Difference between revisions of "2016 Summer Project Week/Segmentations Integration"

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<gallery>
 
<gallery>
 
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
 
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
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Image:SegmentationHighlights01s.png|Highlights of segmentations 1
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Image:SegmentationHighlights02s.png|Highlights of segmentations 2
 
Image:20160526_SegmentationObject.PNG|Segmentation object
 
Image:20160526_SegmentationObject.PNG|Segmentation object
 
Image:20160526_ConversionGraph.PNG|Conversion graph for automated conversions
 
Image:20160526_ConversionGraph.PNG|Conversion graph for automated conversions
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<h3>Progress</h3>
 
<h3>Progress</h3>
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*  
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* Code moved from SlicerRT to Slicer core
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** vtkSegmentationCore to Libs/vtkAddon
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** Segmentations module (MRML, MRMLDM, Widgets, EditorEffects, Logic) to Modules/Loadable
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** SegmentEditor module to Modules/Scripted
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* [https://github.com/Slicer/Slicer/pull/542 Pull request] sent
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** Waiting for the CircleCI test to pass, then Jc's and Steve's nod
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* Outstanding issues
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** One tests fails due to usage of DICOM-RT, need to switch to a scene
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** Add subject hierarchy plugin for Segment Editor
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** Add disclaimer to Editor that there is an updated version of the module and offer a button that takes the user there
 
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'''To try: download latest Slicer nightly build, install SlicerRT extension and open the Segmentations module and Segment editor module.'''
 
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= Segmentation highlights =
 
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* Improved display: real-time synchronized display of segments in 2D (simultaneous contours and solid fill) and 3D; any number of segmentations can be shown
 
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* Segments can now overlap (can be enabled/disabled for individual segments or a group of segments)
 
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* Import/export from/to labelmaps and models
 
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* Read/writ from/to DICOM segmentation objects (WIP) and standard VTK file formats
 
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* Copy/mode segments between segmentations
 
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= Segment editor highlights
 
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* Editing is allowed on arbitrary plane orientation and at different resolution than the master volume
 
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* Any segment (or a group of segments) can be used as mask
 
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* Intensity threshold can be applied for all effects (only modifications to regions of a certain intensity range)
 
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* Overwrite/overlap control is available for all effects (segments may be allowed to overlap with any, visible, or no other segments)
 
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* Editor widget can be very easily embedded into any module's GUI
 
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* Painting on 2D view and 3D views
 
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* Higher-quality erosion and dilation (arbitrarily-sized spherical kernel)
 
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* 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)
 
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* New labelmap smoothing effect: median, morphological opening, closing, Gaussian
 
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* Customizable slice thickness for slice-based effects
 

Latest revision as of 08:33, 25 June 2016

Home < 2016 Summer Project Week < Segmentations Integration

  • Highlights of segmentations 1

  • Highlights of segmentations 2

  • 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

  • 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
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