Research facilities
Microscopy Unit
- Application
- 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’.
- Availability
- The Microscopy Unit is open for All students, PhD students, researchers of the Leiden university as well as guest workers.
- Contact
- Joost Willemse
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 Bas Laan 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 microscopes you need to register.
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 Bas Laan or Joost Willemse immediately.
For information about the microscopes we have as well as the services we provide please go to our wiki page
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.