Tomnl at 14:53, 28 November 2015

2015-11-28T14:53:22Z

UpdateBot: Nightly -> 4.5

2015-11-12T20:18:27Z

Nightly -> 4.5

New page

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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
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Extension: [[Documentation/{{documentation/version}}/Extensions/Wasp|Wasp]]<br>

Watershed Annotation and Segmentation Plugin for 3D Slicer.

Acknowledgments:
This work was done at the Medical Research Council (MRC) Harwell, Oxfordshire. Funded by Mouse Phenotyping Informatics Infrastructure (MPI2) <br>

Author: Thomas Lawson <br>
Contact: Thomas Lawson, <email> tnl495@bham.ac.uk </email><br>
[[File:Slicer-Wasp.png|200px|thumb|left|WASP (MRC Harwell)]]

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The plugin consists of two main components

*Watershed stage: Perform a series of watershed filters on the original image
*Annotation stage: Creating a new label map out of selected components from the watershed stage

==Watershed stage==

It allows the user to perform a series of Watershed segmentations on a 3D image using the SimpleITK “Morphological Watershed” without seeds.

They can edit various parameters but importantly they can choose a range of values to use for the “watershed level”.

*When the watershed value is lower the image will be segmented into more components.
*When the watershed level is higher the image will be segmented into less components

A user can then use a range for this parameter (e.g. 1 to 2 with steps of 0.1 resulting in 20 label map results)

==Annotation stage==

The user can then select individual segmentations out of any of the watershed produced label map using fiducials.

This will create a new label map with only the components the user has chosen. The user can also choose the order of the labels as well.

A model of the label map is generated as well.


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{{documentation/{{documentation/version}}/module-section|Tutorials}}
Tutorial on how to use the WASP extension. Please be aware that a few changes have been made since the tutorial was created.

[[File:Wasp_tutorial.pptx]]

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@@ Line 12: / Line 12: @@
 Watershed Annotation and Segmentation Plugin for 3D Slicer.
-Acknowledgments:
+Acknowledgements:
 This work was done at the Medical Research Council (MRC) Harwell, Oxfordshire. Funded by Mouse Phenotyping Informatics Infrastructure (MPI2) <br>
 Author: Thomas Lawson <br>
-Contact: Thomas Lawson, <email> tnl495@bham.ac.uk </email><br>
 [[File:Slicer-Wasp.png|200px|thumb|left|WASP (MRC Harwell)]]
@@ Line 28: / Line 29: @@
 {{documentation/{{documentation/version}}/module-section|Module Description}}
-The plugin consists of two main components
+The plugin (extension) consists of two main components
 *Watershed stage: Perform a series of watershed filters on the original image
 *Annotation stage: Creating a new label map out of selected components from the watershed stage
 ==Watershed stage==
@@ Line 51: / Line 58: @@
 A model of the label map is generated as well.
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Use Cases}}
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Tutorials}}
-Tutorial on how to use the WASP extension. Please be aware that a few changes have been made since the tutorial was created.
+Tutorial on how to use the WASP extension. Please be aware that a few changes have been made since the tutorial was created. Video link does not work in presentation. See youtube link below for video.

Documentation/4.5/Extensions/Wasp - Revision history

Tomnl at 14:53, 28 November 2015

UpdateBot: Nightly -> 4.5