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Written by Yannick KREMPP   
Friday, 13 July 2007


Confocal Microscope Zeiss LSM 700

This Zeiss LSM700 confocal is mounted on an inverted Zeiss Axio Observer Z1 using a motorized XY stage controller. We have 4 solid state laser lines (445, 488, 555 and 639nm) available on this system.

Currently four objectives are on the system: a Plan Apo 10x Ph1 objective with a 0.45 NA, a Plan Apo 25x Oil immersion DIC objective with 0.8 NA, a Plan Neofluar 40x Oil immersion DIC objective with a 1.3 NA and an Apochromat 63x Water immersion DIC objective with a 1.2 NA.

Two photomultiplier detectors are available, each coupled with 8 emission filters for spectral flexibility on the detection of the fluorescence signal. An additional transmitted light detector may also be selected to allow the users to acquire a transmitted light image of the samples in confocal mode.

The software running the LSM700 is the ZEN ("Zeiss Efficient Navigation") software. That software allows a really easy and straightforward use of the confocal. Using the so-called "Smart Setup" function, the software will drive you in a few clicks through the light path configuration to set up for your own experiments.

Additionally, the focus stabilizer ("Definite Focus") implemented on this confocal microscope enables maintaining the focus stable in the z axis for in long term (typically time-lapse) acquisitions.


Confocal Microscope Leica SP 8 FLIM

This confocal microscope comes with a pulsed supercontinuum (White Laser Line) tunable laser in the visible range from 470nm to 670nm. Tune freely your own BP filter settings for detection that are matching for your fluorescent detection. The fine tunable WLL (every wavelength with 1nm accuracy can be selected from the 470-670nm range) will allow to perform any type of excitation within this range and also measuring the excitation spectrum of your fluorescent dyes. Complete excitation emission spectra can be recorded.

A FLIM (Fluorescence Lifetime Imaging) module is also attached to this system. So with that you can measure precisely fluorescence lifetime of your dyes and perform Single Molecule Detection (SMD). This feature is fully integrated to the confocal system (developed by PicoQuant company using Symphotime software). This SMD FLIM can also be used to make FRET experiments.

The microscope stand is an inverted one fully motorized. The system has a motorized xy stage controller. The motorized z focus can use the microscope motorization or the table top piezo z for fine and fast z movements.

On the detection side of the fluorescence of your samples its fully filter free you can design and fine tune your emission spectrum window freely. Two sensitive HyD + 1 HyD-SMD/FLIM detectors (Hybrid Detectors) are installed with one standard PMT detector. The HyDs are special detection devices that will allow you to time shift the detection of the light coming from the sample using the so called gating feature (adjusting in time gate switches off the data collection during the WLL laser pulse) this will help in many cases to get read of autofluorescence/biological background of the sample used. The HyDs are also generating no electronical noise and can be used for photon counting experiments.

A transmitted light PMT is added to the system for the confocal brightfield recordings.

As complementary lasers on the Leica SP8 we have an Argon ML laser generating the 458, 488 and 514nm lines. A 440nm solid state laser is also present for the FLIM measures.

On the objectives side the system is equipped with a:

10x HC PL FLUOTAR NA 0.30 Dry,

20x HC PL NA 0.75 IMM,


63x HC PL APO NA 1.20 WATER.


In summary this system will enable you to perform all the traditional confocal multi-dimensional experiments as consecutive optical slices (z-stacks), xy tiles stitched automatically together, time lapses, fluorescent multi channels acquisitions, spectral characterized experiments and all these can be combined. Also precise FRAP/FRET or FLIM experiments can be performed.

This brand new system is now installed at the CIF Dorigny campus (Biophore, Room 4416). 





Confocal Microscope Zeiss LSM 510 Meta INVERTED

Available Laser lines :
Diode 30mW 405 nm
Argon Multiline 30mW 458/477/488/514 nm
HeNe 1mW 543 nm
HeNe 2mW 594 nm
HeNe 5mW 633 nm

Equiped with transmited detector for DIC and Phase Contrast.
Meta detector for emission spectra of fluorochromes.

