---

name: annotation-visualization description: "Plan and implement TIAToolbox annotation stores, DSL filters, graph overlays, and visualization/tile-server data layouts." disable-model-invocation: true metadata: disco-role: operating license: NOASSERTION

TIAToolbox Annotation Visualization

Use this sub-skill when a task involves TIAToolbox annotations, annotation stores, GeoJSON or HoVerNet-style overlays, graph overlays, DSL filters, or visualization command planning.

Route here for

• Creating or inspecting Annotation objects and SQLiteStore or DictionaryStore containers.
• Querying annotations by spatial bounds, Shapely geometry, properties, or DSL where filters.
• Converting overlay data among AnnotationStore, GeoJSON-like feature collections, HoVerNet-style .dat records, and graph JSON layouts.
• Planning visualization with tiatoolbox visualize, tiatoolbox show-wsi, or TileServer without launching servers unless the user explicitly asks.
• Diagnosing overlay visibility, coloring, property, filter, and remote/port issues.

Route elsewhere

• Route model-output generation and inference configuration to ../model-inference/SKILL.md.
• Route WSI loading, slide metadata, resolution, and registration image metadata to ../wsi-io/SKILL.md.
• Route exact CLI option tables and global configuration conventions to ../cli-and-configuration/SKILL.md.

Reference map

• API and query patterns: references/api-reference.md
• Overlay and data layout formats: references/data-formats.md
• End-to-end planning workflows: references/workflows.md
• Failure diagnosis: references/troubleshooting.md
• Safe local smoke check: scripts/annotation_store_smoke.py

Safe default approach

1. Identify whether the user needs an in-memory check, a persistent .db, a GeoJSON/dat conversion, a graph overlay, or an interactive viewer plan.
2. Normalize properties early: prefer stable keys such as type, score, color, class labels, and model-specific fields.
3. Use SQLiteStore for large or persistent overlays; use DictionaryStore for tiny examples and quick in-memory manipulation.
4. Validate geometry, basename matching, property ranges, and DSL filters before launching a browser or server.
5. If visualization is needed, prepare commands with --noshow for headless checks or document SSH port forwarding for remote runs.

Minimal smoke check

Run this only as a local sanity check; it does not launch TileServer, Bokeh, or a browser:

python scripts/annotation_store_smoke.py