Slicer Wiki - User contributions [en]

Documentation/4.4/Extensions/Wasp

2015-11-28T15:05:33Z

Tomnl:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/Wasp|Wasp]] 

Watershed Annotation and Segmentation Plugin for 3D Slicer.

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

Author: Thomas Lawson 
Contact: Thomas Lawson, <email> thomas.nigel.lawson@gmail.com </email> 
[[File:Slicer-Wasp.png|200px|thumb|left|WASP (MRC Harwell)]]

{{documentation/{{documentation/version}}/module-introduction-row}}

{{documentation/{{documentation/version}}/module-introduction-end}}


{{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

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)

==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}}
I was primarily working with a micro-CT dataset of a mouse embryo and that is what I get the best results with. However, the extension can be used with other data including the Slicer examples:

RegLib_c01_1
Using Watershed level 2 to 2.5 with default settings. The idea is that you use fiducials to pick out the the good segmentations (say the tumour and eyes) and then they will be created into a new label map and isosurface.

CT-Head
Watershed level 7 to 10 with with 0.5 iterations. Can use fiducials to get out the lungs.

A few notes:
To gauge what watershed level to use I typically run WASP with watershed levels 0.1 to 10 with iteration steps of 1. I can then run more watershed iterations where it is needed e.g. 3 to 4 with iterations of 0.1.

The limits for the parameters were just what fit with the embryo dataset I used. The actual limits are just the same as the SimpleITK methods so I can modify if requested.


{{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. Video link does not work in presentation. See youtube link below for video.

https://www.youtube.com/watch?v=o9DA4gqWNjg&feature=youtu.be

[[File:Wasp_tutorial.pptx]]

{{documentation/{{documentation/version}}/module-section|Panels and their use}}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


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

Documentation/4.5/Extensions/Wasp

2015-11-28T14:53:22Z

Tomnl:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/Wasp|Wasp]] 

Watershed Annotation and Segmentation Plugin for 3D Slicer.

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

Author: Thomas Lawson 

Contact: Thomas Lawson, <email> thomas.nigel.lawson@gmail.com </email> 
[[File:Slicer-Wasp.png|200px|thumb|left|WASP (MRC Harwell)]]

{{documentation/{{documentation/version}}/module-introduction-row}}

{{documentation/{{documentation/version}}/module-introduction-end}}


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

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

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 plugin has been tested and works with 3D Slicer 4.5 stable version and nightly (last tested 28-Nov-2015)

==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}}
I was primarily working with a micro-CT dataset of a mouse embryo and that is what I get the best results with. However, the extension can be used with other data including the Slicer examples:

RegLib_c01_1
Using Watershed level 2 to 2.5 with default settings. The idea is that you use fiducials to pick out the the good segmentations (say the tumour and eyes) and then they will be created into a new label map and isosurface.

CT-Head
Watershed level 7 to 10 with with 0.5 iterations. Can use fiducials to get out the lungs.

A few notes:
To gauge what watershed level to use I typically run WASP with watershed levels 0.1 to 10 with iteration steps of 1. I can then run more watershed iterations where it is needed e.g. 3 to 4 with iterations of 0.1.

The limits for the parameters were just what fit with the embryo dataset I used. The actual limits are just the same as the SimpleITK methods so I can modify if requested.


{{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. Video link does not work in presentation. See youtube link below for video.

https://www.youtube.com/watch?v=o9DA4gqWNjg&feature=youtu.be

[[File:Wasp_tutorial.pptx]]

{{documentation/{{documentation/version}}/module-section|Panels and their use}}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


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

Documentation/4.4/Extensions/Wasp

2015-11-28T14:47:27Z

Tomnl:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/Wasp|Wasp]] 

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) 

Author: Thomas Lawson 
Contact: Thomas Lawson, <email> thomas.nigel.lawson@gmail.com </email> 
[[File:Slicer-Wasp.png|200px|thumb|left|WASP (MRC Harwell)]]

{{documentation/{{documentation/version}}/module-introduction-row}}

{{documentation/{{documentation/version}}/module-introduction-end}}


{{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

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)

==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}}
I was primarily working with a micro-CT dataset of a mouse embryo and that is what I get the best results with. However, the extension can be used with other data including the Slicer examples:

RegLib_c01_1
Using Watershed level 2 to 2.5 with default settings. The idea is that you use fiducials to pick out the the good segmentations (say the tumour and eyes) and then they will be created into a new label map and isosurface.

