2012 Summer Project Week:EditorExtensions

From NAMIC Wiki
Jump to: navigation, search
Home < 2012 Summer Project Week:EditorExtensions

Key Investigators

  • Isomics: Steve Pieper
  • GI: Jim Miller
  • BWH: Yi Gao
  • GaTech: Ivan Kolasev
  • NIH: Brad Lowekamp (C)


Provide a framework for Streered Segmentation in the Editor Module.

Approach, Plan

An example implementation of GrowCut has been implemented as a test.

During project week we would like to:

  • Discuss the implementation with potential users and developers in order to generalize the approach and improve the interface.
  • Discuss other algorithms suitable for this apuproach
  • Possibly test this module on multiple CPU/GPU options to compare performance. (may be tricking since installation is not automated)
  • Identify OpenCL/GPU programming experts to help evaluate and improve the implementation.

See the repository for more information: https://github.com/pieper/SlicerCL

(Note that use of this module requires installation of PyOpenCL into the slicer python build tree - see this example script. Also note that the current implementation depends on some changes to the Editor module that only exist in a threeDEditor branch.)


  • Topic was generalized to include editor effects based on ITK and VTK
    • SimpleITK tools (Brad)
      • Marker based watersheds [1]
      • Binary watershed to split object [1]
      • DoubleThresholding
      • Current prototypes are on github.
    • Porting of CLI tools to run as steered segmenters (Yi, Ivan)
  • Productive discussions with other developers about future strategies and uses of OpenCL (pyopencl)

Delivery Mechanism

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

  1. ITK Module
  2. Slicer Module - YES
    1. Built-in - YES
    2. Extension -- commandline
    3. Extension -- loadable
  3. Other (Please specify)


[1] Beare R., Lehmann G. (2006). The watershed transform in ITK - discussion and new development. http://hdl.handle.net/1926/202