Slicer Wiki - User contributions [en]

Documentation/Nightly/Extensions/IASEM

2013-08-06T15:58:58Z

Ksukri: /* BinShrink Image Filter */

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

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


{{ambox
| type = protection
| image = [[File:InProgress.png|40px|alt=Work in progress]]
| text = WARNING: This module is Work in Progress, which means:
* the functionality provided by this module may change drastically in the future releases of 3D Slicer
* the scenes containing data types specific to this module may not be readable by the future versions of Slicer
* the functionality and user interface may change at any time
* some functionality may not work as intended
* testing and documentation is limited
}}


{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Acknowledgments:
This work is supported by NLM, and the Slicer Community. 
Author: Bradley Lowekamp 
Contact: Bradley Lowekamp <email>blowekamp@mail.nih.gov</email> 
License: [http://raw.github.com/blowekamp/Slicer-IASEM/master/LICENSE Apache License 2.0]
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|nlm}}|{{collaborator|longname|nlm}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/extension-section|Extension Description}}

This extension is a compilation of modules which are useful for segmentation and processing of IASEM Electron Microscopy images. It adds modules which help in general with segmenting large data sets, and has components to deal with images in multi-resolutions.

IASEM stands for ion-abrasion scanning electron microscopy, some times also call dual-beam or focused ion-beam scanning electron microscopy (FIBSEM).

<gallery widths="200px" perrow="4">
Image:IASEM-Screenshot1.png|Segmentation of Gold particles.
</gallery>


{{documentation/{{documentation/version}}/extension-section|Modules}}

* BinShrink Image Filter
* SpacingAwareCurvatureDiffusion Image Filter
* DoubleThreshold Editor Effect
* BinaryWatershed Editor Effect


{{documentation/{{documentation/version}}/extension-section|Use Cases}}
===BinShrink Image Filter===
Bin Shrink is one of the modules used to help ease the process of segmentation. By stipulating a neighborhood size, 5x5x5 for example, it will average the neighboring pixels within that 5x5x5 region and turn them into one pixel. Applying the Bin Shrink will result in reduced resolution and a less noisy image. Based on the features you want to segment, you can apply a more aggressive bin or a less aggressive bin based on the complexity of your features of interest. Binning the image does not significantly affect the quality of the image, it also reduces the amount of memory the computer needs to process the data, so the more an image is binned the faster slicer will work and the more free memory you will have.

{|
|[[Image:GoldGrayscale.png|thumb|Original gray scale image.]]
|[[Image:GoldGrayscaleBin5.png|thumb|After running the BinShrink by a factor of 5x5x5.]]
|}

===SpacingAwareCurvatureDiffusion Image Filter===
===DoubleThreshold Editor Effect===
===BinaryWatershed Editor Effect===


{{documentation/{{documentation/version}}/extension-section|Walk Through}}
===BinShrink Image Filter===
{|
|[[Image:OriginalGoldGrayscale.png|thumb|Step 1: Original gray scale image.]]
|[[Image:BinShrinkSettings.png|thumb|Step 2: BinShrink settings.]]
|[[Image:BinShrinkGoldGrayscale.png|thumb|Step 3: After running the BinShrink by a factor of 5x5x5.]]
|[[Image:ROIToolbar.png|thumb|Step 4: ROI Toolbar.]]
|[[Image:CropGoldGrayscale.png|thumb|Step 5: Cropped gray scale image.]]
|[[Image:ThresholdGoldLabelMap.png|thumb|Step 6: Threshold of the cropped gray scale image.]]
|}
#[[Documentation/{{documentation/version}}/Modules/SlicerWelcome#LoadPanel|Load]] gray scale data.
#Go to the Modules search bar, search and select "BinShrink". Go to the BinShrink settings, change the input to the original gray scale image and change the output to "create a new volume".
#Apply the BinShrink Image Filter.
#Create a Region of Interest (ROI) using the Fiducial Module in the Slicer Toolbar.
#Use the [[Documentation/{{documentation/version}}/Modules/CropVolume|Crop Volume]] module to crop the region of interest.
#Apply [[Documentation/{{documentation/version}}/Modules/Editor#Threshold|Threshold Effect]], or any other editing technique, to your gray scale image to create a label map.
#[[Documentation/{{documentation/version}}/Modules/BRAINSResample|Resample]] the label map so its dimensions match those of the gray scale image.
##Using the [[Documentation/{{documentation/version}}/Modules/Transforms|Transforms]] module, create a new transform and rename it "Identity".
##Search and select "Resample Image (BRAINS)" in the modules search bar. Go to the [[Documentation/{{documentation/version}}/Modules/BRAINSResample|Resample]] settings to resample the label map.
##The Image to Warp should be the label map.
##The Reference Image should be the BinShrink gray scale image.
##Create a new Output Image.
##Change the pixel type to "short".
##Change the Transform file to "Identity".
##Change the Interpolation Mode to "NearestNeighbor".
##Apply the Resampling.
{|
|[[Image:TransformToolbar.png|thumb|Transform Module in the Slicer Toolbar]]
|[[Image:TransformModule.png|thumb|Transform Settings]]
|[[Image:ResampleSettings.png|thumb|Resample settings.]]
|}


{{documentation/{{documentation/version}}/extension-section|Tutorials}}


{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
N/A


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


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


{{documentation/{{documentation/version}}/extension-footer}}

Documentation/Nightly/Extensions/IASEM

2013-08-06T15:53:49Z

Ksukri:

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

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


{{ambox
| type = protection
| image = [[File:InProgress.png|40px|alt=Work in progress]]
| text = WARNING: This module is Work in Progress, which means:
* the functionality provided by this module may change drastically in the future releases of 3D Slicer
* the scenes containing data types specific to this module may not be readable by the future versions of Slicer
* the functionality and user interface may change at any time
* some functionality may not work as intended
* testing and documentation is limited
}}


{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Acknowledgments:
This work is supported by NLM, and the Slicer Community. 
Author: Bradley Lowekamp 
Contact: Bradley Lowekamp <email>blowekamp@mail.nih.gov</email> 
License: [http://raw.github.com/blowekamp/Slicer-IASEM/master/LICENSE Apache License 2.0]
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|nlm}}|{{collaborator|longname|nlm}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/extension-section|Extension Description}}

This extension is a compilation of modules which are useful for segmentation and processing of IASEM Electron Microscopy images. It adds modules which help in general with segmenting large data sets, and has components to deal with images in multi-resolutions.

IASEM stands for ion-abrasion scanning electron microscopy, some times also call dual-beam or focused ion-beam scanning electron microscopy (FIBSEM).

<gallery widths="200px" perrow="4">
Image:IASEM-Screenshot1.png|Segmentation of Gold particles.
</gallery>


{{documentation/{{documentation/version}}/extension-section|Modules}}

* BinShrink Image Filter
* SpacingAwareCurvatureDiffusion Image Filter
* DoubleThreshold Editor Effect
* BinaryWatershed Editor Effect


{{documentation/{{documentation/version}}/extension-section|Use Cases}}
===BinShrink Image Filter===
Bin Shrink is one of the modules used to help ease the process of segmentation. By stipulating a neighborhood size, 5x5x5 for example, it will average the neighboring pixels within that 5x5x5 region and turn them into one pixel. Applying the Bin Shrink will result in reduced resolution and a less noisy image. Based on the features you want to segment, you can apply a more aggressive bin or a less aggressive bin based on the complexity of your features of interest. Binning the image does not significantly affect the quality of the image, it also reduces the amount of memory the computer needs to process the data, so the more an image is binned the faster slicer will work and the more free memory you will have.

{|
|[[Image:GoldGrayscale.png|thumb|Original gray scale image.]]
|[[Image:GoldGrayscaleBin5.png|thumb|After running the BinShrink by a factor of 5x5x5.]]
|}

===SpacingAwareCurvatureDiffusion Image Filter===
===DoubleThreshold Editor Effect===
===BinaryWatershed Editor Effect===


{{documentation/{{documentation/version}}/extension-section|Walk Through}}
===BinShrink Image Filter===
{|
|[[Image:OriginalGoldGrayscale.png|thumb|Step 1: Original gray scale image.]]
|[[Image:BinShrinkSettings.png|thumb|Step 2: BinShrink settings.]]
|[[Image:BinShrinkGoldGrayscale.png|thumb|Step 3: After running the BinShrink by a factor of 5x5x5.]]
|[[Image:ROIToolbar.png|thumb|Step 4: ROI Toolbar.]]
|[[Image:CropGoldGrayscale.png|thumb|Step 5: Cropped gray scale image.]]
|[[Image:ThresholdGoldLabelMap.png|thumb|Step 6: Threshold of the cropped gray scale image.]]
|}
#[[Documentation/{{documentation/version}}/Modules/SlicerWelcome#LoadPanel|Load]] gray scale data.
#Go to the Modules search bar, search and select "BinShrink". Go to the BinShrink settings, change the input to the original gray scale image and change the output to "create a new volume".
#Apply the BinShrink Image Filter.
#Create a Region of Interest (ROI) using the Fiducial Module in the Slicer Toolbar.
#Use the [[Documentation/{{documentation/version}}/Modules/CropVolume|Crop Volume]] module to crop the region of interest.
#Apply [[Documentation/{{documentation/version}}/Modules/Editor#Threshold|Threshold Effect]], or any other editing technique, to your gray scale image to create a label map.
#[[Documentation/{{documentation/version}}/Modules/BRAINSResample|Resample]] the label map so its dimensions match those of the gray scale image.
##Using the [[Documentation/{{documentation/version}}/Modules/Transforms|Transforms]] module, create a new transform and rename it "Identity".
##Go to the [[Documentation/{{documentation/version}}/Modules/BRAINSResample|Resample]] settings to resample the label map.
##The Image to Warp should be the label map.
##The Reference Image should be the BinShrink gray scale image.
##Create a new Output Image.
##Change the pixel type to "short".
##Change the Transform file to "Identity".
##Change the Interpolation Mode to "NearestNeighbor".
##Apply the Resampling.


