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✨ Add OME-TIFF Writer to Utils #929

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@shaneahmed shaneahmed commented Apr 30, 2025

  • This PR saves a NumPy or Zarr Array to OME tiff. This will help to save probability maps from deep learning models as ome.tiff which can be visualized using TIAViz.
  • The image is written as tiles and stitched in OME tiff along with associated necessary metadata.
  • The output file should be readable using multichannel viewer in 🆕Multichannel Image Reading #825
  • Reading with QuPath has been tested.

- This will help to save probability maps from deep learning models as ome tiff which can be visualized using TIAViz.
@shaneahmed shaneahmed self-assigned this Apr 30, 2025
@shaneahmed shaneahmed added the enhancement New feature or request label Apr 30, 2025
@shaneahmed shaneahmed added this to the Release v1.7.0 milestone Apr 30, 2025
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codecov bot commented Apr 30, 2025

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 99.70%. Comparing base (7ba7394) to head (d89f921).

Additional details and impacted files
@@           Coverage Diff            @@
##           develop     #929   +/-   ##
========================================
  Coverage    99.70%   99.70%           
========================================
  Files           71       71           
  Lines         8847     8874   +27     
  Branches      1154     1161    +7     
========================================
+ Hits          8821     8848   +27     
  Misses          23       23           
  Partials         3        3           

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The output file should be readable using multichannel viewer in #825

@shaneahmed shaneahmed mentioned this pull request Apr 30, 2025
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@shaneahmed shaneahmed changed the title ✨ Add OME tiff writer to utils. ✨ Add OME-TIFF Writer to Utils Apr 30, 2025
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