Omero Integration

If you're working with microscopy data stored in OMERO servers, this skill gives you the Python API patterns you need. It covers the full stack: connecting and authenticating, navigating the project/dataset/image hierarchy, pulling pixel data as NumPy arrays, managing ROIs and annotations, and storing analysis results in OMERO tables. The references are organized by task (data access, image processing, ROIs, batch scripts), which is helpful since OMERO's API surface is pretty wide. Most useful when you're building analysis pipelines that need to read from and write back to OMERO rather than working with exported files. The context manager patterns and error handling examples are solid.

skills.sh installs: 203
GitHub stars: 33.2K
last updated: Aug 21, 2026

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Install

$ npx -y skills add davila7/claude-code-templates --skill omero-integration --agent claude-code

Installs into .claude/skills of the current project.

Files

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.

SKILL.md on GitHub