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🆕Multichannel Image Reading#825

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measty wants to merge 154 commits intodevelopfrom
multichannel-reading
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🆕Multichannel Image Reading#825
measty wants to merge 154 commits intodevelopfrom
multichannel-reading

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@measty
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@measty measty commented Jun 21, 2024

Initial draft implementation of multi-channel reading.

multi_channel

Still needs lots of work so its a draft at the moment.

to do:

  • test on other examples
  • unit tests
  • decide what should default behaviour be?
  • decide how will interact with VirtualWSIReader mode flag - should we extend this to all readers?
  • are there better ways to do RGB conversion? simple approach at the moment
  • Get colors from metadata (if existing)
  • Selecting specific channels in viewer
  • Third set of metadata format for COMET
  • For usability join the menus for channel and colour (so not scrolling separately)

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codecov bot commented Jun 21, 2024

Codecov Report

❌ Patch coverage is 96.14512% with 17 lines in your changes missing coverage. Please review.
✅ Project coverage is 99.24%. Comparing base (78b797e) to head (86c8fe9).

Files with missing lines Patch % Lines
tiatoolbox/wsicore/wsireader.py 96.73% 3 Missing and 6 partials ⚠️
tiatoolbox/visualization/bokeh_app/main.py 92.59% 1 Missing and 3 partials ⚠️
tiatoolbox/models/dataset/classification.py 93.75% 2 Missing ⚠️
tiatoolbox/visualization/tileserver.py 92.30% 0 Missing and 2 partials ⚠️
Additional details and impacted files
@@             Coverage Diff             @@
##           develop     #825      +/-   ##
===========================================
- Coverage    99.37%   99.24%   -0.14%     
===========================================
  Files           71       72       +1     
  Lines         9175     9536     +361     
  Branches      1197     1266      +69     
===========================================
+ Hits          9118     9464     +346     
- Misses          31       35       +4     
- Partials        26       37      +11     

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@shaneahmed shaneahmed linked an issue Jun 25, 2024 that may be closed by this pull request
@shaneahmed shaneahmed changed the title ENH: initial draft multichannel reading 🆕Multichannel Image Reading Jun 25, 2024
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Add multichannel viewer [ENH] Get ValueError: Unsupported axes YX when using OME-TIFF for nuclear segmentation

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