CT-Head
Watershed level 7 to 10 with with 0.5 iterations. Can use fiducials to get out the lungs.

A few notes:
To gauge what watershed level to use I typically run WASP with watershed levels 0.1 to 10 with iteration steps of 1. I can then run more watershed iterations where it is needed e.g. 3 to 4 with iterations of 0.1.

The limits for the parameters were just what fit with the embryo dataset I used. The actual limits are just the same as the SimpleITK methods so I can modify if requested.


{{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. Video link does not work in presentation. See youtube link below for video.

https://www.youtube.com/watch?v=o9DA4gqWNjg&feature=youtu.be

[[File:Wasp_tutorial.pptx]]

{{documentation/{{documentation/version}}/module-section|Panels and their use}}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


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

Documentation/4.4/Extensions/Wasp

2015-10-15T09:30:15Z

Tomnl:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/Wasp|Wasp]] 

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) 

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

{{documentation/{{documentation/version}}/module-introduction-row}}

{{documentation/{{documentation/version}}/module-introduction-end}}


{{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

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

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 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

==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}}
I was primarily working with a micro-CT dataset of a mouse embryo and that is what I get the best results with. However, the extension can be used with other data including the Slicer examples:

RegLib_c01_1
Using Watershed level 2 to 2.5 with default settings. The idea is that you use fiducials to pick out the the good segmentations (say the tumour and eyes) and then they will be created into a new label map and isosurface.

CT-Head
Watershed level 7 to 10 with with 0.5 iterations. Can use fiducials to get out the lungs.

A few notes:
To gauge what watershed level to use I typically run WASP with watershed levels 0.1 to 10 with iteration steps of 1. I can then run more watershed iterations where it is needed e.g. 3 to 4 with iterations of 0.1.

The limits for the parameters were just what fit with the embryo dataset I used. The actual limits are just the same as the SimpleITK methods so I can modify if requested.


{{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. Video link does not work in presentation. See youtube link below for video.

https://www.youtube.com/watch?v=o9DA4gqWNjg&feature=youtu.be

[[File:Wasp_tutorial.pptx]]

{{documentation/{{documentation/version}}/module-section|Panels and their use}}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


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

Documentation/4.4/Extensions/Wasp

2015-10-15T09:29:38Z

Tomnl:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/Wasp|Wasp]] 

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) 

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

{{documentation/{{documentation/version}}/module-introduction-row}}

{{documentation/{{documentation/version}}/module-introduction-end}}


{{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

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

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

==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}}
I was primarily working with a micro-CT dataset of a mouse embryo and that is what I get the best results with. However, the extension can be used with other data including the Slicer examples:

RegLib_c01_1
Using Watershed level 2 to 2.5 with default settings. The idea is that you use fiducials to pick out the the good segmentations (say the tumour and eyes) and then they will be created into a new label map and isosurface.

CT-Head
Watershed level 7 to 10 with with 0.5 iterations. Can use fiducials to get out the lungs.

A few notes:
To gauge what watershed level to use I typically run WASP with watershed levels 0.1 to 10 with iteration steps of 1. I can then run more watershed iterations where it is needed e.g. 3 to 4 with iterations of 0.1.

The limits for the parameters were just what fit with the embryo dataset I used. The actual limits are just the same as the SimpleITK methods so I can modify if requested.


{{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. Video link does not work in presentation. See youtube link below for video.

https://www.youtube.com/watch?v=o9DA4gqWNjg&feature=youtu.be

[[File:Wasp_tutorial.pptx]]

{{documentation/{{documentation/version}}/module-section|Panels and their use}}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


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

Documentation/4.4/Extensions/Wasp

2015-10-14T10:58:57Z

Tomnl:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/Wasp|Wasp]] 

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) 

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

{{documentation/{{documentation/version}}/module-introduction-row}}

{{documentation/{{documentation/version}}/module-introduction-end}}


{{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

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://www.dropbox.com/sh/xu6e9wwydnv341m/AADiXr-uQka4xhPBg5ccCDpMa?dl=0

==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}}
I was primarily working with a micro-CT dataset of a mouse embryo and that is what I get the best results with. However, the extension can be used with other data including the Slicer examples:

RegLib_c01_1
Using Watershed level 2 to 2.5 with default settings. The idea is that you use fiducials to pick out the the good segmentations (say the tumour and eyes) and then they will be created into a new label map and isosurface.

