omero-integration
Inspects and automates microscopy data workflows against OMERO.server
by k-dense-aiFree
Description
omero-integration is an agent skill for inspecting and automating microscopy data workflows against an OMERO server, using omero-py, BlitzGateway and the OMERO command-line tool. It covers tables, annotations, regions of interest, image rendering and related tasks. OMERO is an open platform for managing microscopy images and their metadata. The skill asks you to use the current OME documentation and the smallest explicit data scope, because OMERO data can include unpublished images, identifiers, annotations, original files and derived measurements. The skill was refreshed on 30 September 2026 against OMERO.server 5.6.18, released in May 2026, which is the current documented stable server. It was tested by OME with omero-py 5.22.1 and OMERO.web 5.31.0. The omero-py 5.22.1 package requires Python 3.10 or newer. The OMERO support matrix supports Python 3.10 and 3.11, recommends 3.12, and still labels 3.13 and 3.14 as upcoming. OMERO 5.6 uses IcePy 3.6, with prebuilt client wheels documented for Python versions up to 3.12. Use it when you need to script work on an existing OMERO server, such as querying images or adding annotations.…
Highlights
- Scripts OMERO microscopy workflows
- omero-py, BlitzGateway and the OMERO CLI
- Tables, annotations and regions of interest
- Image rendering support
- Targets OMERO.server 5.6.18
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omero-integration FAQ
What is OMERO?
An open platform for managing microscopy images and their metadata, which this skill works against through its server.
What can I automate?
Inspecting and changing data through omero-py, BlitzGateway and the OMERO command-line tool, including tables, annotations, regions of interest and rendering.
Which versions were tested?
OMERO.server 5.6.18, omero-py 5.22.1 and OMERO.web 5.31.0.
Which Python versions work?
omero-py 5.22.1 needs Python 3.10 or newer. The OMERO support matrix lists 3.10 and 3.11, recommends 3.12, and marks 3.13 and 3.14 as upcoming.
How do I install it?
Run npx skills add https://github.com/k-dense-ai/scientific-agent-skills --skill omero-integration.
Is it checked for security?
Its security audits show passes from Gen Agent Trust Hub, Socket and Snyk.
What are the best omero-integration alternatives?
Popular alternatives to omero-integration include data-scraper-agent, django-celery and django-patterns. See all omero-integration alternatives