Slicer Wiki - User contributions [en]

Documentation/Nightly/Extensions/SlicerPathology

2016-05-18T19:02:34Z

Ebremer:

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

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



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/SlicerPathology|SlicerPathology]] 
Acknowledgments:
This work was supported by via the NIH-National Cancer Institute Grant U24 CA180918, as well as, U24 CA180918 Quantitative Image Informatics for Cancer Research (QIICR), http://qiicr.org, PIs Ron Kikinis and Andrey Fedorov, Brigham and Women's Hospital. 
Author: Erich Bremer 

Contributor 1: Yi Gao 
Contributor 2: Nicole Aucoin ({{collaborator|name|spl}}) 
Contributor 3: Andrey Fedorov ({{collaborator|name|spl}}) 
Contributor 4: Jean-Christophe Fillion-Robin ({{collaborator|name|kitware}}) 
Contact: Erich Bremer, <email>erich.bremer@stonybrook.edu</email> 

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


{{documentation/{{documentation/version}}/module-section|Module Description}}
This extension provides tools for automatic and semi-automatic pathology image segmentation.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-section|Tutorials}}
<embedvideo service="youtube">https://www.youtube.com/watch?v=HZ_vSb-C-LA</embedvideo>
{|
|[[File:SlicerPathologyScreenShot2.png|thumb|800px|Step 1 - Go to the SlicerPathology Extension.]]
|}
{|
|[[File:SlicerPathologyScreenShot3.png|thumb|800px|Step 2 - Click the user information tab. Enter your email address. This is used for identification of you in the file data files.]]
|}
{|
|[[File:SlicerPathologyScreenShot4.png|thumb|800px|Step 3 - Click "Load data" to select an image.]]
|}
{|
|[[File:SlicerPathologyScreenShot5.png|thumb|800px|Step 4 - Click the button Quick TCGA Effect button to activate the effect.]]
|}
{|
|[[File:SlicerPathologyScreenShot6.png|thumb|800px|Step 5 - Click "Start TCGA Segmenter and adjust the five segmentation algorithm parameters as needed.]]
|}
{|
|[[File:SlicerPathologyScreenShot7.png|thumb|800px|Step 6 - you can select a subregion to speed up the parameter tuning process. Press "Y" to execute the segmenter on the subregion (if it was selected) or the whole image]]
|}
{|
|[[File:SlicerPathologyScreenShot8.png|thumb|800px|Step 7 - you can click "Clear Selection" to clear the selected sub-region so that the segmenter operates on the whole image.]]
|}
{|
|[[File:SlicerPathologyScreenShot9.png|thumb|800px|Step 8 - "Click the "Submission" tab so that you can save your label masks and related meta data. (meta data will be stored as JSON)]]
|}
{|
|[[File:SlicerPathologyScreenShot-json.png|thumb|800px|Step 9 - "This is a sample of the stored meta data. Notice the addition of your username for identification.]]
|}

{{documentation/{{documentation/version}}/module-section|References}}
* [http://qiicr.org Quantitative Image Informatics for Cancer Research (QIICR)]
* [http://opencv.org Open Source Computer Vision]
* [http://cancergenome.nih.gov/ The Cancer Genome Atlas]


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
The source code for SlicerPathology is available at https://github.com/SBU-BMI/SlicerPathology


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

Documentation/Nightly/Extensions/SlicerPathology

2016-05-13T13:50:42Z

Ebremer:

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

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



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/SlicerPathology|SlicerPathology]] 
Acknowledgments:
This work was supported by via the NIH-National Cancer Institute Grant U24 CA180918, as well as, U24 CA180918 Quantitative Image Informatics for Cancer Research (QIICR), http://qiicr.org, PIs Ron Kikinis and Andrey Fedorov, Brigham and Women's Hospital. 
Author: Erich Bremer 

Contributor 1: Yi Gao 
Contributor 2: Nicole Aucoin ({{collaborator|name|spl}}) 
Contributor 3: Andrey Fedorov ({{collaborator|name|spl}}) 
Contributor 4: Jean-Christophe Fillion-Robin ({{collaborator|name|kitware}}) 
Contact: Erich Bremer, <email>erich.bremer@stonybrook.edu</email> 

