Lionheart, W. R. B. (2015)

OMERO workshop

TOPIM TECH
Chania, July 2018
Will Moore, Petr Walczysko

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 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

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.parade

OMERO.web framework is extensible

Open with... Web apps

OMERO Python scripts

Fiji

CellProfiler and R in Jupyter notebooks

Orbit

Tomorrow's workshop

Tomorrow's workshop

Please bring your laptops
We have an OMERO server prepared:
- User accounts set-up
- Sample data already imported
- Data from IDR: idr0002 and idr0021
Everything is web-based except:
- Fiji. Google Fiji OMERO
- Orbit. www.orbit.bio

Thank you