omero-integration

omero-integration is a skill for Claude Code, Codex from foryourhealth111-pixel/Vibe-Skills. It costs 39 tokens per session (1,836 once invoked), scanned A, a copy of omero-integration, Apache-2.0.

A Python integration for OMERO, an open-source platform that stores, displays, and manages microscopy images and their metadata. It supports working with images, datasets, annotations, and regions of interest.

In plain words
What is it for?
Use it to retrieve microscopy projects or screening data, analyze pixels, create image annotations, store measurements, and run batch processing.
Why use it?
It lets code access and organize microscopy data on an OMERO server instead of handling each image and its metadata manually.

Skill for Claude CodeCodex

Written for no agent in particular: nothing here depends on one.

Good fit Use it to retrieve microscopy projects or screening data, analyze pixels, create image annotations, store measurements, and run batch processing.

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Install with agentmods
npx agentmods add skills/foryourhealth111-pixel/vibe-skills/omero-integration
About the project

Vibe-Skills is a collection and routing system that helps AI agents discover, select, and coordinate specialized skills for completing tasks. It is intended for agents that need to organize workflows across many installed capabilities. The catalogue entries are skills and an agent belonging to this system.

foryourhealth111-pixel/Vibe-Skills · 3,252 stars · on GitHub

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent
npx skills add foryourhealth111-pixel/Vibe-Skills --skill omero-integration
Clone the repo
git clone --depth 1 https://github.com/foryourhealth111-pixel/Vibe-Skills

Made for: Claude Code, Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for omero-integration

README.md
[![agentmods](https://agentmods.dev/badge/skills/foryourhealth111-pixel/vibe-skills/omero-integration/github.svg)](https://agentmods.dev/skills/foryourhealth111-pixel/vibe-skills/omero-integration)
Your own site
<a href="https://agentmods.dev/skills/foryourhealth111-pixel/vibe-skills/omero-integration"><img src="https://agentmods.dev/badge/skills/foryourhealth111-pixel/vibe-skills/omero-integration/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for omero-integration

Your own site · 80×15
<a href="https://agentmods.dev/skills/foryourhealth111-pixel/vibe-skills/omero-integration"><img src="https://agentmods.dev/badge/skills/foryourhealth111-pixel/vibe-skills/omero-integration.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 39 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 1,836 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin 89% copy Near-identical to another mod in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00039 $0.01836
Opus 5 $0.00019 $0.00918
Sonnet 5 $0.00008 $0.00367
Haiku 4.5 $0.00004 $0.00184

Measured 9d ago against content hash 0468f97fbe57, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-12, from the pricing page.

Security

Grade A, and why

omero-integration scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 9d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

Origin

This is a copy

89% identical to omero-integration — 8 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.

bundled/skills/omero-integration/SKILL.md · 253 lines

How it starts

The opening of the file, as written. The whole thing — 253 lines — stays where its author put it; the contents beside it link to each section on GitHub.

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.

Routing Boundary

Use this skill for OMERO server access, OMERO Python API work, microscopy image server data retrieval, ROI annotation, image metadata management, and high-content screening image management. Generic microscopy literature search, DICOM tags, IDC/TCIA retrieval, histolab tiling, PathML computational pathology, scRNA-seq, flow cytometry, and generic image processing are outside this skill.

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.

Common scenarios:

  • Connect to OMERO server with credentials
  • Use existing session IDs
  • Switch between group contexts
  • Manage connection lifecycle with context managers

2. Data Access & Retrieval

File: references/data_access.md

Navigate OMERO's hierarchical data structure (Projects → Datasets → Images) and screening data (Screens → Plates → Wells). Retrieve objects, query by attributes, and access metadata.

Read the full file on GitHub · 253 lines

Files

What ships with it

8 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 9d ago First seen · 253 lines · 39 tokens per session scan A 0468f97fbe57

Subscribe to this mod's changes

omero-integration is a skill published in the GitHub repository foryourhealth111-pixel/Vibe-Skills (3,252 stars, last pushed 12d ago), licensed Apache-2.0. It adds 39 tokens to every session and 1,836 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it A with 0 findings. It is 89% identical to omero-integration, differing in 8 lines, and is treated as a copy.

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