[tieneupin]

This PR adds logic to the Analyser and SIMContext to detect the atlas files and request for them to be processed. A stub FastAPI endpoint has been added to the backend that will log when processing parameters are received. This will be extended in subsequent PRs.

In the cryo-SIM workflow, the atlas stitching service requires three files:

• A mosaic.mrc file, which contains the actual image frames
• A mosaic.txt file, which points to the MRC file and contains the stage position information for each frame
• An optional markers.txt file, which contains annotation information to apply to the stitched image

As long as the two mosaic files are accounted for, a processing request will be sent to the backend. If a markers file is created later on, a new processing request will be sent which will regenerate the image with the annotations.

[codecov]

Codecov Report

❌ Patch coverage is 93.33333% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 55.83%. Comparing base (da1390a) to head (8123597).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #925      +/-   ##
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+ Coverage   55.74%   55.83%   +0.08%     
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  Files         103      103              
  Lines       11643    11671      +28     
  Branches     1553     1560       +7     
==========================================
+ Hits         6490     6516      +26     
- Misses       4802     4803       +1     
- Partials      351      352       +1     

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[stephen-riggs]

Might need to work out what we have across different instruments here, as the .mrc extension might conflict with other things