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Location: Room P2-A-22 ( 47217)
Manufacturer: ZEISS Microscopy
Model: Cell Observer SD
Nickname: "Cell Observer SD"
Software: ZEN 3.2 (blue edition)
Year: 2015
SN: 3851001637
Data will be deleted after: 1 month  
Zeiss Cell Observer SD Quality Control
Zeiss Cell Observer SD Usage Statistics  

System overview

The Zeiss Cell Observer SD spinning disk confocal microscope is a fast imaging system which provides a trade-off between confocality, resolution and speed. It is an inverted microscope ideal for live cell applications which require fast acquisition speeds rather than high resolution images. The scanning unit achieves confocality by directing light through a spinning disk with many small pinholes. Images are then acquired with a sensitive EMCCD which allows for very small exposure times but is limited in resolution to 512×512 pixels. The stage is motorized and furthermore equipped with a piezo for Z displacement so fast 4D imaging is possible in multiple stage positions. The system is also equipped with a large size incubator for temperature control, a stage top incubator for CO2 supply and with Definite Focus.2 for hardware focus control during large tile or multi-position/time-lapse acquisitions (check tutorial videos below). You can also use the system as a widefield microscope, using fast-swicthing LEDs for illumination (Zeiss Colibri.2) and a sCMOS camera for acquisition.

Data files older than 1 month will be automatically deleted on this system, please copy your data to the iMM server using the desktop link.

Booking Rules

  1. Users can book at maximum 8 hours per week
  2. This usage restriction does not apply for weekends and for working days before 9:00 and after 21:00
  3. Exceptions to these rules require approval from José Rino.

System components


Magnification Model Immersion NA WD (mm) Reference
10x EC Plan-Neofluar Ph1 Air 0.30 5.20 420341-9911-000
20x Plan-Apochromat Ph2 Air 0.80 0.55 420651-9911-000
40x LD C-Apochromat Corr Water 1.10 0.62 421867-9970-000
40x Plan-Apochromat DIC Oil 1.40 0.13 420762-9900-000
63x Plan-Apochromat DIC Oil 1.40 0.19 420782-9900-000
100x α Plan-Apochromat DIC Oil 1.46 0.11 420792-9800-000

Upon request:

Magnification Model Immersion NA WD (mm) Reference
10x EC Plan-Neofluar Air 0.30 5.20 420340-9901-000
25x LCI Plan-Neofluar Corr DIC Oil/Glyc/W 0.80 0.21 420852-9972-000

LASERs (Confocal)

Laser Unit Wavelength Maximum Power
Solid State Laser 405 405 nm 50 mW
Solid State Laser 488 488 nm 100 mW
Solid State Laser 561 561 nm 75 mW
Solid State Laser 638 638 nm 75 mW

Emission Filters (Confocal)

Position Transmission
1: BP 450/50 425-475 nm
2: TBP 526 601 688 510-542 nm
586-616 nm
663-713 nm
3: none
4: FE01-520/35 502-537 nm
5: BP 600 50 575-625 nm
6: BP 690/50 665-715 nm

LEDs (Widefield)

Line Wavelength
UV 365 nm
B 470 nm
G 565 nm
R 625 nm

Filtersets (Widefield)

Position Filterset Reference Excitation Dichroic Emission
1 Green FS38HE 450-490 nm 495 nm 500-550 nm
2 Red FS43HE 538-562 nm 570 nm 570-640 nm
3 Blue FS49 335-383 nm 395 nm 420-470 nm
4 Far Red FS50 625-655 nm 660 nm 665-715 nm
5 QUAD FS81HE 357-393 nm 400 nm 407-412 nm
473-496 nm 503 nm 511-528 nm
545-562 nm 570 nm 577-602 nm
620-642 nm 650 nm 658-704 nm
6 Empty


Model Type Frame Size Pixel Size (µm) Quantum Efficiency Mode
Photometrics Evolve 512 EMCCD 512 x 512 16 x 16 > 90% Confocal
Hamamatsu ORCA-flash4.0 V2 sCMOS 2048 x 2048 6.5 x 6.5 82% Widefield

Microscope Turn On Procedure

  • Turn on the HXP 200 fluorescent light source (if used)
  • Turn on the computer (underneath the microscope table)
  • Login in to Windows with your Agendo credentials
  • Turn on the black socket outlet number 1 (back left corner of microscope table)

  • Wait for the Definite Focus controller to show the App-Ver. and OS-Image info

  • Turn on the black socket outlet number 2
  • Turn on the black socket outlet number 3
  • Start the ZEN Blue software

Microscope Turn Off Procedure

If there is another user for this microscope in the next hour:

  • Exit the ZEN software
  • Log off the computer
  • Clean up immersion objectives


  • Exit the ZEN software
  • Shut down the computer (not the UPS!)
  • Clean up immersion objectives
  • Turn off the black socket outlets by reverse order (3→2→1)
  • Turn off the HXP 200 fluorescent light source

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zeiss_cell_observer_sd.txt · Last modified: 2024/04/01 23:53 by bioimaging