Read and insert tomography atlas and search map locations #616
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #616 +/- ##
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+ Coverage 31.86% 32.38% +0.52%
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Files 90 92 +2
Lines 10762 11095 +333
Branches 1422 1460 +38
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+ Hits 3429 3593 +164
- Misses 7215 7377 +162
- Partials 118 125 +7 🚀 New features to boost your workflow:
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tieneupin
reviewed
Jul 7, 2025
Contributor
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With the latest changes, the test workflow now runs on the incompatible tomo dataset, with the missing values replaced with inaccurate arbitrary ones. This should be safe to merge. |
stephen-riggs
added a commit
to DiamondLightSource/cryoem-services
that referenced
this pull request
Jul 17, 2025
Connects to DiamondLightSource/python-murfey#616 The location and ID of the search map for a tomogram will be send in the alignment message, and this inserts those into ispyb with the tomogram.
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Registers the locations of SearchMaps and BatchPositions for tomography data collection.
This requires reading the SearchMap.dm and .xml files, and the BatchPositionsList.xml, plus finding the atlas in the Session.dm
The logic for converting from stage coordinates to pixel positions is non-trivial and does not work perfectly.
For the Krios microscopes with FALCON and K3_FLIPX cameras it appears to give reasonably accurate values (with some ambiguity over whether "zero" is top-left or bottom-left which may need fixing), but for the Talos with K3_FLIPY it does not currently work.
The Murfey database has a new table for SearchMaps and the TiltSeries table now has positions. For ispyb the SearchMaps are inserted as GridSquares. TiltSeries location inserts will be done as part of the em-tomo-align recipe.