Difference between revisions of "2011 Summer Project Week Watersheds"
m (Text replacement - "[http://www.na-mic.org/Wiki/images/" to "[https://na-mic.org/w/images/") |
|||
| (8 intermediate revisions by 2 users not shown) | |||
| Line 2: | Line 2: | ||
<gallery> | <gallery> | ||
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]] | Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]] | ||
| − | Image:SegmentationEditorITK. | + | Image:SegmentationEditorITK.gif|Watersheds Segmentation Editor |
</gallery> | </gallery> | ||
| − | '''Interactive Watersheds Segmentation Module for Slicer for Atrial Fibrillation and HN Cancer''' | + | '''Interactive Watersheds Segmentation Module for Slicer for Atrial Fibrillation and HN Cancer''' ... and general use for segmentation of complex structures! |
==Key Investigators== | ==Key Investigators== | ||
| Line 14: | Line 14: | ||
<h3>Objective</h3> | <h3>Objective</h3> | ||
| − | + | 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. | |
| − | |||
| − | |||
</div> | </div> | ||
| Line 23: | Line 21: | ||
<h3>Approach, Plan</h3> | <h3>Approach, Plan</h3> | ||
| + | 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. | ||
<!-- What specific things you will be doing during the week: writing code? trying code on specific datasets? talking with other attendees? All of the above? --> | <!-- What specific things you will be doing during the week: writing code? trying code on specific datasets? talking with other attendees? All of the above? --> | ||
| Line 32: | Line 31: | ||
<h3>Progress</h3> | <h3>Progress</h3> | ||
| + | <!-- Fill this out before Friday's summary presentations - list what you did and how well it worked. --> | ||
| + | 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: [http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Extensions/Testing/EditorExtensionTemplate/] | ||
| + | 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 [https://na-mic.org/w/images/2/23/AHM-2011-SlicerExtensions.pdf] | ||
</div> | </div> | ||
</div> | </div> | ||
| Line 42: | Line 49: | ||
==References== | ==References== | ||
| − | + | 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 | |
<!-- Add links here to background material: where can we download the data? where is the source code repository? what papers or web sites will help someone quickly learn what the outstanding issues are? --> | <!-- Add links here to background material: where can we download the data? where is the source code repository? what papers or web sites will help someone quickly learn what the outstanding issues are? --> | ||
Latest revision as of 18:27, 10 July 2017
Home < 2011 Summer Project Week Watersheds
Watersheds Segmentation Editor
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
Objective
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.
Progress
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]
References
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
- NITRIC distribution
- Slicer Module
- Built-in:
- Extension -- commandline: NO
- Extension -- loadable: YES
