklová, Ph.D.

Štěpán Kortus, Ph.D.

Assoc. Prof. Jan Malínský, Ph.D.

Iva Švecová, M.Sc.

About Us

The purpose of our group is to provide users with access to cutting-edge microscopic equipment and software for subsequent data analysis. We provide support at every step of the scientific process, from experimental design to data evaluation.  

The following techniques are available:  

  • Transmitted light microscopy  
  • Widefield fluorescence microscopy  
  • Phase contrast and DIC microscopy 
  • Laser scanning confocal microscopy (single- and multichannel) 
  • Spinning disk confocal microscopy  
  • Super-resolution microscopy (Airyscan or SpinSR10)  
  • Two-photo excitation microscopy 
  • 3D ultra-fast laser scanning microscopy with two-photon excitation  
  • Fluorescence recovery after photobleaching (FRAP)  
  • Light-sheet microscopy  

Our group also operates a facility for advanced imaging of behaving animals (BSL2), which offers an advanced two-photon 3D imaging system, as well as equipment for live animal handling and housing.   

For data analysis, two PC workstations equipped with image analysis software are available. We offer support for data analysis, and if needed, we can develop custom-made software for specific applications. 


We currently provide seven microscopes available directly through the reservation system. Access to other devices is possible by prior arrangement at the specific workplace.


PC workstations

  • Algernon (Imaris)

    PC workstation for microscopy image processing


  • Benjy (CellSens)

    PC workstation for microscopy image processing


  • Frankie (freeware)

    PC workstation for microscopy image processing


Intravital imaging laboratory

Our facility operates a BSL-2 certified intravital imaging laboratory, which encompasses a spectrum of essential components to facilitate every stage of the experimental process:

Animal handling and housing: Our laboratory is equipped to provide the requisite space and infrastructure for the care and management of small rodents. It can accommodate a diverse range of animals, including transgenic and transfected strains, with the oversight of trained animal caretakers ensuring their welfare.

Surgery room: The surgery room consists of two surgical workstations. It is furnished with a state-of-the-art stereotaxic surgery setup, complete with the necessary equipment for conducting surgical procedures. These include viral injections and cranial window preparations.

In vivo experimental setup: The centerpiece of the laboratory is the 2-photon Femtonics Femto3D Atlas microscope. This advanced microscopy system supports both functional and structural imaging, affording researchers the capacity to investigate biological systems at cellular and subcellular levels. It is particularly suited for in-depth examinations of neural activity, tissue dynamics, and cellular interactions within living organisms. Additionally, the laboratory can accommodate electrophysiological and behavioral experiments.


Training and consultation

Our facility provides training in methods and techniques available on our microscopes. Introductory training is mandatory for every user. Upon request, additional training can be provided in specialized techniques which are not covered by the basic training. These methods include super-resolution microscopy with Airyscan detector, multiphoton microscopy, FRAP (fluorescence recovery after photobleaching), incubation (temperature and atmosphere control), or DIC (differential interference contrast) setting, among others. We also offer consultation and assistance with experimental design or advanced microscope settings.

Image analysis and data processing support

The facility staff can assist users in selecting the most suitable software for their specific research question and provide training for the software available at the workstations. If needed, direct support with data analysis can be provided, and in specialized cases, custom-made software can be developed on request.


Access to the Service Laboratory

Complete set of rules for accessing the service laboratory can be found on the following page:

Price List

Device/serviceInternal Open Access Cost*External Open Access Cost*

Zeiss LSM880 AiryScan

120 CZK

200 CZK

Olympus FV10i

60 CZK

170 CZK

Olympus FV1200 MPE

120 CZK (multiphoton +50 CZK)

200 CZK (multiphoton +100 CZK)

Femtonics FEMTO3D Atlas

200 CZK

350 CZK

LaVision UltraMicroscope II

100 CZK

180 CZK

Zeiss AxioObserver Z.1

50 CZK

100 CZK

Olympus SpinSR10

120 CZK

200 CZK

Philips Morgagni

150 CZK


150 CZK

200 CZK

Bookings outside of normal working hours (18:00-8:00) and during weekends and holidays are discounted by 25 %. Pilot imaging and training is free of charge. 

Users falling outside the delineated categories are kindly requested to contact us for pricing information.

* Hourly rate without VAT.

Mandatory Publicity

According to the mandatory publicity, please include the following information in your publications if you use the Microscopy service:


“Microscopy was done at the Microscopy Service Centre of the Institute of Experimental Medicine CAS supported by the MEYS CR (LM2023050 Czech-Bioimaging).”

In case of using the devices listed below, please further specify:


Olympus SpinSR10

Funded by the NanoEnviCz project

“This work was funded by the Ministry of Education, Youth and Sports of the Czech Republic (Research Infrastructure NanoEnviCZ, LM2018124) and The European Union-European Structural and Investments Funds in the frame of the Research Development and Education-project Pro-NanoEnviCz operational program (Project No. CZ.02.1.01/0.0/0.0/16_013/0001821).”