CT-Head
Watershed level 7 to 10 with with 0.5 iterations. Can use fiducials to get out the lungs.

A few notes:
To gauge what watershed level to use I typically run WASP with watershed levels 0.1 to 10 with iteration steps of 1. I can then run more watershed iterations where it is needed e.g. 3 to 4 with iterations of 0.1.

The limits for the parameters were just what fit with the embryo dataset I used. The actual limits are just the same as the SimpleITK methods so I can modify if requested.


{{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. Video link does not work in presentation. See youtube link below for video.

https://www.youtube.com/watch?v=o9DA4gqWNjg&feature=youtu.be

[[File:Wasp_tutorial.pptx]]

{{documentation/{{documentation/version}}/module-section|Panels and their use}}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


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

Documentation/4.4/Extensions/Wasp

2015-10-14T10:47:02Z

Tomnl:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/Wasp|Wasp]] 

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) 

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

{{documentation/{{documentation/version}}/module-introduction-row}}

{{documentation/{{documentation/version}}/module-introduction-end}}


{{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

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==

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}}
I was primarily working with a micro-CT dataset of a mouse embryo and that is what I get the best results with. However, the extension can be used with other data including the Slicer examples:

RegLib_c01_1
Using Watershed level 2 to 2.5 with default settings. The idea is that you use fiducials to pick out the the good segmentations (say the tumour and eyes) and then they will be created into a new label map and isosurface.

CT-Head
Watershed level 7 to 10 with with 0.5 iterations. Can use fiducials to get out the lungs.

A few notes:
To gauge what watershed level to use I typically run WASP with watershed levels 0.1 to 10 with iteration steps of 1. I can then run more watershed iterations where it is needed e.g. 3 to 4 with iterations of 0.1.

The limits for the parameters were just what fit with the embryo dataset I used. The actual limits are just the same as the SimpleITK methods so I can modify if requested.


{{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. Video link does not work in presentation. See youtube link below for video.

https://www.youtube.com/watch?v=o9DA4gqWNjg&feature=youtu.be

[[File:Wasp_tutorial.pptx]]

{{documentation/{{documentation/version}}/module-section|Panels and their use}}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


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

Documentation/4.4/Extensions/Wasp

2015-06-30T08:11:29Z

Tomnl:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/Wasp|Wasp]] 

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) 

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

{{documentation/{{documentation/version}}/module-introduction-row}}

{{documentation/{{documentation/version}}/module-introduction-end}}


{{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

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).

==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}}
I was primarily working with a micro-CT dataset of a mouse embryo and that is what I get the best results with. However, the extension can be used with other data including the Slicer examples:

RegLib_c01_1
Using Watershed level 2 to 2.5 with default settings. The idea is that you use fiducials to pick out the the good segmentations (say the tumour and eyes) and then they will be created into a new label map and isosurface.

CT-Head
Watershed level 7 to 10 with with 0.5 iterations. Can use fiducials to get out the lungs.

A few notes:
To gauge what watershed level to use I typically run WASP with watershed levels 0.1 to 10 with iteration steps of 1. I can then run more watershed iterations where it is needed e.g. 3 to 4 with iterations of 0.1.

The limits for the parameters were just what fit with the embryo dataset I used. The actual limits are just the same as the SimpleITK methods so I can modify if requested.


{{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. Video link does not work in presentation. See youtube link below for video.

https://www.youtube.com/watch?v=o9DA4gqWNjg&feature=youtu.be

[[File:Wasp_tutorial.pptx]]

{{documentation/{{documentation/version}}/module-section|Panels and their use}}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


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

Documentation/4.4/Extensions/Wasp

2015-01-24T14:26:48Z

Tomnl:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/Wasp|Wasp]] 

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) 

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

{{documentation/{{documentation/version}}/module-introduction-row}}

{{documentation/{{documentation/version}}/module-introduction-end}}


{{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

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).

