Workflow

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
   or
   Processing tab >
   • Batch in upper left on/off
   • Apotome Raw Convert
   • Add files to list to be processed
     (Ctrl &/or Shift click to add multiple)
   • Select one file to set parameters
   • Set the parameters -- the method for Apootome processing
   • Copy parameters
   • Highlight files to apply parameters to
     Try Ctrl click to choose multiple or Select All in upper right - you can also right click for more options.
   • Paste parameters
   • Upper left, select output folder
   • Apply
     
9. Close files - raw data big files
   

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

last updated 20151230_1458

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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
\\shares.nyumc.org\research\MicroscopyCore\mcammer\mcammer\Zeiss_AxioOberver settings 20151209\files_for_instructions and
E:\equipment profiles\AxioObserver\settings at of 20151209

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