Modules:EM-Segmenter-Documentation
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Module Name
MyModule
General Information
Module Type & Category
Type: Interactive (Template Builder) and CLI (EMSegment Simple)
Category: Segmentation
Authors, Collaborators & Contact
- Kilian Pohl: Harvard
- Brad Davis: Kitware, Inc.
- Sebastien Barre: Kitware, Inc.
- Yumin Yuan: Kitware, Inc.
- Polina Golland: MIT
- Contact: Brad Davis, brad.davis@kitware.com
Module Description
The goal of this project is the creation of interfaces in Slicer3 that integrate the EMSegment algorithm (Pohl et al.), an automatic segmentation algorithm for medical images that previously existed in Slicer 2. As in Slicer 2, the user is able to adjust the algorithm to a variety of imaging protocols as well as anatomical structures and run the segmenter on large data sets. Three views or interfaces to the algorithm are available: a wizard-based module for building and editing parameter sets, a simplified "one-click" GUI module, and a command line interface for script and batch processing.
As of January, 2008, working versions of all EMSegment interfaces are complete and have been checked into the Slicer3 SVN repository. Recent development effort has focused on providing simplified interfaces to the algorithm, reducing assumptions about input data, testing, and validation. The module was demonstrated at the NAMIC All-Hands meetings in Salt Lake City (2007 and 2008). A tutorial has been developed and is available from this page.
Usage
Examples, Use Cases & Tutorials
- Note use cases for which this module is especially appropriate, and/or link to examples.
- Link to examples of the module's use
- Link to any existing tutorials
Quick Tour of Features and Use
List all the panels in your interface, their features, what they mean, and how to use them. For instance:
- Input panel:
- Parameters panel:
- Output panel:
- Viewing panel:
Development
Dependencies
Slicer base modules.
Known bugs
Follow this link to the Slicer3 bug tracker.
Usability issues
Follow this link to the Slicer3 bug tracker. Please select the usability issue category when browsing or contributing.
Source code & documentation
Customize following links for your module.
More Information
For more information about the EM Segmenter project in Slicer3 see the old EMSegment Wiki page here
Acknowledgment
Funding for the EMSegmenter module was provided by NAMIC.
References
Kilian TMI Paper
