Modules:VMTKEasyLevelSetSegmentation - Revision history

Haehn: /* Source code & documentation */

2010-04-20T13:53:09Z

Source code & documentation

Haehn: /* Installation */

2010-04-20T13:43:50Z

Installation

Haehn: /* Notes from the Developer(s) */

2010-04-20T13:08:14Z

Notes from the Developer(s)

Haehn: /* Source code & documentation */

2010-04-20T13:07:34Z

Source code & documentation

Haehn: /* Notes from the Developer(s) */

2010-04-20T13:01:17Z

Notes from the Developer(s)

Haehn: /* Quick Tour of Features and Use */

2010-04-20T12:59:00Z

Quick Tour of Features and Use

Haehn: /* Development */

2010-04-20T12:57:30Z

Development

Haehn: /* Quick Tour of Features and Use */

2010-04-20T12:54:31Z

Quick Tour of Features and Use

Haehn: /* Quick Tour of Features and Use */

2010-04-20T12:48:14Z

Quick Tour of Features and Use

Haehn at 12:43, 20 April 2010

2010-04-20T12:43:23Z

@@ Line 171: / Line 171: @@
 The class ''VMTKEasyLevelSetSegmentationGUI'' derives from ''ScriptedModuleGUI'' and saves the current parameters to its own MRML node. The actual calls to the VMTK libraries as well as the Marching Cubes or Volume Rendering methods are performed in the class ''VMTKEasyLevelSetSegmentationLogic''. Several general supporting functions are outsourced in the class ''VMTKEasyLevelSetSegmentationHelper''.
-The complete source code is available at a [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/VMTKLevelSetSegmentation/?root=slicervmtklvlst NITRC SVN repository].
+The complete source code is available at a [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/VMTKEasyLevelSetSegmentation/?root=slicervmtklvlst NITRC SVN repository].
 == More Information ==

@@ Line 40: / Line 40: @@
 ''This module depends on the [[Modules:VMTKSlicerModule|VmtkSlicerModule]]: see [[Modules:VMTKSlicerModule|this page]] for installation notes.''
-The VMTKVesselEnhancement module can be installed using the '''3D Slicer extension wizard'''. The extension is called ''VMTKEasyLevelSetSegmentation''.
+The VMTKEasyLevelSetSegmentation module can be installed using the '''3D Slicer extension wizard'''. The extension is called ''VMTKEasyLevelSetSegmentation''.
 When the module was successfully installed, it is available within 3D Slicer's module selector inside the category ''Vascular Modeling Toolkit''.

@@ Line 151: / Line 151: @@
 ===Notes from the Developer(s)===
-The algorithms provided by VMTK and used by this module are C++ classes implemented using VTK and ITK. In particular the module uses the Fast Marching Upwind Gradient Image Filter (see http://math.berkeley.edu/~sethian/Explanations/fast_marching_explain.html) for initialization and the Geodesic Active Contours (see http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.21.2196&rep=rep1&type=pdf) and CURVES level set (see http://www.spl.harvard.edu/publications/item/view/179) filters for evolution.
+The algorithms provided by VMTK and used by this module are C++ classes implemented using VTK and ITK. In particular the module uses the Fast Marching Upwind Gradient Image Filter (see http://math.berkeley.edu/~sethian/Explanations/fast_marching_explain.html) for initialization and the Geodesic Active Contours (see http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.21.2196&rep=rep1&type=pdf) and CURVES (see http://www.spl.harvard.edu/publications/item/view/179) level set filters for evolution.
 ===Dependencies===

@@ Line 163: / Line 163: @@
 ===Source code & documentation===
 {|
-|[[Image:VMTKEasyLevelSetSegmentationClassDiagram.png|thumb|280x280px|Class diagram showing the separation of GUI and logic]]
+|[[Image:Easylevelset_classdiagram.png|thumb|280x280px|Class diagram showing the separation of GUI and logic]]
-|[[Image:VMTKEasyLevelSetSegmentationFM.png|thumb|280x280px|Flow chart showing the VTK/VMTK pipeline of the Fast Marching algorithm]]
+|[[Image:Fastmarching_pipeline.png|thumb|280x280px|Flow chart showing the VTK/VMTK pipeline of the Fast Marching algorithm]]
-|[[Image:VMTKEasyLevelSetSegmentationGeodesic.png|thumb|280x280px|Flow chart showing the VTK/VMTK pipeline of the Geodesic Active Contours algorithm]]
+|[[Image:Gac_pipeline.png|thumb|280x280px|Flow chart showing the VTK/VMTK pipeline of the Geodesic Active Contours algorithm]]
 |}
 VMTKEasyLevelSetSegmentation is a Python Scripted Module. It follows the conventions of the Model View Controller pattern of slicer modules. This implies the separation of logic and GUI.