{{documentation/{{documentation/version}}/extension-section|Tutorials}}


{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
N/A


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


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


{{documentation/{{documentation/version}}/extension-footer}}

Documentation/Nightly/Extensions/IASEM

2013-08-06T15:52:25Z

Ksukri:

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

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


{{ambox
| type = protection
| image = [[File:InProgress.png|40px|alt=Work in progress]]
| text = WARNING: This module is Work in Progress, which means:
* the functionality provided by this module may change drastically in the future releases of 3D Slicer
* the scenes containing data types specific to this module may not be readable by the future versions of Slicer
* the functionality and user interface may change at any time
* some functionality may not work as intended
* testing and documentation is limited
}}


{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Acknowledgments:
This work is supported by NLM, and the Slicer Community. 
Author: Bradley Lowekamp 
Contact: Bradley Lowekamp <email>blowekamp@mail.nih.gov</email> 
License: [http://raw.github.com/blowekamp/Slicer-IASEM/master/LICENSE Apache License 2.0]
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|nlm}}|{{collaborator|longname|nlm}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/extension-section|Extension Description}}

This extension is a compilation of modules which are useful for segmentation and processing of IASEM Electron Microscopy images. It adds modules which help in general with segmenting large data sets, and has components to deal with images in multi-resolutions.

IASEM stands for ion-abrasion scanning electron microscopy, some times also call dual-beam or focused ion-beam scanning electron microscopy (FIBSEM).

<gallery widths="200px" perrow="4">
Image:IASEM-Screenshot1.png|Segmentation of Gold particles.
</gallery>


{{documentation/{{documentation/version}}/extension-section|Modules}}

* BinShrink Image Filter
* SpacingAwareCurvatureDiffusion Image Filter
* DoubleThreshold Editor Effect
* BinaryWatershed Editor Effect


{{documentation/{{documentation/version}}/extension-section|Use Cases}}
===BinShrink Image Filter===
Bin Shrink is one of the modules used to help ease the process of segmentation. By stipulating a neighborhood size, 5x5x5 for example, it will average the neighboring pixels within that 5x5x5 region and turn them into one pixel. Applying the Bin Shrink will result in reduced resolution and a less noisy image. Based on the features you want to segment, you can apply a more aggressive bin or a less aggressive bin based on the complexity of your features of interest. Binning the image does not significantly affect the quality of the image, it also reduces the amount of memory the computer needs to process the data, so the more an image is binned the faster slicer will work and the more free memory you will have.

{|
|[[Image:GoldGrayscale.png|thumb|Original gray scale image.]]
|[[Image:GoldGrayscaleBin5.png|thumb|After running the BinShrink by a factor of 5x5x5.]]
|}

===SpacingAwareCurvatureDiffusion Image Filter===
===DoubleThreshold Editor Effect===
===BinaryWatershed Editor Effect===


{{documentation/{{documentation/version}}/extension-section|Walk Through}}
{|
|[[Image:OriginalGoldGrayscale.png|thumb|Step 1: Original gray scale image.]]
|[[Image:BinShrinkSettings.png|thumb|Step 2: BinShrink settings.]]
|[[Image:BinShrinkGoldGrayscale.png|thumb|Step 3: After running the BinShrink by a factor of 5x5x5.]]
|[[Image:ROIToolbar.png|thumb|Step 4: ROI Toolbar.]]
|[[Image:CropGoldGrayscale.png|thumb|Step 5: Cropped gray scale image.]]
|[[Image:ThresholdGoldLabelMap.png|thumb|Step 6: Threshold of the cropped gray scale image.]]
|}
#[[Documentation/{{documentation/version}}/Modules/SlicerWelcome#LoadPanel|Load]] gray scale data.
#Go to the Modules search bar, search and select "BinShrink". Go to the BinShrink settings, change the input to the original gray scale image and change the output to "create a new volume".
#Apply the BinShrink Image Filter.
#Create a Region of Interest (ROI) using the Fiducial Module in the Slicer Toolbar.
#Use the [[Documentation/{{documentation/version}}/Modules/CropVolume|Crop Volume]] module to crop the region of interest.
#Apply [[Documentation/{{documentation/version}}/Modules/Editor#Threshold|Threshold Effect]], or any other editing technique, to your gray scale image to create a label map.
#[[Documentation/{{documentation/version}}/Modules/BRAINSResample|Resample]] the label map so its dimensions match those of the gray scale image.
##Using the [[Documentation/{{documentation/version}}/Modules/Transforms|Transforms]] module, create a new transform and rename it "Identity".
##Go to the [[Documentation/{{documentation/version}}/Modules/BRAINSResample|Resample]] settings to resample the label map.
##The Image to Warp should be the label map.
##The Reference Image should be the BinShrink gray scale image.
##Create a new Output Image.
##Change the pixel type to "short".
##Change the Transform file to "Identity".
##Change the Interpolation Mode to "NearestNeighbor".
##Apply the Resampling.


{{documentation/{{documentation/version}}/extension-section|Tutorials}}


{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
N/A


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


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


{{documentation/{{documentation/version}}/extension-footer}}

Documentation/Nightly/Extensions/IASEM

2013-08-06T15:45:03Z

Ksukri:

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

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


{{ambox
| type = protection
| image = [[File:InProgress.png|40px|alt=Work in progress]]
| text = WARNING: This module is Work in Progress, which means:
* the functionality provided by this module may change drastically in the future releases of 3D Slicer
* the scenes containing data types specific to this module may not be readable by the future versions of Slicer
* the functionality and user interface may change at any time
* some functionality may not work as intended
* testing and documentation is limited
}}


{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Acknowledgments:
This work is supported by NLM, and the Slicer Community. 
Author: Bradley Lowekamp 
Contact: Bradley Lowekamp <email>blowekamp@mail.nih.gov</email> 
License: [http://raw.github.com/blowekamp/Slicer-IASEM/master/LICENSE Apache License 2.0]
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|nlm}}|{{collaborator|longname|nlm}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/extension-section|Extension Description}}

This extension is a compilation of modules which are useful for segmentation and processing of IASEM Electron Microscopy images. It adds modules which help in general with segmenting large data sets, and has components to deal with images in multi-resolutions.

IASEM stands for ion-abrasion scanning electron microscopy, some times also call dual-beam or focused ion-beam scanning electron microscopy (FIBSEM).

<gallery widths="200px" perrow="4">
Image:IASEM-Screenshot1.png|Segmentation of Gold particles.
</gallery>


{{documentation/{{documentation/version}}/extension-section|Modules}}

* BinShrink Image Filter
* SpacingAwareCurvatureDiffusion Image Filter
* DoubleThreshold Editor Effect
* BinaryWatershed Editor Effect


{{documentation/{{documentation/version}}/extension-section|Use Cases}}
===BinShrink Image Filter===
Bin Shrink is one of the modules used to help ease the process of segmentation. By stipulating a neighborhood size, 5x5x5 for example, it will average the neighboring pixels within that 5x5x5 region and turn them into one pixel. Applying the Bin Shrink will result in reduced resolution and a less noisy image. Based on the features you want to segment, you can apply a more aggressive bin or a less aggressive bin based on the complexity of your features of interest. Binning the image does not significantly affect the quality of the image, it also reduces the amount of memory the computer needs to process the data, so the more an image is binned the faster slicer will work and the more free memory you will have.

{|
|[[Image:GoldGrayscale.png|thumb|Original gray scale image.]]
|[[Image:GoldGrayscaleBin5.png|thumb|After running the BinShrink by a factor of 5x5x5.]]
|}

===SpacingAwareCurvatureDiffusion Image Filter===
===DoubleThreshold Editor Effect===
===BinaryWatershed Editor Effect===


{{documentation/{{documentation/version}}/extension-section|Walk Through}}
{|
|[[Image:OriginalGoldGrayscale.png|thumb|Step 1: Original gray scale image.]]
|[[Image:BinShrinkSettings.png|thumb|Step 2: BinShrink settings.]]
|[[Image:BinShrinkGoldGrayscale.png|thumb|Step 3: After running the BinShrink by a factor of 5x5x5.]]
|[[Image:ROIToolbar.png|thumb|Step 4: ROI Toolbar.]]
|[[Image:CropGoldGrayscale.png|thumb|Step 5: Cropped gray scale image.]]
|[[Image:ThresholdGoldLabelMap.png|thumb|Step 6: Threshold of the cropped gray scale image.]]
|}
#[[Documentation/{{documentation/version}}/Modules/SlicerWelcome#LoadPanel|Load]] gray scale data.
#Go to the Modules search bar, search and select "BinShrink". Go to the BinShrink settings, change the input to the original gray scale image and change the output to "create a new volume".
#Apply the BinShrink Image Filter.
#Create a Region of Interest (ROI) using the Fiducial Module in the Slicer Toolbar.
#Use the [[Documentation/{{documentation/version}}/Modules/CropVolume|Crop Volume]] module to crop the region of interest.
#Apply [[Documentation/{{documentation/version}}/Modules/Editor#Threshold|Threshold Effect]], or any other editing technique, to your gray scale image to create a label map.
#[[Documentation/{{documentation/version}}/Modules/BRAINSResample|Resample]] the label map so its dimensions match those of the gray scale image.


