OMERO Microscopy Integration

About

This skill empowers Claude to interact with OMERO servers for high-content screening and microscopy data management. It provides comprehensive patterns for accessing hierarchical data structures such as Projects, Datasets, and Images, while enabling manipulation of raw pixel data as NumPy arrays. Whether performing complex image analysis, managing regions of interest (ROIs), or automating metadata annotations, this skill ensures Claude follows best practices for session management, error handling, and scientific data integrity within the OMERO ecosystem.

Key Features

• Seamless connection and session management for secure OMERO server access
• Robust ROI management including creation, retrieval, and statistics
• Structured data storage and querying via OMERO Tables
• 324 GitHub stars
• Hierarchical data retrieval for projects, datasets, and screening plates
• Advanced image processing and pixel manipulation using NumPy integration

Use Cases

• Programmatically managing metadata and annotations for large scientific datasets
• Automating high-content screening analysis pipelines
• Extracting pixel data for training machine learning models in bioimaging