Omero Integration
If you're working with microscopy data in OMERO, this gives Claude the ability to navigate projects and datasets, pull pixel data into NumPy arrays, manage ROIs and annotations, and write server-side scripts for batch processing. The skill covers eight capability areas from basic connection patterns to creating OMERO tables for storing quantitative measurements. It's genuinely useful if you're doing high-content screening or need to automate analysis workflows across hundreds of images. The reference docs are thorough and include specific code patterns for common tasks like extracting intensities from ROIs or querying screening plates. You'll need access to an OMERO server and omero-py installed to use any of this.
- skills.sh installs
- 2K
- GitHub stars
- 56.6K
- last updated
- Aug 21, 2026
Install
$ npx -y skills add k-dense-ai/scientific-agent-skills --skill omero-integration --agent claude-codeInstalls into .claude/skills of the current project.
Files
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 OMERO data may contain unpublished images, identifiers, annotations, original files, and derived measurements.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 2026-09-30:
- 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==5.22.1requires 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.
Latest client releases: OMERO.py 5.23.0 (2026-07-30) and OMERO.web 5.33.2 are newer than the server history’s tested pairing. The bundled helpers were checked locally with OMERO.py 5.22.1 and 5.23.0, IcePy 3.6.5, and Python 3.12; this did not connect to an OMERO server. Remote snippets in this skill and its references are illustrative, verified against official docs/source, and require adaptation to an authorized server and its object IDs.
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- Repository
- github.com/k-dense-ai/scientific-agent-skills
- Categories
- Backend & APIs, AI & Agent Building, Productivity & Planning, Automation & Workflows, CLI & Terminal
- First seen
- Jun 3, 2026
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