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OMERO Microscopy Integration

Lets an agent inspect, export and plan transfers of microscopy data on an OMERO server, with bounded, read-only defaults.

Source Download skill
Repository
K-Dense-AI/scientific-agent-skills
Stars
55,780
Licence
MIT
Files
15 files

What it does

Once installed, the agent can work with OMERO, a server platform that stores and organises scientific microscope images, using the omero-py Python client and the OMERO command line. It can produce bounded inventories of projects, datasets and images, export annotations and ROI shape geometry for specific image IDs to JSON, and build local import/export plans. Writes such as uploads, annotations or deletions are meant to happen only after an explicit, reviewed target is named.

Great for

  • Lab data managers who need a scoped inventory of what is stored on an OMERO server
  • Bioimaging researchers exporting annotations or ROI geometry for named images
  • Developers writing reviewed scripts that query OMERO with the omero-py client

Skip it if

  • Users who want to connect to an OMERO server without understanding credential handling, since it requires password or session-key setup and network access to a server they are authorised to use
  • Anyone expecting a general image-analysis tool, because it focuses on data access and metadata rather than analysing pixels
  • Use against servers or data without authorisation, because OMERO data may contain unpublished images and identifiers

Try asking

  • “List up to 100 image objects from my OMERO project 12 and summarise them without downloading pixels”
  • “Export annotations and ROI geometry for image IDs 501 and 502 to a JSON file”
  • “Plan an import of my local microscopy folder into OMERO without connecting to the server yet”
  • “Validate my OMERO connection settings before running any remote command”
Step-by-step guide: how to use OMERO Microscopy IntegrationInstall, first run, examples, tips and FAQs

Install in 3 steps

  1. 1

    Download the skill

    The ZIP contains the 15 original files, the MIT licence and an attribution note.

    omero-integration.zip
  2. 2

    Add it to your agent

    Claude Code (all projects)

    mkdir -p ~/.claude/skills && unzip omero-integration.zip -d ~/.claude/skills/

    Claude Code / Agent SDK (this project only)

    mkdir -p .claude/skills && unzip omero-integration.zip -d .claude/skills/

    Claude apps (web/desktop): Settings → Capabilities → Skills → Upload skill, and choose the ZIP.

  3. 3

    Ask for the task

    No special command needed — the agent reads the skill's description and loads it when your request matches. Try one of the prompts above.

Get better results

  • Run the local validation and dry-run modes first; the helpers make no server connection without --execute.
  • Give the agent explicit host, group, object type, IDs and a result limit so that scope stays small.
  • Supply passwords through environment variables or a secret manager, never on the command line, and rotate any session key that has been exposed.

What's inside

  • references/advanced.md
  • references/connection.md
  • references/data_access.md
  • references/image_processing.md
  • references/metadata.md
  • references/rois.md
  • references/scripts.md
  • references/sources.md
  • references/tables.md
  • scripts/export_image_metadata.py
  • scripts/inventory.py
  • scripts/omero_common.py
  • scripts/plan_transfer.py
  • scripts/validate_config.py
  • SKILL.md

Redistributed unmodified from K-Dense-AI/scientific-agent-skills under the MIT licence. The assessment was drafted with AI from the skill's files on 2026-10-29. Skills can instruct your agent to run code — read SKILL.md and any scripts before installing.