New reader for G4X datasets (Singular Genomics)

[ckmah]

👋 Hello @scverse/spatialdata and community,

I would like to contribute the initial version of a spatialdata-io reader for Singular Genomics G4X datasets that I recently developed for internal use (I work at Singular), and now for the spatial community. It is still experimental and not fully battle-tested, but I tried to keep the API consistent with the other readers as much as possible. However, there are few key additions I made to streamline use with our datasets:

Notable features

• Incremental I/O of elements (images, tables etc.) G4X datasets can get pretty large since they are multimodal. Therefore, we made sure the reader saves elements as soon as they are converted to reduce memory Reduce readers' memory consumption #229 and mitigate data loss. This is handled via the g4x(..., mode="append") parameter. The user can also choose mode="overwrite" to turn this off. The constructed SpatialData is also re-read from disk automatically to fully take advantage of lazy loading.
• Read one or more samples at once. This corresponds to our assay design and enables converting an entire experiment with a single function call. The reader will then return a single SpatialData object or a list of them accordingly.

Additional Dependencies

• Some of our images are encoded in the Jpeg2000 (.jp2, j2k) format and require the glympur package to read

Misc.

• The reader corrects the Offset when rasterizing data spatialdata#165 for now. This can be removed when ready.
• Sample dataset PRed to https://github.com/giovp/spatialdata-sandbox/

Are there any other pieces I should have in this PR? Devs please let me know, I'm happy to add them. Here are relevant ones I can think of:

• Documentation/tutorial notebook? (also not sure if I used @injectdocs decorator properly)
• Parse experimental metadata: sample names, positions, acquisition info etc.
• spatialdata-io CLI compatibility

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 17.19298% with 236 lines in your changes missing coverage. Please review.

Project coverage is 46.45%. Comparing base (296d9a5) to head (f670424).
Report is 174 commits behind head on main.

Files with missing lines	Patch %	Lines
src/spatialdata_io/readers/g4x.py	10.26%	236 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #281      +/-   ##
==========================================
+ Coverage   39.16%   46.45%   +7.29%     
==========================================
  Files          26       27       +1     
  Lines        2663     2994     +331     
==========================================
+ Hits         1043     1391     +348     
+ Misses       1620     1603      -17     

Files with missing lines	Coverage Δ
src/spatialdata_io/__init__.py	100.00% <100.00%> (ø)
src/spatialdata_io/_constants/_constants.py	100.00% <100.00%> (ø)
src/spatialdata_io/readers/g4x.py	10.26% <10.26%> (ø)

... and 10 files with indirect coverage changes

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