Zeiss LSM 880

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Skip to Instrument Specifications below.

 

Startup:

      

DO NOT touch any switches except the the ones in these instructions.

If you are only using the computer, only turn on the switches in step 3; leave all the other ones off.

  1. SIGN IN LOG BOOK
  2. SWITCH 1
    MAIN SWITCH

    Turns on: DEFO, HXP, incubation
  3. SWITCH 2
    Red Switch on Power Strip

    Sends power to the PC (computer) and monitor.
    • Press the power button on the front of the CONFOCAL computer on the floor to the right.
    • Only turn on the confocal computer.
    • You can use Zen Blue software for data processing instead of Zen Black (which runs the hardware).
      (Please ask for more training if you want to be shown this.)
    • If you are only doing data processing, stop here.
    • DO NOT TURN ON THE FLIM COMPUTER UNLESS YOU ARE DOING FLIM. If you don't know what FLIM is, you are not using it.
  4. SWITCH 3
    SYSTEMS/PC
    (label not descriptively correct...)
    Turns on additional confocal components.

    STOP. Wait for computer to completely boot up before next step.
     
  5. SWITCH 4
    COMPONENTS

    Turns on: Lasers, scan head, real time PC, etc.
  6. STOP. The microscope control touch pad must be on before you continue.
    If the microscope touch pad does not light up, try pressing the power button at the back left of the microscope stand.
  7. Log in to computer account. (Password taped to screen.)
  8. Run Zen software.
  9. Immediately go in to Lasers window in Acquitiion tab and turn on the lasers you will be using. This will save time by allowing the lasers to power up fully while you find your sample, load settings, etc.
  10. Optional: Incubator may be set by the touchpad on the table.
    Home > Microscope > Incubation
    For Airy Scan, the Incubator should be on at 30 degrees C and make sure the doors and other covers on the incubator box are closed.

General Confocal Best practices:

 

Oil and Water lenses

Use special 30 degrees oil for incubation only.

Use 1.518 oil for RT.

Use Immersol W or GenTeal for water lenses.
DO NOT LEAVE IMMERSOL W BOTTLE ON THE TABLE.
AT THE END OF YOUR IMAGING SESSION, MAKE SURE YOU RETURN IT TO THE SHELVES at the back of the room.

 

Saving Files

All files should be stored in one of these two locations.
   D:\User_Data\
   D:\SWAP\
Files left on the desktop. drive C, or Picture folder will be deleted.

.czi always.

Move data to your lab's shared server space.

Always save files as CZI. These files can be opened directly into image analysis software. These files retain instrument settings, channel integrity, bit depth, and spatial scale that may be necessary for image analysis.

If you save files as TIFor other formats, the integrity of color channels may be lost and you will have no metadata regarding instrument settings and spatial scale.

Tiling or mosaic images need to be stiched in the Process tab with fuse tiles turned on.

 

Detectors

CH1 and CH2 GaAsP detectors require 500V gain minimum.

For BiG use plate, not mirror. Filter blocks installed manually in side. Blocks for red/green and CFP/YFP.

True spectral imaging. An example of a result here.

 

Software Help

Click on ? button in upper right and then click on thing on screen want help with.

 

Tiling

First do 128X128 large area fast overview tile scan.
Put in new container.
Click stage (or use positions to set multiple Z)

12% overlap.

Zen Blue for post processing stitching.

 

Airyscan

I really like this document's description of AiryScan and how to do it: https://imb.uq.edu.au/files/2084/The%20Zeiss%20AiryScan%20System.pdf (and cached here).

Here is Zeiss official document on AiryScan.

Also, this doesn't match our system precisely, but a very good set of instructions by Mt Sinai.

Key points: