Agent skill · software engineering · k-dense-ai
omero-integration
Securely inspect and automate microscopy data workflows against OMERO.server with omero-py, BlitzGateway, OMERO CLI, tables, annotations, ROIs, rendering, and documented OMERO.web APIs. Use for scoped OMERO inventory, metadata export, import/export planning, or reviewed write workflows.
Why this skill is useful
Provides specific commands and workflows for interacting with OMERO.server that the AI wouldn't reliably generate on its own.
What it needs
Requires python installed locally. About 5k tokens when loaded. Last updated 2026-08-03. 32,849 stars on the source repository.
What this skill does
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 OMERO data may contain unpublished images, identifiers, annotations, original files, and derived measurements.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 2026-07-23: 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==5.22.1 requires 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. The pin above is a reproducible skill snapshot, not a promise that every OMERO.server release accepts that client. For another server version, consult its release entry and use the OMERO.py version tested with it. See references/sources.md. Operating Contract 1. Start with local validation or a dry run. Do not connect until the user has selected the host, group, object type, IDs, and result limit. 2. Read credentials only from the named OMERO variables in the frontmatter. Never search parent directories or load .env files. 3. Never place a password or session key in command arguments, source code, output JSON, logs, tracebacks, or chat. A session key is a bearer credential. 4. Default to secure=True. OMERO encrypts login by default, but post-login data and the session ID may otherwise travel unencrypted. secure=True does not by itself guarantee certificate hostname verification. 5. Bound every list, page, ROI, shape, annotation, table row, pixel plane, and local file scan. Do not turn an object request into a group-wide or cross-group export without explicit approval. 6. Treat all writes separately: annotation/link creation, rendering-default saves, image creation, imports, script uploads, table writes, ownership or group changes, and deletion require an exact reviewed target. 7. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills k-dense-ai/omero-integration