Attached software : LSM Software Rel. 3.5

INVERTED Microscope

Zeiss AXIO Vert 200 M
XY motorized Stage

Filter cubes
Set 01 DAPI Ex BP 365/12, FT 395, Em LP 397
Set 09 FITC Ex BP 450-490, FT 510, Em LP 515
Set 15 Rhod Ex BP 546/12, FT 580, Em LP 590

EC Plan-NEOFLUAR 10x/0,30
EC Plan-NEOFLUAR 20x/0,50
EC Plan-NEOFLUAR 40x/1,30 Oil DIC
Plan-APOCHROMAT 63x/1,40 Oil DIC
Plan-APOCHROMAT 100x/1,40 Oil DIC

Camera : AxioCam MRm
Axiovision Software Rel. 4.4

Illumination: HAL 100, HBO 100

Zeiss LSM 710 NLO (Non Linear Optics)

Laser lines

Available visible laser lines 458, 488, 514, 561 and 633 nm for conventional laser scanning confocal microscopy.

The available laser for the 2 Photon acquisitions is a Ti:Sapphire Chameleon Ultra II infrared laser, tunable  from 690 nm to 1040 nm with an maximum output power of  4W at 800 nm.


An upright Zeiss AxioExaminer Z1.

Objectives available on the system, currently 3 objectives are available on the system:

Achroplan 10x W objective with a 0.3 NA

Plan-Apochromat 20x W objective with a 1.0 NA

Apochromat 63x Water-Oil immersion objective with a 1.2 NA

Attached Software

ZEN 2009 (Zeiss Efficient Navigation 2009)

Detection modes

The light may be detected in the confocal scanhead (internal or  'descanned' detection)

Confocal detection on external 'non-descanned' detectors (NDD)

Confocal detection on GaAsP non-descanned detector (GaAsP NDD)

System Capabilities

In depth confocal microscopy for thick samples 3D optical sectioning.

Spectral infrared excitation fingerprinting.

Spectral emission fingerprinting.

FRAP, FRET, Time lapse, fluorescent dyes uncaging



Confocal Microscope Zeiss LSM 510 Meta UPRIGHT

Available Laser lines :
Diode 30mW 405 nm
Argon Multiline 30mW 458/477/488/514 nm
HeNe 1mW 543 nm
HeNe 2mW 594 nm
HeNe 5mW 633 nm

Equiped with transmited detector for DIC and Phase Contrast.
Meta detector for emission spectra of fluorochromes.

Attached software : LSM Software Rel. 3.5

UPRIGHT Microscope

AXIO Imager Z.1
Fully motorized

Filter cubes
Set 49 DAPI Ex G 365, FT 395, EM BP 445/50
Set 38 HE eGFP EX BP 470/40, FT 495, EM BP 525/50
Set 43 HE Cy3 Ex BP 550/25, FT 570, EM BP 605/70
Set GFP Chroma

EC Plan-NEOFLUAR 10x/0,30
ACHROPLAN 10x/0,30 W Ph1
ACHROPLAN 20x/0,50 W Ph2
ACHROPLAN 40x/0.80 W
EC Plan-NEOFLUAR 40x/1,30 Oil DIC
ACHROPLAN 63x/0,95 W
Plan-APOCHROMAT 63x/1,40 Oil DIC

Camera : AxioCam MRm
Axiovision Software Rel. 4.4

Illumination: HAL 100, HBO 100

Stereomicroscope Leica MZ16FA

Standard + Fluorescence
Fluorescence Leica EL6000 (lasts up to 2000 hours)

1x up to 180x

DAPI, GFP, CY3, Transmitted light

Attached software : Leica Application Suite (LAS)

Cameras :
Leica DFC350FX Monochrome
Leica DFC320R2 Color

Motorized filter wheel, focus and zoom.

Laser Microdissection and laser tweezers

Microscope :
Inverted OLYMPUS IX71

Illumination: HBO, HAL

Filters cubes for Dapi, FITC, TRITC:
narrow-band DAPI Ex BP360-370, BS DM400, Em BA420-460
wide-band FITC Ex BP460-495, BS DM505, Em BA510-550
wide-band TRITC Ex BP530-550, BS DM570, Em BA575-625

Plan Fluorite 4X/0.13 PHL wd 17.00mm
Plan Fluorite 10X/0.30 PH1 wd 1.60mm
Plan Fluorite 20X/0.45 PH1 wd 6.40 – 7.6mm.60mm
Plan Fluorite 40X/0.60 PH2 wd 2.70mm – 4.00mm
Plan Fluorite 60X/0.70 PH2 wd 1.50mm – 2.20mm
Plan Super Apochromat 100X/1.40 oil imm wd 0.12mm

