MITK Segmentation Redesign

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Since the MITK Workbench Release 2013.06 the whole segmentation group has been working on an extensive redesign of our segmentation plugin. With the MITK 2013.09 release we are proud to announce that this project is completed! Here is a list of the major changes and new features:

Segmentation 2D and 3D Tools

We cleaned up the segmentation view and removed unused GUI elements. We also extended its functionality with new 2D and 3D segmentation tools

UI improvements

  • The segmentation view contains now two tabs which allows to switch between 2D and 3D tools
  • New tool icons replaced the antiquated old ones
  • A customized mouse cursor is now visible beneath your application cursor while a 2D tool is active
  • A slim view option allows you to hide the tool button names
  • Simplified the interpolation widget

New segmentation tools

  • We extended and improved the 2D tool set:
    • There is now a 2D Fast Marching Tool
    • Better interaction and look and feel for the Live Wire Tool
  • New 3D tool area contains many tools which were formerly located in the Datamanager's context menu:
    • Simple threshold - Segment your image using a single threshold value
    • Upper/Lower Threshold - Segment your image using an upper and lower threshold
    • Fast Marching 3D tool
    • Watershed Segmentation
    • Otsu Segmentation
  • All 3D tools have a dedicated Tool GUI area for setting specific parameters

Segmentation Utilities

Often a segmentation needs some post processing. Lets say you just performed a threshold segmentation and the result contains some "holes". In this case you would like to fill these holes automatically. Or you want to combine two different segmentations within one single segmentation image. For these cases MITK now comes with an extensive set of segmentation utilities in a separate view:

  • Boolean operations:
    • Calculate the difference between two segmentations
    • Calculate the intersection of two segmentations
    • Calculate the union of the segmentations
  • Image masking:
    • You have finished a segmentation and what now? E.g. you can mask the patient image with an existing segmentation or a surface and then proceed with e.g. vessel segmentation/visualization
  • Morphological operations:
    • Postprocess your segmentation by
      • Dilatation/Erosion
      • Opening/Closing
      • Fill Holes
  • Surface To Image:
    • Convert a surface into a segmentation and use all the available segmentation tools to modify the segmentation!


  • The toolmanager can now be accessed using CppMicroServices
  • Switch to mitkContourModel:
    • All 2D tools are now using the new mitkContourModel
    • The old mitkContour is declared as deprecated and will be removed during the next year
  • 3D interpolation can now also be used with planar figures
  • New SegmentationUI module which contains all the segmentation widgets