OMERO Workshop ELMI

Brno, June 2019
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++

Integration

Open with... Web apps

idr.openmicroscopy.org

Today's workshop

Thank you