Documentation/4.4/Extensions/Wasp - Revision history

Tomnl at 15:05, 28 November 2015

2015-11-28T15:05:33Z

Tomnl at 14:47, 28 November 2015

2015-11-28T14:47:27Z

Tomnl at 09:30, 15 October 2015

2015-10-15T09:30:15Z

Tomnl at 09:29, 15 October 2015

2015-10-15T09:29:38Z

Tomnl at 10:58, 14 October 2015

2015-10-14T10:58:57Z

Tomnl at 10:47, 14 October 2015

2015-10-14T10:47:02Z

Tomnl at 08:11, 30 June 2015

2015-06-30T08:11:29Z

Tomnl at 14:26, 24 January 2015

2015-01-24T14:26:48Z

UpdateBot: Nightly -> 4.4

2014-12-24T19:58:56Z

Nightly -> 4.4

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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{{documentation/{{documentation/version}}/module-section|Module Description}}

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.


{{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.

[[File:Wasp_tutorial.pptx]]

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[[Category:Documentation/{{documentation/version}}/Modules/Segmentation]]

@@ Line 16: / Line 16: @@
 Author: Thomas Lawson <br>
-Contact: Thomas Lawson, <email> tnl495@bham.ac.uk </email><br>
+Contact: Thomas Lawson, <email> thomas.nigel.lawson@gmail.com </email><br>
 [[File:Slicer-Wasp.png|200px|thumb|left|WASP (MRC Harwell)]]
@@ Line 33: / Line 33: @@
 *Annotation stage: Creating a new label map out of selected components from the watershed stage
-The primary use cas of the tool is to perform multiple watershed segmentations (watershed stage) of an image and then use fiducials to pick out the good segmentations (annotation stage).
+The primary use case of the tool is to perform multiple watershed segmentations (watershed stage) of an image and then use fiducials to pick out the good segmentations (annotation stage).
 For code of the plugin see: https://github.com/Tomnl/Slicer-Wasp
+This extension has been tested and works with 3D Slicer 4.5. If you are using the 3D slicer 4.4 version you might have to follow the instructions detailed on the github readme page (https://github.com/Tomnl/Slicer-Wasp)

@@ Line 38: / Line 38: @@
-IMPORTANT: The current version of WASP has been tested with the nightly build in july 2015. See below link for the nightly build installer. To get the plugin working with
+IMPORTANT: The current version of WASP has been tested with the nightly build in july 2015. See below link for the nightly build installer. To get WASP working with
-the stable build read the instructions in the readme of https://github.com/Tomnl/Slicer-Wasp
+the stable 4.4.0 build read the instructions in the readme of https://github.com/Tomnl/Slicer-Wasp
 For most recent nighlty version of 3D Slicer tested see: https://www.dropbox.com/sh/xu6e9wwydnv341m/AADiXr-uQka4xhPBg5ccCDpMa?dl=0

← Older revision		Revision as of 09:29, 15 October 2015
Line 36:		Line 36:

	For code of the plugin see: https://github.com/Tomnl/Slicer-Wasp		For code of the plugin see: https://github.com/Tomnl/Slicer-Wasp
		+
		+
		+	IMPORTANT: The current version of WASP has been tested with the nightly build in july 2015. See below link for the nightly build installer. To get the plugin working with
		+	the stable build read the instructions in the readme of https://github.com/Tomnl/Slicer-Wasp

	For most recent nighlty version of 3D Slicer tested see: https://www.dropbox.com/sh/xu6e9wwydnv341m/AADiXr-uQka4xhPBg5ccCDpMa?dl=0		For most recent nighlty version of 3D Slicer tested see: https://www.dropbox.com/sh/xu6e9wwydnv341m/AADiXr-uQka4xhPBg5ccCDpMa?dl=0
−

← Older revision		Revision as of 10:58, 14 October 2015
Line 37:		Line 37:
	For code of the plugin see: https://github.com/Tomnl/Slicer-Wasp		For code of the plugin see: https://github.com/Tomnl/Slicer-Wasp

−	For most recent nighlty version of 3D Slicer tested see: https://~~github~~.com/~~Tomnl~~/~~wasp~~/~~slicer~~	+	For most recent nighlty version of 3D Slicer tested see: https://www.dropbox.com/sh/xu6e9wwydnv341m/AADiXr-uQka4xhPBg5ccCDpMa?dl=0

← Older revision		Revision as of 10:47, 14 October 2015
Line 34:		Line 34:

	The primary use cas of the tool is to perform multiple watershed segmentations (watershed stage) of an image and then use fiducials to pick out the good segmentations (annotation stage).		The primary use cas of the tool is to perform multiple watershed segmentations (watershed stage) of an image and then use fiducials to pick out the good segmentations (annotation stage).
		+
		+	For code of the plugin see: https://github.com/Tomnl/Slicer-Wasp
		+
		+	For most recent nighlty version of 3D Slicer tested see: https://github.com/Tomnl/wasp/slicer
		+
		+

	==Watershed stage==		==Watershed stage==

@@ 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>

@@ Line 72: / Line 72: @@
 <!-- ---------------------------- -->
 {{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.

@@ Line 32: / Line 32: @@
 *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 54: / Line 56: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Use Cases}}