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+41 21 692 51 06
CIF Coordinator: jean-yves.chatton@unil.ch

Epalinges Instruments

Acquisition systems

Confocal

Confocal microscopy, most frequently confocal laser scanning microscopy (CLSM) or laser confocal scanning microscopy (LCSM), is an optical imaging technique for increasing optical resolution and contrast of a micrograph by means of using a spatial pinhole to block out-of-focus light in image formation.[1] Capturing multiple two-dimensional images at different depths in a sample enables the reconstruction of three-dimensional structures (a process known as optical sectioning) within an object.

Zeiss LSM 800

Stage
  • Zeiss AxioObserver, Inverted

Illumination

  • HXP 120V

Lasers

  • 405nm

  • 488nm

  • 561nm

  • 640nm

Objectives

  • Plan Apochromat 10x / 0.45 NA DIC II

  • Plan Apochromat 20x / 0.80 DIC II

  • Plan Apochromat 40x / 1.30 NA / oil immersion DIC II

  • Plan Apochromat 63x /1.40 NA / oil immersion DIC II

Stage

  • Motorized XY

Contrast

  • DIC

CO2 | T° control

  • No

Detector type

  • 3x GaAsP

Optional modules

  • Multiposition and Tiling

Software

  • Zen Blue 2.6

Room

  • CLF-212a

Zeiss LSM 880

Stage
  • Zeiss AxioObserver Z1, Inverted

Illumination

  • HXP 120V

Lasers

  • 405nm

  • 458nm, 488nm, 514nm

  • 561nm

  • 640nm

Objectives

  • EC Plan Neofluar 10x/0.3 NA Ph1 DIC I

  • EC Plan Neofluar 20x/0.5 NA Ph2 DIC II

  • EC Plan Neofluar 40x/1.3 NA oil immersion DIC III

  • Plan Neofluar 63x/1.25 NA oil immersion DIC III

  • EC Plan Neofluar 100x/1.3 NA oil immersion DIC III

Stage

  • Motorized XY

Contrast

  • Phase (10x & 20x)

CO2 | T° control

  • No | No

Optional modules

  • Multiposition (Mark and Find)
  • Time-Lapse

Software

  • Zen Black

Room

  • CLF-212a

Leica SP5

Stage
  • Leica DM 5000, Upright

Illumination

  • HXP 120V

Lasers

  • 405nm

  • 458nm, 477nm, 488nm, 514nm

  • 543nm

  • 633nm

Objectives

  • HCX PL FLUOTAR 10x/0.30.

  • HC PL APO 20x/0.70 imm corr.

  • HCX PL APO CS 40x/ 1.25-0.75 Oil.

  • HCX PL APO 63x/1.40-0.60 Oil.

  • HCX PL APO 100x/1.40-0.70 Oil CS.

Stage

  • Motorized XY

  • Galvo Z

Contrast

  • DIC

CO2 | T° control

  • No

Detector type

  • 3x PMT

  • Resonnant scanner

Optional modules

  • Multiposition and Tiling

Software

  • LAS AF

Room

  • CLF-213a

Zeiss LSM 800 P2 Lab [SPECIAL AUTHORIZATION REQUIRED]

This particular setup being place in a P2 Lab, special authorization is required to access it. Contact the technical manager for further information

Stage
  • Zeiss AxioObserver, Inverted

Illumination

  • HXP 120V

Lasers

  • 405nm

  • 488nm

  • 561nm

  • 640nm

Objectives

  • Plan Apochromat 10x / 0.45 NA DIC II

  • Plan Apochromat 20x / 0.80 DIC II

  • Plan Apochromat 40x / 0.95 DIC III
  • Plan Apochromat 40x / 1.30 NA / oil immersion DIC II

  • Plan Apochromat 63x /1.40 NA / oil immersion DIC II

Stage

  • Motorized XY

  • Definite Focus

Contrast

  • DIC

CO2 | T° control

  • Yes
  • Full enclosure

Detector type

  • 3x GaAsP

Optional modules

  • Multiposition and Tiling

Software

  • Zen Blue 2.6

Room

  • P2 Lab (F, 4th floor)

Slide Scanner

A slide scanner allows you to digitize full microscopy slides in an automated manner. This is a high throughput system able to process around a hundred of slides in one batch.

The NanoZoomer S60 slide-scanner can work as an intuitive microscope designed for slides or as a regular slide-scanner. The way a slide scanner works implies that designing a specific profile for each of your sample type is needed.
This profile is very dependent of the way you have prepared your slides. Since this processe is time-consuming, it is only useful if you have at least a dozen or more slides of the exact same type to acquire (1-2 hours with testing).

Here are some general guidelines before thinking of using the slide scanner for your experiments:

 

SCAN PROFILE

If the samples vary in any one of these categories:

  • Thickness of the slices
  • Layout of the cuts
  • Size of the cuts
  • Intensity / color of the staining

Fluorescence specific:

  • Number of fluorescent dyes
  • target of the staining used as reference

The profile will have to be updated and saved as a new variant or it will probably fail (not focused, over/underexposed, stitching failing).

ACQUISITION TIME

 The acquisition time depends on:

  • Number of sample / blade
  • Sample size / blade
  • Lens used
  • Exposure time (not important in BF)
  • Z Stack or not and EDF(extend focus) or not
  • Accuracy of the focus map

Each of these parameters can greatly vary the acquisition time, which can range from a few minutes to an hour or more per slide.
If you want to change the objective used for the acquisition, you will also need to update most of the previous parameters of the scan profile.

