2011 Summer Project Week Watersheds

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Interactive Watersheds Segmentation Module for Slicer for Atrial Fibrillation and HN Cancer ... and general use for segmentation of complex structures!

Key Investigators

  • University of Utah: Josh Cates, Ross Whitaker


The watersheds algorithm produces a hierarchical set of segmented objects. For some applications, an interface exploring this hierarchical set has proven useful for assembling segmentations of complex anatomical structures. The goal of this project is to re-engineer the old ITKApps Watershed Segmentation Editor in Slicer. The resulting tool will allow a user to interactively assemble 3D segmentations of image data using the output of the itk::WatershedImageFilter. During Project Week, we anticipate finalizing the watershed tool design, taking advantage of the available Slicer engineering expertise to resolve any remaining technical challenges.

Approach, Plan

Work on the Slicer version of the Watershed Segmenter is currently underway. Project week activities include planning for integration into Slicer 4. Some additional Slicer infrastructure will be required to provide the level of interaction needed for this tool.


The design is not completely finalized, but we have made good progress towards that goal. Tentatively, we plan to python wrapping of the Watersheds logic and custom VTK classes, and integration through the new EditorExtension module type. Some experimentation with the new EditorExtensionTemplate will be required in order to finalize our design.

Example: create editor extension with ModuleWizard:

./Scripts/ModuleWizard.py --template ./Extensions/Testing/EditorExtensionTemplate --target ../MyEditorTool MyEditorTool

Makes a new "MyEditorTool" based on the code here: [1]

Add it to slicer by adding the path to "../MyEditorTool" to the View->Application Settings->Module Settings list.

Extension can also be registered with slicer nightly builds by constructing an s4ext file and giving it to slicer developers [see instructions in tutorial [2]


J. Cates, R. Whitaker, G. Jones, Case Study: An Evaluation of User-Assisted Hierarchical Watershed Segmentation, Medical Image Analysis, V.9, No.6, Dec. 2005

Delivery Mechanism

This work will be delivered to the NAMIC Kit as a

  1. NITRIC distribution
  2. Slicer Module
    1. Built-in:
    2. Extension -- commandline: NO
    3. Extension -- loadable: YES