Documentation/Nightly/Extensions/SlicerPathology - Revision history

Fedorov at 20:54, 7 December 2016

2016-12-07T20:54:40Z

Ebremer at 19:02, 18 May 2016

2016-05-18T19:02:34Z

Ebremer at 13:50, 13 May 2016

2016-05-13T13:50:42Z

Ebremer at 13:49, 13 May 2016

2016-05-13T13:49:14Z

Ebremer at 13:46, 13 May 2016

2016-05-13T13:46:29Z

Ebremer at 13:44, 13 May 2016

2016-05-13T13:44:33Z

Ebremer at 13:43, 13 May 2016

2016-05-13T13:43:47Z

Ebremer at 19:01, 12 May 2016

2016-05-12T19:01:07Z

Ebremer at 15:24, 12 May 2016

2016-05-12T15:24:23Z

Ebremer at 20:46, 11 May 2016

2016-05-11T20:46:25Z

@@ Line 31: / Line 31: @@
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 {{documentation/{{documentation/version}}/module-section|Tutorials}}
-<embedvideo service="youtube">https://www.youtube.com/watch?v=HZ_vSb-C-LA</embedvideo>
+<embedvideo service="youtube">https://www.youtube.com/watch?v=n6RtJoU9nGQ</embedvideo>
 {|
 |[[File:SlicerPathologyScreenShot2.png|thumb|800px|Step 1 - Go to the SlicerPathology Extension.]]

@@ Line 31: / Line 31: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Tutorials}}
 {|
 |[[File:SlicerPathologyScreenShot2.png|thumb|800px|Step 1 - Go to the SlicerPathology Extension.]]

@@ Line 62: / Line 62: @@
 * [http://qiicr.org Quantitative Image Informatics for Cancer Research (QIICR)]
 * [http://opencv.org Open Source Computer Vision]
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@@ Line 23: / Line 23: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Module Description}}
-{{documentation/{{documentation/version}}/module-developerinfo}}
+This extension provides tools for automatic and semi-automatic pathology image segmentation.
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@@ Line 56: / Line 56: @@
 |}
 {|
-|[[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]]
+|[[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.]]
 |}
 <!-- ---------------------------- -->
@@ Line 65: / Line 65: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Information for Developers}}
-{{documentation/{{documentation/version}}/module-developerinfo}}
+The source code for SlicerPathology is available at https://github.com/SBU-BMI/SlicerPathology
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@@ Line 54: / Line 54: @@
 {|
 |[[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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@@ Line 31: / Line 31: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Tutorials}}
-Go to Module, Pathology.
+{|
-[[File:SlicerPathologyScreenShot2.png|500px|thumb|left|alt text]]<p>
+|[[File:SlicerPathologyScreenShot2.png|thumb|800px|Step 1 - Go to the SlicerPathology Extension.]]
-Click "Load data directly from file" to select an image.
+|}
-[[File:SlicerPathologyScreenShot3.png|500px|thumb|left|alt text]]<p>
+{|
-[[File:SlicerPathologyScreenShot4.png|500px|thumb|left|alt text]]<p>
+|[[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:SlicerPathologyScreenShot5.png|500px|thumb|left|alt text]]<p>
+|}
-[[File:SlicerPathologyScreenShot6.png|500px|thumb|left|alt text]]<p>
+{|
-[[File:SlicerPathologyScreenShot7.png|500px|thumb|left|alt text]]<p>
+|[[File:SlicerPathologyScreenShot4.png|thumb|800px|Step 3 - Click "Load data" to select an image.]]
-[[File:SlicerPathologyScreenShot8.png|500px|thumb|left|alt text]]<p>
+|}
-[[File:SlicerPathologyScreenShot9.png|500px|thumb|left|alt text]]<p>
+{|
-[[File:SlicerPathologyScreenShot-json.png|500px|thumb|left|alt text]]
+|[[File:SlicerPathologyScreenShot5.png|thumb|800px|Step 4 - Click the button Quick TCGA Effect button to activate the effect.]]
+|}
-Click the button labeled Quick TCGA Effect.
+{|
-This adds a palette to the interface where you can change the parameters of the run.
+|[[File:SlicerPathologyScreenShot6.png|thumb|800px|Step 5 - Click "Start TCGA Segmenter and adjust the five segmentation algorithm parameters as needed.]]
+|}
-Click segmentation button to run an algorithm over the image with the current parameters.
+{|
-Hit the "Y" key to continue.
+|[[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]]
+|}
-After a few moments it’ll come back segmented.
+{|
+|[[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.]]
-Left-click & drag to select a subregion.
+|}
-Now you can run the function on that area only.
+{|
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 {{documentation/{{documentation/version}}/module-section|Panels and their use}}

← Older revision		Revision as of 20:46, 11 May 2016
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	{{documentation/{{documentation/version}}/module-introduction-end}}		{{documentation/{{documentation/version}}/module-introduction-end}}
−	~~{{documentation/{{documentation/version}}/module-developerinfo}}~~

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