OMERO workshop

Canada BioImaging

July 2023

OME Team

Outline

What is OME?
What is OMERO?
Workshop overview

OME: Interoperability

OMERO is a server with clients

Image Data - Read by Bio-Formats

Support for reading > 160 image formats
Read pixel data and metadata
Includes 5D images, HCS data, Tiled WSI images
Domains: biological, medical, general (tiff, png, etc.)

Metadata

Stored in a Relational Database
Acquisition Metadata
User-added Annotations
ROIs / Segmentations

Search

Text and Annotations indexed with Lucene
Allows keyword searches

OMERO.tables

HDF5 tables for analysis results
Flexible columns

OMERO API

Python | Java | Matlab | R | C++

Integration

Open with... Web apps

idr.openmicroscopy.org

OMERO guide

Workshop content is in OMERO guides

https://omero-guides.readthedocs.io

What should OME user know ?

Routine training and user inductions

Attracting users to OMERO

See the OMERO guide for facility managers
Especially see getting users started guide
See the OMERO guide for users
Videos
See Train-the-trainer presentation

Support on image.sc - community

OMERO setups - community

Implementation of OMERO at the Münster Imaging Network, setup from Zobel et al. 2022:

Read-annotate setup example

Group Owner (PI) can always see all data in every setup

Import: Desktop Application

Read the import guide or watch the import video

Import: Advanced options

Read the import guides

Thank you