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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 82.21709% with 77 lines in your changes missing coverage. Please review.
✅ Project coverage is 98.51%. Comparing base (adc18c9) to head (eecdf59).

Files with missing lines Patch % Lines
tiatoolbox/utils/postproc_defs.py 52.72% 19 Missing and 7 partials ⚠️
tiatoolbox/visualization/bokeh_app/main.py 66.66% 16 Missing and 2 partials ⚠️
tiatoolbox/visualization/tileserver.py 34.61% 16 Missing and 1 partial ⚠️
tiatoolbox/wsicore/wsireader.py 94.71% 3 Missing and 11 partials ⚠️
tiatoolbox/models/dataset/classification.py 93.75% 2 Missing ⚠️
Additional details and impacted files
@@             Coverage Diff             @@
##           develop     #825      +/-   ##
===========================================
- Coverage    99.27%   98.51%   -0.77%     
===========================================
  Files           71       72       +1     
  Lines         9162     9519     +357     
  Branches      1195     1265      +70     
===========================================
+ Hits          9096     9378     +282     
- Misses          40       94      +54     
- Partials        26       47      +21     

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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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