omero-integration

Files (11)

• SKILL.md
• advanced.md · references/
• connection.md · references/
• data_access.md · references/
• image_processing.md · references/
• metadata.md · references/
• rois.md · references/
• scripts.md · references/
• tables.md · references/
• demo.cpython-313.pyc · scripts/__pycache__/
• demo.py · scripts/

SKILL.md (first lines)

# 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`

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

**Common scenarios:**
- List all projects and datasets for a user
- Retrieve images by ID or dataset
- Access screening plate data
- Query objects with filters

### 3. Metadata & Annotations
**File**: `references/metadata.md`

Create and manage annotations including tags, key-value pairs, file attachments, and comments. Link annotations to images, datasets, or other objects.

**Common scenarios:**
- Add tags to images
- Attach analysis results as files
- Create custom key-value metadata
- Query annotations by namespace

### 4. Image Processing & Rendering
**File**: `references/image_processing.md`

Access raw pixel data as NumPy arrays, manipulate rendering settings, create derived images, and manage physical dimensions.

**Common scenarios:**
- Extract pixel data for computational analysis
- Generate thumbnail images
- Create maximum intensity projections
- Modify channel rendering settings

### 5. Regions of Interest (ROIs)
**File**: `references/rois.md`

Create, retrieve, and analyze ROIs with various shapes (rectangles, ellipses, polygons, masks, points, lines). Extract intensity statistics from ROI regions.

**Common scenarios:**
- Draw rectangular ROIs on images
- Create polygon masks for segmentation
- Analyze pixel intensities within ROIs
- Export ROI coordinates

### 6. OMERO Tables
**File**: `references/tables.md`

Store and query structured tabular data associated with OMERO objects. Useful for analysis results, measurements, and metadata.

**Common scenarios:**
- Store quantitative measurements for images
- Create tables with multiple column types
- Query table data with conditions
- Link tables to specific images or datasets

### 7. Scripts & Batch Operations
**File**: `references/scripts.md`

Create OMERO.scripts that run server-side for batch processing, automated workflows, and integration with OMERO clients.

**Common scenarios:**
- Process multiple images in batch
- Create automated analysis pipelines
- Generate summary statistics across datasets
- Export data in custom formats

### 8. Advanced Features
**File**: `references/advanced.md`

Covers permissions, filesets, cross-group queries, delete operations, and other advanced functionality.

**Common scenarios:**
- Handle group permissions
- Access original imported files
- Perform cross-group queries
- Delete objects with callbacks

## Installation

```bash
uv pip install omero-py
```

**Requirements:**
- Python 3.7+
- Zeroc Ice 3.6+

From lamm-mit/scienceclaw, Apache-2.0.

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