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🆕Multichannel Image Reading#825

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measty wants to merge 164 commits intodevelopfrom
multichannel-reading
Open

🆕Multichannel Image Reading#825
measty wants to merge 164 commits intodevelopfrom
multichannel-reading

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@measty
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@measty measty commented Jun 21, 2024

Initial implementation of multi-channel reading.

multi_channel

The core tasks are done, the others can be a later PR if we decide they are necessary.

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 better 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 99.77629% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 99.41%. Comparing base (78b797e) to head (ae7e2ca).

Files with missing lines Patch % Lines
tiatoolbox/visualization/bokeh_app/main.py 98.07% 0 Missing and 1 partial ⚠️
Additional details and impacted files
@@             Coverage Diff             @@
##           develop     #825      +/-   ##
===========================================
+ Coverage    99.37%   99.41%   +0.03%     
===========================================
  Files           71       72       +1     
  Lines         9175     9540     +365     
  Branches      1197     1267      +70     
===========================================
+ Hits          9118     9484     +366     
+ Misses          31       29       -2     
- Partials        26       27       +1     

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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
@measty measty marked this pull request as ready for review February 6, 2026 22:24
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@shaneahmed shaneahmed left a comment

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This looks good and I can successfully load the images in TIAViz. However, I am not clear how to read the channels in python. Could you add some examples in the docstring?

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Add multichannel viewer [ENH] Get ValueError: Unsupported axes YX when using OME-TIFF for nuclear segmentation

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