Add Visium HD end-to-end tests for Space Ranger 4.x segmentation and cell-type annotation

[jakubmajercik]

Context

PR #64 updated Space Ranger to 4.1.0 and exposed the new 4.x arguments for nucleus/cell segmentation (--nucleus_segmentation, --custom_segmentation_file, --nucleus_expansion_distance_micron, --max_nucleus_diameter_px), UMI-based registration (--umi_registration, --umi_to_image_offset), cell-type annotation (--cell_annotation_model, --tenx_cloud_token_path, --disable_cell_annotation), and --include_introns.

These were reviewed and merged with unit-level coverage (optional --probe_set, --unknown-slide no-slidefile path, converter without a probe set). However, the segmentation/annotation features only trigger on Visium HD / HD 3' data with an H&E image, so they can't be exercised by the current FFPE (visium) fixture.

Why deferred

Truly testing these end-to-end requires:

1. Running Space Ranger 4.1 on the Visium HD fixture with an H&E image so segmented_outputs/ (+ nucleus_segmentations.geojson, cell_types/) are produced.
2. An HD-aware from_spaceranger_to_h5mu (or a new converter): the current one reads a flat bundle and CSV tissue_positions, whereas HD output uses binned_outputs/square_XXXum/, segmented_outputs/, and parquet tissue positions.
3. An HD ingestion workflow in openpipeline_spatial (currently HD ingestion lives in pfizer-spatial).

Scope of this issue

• HD-aware output handling in the converter (bins vs cells, parquet positions, segmented_outputs/).
• An HD (or HD 3') integration test that runs spaceranger_count with segmentation enabled and asserts the segmentation/annotation outputs.
• Coverage for --include_introns and the segmentation/annotation params on real HD data.

Related

• Requested during review of PR Update Space Ranger to 4.1.0 #64.
• Also relevant: resources_test_scripts/visium_hd_tiny.sh currently downloads a probe set for an HD 3' dataset, but per 10x, Visium HD 3' must NOT be given --probe_set -- worth reconciling as part of this work.