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


{{documentation/{{documentation/version}}/module-section|Module Description}}
This extension provides tools for automatic and semi-automatic pathology image segmentation.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-section|Tutorials}}
{|
|[[File:SlicerPathologyScreenShot2.png|thumb|800px|Step 1 - Go to the SlicerPathology Extension.]]
|}
{|
|[[File:SlicerPathologyScreenShot3.png|thumb|800px|Step 2 - Click the user information tab. Enter your email address. This is used for identification of you in the file data files.]]
|}
{|
|[[File:SlicerPathologyScreenShot4.png|thumb|800px|Step 3 - Click "Load data" to select an image.]]
|}
{|
|[[File:SlicerPathologyScreenShot5.png|thumb|800px|Step 4 - Click the button Quick TCGA Effect button to activate the effect.]]
|}
{|
|[[File:SlicerPathologyScreenShot6.png|thumb|800px|Step 5 - Click "Start TCGA Segmenter and adjust the five segmentation algorithm parameters as needed.]]
|}
{|
|[[File:SlicerPathologyScreenShot7.png|thumb|800px|Step 6 - you can select a subregion to speed up the parameter tuning process. Press "Y" to execute the segmenter on the subregion (if it was selected) or the whole image]]
|}
{|
|[[File:SlicerPathologyScreenShot8.png|thumb|800px|Step 7 - you can click "Clear Selection" to clear the selected sub-region so that the segmenter operates on the whole image.]]
|}
{|
|[[File:SlicerPathologyScreenShot9.png|thumb|800px|Step 8 - "Click the "Submission" tab so that you can save your label masks and related meta data. (meta data will be stored as JSON)]]
|}
{|
|[[File:SlicerPathologyScreenShot-json.png|thumb|800px|Step 9 - "This is a sample of the stored meta data. Notice the addition of your username for identification.]]
|}

{{documentation/{{documentation/version}}/module-section|References}}
* [http://qiicr.org Quantitative Image Informatics for Cancer Research (QIICR)]
* [http://opencv.org Open Source Computer Vision]
* [http://cancergenome.nih.gov/ The Cancer Genome Atlas]


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
The source code for SlicerPathology is available at https://github.com/SBU-BMI/SlicerPathology


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

Documentation/Nightly/Extensions/SlicerPathology

2016-05-13T13:49:14Z

Ebremer:

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

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



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/SlicerPathology|SlicerPathology]] 
Acknowledgments:
This work was supported by via the NIH-National Cancer Institute Grant U24 CA180918, as well as, U24 CA180918 Quantitative Image Informatics for Cancer Research (QIICR), http://qiicr.org, PIs Ron Kikinis and Andrey Fedorov, Brigham and Women's Hospital. 
Author: Erich Bremer 

Contributor 1: Yi Gao 
Contributor 2: Nicole Aucoin ({{collaborator|name|spl}}) 
Contributor 3: Andrey Fedorov ({{collaborator|name|spl}}) 
Contributor 4: Jean-Christophe Fillion-Robin ({{collaborator|name|kitware}}) 
Contact: Erich Bremer, <email>erich.bremer@stonybrook.edu</email> 

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


{{documentation/{{documentation/version}}/module-section|Module Description}}
This extension provides tools for automatic and semi-automatic pathology image segmentation.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-section|Tutorials}}
{|
|[[File:SlicerPathologyScreenShot2.png|thumb|800px|Step 1 - Go to the SlicerPathology Extension.]]
|}
{|
|[[File:SlicerPathologyScreenShot3.png|thumb|800px|Step 2 - Click the user information tab. Enter your email address. This is used for identification of you in the file data files.]]
|}
{|
|[[File:SlicerPathologyScreenShot4.png|thumb|800px|Step 3 - Click "Load data" to select an image.]]
|}
{|
|[[File:SlicerPathologyScreenShot5.png|thumb|800px|Step 4 - Click the button Quick TCGA Effect button to activate the effect.]]
|}
{|
|[[File:SlicerPathologyScreenShot6.png|thumb|800px|Step 5 - Click "Start TCGA Segmenter and adjust the five segmentation algorithm parameters as needed.]]
|}
{|
|[[File:SlicerPathologyScreenShot7.png|thumb|800px|Step 6 - you can select a subregion to speed up the parameter tuning process. Press "Y" to execute the segmenter on the subregion (if it was selected) or the whole image]]
|}
{|
|[[File:SlicerPathologyScreenShot8.png|thumb|800px|Step 7 - you can click "Clear Selection" to clear the selected sub-region so that the segmenter operates on the whole image.]]
|}
{|
|[[File:SlicerPathologyScreenShot9.png|thumb|800px|Step 8 - "Click the "Submission" tab so that you can save your label masks and related meta data. (meta data will be stored as JSON)]]
|}
{|
|[[File:SlicerPathologyScreenShot-json.png|thumb|800px|Step 9 - "This is a sample of the stored meta data. Notice the addition of your username for identification.]]
|}

