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O3 autofocus improvement #165

Merged
merged 26 commits into from
Dec 11, 2024
Merged

O3 autofocus improvement #165

merged 26 commits into from
Dec 11, 2024

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ieivanov
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@ieivanov ieivanov commented Oct 16, 2024

This PR contains the following improvements to the shrimPy acquisition engine:

  • more robust O3 autofocus
    • re-running O3 autofocus with extended range if it is out of range on the first try
    • removing the O3 travel limits to account for both O2 and O3 drifting together
    • backlash correction of the O3 piezo for more consistent refocusing
    • ability to skip O3 refocus in given wells, e.g. if they don't contain fluorescent markers
    • increased focus finder threshold to safeguard against false peaks
    • updating laser powers immediately after autoexposure rather than in hook functions to prevent O3 refocus running with incorrect illumination settings
  • turning off Live mode if it is running
  • checking if the illumination.csv file is present during setup when manual autoexposure is enabled
  • moving scripts folder to top level

This PR is tested and ready to merge.

@ieivanov ieivanov marked this pull request as ready for review December 5, 2024 00:27
@ieivanov ieivanov merged commit faa33db into main Dec 11, 2024
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@ieivanov ieivanov deleted the o3_autofocus_improvement branch December 11, 2024 01:41
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