What are the technical requirements for this skill?

You need Python 3.7+, the omero-py library, and access to an OMERO server (host, port, and credentials) to perform data operations.

Can I perform image analysis with this skill?

Yes, the skill provides patterns for accessing raw pixel data as NumPy arrays, allowing you to integrate with analysis libraries like scikit-image, OpenCV, or TensorFlow.

What is the OMERO Integration skill?

It is a specialized capability for Claude Code that provides implementation patterns and best practices for interacting with the OMERO microscopy platform using the Python API.

How does it handle metadata and annotations?

It provides comprehensive support for managing tags, key-value pairs, file attachments, and structured data through OMERO Tables linked to specific images or datasets.

Does it support high-content screening (HCS)?

Absolutely. It includes specific capabilities for navigating HCS data structures such as Screens, Plates, and Wells.

OMERO Microscopy Integration

Name: OMERO Microscopy Integration
Author: Sologa

bySologa

0•

Data Science & ML

Manages and analyzes microscopy data through the OMERO Python API for scientific imaging and high-content screening workflows.

The OMERO Integration skill provides a comprehensive framework for interacting with the OMERO microscopy platform directly from Claude Code. It simplifies complex bio-imaging workflows by offering standardized patterns for session management, hierarchical data retrieval, and raw pixel analysis using NumPy. This skill is essential for researchers and developers who need to programmatically manage large-scale microscopy datasets, perform automated ROI analysis, and store structured measurements. By bridging the gap between raw scientific data and Python-based analysis, it enables the creation of robust, reproducible microscopy pipelines.

Key Features

01Pixel data extraction and manipulation via NumPy for computational analysis

02Hierarchical data navigation across Projects, Datasets, Screens, and Plates

03Programmatic ROI creation and intensity measurement for various shapes

04Secure session and multi-group context management for OMERO servers

05Structured metadata handling using OMERO Tables and custom annotations

060 GitHub stars

Use Cases

01Integrating microscopy image data into machine learning and AI training pipelines

02Automating high-content screening analysis and data extraction

03Batch processing large scientific datasets with server-side OMERO scripts

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add sologa/codex-pipeline omero-integration

For use in Claude.ai and ChatGPT

Download Skill