omero-integration
Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows.
npx skills add LeonChaoX/qinyan-academic-skills --skill omero-integration --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# OMERO Integration ## Overview OMERO is an open-source platform for managing, visualizing, and analyzing microscopy images and metadata. Access images via Python API, retrieve datasets, analyze pixels, manage ROIs and annotations, for high-content screening and microscopy workflows. ## When to Use This Skill This skill should be used when: - Working with OMERO Python API (omero-py) to access microscopy data - Retrieving images, datasets, projects, or screening data programmatically - Analyzing pixel data and creating derived images - Creating or managing ROIs (regions of interest) on microscopy images - Adding annotations, tags, or metadata to OMERO objects - Storing measurement results in OMERO tables - Creating server-side scripts for batch processing - Performing high-content screening analysis ## Core Capabilities This skill covers eight major capability areas. Each is documented in detail in the references/ directory: ### 1. Connection & Session Management **File**: `references/connection.md` Establish secure connections to OMERO servers, manage sessions, handle authentication, and work with group contexts. Use this for initial setup and connection patterns. **Common scenario
- Overview
- When to Use This Skill
- Core Capabilities
- 1. Connection & Session Management
- 2. Data Access & Retrieval
- 3. Metadata & Annotations
- 4. Image Processing & Rendering
- 5. Regions of Interest (ROIs)
- 6. OMERO Tables
- 7. Scripts & Batch Operations
- 8. Advanced Features
- Installation
- Quick Start
- Selecting the Right Capability
uv pip install omero-py
What does the omero-integration skill do?
Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows.
How do I install it?
Run `npx skills add LeonChaoX/qinyan-academic-skills --skill omero-integration --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From LeonChaoX/qinyan-academic-skills, a repository with 759 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.