Hamamatsu NanoZoomer S60

Brochure available here for more information : https://www.hamamatsu.com/resources/pdf/sys/SBIS0043E_NanoZoomers.pdf

Illumination

  • See filters below

Filters

  • DAPI
  • FITC – AF488
  • Cy3 (or TxRed)
  • Cy5
  • Cy7 – AF750 (unique at the CIF at the moment)

Objectives

  • The NanoZoomer S60 uses a 40x objective allowing for multiple magification through pixel binning.

Stage

  • Motorized

Contrast

  • Brightfield, Fluorescence

CO2 | T° control

  • No

Cameras

Color camera

  • Color CMOS camera

Black and White Camera

  • sCMOS Orca Flash LT Plus

Optional modules

  •  

Software

  • NDP.view2

Room

  • CLF-212

Widefield | Fluorescence

The majority of fluorescence microscopes, especially those used in the life sciences, are of the epifluorescence design shown in the diagram. Light of the excitation wavelength illuminates the specimen through the objective lens. The fluorescence emitted by the specimen is focused to the detector by the same objective that is used for the excitation which for greater resolution will need objective lens with higher numerical aperture. Since most of the excitation light is transmitted through the specimen, only reflected excitatory light reaches the objective together with the emitted light and the epifluorescence method therefore gives a high signal-to-noise ratio. The dichroic beamsplitter acts as a wavelength specific filter, transmitting fluoresced light through to the eyepiece or detector, but reflecting any remaining excitation light back towards the source.

Zeiss Axiovision Upright

Stage
  • Zeiss ImagerZ1, Upright

Illumination

  • HXP 120V

Filter Cubes

  • DAPI
  • CFP
  • GFP
  • Rhodamin
  • CY5
  • FRET
  • YellowFP
  • mCherry
  • DsRed

Objectives

  • EC Plan Neofluar 10X, N.A. 0.3 DIC
  • EC Plan Neofluar 20X, N.A. 0.5 DIC
  • EC Plan Neofluar 40X, N.A. 1.3 Oil DIC
  • Plan Neofluar 63X, N.A. 1.4 Oil DIC
  • EC Plan Neofluar 100X, N.A. 1.3 Oil DIC

Stage

  • Motorized

Contrast

  • NC

CO2 | T° control

  • No | No

Cameras

  • Axiocam MRm
  • Axiocam MRc5

Optional modules

  • Mosaix (Image stitching)

Software

  • Axiovision SE64 rel 4.9.1

Room

  • CLF-212

Zeiss Axiovision Upright B

Stand
  • Zeiss AxioImager Z1, Upright

Illumination

  • EBQ100 Isolated

Filters

  • DAPI BP
  • YFP
  • FITC – GFP
  • Rhodamin – CY3
  • Alexa 660
  • CY5.5
  • DAPI LP

Objectives

  • EC Plan Neofluar 10x/0.3 NA DIC I

  • EC Plan Neofluar 20x/0.5 NA DIC II

  • EC Plan Neofluar 40x/0.75 NA DIC II
  • EC Plan Neofluar 40x/1.3 NA oil immersion DIC III

  • Plan Neofluar 63x/1.25 NA oil immersion DIC III

  • EC Plan Neofluar 100x/1.3 NA oil immersion DIC III

Stage

  • Motorized XY

Contrast

  • DIC

CO2 | T° control

  • No

Cameras

Color camera

  • Zeiss Axiocam MRc

Black and White Camera

  • Zeiss Axiocam MRm

Optional modules

  • Mosaix (Tile Scan)

Software

  • Zeiss Axiovision rel 4.8

Room

  • CLF-213

Time-Lapse microscopy

Time-lapse microscopy is time-lapse photography applied to microscopy. Microscope image sequences are recorded and then viewed at a greater speed to give an accelerated view of the microscopic process. Before the introduction of the video tape recorder in the 1960s, time-lapse microscopy recordings were made on photographic film. During this period, time-lapse microscopy was referred to as microcinematography. With the increasing use of video recorders, the term time-lapse video microscopy was gradually adopted. Today, the term video is increasingly dropped, reflecting that a digital still camera is used to record the individual image frames, instead of a video recorder.

Zeiss Axiovision Inverted (Time-Lapse)

Stage
  • Zeiss AxioObserver Z1, Inverted

Illumination

  • HXP 120V

Filter Cubes

  • DAPI
  • CFP
  • GFP
  • Rhodamin
  • CY5

Objectives

  • EC Plan Neofluar 10X, N.A. 0.3 Ph1
  • EC Plan Neofluar 20X, N.A. 0.5 Ph2
  • EC Plan Neofluar 40X, N.A. 1.3 Oil DIC
  • Plan Neofluar 63X, N.A. 1.25 Oil DIC
  • EC Plan Neofluar 100X, N.A. 1.3 Oil DIC

Stage

  • Motorized

Contrast

  • Phase only

CO2 | T° control

  • Yes [Full enclosure]

Cameras

  • Photometrics CoolSnap HQ2

Optional modules

  • Multi-position

Software

  • Axiovision 4.8

Room

  • CLF-213

Stereomicroscopy

The stereo, stereoscopic or dissecting microscope is an optical microscope variant designed for low magnification observation of a sample, typically using light reflected from the surface of an object rather than transmitted through it. The instrument uses two separate optical paths with two objectives and eyepieces to provide slightly different viewing angles to the left and right eyes. This arrangement produces a three-dimensional visualization of the sample being examined.[1] Stereomicroscopy overlaps macrophotography for recording and examining solid samples with complex surface topography, where a three-dimensional view is needed for analyzing the detail.

Leica M205-FA