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alterlab-omero

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Plug-and-play OMERO data workflows for microscopy.

Education & Research#automation#python#roi#annotations#microscopy#omero
AuthorAlterLab-IEU
Version1.0.0
Installs0

System Documentation

What problem does it solve?

OMERO is a powerful data management platform for microscopy that can be complex to use directly from code; this Skill provides a structured, scriptable integration to simplify connections, data access, ROI/annotation workflows, and batch processing.

Core Features & Use Cases

  • Connection and session management to OMERO servers using BlitzGateway with context management for reliable workflows.
  • Data access, navigation of Project -> Dataset -> Image (and Screen -> Plate -> Well) and management of ROIs and annotations for batch analyses.
  • Script-driven automation: batch processing of images, ROI analysis, and metadata handling, enabling reproducible pipelines for microscopy experiments.
  • Use Case: Automate retrieval of images from a dataset, apply ROI computations, and attach results as file annotations for reporting.

Quick Start

Connect to your OMERO server and list the available projects to verify access before proceeding.

Dependency Matrix

Required Modules

None required

Components

Standard package

💻 Claude Code Installation

Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.

Please help me install this Skill:
Name: alterlab-omero
Download link: https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/archive/main.zip#alterlab-omero

Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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