Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows.
npxskills add davila7/claude-code-templates--skill omero-integrationLoading…
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.
This skill should be used when:
This skill covers eight major capability areas. Each is documented in detail in the references/ directory:
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:
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:
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:
File: references/image_processing.md
Access raw pixel data as NumPy arrays, manipulate rendering settings, create derived images, and manage physical dimensions.
Common scenarios:
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:
File: references/tables.md
Store and query structured tabular data associated with OMERO objects. Useful for analysis results, measurements, and metadata.
Common scenarios:
File: references/scripts.md
Create OMERO.scripts that run server-side for batch processing, automated workflows, and integration with OMERO clients.
Common scenarios:
File: references/advanced.md
Covers permissions, filesets, cross-group queries, delete operations, and other advanced functionality.
Common scenarios:
uv pip install omero-py
Requirements:
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
For data exploration:
references/connection.md to establish connectionreferences/data_access.md to navigate hierarchyreferences/metadata.md for annotation detailsFor image analysis:
references/image_processing.md for pixel data accessreferences/rois.md for region-based analysisreferences/tables.md to store resultsFor automation:
references/scripts.md for server-side processingreferences/data_access.md for batch data retrievalFor advanced operations:
references/advanced.md for permissions and deletionreferences/connection.md for cross-group queriesreferences/connection.md)references/data_access.md)references/data_access.md)references/image_processing.md)references/tables.md or references/metadata.md)references/rois.md)references/rois.md)references/tables.md)references/scripts.md)Always wrap OMERO operations in try-except blocks and ensure connections are properly closed:
from omero.gateway import BlitzGateway
import traceback
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()
Create or update AgentSkills. Use when designing, structuring, or packaging skills with scripts, references, and assets.
Create or update AgentSkills. Use when designing, structuring, or packaging skills with scripts, references, and assets.
Set up and use 1Password CLI (op). Use when installing the CLI, enabling desktop app integration, signing in (single or multi-account), or reading/injecting/running secrets via op.
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Create or update AgentSkills. Use when designing, structuring, or packaging skills with scripts, references, and assets.
Create or update AgentSkills. Use when designing, structuring, or packaging skills with scripts, references, and assets.
Set up and use 1Password CLI (op). Use when installing the CLI, enabling desktop app integration, signing in (single or multi-account), or reading/injecting/running secrets via op.
CLI to manage emails via IMAP/SMTP. Use `himalaya` to list, read, write, reply, forward, search, and organize emails from the terminal. Supports multiple accounts and message composition with MML (MIME Meta Language).