==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}}
I was primarily working with a micro-CT dataset of a mouse embryo and that is what I get the best results with. However, the extension can be used with other data including the Slicer examples:

RegLib_c01_1
Using Watershed level 2 to 2.5 with default settings. The idea is that you use fiducials to pick out the the good segmentations (say the tumour and eyes) and then they will be created into a new label map and isosurface.

CT-Head
Watershed level 7 to 10 with with 0.5 iterations. Can use fiducials to get out the lungs.

A few notes:
To gauge what watershed level to use I typically run WASP with watershed levels 0.1 to 10 with iteration steps of 1. I can then run more watershed iterations where it is needed e.g. 3 to 4 with iterations of 0.1.

The limits for the parameters were just what fit with the embryo dataset I used. The actual limits are just the same as the SimpleITK methods so I can modify if requested.


{{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]]

{{documentation/{{documentation/version}}/module-section|Panels and their use}}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}


{{documentation/{{documentation/version}}/module-section|References}}


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


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

File:Slicer-Wasp.png

2015-01-07T21:06:02Z

Tomnl: uploaded a new version of "File:Slicer-Wasp.png"

Logo for WASP extension (MRC Harwell).

Documentation/Nightly/Extensions/Wasp

2014-12-22T19:03:23Z

Tomnl:

Documentation/Nightly/Extensions/Wasp

2014-12-22T19:02:03Z

Tomnl:

File:Wasp tutorial.pptx

2014-12-22T19:01:15Z

Tomnl: Tutorial on how to use the WASP extension. Contains a video demo. Please be aware that a few changes have been made to the tool since this tutorial was made.

Tutorial on how to use the WASP extension. Contains a video demo. Please be aware that a few changes have been made to the tool since this tutorial was made.

Documentation/Nightly/Extensions/Wasp

2014-12-22T18:43:39Z

Tomnl:

Documentation/Nightly/Extensions/Wasp

2014-12-22T18:42:45Z

Tomnl:

Documentation/Nightly/Extensions/Wasp

2014-12-22T18:41:49Z

Tomnl:

Documentation/Nightly/Extensions/Wasp

2014-12-22T18:41:14Z

Tomnl:

Documentation/Nightly/Extensions/Wasp

2014-12-22T18:35:30Z

Tomnl:

Documentation/Nightly/Extensions/Wasp

2014-12-22T18:35:06Z

Tomnl:

Documentation/Nightly/Extensions/Wasp

2014-12-22T18:34:07Z

Tomnl:

Documentation/Nightly/Extensions/Wasp

2014-12-22T18:33:49Z

Tomnl:

Documentation/Nightly/Extensions/Wasp

2014-12-22T18:33:34Z

Tomnl:

File:Slicer-Wasp.png

2014-12-22T18:30:08Z

Tomnl: Logo for WASP extension (MRC Harwell).

Logo for WASP extension (MRC Harwell).

Documentation/Nightly/Extensions/Wasp

2014-09-25T11:17:34Z

Tomnl: Created page with '<noinclude>{{documentation/versioncheck}}</noinclude>  {{documentation/{{documentation/version}}/module-header}} <!-- -----------------------…'

Documentation/Nightly/Extensions

2014-09-25T11:09:46Z

Tomnl:

<noinclude>{{documentation/versioncheck}}</noinclude>
<noinclude>
__TOC__
</noinclude>= Extensions by Category =

