2016 Summer Project Week/Segmentations Integration

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Home < 2016 Summer Project Week < Segmentations Integration

Key Investigators

  • Csaba Pinter
  • Andras Lasso
  • Steve Pieper
  • Jean-Christophe Fillion-Robin (to be consulted remotely)

Project Description


  • Integration of the Segmentation infrastructure into Slicer core
  • The infrastructure contains the following components:
    • SegmentationCore: Pure VTK implementation of the segmentation object, oriented VTK image data and utilities, and the automated conversion mechanism
    • Segmentation MRML: Segmentation MRML node, display node, storage node, displayable managers
    • Segmentations module: Slicer module for handling segmentation nodes, various re-usable widgets, and subject hierarchy plugins
    • Segment Editor: Slicer module for editing segmentation nodes directly. Similar to Editor, but has a C++ core, and extended functionality that makes use of the advanced Segmentations features
    • Segment Morphology: Slicer module for performing expand/shrink and logical operations (union, intersection, subtraction) on segments. Its logic can be used in Segment Editor effects
    • Segment Registration (?): Distance map based registration of segmentations (from SlicerProstate::DistanceMapBasedRegistration, integration TBD)
  • Presentation slides explaining the motivation, features, and details of the infrastructure

Approach, Plan

  • Move classes into Slicer core
    • Convert to Slicer core coding conventions (curly brackets in line with the contained block)
    • vtkSegmentationCore -> vtkAddon?
    • Segmentations/MRML -> Libs/MRML/Core
    • Segmentations/MRMLDM -> Libs/MRML/DisplayableManager
    • Segmentations/Widgets -> MRML/Widgets?
    • Segmentations/EditorEffects -> ?
    • Segmentations -> Modules/Loadable
    • SegmentEditor -> Modules/Scripted
  • Discuss possible integration vtkOrientedImageData to VTK core


  • Code moved from SlicerRT to Slicer core
    • vtkSegmentationCore to Libs/vtkAddon
    • Segmentations module (MRML, MRMLDM, Widgets, EditorEffects, Logic) to Modules/Loadable
    • SegmentEditor module to Modules/Scripted
  • Pull request sent
    • Waiting for the CircleCI test to pass, then Jc's and Steve's nod
  • Outstanding issues
    • One tests fails due to usage of DICOM-RT, need to switch to a scene
    • Add subject hierarchy plugin for Segment Editor
    • Add disclaimer to Editor that there is an updated version of the module and offer a button that takes the user there