Difference between revisions of "2012 Summer Project Week:EditorExtensions"
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Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]] | Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]] | ||
Image:Slicer-GrowCutCL.png|OpenCL Implementation of GrowCut running in the Editor Module. (See [http://www.youtube.com/watch?v=dfu2gugHLHs&feature=plcp demo video]) | Image:Slicer-GrowCutCL.png|OpenCL Implementation of GrowCut running in the Editor Module. (See [http://www.youtube.com/watch?v=dfu2gugHLHs&feature=plcp demo video]) | ||
| + | IMAGE:Slicer-WatershedMarkers.png|Input into the ITK's morphological watershed from markers. | ||
| + | Image:Slicer-WatershedFromMarkers.png|Resulting segmentation by morphological watershed from markers. | ||
</gallery> | </gallery> | ||
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* Isomics: Steve Pieper | * Isomics: Steve Pieper | ||
* GI: Jim Miller | * GI: Jim Miller | ||
| + | * BWH: Yi Gao | ||
| + | * GaTech: Ivan Kolasev | ||
| + | * NIH: Brad Lowekamp (C) | ||
<div style="margin: 20px;"> | <div style="margin: 20px;"> | ||
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During project week we would like to: | 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 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) | * 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. | * Identify OpenCL/GPU programming experts to help evaluate and improve the implementation. | ||
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See the repository for more information: https://github.com/pieper/SlicerCL | 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 [https://github.com/pieper/SlicerCL/blob/master/Experiments/slicercl.sh this example script]) | + | (Note that use of this module requires installation of PyOpenCL into the slicer python build tree - see [https://github.com/pieper/SlicerCL/blob/master/Experiments/slicercl.sh this example script]. Also note that the current implementation depends on some changes to the Editor module that only exist in [https://github.com/pieper/Slicer/tree/threeDEditor a threeDEditor branch].) |
</div> | </div> | ||
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<h3>Progress</h3> | <h3>Progress</h3> | ||
| − | + | * 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 [https://github.com/blowekamp/Slicer-IASEM 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) | ||
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==References== | ==References== | ||
| + | |||
| + | [1] Beare R., Lehmann G. (2006). The watershed transform in ITK - discussion and new development. http://hdl.handle.net/1926/202 | ||
</div> | </div> | ||
Latest revision as of 13:51, 22 June 2012
Home < 2012 Summer Project Week:EditorExtensions
OpenCL Implementation of GrowCut running in the Editor Module. (See demo video)
Input into the ITK's morphological watershed from markers.
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)
- SimpleITK tools (Brad)
- 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)
- ITK Module
- Slicer Module - YES
- Built-in - YES
- Extension -- commandline
- Extension -- loadable
- 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