==Cat 1==

==Cat 2==
*[[Documentation/{{documentation/version}}/Extensions/CarreraSliceInteractiveSegmenter|CarreraSlice Interactive Segmenter]] (Ivan Kolesov, LiangJia Zhu, Yi Gao, Peter Karasev, Patricio Vela, Allen Tannenbaum, Karl Fritscher, Steve Pieper )
* [[Documentation/{{documentation/version}}/Extensions/SurfaceReconstruction|SurfaceReconstruction]] (Chenxi-Zhang David-Doria Arnaud-Gelas Michael-Kazhdan Matthew-Bolitho Hugues-Hoppe Jean-Christophe Fillion-Robin )
* [[Documentation/{{documentation/version}}/Extensions/SkullStripper|SkullStripper]] (Xiaodong Tao)
* [[Documentation/{{documentation/version}}/Extensions/MABMIS|MABMIS]] (Xiaofeng Liu)
* [[Documentation/{{documentation/version}}/Extensions/SwissSkullStripper|SwissSkullStripper]] (Bill Lorensen)
* [[Documentation/{{documentation/version}}/Extensions/CARMA|Cardiac MRI Toolkit]] (Alan Morris, Salma Bengali)[[image:UnderConstruction.png|tumb|10px]]
* [[Documentation/{{documentation/version}}/Extensions/PkModeling|PkModeling]] (Emma Zhu, Jim Miller)
* [[Documentation/{{documentation/version}}/Extensions/FacetedVisualizer|FacetedVisualizer]] (Harini Veeraraghavan, Jim Miller)
* [[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting]] (Andrey Fedorov, Nicole Aucoin, Steve Pieper) (work in progress)
* [[Documentation/{{documentation/version}}/Extensions/TCIABrowser|TCIA Browser]] (Alireza Mehrtash, Andrey Fedorov) (work in progress)
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT|SlicerRT]] (Csaba Pinter, Kevin Wang, Adam Rankin, Greg Sharp, Andras Lasso, Steve Pieper)
** [[Documentation/{{documentation/version}}/Modules/DicomRtImport|DICOM-RT import]]
** [[Documentation/{{documentation/version}}/Modules/DicomRtExport|DICOM-RT export]]
** [[Documentation/{{documentation/version}}/Modules/Contours|Contours]]
** [[Documentation/{{documentation/version}}/Modules/DoseVolumeHistogram|Dose volume histogram]]
** [[Documentation/{{documentation/version}}/Modules/DoseAccumulation|Dose accumulation]]
** [[Documentation/{{documentation/version}}/Modules/DoseComparison|Dose comparison]]
** [[Documentation/{{documentation/version}}/Modules/Isodose|Isodose line and surface display]]
** [[Documentation/{{documentation/version}}/Modules/ContourComparison|Contour comparison]]
** [[Documentation/{{documentation/version}}/Modules/ContourMorphology|Contour morphology]]