{{documentation/{{documentation/version}}/extension-section|Tutorials}}


{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
N/A


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


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


{{documentation/{{documentation/version}}/extension-footer}}

Documentation/Nightly/Extensions/IASEM

2013-08-06T15:44:34Z

Ksukri:

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

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


{{ambox
| type = protection
| image = [[File:InProgress.png|40px|alt=Work in progress]]
| text = WARNING: This module is Work in Progress, which means:
* the functionality provided by this module may change drastically in the future releases of 3D Slicer
* the scenes containing data types specific to this module may not be readable by the future versions of Slicer
* the functionality and user interface may change at any time
* some functionality may not work as intended
* testing and documentation is limited
}}


{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Acknowledgments:
This work is supported by NLM, and the Slicer Community. 
Author: Bradley Lowekamp 
Contact: Bradley Lowekamp <email>blowekamp@mail.nih.gov</email> 
License: [http://raw.github.com/blowekamp/Slicer-IASEM/master/LICENSE Apache License 2.0]
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|nlm}}|{{collaborator|longname|nlm}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/extension-section|Extension Description}}

This extension is a compilation of modules which are useful for segmentation and processing of IASEM Electron Microscopy images. It adds modules which help in general with segmenting large data sets, and has components to deal with images in multi-resolutions.

IASEM stands for ion-abrasion scanning electron microscopy, some times also call dual-beam or focused ion-beam scanning electron microscopy (FIBSEM).

<gallery widths="200px" perrow="4">
Image:IASEM-Screenshot1.png|Segmentation of Gold particles.
</gallery>


{{documentation/{{documentation/version}}/extension-section|Modules}}

* BinShrink Image Filter
* SpacingAwareCurvatureDiffusion Image Filter
* DoubleThreshold Editor Effect
* BinaryWatershed Editor Effect


{{documentation/{{documentation/version}}/extension-section|Use Cases}}
===BinShrink Image Filter===
Bin Shrink is one of the modules used to help ease the process of segmentation. By stipulating a neighborhood size, 5x5x5 for example, it will average the neighboring pixels within that 5x5x5 region and turn them into one pixel. Applying the Bin Shrink will result in reduced resolution and a less noisy image. Based on the features you want to segment, you can apply a more aggressive bin or a less aggressive bin based on the complexity of your features of interest. Binning the image does not significantly affect the quality of the image, it also reduces the amount of memory the computer needs to process the data, so the more an image is binned the faster slicer will work and the more free memory you will have.

{|
|[[Image:GoldGrayscale.png|thumb|Original gray scale image.]]
|[[Image:GoldGrayscaleBin5.png|thumb|After running the BinShrink by a factor of 5x5x5.]]
|}

===SpacingAwareCurvatureDiffusion Image Filter===
===DoubleThreshold Editor Effect===
===BinaryWatershed Editor Effect===


{{documentation/{{documentation/version}}/extension-section|Walk Through}}
{|
|[[Image:OriginalGoldGrayscale.png|thumb|Step 1: Original gray scale image.]]
|[[Image:BinShrinkSettings.png|thumb|Step 2: BinShrink settings.]]
|[[Image:BinShrinkGoldGrayscale.png|thumb|Step 3: After running the BinShrink by a factor of 5x5x5.]]
[[Image:ROIToolbar.png|thumb|Step 4: ROI Toolbar.]]
|[[Image:CropGoldGrayscale.png|thumb|Step 5: Cropped gray scale image.]]
|[[Image:ThresholdGoldLabelMap.png|thumb|Step 6: Threshold of the cropped gray scale image.]]
|}
#[[Documentation/{{documentation/version}}/Modules/SlicerWelcome#LoadPanel|Load]] gray scale data.
#Go to the Modules search bar, search and select "BinShrink". Go to the BinShrink settings, change the input to the original gray scale image and change the output to "create a new volume".
#Apply the BinShrink Image Filter.
#Create a Region of Interest (ROI) using the Fiducial Module in the Slicer Toolbar.
#Use the [[Documentation/{{documentation/version}}/Modules/CropVolume|Crop Volume]] module to crop the region of interest.
#Apply [[Documentation/{{documentation/version}}/Modules/Editor#Threshold|Threshold Effect]], or any other editing technique, to your gray scale image to create a label map.
#[[Documentation/{{documentation/version}}/Modules/BRAINSResample|Resample]] the label map so its dimensions match those of the gray scale image.


{{documentation/{{documentation/version}}/extension-section|Tutorials}}


{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
N/A


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


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


{{documentation/{{documentation/version}}/extension-footer}}

File:ROIToolbar.png

2013-08-06T15:37:57Z

Ksukri:

Documentation/Nightly/Extensions/IASEM

2013-08-06T15:33:44Z

Ksukri:

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

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


{{ambox
| type = protection
| image = [[File:InProgress.png|40px|alt=Work in progress]]
| text = WARNING: This module is Work in Progress, which means:
* the functionality provided by this module may change drastically in the future releases of 3D Slicer
* the scenes containing data types specific to this module may not be readable by the future versions of Slicer
* the functionality and user interface may change at any time
* some functionality may not work as intended
* testing and documentation is limited
}}


{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Acknowledgments:
This work is supported by NLM, and the Slicer Community. 
Author: Bradley Lowekamp 
Contact: Bradley Lowekamp <email>blowekamp@mail.nih.gov</email> 
License: [http://raw.github.com/blowekamp/Slicer-IASEM/master/LICENSE Apache License 2.0]
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|nlm}}|{{collaborator|longname|nlm}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/extension-section|Extension Description}}

This extension is a compilation of modules which are useful for segmentation and processing of IASEM Electron Microscopy images. It adds modules which help in general with segmenting large data sets, and has components to deal with images in multi-resolutions.

IASEM stands for ion-abrasion scanning electron microscopy, some times also call dual-beam or focused ion-beam scanning electron microscopy (FIBSEM).

<gallery widths="200px" perrow="4">
Image:IASEM-Screenshot1.png|Segmentation of Gold particles.
</gallery>


{{documentation/{{documentation/version}}/extension-section|Modules}}

* BinShrink Image Filter
* SpacingAwareCurvatureDiffusion Image Filter
* DoubleThreshold Editor Effect
* BinaryWatershed Editor Effect


{{documentation/{{documentation/version}}/extension-section|Use Cases}}
===BinShrink Image Filter===
Bin Shrink is one of the modules used to help ease the process of segmentation. By stipulating a neighborhood size, 5x5x5 for example, it will average the neighboring pixels within that 5x5x5 region and turn them into one pixel. Applying the Bin Shrink will result in reduced resolution and a less noisy image. Based on the features you want to segment, you can apply a more aggressive bin or a less aggressive bin based on the complexity of your features of interest. Binning the image does not significantly affect the quality of the image, it also reduces the amount of memory the computer needs to process the data, so the more an image is binned the faster slicer will work and the more free memory you will have.

{|
|[[Image:GoldGrayscale.png|thumb|Original gray scale image.]]
|[[Image:GoldGrayscaleBin5.png|thumb|After running the BinShrink by a factor of 5x5x5.]]
|}

===SpacingAwareCurvatureDiffusion Image Filter===
===DoubleThreshold Editor Effect===
===BinaryWatershed Editor Effect===


{{documentation/{{documentation/version}}/extension-section|Walk Through}}
{|
|[[Image:OriginalGoldGrayscale.png|thumb|Original gray scale image.]]
|[[Image:BinShrinkSettings.png|thumb|BinShrink settings.]]
|[[Image:BinShrinkGoldGrayscale.png|thumb|After running the BinShrink by a factor of 5x5x5.]]
|[[Image:CropGoldGrayscale.png|thumb|Cropped gray scale image.]]
|[[Image:ThresholdGoldLabelMap.png|thumb|Threshold of the cropped gray scale image.]]
|}
#[[Documentation/{{documentation/version}}/Modules/SlicerWelcome#LoadPanel|Load]] gray scale data.
#Go to the Modules search bar, search and select "BinShrink". Go to the BinShrink settings, change the input to the original gray scale image and change the output to "create a new volume", then apply the BinShrink Image Filter.
#Use the [[Documentation/{{documentation/version}}/Modules/CropVolume|Crop Volume]] module to crop a region of interest.
#Apply [[Documentation/{{documentation/version}}/Modules/Editor#Threshold|Threshold Effect]], or any other editing technique, to your gray scale image to create a label map.
#[[Documentation/{{documentation/version}}/Modules/BRAINSResample|Resample]] the label map so its dimensions match those of the gray scale image.


