ome-zarr-skills

Agentic Skills for OME-Zarr.

Install

Requires Node.js (for npx). Then:

DISABLE_TELEMETRY=1 npx skills add BioImageTools/ome-zarr-skills -g

Skills

Skill	Invoke	What it does
ome-zarr-primer	automatic, loaded first	Background on bioimage analysis and OME-Zarr: image concepts, formats, Zarr chunks/shards, OME-Zarr layout and versions, tooling, pipelines, large-image patterns. The other skills build on it.
setup-ome-zarr-skills	/setup-ome-zarr-skills, by you only	Run once per repo. Records the spec version, RFCs in use, and imaging domain in docs/agents/ome-zarr.md.
reading-ome-zarr-spec	automatic	Infers the OME-Zarr version in play and fetches that version's spec from the official site.
inspect-ome-zarr	automatic	Read-only summary of an OME-Zarr store (local, zip, http, s3, gs): structure, axes, pixel size, pyramid, channels, storage, labels, plus anomalies with fixes. Optional JSON for other skills.
planning-ome-zarr-layout	automatic	Chooses chunk, shard and tile shapes from how downstream tools read and write the data (tiled segmentation, pixel classification, tracking, viewers, cluster jobs); spec rules such as DCA are applied afterwards.

How the skills compose

Per-repo preferences live in docs/agents/ome-zarr.md, written by setup-ome-zarr-skills. Every skill in this set follows one rule: read that file if it exists, infer from context if it doesn't. No skill requires setup to have run.

Dev install

Symlink the skills into Claude Code (.claude/skills) and the cross-agent .agents/skills dir so edits in this repo are picked up on the next session:

scripts/link-skills.sh              # all projects (~/.claude/skills, ~/.agents/skills)
scripts/link-skills.sh <project>    # one project (<project>/.claude/skills, <project>/.agents/skills)
scripts/link-skills.sh --unlink     # remove

Don't combine this with a plugin install of the same repo, or every skill appears twice.

License

See LICENSE.