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@stephen-riggs stephen-riggs commented Oct 17, 2025

DLS B24 runs cryo-SXT which is compatible with AreTomo3, denoising and segmentation.

This adds capacity to read in a txrm file using txrm2tiff and then align it in AreTomo3. Less information needs to be provided as pixel size and angles are in the txrm file.

Reconstruction is set to use WBP as SART seems to work less well.

Still to sort out:

  • pixel size needs adjusting for segmentation
  • support for external reference image?

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codecov bot commented Oct 17, 2025

Codecov Report

❌ Patch coverage is 71.42857% with 18 lines in your changes missing coverage. Please review.
✅ Project coverage is 82.68%. Comparing base (9c64f9f) to head (5f45b2b).

Additional details and impacted files
@@            Coverage Diff             @@
##             main     #203      +/-   ##
==========================================
- Coverage   82.71%   82.68%   -0.04%     
==========================================
  Files          62       62              
  Lines        8112     8148      +36     
  Branches     1130     1136       +6     
==========================================
+ Hits         6710     6737      +27     
- Misses        960      967       +7     
- Partials      442      444       +2     
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@stephen-riggs stephen-riggs changed the title Add recipe for B24 tomogram alignment Add recipe and tomogram processing for B24 tomogram alignment Dec 9, 2025
@stephen-riggs stephen-riggs marked this pull request as ready for review December 9, 2025 15:05
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2 participants