OMERO.figure ?

Tuesday Group Meeting
14th Jan 2014

Will Moore

OMERO.figure

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

Figure creation takes time

No metadata, context,
links to data, etc

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

• ✿ github.com/will-moore/weblabs Initial Commit - May 2013
• ✿ github.com/will-moore/webfigure New Repo - Sept 2013
• ✿ PR #1690 for dev_4_4 (TEMP)
• ✿ Tested on howe by several users - positive feedback ☺
• ✿ Many issues & new features addressed...

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
                    

Demo...

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

• backbone.js (MVC - also angular.js, ember.js etc)
  • model
  • events
  • view
  • templating
  • router
• Bootstrap - css, icons, js
• Mousetrap - Keyboard bindings
• Raphael - Drag handles etc
• Reportlab - PDF generation

Data Model

    panel = {
        "imageId":205,
        "name":"121-Control siRNA.ome.tiff",
        "orig_width":163,
        "orig_height":194,
        "sizeT":23,
        "sizeZ":6,
        "theZ":2,
        "theT":17,
        "pixel_size":0.3312,
        "zoom":188,
        "dx":9.15,
        "dy":12.7,
        "width":102.4,
        "height":102.5,
        "y":641.1,
        "x":191.9
        "labels":[{"time":"hrs:mins","size":"14","position":"top","color":"000000"}],
        "channels":[{"color":"FFFFFF","active":true,"window":{"max":743,"min":87,"end":345,"start":119},"emissionWave":528,"label":"528"}],
        "deltaT":[5744,6047,6348,6649,6951,7254,7556,7858,8162,8464,8764,9065,9368,9671,9973,10274,10577,10879,11178,11483,11786,12090,12387],
        "selected":false,
        "datasetId":"",
        "datasetName":"Multiple",
    }

                    

Data Flow & Storage
 

FigureJ

Scientifig

Macnification "Light Table"

Figure Zero & FigShare

JCB

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.?