OME Users' meeting, Dundee

1st June 2016

Will Moore

Presentation Outline

  • Figures
  • Design goals
  • OMERO.figure app
  • Technical
  • Demo

What's in a Figure?

Porter 2007

Manual Figure Creation

  • Export of images as TIFFs
    • Decide on which Z sections or projections
    • Choose timepoints for movies
    • Correct channels and rendering settings
    • Make notes in case you need to repeat!
  • Import into Illustrator / Photoshop / etc.
  • Cropping (same region in multiple images)
  • Align into rows / grids
  • Add scalebars, labels, ROIs

Important to preserve image quality & integrity


  • SLOW!!!
  • Need to know exactly what to export at start
  • Loss of Metadata:
    • pixel sizes
    • channel names
    • rendering settings
  • Loss of Pixel data:
    • Export as 8-bit TIFF
    • Resizing images may resample them
  • No links between Figure and original images

Figure export scripts

OMERO 4.2 (July 2010) Demo Movie

OMERO.figure Design Goals

  • Keep it fast!
  • Combine images into figure in OMERO (no export)
  • Flexible layout with shortcuts for grids
  • Each panel is a fully editable image viewer
  • Edits applied to multiple selected images
  • Exportable as PDF / TIFF

History of a "side project"

What is OMERO.figure?

  • OMERO.web app, same as OMERO.webclient
  • Download, put on $PYTHONPATH and add to web 'apps'
  • $ bin/omero config append omero.web.apps '"figure"'

Services used by OMERO.figure

OMERO.figure tech



Z-index, Time

Labels & Scalebars


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

Export as PDF / TIFF

What's next?

  • Improve ROI support:
    • Load ROIs from OMERO
    • Save ROIs back to OMERO
    • More shapes (freehand, polygon, label)
  • Improved integration with OMERO.webclient
  • Embeddable Preview
  • Labels from Tags

More information

Thank you

  • Jason Swedlow
  • OME team