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Laboratory of Confocal and Fluorescence Microscopy

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Laboratory Equipment

Confocal microscopes

High-end confocal microscope Leica TCS SP8 with one standard PMT and one sensitive HyD detector. Allows acquisition of fixed and living samples. The environmental chamber PECON with the CO2 regulation provides a suitable atmosphere for living cells experiments. The microscope offers several modes including lambda scanning, FRET and FRAP measurements, and is also equipped with a MATRIX module for object tracking during acquisition (e.g. growing oocytes or roots)

The laboratory is equipped with a high-end inverted confocal microscope Leica TCS SP2 with AOBS (Acousto-Optical Beam Splitter) system, which ensures high sensitivity and the possibility to combine up to four fluorescence markers. The microscope allows structure analysis of fixed samples. It is possible to do multicolor analysis, 3D reconstructions, FRAP (Fluorescence Recovery After Photobleaching), FRET (Fluorescence Resonance Energy Transfer) analysis, and tile scans. There is a diode 405 nm laser installed.

The most up-to-date confocal microscope Zeiss LSM 880 NLO is equipped with a set of lasers for one-photon excitation and with tunable  Ti:Sa pulsed laser for two-photon excitation. High-sensitive 32-channel GaAsp spectral detector gets unrivaled clear images. It is possible to do one-channel FLIM (Fluorescence Lifetime IMaging), FCS (Fluorescence Correlation Spectroscopy), and RICS (Raster Image Correlation Microscopy) measurements which allow us to uncover molecular relationships and functions. The microscope works with high speed and high resolution. Live-cell imaging heated chamber with CO2 atmosphere is available as well.

Wide-field microscopes

There is also a great wide-field system Olympus Scan^R available. It is equipped with a stabilized light source, high sensitive Hamamatsu camera, motorized stage, filter, and objective turrets and shutters. It is possible to do high-quality imaging as well as high throughput imaging and mosaic imaging. A high-quality stage chamber with the regulation of temperature (-5 to 65 °C) and gas level (CO2, O2) can maintain also multiwell dishes and allow high throughput imaging under different environmental conditions.

Fully motorized fluorescence wide-field microscope NIKON TiE2 serves for fixed and living samples. It is equipped with a high-speed monochromatic ORCA Flash camera able to get 100 fps as well as with a nice RGB camera. Excitation Cool-LED P-4000 with 16 LEDs cover the full spectrum as well as SEDAT system of emission filters and multiband dichroic. OKOLab environmental chamber suits most common living cells demands. The microscope is driven by the full version of NIS-elements with High Content Imaging possibilities (JOBs module).

A fully automated microscope ZEISS Axioscan Z.1 with the dock for 100 slides can easily and autonomously scan all of them at once. It is a workhorse for High Throughput Imaging of all of your tissue sections which could be reconstructed back to the 3D image of the sample.






Super-resolution microscopes

Microscope Zeiss Elyra PS.1 uses technologies of structured illumination (SIM) and precise localization (PALM/STORM) to overcome the so-called diffraction barrier, which limits us to the resolution of around 200 nm in conventional light microscopy. Nanoscopy allows us to observe structures with 2-3x higher resolution with SIM and up to 5 nm with localization microscopy. The microscope can use a technology of TIRF (Total Internal Reflection Fluorescence) to increase the signal-to-noise ratio in the space near to cover glass. A set of high-quality lasers and cameras help us to make great super-resolution images.

Ligthsheet microscopes

Zeiss Lightsheet Z.1 microscope is great for rapid acquisition of fixed, living, or cleared samples in selective plane illumination. There are two pairs of 5x and 10x illumination objectives. Detection objective of 5x, 10x, 20x, and 40x and two objectives 20x for clearing  RI 1.38 and 1.45. The chamber size is roughly 2x2x2 cm. The two-channel acquisition is driven by two cooled PCO cameras.



For optimal performance, all microscopes stay on antivibration tables in air-conditioned rooms. Our core facility serves people of many different fields of research and contributes significantly to results published in peer-reviewed scientific journals.


If you are really interested in work with our microscopes, please, 
1) join a  google group of users. 
2) join a Ceitec reservation system.
3) Students and employees of Charles University in Prague only:
You will need a permission to entry laboratory rooms via chip or your employee card. Fill up this form.
If you are only interested in workshop and other microscopy related events announcements join a group lab.konfmi. Active users are going to receive lab.konfmi announcements automatically.

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Price list

lamp WF cena s DPH Rezervace
Olympus Cell^R (widefield) 119 Kč  
NIKON TiE2 119 Kč  
Zeiss Elyra PS.1 (lamp WF) 119 Kč  
Konfokální mikroskopy    
Zeiss LSM 880 1198 Kč  
Leica TCS SP8 1198 Kč  
Leica TCS SP2 697 Kč  
Super Resolution    
Zeiss Elyra PS.1 (superresolution, TIRF, laser WF) 774 Kč  
Zeiss Elyra PS.1 (superresolution, TIRF, laser WF) s assistencí 1655 Kč  
High Throughput Imaging - live cell    
Olympus Scan^R (widefield) 173 Kč 505 Kč
NIKON TiE 2 173 Kč 505 Kč
Leica TCS SP8 (konfokál) 347 Kč 505 Kč
Zeiss LSM 880 (konfokál) 347 Kč 505 Kč
High Throughput Imaging - fixed samples    
Olympus Scan^R (widefield) 85 Kč 505 Kč
NIKON TiE 2 85 Kč 505 Kč
Leica TCS SP8 (konfokál) 135 Kč 505 Kč
Zeiss LSM 880 (konfokál) 135 Kč 505 Kč
Axioscan – virtual slider 67 Kč 505 Kč
Any sample up to 24 hours 253 Kč 505 Kč
Long-term experiments (longer than 24 hours) 127 Kč 505 Kč
Image Analysis    
Consultations 50 Kč  
Workflow establishment 101 Kč  
Manual Analysis/scripting 390 Kč  
Computing time 469 Kč  

More prices on intranet here.



Mgr. Ondřej Šebesta
+420 22195 1061 (S47 - office / Cell^R)
+420 22195 1943 (S39 - konfokální mikroskopy)
+420 22195 1060 (S47 - superresolution)
+420 22195 1033 (108 - Axioscan and Nikon)
+420 777 988 925
Email: Ondrej.Sebesta@natur.cuni.cz

Asistence Lightsheet:

Mgr. Zuzana Burdíková Ph.D.
Telefony: 22195 1061
Mobilní: +420 775 305 602
Email: Burdikova.zuzana@gmail.com

Asistence Elyra PS.1:

Mgr. Peter Hoboth Ph.D.
+420 601 507 170
Email: peter.hoboth@natur.cuni.cz
Available on demand

Image data analysis:

Ing. Martin Schätz Ph.D.
+420 22195 1061 (office)
Email: Martin.Schatz@natur.cuni.cz
Available on Wednesday and Thursday
Book a consultation


Mgr. Judith Garcia Gonzales
Email: garcia.judith@natur.cuni.cz

Mgr. Jakub Soukup
Email: jakub.soukup@natur.cuni.cz

Available on Wednesday and Thursday


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