Zeiss 800 upright microscope SB401
SN 2633000142

Michael Cammer & Yan Deng are the contact people for the microscope and to use it you need to be part of the group that purchased it.

Signup to use microscope http://signups.med.nyu.edu/facilities/equipment/signups/zeiss-800-confocal


All files must be saved on Drive D:
All files should be copied to Medical Center maintained server. Read these instructions or look for these shortcuts which are in multiple locations on the computer

If you are asked to install an update, just say no!

About the microscope

Laser lines Useful for...
405 nm Dapi, CFP, Pacific Blue
488 nm FITC, Alexa488, GFP, YFP
561 nm RFP, mCherry, rhodamine, Cy3, Alexa568, Alexa594, propidium iodide
640 nm Cy5, Alexa647, To-Pro

There are two ways to choose the spectral detection. One is by filter and the other is by a user adjustable mask. If you are using multiple channels, imaging will be much faster if the mask does not move between channels.

Emission filters & splitter Useful for...
  Dapi, CFP, Pacific Blue
  FITC, Alexa488, GFP, YFP; (May collect spillover from blue)
  RFP, mCherry, rhodamine, Cy3, Alexa568, Alexa594, propidium iodide; (May collect spillover from green)
  Cy5, Alexa647, To-Pro; (May collect spillover from red)



Use oil that says RI 1.518 on the bottle.

For best results, use #1.5 coverslips as explained here.



  1. Make sure you are signed up in advance at http://signups.med.nyu.edu/facilities/equipment/signups/zeiss-800-confocal
  2. Under computer table, "Systems" switch.
  3. "Components" switch.
  5. Power strip strapped to right side of air table, turn on.
  6. Computer on. As of March 2022, the computer may now be used without tunring on the confocal.
  7. Log in to LSM User account. 
  8. Make sure the touchpad on the right side of the microscope is fully ready before next step.
  9. Run Zen software (icon is above center of screen).
  10. There are two tabs in the upper left of the software labeled “Locate” and “Acquisition”.

    The Locate tab is for looking through the microscope oculars.
    The Acquisition tab is for using the confocal microscope.
    The Processing tab is for working on images after they have been collected and saved.
    Analysis can generate numbers from the images, but you may find ImageJ or Volocity better.
  11. The Locate tab has buttons to turn the light on/off to look by eye.

    Do not use the touch pad on the microscope.
    Do not change any of the settings in the window titled "Microscope Control".
  12. Best way to set up imaging method:
    Acquisition tab
    Open image from earlier session with same settings.
    Click Reuse button.

To look by eye, the slider on the right side of the microscope must be pushed in, all the way to the left.
To use the confocal, the slider must be pulled out all the way to the right.
Put slide on the stage.

Put it in the recessed are of the stage closest to you and push it back under the metal tabs.
This means that samples should be at the center of the slide, not at the far edge.
Use joystick to move stage.  F1 button in top right corner toggles from fine to coarse and back.
Find sample. 
Then set up tracks in Acquisition tab.

The behavior of the Live scan button is different than previous versions of the Zeiss confocals. You cannot image multiple tracks simultaneously, details here.

This microscope has GaAsP detectors which can be burned out by excessive voltage. Saturating your images can damage the microscope as well as confound quantification. We are happy to explain this further; please let us know.

Always leave the Digital Offset at 0 and the Digital Gain at 1.
DO NOT use these to reduce background or brighten the image. Especially if you want to do intensity quantification later, using these will complicate or nullify the ability to do so.
Pinhole always at 1 or smaller. Greater than 1, go use widefield microscope with camera instead.
In the images below, note that you can click off the Show All box at the top of the Channels window so that the sliders for Digital Gain and Offset will disappear so you won't be tempted to touch them.


Save all images on drive D: only.  Files stored on drive C: may be deleted without warning.
All files should be copied to Medical Center maintained server. Read these instructions or look for these shortcuts which are in multiple locations on the computer

Click here for screen snap of how to export TIFs from the Processing tab, especially useful after stitching.


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. Tiling works best at a zoom of 1 or greater with 10% overlap.



  1. Quit software.
  2. Transfer data to server of your choice.
  3. Shut down computer.
  4. Switches in reverse order.
  5. Before you leave the room, stop, look down and around, and if you see stuff on the floor, pick it up and throw it out.


SN 2633000142

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comments, questions, suggestions for this web page: Michael.Cammer@med.nyu.edu or mcammer@gmail.com