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OMERO Integration (Microscopy Data)

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

Data & AnalyticsAdvanced★ 33,030⑂ 3,248AI score 8/10Last updated: Aug 9, 2026

What it does

  • Guides you to the right interface: BlitzGateway (omero-py), the OMERO CLI, or the officially stable OMERO.web api/webgateway endpoints.
  • Covers Project/Dataset/Image traversal, tags and map annotations, ROIs, OMERO.tables, thumbnails, and rendering settings.
  • Ships local helper scripts (validate_config.py, inventory.py, export_image_metadata.py, plan_transfer.py) that are dry-run by default and require --execute for remote action.
  • Enforces credential hygiene: read only the named OMERO_* variables, never load .env, never echo a password or session key into args, logs, or output.
  • Requires hard limits on every list, page, ROI, and table read, and treats every write (annotation, import, delete, permission change) as a separately reviewed operation with exact target IDs.

Who it's for

  • Imaging core facility staff and lab admins running OMERO.server.
  • Bioimage analysts who need bulk image metadata exported as JSON for downstream pipelines.
  • Teams handling unpublished data who need strict scoping before anything leaves the server.

Example uses

  1. "Check my OMERO connection settings without touching the server" → validate_config.py validates env vars (and optionally DNS) locally.
  2. "List the first 25 images in Dataset 481 by ID" → inventory.py produces a paged, read-only JSON inventory.
  3. "Export tags and ROIs for these 10 image IDs as JSON, no pixels" → export_image_metadata.py with per-category limits and redaction defaults.
  4. "Scan this folder and draft an import plan" → plan_transfer.py runs entirely offline, never emitting credential flags.

· · · Install guide · · ·

Try it now, no install

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Read the instructions in this file and follow them to help me:
https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/HEAD/skills/omero-integration/SKILL.md

What I want: (describe your task here)

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↓ If it works for you, download the ZIP below and install it. Then it runs on its own — no pasting each time.

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.
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Install in Claude Code

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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 Claude Code: 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 IcePy 3.6.5 wheel matching your interpreter/OS/architecture from the official OMERO-linked matrix and install it: uv pip install /abs/path/zeroc_ice-3.6.5-<tags>.whl (do not substitute Ice 3.7).
  5. Install the client: uv pip install "omero-py==5.22.1"
  6. Export connection variables: export OMERO_HOST=..., OMERO_PORT=4064, OMERO_USER=..., OMERO_SECURE=true. Supply OMERO_PASSWORD or OMERO_SESSION_KEY via your secret manager — never commit them.
  7. Restart Claude Code and try "validate my OMERO configuration". Only set OMERODIR (pointing to an extracted OMERO.server tree) if you need import/admin CLI commands.
View source on GitHub ↗License: MIT