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Register FIB data#766

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tieneupin wants to merge 26 commits intomainfrom
register-fib-data
Open

Register FIB data#766
tieneupin wants to merge 26 commits intomainfrom
register-fib-data

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@tieneupin tieneupin commented Mar 25, 2026

This PR adds the components needed to begin analysing and processing FIB data.

  • Added a new FastAPI router, API end point, workflow, and entry point to use for registering FIB atlas images
  • Added logic to the FIB Context to trigger the registration of FIB atlas images
  • Added new columns to the ImagingSite table to keep track of stage position information in the FIB
  • Enabled and fixed a prior workflow that was set up to create GIFs of the milling sites as images are acquired
  • Added tests and fixed old ones

Actual changes to the code make up about 400 insertions and 200 deletions, with the updating and adding of tests taking up the remainder of the diff.

* Removed previous logic for parsing 'EMproject.emxml' file, since it's no longer needed
* Added class function to post to backend server to trigger FIB atlas registration
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codecov bot commented Mar 25, 2026

Codecov Report

❌ Patch coverage is 86.14458% with 23 lines in your changes missing coverage. Please review.
✅ Project coverage is 49.92%. Comparing base (24e6c5f) to head (0d96dfe).

Additional details and impacted files
@@            Coverage Diff             @@
##             main     #766      +/-   ##
==========================================
+ Coverage   49.33%   49.92%   +0.59%     
==========================================
  Files          92       94       +2     
  Lines        9826     9922      +96     
  Branches     1298     1295       -3     
==========================================
+ Hits         4848     4954     +106     
+ Misses       4726     4714      -12     
- Partials      252      254       +2     
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…age position, image field of view, and rotation
@tieneupin tieneupin self-assigned this Mar 27, 2026
@tieneupin tieneupin added enhancement New feature or request server Relates to the server component client Relates to the client component fib Part of the FIB pipeline extension labels Mar 27, 2026
@tieneupin tieneupin marked this pull request as ready for review March 30, 2026 14:22
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client Relates to the client component enhancement New feature or request fib Part of the FIB pipeline extension server Relates to the server component

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