What is the OMERO Integration skill?

It is a specialized capability for Claude that provides patterns, best practices, and implementation guidance for the OMERO Python API (omero-py) to manage microscopy data.

Does this skill help with ROI management?

Absolutely. It covers creating, retrieving, and analyzing various Regions of Interest (ROIs) such as rectangles, polygons, and masks, including intensity statistics.

What software is required to use this skill?

You will need Python 3.7+, the omero-py library installed via pip, and access to an active OMERO server (host, port, and credentials).

Can I perform image analysis with this skill?

Yes, it provides specific guidance on accessing raw pixel data as NumPy arrays, allowing you to perform computational analysis and create derived images.

OMERO Microscopy Integration

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

byK-Dense-AI

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2,188

Data Science & ML

Manages and analyzes microscopy data programmatically using the OMERO Python API and data management platform.

About

The OMERO Integration skill enables seamless interaction with the OMERO open-source platform for managing, visualizing, and analyzing microscopy images. It provides Claude with specialized knowledge to navigate complex data hierarchies, manage sessions, and perform pixel-level analysis using the omero-py library. This skill is essential for researchers and bioimage analysts who need to automate high-content screening workflows, retrieve specific datasets, handle Regions of Interest (ROIs), or store quantitative measurements in OMERO tables directly through programmatic interfaces.

Key Features

Secure session and connection management for OMERO servers
Hierarchical data navigation for Projects, Datasets, and Plates
2,188 GitHub stars
Metadata handling via tags, key-value pairs, and file attachments
Pixel data extraction and conversion to NumPy arrays for analysis
Comprehensive ROI management including polygons, masks, and statistics

Use Cases

Creating server-side batch processing scripts for microscopy pipelines
Managing and querying complex spatial annotations and image metadata
Automating high-content screening analysis and data retrieval

About

Key Features

Secure session and connection management for OMERO servers
Hierarchical data navigation for Projects, Datasets, and Plates
2,188 GitHub stars
Metadata handling via tags, key-value pairs, and file attachments
Pixel data extraction and conversion to NumPy arrays for analysis
Comprehensive ROI management including polygons, masks, and statistics

Use Cases

Creating server-side batch processing scripts for microscopy pipelines
Managing and querying complex spatial annotations and image metadata
Automating high-content screening analysis and data retrieval