OMERO Workshop Day 1

Oxford, May 2019
Dominik Lindner, 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 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++

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

Open with... Web apps

idr.openmicroscopy.org

Data organisation

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

Each other's data – read-annotate setup

Thank you