{{documentation/{{documentation/version}}/extension-section|Tutorials}}


{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
N/A


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


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


{{documentation/{{documentation/version}}/extension-footer}}

Documentation/Nightly/Extensions/IASEM

2013-08-06T15:32:07Z

Ksukri:

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

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


{{ambox
| type = protection
| image = [[File:InProgress.png|40px|alt=Work in progress]]
| text = WARNING: This module is Work in Progress, which means:
* the functionality provided by this module may change drastically in the future releases of 3D Slicer
* the scenes containing data types specific to this module may not be readable by the future versions of Slicer
* the functionality and user interface may change at any time
* some functionality may not work as intended
* testing and documentation is limited
}}


{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Acknowledgments:
This work is supported by NLM, and the Slicer Community. 
Author: Bradley Lowekamp 
Contact: Bradley Lowekamp <email>blowekamp@mail.nih.gov</email> 
License: [http://raw.github.com/blowekamp/Slicer-IASEM/master/LICENSE Apache License 2.0]
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|nlm}}|{{collaborator|longname|nlm}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/extension-section|Extension Description}}

This extension is a compilation of modules which are useful for segmentation and processing of IASEM Electron Microscopy images. It adds modules which help in general with segmenting large data sets, and has components to deal with images in multi-resolutions.

IASEM stands for ion-abrasion scanning electron microscopy, some times also call dual-beam or focused ion-beam scanning electron microscopy (FIBSEM).

<gallery widths="200px" perrow="4">
Image:IASEM-Screenshot1.png|Segmentation of Gold particles.
</gallery>


{{documentation/{{documentation/version}}/extension-section|Modules}}

* BinShrink Image Filter
* SpacingAwareCurvatureDiffusion Image Filter
* DoubleThreshold Editor Effect
* BinaryWatershed Editor Effect


{{documentation/{{documentation/version}}/extension-section|Use Cases}}
===BinShrink Image Filter===
Bin Shrink is one of the modules used to help ease the process of segmentation. By stipulating a neighborhood size, 5x5x5 for example, it will average the neighboring pixels within that 5x5x5 region and turn them into one pixel. Applying the Bin Shrink will result in reduced resolution and a less noisy image. Based on the features you want to segment, you can apply a more aggressive bin or a less aggressive bin based on the complexity of your features of interest. Binning the image does not significantly affect the quality of the image, it also reduces the amount of memory the computer needs to process the data, so the more an image is binned the faster slicer will work and the more free memory you will have.

{|
|[[Image:GoldGrayscale.png|thumb|Original gray scale image.]]
|[[Image:GoldGrayscaleBin5.png|thumb|After running the BinShrink by a factor of 5x5x5.]]
|}

===SpacingAwareCurvatureDiffusion Image Filter===
===DoubleThreshold Editor Effect===
===BinaryWatershed Editor Effect===


{{documentation/{{documentation/version}}/extension-section|Walk Through}}
{|
|[[Image:OriginalGoldGrayscale.png|thumb|Original gray scale image.]]
|[[Image:BinShrinkSettings.png|thumb|BinShrink settings.]]
|[[Image:BinShrinkGoldGrayscale.png|thumb|After running the BinShrink by a factor of 5x5x5.]]
|[[Image:CropGoldGrayscale.png|thumb|Cropped gray scale image.]]
|[[Image:ThresholdGoldLabelMap.png|thumb|Threshold of the cropped gray scale image.]]
|}
#[[Documentation/{{documentation/version}}/Modules/SlicerWelcome#LoadPanel|Load]] gray scale data.
#Go to the BinShrink settings, change the input to the original gray scale image and change the output to "create a new volume", then apply the BinShrink Image Filter.
#Use the [[Documentation/{{documentation/version}}/Modules/CropVolume|Crop Volume]] module to crop a region of interest.
#Apply [[Documentation/{{documentation/version}}/Modules/Editor#Threshold|Threshold Effect]], or any other editing technique, to your gray scale image to create a label map.
#[[Documentation/{{documentation/version}}/Modules/BRAINSResample|Resample]] the label map so its dimensions match those of the gray scale image.


{{documentation/{{documentation/version}}/extension-section|Tutorials}}


{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
N/A


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


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


{{documentation/{{documentation/version}}/extension-footer}}

Documentation/Nightly/Extensions/IASEM

2013-08-06T15:20:33Z

Ksukri:

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

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


{{ambox
| type = protection
| image = [[File:InProgress.png|40px|alt=Work in progress]]
| text = WARNING: This module is Work in Progress, which means:
* the functionality provided by this module may change drastically in the future releases of 3D Slicer
* the scenes containing data types specific to this module may not be readable by the future versions of Slicer
* the functionality and user interface may change at any time
* some functionality may not work as intended
* testing and documentation is limited
}}


{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Acknowledgments:
This work is supported by NLM, and the Slicer Community. 
Author: Bradley Lowekamp 
Contact: Bradley Lowekamp <email>blowekamp@mail.nih.gov</email> 
License: [http://raw.github.com/blowekamp/Slicer-IASEM/master/LICENSE Apache License 2.0]
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|nlm}}|{{collaborator|longname|nlm}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/extension-section|Extension Description}}

This extension is a compilation of modules which are useful for segmentation and processing of IASEM Electron Microscopy images. It adds modules which help in general with segmenting large data sets, and has components to deal with images in multi-resolutions.

IASEM stands for ion-abrasion scanning electron microscopy, some times also call dual-beam or focused ion-beam scanning electron microscopy (FIBSEM).

<gallery widths="200px" perrow="4">
Image:IASEM-Screenshot1.png|Segmentation of Gold particles.
</gallery>


{{documentation/{{documentation/version}}/extension-section|Modules}}

* BinShrink Image Filter
* SpacingAwareCurvatureDiffusion Image Filter
* DoubleThreshold Editor Effect
* BinaryWatershed Editor Effect


{{documentation/{{documentation/version}}/extension-section|Use Cases}}
===BinShrink Image Filter===
Bin Shrink is one of the modules used to help ease the process of segmentation. By stipulating a neighborhood size, 5x5x5 for example, it will average the neighboring pixels within that 5x5x5 region and turn them into one pixel. Applying the Bin Shrink will result in reduced resolution and a less noisy image. Based on the features you want to segment, you can apply a more aggressive bin or a less aggressive bin based on the complexity of your features of interest. Binning the image does not significantly affect the quality of the image, it also reduces the amount of memory the computer needs to process the data, so the more an image is binned the faster slicer will work and the more free memory you will have.

{|
|[[Image:GoldGrayscale.png|thumb|Original gray scale image.]]
|[[Image:GoldGrayscaleBin5.png|thumb|After running the BinShrink by a factor of 5x5x5.]]
|}

===SpacingAwareCurvatureDiffusion Image Filter===
===DoubleThreshold Editor Effect===
===BinaryWatershed Editor Effect===


{{documentation/{{documentation/version}}/extension-section|Walk Through}}
{|
|[[Image:OriginalGoldGrayscale.png|thumb|Original gray scale image.]]
|[[Image:BinShrinkSettings.png|thumb|BinShrink settings.]]
|[[Image:BinShrinkGoldGrayscale.png|thumb|After running the BinShrink by a factor of 5x5x5.]]
|[[Image:CropGoldGrayscale.png|thumb|Cropped gray scale image.]]
|[[Image:ThresholdGoldLabelMap.png|thumb|Threshold of the cropped gray scale image.]]
|}
#Upload gray scale data.
#Go to the BinShrink settings, change the input to the original gray scale image and change the output to "create a new volume", then apply the BinShrink Image Filter.
#Use the [[Documentation/{{documentation/version}}/Modules/CropVolume|Crop Volume]] module to crop a region of interest.
#Apply [[Documentation/{{documentation/version}}/Modules/Editor#Threshold|Threshold Effect]], or any other editing technique, to your gray scale image to create a label map.
#[[Documentation/{{documentation/version}}/Modules/BRAINSResample|Resample]] the label map so its dimensions match those of the gray scale image.


{{documentation/{{documentation/version}}/extension-section|Tutorials}}


{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
N/A


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


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


{{documentation/{{documentation/version}}/extension-footer}}

File:ThresholdGoldLabelMap.png

2013-08-06T15:19:24Z

Ksukri:

File:BinShrinkSettings.png

2013-08-06T15:18:02Z

Ksukri:

Documentation/Nightly/Extensions/IASEM

2013-08-06T15:17:00Z

Ksukri:

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

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


{{ambox
| type = protection
| image = [[File:InProgress.png|40px|alt=Work in progress]]
| text = WARNING: This module is Work in Progress, which means:
* the functionality provided by this module may change drastically in the future releases of 3D Slicer
* the scenes containing data types specific to this module may not be readable by the future versions of Slicer
* the functionality and user interface may change at any time
* some functionality may not work as intended
* testing and documentation is limited
}}


{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Acknowledgments:
This work is supported by NLM, and the Slicer Community. 
Author: Bradley Lowekamp 
Contact: Bradley Lowekamp <email>blowekamp@mail.nih.gov</email> 
License: [http://raw.github.com/blowekamp/Slicer-IASEM/master/LICENSE Apache License 2.0]
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|nlm}}|{{collaborator|longname|nlm}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/extension-section|Extension Description}}

This extension is a compilation of modules which are useful for segmentation and processing of IASEM Electron Microscopy images. It adds modules which help in general with segmenting large data sets, and has components to deal with images in multi-resolutions.

