alterlab-omero

name	alterlab-omero
description	Manages microscopy image data on an OMERO server via the OMERO Python API (BlitzGateway) — access images, retrieve datasets, read pixel data, manage ROIs and annotations, and batch-process. Use when connecting to an OMERO server, pulling microscopy images or datasets, analyzing pixels, managing ROIs/annotations, or running high-content screening and microscopy workflows. Part of the AlterLab Academic Skills suite.
license	MIT
allowed-tools	Read, Write, Edit, Bash(uv:*)
compatibility	Requires a reachable OMERO server (host, port, credentials) and the omero-py client (uv pip install omero-py) for BlitzGateway access
metadata	{"skill-author":"AlterLab","version":"1.0.0"}

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

uv pip install omero-py

Requirements (omero-py 5.22.x):

• Python 3.10+
• Zeroc Ice: omero-py pins zeroc-ice>=3.6.5,<3.7 — Ice 3.7 is NOT supported, so don't install a 3.7 wheel.
• Access to an OMERO server (host, port, credentials)

Quick Start

Basic connection pattern:

from omero.gateway import BlitzGateway

# Connect to OMERO server
conn = BlitzGateway(username, password, host=host, port=port)
connected = conn.connect()

if connected:
    # Perform operations
    for project in conn.listProjects():
        print(project.getName())

    # Always close connection
    conn.close()
else:
    print("Connection failed")

Recommended pattern with context manager:

from omero.gateway import BlitzGateway

with BlitzGateway(username, password, host=host, port=port) as conn:
    # Connection automatically managed
    for project in conn.listProjects():
        print(project.getName())
    # Automatically closed on exit

Selecting the Right Capability

For data exploration:

• Start with references/connection.md to establish connection
• Use references/data_access.md to navigate hierarchy
• Check references/metadata.md for annotation details

For image analysis:

• Use references/image_processing.md for pixel data access
• Use references/rois.md for region-based analysis
• Use references/tables.md to store results

For automation:

• Use references/scripts.md for server-side processing
• Use references/data_access.md for batch data retrieval

For advanced operations:

• Use references/advanced.md for permissions and deletion
• Check references/connection.md for cross-group queries

Common Workflows

Workflow 1: Retrieve and Analyze Images

1. Connect to OMERO server (references/connection.md)
2. Navigate to dataset (references/data_access.md)
3. Retrieve images from dataset (references/data_access.md)
4. Access pixel data as NumPy array (references/image_processing.md)
5. Perform analysis
6. Store results as table or file annotation (references/tables.md or references/metadata.md)

Workflow 2: Batch ROI Analysis

1. Connect to OMERO server
2. Retrieve images with existing ROIs (references/rois.md)
3. For each image, get ROI shapes
4. Extract pixel intensities within ROIs (references/rois.md)
5. Store measurements in OMERO table (references/tables.md)

Workflow 3: Create Analysis Script

1. Design analysis workflow
2. Use OMERO.scripts framework (references/scripts.md)
3. Access data through script parameters
4. Process images in batch
5. Generate outputs (new images, tables, files)

Error Handling

Always wrap OMERO operations in try-except blocks and ensure connections are properly closed:

from omero.gateway import BlitzGateway
import traceback

conn = None  # bind first so the finally block is safe if the constructor raises
try:
    conn = BlitzGateway(username, password, host=host, port=port)
    if not conn.connect():
        raise Exception("Connection failed")

    # Perform operations

except Exception as e:
    print(f"Error: {e}")
    traceback.print_exc()
finally:
    if conn:
        conn.close()

Additional Resources

• Official Documentation: https://omero.readthedocs.io/en/stable/developers/Python.html
• BlitzGateway API: https://omero.readthedocs.io/en/stable/developers/Python.html#omero-blitzgateway
• OMERO Model: https://omero.readthedocs.io/en/stable/developers/Model.html
• Community Forum: https://forum.image.sc/tag/omero

Notes

• OMERO uses group-based permissions (READ-ONLY, READ-ANNOTATE, READ-WRITE)
• Images in OMERO are organized hierarchically: Project > Dataset > Image
• Screening data uses: Screen > Plate > Well > WellSample > Image
• Always close connections to free server resources
• Use context managers for automatic resource management
• Pixel data is returned as NumPy arrays for analysis