Sharing scientific knowledge
on the web with the
Open Microscopy Environment (OME)

MozFest 2013

Will Moore @will_j_moore
Aleksandra Tarkowska
Petr Walczysko

University of Dundee

Biological Image Data

Images: Wakana 2013, Horn 2013, Hagedorn 2013

Images are Quantitative

Images: Nunes Bastos 2013

Images are Multi-dimensional

Image: Civelekoglu-Scholey 2010

Images are Big

Data from Paul Felts, University of Dundee

Large numbers of Images per Dataset

Images: Rohn 2013

Many different image formats

  • Interoperability is a problem
  • Bio-Formats Java library reads over 130 formats...
  • ...and growing (send us the data!)



What do we want to do with
the images?

  • Exchange between formats / packages
  • Remote Access
  • View Images & Metadata
  • Share & Collaborate
  • Publish

OMERO: Java Server with open API

OMERO API OMERO documentation

OMERO.web Framework

OMERO.web Framework OMERO.web documentation

OMERO webclient:
manage your images

webclient demo login

OMERO Public Image Repositories

  • JCB Dataviewer (Publishing)
  • ASCB 'The Cell' Image Library (Educational)
  • Stowers Original Data Repository (Institution)
  • EM Data Bank (Reference Library)

Glencoe Software

Journal of Cell Biology

  • JCB Dataviewer Launched in 2008
  • Allows access to original data for reviewers and readers
  • Over 400,000 multi-dimensional images available
  • Over 5 TB of data

JCB Data-viewer: Raw data access

Posch et al 2010: Images | Article

Rendering Settings (min/max)

JCB Data-viewer: Screening Data

Example Data | Editorial

  • OMERO supports HCS data 'out of the box'
  • Graphs of 'hits' are custom additions for JCB
  • Browse via Screen / Plate / Well -> Results
    OR via Results -> Image

JCB Data-viewer: 'Big' Image

'Big Fish' - EM of whole zebra-fish.
281 gigapixels (1,843,206 x 380,932), 500 GB
Image | Editorial

'The Cell' ASCB Image Library

Metadata include annotations of Cell Type, Cell Component etc. E.g. Search for 'Growth Cone'

Stowers Original Data Repositiory (ODR)

Electron Microscopy Data Bank (EMDB)

EMDB Entries E.g. Entry EMD-1906

Protein 3D volumes (electron density) determined by EM

OMERO customisation

  • Extend Blitz Gateway (Python)
  • Create Django App (Python, html)
  • Embed Images or Viewer in existing pages (html, js)
OMERO.web Framework

WebGateway Rendering and


Try it yourself...

See the Pen 3D image stack by Will Moore (@will-moore) on CodePen