Rue du Bugnon 9, CH-1005, Lausanne, VD, Switzerland
+41 21 692 51 06
CIF Coordinator: jean-yves.chatton@unil.ch

Bugnon 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 710

Stand
  • Zeiss AxioObserver Z1, Inverted

Illumination

  • X-Cite

Lasers

  • 405nm

  • 458nm, 476nm, 488nm, 514nm

  • 561nm

  • 633nm

Objectives

  • Plan neofluar 10x / 0.30 NA (No DIC)

  • Plan neofluar 20x / 0.50 NA

  • Plan neofluar 40x dry

  • Plan neofluor 25x oil immersion

  • Plan neofluar 40x / 1.30 NA / oil immersion

  • Plan apochromat 63x /1.20 NA / oil immersion

  • Plan neofluar 100x /1.30 NA / oil immersion

Stage

  • Motorized

Contrast

  • DIC

CO2 | T° control

  • Yes

Detector type

  • 2x PMT

  • Quasar detector (spectral imaging)

Optional modules

  •  

Software

  • Zen black 2012

Room

  • B9-150

Zeiss LSM 780 with Airyscan

Stand
  • Zeiss AxioObserver Z1, Inverted
Widefield Illumination
  • X-Cite
Lasers
  • 405nm
  • 458nm, 476nm, 488nm, 514nm
  • 561nm
  • 633nm
Objectives
  • Plan Neofluar 10x / 0.30 NA
  • Plan Apochromat 20x / 0.8 NA
  • Plan Neofluar 40x /0.6 NA
  • Plan Apochromat 40x / 1.30 NA / oil immersion
  • Plan Apochromat 63x /1.40 NA / oil immersion
Stage
  • Motorized
Contrast
  • DIC
CO2 | T° control
  • No
Detector type
  • 2x GaAsP
  • Quasar detector (spectral imaging)
  • Airyscan (enhanced resolution and SNR)
Optional modules
  •  
Software
  • Zen black 2012
Location
  • B9-152

Zeiss LSM 900

Stand
  • Zeiss AxioObserver Z1, Inverted
Widefield Illumination
  • HXP 120W
Lasers
  • 405nm
  • 488nm
  • 561nm
  • 640nm
Objectives
  • Plan Apochromat 10x | 0.45 NA
  • Plan Apochromat 20x | 0.80 NA
  • Plan Apochromat 40x | 1.30 NA | oil immersion
  • Plan Apochromat 63x | 1.40 NA | oil immersion
Stage
  • Motorized
Contrast
  • DIC
Cubes
  • FL set 10 (ExBP450-490 shift free)
  • FL set 20 (Rhodamin shift free)
  • FL set 49 (DAPI, ExG365 shift free)
CO2 | T° control
  • No
Detector type
  • 3x GaAsP
  • 1x ESID (bright field)
Optional modules
  • Tiles and Positions
  • FRAP
  • Experiment Designer
Software
  • Zen blue 2019
Location
  • B9-152

Spinning Disk | Time-Lapse

Spinning-disk (Nipkow disk) confocal microscopes use a series of moving pinholes on a disc to scan spots of light. Since a series of pinholes scans an area in parallel, each pinhole is allowed to hover over a specific area for a longer amount of time thereby reducing the excitation energy needed to illuminate a sample when compared to laser scanning microscopes. Decreased excitation energy reduces phototoxicity and photobleaching of a sample often making it the preferred system for imaging live cells or organisms.

Nikon Ti2 | CrEST Optics V2

Stand
  • Nikon Ti2, Inverted

Spinning Disk Head

  • Crest Optics X-Light V2 – Single Pattern Disk for large FOV

Widefield LED Illumination

Lumencore Sola LED

Filter Cubes

  • DAPI
  • CFP
  • YFP
  • GFP
  • CY3
  • CY5

Spinning Disk + DMD LED excitation

Lumencore Spectra X LED x2 (1x SD + 1x DMD)

  • 395nm

  • 440nm

  • 470nm

  • 508nm

  • 555nm

  • 640nm

Objectives

  • CFI Plan Apochromat Lambda 10X, N.A. 0.45, W.D. 4.0mm
  • CFI Plan Apochromat Lambda 20X, N.A. 0.75, W.D. 1.0mm, spring-loaded
  • CFI Plan Apochromat Lambda 40XC N.A. 0.95, W.D. 0.21mm, Spring-loaded, Cover glass correction: 0.11-0.23mm
  • CFI Plan Apochromat Lambda 60XC N.A 0.95, WD 0.21mm
  • CFI Plan Apochromat Lambda 60X Oil, N.A1.40, W.D. 0.13mm

