ROIs in OMERO.web

Tuesday Group Meeting
18th August, 2015

Will Moore

Talk outline

  • Current state of ROI support
  • Use cases:
    • ROI Annotations
    • Large ROI counts
    • Editing of ROIs in webclient
    • Adding ROIs to OMERO.figure
    • Others? (3D ROIS ?!)
  • Current work: Shape Editor
  • Next: Shape Editor | OMERO.figure | webclient

Current state of ROI support

  • Show ROI count in general pane
  • In image viewer we load all ROIs as json on "Show ROIs"
  • All Shapes shown in table (and ROIs if >1 shape)
  • Shapes are shown on image for currently selected plane
  • Click shape in table -> shown in viewer
  • NO creating or editing of ROIs or Shapes
  • Filter Shapes & Load external ROIs (CRS4)

Use Case: ROI Annotations

  • Teaching applications: CRS4 & Virtual Microscope
  • Need different categories (namespaces?) of Shapes
  • Annotations have name, description? etc?
  • Linked to external resources / terms E.g. Ontology
  • Filter by type, owner, etc?
  • First question: use Tags, Map Annotations or something else?

Use Case: Large ROI counts

  • Loading ALL ROIs & shapes for image fails if there are too many
  • Could load shapes for current plane only (for multi-plane images)
  • For even larger numbers, might need to load by region or
    render shapes on tiles
  • Editing ROIS & shapes is harder, but probably not needed?

Use Case: Create shapes in web

  • Need to support same use-cases as in Insight
  • But, room for improvement of usability
  • No restriction on 1 shape per plane per ROI
  • Create new shapes with chosen Color, Line thickness etc
  • While creating shapes, allow tweaking of last-added shape
  • No support for 'smooth' shapes & Arrows
  • ImageJ can serve as useful example of what users want

Use Case: Adding shapes to OMERO.figure...

...Adding shapes to OMERO.figure

  • Don't need "ROI" support - just need "shapes"
  • Shapes on figures tend to have NO fill (outline only)
  • Want to add shapes from OMERO onto figures, AND draw shapes in figure
  • 2 Use cases:
    • 'Page' shapes - Drawn across whole page
    • 'Panel' shapes - Attached to image panel
  • Copy and paste a 'crop' region -> Rectangle and vice versa
  • Need to be able to export shapes to PDF & TIFF figures
  • Image panel rotation will be tricky (not supported)?

Getting Started: Editing shapes

  • Couldn't find an existing shape editing library with desired functionality. E.g:
  • Decided to try creating a toolkit using Raphael.js (as in webclient ROIs and OMERO.figure panel selection)...

Shape Editor

  • In order to support shapes in OMERO.figure (and webclient?), started working on shape-editor-js
  • Handles shapes only (No ROIs)
  • Currently only supports Line, Arrow, Rectangle, Ellipse.
    • Poly-lines etc to come later
  • No shape fill colors (transparent)
  • Followed ImageJ behaviour for creation & tweaking of shapes

Next Tasks: OMERO.figure

  • Integrate Shape Editor into OMERO.figure (Done)
  • Export of shapes on PDF and TIFF figures
  • Import of shapes from OMERO
  • Copy & Paste of shapes / crop-regions etc

Next Tasks: Shape Editor

  • Fix model - E.g. 'lineWidth' -> 'strokeWidth'
  • Polygon & Freehand shapes
  • Any need for Polyline or other shapes?
  • Dashed lines
  • Support for rotated images?!?

Next Tasks: ROI editing in webclient?

Saving ROIS/shapes to OMERO

  • Can save 'Arrow' to OMERO with line.markerStart = 'Arrow' but not supported in Insight
  • Can save a 'Polygon' but can't distinguish it from 'Freehand' shape
  • Use shape.strokeDashArray for dashed shapes. Insight support?