Instructions for Apotome mode of Zeiss AxioObserver microscope



Either process each image or Z stack as you go or collect raw data and batch process in one shot at end.


  1. ApoTome in light path.

    Apotome in light path
    One click to right
    Apotome out of light path
  2. Locate tab
    Click on Apotome in lower right to make sure camera selected. (picture here)
  3. Optional: check calibration by clicking on Grid in lightpath. (picture here)
  4. Acquisition tab
    Click Apotome window and choose number of phases (5 should be ok -- you can test on your sample whether more better).
  5. Grid visible.
  6. Live to move around and focus.
  7. Use Snap to take image.
  8. Apotome tab below image,
    set parameters
    Create Image
    Processing tab >
  9. Close files - raw data big files



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last updated 20151230_1458


Calibration should be done by staff only!

Use Apotome sample.

Phase calibration, cemera rotation

Tools > Focus Calibration

Calibration of Apotome per color, per lens

Grid focus calibration

Acqisition menu > Apotome focus calibration wizard

Focus -- exposure

Start Full scan (or local)

Also see
\\\research\MicroscopyCore\mcammer\mcammer\Zeiss_AxioOberver settings 20151209\files_for_instructions and
E:\equipment profiles\AxioObserver\settings at of 20151209


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