{{documentation/{{documentation/version}}/module-section|References}}
* [http://qiicr.org Quantitative Image Informatics for Cancer Research (QIICR)]
* [http://opencv.org Open Source Computer Vision]


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
The source code for SlicerPathology is available at https://github.com/SBU-BMI/SlicerPathology


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

Documentation/Nightly/Extensions/SlicerPathology

2016-05-13T13:46:29Z

Ebremer:

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

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



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/SlicerPathology|SlicerPathology]] 
Acknowledgments:
This work was supported by via the NIH-National Cancer Institute Grant U24 CA180918, as well as, U24 CA180918 Quantitative Image Informatics for Cancer Research (QIICR), http://qiicr.org, PIs Ron Kikinis and Andrey Fedorov, Brigham and Women's Hospital. 
Author: Erich Bremer 

Contributor 1: Yi Gao 
Contributor 2: Nicole Aucoin ({{collaborator|name|spl}}) 
Contributor 3: Andrey Fedorov ({{collaborator|name|spl}}) 
Contributor 4: Jean-Christophe Fillion-Robin ({{collaborator|name|kitware}}) 
Contact: Erich Bremer, <email>erich.bremer@stonybrook.edu</email> 

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


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


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-section|Tutorials}}
{|
|[[File:SlicerPathologyScreenShot2.png|thumb|800px|Step 1 - Go to the SlicerPathology Extension.]]
|}
{|
|[[File:SlicerPathologyScreenShot3.png|thumb|800px|Step 2 - Click the user information tab. Enter your email address. This is used for identification of you in the file data files.]]
|}
{|
|[[File:SlicerPathologyScreenShot4.png|thumb|800px|Step 3 - Click "Load data" to select an image.]]
|}
{|
|[[File:SlicerPathologyScreenShot5.png|thumb|800px|Step 4 - Click the button Quick TCGA Effect button to activate the effect.]]
|}
{|
|[[File:SlicerPathologyScreenShot6.png|thumb|800px|Step 5 - Click "Start TCGA Segmenter and adjust the five segmentation algorithm parameters as needed.]]
|}
{|
|[[File:SlicerPathologyScreenShot7.png|thumb|800px|Step 6 - you can select a subregion to speed up the parameter tuning process. Press "Y" to execute the segmenter on the subregion (if it was selected) or the whole image]]
|}
{|
|[[File:SlicerPathologyScreenShot8.png|thumb|800px|Step 7 - you can click "Clear Selection" to clear the selected sub-region so that the segmenter operates on the whole image.]]
|}
{|
|[[File:SlicerPathologyScreenShot9.png|thumb|800px|Step 8 - "Click the "Submission" tab so that you can save your label masks and related meta data. (meta data will be stored as JSON)]]
|}
{|
|[[File:SlicerPathologyScreenShot-json.png|thumb|800px|Step 9 - "This is a sample of the stored meta data. Notice the addition of your username for identification]]
|}

{{documentation/{{documentation/version}}/module-section|References}}
* [http://qiicr.org Quantitative Image Informatics for Cancer Research (QIICR)]
* [http://opencv.org Open Source Computer Vision]


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


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

Documentation/Nightly/Extensions/SlicerPathology

2016-05-13T13:44:33Z

Ebremer:

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

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



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/SlicerPathology|SlicerPathology]] 
Acknowledgments:
This work was supported by via the NIH-National Cancer Institute Grant U24 CA180918, as well as, U24 CA180918 Quantitative Image Informatics for Cancer Research (QIICR), http://qiicr.org, PIs Ron Kikinis and Andrey Fedorov, Brigham and Women's Hospital. 
Author: Erich Bremer 

Contributor 1: Yi Gao 
Contributor 2: Nicole Aucoin ({{collaborator|name|spl}}) 
Contributor 3: Andrey Fedorov ({{collaborator|name|spl}}) 
Contributor 4: Jean-Christophe Fillion-Robin ({{collaborator|name|kitware}}) 
Contact: Erich Bremer, <email>erich.bremer@stonybrook.edu</email> 

