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
Measurements


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

Metadata is important


OME Data Model

Many different image formats

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

 

Bio-Formats

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

http://jcb-dataviewer.rupress.org/

  • 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


www.cellimagelibrary.org

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

Stowers Original Data Repositiory (ODR)

http://odr.stowers.org

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
Viewports


WebGateway

Try it yourself...

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

www.openmicroscopy.org