2015 Winter Project Week Segmentations Breakout

Back to Winter project week 2015 Agenda

Introduction

• Purpose: Discuss present and future of Segmentation object support
• Time: Tuesday 3:15 - 4:00
• Participants: Csaba Pinter, Andriy Fedorov, Steve Pieper, Jc, Andras Lasso (via skype) and everybody who is interested

Agenda

• Present latest plans and progress regarding Segmentation object support (Csaba) slides
  • Background, objectives
  • Design, issues, and future work
• Labelmap node class - integration to Slicer core
• Discussion on the features and implementation details
• Come to an agreement
  • Features and architecture
  • Integration
  • Tentative roadmap

Links

• Segmentations project page
• Main page for Segmentations project: https://www.assembla.com/spaces/slicerrt/wiki/Segmentation

Notes

• Important use cases
  • Huge number of segments (Bill, Brad, etc.)
    • Issue: efficient storage and processing
    • Fire segment-specific events from segmentation node (with segment ID)
    • Load subsets of data based on spatial constraints in an on-demand fashion
      • Need to support geometrical decision functions by default (contain, overlap, etc.), maybe even on the CLI level
    • Storage of at the moment non-displayed segments in a compressed way?
  • Tractography (Nicole): ask Alex or Lauren
  • SceneViews
    • They are defined by display node on/off states basically
• Relevant existing implementations / interfaces
  • Similar notions in ITK as the proposed labelmap types: LabelImage ~ LabelMap, LabelMap ~ RLE (ImageStencil)
  • VTK6 color table additions
  • vtkCompositeDataset, vtkMultiBlockDataset: both composite objects already defined in VTK
• Design alternatives
  • vtkSegment subclass of vtkDataObject or vtkCompositeDataset or vtkMultiBlockDataset
  • Explicit ID for segments: need to uniquely identify segments
    • Segmentation vector index not good because of its non-unique nature (remove, etc.) (Jim)
    • Tags are one option but not too explicit
    • Need to unambiguosly link segment to color table
  • Color, opacity stored elsewhere than the segment
    • Color information is needed to be stored at at least two locations (segment, color table of merged labelmap, ?)
    • Display node? Segment could still store a "default" color (Andras)
  • Volume reference in segmentation could be FrameOfReferenceUID (transforms would need to support that anyway; ensuring equality is the most important so UID is just as good for this as matrices or something else)
  • Extending CLI to be able to tell the desired representation will be necessary (Jim)
    • Similar to existing ContourSelectorWidget?
• Encoding antology (hierarchies, colors, groupings) is important (Nicole, Andrey)
  • Tags can be used, or something more explicit, need ideas
• Other ideas
  • Compute/show estimated data loss of conversion