OMERO.figure ?

Tuesday Group Meeting
14th Jan 2014

Will Moore


  • Background
  • Demo
  • Tech
  • Related software
  • Next steps

Figure creation takes time

Porter 2007

No metadata, context,
links to data, etc

Porter 2007

Figures in OMERO 4.4.10...

  • ✔ Various scripts for different figures
  • ✔ Use metadata (E.g. pixel size, channels, ROIs etc)
  • ✔ Figure is linked to data

OMERO 4.4.10 Script UIs

Figures in OMERO 4.4.10

  • ✘ No flexibility
    • - fixed layouts with params
    • - requests for more (forums / Leuven / Dundee)
  • ✘ Layout code in Python is horrible!
  • ✘ Export as bitmap: Can't edit layout / text

Feature Wish List

  • Flexible Layout (drag to move)
  • Edit multiple panels at once
  • Full use of OMERO metadata
  • Export as PDF (edit in Illustrator etc)
  • Bonus: share/publish figures

Brief History

RFEs & Bugs

---- Before deploying on nightshade ----
Save to OMERO (and open saved Figures)      Done
Free-text, figure name                      Done
Open files list                             Done
Drag to select panels                       Done
Arrow keys to nudge selected panels         Done
Show actual times                           Done

---- Other feedback RFEs ----
Address interpolation issues
Landscape canvas
Set Image ID                                Done
Max Intensity Projection
Copy viewport location -> Rectangle
User-defined spacing
Attach pdf to ALL source images             Done
2nd page of pdf with image links etc
Vertical labels                             Done
Keep-alive ping from webfigure              Done
Bug: Zoom centering                         Done
Grid alignment with labels
Label edits saved with loss of focus        Done
Free label for titles/row headers etc.

---- Will's other TODOs ---
Panel Borders
Export tiffs with pdf (tiffs -> pdf)
Export to image (png/jpeg)
Send to Panel to Back / Bring to Front
Set x, y, w, h
Alignment guides on drag / resize
Rotate Image within panel
Shapes from OMERO ROIs


See Older Demo on youtube

Key Features

  • Each ‘panel’ is an independent viewer
  • Select multiple panels to co-edit
  • Full undo/redo
  • Save as orig file (json)
  • URL per file - bookmark, share, 'publish' etc
  • Script to create PDF from json
  • "Template" for figures

Tools & Tech

Data Model

    panel = {
        "name":"121-Control siRNA.ome.tiff",


Data Flow & Storage

Javascript (Backbone.Model)
POST json string
↕                         ↓
Save as Orig File
(retrieved by namespace)
Export to PDF
(attached to all images)





Macnification "Light Table"

Macnification - Light Table

Figure Zero & FigShare

Figure Zero | FigShare


Posch 2010

Next Steps...

  • Name ?
    • ✘ FigureShop
    • ✘ FigureO
    • ? OMERO.figure
    • ? OMERO.paper
    • ? OMERO.LightTable
  • Version number for data model
  • Install on nightshade
    • - Get feedback, fix bugs etc
  • PR for develop
  • Release for OMERO 5.?