Modules :
mmi CellCut® Laser Microdissection System
Computer controlled xy-table

mmi CellManipulator Laser tweezer

Multi Cap System
Multi-Slide System

Attached Camera :
3 Chip RGB CCD Sony camera
20´´ Interactive Pen-Screen Display

Laser for cutting and isolation of tissue samples :
Solid state UV-A laser, 350 nm

Trapping Laser CellManipulation :
YAG IR-laser, 3 W, 1064 nm

Attached Software :
mmi UV Cut Software
Cellexplorer image analysis software package
CellManipulator Software Package

TIME LAPSE / ION-imaging, Multidimentional acquisition station

Illumination :
Visichrome monochromator
Halogen lamp

Microscope stand :
Inverted microscope Zeiss Axiovert 200 M
with XY motorized stage controller
Full automatic Objective changer
Automatic Z-focus
Automatic filter change

Installed filter cubes :
Single Filter sets for DAPI, FITC, Rhodamine
Triple Filter set for DAPI, FITC, Rhodamine

Objectives :
Plan-Neofluar 20x/0.50 Ph2
Plan-Neofluar 40x/1.30 Oil DIC
Plan-Apochromat 63x/1.40 Oil DIC
Plan-Apochromat 100X/1.40 Oil DIC

Camera :
Roper Scientific CoolSnap HQ

Objective Heating Ring system
Thermostatized Heating tabletop incubation chamber
CO2 controller

Attached Softwares :
MetaMorph 6.3 (Universal Imaging)
MetaFluor 6.3 (Universal Imaging)


Stations short description :
Dell Precision 670
2x Intel Xeon 3.00 GHz (800MHz FSB / 2 MB L2 cache), processor Hyper-threading
2.0 GB (2x1024MB DIMM) 400MHz DDR2 ECC SDRAM
128Mo PCIe x16 (DVI/VGA) nVidia Quadro FX1400
20" LCD TFT flat wide aspect screen

Installed softwares :

Image acquisition and analysis.

NIH Image / Scion Image / Visilog / Image J
General purpose image analysis software with programming language.

Bitplane IMARIS suite 4.1
Consisting of Imaris, ImarisMeasurement Pro, ImarisTrack and ImarisColoc.
Large range of specific image file readers for 3D microscopes. SLicer, Section, Gallery,
Easy 3D shadow Projection, real time volume rendering.
Interactive 3D distance measurement, volume and voxel intensity statistics in 3D and 4D,
manual object segmentation with contours. Leading 3D and 4D colocalization.

Bitplane ImarisXT - programing interface
Bitplane Filament Tracer 4.1, to segment and visualize filamentous structures
AutoAligner 2.0, for automatic and manual registration of serial 2D images

SVI HUYGENS Essential Rel. 2.8
3D Deconvolution software
Huygens® Essential is an image processing software package tailored for deconvolution of microscopic images.
Huygens Essential is able to deconvolve a wide variety of images ranging from 2D widefield (WF) images
to 4D multi-channel two-photon confocal images. To facilitate comparison of raw and deconvolved data,
or results from different deconvolution runs the Essential is equipped with a dual 4D slicer tool.
Powerful and fast renderers produce different representations of your data, not needing any special graphic card.

Xenogen Living Image 2.5.1
Xenogen 3D analysis package
Imaging software from the Whole animal imaging system, IVIS 3D from Xenogen.

Leica Confocal Software

Zeiss LSM 510 software

Zeiss Axiovision


ROOM System
CIFD_1A Confocal Zeiss LSM 510 Meta
CIFD_2A Time lapse / Ion imaging
Laser Microdissection
CIFD_4A Leica Macro Fluo
CIFD_4B Whole Animal Imaging
CIFD_5A Culture Lab
CIFD_6A Workstations
Phone numbers :
Confocal Leica SP2 AOBS (Biophore)
+41 (0)21 692 4109
CIFD_6A +41 (0)21 692 4099
CIFD Office Technical Manager +41 (0)21 692 4090


Last Updated ( Monday, 30 October 2017 )
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