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


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


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-section|Tutorials}}
{|
|[[File:SlicerPathologyScreenShot2.png|thumb|800px|Step 1 - Go to the SlicerPathology Extension.]]
|}
{|
|[[File:SlicerPathologyScreenShot3.png|thumb|800px|Step 2 - Click the user information tab. Enter your email address. This is used for identification of you in the file data files.]]
|}
{|
|[[File:SlicerPathologyScreenShot4.png|thumb|800px|Step 3 - Click "Load data" to select an image.]]
|}
{|
|[[File:SlicerPathologyScreenShot5.png|thumb|800px|Step 4 - Click the button Quick TCGA Effect button to activate the effect.]]
|}
{|
|[[File:SlicerPathologyScreenShot6.png|thumb|800px|Step 5 - Click "Start TCGA Segmenter and adjust the five segmentation algorithm parameters as needed.]]
|}
{|
|[[File:SlicerPathologyScreenShot7.png|thumb|800px|Step 6 - you can select a subregion to speed up the parameter tuning process. Press "Y" to execute the segmenter on the subregion (if it was selected) or the whole image]]
|}
{|
|[[File:SlicerPathologyScreenShot8.png|thumb|800px|Step 7 - you can click "Clear Selection" to clear the selected sub-region so that the segmenter operates on the whole image.]]
|}
{|
|[[File:SlicerPathologyScreenShot9.png|thumb|800px|Step 8 - "Click the "Submission" tab so that you can save your label masks and related meta data. (meta data will be stored as JSON)]]
|}

{{documentation/{{documentation/version}}/module-section|References}}
* [http://qiicr.org Quantitative Image Informatics for Cancer Research (QIICR)]
* [http://opencv.org Open Source Computer Vision]


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


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

Documentation/Nightly/Extensions/SlicerPathology

2016-05-13T13:43:47Z

Ebremer:

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

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



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/SlicerPathology|SlicerPathology]] 
Acknowledgments:
This work was supported by via the NIH-National Cancer Institute Grant U24 CA180918, as well as, U24 CA180918 Quantitative Image Informatics for Cancer Research (QIICR), http://qiicr.org, PIs Ron Kikinis and Andrey Fedorov, Brigham and Women's Hospital. 
Author: Erich Bremer 

Contributor 1: Yi Gao 
Contributor 2: Nicole Aucoin ({{collaborator|name|spl}}) 
Contributor 3: Andrey Fedorov ({{collaborator|name|spl}}) 
Contributor 4: Jean-Christophe Fillion-Robin ({{collaborator|name|kitware}}) 
Contact: Erich Bremer, <email>erich.bremer@stonybrook.edu</email> 

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


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


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-section|Tutorials}}
{|
|[[File:SlicerPathologyScreenShot2.png|thumb|800px|Step 1 - Go to the SlicerPathology Extension.]]
|}
{|
|[[File:SlicerPathologyScreenShot3.png|thumb|800px|Step 2 - Click the user information tab. Enter your email address. This is used for identification of you in the file data files.]]
|}
{|
|[[File:SlicerPathologyScreenShot4.png|thumb|800px|Step 3 - Click "Load data" to select an image.]]
|}
{|
|[[File:SlicerPathologyScreenShot5.png|thumb|800px|Step 4 - Click the button Quick TCGA Effect button to activate the effect.]]
|}
{|
|[[File:SlicerPathologyScreenShot6.png|thumb|800px|Step 5 - Click "Start TCGA Segmenter and adjust the five segmentation algorithm parameters as needed.]]
|}
{|
|[[File:SlicerPathologyScreenShot7.png|thumb|800px|Step 6 - you can select a subregion to speed up the parameter tuning process. Press "Y" to execute the segmenter on the subregion (if it was selected) or the whole image]]
|}
{|
|[[File:SlicerPathologyScreenShot8.png|thumb|800px|Step 7 - you can click "Clear Selection" to clear the selected sub-region so that the segmenter operates on the whole image.]]
|}
{|
|[[File:SlicerPathologyScreenShot9.png|thumb|800px|Step 8 - "Click the "Submission" tab so that you can save your label masks and related meta data. (meta data will be stored as JSON)]]
|}

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


{{documentation/{{documentation/version}}/module-section|References}}
* [http://qiicr.org Quantitative Image Informatics for Cancer Research (QIICR)]
* [http://opencv.org Open Source Computer Vision]


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


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

Documentation/Nightly/Extensions/SlicerPathology

2016-05-12T19:01:07Z

Ebremer:

