Zeiss Elyra microscope
Skirball 2nd floor, Room 063

Signup to use microscope.  (During covid one person per room rules, need to book Nikon Ti at same time.)


Instrument on/off, incubation, definite focus, other general tasks [Word doc]   [PDF]
TIRF [Word doc]   [PDF]
SIM [Word doc]   [PDF]
High speed transmitted light [Word doc]   [PDF]
Complete Operating Manual [PDF Zeiss manual 49MB]
Super Resolution sample prep [PDF Zeiss manual]
3D PALM calibration & Alignment [PDF Zeiss manual] [beampath]
PALM grouping

[PDF Zeiss manual]

PALM rendering [PDF Zeiss manual]


This microscope is for TIRF, Lattice SIM, high speed brightfield, and super-resolution localization techniques such as GSD, STORM, PALM.

  • Elyra 7 Lattice SIM and Single Molecular Localization System System equipped with TIRF and 3D PALM
  • Dual PCO.Edge 4.2 sCMOS camera with Duolink motorized Dual Camera Adapter for simultaneous 2 channel acquisitions; 1280 x 1280 pixels; beamsplitter 560 nm LP
  • 4 Laser system. with 500 mW power on 488, 561 and 640 nm lasers. 50 mW 405 nm laser
  • Axio Observer 7 inverted microscope with piezo x-y stage and z-piezo
  • Definite Focus.2
  • Transmitted Light Illumination
  • Epifluorescence Illumination
  • Plan Neofluar 10x/0.3 air
  • C-Apochromat 40x/1.2 and 63x 1.2 water objectives
    With 40X lens, full frame is 195.11 µm X 195.11 µm with 0.15 µm pixel size. (0.1524296875 um)
  • Plan Apochromat 40x/1.4 and 63x/1.4 oil objectives
  • Alpha Plan Apochromat 63x/1.46 TIRF objective
  • Incubation: stage-top temperature, CO2 and humidity supply
  • Dark, laser-safe plexi-glass chamber with heating supply
  • Premium Workstation with Zen Software System Table Offline Work Station with Zen Desk License

A few of the specifications:

  • Lasers:
    405nm laser 50mW
    488nm Laser 500mW
    561 nm laser 500 mW
    642 nm laser 500 mW
  • 100W halogen for brightfield
  • Two cameras separated by 560 nm LP beamsplitter
  • The following italics need to be better explained; to be updated after training:
    Filter module Duolink SR QUAD consists of one double filter cube with the following secondary beam splitter (SBS) and emission filters (EF):
  • Filter cube 1: SBS LP 560 with EF BP420-480/BP495-550 & EF BP570-620 & LP655
  • Filter cube 2: SBS SBS BP490-560/LP640 with EF BP420-480/BP570-620/LP740 & EF BP495-560/LP655
  • The filter module Duolink SR QUAD consists of dual emission bands und hence allows fast four channel imaging by fast switching of laser lines via AOTF. Emission bands allow hereby the parallel acquisition in the blue & orange as well as orange & red spectral range (Filter cube 1) or parallel acquisition in the blue & green and the orange & red spectral range (Filter cube 2).
    Note that there are no single narrow band pass filters on this microscope. If concerned about spillover, samples must be labeled according to the hardware strictures of this instrument or spillover well characterized using other microscopes.
  • lenses need to be confirmed; list above may not be correct

People often ask, what about 100X? The 63X lenses have the same spatial resolution 100X lenses with the same N.A. lens when matched with the small pixel cameras on this microscope but with benefits such as a wider field of view, longer working distance, and better light collection. Also, a magnification lens my be placed in the lightpath for spatial oversampling.

Click here for lightpath schematic. (Camera beam splitter very similar to Nikon spinning disk except before the splitter Nikon has an additional narrow pass filter wheel and no additional magnification.)

Click here for full PDF manual. (49 MB)


Lens Standard widefield TIRF Lattice SIM Apotome
Plan Neofluar 10x/0.3 air X      
C-Apochromat 40x/1.2 water X     X
C-Apochromat 63x 1.2 water X     X
Plan Apochromat 40x/1.4 oil X     X
Plan Apochromat 63x/1.4 oil X   X  
Alpha Plan Apochromat 63x/1.46 oil TIRF X X X  


For application of high speed brightfield, the fastest we have driven the camera full frame (1280 x 1280 pixels) is 135 FPS with 1 ms exposure with light on continuously. (There appears to be a lower limit of 3 ms cycle time.)



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