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Timothy Kassis
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scientific-integrations/omero-integration/SKILL.md
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scientific-integrations/omero-integration/SKILL.md
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name: omero-integration
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description: Toolkit for interacting with OMERO microscopy data management systems using Python. Use this skill when working with microscopy images stored in OMERO servers, retrieving datasets and screening data, analyzing pixel data from scientific images, creating or managing annotations and metadata, working with regions of interest (ROIs), batch processing images, creating OMERO scripts, or integrating OMERO data into computational workflows. Essential for researchers working with high-content screening data, multi-dimensional microscopy datasets, or collaborative image repositories.
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---
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# OMERO Integration
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## Overview
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OMERO is an open-source client-server platform for managing, visualizing, and analyzing microscopy images and associated metadata. This skill provides comprehensive guidance for using OMERO's Python API (omero-py) to programmatically interact with OMERO servers for data retrieval, analysis, and management.
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## Core Capabilities
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This skill covers eight major capability areas. Each is documented in detail in the references/ directory:
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### 1. Connection & Session Management
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**File**: `references/connection.md`
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Establish secure connections to OMERO servers, manage sessions, handle authentication, and work with group contexts. Use this for initial setup and connection patterns.
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**Common scenarios:**
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- Connect to OMERO server with credentials
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- Use existing session IDs
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- Switch between group contexts
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- Manage connection lifecycle with context managers
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### 2. Data Access & Retrieval
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**File**: `references/data_access.md`
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Navigate OMERO's hierarchical data structure (Projects → Datasets → Images) and screening data (Screens → Plates → Wells). Retrieve objects, query by attributes, and access metadata.
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**Common scenarios:**
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- List all projects and datasets for a user
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- Retrieve images by ID or dataset
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- Access screening plate data
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- Query objects with filters
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### 3. Metadata & Annotations
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**File**: `references/metadata.md`
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Create and manage annotations including tags, key-value pairs, file attachments, and comments. Link annotations to images, datasets, or other objects.
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**Common scenarios:**
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- Add tags to images
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- Attach analysis results as files
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- Create custom key-value metadata
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- Query annotations by namespace
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### 4. Image Processing & Rendering
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**File**: `references/image_processing.md`
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Access raw pixel data as NumPy arrays, manipulate rendering settings, create derived images, and manage physical dimensions.
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**Common scenarios:**
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- Extract pixel data for computational analysis
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- Generate thumbnail images
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- Create maximum intensity projections
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- Modify channel rendering settings
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### 5. Regions of Interest (ROIs)
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**File**: `references/rois.md`
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Create, retrieve, and analyze ROIs with various shapes (rectangles, ellipses, polygons, masks, points, lines). Extract intensity statistics from ROI regions.
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**Common scenarios:**
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- Draw rectangular ROIs on images
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- Create polygon masks for segmentation
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- Analyze pixel intensities within ROIs
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- Export ROI coordinates
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### 6. OMERO Tables
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**File**: `references/tables.md`
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Store and query structured tabular data associated with OMERO objects. Useful for analysis results, measurements, and metadata.
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**Common scenarios:**
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- Store quantitative measurements for images
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- Create tables with multiple column types
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- Query table data with conditions
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- Link tables to specific images or datasets
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### 7. Scripts & Batch Operations
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**File**: `references/scripts.md`
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Create OMERO.scripts that run server-side for batch processing, automated workflows, and integration with OMERO clients.
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**Common scenarios:**
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- Process multiple images in batch
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- Create automated analysis pipelines
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- Generate summary statistics across datasets
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- Export data in custom formats
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### 8. Advanced Features
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**File**: `references/advanced.md`
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Covers permissions, filesets, cross-group queries, delete operations, and other advanced functionality.
