2016 Summer Project Week/Segmentations Integration

• 

  Projects List

• 

  Segmentation object

• 

  Conversion graph for automated conversions

• 

  Segmentations architecture

• 

  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

To try: download latest Slicer nightly build, install SlicerRT extension and open the Segmentations module and Segment editor module.

Segmentation highlights

• Improved display: real-time synchronized display of segments in 2D (simultaneous contours and solid fill) and 3D; any number of segmentations can be shown
• Segments can now overlap (can be enabled/disabled for individual segments or a group of segments)
• Import/export from/to labelmaps and models
• Read/writ from/to DICOM segmentation objects (WIP) and standard VTK file formats
• Copy/mode segments between segmentations

= Segment editor highlights

• Editing is allowed on arbitrary plane orientation and at different resolution than the master volume
• Any segment (or a group of segments) can be used as mask
• Intensity threshold can be applied for all effects (only modifications to regions of a certain intensity range)
• Overwrite/overlap control is available for all effects (segments may be allowed to overlap with any, visible, or no other segments)
• Editor widget can be very easily embedded into any module's GUI
• Painting on 2D view and 3D views
• Higher-quality erosion and dilation (arbitrarily-sized spherical kernel)
• New logical operations effects: combine segments by add/remove/copy operations, invert/fill/clear segment (for example for scaffolding or mold generation for 3D printing)
• New labelmap smoothing effect: median, morphological opening, closing, Gaussian
• Customizable slice thickness for slice-based effects