Difference between revisions of "MITK Segmentation Redesign"

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__NOTOC__
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[[File:MITK$$SegmentationRedesign$SegmentationRedesign.png|thumb|300px]]
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= Segmentation Redesign =
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Since the MITK Workbench Release 2013.06 the whole segmentation group has been working on an extensive redesign of our segmentation plugin. With the MITK 2013.09 release we are proud to announce that this project is completed! Here is a list of the major changes and new features:
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[[Media:MITK$$SegmentationRedesign$SegmentationRedesign.png||align="middle",|width="350px"]]
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__TOC__
  
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Since the last release from 2013.06 the whole segmentation group has been working on an extensive redesign of our segmentation plugin. With the MITK 2013.09 release we are proud to announce that this project is completed! Here is a list of the major changes and new features:
 
  
 
== Segmentation 2D and 3D Tools ==
 
== Segmentation 2D and 3D Tools ==
  
−
We cleaned up the segmentation view and removed unused GUI elements. We also extended the functionality with new 2D and 3D tools
+
We cleaned up the segmentation view and removed unused GUI elements. We also extended its functionality with new 2D and 3D segmentation tools
 +
 
  
 
=== UI improvements ===
 
=== UI improvements ===
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* The segmentation view contains now two tabs which allows to '''switch between 2D and 3D tools'''
 
* The segmentation view contains now two tabs which allows to '''switch between 2D and 3D tools'''
 
* '''New tool icons''' replaced the antiquated old ones
 
* '''New tool icons''' replaced the antiquated old ones
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* '''Customized mouse cursor''' - The icon of the active 2D tool is now visible beneath your mouse cursor
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* A '''customized mouse cursor''' is now visible beneath your application cursor while a 2D tool is active
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* '''Slim view''' - Hide button names
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* A '''slim view''' option allows you to hide the tool button names
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* Improved the '''interpolation widget'''
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* Simplified the '''interpolation widget'''
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* Improved the '''interpolation widget'''
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 +
<gallery>
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File:MITK$$SegmentationRedesign$2DTools.png|'''2D Tools'''
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File:MITK$$SegmentationRedesign$2DTools_Slimview.png|'''2D Tools Slimview'''
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File:MITK$$SegmentationRedesign$3DTools.png|'''3D Tools'''
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File:MITK$$SegmentationRedesign$LiveWireTool.png|'''Live Wire Tool with cursor icon'''
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</gallery>
  
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{| border="1" cellpadding="2" cellspacing="0"
 
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|align="center" |[[Media:MITK$$SegmentationRedesign$2D3DToolsTab.png
 
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| align="right",width="300px"}}
 
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|align="center" |{{attachment:Segmentation_Slimview.png
 
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| align="middle",width="300px"]]
 
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|-
 
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|align="center" |2D / 3D Tabs
 
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|align="center" | Slimview
 
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|}
 
  
 
=== New segmentation tools ===
 
=== New segmentation tools ===
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** There is now a '''2D Fast Marching Tool'''
 
** There is now a '''2D Fast Marching Tool'''
 
** '''Better interaction''' and '''look and feel''' for the Live Wire Tool
 
** '''Better interaction''' and '''look and feel''' for the Live Wire Tool
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* New '''3D tool area''' contains many tools which were formerly located in the Datamanager's context menu
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* New '''3D tool area''' contains many tools which were formerly located in the Datamanager's context menu:
 
** '''Simple threshold''' - Segment your image using a single threshold value
 
** '''Simple threshold''' - Segment your image using a single threshold value
 
** '''Upper/Lower Threshold''' - Segment your image using an upper '''and''' lower threshold
 
** '''Upper/Lower Threshold''' - Segment your image using an upper '''and''' lower threshold
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** '''Fast Marching 3D'''
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** '''Fast Marching 3D tool'''
 
** '''Watershed Segmentation'''
 
** '''Watershed Segmentation'''
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* All 3D tool have a '''dedicated Tool GUI area''' for setting specific parameters
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** '''Otsu Segmentation'''
 +
* All 3D tools have a '''dedicated Tool GUI area''' for setting specific parameters
 +
 
 +
<gallery>
 +
File:MITK$$SegmentationRedesign$FastMarching.png|'''Fast Marching Tool'''
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File:MITK$$SegmentationRedesign$UL_Threshold.png|'''Upper/Lower Threshold'''
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File:MITK$$SegmentationRedesign$Otsu_1.png|'''Otsu Tool'''
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File:MITK$$SegmentationRedesign$Otsu_2.png|'''Otsu Region Selection'''
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File:MITK$$SegmentationRedesign$Watershed.png|'''Watershed Tool'''
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File:MITK$$SegmentationRedesign$3DRegiongrowing.png|'''3D Regiongrowing'''
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</gallery>
  
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{| border="1" cellpadding="2" cellspacing="0"
 
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| [[Media:MITK$$SegmentationRedesign$FastMarching.png
 
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| align="middle",width="300px"}}
 
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| {{attachment:UL_Threshold.png
 
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| align="middle",width="300px"]]
 
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|-
 
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|align="center" |Fast Marching Tool
 
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|align="center" |Upper/Lower Threshold
 
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|-
 
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| [[Media:MITK$$SegmentationRedesign$Otsu_1.png
 
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| align="left",width="300px"}}
 
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| {{attachment:Otsu_2.png
 
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| align="right",width="300px"]]
 
−
|-
 
−
|align="center" |Otsu Tool
 
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|align="center" |Otsu Region Selection
 
−
|-
 
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| [[Media:MITK$$SegmentationRedesign$Watershed.png
 
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| align="middle",width="300px"}}
 
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| {{attachment:3DRegiongrowing.png
 
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| align="middle",width="300px"]]
 
