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Carl Zeiss Reference Center for Confocal Microscopy is equipped with:

- LSM780 microscope, with the Faraday cage the spectral PMT array detector (GaAsP), diode laser 405, Argon laser 458, 488, 514, DPSS laser 561 and He/Ne 633 nm).

- LSM510 microscope with the Meta PMT array detector (spectral detection, He/Ne and Argon lasers (458, 488, 514, 543, 633 nm).

- LSM7MP two photon microscope
680 nm to 1080 nm 3,5 W, 140 fs, 80 MHz.
Filter set: blue-green  420-475 / 500-550
Filter set: cian-yellow 460-500 / 525-560
Filter set: green-red 500-550 / 575-610 nm

- two Till Photonics imaging systems, equipped with  Polychrome IV and Polychrome V monochromators, Imago Type QE CCD Camera (-12C), Zeiss Axio Observer microscopes.

- Atomic Force Microscopy JPK Bioscope II.

- SIM, Zeiss ELYRA PS.1 microscope

- a custom-built STED microscope with a supercontinuum fiber laser (ALP-710-745-SC, Fianium Ltd, Southampton, UK) running at 20 MHz.

Center's open hours: 9:00 a.m. - 5:00 p.m.

Overview. The confocal microscopy offers several advantages over conventional fluorescence microscopy. Information is collected from a well-defined optical section; thus out of focus fluorescence is eliminated, which results in an increase in contrast, clarity and detection of optical objects. Stacks of optical sections taken at successive focal planes can be reconstructed to produce a three dimensional view of a specimen. Thus confocal microscopy provides means to observe structural components and physiological processes of living cells and tissues in three-dimensional space without physical sectioning.


Our laboratories operate a quality management system compliant with the SIST EN ISO/IEC 17025:2005 standard. In the field of advanced microscopy which is run within the Carl Zeiss Reference Center for Confocal Microscopy we received accreditation certificates LK-024 and LK-025 (since November 13th, 2008) for calibration laboratories accredited by the Slovenian Accreditation, an ILAC-MRA signee (www.ilac.org, International Accreditation Laboratory Cooperation)). In addition to quantitative advanced microscopy imaging services for which our customers receive calibration certificates for the twodimensional measuring image system, we offer the international support for interlaboratory quality/validation of laser scanning confocal microscopes for external users, which is based on a special certified sample and an algorithm to perform the measurements which are then compared with those from the international lab database. Each lab receives a feedback on their results of how their results compare with the ones from the database. This is an important service for the laboratories providing their R&D services to credible industrial partners.

Quantitative analysis of confocal fluorescence microscopy images 

Fluorescent proteins like green fluorescent proteins (GFP) are markers of subcellular protein location and trafficking. After transfection of GFPs, cells or tissue is imaged. Together with methods of quantitative image analysis confocal microscopy provide a powerful tool in molecular cell biology-physiology studies.

We developed several software tools, which are now available on-line.

References of the Confocal Center