Imaging workflows in OMERO

GBI course

July 2023

OME Team

Outline

  • What is OME?
  • What is OMERO?
  • From data acquisition to publication
  • 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

Integration

Import: Desktop Application

Read the import guide or watch the import video

Import: Advanced options

Read the import guides

Data management

Groups & Users: cooperation, sharing

  • Users are organized in groups
  • Users in one group can share & cooperate

Read-annotate setup example

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

    • Groups & Users: switch displayed user

    • Click on group name
    • Select group and user to display

    Annotations

    • Tags
    • Key-Value Pairs
    • Ratings
    • File Attachments
      • Attach any file to an object in OMERO

    Annotations - filtering

    • By Tags AND Key-Value Pairs
    • By Rating
    • ...

    Annotations

    Open with... Web apps

    Viewing - OMERO.iviewer

    • View multi-z and multi-t images
    • Draw and Save ROIs
    • Simple image analysis

    OMERO.iviewer

    Analysis

    OMERO.figure

    Publication in OMERO

    Retrieve workshop content

    What should OME user know ?

    Support on image.sc - community

    OMERO setups - community

    Thank you