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Seg3D Design


Diagram describing dataflow in the app.
  • 3D analog to Photoshop
  • Work with multiple volumes simultaneously
  • Volumes are organized in Layers
  • Layers may be visualized separately or as blended overlays
  • Each layer is assigned its own color map
  • Layers may be piped to Filters (ITK or other)
  • Filter output is piped back into a new Layer
  • Any number of Label Layers may be created
  • Label Layers are bit masks that represent a hierarchy of binary segmentations
  • Segmentations are either produced manually by slice-by-slice painting, or produced using Filter operations.
  • File IO via ITK (Analyze, DICOM, Nrrd, MetaImage, tiff, jpeg, png, and more)
  • Users may save work in sessions and reload

Hand Contouring / Painting

  • Each label represented as 1-bit in memory
  • Respects logical operations (AND, OR, NOT, etc)
  • Heierarchical label management
  • Ontologies may be enforced by mapping to these logical operations

Image Processing and Segmentation

  • ITK Filters, Teem Filters, & custom filters
  • Focus on integration of filters versus simple wrapping
    • Integrated with the manual segmentation interface
    • Real-time visualization of automated processing
    • Minimize number of parameters that need to be exposed to user


  • Customizable 2D layouts (specified by XML)
  • 3D slice views with isosurfacing
  • Real-time volume rendering