From OpenProblems Spatial Co-pilot
Validate and inspect spatial transcriptomics data files (SpatialData/zarr/AnnData) before any analysis. Use when the user points at a spatial data file, reports a loading/format error, or asks whether data is suitable for a method.
How this skill is triggered — by the user, by Claude, or both
Slash command
/openproblems-spatial:spatial-data-validationThe summary Claude sees in its skill listing — used to decide when to auto-load this skill
Validate first, reason second. Never assume a file's format or contents from its
Validate first, reason second. Never assume a file's format or contents from its extension.
Detect & validate format. Call the MCP tool validate_spatial_data with
the file path. Choose validation_level:
basic — extension/existence only.structure (default) — format + structural integrity.integrity — deeper content checks.domain — spatial-biology-specific expectations.
For several files, use validate_multiple_spatial_files.Read the metadata. Call analyze_spatial_metadata to extract dimensions,
spatial coordinates, and gene/feature info. Confirm obsm['spatial'] (AnnData)
or coordinate systems (SpatialData) are present when spatial analysis is
intended.
Check raw vs. processed. Integer-valued matrices are likely raw counts; non-integer/log-scaled values are processed. State which the downstream method expects and flag a mismatch.
Check compatibility when combining files: check_spatial_data_compatibility
(coordinate systems + gene overlap).
context/data-formats.md).zarr store is SpatialData only if it has SpatialData markers or ≥2 of
images/ labels/ points/ shapes/ tables/. Otherwise it's a plain zarr array.pip install -e ".[spatial]")
is optional — the validators degrade gracefully without it.run_nextflow_workflow) — they aren't
implemented. Drive local CLIs directly if execution is needed.Guides creation, editing, and verification of skills for AI coding agents using test-driven development with subagent scenarios. Use when authoring or debugging skills.
npx claudepluginhub rebell-leader/spatialai_mcp --plugin openproblems-spatial