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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 IBL as well as guest workers.
Contact
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 Molecular Cell Biology group 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

Zeiss LSM5 Exciter / AxioObserver

  • Location: Sylvius, Rm. 6.5.32
  • Specifications: Inverted confocal laser scanning microscope, automated stage control, two detector channels for fluorescence and one transmitted light channel, available laser lines: 405, 458, 488, 514, 543, and 633 nm

Zeiss LSM5 Exciter / AxioImager

  • 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: 458, 488, 514, 543, and 633 nm

Leica TCS SPE

  • 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

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

Electron Microscopes

JEOL SEM 6400

  • Location: Sylvius, Rm. 6.5.34
  • SEM JEOL 6400: Conventional high vacuum scanning electron microscope equipped with Image Convert for windows (digital imaging)

JEOL TEM 1010

  • Location: Cell Observatory GW2.24a
  • TEM JEOL 1010: 100 kV transmission electron microscope

Phenom

  • Location: Sylvius, Rm. 6.5.35
  • Scanning electron microscope. For examining surfaces at nanometer resolution

Fluorescence microscopes

Zeiss Axioplan 2

  • Location: Sylvius, Rm. 6.5.35
  • Specifications: Upright fluorescence microscope, DIC optics. Equipped with Zeiss AxioCam MRc 5 digital color camera

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

LEICA DM6000

  • 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

LEICA M205 FA

  • Location Cell Observatory GW2.26
  • Stereo fluorescence microscope, filters GFP, DSR, YFP, CFP, CY5, Alexa 405, Leica DFC 345FX camera

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

Zeiss Axioscope A1

  • Location: Sylvius, Rm. 6.5.31a
  • Widefield fluorescence microscope with Colibri system. Filters for DAPI, GFP and mCherry.  Equipped with Axiocam Mrc5

Zeiss Lumar V12

  • Location: Sylvius, Rm. 6.5.31a
  • Stereo Fluorescence microscope. Filters for CFP, YFP and GFP. Magnification 5-150x

Stereo light microscope

Leica MZ12

  • Location: Sylvius, Rm. 6.5.31a
  • Specifications: Stereo light microscope, automated focus and zoom control. Equipped with Leica DC500 digital color camera

Other equipment in the cell observatory not managed by the IBL microscopy unit can be found via OARI.

 

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

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