Zeiss 700 microscope
Alexandria Center East 3rd floor, 349 (click here for a map)
Badge Access Request Here
Phone in room x42677 or 646-754-2677

To use microscope you must be trained by Michael Cammer or Yan Deng via the Microscopy Core.

**  Sign up to use microscope  **  Official Zeiss instructions "Quick Guide"



  1. Appointment in iLab.
  2. Only if need environmental chamber heat on, power strip #3 for incubator.
  3. Hg arc lamp for viewing fluorescence by eye.
  4. Power strip switch #1.
  5. Power strip switch #2.
  6. Computer:
    • Check if already on. If logged in, then log out and log in.
    • If off, turn on with power on front of computer.
  7. Zen software. Do not touch microscope while blue bar is progressing during software startup.
  8. If you get a Keyserver error, this means that you must start a session using ilab Kiosk.
  9. Make sure the microscope stage plate is properly inserted flat and recessed. Before doing this, make sure the lens is at the lowest focus position.
  10. Save all files in CZI format.
  11. Save all files in Drive D:


  1. If oil lens used, lightly clean.
  2. Switch to 10X lens.
  3. Focus the microscope as low as it will go. The touch pad will Say Lowest Z Limit.
  4. Copy your files over network or to USB device to take with you.
  5. Quit software.
  6. Log out of computer account. Computer may be left on.
  7. Switches in reverse order.
  8. DO NOT turn off computer monitor


Please read this document: https://microscopynotes.com/700/safety_update_20230411.pdf


General Confocal Best practices:

Highly recommended reading: Tutorial: guidance for quantitative confocal microscopy


About the microscope

Laser lines Useful for...
405 nm Dapi, CFP, Pacific Blue, Alexa 405, Brilliant Violets
488 nm FITC, Alexa488, GFP, YFP, NBD
555 nm RFP, mCherry, rhodamine, Cy3, Alexa568, Alexa594, propidium iodide
639 nm Cy5, Alexa647, To-Pro



Setting up multiple channels for detection:

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. We typically leave it at 555 nm. But custom selection may provide fine tuning of spectral detection.

In the above example, the splitter is moved for the red channel because there is no short pass 630 filter in the system to allow for red only collection. If the splitter were not set at 630 nm with the red detection in PMT1, then there is a possibility that far-red probe excited by the 555 nm laser could be detected as spill over in the red channel.

There is no worry of green being imaged in this channel because fluorescence is always red shifted; a photon of less energy is emitted.


Method for Manual uncaging / photo activation using widefield illumination.


Partial list of publications with data from this microscope, last updated 2018:


LSM 700 Serial# 2601000862 which is currently located in Alexandria East

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