2016 Summer Project Week/Segmentations Integration

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  Projects List

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  Highlights of segmentations 1

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  Highlights of segmentations 2

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  Segmentation object

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  Conversion graph for automated conversions

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  Segmentations architecture

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  Representations

Key Investigators

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

Project Description

Objective

• 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

Progress

• 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