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 → Data...