Agent skill · research science · aiskillstore
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.
Why this skill is useful
Adds executable scripts for batch processing and advanced image analysis workflows that are not covered in general programming knowledge.
What it needs
Requires python installed locally. Requires omero account access. About 4k tokens when loaded. Last updated 2026-08-07. 405 stars on the source repository.
What this skill does
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 scenarios: Connect to OMERO server with credentials Use existing session IDs Switch between group contexts Manage connection lifecycle with context managers 2. Data Access & Retrieval File: references/dataaccess.md Navigate OMERO's hierarchical data structure (Projects → Datasets → Images) and screening data (Screens → Plates → Wells). Retrieve objects, query by attributes, and access metadata. Common scenarios: List all projects and datasets for a user Retrieve images by ID or dataset Access screening plate data Query objects with filters 3. Metadata & Annotations File: references/metadata.md Create and manage annotations including tags, key-value pairs, file attachments, and comments. Link annotations to images, datasets, or other objects. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills aiskillstore/omero-integration