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Research facilities

Microscopy Unit

The Microscopy Unit houses, maintains and coordinates most of the microscopy equipment of the IBL. The available equipment ranges from conventional light and fluorescence microscopes, to confocal laser scanning and electron microscopes. In addition, infrastructure is available for histology, including embedding, sectioning and staining. We offer support in automated image analysis for microscopy data. The equipment is housed at two locations: on the 6th floor of the Sylvius building and at the Cell Observatory in the Gorlaeus Laboratory. For an overview of the available equipment go to ‘Equipment’.
The Microscopy Unit is open for All students, PhD students, researchers of the Leiden university as well as guest workers.
Gerda Lamers

Location Sylvius
On the 6th floor of the Sylvius laboratory equipment can be found that enables researchers to perform many microscopical applications. Several light microscopes (conventional compound and stereo), upright and inverted fluorescence microscopes, stereo fluorescence microscopes, confocal laser scanning microscopes and scanning electron microscopes are present. In addition, sample preparation equipment is available for histology as well as electron microscopy techniques.

Location Cell Observatory
The Cell Observatory, located at the second floor of the GW wing of the Gorlaeus Laboratory is a specialised imaging center in which several institutes of the science faculty participate, among which the IBL. In the Cell Observatory more specialised microscopy equipment is present, in order to apply more advanced technology like fluorescence correlation spectroscopy and multi-photon excitation. Besides this, the Cell Observatory houses the microscopes of the IBL.

Rules and Regulations
The Microscopy Unit is open for All students, PhD students, researchers of the IBL as well as guest workers. However, the equipment can only be used after appropriate introduction and/or training. Please contact Gerda Lamers or Joost Willemse for an introduction on the equipment before starting experiments. It is not allowed to use any equipment before being properly trained.

Booking of equipment is done via Supersaas, for access to the Confocal, SEM, TEM, and VAST you need to register. For stereo microscopes (Stereo_sylvius, Stereo_Gorlaeus), as well as Fluorescence widefield microscopes you can create a login yourself.

Furthermore if you have questions about experimental set up feel free to walk into our office to discuss which type of microscopy, histology or image analysis you need. If a microscope malfunctions during operation or you are not sure how to use it properly, contact Gerda Lamers or Joost Willemse immediately.

Confocal Microscopes

Airyscan confocal microscope

Zeiss Airyscan 900

  • Location: Sylvius, Rm. 6.5.32
  • Specifications: Inverted confocal laser scanning microscope, incubation (temperature only), automated stage control, three detector channels for fluorescence and one transmitted light channel, available laser lines: 405, 488, 543, and 633 nm
  • Agenda
  • Instruction movie

Nikon AX

  • Location: Sylvius, Rm. 6.5.32
  • Specifications: Upright confocal laser scanning microscope, two detector channels for fluorescence and one transmitted light channel, available laser lines: 405, 458, 488, 514, 561, and 640 nm
  • Agenda
  • Instruction manual


  • Location: Cell Observatory GW 2.26
  • Specifications: Inverted confocal laser scanning microscope, one spectral detector channel for fluorescence and one transmitted light channel, available laser lines 488, 532, and 633 nm
  • Agenda
  • Instruction movie (in dutch)

Leica SP8

  • Location: Cell Observatory GW 2.28
  • Specifications: Inverted confocal laser scanning microscope, three spectral detector channels for fluorescence (2 PMT, one GASP) and one transmitted light channel, available laser lines 405, 488, 532, and 633 nm
  • Agenda
  • Instruction movie

Electron Microscopes

Jeol 7600 Scanning electron microscope


  • Location: Sylvius, Rm. 6.5.34
  • Specifications:
    • Conventional high vacuum scanning electron microscope equipped with digital imaging
    • Cryo-unit for freezing, coating and imaging of samples
    • EDS for elemental analysis
  • Agenda
  • Manual

JEOL TEM 1400+

  • Location: Cell Observatory GW2.24a
  • TEM JEOL 1400: 120 kV transmission electron microscope
  • Agenda
  • Manual

Fluorescence compound microscopes

Widefield Observer

Zeiss Observer

  • Location: Sylvius, Rm. 6.5.31a
  • Widefield fluorescence microscope with Colibri system. Filters for DAPI, GFP and mCherry. Automated stage. Equipped with a Hamamatsu EMCCD
  • Agenda
  • Manual (tiles imaging only)

Zeiss Axioscope A1

  • Location: Sylvius, Rm. 6.5.31a
  • Widefield fluorescence microscope with Colibri system. Filters for DAPI, GFP and mCherry.  
  • Agenda
  • Manual

