OMERO.figure

Technique Tapas

5th November 2014

Will Moore

OMERO.figure

Presentation Outline

  • OME Project
  • OMERO
  • Figures
  • Demo

OME

Open Microscopy Environment

OME Project

  • Open Source Software Project
  • Largely funded by Wellcome Trust
  • Founded in 2000 by J. Swedlow, P. Sorger, I. Goldberg
  • Now based in Dundee

A typical microscopy
workflow

Interoperability

OMERO is a server with clients

OMERO.insight

OMERO in CLS

  • nightshade.openmicroscopy.org
  • Available to all in CLS (Dundee Uni login)
  • ~300 users, ~50 groups, lots of Data!
  • We're happy to help:
    • Drop-in sessions: Thursdays 10.00 - 12.00
    • "Getting Started" Workshops: 10th & 24th November

Figures

What's in a Figure?

Porter 2007

Problems

  • SLOW
  • Loss of Metadata:
    - pixel sizes
    - channel names
    - rendering settings
  • No links between Figure and original images

OMERO.figure

OMERO.figure

  • Web-based application
  • Beta release in March 2014
  • Small number of CLS users, created over 300 figures
  • Positive feedback from several external sites
  • OMERO.figure 1.0.0 released October 2014

Layout


Rendering


Z-index, Time


Rotation & Zoom


Labels & Scalebars


Finally...

  • Save to OMERO
  • Export to PDF
  • Share url
  • Links to images in OMERO

Export as PDF


More information

Thank you

  • Jason Swedlow
  • OME team
  • Beta testers
    • Katharina Schleicher
    • Amy Gerc
    • Many others here and elsewhere
  • Iain Porter for Data