** Modules from [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]] (Greg Sharp)
*** [[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]]
*** [[Documentation/{{documentation/version}}/Modules/PlmLANDWARP|Plastimatch LANDWARP Landmark]]
*** [[Documentation/{{documentation/version}}/Modules/PlmXFORMWARP|Plastimatch XFORMWARP]] [[image:UnderConstruction.png|tumb|10px]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT|SlicerIGT]] (Tamas Ungi, Adam Rankin, Andras Lasso, Junichi Tokuda, Laurent Chauvin)
** [[Documentation/{{documentation/version}}/Modules/CollectFiducials|CollectFiducials]] (Tamas Ungi)
** [[Documentation/{{documentation/version}}/Modules/CreateModels|CreateModels]] (Tamas Ungi, Matthew Holden)
** [[Documentation/{{documentation/version}}/Modules/OpenIGTLinkRemote|OpenIGTLinkRemote]] (Tamas Ungi, Andras Lasso)
** [[Documentation/{{documentation/version}}/Modules/UltrasoundSnapshots|UltrasoundSnapshots]] (Tamas Ungi, Franklin King)
** [[Documentation/{{documentation/version}}/Extensions/VolumeResliceDriver|VolumeResliceDriver]] (Junichi Tokuda, Tamas Ungi, Laurent Chauvin)
** [[Documentation/{{documentation/version}}/Extensions/PathExplorer|PathExplorer]] (Laurent Chauvin, Junichi Tokuda)
* [[Documentation/{{documentation/version}}/Extensions/MatlabBridge|Matlab Bridge]] (Andras Lasso, Jean-Christophe Fillion-Robin, Kevin Wang)
* [[Documentation/{{documentation/version}}/Extensions/iGyne|iGyne]] (Xiaojun Chen and iGyne Team)
* [[Documentation/{{documentation/version}}/Extensions/LongitudinalPETCT|LongitudinalPETCT]] (Paul Mercea, Andrey Fedorov)
* [[Documentation/{{documentation/version}}/Extensions/DTIProcess|DTIProcess]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIAtlasFiberAnalyzer|DTIAtlasFiberAnalyzer]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/FiberViewerLight|FiberViewerLight]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIPrep|DTIPrep]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIAtlasBuilder|DTIAtlasBuilder]] (Adrien Kaiser)
* [[Documentation/{{documentation/version}}/Extensions/IntensitySegmenter|IntensitySegmenter]] (Francois Budin, Pengdong Xiao, Beatriz Paniagua)
* [[Documentation/{{documentation/version}}/Extensions/ShapePopulationViewer|ShapePopulationViewer]] (Alexis Girault)
* [[Documentation/{{documentation/version}}/Extensions/ModelToModelDistance|ModelToModelDistance]] (Francois Budin, Juliette Pera, Beatriz Paniagua)
* [[Documentation/{{documentation/version}}/Extensions/SpharmPdm|SPHARM-PDM]] (Beatriz Paniagua, Francois Budin, Martin Styner)
* [[Documentation/{{documentation/version}}/Extensions/TubeTK|TubeTK]] (Stephen Aylward, Jean-Christophe Fillion-Robin, Christopher Mullins, Michael Jeulin-L, Matthew McCormick)
* [[Documentation/{{documentation/version}}/Extensions/UKFTractography|UKFTractography]] (Ryan Eckbo, Yogesh Rathi)
* [[Documentation/{{documentation/version}}/Extensions/TrackerStabilizer|TrackerStabilizer]] (Laurent Chauvin, Jayender Jagadeesan)
* [[Documentation/{{documentation/version}}/Extensions/ChangeTracker|ChangeTracker]] (Andrey Fedorov)
* [[Documentation/{{documentation/version}}/Extensions/SobolevSegmenter|SobolevSegmenter]] (Arie Nakhmani)
* [[Documentation/{{documentation/version}}/Extensions/QuickTools|QuickTools]] (Julien Finet)
** [[Documentation/{{documentation/version}}/Modules/ImageMaker|Image Maker]]
* [[Documentation/{{documentation/version}}/Extensions/XNATSlicer|XNATSlicer]]
* [[Documentation/{{documentation/version}}/Extensions/ErodeDilateLabel|ErodeDilateLabel]] (Junichi)
* [[Documentation/{{documentation/version}}/Extensions/ThingiverseBrowser|ThingiverseBrowser]] (Nigel Goh)
* [[Documentation/{{documentation/version}}/Extensions/VirtualFractureReconstruction|Virtual Fracture Reconstruction]] (Karl Fritscher, Peter Karasev)
* [[Documentation/{{documentation/version}}/Extensions/AirwaySegmentation|AirwaySegmentation]] (Pietro Nardelli)
* [[Documentation/{{documentation/version}}/Extensions/ModelClip|ModelClip]] (Jun Lin, Xiaojun Chen)
* [[Documentation/{{documentation/version}}/Extensions/SurfaceMirror|SurfaceMirror]] (Jiaxi Luo, Ruqing Ye, Xiaojun Chen)
