2012 Summer Project Week:EditorExtensions

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  Projects List

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  OpenCL Implementation of GrowCut running in the Editor Module. (See demo video)

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  Input into the ITK's morphological watershed from markers.

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  Resulting segmentation by morphological watershed from markers.

Key Investigators

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

Objective

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.)

Progress

• 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)

References

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