Equipment & Resources

The Imaging and Optics Facility is facilitating the use and maintenance of an wide variety of advanced Microscopy, Imaging analysis and Cytometry devices, as well as software licenses and system accessories. Before anyone can make use of any system, users need to complete a training by the Imaging and Optics Facility Facility team before bookings can be made.



Grouped Equipment Overview:


00. Flow Cytometry: Fluorescence-Activated Cell Sorting (FACS)

The Imaging and Optics Facility provides an high-end Flow Cytometry machine park and analysis infrastructure.

Overview Flow Cytometry Equipment
  1. BC Cytoflex LX Cell Analyser (room i04.EG.017): book in PPMS
  2. BD Aria III Cell sorter (room i04.EG.017): book in PPMS
  3. SONY SH800 Cell sorter (room i04.EG.017): book in PPMS
  4. Cytometry analysis workstation (remote): book in PPMS


01. Widefield Microscopes

Our widefield equipment park consists of automated widefield microscopes, as well as slidescanners. The  slidescanner are best used for large volume imaging; the inverted Nikon Ti2E microscopes allow diverse options for automation routines – using JOBS, and have been equipped with incubators chambers, CO2 gas mixers and a variety of (custom) stage inserts. the Zeiss upright systems – and the Axioscan Slide scanner service – excell for quick scans and making overiew images that can be used on confocal – using ZEN Connect. Luminescent samples can be images on our dark-box.

Overview Widefield Microscopes
  1. Olympus VS120 slide scanner (room i06.U1.406): book in PPMS
  2. Nikon Eclipse Ti inverted (room i023.U1.015) → to be reactivated in 2022
  3. Nikon Eclipse Ti2E-01 inverted (room i06.U1.406): book in PPMS
  4. Nikon Eclipse Ti2E-02 inverted (room i04.U1.015): book in PPMS
  5. Nikon Eclipse Ti2E-03 (PRIMO) inverted (room i04.U1.019): book in PPMS → implementation (2022)
  6. Zeiss AxioScan Slidescanner (service-based): book in PPMS
  7. Zeiss Axioscope (room i06.U1.403): book in PPMS
  8. Zeiss Examiner D1 (room i04.U1.018): book in PPMS
  9. Biolumenescence imaging (room i04.U1.018): book in PPMS

02. Confocal Microscopes

Confocal laser scanning microscopy is a flexible technology that suite many imaging applications. Our confocal  machine park consists a diverse set of confocals micrscopes in upright (), inverted () and vertical () orientation. Different applications are available, such as Airyscan, FRAP, FLIM, as well as options to automation routines, such as ‘experiment designer’. Using ZEN Connect, widefield image data (e.g. slidescanner images) can be opened and navigated trough to assist setup of imaging, or add multidimnetional data-sets. Many of the confocal setups have been equipped with incubators or (custom) heated-controlled stage inserts and/or CO2 gas mixers. A dual pipette Aspiration assay has been added to the Leica sp5 inverder microscope.

03. Multiphoton Microscopes

Multiphoton microscopy relies on the simultaneous absorption of two or more photons by a fluorophore, most often using infra-red laser. Multiphoton microscopy most significan atvanteage over other technoligies is that it allows exceptionally deep light penetration with less phototoxicity. It therefore best used for ‘non-invasive’ imaging in living samples / organism. Our multiphoton system allows a very large working space, resonance scanner and allows Fluorescent Life-Time imaging applications (FLIM).

04. Spinning Disk / Multi-point Confocal

Spinning Disk microscopes – also known as ‘Multi-point Confocal microscope’ are fast camera-based imaging systems. Spining Disk Confocals technology induces low phototoxicity and reduced photo-bleaching effects compared to point scanning micrscopes and are therefore a good match for live imaging but als excell in aquisition of large data volumes (cleared tissues, expanded samples or brain sections). Most systems have been equipped with incubators chambers or temperature-contolled stages inserts, CO2 gas mixers and/or a variety of (custom) stage inserts. In addition, Spinning-disk confocal machine park allows many options to cusomize automation routines, as well as feed-back routines allow the triggering of external hard-ware during aquisition → please approach for custom automation project request.

Overview Spinning Disk / Multi-point Confocal Confocal Microscopes

05. Multi-modal multi-point Confocal

Multi-modal multi-point confocal system‘ are also fast camera-based imaging system – similar to our Spining Disk Confocal Micrscopes – but host additional modalities, such as Widefield, Super-resolution (SRRF, SoRa) or TIRF modalities. Different modalities can be combined in both live and fixed samples of different volumes. The systems have been equipped with temperature incubators, CO2 gas mixers and/or a variety of (custom) stage inserts. 

