I2K OMERO Workshop

Heidelberg, December 2018
Jean-Marie Burel

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 > 150 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

OMERO.web framework is extensible

Different clients for different jobs

OMERO clients

OMERO.insight
OMERO.webclient
- Browsing images
- Viewing metadata
- Data management
- Searching
OMERO web apps
- OMERO.iviewer
- OMERO.figure
- OMERO.parade
- ...
...

OMERO.iviewer

OMERO.figure

OMERO.parade

Open with... Web apps

Today's workshop

Today's workshop

Data organisation

Francis-data ≠ Ada-data
Francis-data similar to Ada-data

Each others data – read-annotate setup

Thank you