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Advanced Optical Microscopy Centre

Equipment & expertise

Advanced Optical Microscopy Centre

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Perform fast, live-cell fluorescence imaging experiments on this powerful widefield fluorescence microscope with TIRF and 3D super-resolution (SIM and SMLM) capabilities. This commercial Zeiss microscope is equipped with 4 laser lines (405, 488, 561 & 642nm), an incubation chamber, a dedicated SIM camera and SMLM camera, Definite Focus system and piezo stage. Additionally, the microscope is combined with a patch clamp setup allowing simultaneous fluorescence and electrophysiology recordings.

Use and training

To access this microscope, contact the facility to schedule a hands-on training session. Trained users have 24/7 access to the microscope and are free to schedule experiments using the online booking system. Training can only be given by facility staff.




X-Cite Series 120PC Q fluorescence lamp
405nm laser
488nm laser
561nm laser
642nm laser

Filter sets

There are 2 filter turrets with a selection of different filter sets available for use with the Elyra PS.1. Single color experiments are preferentially performed with filter turret 1. Multi-color experiments can be performed with filter turret 2 to allow for fast-frame-switching between different acquisitions.

Filter turret 1 (single-band)
position filter name emission filter beam splitter example fluorophores
1 Transmission Light transmission N/A N/A
2 FSet77 HE triple band splitter N/A common fluorophores
3 BP 420-480 + LP 750 BP 420-480 + LP 750 MBS 405 DAPI, BFP
4 BP 495-575 + LP 750 BP 495-575 + LP 750 MBS -488 GFP, Alexa Fluor 488
5 BP 570-650 + LP 750 BP 570-650 + LP 750 MBS -561 mCherry, mScarlet, Alexa Fluor 568
6 LP 655 LP 655 MBS -642 Cy5, Alexa Fluor 647

Filter turret 2 (multi-band)
position filter name emission filter beam splitter example fluorophores
1 Transmission Light transmission N/A N/A
2 empty N/A N/A N/A
3 BP 420-480 + BP 570-640 + LP 740 BP 420-480 + BP 570-640 + LP 740 MBS 405/561 DAPI & mCherry
4 BP 420-480 + BP 495-550 + LP 650 BP 420-480 + BP 495-550 + LP 650 MBS 405/488/642 DAPI & Alexa Fluor 488 & Alexa Fluor 647
5 LBF -561/642 LBF -561/642 MBS -561/642 Alexa Fluor 568 & Alexa Fluor 647
6 LBF -488/561 LBF -488/561 MBS -488/561 GFP & mCherry


The microscope is equipped with a PCO Edge 4.2 sCMOS camera (6.5µm pixels, 1280x1280) connected to the bottom port, and an Ander iXon+ 897 EMCCD camera (16µm pixels, 512x512) connected to the right-side port.

Objective lenses

The microscope can be equipped with a set of low-magnification air objectives (5x, 10x, 20x and 40x) for fast and easy visualization of samples. Additionally, the microscope is equipped with two high-magnification oil immersion objectives for high-resolution (TIRF, SIM, SMLM) imaging. Additional 1.6x magnification can be achieved using the OptoVar lens (choice between 1x and 1.6x magnification).

  • SIM: Plan-Apochromat 63x/1.40 Oil DIC M27.
  • TIRF & SMLM: Alpha Plan-Apochromat 100x/1.46 Oil DIC M27. (contains a rotatable TIRF back-reflection blocking pin)

Other features

  • A PECON incubation system allowing precise control of experimental conditions (Temperature and CO2).
  • Zeiss Definite Focus system to counter axial drift during long-term experiments (e.g. timelapse, super-resolution).
  • 3D single-molecule super-resolution imaging with the 3D-PALM slider.
  • High precision Piezo stage for fast and precise Z-control.
  • Access to a patch-clamp setup for simultaneous fluorescence and electrophysiology experiments.


Typical research applications of the Elyra PS.1 include:

  • patch-clamp fluorometry experiments, combining TIRF microscopy and patch-clamping to study signalling pathways.
  • cell-tracking of fluorescently labelled cells passed through cell culture flow chambers.
  • super-resolution dSTORM imaging of cellmembrane receptors.
  • live-cell super-resolution SIM imaging of calcium signalling.
  • single-particle tracking PALM.
  • single molecule and image correlation studies.
  • ...