* [[Documentation/{{documentation/version}}/Extensions/Scoliosis|Scoliosis]] (Franklin King, Tamas Ungi)
**[[Documentation/{{documentation/version}}/Modules/SpinalCurvatureMeasurement|Spinal Curvature Measurement]] (Franklin King, Tamas Ungi)
* [[Documentation/{{documentation/version}}/Extensions/PortPlacement|Port Placement]] (Luis G. Torres and Andinet Enquobahrie)
* [[Documentation/{{documentation/version}}/Extensions/AutoPortPlacement|Auto Port Placement]] (Luis G. Torres, Andinet Enquobahrie)
* [[Documentation/{{documentation/version}}/Extensions/PlusRemote|Plus Remote]] (Franklin King, Tamas Ungi)
* [[Documentation/{{documentation/version}}/Extensions/TransformVisualizer|Transform Visualizer]] (Franklin King, Andras Lasso, Csaba Pinter)
* [[Documentation/{{documentation/version}}/Extensions/WindowLevelEffect|WindowLevelEffect]] (Andrey Fedorov, Steve Pieper)
* [[Documentation/{{documentation/version}}/Extensions/PerkTutor|PerkTutor]] (Tamas Ungi, Matthew Holden)
** [[Documentation/{{documentation/version}}/Modules/PerkEvaluator|PerkEvaluator]]
** [[Documentation/{{documentation/version}}/Modules/TransformRecorder|TransformRecorder]]
** [[Documentation/{{documentation/version}}/Modules/WorkflowSegmentation|WorkflowSegmentation]]
* [[Documentation/{{documentation/version}}/Modules/SlicerToKiwiExporter|SlicerToKiwiExporter]] (Jean-Christophe Fillion-Robin)
* [[Documentation/{{documentation/version}}/Modules/GelDosimetry|GelDosimetry]] (Csaba Pinter)
* [[Documentation/{{documentation/version}}/Extensions/MultidimData|Multidimensional data]] (Andras Lasso, Matthew Holden, Kevin Wang)
* [[Documentation/{{documentation/version}}/Extensions/GyroGuide|GyroGuide]] (Ruifeng Chen,Luping Fang, Qing Pan, Xiaolei Chen, Jiashu Zhang)
* [[Documentation/{{documentation/version}}/Modules/MRI SNR Measurement|MRI SNR Measurement]] (Babak Matinfar)
* [[Documentation/{{documentation/version}}/Extensions/OpenCAD|OpenCAD]] (Vivek Narayan, Jayender Jagadeesan)
* [[Documentation/{{documentation/version}}/PercutaneousApproachAnalysis|Percutaneous Approach Analysis]] (Koichiro Murakami, Laurent Chauvin, Junichi Tokuda)
* [[Documentation/{{documentation/version}}/Extensions/FinslerTractography|Finsler Tractography]] (Antonio Tristan Vega, Demian Wassermann and Carl-Fredrik Westin)
** [[Documentation/{{documentation/version}}/Modules/FinslerTractography|Finsler Tractography]]
** [[Documentation/{{documentation/version}}/Modules/FinslerBacktracing|Finsler Backtracing]]
* [[Documentation/{{documentation/version}}/Extensions/CurveMaker|CurveMaker]] (Junichi Tokuda)
* [[Documentation/{{documentation/version}}/Extensions/CBC_3D_I2MConversion | CBC 3D I2MConversion]] (Fotis Drakopoulos, Yixun Liu, Andrey Fedorov and Nikos Chrisochoides)
** [[Documentation/{{documentation/version}}/Modules/BodyCentricCubicMesh|Body Centric Cubic Mesh]]
** [[Documentation/{{documentation/version}}/Modules/MeshCompression|Mesh Compression]]
* [[Documentation/{{documentation/version}}/Extensions/PBNRR|Physics-Based Non-Rigid Registration (PBNRR)]] (Fotis Drakopoulos, Yixun Liu, Andriy Kot, Andrey Fedorov, Olivier Clatz and Nikos Chrisochoides)
* [[Documentation/{{documentation/version}}/Extensions/ResectionPlanner|ResectionVolume]] (Matt Lougheed)
* [[Documentation/{{documentation/version}}/Extensions/PETDICOM|PET DICOM]] (Andrey Fedorov, Ethan Ulrich)
* [[Documentation/{{documentation/version}}/Modules/CornerAnnotation|CornerAnnotation]] (Atsushi Yamada)
* [[Documentation/{{documentation/version}}/Extensions/Wasp|Watershed Annotation and Segmentation Plugin.]] (Thomas Lawson)
==Cat 3==
* [[Documentation/{{documentation/version}}/Extensions/LesionSegmentation|LesionSegmentation]] (Mark Scully)
**[[Documentation/{{documentation/version}}/Modules/TrainModel|LesionSegmentation->TrainModel]] (Mark Scully)
**[[Documentation/{{documentation/version}}/Modules/PredictLesions|LesionSegmentation->PredictLesions]] (Mark Scully)
* [[Documentation/{{documentation/version}}/Extensions/IASEM|IASEM]] (Bradley Lowekamp)
* [[Documentation/{{documentation/version}}/Extensions/PyDevRemoteDebug|Python debugger]] (Andras Lasso)
<noinclude>
{{:Documentation/{{documentation/version}}/FAQ/Extensions|Extensions}}
</noinclude>