omero-integration

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/data_access.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.