@@ Line 151: / Line 151: @@
 ===Notes from the Developer(s)===
-The algorithms provided by VMTK and used by this module are C++ classes implemented using VTK and ITK. In particular the module uses the Fast Marching Upwind Gradient Image Filter for initialization and the Geodesic Active Contours and CURVES level set filters for evolution.
+The algorithms provided by VMTK and used by this module are C++ classes implemented using VTK and ITK. In particular the module uses the Fast Marching Upwind Gradient Image Filter (see http://math.berkeley.edu/~sethian/Explanations/fast_marching_explain.html) for initialization and the Geodesic Active Contours (see http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.21.2196&rep=rep1&type=pdf) and CURVES level set (see http://www.spl.harvard.edu/publications/item/view/179) filters for evolution.
 ===Dependencies===

@@ Line 139: / Line 139: @@
 * Evolution panel:
 Different weights are available to configure the inflation of the initial level-set. Is is possible to adjust the importance of inflation, curvature shape and attraction to the gradient ridges.
 The number of iterations defines how many steps of evolution are performed.

← Older revision		Revision as of 12:57, 20 April 2010
Line 147:		Line 147:

	== Development ==		== Development ==
		+
		+	===Notes from the Developer(s)===
		+	The algorithms provided by VMTK and used by this module are C++ classes implemented using VTK and ITK. In particular the module uses the Fast Marching Upwind Gradient Image Filter for initialization and the Geodesic Active Contours and CURVES level set filters for evolution.

	===Dependencies===		===Dependencies===

@@ Line 122: / Line 122: @@
 ===Quick Tour of Features and Use===
-The VMTKEasyLevelSetSegmentation has four panels.
+The graphical user interface of the VMTKEasyLevelSetSegmentation module consists of four panels.
+[[Image:Easylevelsetgui.png|thumb|500x500px|The GUI of VMTKEasyLevelSetSegmentation. Click to enlarge.]]
 The current parameters are stored to the MRML node of the module and therefore it is possible to work with different parameter sets.
 * I/O panel:
 The input volume and the output volumes for the initialization and evolution stage can be selected using this panel.
 The output volume of the initialization stage is used as an input for the evolution stage.
 Fiducial lists can be configured as source and target seeds. If the selected fiducial lists are equal, target seeds will be ignored. This is useful for the segmentation of vessel trees.
 A switch to choose between 3D visualization using models generated by Marching Cubes or Volume Rendering is available.
 * Initialization panel:
 The threshold slider is used as a parameter for the Fast Marching Upwind Gradient Image Filter and updates the slice viewers during change for visualization.
 * Evolution panel:
-* Evolution panel
+Different weights are available to configure the inflation of the initial level-set. Is is possible to adjust the importance of inflation, curvature shape and attraction to the gradient ridges.
 The number of iterations defines how many steps of evolution are performed.
 The module supports the 3D Slicer built-in ''Undo'' function.
-All generated binary volumes and used fiducials are saved as MRML nodes in the current MRML scene. Therefore these can be exported or saved.
+All generated models, binary volumes and used fiducials are saved as MRML nodes in the current MRML scene. Therefore these can be exported or saved.
 == Development ==

← Older revision		Revision as of 12:48, 20 April 2010
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	\|}		\|}

		+
		+	===Tutorials===
		+	The following tutorials demonstrate the use of VMTKEasyLevelSetSegmentation in a pipeline of VMTK modules to extract the centerlines of coronary arteries.
		+
		+	{\|
		+	\|[[Image:Vmtkaftercenterline.png\|thumb\|260x260px\|Step-by-step online tutorial: Segmentation of the Right Coronary Artery using VMTK in 3D Slicer. View online [[Modules:VMTK_in_3D_Slicer_Tutorial:_Coronary_Artery_Centerline_Extraction\|here]].]]
		+	\|[[Image:VMTKCenterlines_Tutorial_first_slide.png\|thumb\|280x280px\|Step-by-step tutorial including example dataset: The first slide of the Centerline Extraction tutorial. Download [http://www.na-mic.org/Wiki/images/4/40/TutorialVMTKCoronariesCenterlinesMRI_Winter2010AHM.pdf here].]]
		+	\|}

	===Quick Tour of Features and Use===		===Quick Tour of Features and Use===

@@ Line 93: / Line 93: @@
 |}
-* '''Example segmentation''': The following images demonstrate the application of this tool. An AV fistula is segmented in a contrast-enhanced three-dimensional image acquired from a MR scanner.
+* '''Example segmentation''': The following images show results of an example segmentation using this tool. An AV fistula is segmented in a contrast-enhanced three-dimensional image acquired from a MR scanner.
 {|
 |-valign="top"
 ===Quick Tour of Features and Use===