Merge `recOrder` into `waveorder` #183

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talonchandler merged 1377 commits intomainfrom

Apr 2, 2025

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add notification for potential delay before update
ziw-liu
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Call `enter_phase_denoiser` to create attributes
talonchandler
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Check for non-physical NA arguments
talonchandler
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Merge pull request #292 from mehta-lab/bf-keep-shutter-open
talonchandler
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Merge pull request #286 from mehta-lab/restore-mda-after-acq
talonchandler
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initial draft
talonchandler
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Only disable "Phase From BF"
talonchandler
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Fix typo
talonchandler
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Initial draft
Talon Chandler
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Open select positions
Talon Chandler
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Support channels and positions to layers
Talon Chandler
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Add channel_name text overlay to napari window
talonchandler
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Merge pull request #294 from mehta-lab/no-bf-channel
talonchandler
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pin numpy version (#301)
ziw-liu
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Update setup.cfg for macos_arm64 specific dependencies (#313)

mattersoflight
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ziw-liu
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Fix cli entry points
Talon Chandler
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Move imports into cli functions
Talon Chandler
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black formatting
talonchandler
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remove transpose+copy (#322)
talonchandler
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Depend on `iohub` (#331)

talonchandler
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ziw-liu
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Write to single zarr store (#340)
talonchandler
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Install iohub from PyPI (#342)
ziw-liu
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Minor documentation updates for 0.3.0 (#344)
talonchandler
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pin README links (#345)
talonchandler
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Test docking the plugin widget (#346)
ziw-liu
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Bump dependencies and enable widget test (#391)
ziw-liu
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0.4.0 installation documentation (#395)
talonchandler
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Reconstruct a subset of time indices (#398)

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Standardize CLI (#402)

talonchandler
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clinton-huynh
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Implement schema (#424)

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Redo overlay2 (#425)

talonchandler
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edyoshikun
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Improved birefringence overlays (#426)

talonchandler
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ziw-liu
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Background scaling, naming, and squeezing (#429)
talonchandler
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update links (#439)
talonchandler
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fix bug loading timepoints in apply_inverse_to_zyx_and_save (#441)
ieivanov
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Optional GUI/PM dependencies (#456)

ziw-liu
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talonchandler
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Chunk transfer functions (#463)
talonchandler
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Pass metadata (#464)

talonchandler
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ziw-liu
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Collect and unify color overlays (#473)
talonchandler
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pin ome-zarr (#475)
talonchandler
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Fix background-check bug (#469)
talonchandler
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Default HSV colormap (#471)

talonchandler
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ziw-liu
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Bump Python, iohub, and waveorder (#478)

ziw-liu
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aaronalvarezcz
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Parallelize reconstructions with `submitit` (#477)
talonchandler
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Buyer's guide (#486)

talonchandler
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mattersoflight
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Standalone auto-generated reconstruction GUI (#487)
amitabhverma
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remove pyqt6 dependency and re-worked setup cfgs (#503)

amitabhverma
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talonchandler
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Commits on Feb 23, 2025

Fix non-example pytests (#186)
talonchandler
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Clean up examples and temp files (#187)
talonchandler
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Remove recorder image references (#189)
talonchandler
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