omero-integration
Securely inspect and automate microscopy data workflows against OMERO.server with omero-py, BlitzGateway, OMERO CLI, tables, annotations, ROIs, rendering, and documented OMERO.web APIs. Use for scoped OMERO inventory, metadata export, import/export planning, or reviewed write workflows.
npx skills add K-Dense-AI/scientific-agent-skills --skill omero-integration --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# OMERO Integration Use current OME documentation and the smallest explicit data scope. OMERO data may contain unpublished images, identifiers, annotations, original files, and derived measurements. ## Verified Baseline This skill was refreshed on **2026-07-23**: - **OMERO.server 5.6.18** (May 2026) is the current documented stable server. - It was tested by OME with **OMERO.py/omero-py 5.22.1** and **OMERO.web 5.31.0**. - `omero-py==5.22.1` requires Python 3.10 or newer. The OMERO support matrix supports 3.10 and 3.11, recommends 3.12, and still labels 3.13/3.14 “upcoming.” - OMERO 5.6 uses **IcePy 3.6**, with 3.6.5 prebuilt client wheels documented for Python versions through 3.12. The pin above is a reproducible skill snapshot, not a promise that every OMERO.server release accepts that client. For another server version, consult its release entry and use the OMERO.py version tested with it. See [`references/sources.md`](references/sources.md). ## Operating Contract 1. Start with local validation or a dry run. Do not connect until the user has selected the host, group, object type, IDs, and result limit. 2. Read credentials only from the named `OMERO_*` variables in the frontmatt
- Verified Baseline
- Operating Contract
- Choose the Interface
- Install a Reproducible Client
- Credentials and Connection
- Bundled Safe Helpers
- Capability Guide
- Final Review Before Remote Work
uv venv --python 3.12 .venv source .venv/bin/activate Download the matching 3.6.5 wheel from the official OMERO-linked matrix. uv pip install "/absolute/path/to/zeroc_ice-3.6.5-<matching-tags>.whl" uv pip install "omero-py==5.22.1" export OMERO_HOST="omero.example.org" export OMERO_PORT="4064" export OMERO_USER="researcher" export OMERO_SECURE="true" Supply OMERO_PASSWORD through the environment/secret manager, or use
What does the omero-integration skill do?
Securely inspect and automate microscopy data workflows against OMERO.server with omero-py, BlitzGateway, OMERO CLI, tables, annotations, ROIs, rendering, and documented OMERO.web APIs. Use for scoped OMERO inventory, metadata export, import/export planning, or reviewed write workflows.
How do I install it?
Run `npx skills add K-Dense-AI/scientific-agent-skills --skill omero-integration --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From K-Dense-AI/scientific-agent-skills, a repository with 32,619 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.