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

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



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/SlicerPathology|SlicerPathology]] 
Acknowledgments:
This work was supported by via the NIH-National Cancer Institute Grant U24 CA180918, as well as, U24 CA180918 Quantitative Image Informatics for Cancer Research (QIICR), http://qiicr.org, PIs Ron Kikinis and Andrey Fedorov, Brigham and Women's Hospital. 
Author: Erich Bremer 

Contributor 1: Yi Gao 
Contributor 2: Nicole Aucoin ({{collaborator|name|spl}}) 
Contributor 3: Andrey Fedorov ({{collaborator|name|spl}}) 
Contributor 4: Jean-Christophe Fillion-Robin ({{collaborator|name|kitware}}) 
Contact: Erich Bremer, <email>erich.bremer@stonybrook.edu</email> 

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


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


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-section|Tutorials}}
Go to Module, Pathology.
[[File:SlicerPathologyScreenShot2.png|500px|thumb|left|alt text]]
Click "Load data directly from file" to select an image.
[[File:SlicerPathologyScreenShot3.png|500px|thumb|left|alt text]]
[[File:SlicerPathologyScreenShot4.png|500px|thumb|left|alt text]]
[[File:SlicerPathologyScreenShot5.png|500px|thumb|left|alt text]]
[[File:SlicerPathologyScreenShot6.png|500px|thumb|left|alt text]]
[[File:SlicerPathologyScreenShot7.png|500px|thumb|left|alt text]]
[[File:SlicerPathologyScreenShot8.png|500px|thumb|left|alt text]]
[[File:SlicerPathologyScreenShot9.png|500px|thumb|left|alt text]]
[[File:SlicerPathologyScreenShot-json.png|500px|thumb|left|alt text]]

Click the button labeled Quick TCGA Effect.
This adds a palette to the interface where you can change the parameters of the run.

Click segmentation button to run an algorithm over the image with the current parameters.
Hit the "Y" key to continue.

After a few moments it’ll come back segmented.

Left-click & drag to select a subregion.
Now you can run the function on that area only.

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


{{documentation/{{documentation/version}}/module-section|References}}
* [http://qiicr.org Quantitative Image Informatics for Cancer Research (QIICR)]
* [http://opencv.org Open Source Computer Vision]


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


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

File:SlicerPathologyScreenShot-json.png

2016-05-12T18:53:19Z

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File:SlicerPathologyScreenShot9.png

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File:SlicerPathologyScreenShot7.png

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File:SlicerPathologyScreenShot6.png

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File:SlicerPathologyScreenShot5.png

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File:SlicerPathologyScreenShot4.png

2016-05-12T18:49:33Z

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File:SlicerPathologyScreenShot3.png

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File:SlicerPathologyScreenShot2.png

2016-05-12T18:48:46Z

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Documentation/Nightly/Extensions/SlicerPathology

2016-05-12T15:24:23Z

Ebremer:

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

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



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/SlicerPathology|SlicerPathology]] 
Acknowledgments:
This work was supported by via the NIH-National Cancer Institute Grant U24 CA180918, as well as, U24 CA180918 Quantitative Image Informatics for Cancer Research (QIICR), http://qiicr.org, PIs Ron Kikinis and Andrey Fedorov, Brigham and Women's Hospital. 
Author: Erich Bremer 

Contributor 1: Yi Gao 
Contributor 2: Nicole Aucoin ({{collaborator|name|spl}}) 
Contributor 3: Andrey Fedorov ({{collaborator|name|spl}}) 
Contributor 4: Jean-Christophe Fillion-Robin ({{collaborator|name|kitware}}) 
Contact: Erich Bremer, <email>erich.bremer@stonybrook.edu</email> 

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


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


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-section|Tutorials}}
{{documentation/{{documentation/version}}/module-developerinfo}}

Go to Module, Pathology.

Click "Load data directly from file" to select an image.

Click the button labeled Quick TCGA Effect.
This adds a palette to the interface where you can change the parameters of the run.

Click segmentation button to run an algorithm over the image with the current parameters.
Hit the "Y" key to continue.

After a few moments it’ll come back segmented.

Left-click & drag to select a subregion.
Now you can run the function on that area only.

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


{{documentation/{{documentation/version}}/module-section|References}}
* [http://qiicr.org Quantitative Image Informatics for Cancer Research (QIICR)]
* [http://opencv.org Open Source Computer Vision]


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

Documentation/Nightly/Extensions/SlicerPathology

2016-05-11T20:46:25Z

Ebremer:

Documentation/Nightly/Extensions/SlicerPathology

2016-05-11T20:42:07Z

Ebremer: skeleton for coming documentation