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Add metadata extraction logic to lamella evaluation image registration workflow - #868

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register-lamella-evaluation-image
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Add metadata extraction logic to lamella evaluation image registration workflow#868
tieneupin wants to merge 5 commits into
mainfrom
register-lamella-evaluation-image

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@tieneupin

@tieneupin tieneupin commented Aug 19, 2026

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Extends the existing logic of the lamella evaluation image registration workflow so that it will extract the relevant metadata from the image. This involves:

  • Setting up a Pydantic model to parse the incoming workflow message
  • Making a database call to get the visit and instrument names
  • Parsing the image metadata tags to look for the XML metadata, extracting the values of interest, and validating them with another Pydantic model

There is a significant degree of overlap between the way the metadata in the FIB atlas and lamella evaluation images are extracted, so a future housekeeping PR could involve migrating the logic out into a shared function in murfey.util.fib.

The bulk of the diff is due to the addition of tests. The actual change in the code is +195/-7 lines.

@tieneupin tieneupin self-assigned this Aug 19, 2026
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Codecov Report

❌ Patch coverage is 84.09091% with 14 lines in your changes missing coverage. Please review.
✅ Project coverage is 54.95%. Comparing base (1476890) to head (d0be51f).

Additional details and impacted files
@@            Coverage Diff             @@
##             main     #868      +/-   ##
==========================================
+ Coverage   54.73%   54.95%   +0.21%     
==========================================
  Files         101      101              
  Lines       11241    11326      +85     
  Branches     1489     1492       +3     
==========================================
+ Hits         6153     6224      +71     
- Misses       4763     4774      +11     
- Partials      325      328       +3     
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@tieneupin tieneupin added enhancement New feature or request server Relates to the server component fib Part of the FIB pipeline extension labels Aug 19, 2026
@tieneupin
tieneupin force-pushed the register-lamella-evaluation-image branch from b043e2c to f5fad07 Compare August 20, 2026 08:56
@tieneupin
tieneupin marked this pull request as ready for review August 20, 2026 10:17
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enhancement New feature or request fib Part of the FIB pipeline extension server Relates to the server component

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