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name: datasets-and-io description: "Load Squidpy datasets and local spatial inputs with safe cache, layout, AnnData, and SpatialData validation." disable-model-invocation: true metadata: disco-role: operating license: BSD 3-Clause

Squidpy Datasets and IO

Use this sub-skill when a task starts with Squidpy sample data, local spatial omics outputs, saved .h5ad files, or SpatialData tables that must be checked before analysis, imaging, or plotting.

Route Here For

• Choosing between squidpy.datasets download/cache helpers and local no-download readers.
• Loading local 10x Visium, Vizgen, or Nanostring/CosMx outputs with sq.read.*.
• Validating Squidpy-ready AnnData structure: .obsm['spatial'], .uns['spatial'], library_id, image metadata, and scalefactors.
• Checking SpatialData table availability and table_key before routing to graph or experimental imaging workflows.
• Diagnosing registry, cache, network/hash, spatial/ layout, non-numeric coordinates, or image/scalefactor problems.

Start Here

1. Read references/data-loading.md to pick a no-download local reader or a registry-backed dataset loader.
2. Check exact public signatures and required file conventions in references/api-reference.md.
3. Use scripts/check_spatial_adata.py --help to validate a saved .h5ad or an importable callable returning AnnData/SpatialData.
4. Use references/troubleshooting.md when loading succeeds but downstream workflows cannot find coordinates, library_id, images, scalefactors, or table_key.

Safe Defaults

• Prefer sq.read.visium, sq.read.vizgen, sq.read.nanostring, anndata.read_h5ad, or spatialdata.read_zarr for user-owned local data; these do not consult Squidpy's dataset registry.
• Treat sq.datasets.* calls as potentially networked unless the needed files already exist in the chosen cache directory.
• Pass an explicit cache or input path instead of relying on global Scanpy settings.
• For Visium, use load_images=False only as a count/metadata fallback; it does not create .obsm['spatial'], images, or scalefactors.

Boundaries

• Route spatial graph construction and statistics to graph-analysis after coordinates and table routing are clear.
• Route stable ImageContainer, image processing, segmentation, and image features to image-analysis.
• Route plot rendering and visual styling to visualization.
• Route experimental SpatialData tiling, tissue detection, QC, stitching, and stain workflows to experimental-imaging.