IASEM stands for ion-abrasion scanning electron microscopy, some times also call dual-beam or focused ion-beam scanning electron microscopy (FIBSEM).

<gallery widths="200px" perrow="4">
Image:IASEM-Screenshot1.png|Segmentation of Gold particles.
</gallery>


{{documentation/{{documentation/version}}/extension-section|Modules}}

* BinShrink Image Filter
* SpacingAwareCurvatureDiffusion Image Filter
* DoubleThreshold Editor Effect
* BinaryWatershed Editor Effect


{{documentation/{{documentation/version}}/extension-section|Use Cases}}
===BinShrink Image Filter===
Bin Shrink is one of the modules used to help ease the process of segmentation. By stipulating a neighborhood size, 5x5x5 for example, it will average the neighboring pixels within that 5x5x5 region and turn them into one pixel. Applying the Bin Shrink will result in reduced resolution and a less noisy image. Based on the features you want to segment, you can apply a more aggressive bin or a less aggressive bin based on the complexity of your features of interest. Binning the image does not significantly affect the quality of the image, it also reduces the amount of memory the computer needs to process the data, so the more an image is binned the faster slicer will work and the more free memory you will have.

{|
|[[Image:GoldGrayscale.png|thumb|Original gray scale image.]]
|[[Image:GoldGrayscaleBin5.png|thumb|After running the BinShrink by a factor of 5x5x5.]]
|}

===SpacingAwareCurvatureDiffusion Image Filter===
===DoubleThreshold Editor Effect===
===BinaryWatershed Editor Effect===


{{documentation/{{documentation/version}}/extension-section|Walk Through}}
{|
|[[Image:OriginalGoldGrayscale.png|thumb|Original gray scale image.]]
|[[Image:BinShrinkGoldGrayscale.png|thumb|After running the BinShrink by a factor of 5x5x5.]]
|[[Image:CropGoldGrayscale.png|thumb|Cropped gray scale volume.]]
|}
#Upload gray scale data.
#Go to the BinShrink tool, change the input to the original gray scale image and change the output to "create a new volume", then apply the BinShrink Image Filter.
#Use the [[Documentation/{{documentation/version}}/Modules/CropVolume|Crop Volume]] module to crop a region of interest.
#Apply [[Documentation/{{documentation/version}}/Modules/Editor#Threshold|Threshold Effect]], or any other editing technique, to your gray scale image to create a label map.
#[[Documentation/{{documentation/version}}/Modules/BRAINSResample|Resample]] the label map so its dimensions match those of the gray scale image.


{{documentation/{{documentation/version}}/extension-section|Tutorials}}


{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
N/A


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


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


{{documentation/{{documentation/version}}/extension-footer}}

File:CropGoldGrayscale.png

2013-08-06T15:16:05Z

Ksukri:

File:BinShrinkGoldGrayscale.png

2013-08-06T15:14:31Z

Ksukri:

File:OriginalGoldGrayscale.png

2013-08-06T15:13:28Z

Ksukri:

Documentation/Nightly/Extensions/IASEM

2013-08-06T15:11:41Z

Ksukri:

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

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


{{ambox
| type = protection
| image = [[File:InProgress.png|40px|alt=Work in progress]]
| text = WARNING: This module is Work in Progress, which means:
* the functionality provided by this module may change drastically in the future releases of 3D Slicer
* the scenes containing data types specific to this module may not be readable by the future versions of Slicer
* the functionality and user interface may change at any time
* some functionality may not work as intended
* testing and documentation is limited
}}


{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Acknowledgments:
This work is supported by NLM, and the Slicer Community. 
Author: Bradley Lowekamp 
Contact: Bradley Lowekamp <email>blowekamp@mail.nih.gov</email> 
License: [http://raw.github.com/blowekamp/Slicer-IASEM/master/LICENSE Apache License 2.0]
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|nlm}}|{{collaborator|longname|nlm}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/extension-section|Extension Description}}

This extension is a compilation of modules which are useful for segmentation and processing of IASEM Electron Microscopy images. It adds modules which help in general with segmenting large data sets, and has components to deal with images in multi-resolutions.

IASEM stands for ion-abrasion scanning electron microscopy, some times also call dual-beam or focused ion-beam scanning electron microscopy (FIBSEM).

<gallery widths="200px" perrow="4">
Image:IASEM-Screenshot1.png|Segmentation of Gold particles.
</gallery>


{{documentation/{{documentation/version}}/extension-section|Modules}}

* BinShrink Image Filter
* SpacingAwareCurvatureDiffusion Image Filter
* DoubleThreshold Editor Effect
* BinaryWatershed Editor Effect


{{documentation/{{documentation/version}}/extension-section|Use Cases}}
===BinShrink Image Filter===
Bin Shrink is one of the modules used to help ease the process of segmentation. By stipulating a neighborhood size, 5x5x5 for example, it will average the neighboring pixels within that 5x5x5 region and turn them into one pixel. Applying the Bin Shrink will result in reduced resolution and a less noisy image. Based on the features you want to segment, you can apply a more aggressive bin or a less aggressive bin based on the complexity of your features of interest. Binning the image does not significantly affect the quality of the image, it also reduces the amount of memory the computer needs to process the data, so the more an image is binned the faster slicer will work and the more free memory you will have.

{|
|[[Image:GoldGrayscale.png|thumb|Original gray scale image.]]
|[[Image:GoldGrayscaleBin5.png|thumb|After running the BinShrink by a factor of 5x5x5.]]
|}

===SpacingAwareCurvatureDiffusion Image Filter===
===DoubleThreshold Editor Effect===
===BinaryWatershed Editor Effect===


{{documentation/{{documentation/version}}/extension-section|Walk Through}}
#Upload gray scale data.
#Go to the BinShrink tool, change the input to the original gray scale image and change the output to "create a new volume", then apply the BinShrink Image Filter.
#Use the [[Documentation/{{documentation/version}}/Modules/CropVolume|Crop Volume]] module to crop a region of interest.
#Apply [[Documentation/{{documentation/version}}/Modules/Editor#Threshold|Threshold Effect]], or any other editing technique, to your gray scale image to create a label map.
#[[Documentation/{{documentation/version}}/Modules/BRAINSResample|Resample]] the label map so its dimensions match those of the gray scale image.


{{documentation/{{documentation/version}}/extension-section|Tutorials}}


{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
N/A


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


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


{{documentation/{{documentation/version}}/extension-footer}}

Documentation/Nightly/Modules/Editor/WatershedFromMarkers

2013-08-06T15:08:17Z

Ksukri:

<noinclude>{{documentation/versioncheck}}</noinclude>
{{ambox
| type = protection
| image = [[File:InProgress.png|40px|alt=Work in progress]]
| text = WARNING: This module is Work in Progress, which means:
* the functionality provided by this module may change drastically in the future releases of 3D Slicer
* the scenes containing data types specific to this module may not be readable by the future versions of Slicer
* the functionality and user interface may change at any time
* some functionality may not work as intended
* testing and documentation is limited
}}


{{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}}
: '''Author(s)/Contributor(s):''' Bradley Lowekamp (MSC/NLM), Steve Piepe(Isomics Inc.) 
: '''Acknowledgements:''' This work is supported by NLM, and the Slicer Community. 
: '''Contact:''' Bradley Lowekamp, <email>blowekamp@mail.nih.gov</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|nlm}}|{{collaborator|longname|nlm}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
Watershed from Markers is an edge based editing tool that detects edges and fills in a specific area based on the given outlines created in the label map. It is an effective way to segment features with robust outlines more efficiently.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{|
|[[Image:step1_grayscale.png|thumb|Step 1: Tumor Gray Scale]]
|[[Image:step2_originallabel.png|thumb|Step 2: Original Label Map]]
|[[Image:step3_watershed.png|thumb|Step 3: Label Map after Watershed]]
|[[Image:step4_changelabelmap.png|thumb|Step 4: Label Map after Change Label effect]]
|[[Image:step5_leakedpixels.png|thumb|Step 5: Leaked Pixels]]
|[[Image:step6_finallabel.png|thumb|Step 6: Final Label Map]]
|}
# Use MRBrain Tumor Time Point 1 from Slicer's [[Documentation/{{documentation/version}}/Modules/SampleData|Sample Data]]. Scroll through the data and find a feature of interest, for example the tumor.
# With the [[Documentation/{{documentation/version}}/Modules/Editor#Paint|Paint]] tool, create an original label map as the input for the Watershed from Markers tool. Using one color, paint the tumor precisely. Watershed from Markers is an edge based algorithm and labeling pixels outside of the tumor outline will result in an inaccurate label map. In another color, outline the tumor and fill in part of the background. This can be done for one slide or multiple slides in which the tumor is visible. Labeling more slides will result in a more accurate watershed.
# After the Watershed from Markers is applied, the tumor will be represented by one color and the background will be represented by another color.
# Using the [[Documentation/{{documentation/version}}/Modules/Editor#Change Label|Change Label]] effect, change the background color to black.
# Once the background label has been changed, look through each slice for leaked pixels.
# To fix leaked pixels, use the [[Documentation/{{documentation/version}}/Modules/Editor#Paint|Paint]] tool to erase extra pixels from the label map. Another way to edit your label map is to apply the [[Documentation/{{documentation/version}}/Modules/Editor#Undo/Redo|Undo/Redo]] tools. Using the undo, the watershed can be undone and the original label map can be edited. The redo tool can reapply an updated version of the Watershed from Markers effect. After looking through each slice for leaked pixels, the label map should accurately represent your tumor.


