Skill · em Dados, IA e pesquisa

omero-integration

Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows.

Procedência

Origem: davila7/claude-code-templates
Caminho: cli-tool/components/skills/scientific/omero-integration
Versão fixada: 57f899e5394bb8ca166f38eacae8f0853cbfe033
Licença: MIT
Espelhado em 25/09/2026
nenhum download no Claude Code Templates (lido em 25/09/2026)

Antes de instalar

9 arquivos · 123,3 KB · só texto, nenhum script

Instalar na sua CLI

O comando baixa a versão fixada (commit 57f899e) direto da origem, para a pasta que a CLI lê. Precisa de curl (macOS e Linux); no Windows não há comando, porque o Rook Labs é para macOS.

Claude Code

Neste projeto: instala em .claude/skills/omero-integration/.

d=".claude/skills/omero-integration"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/omero-integration"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/advanced.md" "$u/references/advanced.md" \
  -o "$d/references/connection.md" "$u/references/connection.md" \
  -o "$d/references/data_access.md" "$u/references/data_access.md" \
  -o "$d/references/image_processing.md" "$u/references/image_processing.md" \
  -o "$d/references/metadata.md" "$u/references/metadata.md" \
  -o "$d/references/rois.md" "$u/references/rois.md" \
  -o "$d/references/scripts.md" "$u/references/scripts.md" \
  -o "$d/references/tables.md" "$u/references/tables.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Global: instala em ~/.claude/skills/omero-integration/.

d="$HOME/.claude/skills/omero-integration"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/omero-integration"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/advanced.md" "$u/references/advanced.md" \
  -o "$d/references/connection.md" "$u/references/connection.md" \
  -o "$d/references/data_access.md" "$u/references/data_access.md" \
  -o "$d/references/image_processing.md" "$u/references/image_processing.md" \
  -o "$d/references/metadata.md" "$u/references/metadata.md" \
  -o "$d/references/rois.md" "$u/references/rois.md" \
  -o "$d/references/scripts.md" "$u/references/scripts.md" \
  -o "$d/references/tables.md" "$u/references/tables.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Codex

Neste projeto: instala em .agents/skills/omero-integration/.

d=".agents/skills/omero-integration"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/omero-integration"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/advanced.md" "$u/references/advanced.md" \
  -o "$d/references/connection.md" "$u/references/connection.md" \
  -o "$d/references/data_access.md" "$u/references/data_access.md" \
  -o "$d/references/image_processing.md" "$u/references/image_processing.md" \
  -o "$d/references/metadata.md" "$u/references/metadata.md" \
  -o "$d/references/rois.md" "$u/references/rois.md" \
  -o "$d/references/scripts.md" "$u/references/scripts.md" \
  -o "$d/references/tables.md" "$u/references/tables.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Global: instala em ~/.agents/skills/omero-integration/.

d="$HOME/.agents/skills/omero-integration"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/omero-integration"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/advanced.md" "$u/references/advanced.md" \
  -o "$d/references/connection.md" "$u/references/connection.md" \
  -o "$d/references/data_access.md" "$u/references/data_access.md" \
  -o "$d/references/image_processing.md" "$u/references/image_processing.md" \
  -o "$d/references/metadata.md" "$u/references/metadata.md" \
  -o "$d/references/rois.md" "$u/references/rois.md" \
  -o "$d/references/scripts.md" "$u/references/scripts.md" \
  -o "$d/references/tables.md" "$u/references/tables.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Antigravity

Neste projeto: instala em .agents/skills/omero-integration/.

d=".agents/skills/omero-integration"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/omero-integration"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/advanced.md" "$u/references/advanced.md" \
  -o "$d/references/connection.md" "$u/references/connection.md" \
  -o "$d/references/data_access.md" "$u/references/data_access.md" \
  -o "$d/references/image_processing.md" "$u/references/image_processing.md" \
  -o "$d/references/metadata.md" "$u/references/metadata.md" \
  -o "$d/references/rois.md" "$u/references/rois.md" \
  -o "$d/references/scripts.md" "$u/references/scripts.md" \
  -o "$d/references/tables.md" "$u/references/tables.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Global: instala em ~/.gemini/antigravity-cli/skills/omero-integration/.

d="$HOME/.gemini/antigravity-cli/skills/omero-integration"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/omero-integration"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/advanced.md" "$u/references/advanced.md" \
  -o "$d/references/connection.md" "$u/references/connection.md" \
  -o "$d/references/data_access.md" "$u/references/data_access.md" \
  -o "$d/references/image_processing.md" "$u/references/image_processing.md" \
  -o "$d/references/metadata.md" "$u/references/metadata.md" \
  -o "$d/references/rois.md" "$u/references/rois.md" \
  -o "$d/references/scripts.md" "$u/references/scripts.md" \
  -o "$d/references/tables.md" "$u/references/tables.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Peça ao Rook

Já usa o Rook Labs? Cole no chat do Rook: instale a skill https://rooklabs.sh/marketplace/cct.omero-integration

Prévia do SKILL.md

---
name: omero-integration
description: "Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows."
---

# 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.

**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`
…

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