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|-
 
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|align="center" |3D Regiongrowing
 
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| <-2>
 
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|}
 
  
 
== Segmentation Utilities ==
 
== Segmentation Utilities ==
  
−
Often a segmentation needs some post processing. Lets say you just performed a threshold segmentation and the result contains some "holes". In this case you would like to fill these holes automatically. Or you want to combine to different segmentation into one single segmentation. For these cases MITK now comes with a extensive set of segmentation utilities in a separate view:
+
Often a segmentation needs some post processing. Lets say you just performed a threshold segmentation and the result contains some "holes". In this case you would like to fill these holes automatically. Or you want to combine two different segmentations within one single segmentation image. For these cases MITK now comes with an extensive set of segmentation utilities in a separate view:
  
 +
[[File:MITK$$SegmentationRedesign$SegmentationUtilities.png|thumb|300px]]
 
* '''Boolean operations''':
 
* '''Boolean operations''':
 
** Calculate the '''difference''' between two segmentations
 
** Calculate the '''difference''' between two segmentations
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** Calculate the '''union''' of the segmentations
 
** Calculate the '''union''' of the segmentations
 
* '''Image masking''':
 
* '''Image masking''':
−
** You have finished a segmentation and what now? E.g. you can '''mask the patient image with your segmentation or a surface''' and then proceed with e.g. vessel segmentation/visualization
+
** You have finished a segmentation and what now? E.g. you can '''mask the patient image with an existing segmentation or a surface''' and then proceed with e.g. vessel segmentation/visualization
 
* '''Morphological operations''':
 
* '''Morphological operations''':
 
** Postprocess your segmentation by
 
** Postprocess your segmentation by
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*** Fill Holes
 
*** Fill Holes
 
* '''Surface To Image''':
 
* '''Surface To Image''':
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** Convert a surface into a segmentation and use all the available segmentation tools!
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** Convert a surface into a segmentation and use all the available segmentation tools to modify the segmentation!
 +
 
  
 
== General ==
 
== General ==
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* '''Switch to mitkContourModel''':
 
* '''Switch to mitkContourModel''':
 
** All 2D tools are now using the new mitkContourModel
 
** All 2D tools are now using the new mitkContourModel
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** There is also a '''new data structure called mitkContourModelSet''' which allow the storage of a set of ContourModels
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** The old '''mitkContour is declared as deprecated''' and will be removed during the next year
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** The old mitkContour and mitkContourSet are declared as '''deprecated''' and will be removed during the next year
 
 
* '''3D interpolation''' can now also be used with '''planar figures'''
 
* '''3D interpolation''' can now also be used with '''planar figures'''
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* '''New !SegmentationUI module''' which contains all the segmentation widgets
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* '''New SegmentationUI module''' which contains all the segmentation widgets

Latest revision as of 16:21, 4 December 2014

MITK$$SegmentationRedesign$SegmentationRedesign.png

Since the MITK Workbench Release 2013.06 the whole segmentation group has been working on an extensive redesign of our segmentation plugin. With the MITK 2013.09 release we are proud to announce that this project is completed! Here is a list of the major changes and new features:


Segmentation 2D and 3D Tools

We cleaned up the segmentation view and removed unused GUI elements. We also extended its functionality with new 2D and 3D segmentation tools


UI improvements

  • The segmentation view contains now two tabs which allows to switch between 2D and 3D tools
  • New tool icons replaced the antiquated old ones
  • A customized mouse cursor is now visible beneath your application cursor while a 2D tool is active
  • A slim view option allows you to hide the tool button names
  • Simplified the interpolation widget

  • 2D Tools

  • 2D Tools Slimview

  • 3D Tools

  • Live Wire Tool with cursor icon


New segmentation tools

  • We extended and improved the 2D tool set:
    • There is now a 2D Fast Marching Tool
    • Better interaction and look and feel for the Live Wire Tool
  • New 3D tool area contains many tools which were formerly located in the Datamanager's context menu:
    • Simple threshold - Segment your image using a single threshold value
    • Upper/Lower Threshold - Segment your image using an upper and lower threshold
    • Fast Marching 3D tool
    • Watershed Segmentation
    • Otsu Segmentation
  • All 3D tools have a dedicated Tool GUI area for setting specific parameters

  • Fast Marching Tool

  • Upper/Lower Threshold

  • Otsu Tool

  • Otsu Region Selection

  • Watershed Tool

  • 3D Regiongrowing


Segmentation Utilities

Often a segmentation needs some post processing. Lets say you just performed a threshold segmentation and the result contains some "holes". In this case you would like to fill these holes automatically. Or you want to combine two different segmentations within one single segmentation image. For these cases MITK now comes with an extensive set of segmentation utilities in a separate view:

MITK$$SegmentationRedesign$SegmentationUtilities.png
  • Boolean operations:
    • Calculate the difference between two segmentations
    • Calculate the intersection of two segmentations
    • Calculate the union of the segmentations
  • Image masking:
    • You have finished a segmentation and what now? E.g. you can mask the patient image with an existing segmentation or a surface and then proceed with e.g. vessel segmentation/visualization
  • Morphological operations:
    • Postprocess your segmentation by
      • Dilatation/Erosion
      • Opening/Closing
      • Fill Holes
  • Surface To Image:
    • Convert a surface into a segmentation and use all the available segmentation tools to modify the segmentation!


General

  • The toolmanager can now be accessed using CppMicroServices
  • Switch to mitkContourModel:
    • All 2D tools are now using the new mitkContourModel
    • The old mitkContour is declared as deprecated and will be removed during the next year
  • 3D interpolation can now also be used with planar figures
  • New SegmentationUI module which contains all the segmentation widgets
Retrieved from "http://mitk.org/w/index.php?title=MITK_Segmentation_Redesign&oldid=2267"