omero-integration SKILL.md skillA
omero-integration from jaechang-hits/sciagent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jaechang-hits/sciagent-skills/omero-integration@git:20260528.a140b59Pins git:20260528.a140b59 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jaechang-hits/sciagent-skills
- Path
skills/medical-imaging/omero-integration/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260528.a140b59, committed May 28, 2026
- Size
- 16,105 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
Open-source bio-image data management. Use the omero-py client to connect to an OMERO server, retrieve images as numpy arrays, annotate with tags and key-value pairs, manage ROIs, and feed image data into Python analysis pipelines — programmatically, no GUI.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# omero-integration ## Overview OMERO is an open-source image data management system widely used in microscopy facilities and core labs. The `omero-py` library provides a Python client (`BlitzGateway`) that connects to an OMERO server, allowing programmatic access to images, datasets, projects, tags, annotations, and ROIs. Use it to build automated analysis workflows that pull images from OMERO, process them in Python, and write results back as annotations. ## When to Use - **Programmatic image retrieval from OMERO**: Downloading microscopy images as numpy arrays for downstream analysis without using the OMERO Insight GUI. - **Bulk annotation and tagging**: Applying tags, key-value pair annotations, or comments to large numbers of images/datasets based on analysis results. - **ROI access and management**: Reading segmentation ROIs (shapes) stored in OMERO for downstream quantification or export. - **Integrating OMERO into Python analysis pipelines**: Connecting OMERO image data to scikit-image, OpenCV, CellPose, or other image analysis tools. …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/omero-integration@sha256:e5ecef7263fdcaa9The line at the top of this page pins the label git:20260528.a140b59, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_zwtxokdv67qrx22f)
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Versions
The registry has recorded 1 version of this file, committed on May 28, 2026.
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (16105 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
jaechang-hits/sciagent-skills · 381 stars · license a license file GitHub does not identify · pushed 2026-10-16 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_zwtxokdv67qrx22f GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/omero-integration GET https://markdownregistry.com/api/v1/blob/e5ecef7263fdcaa96af76806e39597c5a854b812bfba1b75f8fa72146e8adfc3
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Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.
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