{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


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


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

Documentation/Nightly/Extensions/IASEM

2013-08-06T14:48:32Z

Ksukri:

Documentation/Nightly/Extensions/IASEM

2013-08-06T14:07:22Z

Ksukri:

Documentation/Nightly/Extensions/IASEM

2013-08-06T14:05:17Z

Ksukri:

Documentation/Nightly/Modules/Editor/WatershedFromMarkers

2013-08-06T13:59:28Z

Ksukri:

<noinclude>{{documentation/versioncheck}}</noinclude>
{{ambox
| type = protection
| image = [[File:InProgress.png|40px|alt=Work in progress]]
| text = WARNING: This module is Work in Progress, which means:
* the functionality provided by this module may change drastically in the future releases of 3D Slicer
* the scenes containing data types specific to this module may not be readable by the future versions of Slicer
* the functionality and user interface may change at any time
* some functionality may not work as intended
* testing and documentation is limited
}}


{{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}}
: '''Author(s)/Contributor(s):''' Bradley Lowekamp (MSC/NLM), Steve Piepe(Isomics Inc.) 
: '''Acknowledgements:''' This work is supported by NLM, and the Slicer Community. 
: '''Contact:''' Bradley Lowekamp, <email>blowekamp@mail.nih.gov</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|nlm}}|{{collaborator|longname|nlm}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
Watershed from Markers is an edge based editing tool that detects edges and fills in a specific area based on the given outlines created in the label map. It is an effective way to segment features with robust outlines more efficiently.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{|
|[[Image:step1_grayscale.png|thumb|Step 1: Tumor Gray Scale]]
|[[Image:step2_originallabel.png|thumb|Step 2: Original Label Map]]
|[[Image:step3_watershed.png|thumb|Step 3: Label Map after Watershed]]
|[[Image:step4_changelabelmap.png|thumb|Step 4: Label Map after Change Label effect]]
|[[Image:step5_leakedpixels.png|thumb|Step 5: Leaked Pixels]]
|[[Image:step6_finallabel.png|thumb|Step 6: Final Label Map]]
|}
# Use MRBrain Tumor Time Point 1 from Slicer's [[Documentation/{{documentation/version}}/Modules/SampleData|Sample Data]]. Scroll through the data and find a feature of interest, for example the tumor.
# With the [[Documentation/{{documentation/version}}/Modules/Editor#Paint|Paint]] tool, create an original label map as the input for the Watershed from Markers tool. Using one color, paint the tumor precisely. Watershed from Markers is an edge based algorithm and labeling pixels outside of the tumor outline will result in an inaccurate label map. In another color, outline the tumor and fill in part of the background. This can be done for one slide or multiple slides in which the tumor is visible. Labeling more slides will result in a more accurate watershed.
# After the Watershed from Markers is applied, the tumor will be represented by one color and the background will be represented by another color.
# Using the [[Documentation/{{documentation/version}}/Modules/Editor#Change Label|Change Label]] effect, change the background color to black.
# Once the background label has been changed, look through each slice for leaked pixels.
# To fix leaked pixels, use the [[Documentation/{{documentation/version}}/Modules/Editor#Paint|Paint]] tool to erase extra pixels from the label map. After looking through each slice for leaked pixels, the label map should accurately represent your tumor.


{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


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


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

File:Step6 finallabel.png

2013-08-06T13:59:06Z

Ksukri:

Documentation/Nightly/Modules/Editor/WatershedFromMarkers

2013-08-06T13:58:36Z

Ksukri:

<noinclude>{{documentation/versioncheck}}</noinclude>
{{ambox
| type = protection
| image = [[File:InProgress.png|40px|alt=Work in progress]]
| text = WARNING: This module is Work in Progress, which means:
* the functionality provided by this module may change drastically in the future releases of 3D Slicer
* the scenes containing data types specific to this module may not be readable by the future versions of Slicer
* the functionality and user interface may change at any time
* some functionality may not work as intended
* testing and documentation is limited
}}


{{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}}
: '''Author(s)/Contributor(s):''' Bradley Lowekamp (MSC/NLM), Steve Piepe(Isomics Inc.) 
: '''Acknowledgements:''' This work is supported by NLM, and the Slicer Community. 
: '''Contact:''' Bradley Lowekamp, <email>blowekamp@mail.nih.gov</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|nlm}}|{{collaborator|longname|nlm}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
Watershed from Markers is an edge based editing tool that detects edges and fills in a specific area based on the given outlines created in the label map. It is an effective way to segment features with robust outlines more efficiently.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{|
|[[Image:step1_grayscale.png|thumb|Step 1: Tumor Gray Scale]]
|[[Image:step2_originallabel.png|thumb|Step 2: Original Label Map]]
|[[Image:step3_watershed.png|thumb|Step 3: Label Map after Watershed]]
|[[Image:step4_changelabelmap.png|thumb|Step 4: Label Map after Change Label effect]]
|[[Image:step5_leakedpixels.png|thumb|Step 5: Leaked Pixels]]
|[[Image:61.png|thumb|Step 6: Final Label Map]]
|}
# Use MRBrain Tumor Time Point 1 from Slicer's [[Documentation/{{documentation/version}}/Modules/SampleData|Sample Data]]. Scroll through the data and find a feature of interest, for example the tumor.
# With the [[Documentation/{{documentation/version}}/Modules/Editor#Paint|Paint]] tool, create an original label map as the input for the Watershed from Markers tool. Using one color, paint the tumor precisely. Watershed from Markers is an edge based algorithm and labeling pixels outside of the tumor outline will result in an inaccurate label map. In another color, outline the tumor and fill in part of the background. This can be done for one slide or multiple slides in which the tumor is visible. Labeling more slides will result in a more accurate watershed.
# After the Watershed from Markers is applied, the tumor will be represented by one color and the background will be represented by another color.
# Using the [[Documentation/{{documentation/version}}/Modules/Editor#Change Label|Change Label]] effect, change the background color to black.
# Once the background label has been changed, look through each slice for leaked pixels.
# To fix leaked pixels, use the [[Documentation/{{documentation/version}}/Modules/Editor#Paint|Paint]] tool to erase extra pixels from the label map. After looking through each slice for leaked pixels, the label map should accurately represent your tumor.


{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


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


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

File:Step5 leakedpixels.png

2013-08-06T13:58:17Z

Ksukri:

Documentation/Nightly/Modules/Editor/WatershedFromMarkers

2013-08-06T13:57:45Z

Ksukri:

<noinclude>{{documentation/versioncheck}}</noinclude>
{{ambox
| type = protection
| image = [[File:InProgress.png|40px|alt=Work in progress]]
| text = WARNING: This module is Work in Progress, which means:
* the functionality provided by this module may change drastically in the future releases of 3D Slicer
* the scenes containing data types specific to this module may not be readable by the future versions of Slicer
* the functionality and user interface may change at any time
* some functionality may not work as intended
* testing and documentation is limited
}}


{{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}}
: '''Author(s)/Contributor(s):''' Bradley Lowekamp (MSC/NLM), Steve Piepe(Isomics Inc.) 
: '''Acknowledgements:''' This work is supported by NLM, and the Slicer Community. 
: '''Contact:''' Bradley Lowekamp, <email>blowekamp@mail.nih.gov</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|nlm}}|{{collaborator|longname|nlm}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
Watershed from Markers is an edge based editing tool that detects edges and fills in a specific area based on the given outlines created in the label map. It is an effective way to segment features with robust outlines more efficiently.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{|
|[[Image:step1_grayscale.png|thumb|Step 1: Tumor Gray Scale]]
|[[Image:step2_originallabel.png|thumb|Step 2: Original Label Map]]
|[[Image:step3_watershed.png|thumb|Step 3: Label Map after Watershed]]
|[[Image:step4_changelabelmap.png|thumb|Step 4: Label Map after Change Label effect]]
|[[Image:51.png|thumb|Step 5: Leaked Pixels]]
|[[Image:61.png|thumb|Step 6: Final Label Map]]
|}
# Use MRBrain Tumor Time Point 1 from Slicer's [[Documentation/{{documentation/version}}/Modules/SampleData|Sample Data]]. Scroll through the data and find a feature of interest, for example the tumor.
# With the [[Documentation/{{documentation/version}}/Modules/Editor#Paint|Paint]] tool, create an original label map as the input for the Watershed from Markers tool. Using one color, paint the tumor precisely. Watershed from Markers is an edge based algorithm and labeling pixels outside of the tumor outline will result in an inaccurate label map. In another color, outline the tumor and fill in part of the background. This can be done for one slide or multiple slides in which the tumor is visible. Labeling more slides will result in a more accurate watershed.
# After the Watershed from Markers is applied, the tumor will be represented by one color and the background will be represented by another color.
# Using the [[Documentation/{{documentation/version}}/Modules/Editor#Change Label|Change Label]] effect, change the background color to black.
# Once the background label has been changed, look through each slice for leaked pixels.
# To fix leaked pixels, use the [[Documentation/{{documentation/version}}/Modules/Editor#Paint|Paint]] tool to erase extra pixels from the label map. After looking through each slice for leaked pixels, the label map should accurately represent your tumor.