Overview Multi-modal 'Multi-point Confocal Microscopes'
  1. Andor Dragonfly 505 (room i04.U1.015): book in PPMS
  2. Nikon CSU-W1-01 Sora (room i04.U1.015): book in PPMS

06. TIRF Microscopes

Total Internal Reflection Fluorescence (TIRF) Microscopy uses the properties of an induced evanescent wave – by exciting the sample under a ‘critical angle’ – immediately adjacent to the interface between two media having different refractive indices (RI): the contact area between the specimen (e.g. liquid, cells) and the glass coverslip or culture dish. This means that fluorophores are only excted in a very limited volume, also increase in signal-to-noise ratio from the restricted of the excitation volume. TIRF is mostly applied for ‘high resolution’ imaging application and is often comined with fluorescence photobleaching recovery (FRAP). All our TIRF setups have enclosed interlocked incubation chambers to guarentee laser safety. Most systems are equipped with temperature incubator and CO2 gas mixers.

Overview TIRF Microscopes
  1. Olympus IX83 TIRF (room i06.O2.031): book in PPMS
  2. Visitron iLAS2 TIRF + FRAP (room i04.U1.018): book in PPMS
  3. TILL Photonics SD & TIRF (room i06.U1.403): book in PPMS
  4. Nikon TIRF + FRAP (room i023.U1.015) → implementation 2022

07. Light sheet Microscopes

Lightsheet microscopy – otherwise known as selective plane illumination microscopy (SPIM) is a powerful technique for (large) volumetric imaging data with isotropic resolution. Light sheet microscopy is a fast cameras based imaging application that restricts photobleaching and phototoxicity effects. Due to these benefits, Light Sheet micrscopy is often used for in-depth analyses of large, optically cleared (or expanded) samples and for long-term three-dimensional (3D) observations of live biological specimens at high spatio-temporal resolution.

08. Force probing equipment

09. Stereo Microscopes (No Charge)

As part of the Imaging and Optics Facility infrastructure, a number of stereo microscope are available for sample-inspection and -mounting near to our imaging setups. Two stereo microscopes are equipped with an monochrome camera.

Overview Stereo Microscopes
  1. Leica stereo microscope (room i04.U1.019): book in PPMS
  2. Olympus Stereo BFB (room i04.U1.018): book in PPMS
  3. Olympus Stereo LBE (room i06.U1.403): book in PPMS
  4. Zeiss Stereo Discovery (room i06.U1.406)
  • Note: Also the Leica Stereo micrscope can be equipped with our occular camera – available in the Automated Rental System. 


The Imaging and Optics Facility provides an sate-of the arte image analysis infrastructure that includes a large number of high-end analysis workstations  as well as a broad spectrum of different image analysis software applications.

In addition, we provide project based solutions for custom-tailored image analysis tasks: we help you to automate your image analysis workflow, or establish new image analysis routines using the image analysis programs available.

10. Image Analysis Workstations

Workstations machine park consits of 9 PCs and 5 Virtual Machines (VDI), where VDI machines are based on an ‘golden image’ – that is shared over multiple workstations. Analysis workstations are specified for specific image analysis applications: ‘classical image analysis‘ & ‘machine learning-based‘ analysis. All our workstation can be accessed from remote, and a large portion can also be used from dedicated ‘connection terminals’ in room i01.O3.52a/b.

Overview Image Analysis Workstations

11. Image Analysis Software

Workstations (both PCs and VDIs) have preinstalled software, where some ‘propriety software’ will need to be booked seperately – as resources are limited by the number of lisences available.

In addition, we provide project based solutions for custom-tailored image analysis tasks: we help you to automate your image analysis workflow, or establish new image analysis routines using the image analysis programs available*.

Overview Image Analysis Software
  1. Arivis Vision4D (1x float) –
  2. Bitplane Imaris (8x float) + clearview (1x) + stitcher (2x) –
  3. SVI Huygens (2x float) –
  4. Fiji / Image J
  5. FlowJo
  6. Ilastik
  7. Mathworks Matlab
  8. Wolfram Mathematica
  9. Zeiss ZEN (v2.1 / v2.3 /  v2.5 / v3.1)

Note: € – seperate booking of lisence required

Note: overview or the Workstationstechnical specifications


The Imaging and Optics facility released an “Automated Rental System” for Experimental Accessories, Optical Tools, (high-end) Objectives. The Automated Rental System helps to coordinate access-rights and the utilization of the available rental items and allows the Imaging and Optics facility to make the rentals available during the weekends → A brief trainings is required to get booking rights.

Overview Image Analysis Software
12. Rental Accessories
13. Rental Optical Tools
  • Optical Tools: power meter, spectral meter, wavefront sensorinfo (location: i04.U1.Rentals)
14. Rental High-end objectives


Retired systems are not available anymore, but the pages are kept for system information

Overview Retired Equipment

BD CANTO II analyzer (room i04.EG.017): RETIRED

– Neurolucida (room i04.U1.018): RETIRED

Leica SP5 upright *(room i04.U1.019): RETIRED

LaVision TRIMscope MP inverted + FLIM (room i04.U1.019): RETIRED

LaVision TRIMscope MP upright (room i04.U1.018): RETIRED