Zeiss Axioplan 2 aka DIC

  • Location: Sylvius, Rm. 6.5.35
  • Specifications:
    • Upright fluorescence microscope, DIC optics. Equipped with Zeiss AxioCam MRc 5 digital color camera
    • Filter blocks for DAPI, CFP, GFP, YFP, mCherry,DIC are present others can be custom built via consulation with Gerda or Joost
  • Agenda
  • Manual


  • Location Cell Observatory GW2.26
  • Leica SL confocal CTR 6000 +DFC 450C camera, Vast BioImager + LP Sampler (Union Biometrica), Ar laser 457, 488, 515, HeNe 543, HeNe 633
  • Agenda

Stereo Fluorescence/Light microscopes

Stereo fluorescence microscopy

Leica MZ16FA

  • Location: Sylvius, Rm. 6.5.31b
  • Specifications: Stereo fluorescence microscope, automated focus, zoom and stage control. Equipped with Leica DFC 420 C digital color camera. filters for GFP, DSR, YFP, CFP, CY5, Alexa 405
  • Agenda

LEICA M205 FA (2)

  • Location Cell Observatory GW2.28
  • Stereo fluorescence microscope, filters GFP, DSR, YFP, CFP, CY5, Alexa 405, Leica DFC 345FX camera
  • Agenda

Zeiss V8

  • Location: Sylvius, Rm. 6.5.31a
  • Specifications: Stereo light microscope, manual focus and zoom control. Equipped with bresser digital color camera
  • Agenda

By discussing your experiments with us our histology expertise will help you identify:

  • Which type of microscopy you need to solve you research question
  • which staining’s you might need
    (Hematoxylin/Eosin, DAPI, Syto 9, a.o.)
  • If embedding and sectioning is needed, and if so which type
    (Gelatin, Paraffin, Epon)
  • Train/Assist you in embedding/sectioning of samples

We also can provide image analysis solutions. Our Photoshop and FIJI / ImageJ experience can help you identify what you want to quantify in your images and how to do this. For this we have a set of ready to use FIJI plugins which can be downloaded from the ImageJ update sites. To do this start-up FIJI, click > Help > Update. After the check is finished go to > Manage Update Sites and tick the box with Leiden University. Click > Close, and > Apply Changes. After a restart the plugins will be available.

In addition we can program custom solutions for your image analysis problems. This can range from fully automated image analysis on 4D images, to an explanation on how to perform manual analysis on 2D images and anything in between.

Furthermore we have access to Huygens deconvolution software, Imaris, and Amira.

Every year a PhD course on microscopy will be organised where you will learn the basics of microscopy. 

Topics include:

  • Kohler illumination
  • Phase contrast
  • DIC
  • Fluorescence microscopy
  • Confocal microscopy
  • Image analysis

Read more about the microscopy course in this news article

OMERO is our envisioned data storage solution. For all microscopes operating under the latest windows version we offer the option to directly upload your data from the microscope into the OMERO database.


The Cell Observatory within the Faculty of Science at Leiden University contributes to scientific excellence in the life sciences through innovative state-of-the-art imaging technologies. Several institutes, e.g. LACDR, IBL, LION, LICand LIACS contribute to these Advanced Optical Microscopy (AOM) techniques and data analysis workflows. National  and  international  bio-imaging  communities  have  taken  on  the  challenge  of  structured  image  data-management following the FAIR (Findable Accessible Interoperable Reusable) principles. A major challenge for a local infrastructure is therefore the harmonisation of solutions and best practices, standardising the collection of rich metadata and providing a centralized archiving solution for researchers. In all cases, the links between data and  data  analysis  tools  need  improvements,  and  more  support  for  data  stewardship  is  required  throughout  the data life cycle. The data management and image analysis processes have common requirements across all imaging modalities, although different techniques give rise to specific problems and must all be addressed in a common data management and analysis framework. 

Leiden  University  was  one  of  the  first  in  the  Netherlands  to  successfully adopt the  OMERO  database. A centralized OMERO database  will  facilitate  preserving  and  archiving  raw  data,  collaboration  on  data  analysis workflows, and FAIR data management. To advance in archiving, processing and sharing of bio-imaging data, the first Faculty wide OMERO instance was set up as a pilot. This  pilot was  made available  to multiple  researchers  (from LACDR, IBL, LIC and LIACS) who worked with a selection of 4 microscopes from different suppliers. During the course of the pilot (6 months), the OMERO instance has been evaluated. Since september 2020 the pilot has gone live and all researchers can and should upload their microscopic data into OMERO.  

Acccess to OMERO 

Everyone at Leiden University can access OMERO after registration for access (Including bachelor and Master students), for registration fill in the OMERO registration form. All data can be accessed via the omero webbrowser of after installing the omero insight client. The latter is especially useful when downloading large datasets. All communication about OMERO is done via Teams

OMERO team:
Joost Willemse
Sylvia Le Dévédec
Rohola Hosseini

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