Can I manage annotations and ROIs with this skill?

Absolutely. It covers creating and querying various ROI shapes (rectangles, polygons, masks) and managing annotations like tags and file attachments.

Does this skill require an active OMERO server?

Yes, you must have access to an OMERO server (host, port, and credentials) and have the omero-py library installed in your Python environment.

Can I use this skill for high-content screening (HCS)?

Yes, the skill includes specific capabilities for navigating Screens, Plates, and Wells, making it ideal for high-content screening workflows.

What is the OMERO Integration skill?

It is a specialized capability for Claude Code that provides patterns and best practices for interacting with the OMERO microscopy data management platform via its Python API.

How does this skill handle image pixel data?

It provides standardized methods to access raw pixel data as NumPy arrays, modify rendering settings, and create derived images or projections.

OMERO Microscopy Integration

Name: OMERO Microscopy Integration
Author: K-Dense-AI

byK-Dense-AI

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3,719

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Data Science & ML

Integrates OMERO microscopy data management with Python for advanced image analysis, metadata handling, and automated screening workflows.

The OMERO Integration skill empowers researchers and developers to interact seamlessly with the OMERO open-source platform for microscopy data. By providing standardized patterns for the OMERO Python API (omero-py), this skill facilitates secure connection management, hierarchical data retrieval across projects and datasets, and sophisticated pixel-level image processing. Whether you are automating high-content screening, managing regions of interest (ROIs), or storing structured measurement results in OMERO tables, this skill offers the domain-specific guidance required to build robust, reproducible scientific analysis pipelines.

Key Features

013,719 GitHub stars

02Metadata and annotation handling for tags, file attachments, and key-value pairs

03Advanced pixel data extraction and manipulation using NumPy arrays

04Hierarchical data navigation across Projects, Datasets, and Screening Plates

05Comprehensive ROI management including polygon, mask, and shape analysis

06Secure session and connection management for OMERO servers

Use Cases

01Managing and querying multi-dimensional scientific image metadata and ROIs

02Developing server-side scripts for automated microscopy image processing

03Automating high-content screening data retrieval and batch analysis

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add k-dense-ai/claude-scientific-skills omero-integration

For use in Claude.ai and ChatGPT

Download Skill