UpdateBot: Nightly -> 4.10

2018-10-19T00:44:56Z

Nightly -> 4.10

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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
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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> 

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{{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}}
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{{documentation/{{documentation/version}}/module-section|Tutorials}}
<embedvideo service="youtube">https://www.youtube.com/watch?v=n6RtJoU9nGQ</embedvideo>
{|
|[[File:SlicerPathologyScreenShot2.png|thumb|800px|Step 1 - Go to the SlicerPathology Extension.]]
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{|
|[[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.]]
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|[[File:SlicerPathologyScreenShot4.png|thumb|800px|Step 3 - Click "Load data" to select an image.]]
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|[[File:SlicerPathologyScreenShot5.png|thumb|800px|Step 4 - Click the button Quick TCGA Effect button to activate the effect.]]
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|[[File:SlicerPathologyScreenShot6.png|thumb|800px|Step 5 - Click "Start TCGA Segmenter and adjust the five segmentation algorithm parameters as needed.]]
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|[[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]]
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|[[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.]]
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|[[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)]]
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|[[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.]]
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{{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


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Documentation/4.10/Extensions/SlicerPathology - Revision history

UpdateBot: Nightly -> 4.10