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Location: Room P2-A-24 ( 47219)
Manufacturer: ZEISS Microscopy
Model: LSM 980 with Airyscan 2
Nickname: "980"
Software: ZEN 3.8 (blue edition)
Year: 2021
SN: 2841000239
Data will be deleted after: 1 month  
Zeiss LSM 980 Quality Control
Zeiss LSM 980 Usage Statistics

Microscope overview

The Zeiss LSM 980 with Airyscan 2 is a point scanning confocal microscope able to generate high-resolution three-dimensional images of thick specimens with high sensitivity, high speed and low photodamage. It is an inverted microscope especially suitable for live cell imaging and photobleaching experiments, equipped with a dark large cage incubator and a stage top incubator for temperature control and CO2 supply and with Definite Focus.3 for hardware focus control during long time-lapse acquisitions. The stage is motorized and furthermore equipped with a piezo for Z displacement so fast 4D imaging is possible in multiple stage positions, using the Tiles Advanced Setup of ZEN blue. Its Airyscan 2 with 32 concentrically arranged GaAsP detection elements is able to collect all light from an Airy pattern simultaneously, allowing for increased resolution (120 nm laterally and 350 nm axially in SR mode, at 488 nm). It can also be used in Multiplex Mode, which enables parallel excitation and detection in 4Y or 8Y modes. The result is a speed improvement by a factor of 4x/8x, while maintaining the sensitivity of Airyscan. Its scanning unit further includes two PMT detectors as well as a GaAsP detector for increased sensitivity (45% QE compared to ~25% QE for conventional PMT). It is equipped with lasers from violet to far red (405, 488, 561 and 639 nm excitation wavelengths). The LSM Plus deconvolution mode enhances signal-to-noise ratio by acting as a denoising step post image acquisition, allowing for high acquisition speed and low laser power. With Airyscan Joint Deconvolution (jDCV) the resolution can be improved to 90 nm (XY) and 270 nm (Z).

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


Laser Unit Wavelength Maximum Power
405 405 nm 15 mW
488 488 nm 13 mW
561 561 nm 13 mW
639 639 nm 10 mW


Magnification Model Immersion NA WD (mm) Reference
10x EC Plan-Neofluar Air 0.30 5.20 420340-9901-000
20x Plan-Apochromat Air 0.80 0.55 420650-9903-000
40x LD C-Apochromat Corr Water 1.10 0.62 421867-9970-000
63x Plan-Apochromat DIC Oil 1.40 0.19 420782-9900-799

LEDs (Ocular)

Line Wavelength
UV 385 nm
B 475 nm
G 555 nm
R 630 nm

Filterset (Ocular)

Position Filterset Reference Excitation Dichroic Emission
1 QUAD FS90HE 370-400 nm 405 nm 410-440 nm
450-488 nm 493 nm 499-529 nm
540-570 nm 575 nm 580-605 nm
615-648 nm 653 nm 659-759 nm

How to start your session

The system should be always on, you only need to:

  • Turn on the computer
  • Log into Windows with your Agendo credentials
  • Start ZEN

How to end your session

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

  • Exit the ZEN software, leave the lasers on
  • Log off the computer
  • Clean up immersion objectives


  • Turn off the lasers on ZEN
  • Clean up immersion objectives
  • Exit the ZEN software
  • Shutdown the computer

Microscope Turn On Procedure (after complete shutdown)

If the system is completely off, please follow this procedure:

  • Turn on the MAIN SWITCH

  • Turn on the COMPONENTS switch

  • Turn on the computer
  • Log into Windows with your Agendo credentials
  • Start the ZEN software

Microscope Turn Off Procedure (for complete shutdown)

Please only shutdown the system if instructed to do so by the Bioimaging Unit.

  • Turn off the lasers on ZEN
  • Exit the ZEN software
  • Shutdown the computer
  • Turn off the COMPONENTS switch (do not turn off the Laser key!)
  • Turn off the MAIN SWITCH

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zeiss_lsm_980.txt · Last modified: 2024/07/16 23:44 by bioimaging