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**Common scenarios:**
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- Handle group permissions
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- Access original imported files
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- Perform cross-group queries
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- Delete objects with callbacks
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## Installation
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Install the OMERO Python bindings using pip or conda:
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```bash
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# Using pip
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pip install omero-py
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# Using conda
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conda install -c conda-forge omero-py
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```
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**Requirements:**
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- Python 3.7+
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- Zeroc Ice 3.6+
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- Access to an OMERO server (host, port, credentials)
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**Best practice:** Use a Python virtual environment (venv, conda, or mamba) to isolate dependencies.
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## Quick Start
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Basic connection pattern:
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```python
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from omero.gateway import BlitzGateway
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# Connect to OMERO server
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conn = BlitzGateway(username, password, host=host, port=port)
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connected = conn.connect()
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if connected:
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# Perform operations
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for project in conn.listProjects():
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print(project.getName())
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# Always close connection
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conn.close()
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else:
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print("Connection failed")
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```
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**Recommended pattern with context manager:**
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```python
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from omero.gateway import BlitzGateway
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with BlitzGateway(username, password, host=host, port=port) as conn:
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# Connection automatically managed
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for project in conn.listProjects():
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print(project.getName())
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# Automatically closed on exit
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```
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## Selecting the Right Capability
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**For data exploration:**
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- Start with `references/connection.md` to establish connection
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- Use `references/data_access.md` to navigate hierarchy
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- Check `references/metadata.md` for annotation details
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**For image analysis:**
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- Use `references/image_processing.md` for pixel data access
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- Use `references/rois.md` for region-based analysis
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- Use `references/tables.md` to store results
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**For automation:**
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- Use `references/scripts.md` for server-side processing
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- Use `references/data_access.md` for batch data retrieval
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**For advanced operations:**
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- Use `references/advanced.md` for permissions and deletion
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- Check `references/connection.md` for cross-group queries
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## Common Workflows
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### Workflow 1: Retrieve and Analyze Images
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1. Connect to OMERO server (`references/connection.md`)
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2. Navigate to dataset (`references/data_access.md`)
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3. Retrieve images from dataset (`references/data_access.md`)
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4. Access pixel data as NumPy array (`references/image_processing.md`)
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5. Perform analysis
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6. Store results as table or file annotation (`references/tables.md` or `references/metadata.md`)
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### Workflow 2: Batch ROI Analysis
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1. Connect to OMERO server
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2. Retrieve images with existing ROIs (`references/rois.md`)
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3. For each image, get ROI shapes
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4. Extract pixel intensities within ROIs (`references/rois.md`)
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5. Store measurements in OMERO table (`references/tables.md`)
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### Workflow 3: Create Analysis Script
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1. Design analysis workflow
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2. Use OMERO.scripts framework (`references/scripts.md`)
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3. Access data through script parameters
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4. Process images in batch
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5. Generate outputs (new images, tables, files)
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## Error Handling
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Always wrap OMERO operations in try-except blocks and ensure connections are properly closed:
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```python
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from omero.gateway import BlitzGateway
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import traceback
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try:
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conn = BlitzGateway(username, password, host=host, port=port)
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if not conn.connect():
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raise Exception("Connection failed")
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# Perform operations
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except Exception as e:
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print(f"Error: {e}")
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traceback.print_exc()
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finally:
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if conn:
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conn.close()
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```
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## Additional Resources
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- **Official Documentation**: https://omero.readthedocs.io/en/stable/developers/Python.html
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- **BlitzGateway API**: https://omero.readthedocs.io/en/stable/developers/Python.html#omero-blitzgateway
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- **OMERO Model**: https://omero.readthedocs.io/en/stable/developers/Model.html
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- **Community Forum**: https://forum.image.sc/tag/omero
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## Notes
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- OMERO uses group-based permissions (READ-ONLY, READ-ANNOTATE, READ-WRITE)
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- Images in OMERO are organized hierarchically: Project > Dataset > Image
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- Screening data uses: Screen > Plate > Well > WellSample > Image
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- Always close connections to free server resources
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- Use context managers for automatic resource management
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- Pixel data is returned as NumPy arrays for analysis
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