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OMERO Integration (Microscopy Data)

Safely inspect, export, and plan microscopy data workflows on an OMERO.server using omero-py, BlitzGateway, and the CLI.

Data & AnalyticsAdvanced★ 33,030⑂ 3,248AI score 7/10Last updated: Aug 9, 2026

What it does

Connects to OMERO.server, the bioimage data management platform, to traverse Project/Dataset/Image hierarchies and export metadata — tags, map annotations, ROIs, and OMERO.tables — as tightly scoped JSON. The skill explains when to reach for BlitzGateway (Python), the OMERO CLI, or the officially supported OMERO.web api/webgateway endpoints, and walks through a reproducible client setup (OMERO.py 5.22.1 with IcePy 3.6.5 on Python 3.12).

Its strongest feature is the operating contract: credentials are read only from declared OMERO_* variables, never echoed into arguments, logs, or output; bundled remote helpers are dry-run by default and require --execute; every write (annotation creation, import, rendering-default save, deletion) needs an explicitly reviewed target ID. Connections, table handles, and raw stores must be closed in finally blocks.

Who it's for

  • Researchers who store microscopy images in OMERO and need recurring inventories or metadata dumps
  • Core imaging facility data managers planning imports and OME-TIFF exports
  • Teams that must strictly bound scope so unpublished images never leave the server

Examples

  1. "List 25 images under Project 42 ordered by ID" → inventory.py produces a paged, read-only JSON inventory
  2. "Export tags and ROIs for images 1011 and 1012, no pixel bytes" → export_image_metadata.py applies per-category limits and redaction defaults
  3. "Show me the import plan for this local folder first" → plan_transfer.py runs entirely offline and never touches OMERO

· · · Install guide · · ·

Install in the Claude app (no terminal)
  1. Download the ZIP with the button below.
  2. In Claude, open Settings → Capabilities and turn on 'Code execution and file creation'. (one time)
  3. Go to Customize → Skills → + → 'Upload a skill' and upload the ZIP.
↓ Download ZIP
Install in Claude Code

Let Claude do it — paste this into Claude Code

Install the skill I found on Claude Skill Mart.
Copy the skills/omero-integration folder from the GitHub repo K-Dense-AI/scientific-agent-skills into my ~/.claude/skills/omero-integration/.
When it's done, tell me in one line what this skill can do.

Install with a command instead

git clone https://github.com/K-Dense-AI/scientific-agent-skills.git /tmp/scientific-agent-skills && mkdir -p ~/.claude/skills && cp -r /tmp/scientific-agent-skills/skills/omero-integration ~/.claude/skills/

⚠ This is a third-party skill. Check the source repository before installing.

  1. Clone the repository: git clone https://github.com/K-Dense-AI/scientific-agent-skills.git
  2. Copy the skill into place: mkdir -p ~/.claude/skills && cp -r scientific-agent-skills/skills/omero-integration ~/.claude/skills/
  3. Create a Python 3.12 environment: uv venv --python 3.12 .venv && source .venv/bin/activate
  4. Download the zeroc_ice-3.6.5 wheel matching your OS, architecture, and interpreter from the official OMERO-linked matrix and install it (do not substitute Ice 3.7).
  5. Install the client: uv pip install "omero-py==5.22.1"
  6. Export connection variables: OMERO_HOST, OMERO_PORT=4064, OMERO_USER, and OMERO_SECURE=true. Supply the password or session key through a secret manager so it never lands in shell history.
  7. Restart Claude Code, then dry-run python -B ~/.claude/skills/omero-integration/scripts/validate_config.py --help before doing any real remote work.
View source on GitHub ↗License: MIT