Difference between revisions of "Documentation/4.1/SlicerApplication/LookupTables"

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=Overview=
 
=Overview=
Slicer offers a variety of predefined lookup tables (LUT). Volumes can be associated with a LUT in the volumes module. Also, see the [[Documentation/4.1/Modules/Colors|Colors Module]].
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In Slicer, the simplest and most widespread application of medicine-specific knowledge are the color lookup tables (LUT) that Slicer uses to map the integer values contained in label map images into structure names and colors. We have begun to use this wiki as both a centralized repository for lookup table information as well as a collaborative tool for creating new mappings. The following wiki pages are in a special format that allows conversion into Slicer lookup tables. Slicer offers a variety of predefined lookup tables (LUT). Volumes can be associated with a LUT in the volumes module. Also, see the [[Documentation/4.1/Modules/Colors|Colors Module]].
  
 
==LUTs==
 
==LUTs==
<gallery widths=200px>
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file:DiscreteLUTs-2012-02-18.png|''Discrete LUTs''
 
file:DiscreteLUTs-2012-02-18.png|''Discrete LUTs''
 
file:Shade-LUTs-2012-02-18.png|''Shade LUTs''
 
file:Shade-LUTs-2012-02-18.png|''Shade LUTs''
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file:CartilageMRI-LUTs-2012-02-18.png|''Cartilage MRI LUTs''
 
file:CartilageMRI-LUTs-2012-02-18.png|''Cartilage MRI LUTs''
 
file:Labelmap-LUTs-2012-02-18.png|''Labelmap LUTs''<br>-[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/2010BrainLabels|Brain Labels]]: Label colors for brain segmentation<br>-[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/2010LabelColors|Label Colors]]: Colors for a generic labelmap
 
file:Labelmap-LUTs-2012-02-18.png|''Labelmap LUTs''<br>-[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/2010BrainLabels|Brain Labels]]: Label colors for brain segmentation<br>-[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/2010LabelColors|Label Colors]]: Colors for a generic labelmap
file:GenericLabel-LUTs-2012-02-18.png|''Generic Labelmap LUTs''<br>-[[Documentation/4.1/SlicerApplication/LookupTables/GenericAnatomyColors|Default Generic Anatomy Colors]]<br>-[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/GenericColors|Generic Colors]]
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file:GenericLabel-LUTs-2012-02-18.png|''Generic Labelmap LUTs''<br>-[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/GenericAnatomyColors|Default Generic Anatomy Colors]]<br>-[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/GenericColors|Generic Colors]]
 
</gallery>
 
</gallery>
  
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===Custom LUT Examples===
 
===Custom LUT Examples===
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*[[Documentation/4.1/SlicerApplication/LookupTables/AbdominalAtlasLabels|Abdominal Atlas Labels]]
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*[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/HNAtlasLabels|Head and Neck Atlas Labels]]
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*[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/HNLabels|Head and Neck Muscles Labels]]
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*[[Documentation/4.1/SlicerApplication/LookupTables/FemalePelvisColors|Female Pelvis Labels]]
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*[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/Freesurfer_labels|Freesurfer Labels]]
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*[[Documentation/4.1/SlicerApplication/LookupTables/KneeAtlasLabels|Knee Atlas Labels]]
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*[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/Lauras-labels|Laura's Labels]]
 
*[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/Mori-Atlas_labels|Mori-Atlas Labels]]
 
*[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/Mori-Atlas_labels|Mori-Atlas Labels]]
*[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/Lauras-labels|Laura's Labels]]
 
*[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/Freesurfer_labels|Freesurfer Labels]]
 
*[[Documentation/{{documentation/version}}/SlicerApplication/LookupTables/HNLabels|Head and Neck Muscles Labels]]
 
  
 
==Useful Links==
 
==Useful Links==

Latest revision as of 07:28, 14 June 2013

Home < Documentation < 4.1 < SlicerApplication < LookupTables


For the latest Slicer documentation, visit the read-the-docs.



Overview

In Slicer, the simplest and most widespread application of medicine-specific knowledge are the color lookup tables (LUT) that Slicer uses to map the integer values contained in label map images into structure names and colors. We have begun to use this wiki as both a centralized repository for lookup table information as well as a collaborative tool for creating new mappings. The following wiki pages are in a special format that allows conversion into Slicer lookup tables. Slicer offers a variety of predefined lookup tables (LUT). Volumes can be associated with a LUT in the volumes module. Also, see the Colors Module.

LUTs

LUTs for Charting

Please see the Generic Chart Colors page.

LUTs in Slicer

You can review and edit LUTs in Slicer via the Colors module.

Slicer ColorPicker

The slicer colorpicker allows to select colors from a label map and to assign them to objects such as surface models or streamlines.

SlicerColorPicker-2012-02-18.png

LUTs for Slicer4

Brain Atlas LUTs

Custom LUTs

It is relatively easy to create custom LUTs by creating a table with the colors on the wiki. This allows to select specific names and colors when segmenting. See below for an example.

integer_label text_label color notes
0 background rgba(0,0,0,0)
1 tissue rgb(128,174,128) Default label for bodily tissues
2 bone rgb(241,214,145)
3 skin rgb(177,122,101)
4 connective tissue rgb(111,184,210)


Custom LUT Examples

Useful Links