{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


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


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

File:Step4 changelabelmap.png

2013-08-06T13:57:21Z

Ksukri:

Documentation/Nightly/Modules/Editor/WatershedFromMarkers

2013-08-06T13:56:29Z

Ksukri:

<noinclude>{{documentation/versioncheck}}</noinclude>
{{ambox
| type = protection
| image = [[File:InProgress.png|40px|alt=Work in progress]]
| text = WARNING: This module is Work in Progress, which means:
* the functionality provided by this module may change drastically in the future releases of 3D Slicer
* the scenes containing data types specific to this module may not be readable by the future versions of Slicer
* the functionality and user interface may change at any time
* some functionality may not work as intended
* testing and documentation is limited
}}


{{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}}
: '''Author(s)/Contributor(s):''' Bradley Lowekamp (MSC/NLM), Steve Piepe(Isomics Inc.) 
: '''Acknowledgements:''' This work is supported by NLM, and the Slicer Community. 
: '''Contact:''' Bradley Lowekamp, <email>blowekamp@mail.nih.gov</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|nlm}}|{{collaborator|longname|nlm}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
Watershed from Markers is an edge based editing tool that detects edges and fills in a specific area based on the given outlines created in the label map. It is an effective way to segment features with robust outlines more efficiently.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{|
|[[Image:step1_grayscale.png|thumb|Step 1: Tumor Gray Scale]]
|[[Image:step2_originallabel.png|thumb|Step 2: Original Label Map]]
|[[Image:step3_watershed.png|thumb|Step 3: Label Map after Watershed]]
|[[Image:41.png|thumb|Step 4: Label Map after Change Label effect]]
|[[Image:51.png|thumb|Step 5: Leaked Pixels]]
|[[Image:61.png|thumb|Step 6: Final Label Map]]
|}
# Use MRBrain Tumor Time Point 1 from Slicer's [[Documentation/{{documentation/version}}/Modules/SampleData|Sample Data]]. Scroll through the data and find a feature of interest, for example the tumor.
# With the [[Documentation/{{documentation/version}}/Modules/Editor#Paint|Paint]] tool, create an original label map as the input for the Watershed from Markers tool. Using one color, paint the tumor precisely. Watershed from Markers is an edge based algorithm and labeling pixels outside of the tumor outline will result in an inaccurate label map. In another color, outline the tumor and fill in part of the background. This can be done for one slide or multiple slides in which the tumor is visible. Labeling more slides will result in a more accurate watershed.
# After the Watershed from Markers is applied, the tumor will be represented by one color and the background will be represented by another color.
# Using the [[Documentation/{{documentation/version}}/Modules/Editor#Change Label|Change Label]] effect, change the background color to black.
# Once the background label has been changed, look through each slice for leaked pixels.
# To fix leaked pixels, use the [[Documentation/{{documentation/version}}/Modules/Editor#Paint|Paint]] tool to erase extra pixels from the label map. After looking through each slice for leaked pixels, the label map should accurately represent your tumor.


{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


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


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

File:Step3 watershed.png

2013-08-06T13:56:06Z

Ksukri:

Documentation/Nightly/Modules/Editor/WatershedFromMarkers

2013-08-06T13:55:24Z

Ksukri:

<noinclude>{{documentation/versioncheck}}</noinclude>
{{ambox
| type = protection
| image = [[File:InProgress.png|40px|alt=Work in progress]]
| text = WARNING: This module is Work in Progress, which means:
* the functionality provided by this module may change drastically in the future releases of 3D Slicer
* the scenes containing data types specific to this module may not be readable by the future versions of Slicer
* the functionality and user interface may change at any time
* some functionality may not work as intended
* testing and documentation is limited
}}


{{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}}
: '''Author(s)/Contributor(s):''' Bradley Lowekamp (MSC/NLM), Steve Piepe(Isomics Inc.) 
: '''Acknowledgements:''' This work is supported by NLM, and the Slicer Community. 
: '''Contact:''' Bradley Lowekamp, <email>blowekamp@mail.nih.gov</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|nlm}}|{{collaborator|longname|nlm}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
Watershed from Markers is an edge based editing tool that detects edges and fills in a specific area based on the given outlines created in the label map. It is an effective way to segment features with robust outlines more efficiently.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{|
|[[Image:step1_grayscale.png|thumb|Step 1: Tumor Gray Scale]]
|[[Image:step2_originallabel.png|thumb|Step 2: Original Label Map]]
|[[Image:31.png|thumb|Step 3: Label Map after Watershed]]
|[[Image:41.png|thumb|Step 4: Label Map after Change Label effect]]
|[[Image:51.png|thumb|Step 5: Leaked Pixels]]
|[[Image:61.png|thumb|Step 6: Final Label Map]]
|}
# Use MRBrain Tumor Time Point 1 from Slicer's [[Documentation/{{documentation/version}}/Modules/SampleData|Sample Data]]. Scroll through the data and find a feature of interest, for example the tumor.
# With the [[Documentation/{{documentation/version}}/Modules/Editor#Paint|Paint]] tool, create an original label map as the input for the Watershed from Markers tool. Using one color, paint the tumor precisely. Watershed from Markers is an edge based algorithm and labeling pixels outside of the tumor outline will result in an inaccurate label map. In another color, outline the tumor and fill in part of the background. This can be done for one slide or multiple slides in which the tumor is visible. Labeling more slides will result in a more accurate watershed.
# After the Watershed from Markers is applied, the tumor will be represented by one color and the background will be represented by another color.
# Using the [[Documentation/{{documentation/version}}/Modules/Editor#Change Label|Change Label]] effect, change the background color to black.
# Once the background label has been changed, look through each slice for leaked pixels.
# To fix leaked pixels, use the [[Documentation/{{documentation/version}}/Modules/Editor#Paint|Paint]] tool to erase extra pixels from the label map. After looking through each slice for leaked pixels, the label map should accurately represent your tumor.


{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


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


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

File:Step2 originallabel.png

2013-08-06T13:55:02Z

Ksukri:

Documentation/Nightly/Modules/Editor/WatershedFromMarkers

2013-08-06T13:54:11Z

Ksukri:

<noinclude>{{documentation/versioncheck}}</noinclude>
{{ambox
| type = protection
| image = [[File:InProgress.png|40px|alt=Work in progress]]
| text = WARNING: This module is Work in Progress, which means:
* the functionality provided by this module may change drastically in the future releases of 3D Slicer
* the scenes containing data types specific to this module may not be readable by the future versions of Slicer
* the functionality and user interface may change at any time
* some functionality may not work as intended
* testing and documentation is limited
}}


{{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}}
: '''Author(s)/Contributor(s):''' Bradley Lowekamp (MSC/NLM), Steve Piepe(Isomics Inc.) 
: '''Acknowledgements:''' This work is supported by NLM, and the Slicer Community. 
: '''Contact:''' Bradley Lowekamp, <email>blowekamp@mail.nih.gov</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|nlm}}|{{collaborator|longname|nlm}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
Watershed from Markers is an edge based editing tool that detects edges and fills in a specific area based on the given outlines created in the label map. It is an effective way to segment features with robust outlines more efficiently.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{|
|[[Image:step1_grayscale.png|thumb|Step 1: Tumor Gray Scale]]
|[[Image:21.png|thumb|Step 2: Original Label Map]]
|[[Image:31.png|thumb|Step 3: Label Map after Watershed]]
|[[Image:41.png|thumb|Step 4: Label Map after Change Label effect]]
|[[Image:51.png|thumb|Step 5: Leaked Pixels]]
|[[Image:61.png|thumb|Step 6: Final Label Map]]
|}
# Use MRBrain Tumor Time Point 1 from Slicer's [[Documentation/{{documentation/version}}/Modules/SampleData|Sample Data]]. Scroll through the data and find a feature of interest, for example the tumor.
# With the [[Documentation/{{documentation/version}}/Modules/Editor#Paint|Paint]] tool, create an original label map as the input for the Watershed from Markers tool. Using one color, paint the tumor precisely. Watershed from Markers is an edge based algorithm and labeling pixels outside of the tumor outline will result in an inaccurate label map. In another color, outline the tumor and fill in part of the background. This can be done for one slide or multiple slides in which the tumor is visible. Labeling more slides will result in a more accurate watershed.
# After the Watershed from Markers is applied, the tumor will be represented by one color and the background will be represented by another color.
# Using the [[Documentation/{{documentation/version}}/Modules/Editor#Change Label|Change Label]] effect, change the background color to black.
# Once the background label has been changed, look through each slice for leaked pixels.
# To fix leaked pixels, use the [[Documentation/{{documentation/version}}/Modules/Editor#Paint|Paint]] tool to erase extra pixels from the label map. After looking through each slice for leaked pixels, the label map should accurately represent your tumor.


