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Location: Room P3-A-10 ( 47331)
Manufacturer: Carl Zeiss MicroImaging
Model: Axio Observer
Nickname: "Cell Observer"
Software: ZEN 2 (blue edition)
Year: 2015
SN: 3851002396
Zeiss Cell Observer Booking
Zeiss Cell Observer Quality Control
Zeiss Cell Observer Usage Statistics

Microscope overview

The Zeiss Cell Observer is a fully motorized inverted widefield fluorescence microscope ideal for live-cell imaging applications. It is equipped with a large cage incubator and a small stage incubator for temperature control and CO2 supply and with Definite Focus for hardware focus control during long time-lapse acquisitions. Using the ZEN 2 software you can control the motorized filters, shutters and stage to simultaneously set up multi-color time-lapse imaging experiments in multiple stage positions. Its sensitive cooled Axiocam 506m camera allows you to capture weak fluorescent signals and minimize photobleaching/photodamage in light sensitive samples. You can also perform Z-stack acquisition and use our deconvolution server Brainstorm to significantly improve image resolution even in thick samples. If don't want to use deconvolution, check out one of the confocal systems such as the point scanners Zeiss LSM 710 and Zeiss LSM 880 or spinning disks 3i Marianas SDC and Zeiss Cell Observer SD. If your personal computer cannot handle all the data you collected, check out the Big Guy or Colossus. If you have FISH or other fixed fluorescence slides try the Leica DM5000B instead.

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

The Zeiss Cell Observer booking is divided in three daily slots:

9:00 to 13:00 13:00 to 17:00 17:00 to 21:00
  1. A user can book at maximum 2 sessions per week
  2. Each session must fit inside one of the three daily slots (i.e. a session booked from 11:00 to 14:00 counts as 2 sessions)
  3. The above rules do not apply for weekends and for work days before 9:00 and after 21:00
  4. The above rules do not apply for sessions booked on the very same day or 24 hours ahead
  5. Exceptions to these rules require approval from José Rino.
  6. Users must indicate if they will use the incubator in the booking Description field (write down 37C INCUBATOR)

System components


Position Filterset Reference Excitation Emission
1 HE GFP FS38HE 450-490 nm 500-550 nm
2 HE DsRed FS43HE 538-562 nm 570-640 nm
3 DAPI FS49 335-383 nm 420-470 nm
4 Cy5 FS50 625-655 nm 665-715 nm
5 none none none none
6 none none none none


Magnification Model Type NA WD (mm)
10x EC Plan-Neofluar Dry 0.30 5.2
20x Plan-Apochromat Dry 0.80 0.55
40x EC Plan-NeoFluar Dry 0.75 0.71
63x Plan-Apochromat Oil 1.40 0.19

Upon request:

Magnification Model Type NA WD (mm)
1.25x EC Epiplan-Neofluar Dry 0.035 4
5x EC Plan-NeoFluar Dry 0.16 18.5
20x EC Plan-Neofluar Ph 2 Dry 0.50 2
40x Plan-Apochromat Dry 0.95 0.25
40x Plan-Neofluar Ph3 Oil 1.30 0.20
63x Plan-Apochromat Ph3 Oil 1.4 0.19
100x Plan-Apochromat Oil 1.40 0.17

System Turn On Procedures

  • Turn on the HXP 120 fluorescence light.

  • Turn on the Temperature and CO2 controller (if you need them).

  • If you need CO2, open the valve

  • Turn on the Motorized Stage controller (A)

  • Turn on the Definite Focus controller (if you are going to use it)

  • Turn on the Microscope power supply (B)

  • Turn on the computer
  • Log in Windows with Cell Observer user account.
  • Start the ZEN 2 software

Microscope Turn Off procedures

  • Exit the ZEN 2 software
  • Turn off the computer (not the UPS!)

  • If you used any immersion oil in the objectives, clean them up.
  • Turn off the microscope power supply (B)
  • Turn off the Definite Focus controller (if used)
  • Turn off the Motorized Stage controller (A)
  • Turn off the Temperature and CO2 controller (if used)
  • If there's another user for this microscope in the next hour leave the mercury lamp power source on, else turn it off.
  • Be extra careful in weekends and at the end of the day to make sure that the mercury lamp is not going to be turned on for an excessive time.

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zeiss_cell_observer.txt · Last modified: 2019/07/12 11:07 by bioimaging