Stage

  • Motorized

  • Piezo (Z direction)
  • Nikon PFS (Perfect Focus System)

Contrast

  • DIC

CO2 | T° control

  • Yes [Full enclosure]

Cameras

  • 1x Photometrics Prime 95B

  • 1x Nikon DS-Qi2

DMD

  • DMD module for multipoint photoactivation

Optional modules

  • JOBS
  • General Analysis 3

Software

  • Nikon NIS-Elements AR 5.0

Room

  • B9-145c

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.

Leica DMi8

Stand
  • Leica DMi 8, Inverted

Illumination

  • SOLASMII, Light source (365nm Version)

Filters

  • DAPI
  • YFP
  • CFP
  • CY3
  • Y5
  • GFP

Objectives

  • HCX FL PLAN 5/0,12 working distance 14,2mm
  • HC PL Fluotar 10x/0.32 PH1

  • HC PL FL L 20x/0.40 CORR PH1

  • HCX PL FLUOTAR L 40x/0.60 CORR

  • HC PL Fluotar (340) 40x/1.30 oil

  • HC PL APO 63x/1.400.60 oil

Stage

  • Motorized

Contrast

  • Phase

CO2 | T° control

  • No

Cameras

Color camera

  • Leica DFC7000T

Black and White Camera

  • Andor Zyla

Optional modules

  • Navigator
  • Multi-well holder (Universal holding frame KM, Click-In)

Software

  • LAS X Premium

Room

  • B9-152c

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.

Nikon SMZ25 Stereomicroscope | Macroscope

Stand
  • Nikon SMZ-25, Upright

Illumination

  • Bright field from the base
  • Fluorescence
  • Ring illumination module for macro shots
  • Optional screw-in polarizer

Filters

  • DAPI
  • GFP
  • TXR

Objectives

  • Plan Apochromat 0.5x SHR WD 71mm
  • Plan Apochromat 1x SHR WD 60mm
  • Plan Apochromat 2x SHR WD 20mm
  • Motorized 25x zoom

Stage

  • Manual XY

  • Motorized Z

Contrast

  • Brightfield + Fluorescence

CO2 | T° control

  • No

Cameras

  • Nikon DS-Ri2 16 Mpx color camera

Optional modules

  • Extended Depth of Field
  • JOBS
  • Multi-position

Software

  • Nikon NIS-BR 4.20

Room

  • B9-152

Slide scanner

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

Zeiss Axioscan Z.1

The way the Zeiss slide scanner works at the CIF 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 two focus maps

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.

DATA SETS

 The files are acquired in the .CZI format.

  • The typical file size ranges from 100 Mb to several Gb
  • Files exported in TIFF will see their size increased AND multiplied several times depending on the number of channels
  • It is thus key to minimize the size of the dataset to be acquired to avoid further analysis problems -> always prefer the minimum magnification that will answer your scientific question. For screening purposes, use the lowest magnification.

Illumination

Zeiss Colibri 7 Type R[G/Y]CBV-UV

  • Red (630nm) for excitation of Cy5, Alexa 631, TOTO-3 and similar dyes
  • Yellow (590nm) for excitation of mCherry, Alexa 568, mPlum and similar dyes
  • Green (555nm) for excitation of Cy3, TRITC, DsRed and similar dyes
  • Cyan (511nm) for excitation of eYFP, Eosin, TOTO-1 and similar dyes
  • Blue (475nm) for excitation of eGFP, Fluo4, FITC and similar dyes
  • Violet (430nm) for excitation of eCFP, Lucifer Yellow, Alexa 430 and similar dyes
  • UV (385nm) for excitation of DAPI, Alexa 405, Hoechst 33258 and similar dyes

Filters

Objectives

  • Fluar 5x/0.25
  • Plan Apochromat 10x/0.45

  • Plan Apochromat 20x/0.80

  • Plan Apochromat 40x/0.95

Stage

  • Motorized

Contrast

  • Brightfield, RAC, Fluorescence

CO2 | T° control

  • No

Cameras

Color camera

Black and White Camera

Optional modules

  •  

Software

  • Zen Blue 2.6

Room

  • B9-152c

Image Processing

[Under construction]