{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


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


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

File:Step1 grayscale.png

2013-08-06T13:53:09Z

Ksukri:

Documentation/Nightly/Modules/Editor/WatershedFromMarkers

2013-08-02T15:46:32Z

Ksukri:

<noinclude>{{documentation/versioncheck}}</noinclude>
{{ambox
| type = protection
| image = [[File:InProgress.png|40px|alt=Work in progress]]
| text = WARNING: This module is Work in Progress, which means:
* the functionality provided by this module may change drastically in the future releases of 3D Slicer
* the scenes containing data types specific to this module may not be readable by the future versions of Slicer
* the functionality and user interface may change at any time
* some functionality may not work as intended
* testing and documentation is limited
}}


{{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}}
: '''Author(s)/Contributor(s):''' Bradley Lowekamp (MSC/NLM), Steve Piepe(Isomics Inc.) 
: '''Acknowledgements:''' This work is supported by NLM, and the Slicer Community. 
: '''Contact:''' Bradley Lowekamp, <email>blowekamp@mail.nih.gov</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|nlm}}|{{collaborator|longname|nlm}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
Watershed from Markers is an edge based editing tool that detects edges and fills in a specific area based on the given outlines created in the label map. It is an effective way to segment features with robust outlines more efficiently.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{|
|[[Image:11.png|thumb|Step 1: Tumor Gray Scale]]
|[[Image:21.png|thumb|Step 2: Original Label Map]]
|[[Image:31.png|thumb|Step 3: Label Map after Watershed]]
|[[Image:41.png|thumb|Step 4: Label Map after Change Label effect]]
|[[Image:51.png|thumb|Step 5: Leaked Pixels]]
|[[Image:61.png|thumb|Step 6: Final Label Map]]
|}
# Use MRBrain Tumor Time Point 1 from Slicer's [[Documentation/{{documentation/version}}/Modules/SampleData|Sample Data]]. Scroll through the data and find a feature of interest, for example the tumor.
# With the [[Documentation/{{documentation/version}}/Modules/Editor#Paint|Paint]] tool, create an original label map as the input for the Watershed from Markers tool. Using one color, paint the tumor precisely. Watershed from Markers is an edge based algorithm and labeling pixels outside of the tumor outline will result in an inaccurate label map. In another color, outline the tumor and fill in part of the background. This can be done for one slide or multiple slides in which the tumor is visible. Labeling more slides will result in a more accurate watershed.
# After the Watershed from Markers is applied, the tumor will be represented by one color and the background will be represented by another color.
# Using the [[Documentation/{{documentation/version}}/Modules/Editor#Change Label|Change Label]] effect, change the background color to black.
# Once the background label has been changed, look through each slice for leaked pixels.
# To fix leaked pixels, use the [[Documentation/{{documentation/version}}/Modules/Editor#Paint|Paint]] tool to erase extra pixels from the label map. After looking through each slice for leaked pixels, the label map should accurately represent your tumor.


{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


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


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

Documentation/Nightly/Modules/Editor/WatershedFromMarkers

2013-08-02T15:44:18Z

Ksukri:

<noinclude>{{documentation/versioncheck}}</noinclude>
{{ambox
| type = protection
| image = [[File:InProgress.png|40px|alt=Work in progress]]
| text = WARNING: This module is Work in Progress, which means:
* the functionality provided by this module may change drastically in the future releases of 3D Slicer
* the scenes containing data types specific to this module may not be readable by the future versions of Slicer
* the functionality and user interface may change at any time
* some functionality may not work as intended
* testing and documentation is limited
}}


{{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}}
: '''Author(s)/Contributor(s):''' Bradley Lowekamp (MSC/NLM), Steve Piepe(Isomics Inc.) 
: '''Acknowledgements:''' This work is supported by NLM, and the Slicer Community. 
: '''Contact:''' Bradley Lowekamp, <email>blowekamp@mail.nih.gov</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|nlm}}|{{collaborator|longname|nlm}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
Watershed from Markers is an edge based editing tool that detects edges and fills in a specific area based on the given outlines created in the label map.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{|
|[[Image:11.png|thumb|Step 1: Tumor Gray Scale]]
|[[Image:21.png|thumb|Step 2: Original Label Map]]
|[[Image:31.png|thumb|Step 3: Label Map after Watershed]]
|[[Image:41.png|thumb|Step 4: Label Map after Change Label effect]]
|[[Image:51.png|thumb|Step 5: Leaked Pixels]]
|[[Image:61.png|thumb|Step 6: Final Label Map]]
|}
# Use MRBrain Tumor Time Point 1 from Slicer's [[Documentation/{{documentation/version}}/Modules/SampleData|Sample Data]]. Scroll through the data and find a feature of interest, for example the tumor.
# With the [[Documentation/{{documentation/version}}/Modules/Editor#Paint|Paint]] tool, create an original label map as the input for the Watershed from Markers tool. Using one color, paint the tumor precisely. Watershed from Markers is an edge based algorithm and labeling pixels outside of the tumor outline will result in an inaccurate label map. In another color, outline the tumor and fill in part of the background. This can be done for one slide or multiple slides in which the tumor is visible. Labeling more slides will result in a more accurate watershed.
# After the Watershed from Markers is applied, the tumor will be represented by one color and the background will be represented by another color.
# Using the [[Documentation/{{documentation/version}}/Modules/Editor#Change Label|Change Label]] effect, change the background color to black.
# Once the background label has been changed, look through each slice for leaked pixels.
# To fix leaked pixels, use the [[Documentation/{{documentation/version}}/Modules/Editor#Paint|Paint]] tool to erase extra pixels from the label map. After looking through each slice for leaked pixels, the label map should accurately represent your tumor.


{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


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


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

File:61.png

2013-08-02T15:41:00Z

Ksukri:

File:51.png

2013-08-02T15:40:12Z

Ksukri:

File:41.png

2013-08-02T15:39:49Z

Ksukri:

File:31.png

2013-08-02T15:39:28Z

Ksukri:

File:21.png

2013-08-02T15:39:00Z

Ksukri:

File:11.png

2013-08-02T15:38:40Z

Ksukri:

Documentation/Nightly/Modules/Editor/WatershedFromMarkers

2013-08-02T15:31:51Z

Ksukri:

<noinclude>{{documentation/versioncheck}}</noinclude>
{{ambox
| type = protection
| image = [[File:InProgress.png|40px|alt=Work in progress]]
| text = WARNING: This module is Work in Progress, which means:
* the functionality provided by this module may change drastically in the future releases of 3D Slicer
* the scenes containing data types specific to this module may not be readable by the future versions of Slicer
* the functionality and user interface may change at any time
* some functionality may not work as intended
* testing and documentation is limited
}}


{{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}}
: '''Author(s)/Contributor(s):''' Bradley Lowekamp (MSC/NLM), Steve Piepe(Isomics Inc.) 
: '''Acknowledgements:''' This work is supported by NLM, and the Slicer Community. 
: '''Contact:''' Bradley Lowekamp, <email>blowekamp@mail.nih.gov</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|nlm}}|{{collaborator|longname|nlm}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
N/A
Watershed from Markers is an edge based editing tool that detects edges and fills in a specific area based on the given outlines created in the label map.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
N/A


{{documentation/{{documentation/version}}/module-section|Walk Through}}
{|
|[[Image:1.png|thumb|Step 1: Tumor Gray Scale]]
|[[Image:2.png|thumb|Step 2: Original Label Map]]
|[[Image:3.png|thumb|Step 3: Label Map after Watershed]]
|[[Image:4.png|thumb|Step 4: Label Map after Change Label effect]]
|[[Image:5.png|thumb|Step 5: Leaked Pixels]]
|[[Image:6.png|thumb|Step 6: Final Label Map]]
|}
# Use MRBrain Tumor Time Point 1 from Slicer's [[Documentation/{{documentation/version}}/Modules/SampleData|Sample Data]]. Scroll through the data and find a feature of interest, for example the tumor.
# With the [[Documentation/{{documentation/version}}/Modules/Editor#Paint|Paint]] tool, create an original label map as the input for the Watershed from Markers tool. Using one color, paint the tumor precisely. Watershed from Markers is an edge based algorithm and labeling pixels outside of the tumor outline will result in an inaccurate label map. In another color, outline the tumor and fill in part of the background. This can be done for one slide or multiple slides in which the tumor is visible. Labeling more slides will result in a more accurate watershed.
# After the Watershed from Markers is applied, the tumor will be represented by one color and the background will be represented by another color.
# Using the [[Documentation/{{documentation/version}}/Modules/Editor#Change Label|Change Label]] effect, change the background color to black.
# Once the background label has been changed, look through each slice for leaked pixels.
# To fix leaked pixels, use the [[Documentation/{{documentation/version}}/Modules/Editor#Paint|Paint]] tool to erase extra pixels from the label map. After looking through each slice for leaked pixels, the label map should accurately represent your tumor.


{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


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


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

File:6.png

2013-08-02T15:09:22Z

Ksukri:

File:5.png

2013-08-02T15:08:15Z

Ksukri:

File:4.png

2013-08-02T15:07:32Z

Ksukri:

File:3.png

2013-08-02T15:06:55Z

Ksukri:

File:2.png

2013-08-02T15:05:57Z

Ksukri:

File:1.png

2013-08-02T14:48:02Z

Ksukri:

Documentation/Nightly/Modules/Editor/WatershedFromMarkers

2013-08-01T18:28:46Z

Ksukri: