Modules:Colors-Documentation-3.6

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Gallery of New Features

Color Module

Color

Color Display

Module Settings

Edit panel

General Information

Module Type & Category

Type: Interactive

Category: Base

Authors, Collaborators & Contact

• Nicole Aucoin: Brigham and Women's Hospital
• Sebastien Barre, Kitware Inc.
• Contact: Nicole Aucoin, nicole@bwh.harvard.edu

Module Description

The Color Module manages color look up tables.

Look-up Tables (LUTs) are used by mappers to translate between an integer and a color value for display of models and volumes.

Usage

Use Cases, Examples

This module is especially appropriate for these use cases:

• Use Case 1: change the color mapping of volumes
  • In the Volumes module, Display tab, you can select a new color table for grey scale or label map volumes.
• Use Case 2: change model scalar overlays
  • In the Models module, Display tab, you can select a new color table to map scalar overlays associated with the model.
• Use Case 3: create new color tables
  • Either copy an existing color node or create a new one in the Colors module, Edit tab.
  • You can then save it with the scene so it gets loaded again whenever that scene is opened. or copy it into a special directory where it will be loaded whenever Slicer is run.

Examples of the module in use:

• Create a custom color file for a brain segmentation

Tutorials

Links to tutorials explaining how to use this module:

• The Slicer3 Visualization Tutorial uses the Colors module.
  • Slicer3VisualizationDataset.zip

Quick Tour of Features and Use

You can specify a directory from which to read color files using the View -> Application Settings window, Module Settings frame. Click on the Add a preset button to add one or more new user color file paths. The directory will be searched for color files with names ending in .txt or .ctbl and loaded on start up. You have to restart Slicer to load the new files after setting the paths the first time.

You can deactivate paths or delete them as well using this interface.

Color files have one color per line:

label name R G B A

label is an integer, name a string, and there are four integers for RGBA in the inclusive range 0-255. The A stands for opacity, use 255 for opaque.

In a the binary directory of Slicer3, the default color files live in share/Slicer3/SlicerBaseLogic/Resources/ColorFiles. In the source directory, they live in Base/Logic/Resources/ColorFiles.

Display panel

Color Display

This is a stand alone widget that can be popped up by other modules, for example the Editor. Here it lets you inspect the values of the selected colour look up table.

Slicer supports three kinds of tables:

1. Continuous scales, like the greyscale table.
2. Parametric tables, defined by an equation, such as the FMRIPA table.
3. Discrete tables, such as those read in from a file.

• Color Select: Choose from a drop down list of color nodes.

The colors are divided up into categories. These descriptions can be found in the Help and Acknowlegements tab at the top of the module's GUI.

• Discrete
  • Labels: A legacy colour table that contains some anatomical mapping
  • FullRainbow: A full rainbow of 256 colors, goes from red to red with all rainbow colors in between. Useful for colourful display of a label map
  • Grey: A grey scale ranging from black at 0 to white at 255. Useful for displaying MRI volumes.
  • Iron: A scale from red to yellow, 157 colours, useful for
  • Rainbow: Goes from red to purple, passing through the colors of the rainbow in between. Useful for a colorful display of a label map
  • Ocean: A lighter blue scale of 256 values, useful for showing registration results.
  • Desert: Red to yellow/orange scale, 256 colours, useful for
  • InvertedGrey: A white to black scale, 256 colours, useful to highlight negative versions, or to flip intensities of signal values.
  • ReverseRainbow: A colourful display option, 256 colours going from purple to red
  • fMRI: A combination of Ocean (0-22) and Desert (23-42), useful for displaying functional MRI volumes (highlights activation)
  • fMRIPA: A small fMRI positive activation scale going from red to yellow from 0-19, useful for displaying functional MRI volumes when don't need the blue of the fMRI scale.
  • Random: A random selection of 256 rgb colours, useful to distinguish between a small number of labeled regions (especially outside of the brain)
  • UserDefined: A user defined colour table, use the editor to specify it
  • Red: A red scale of 256 values. Useful for layering with Cyan
  • Green: A green scale of 256 values, useful for layering with Magenta
  • Blue: A blue scale of 256 values from black to pure blue, useful for layering with Yellow
  • Yellow: A yellow scale of 256 values, from black to pure yellow, useful for layering with blue (it's complementary, layering yields gray)
  • Cyan: A cyan ramp of 256 values, from black to cyan, complementary ramp to red, layering yeilds gray
  • Magenta: A magenta scale of 256 colors from black to magenta, complementary ramp to green, layering yeilds gray
  • Warm1: A scale from yellow to red, of 256 colors, ramp of warm colours that's complementary to Cool1
  • Warm2: A scale from green to yellow, 256 colours, ramp of warm colours that's complementary to Cool2
  • Warm3: A scale from cyan to green, 256 colours, ramp of warm colours that's complementary to Cool3
  • Cool1: A scale from blue to cyan, 256 colours, ramp of cool colours that's complementary to Warm1
  • Cool2: A scale from magenta to blue, 256 colours, ramp of cool colours that's complementary to Warm2
  • Cool3: A scale from red to magenta, ramp of cool colours that's complementary to Warm3
  • RandomIntegers: A random scale
• Shade:
  • WarmShade1: A scale from black to red, of 256 colors, ramp of warm colors with variation in value that's complementary to CoolShade1
  • WarmShade2: A scale from black to yellow, through green, of 256 colors, ramp of warm colors with variation in value that's complementary to CoolShade2
  • WarmShade3: A scale from black to green, of 256 colours, ramp of warm colors with variation in value that's complementary to CoolShade3
  • CoolShade1: A scale from black to cyan, 256 colours, ramp of cool colours with variation in value that is complementary to WarmShade1
  • CoolShade2: A scale from black to blue through purple, 256 colors, ramp of cool colours with variation in value that is complementary to WarmShade2
  • CoolShade3: A scale from black to magenta, 256 colours, ramp of cool colours with variation in value that is complementary to WarmShade3
• Tint:
  • WarmTint1: A scale from white to red, 256 colours, ramp of warm colours with variation in saturation that's complementary to CoolTint1
  • WarmTint2: A scale from white to yellow, 256 colours, ramp of warm colours with variation in saturation that's complementary to CoolTint2
  • WarmTint3: A scale from white to green, 256 colours, ramp of warm colours with variation in saturation that's complementary to CoolTint3
  • CoolTint1: A scale from white to cyan, 256 colours, ramp of cool colours with variations in saturation that's complementary to WarmTint1
  • CoolTint2: A scale from white to blue, 256 colours, ramp of cool colours with variations in saturation that's complementary to WarmTint2
  • CoolTint3: A scale from white to magenta, 256 colours, ramp of cool colours with variations in saturation that's complementary to WarmTint3
• FreeSurfer
  • Heat: The Heat FreeSurfer colour table, shows hot spots with high activation
  • BlueRed: A FreeSurfer color scale, 256 colours, from blue to red
  • RedBlue: A FreeSurfer color scale, 256 colours, from red to blue
  • RedGreen: A FreeSurfer color scale, 256 colours, from red to green, used to highlight sulcal curvature
  • GreenRed: A FreeSurfer color scale, 256 colours, from green to red, used to highlight sulcal curvature
  • FreeSurferLabels: A color table read in from a text file, each line of the format: IntegerLabel Name R G B Alpha
• PET
  • PET-Heat: Useful for displaying colorized PET data.
  • PET-Rainbow: Useful for displaying colorized PET data.
  • PET-MaximumIntensityProjection: Useful for displaying inverse grey PET data.
• Cartilage MRI
  • dGEMRIC-1.5T: Useful for displaying 1.5 tesla delayed gadolinium-enhanced MRI of cartilage
  • dGEMRIC-3T: Useful for displaying 3 Tesla delayed gadolinium-enhanced MRI of cartilage
• Default Labels from File:
  • a list of color nodes loaded from files, from the default Slicer color directory
  • PelvisColor: useful for displaying segmented pelvic MRI volumes
  • 64Color-Nonsemantic: A color table with no semantic labels, pure color information
  • AbdomenColors: useful for displaying segmented abdominal MRI volumes
  • SPL-BrainAtlas-ColorFile: useful for displaying segmented brain MRI volumes
  • SPL-BrainAtlas-2009-ColorFile: an updated brain segmentation node
  • Slicer3_2010_Short_LUT: a table with 16 labels defined.
• Slicer3_2010_Default_Brain_Lut: a brain segementation table with 16 labels defined.
• Auto Loaded User Color Files:
  • Files loaded from the user specified color paths in the Module Settings, can be saved with the scene
• File
  • If you load a color file from File -> Add Data, it will appear here
• User Generated
  • If you create a new color node in the Editor panel, it will appear here

• Node Type: a label updated to give the type of the node currently being displayed
• Total Number of Colours in Table: a label updated to display the number of entries in the color look up table.
• Selected Color Label: used especially in the Editor module, draw with the colour last clicked upon in the table.
• List box: The contents of the colour table, the entry is the integer label value, the name will show up in the label map layer of th 22d slice windows when you mouse over voxels with the corresponding value, the Color column shows how the voxel will be rendered.
• Show Only Named Colors: when this box is checked, the list box will only be populated by named colours. Some colour tables can have memtpy entries that have no name and default to black, this option lets you hide or show them.
• Lookup Table Range Min Max': Changes the range of values displayed, doesn't change the number of values in the table.

Scalar Bar

Scalar Bar

This panel lets you add a scalar bar widget to the 3D view showing the mapping between the integers and the colors in the color node.

• Display Scalar Bar: click on this to add a scalar bar to the scene, showing the currently selected color node in the Color Select drop down menu
• Title: set the title of the scalar bar, mm is used by default
• Title Properties: set the text display properties of the title text
  • Color
  • Font
  • Style
  • Opacity
• Label Format: The label format entry box uses the standard C++ string format. Format documentation
• Label Text Properties: Define how the labels are displayed along the length of the scalar bar widget.
  • Color
  • Font
  • Style
  • Opacity
• Maximum number of Colors: set the maximum number of scalar bar segments to show
• Number of labels: set the number of labels to show.

Edit panel

This panel lets users create a new colour look up table file, or edit an existing one.

Use the Edit frame to create a new color table, and save it to the mrml scene.

To create a new color node:

First, give your new color table a name in the Name entry.

Then fill in the Number of Colors. The list box will be populated with the corresponding number of entries. You can reset this to a larger number w/o losing your current settings.

Then click on Generate to populate a new node from the GUI contents. The color node is now available to use in the Volumes or Edit or Save modules.

To edit an existing color node, click on Select a Color Table to Copy. Pick a node from the drop down list, then click on the Copy Node button, it will fill in the edit box with those values. Make any changes you want, then click on the Generate a New Color Node button. At that point, the new node will show up in the File -> Save Data widget.

Development

Notes from the Developer(s)

A wiki page on LUTs and Ontologies where you can generate a Slicer Color file from a wiki page table.

Dependencies

The Volumes, Editor, and Models modules require this module.

Tests

On the Dashboard, these tests verify that the module is working on various platforms:

• vtkMRMLColorNodeTest1 vtkMRMLColorNodeTest1
• vtkMRMLColorTableNodeTest1 vtkMRMLColorTableNodeTest1
• vtkMRMLColorTableStorageNodeTest1 vtkMRMLColorTableStorageNodeTest1
• vtkMRMLdGEMRICProceduralColorNodeTest1 vtkMRMLdGEMRICProceduralColorNodeTest1
• vtkMRMLFreeSurferProceduralColorNodeTest1 vtkMRMLFreeSurferProceduralColorNodeTest1
• vtkMRMLPETProceduralColorNodeTest1 vtkMRMLPETProceduralColorNodeTest1
• vtkMRMLProceduralColorNodeTest1 vtkMRMLProceduralColorNodeTest1
• Slicer3ColorStorageNodeSceneTest Libs/MRML/Testing/Tcl/TestColorStorageNodeInScene.tcl

Known bugs

Follow this link to the Slicer3 bug tracker.

Usability issues

Follow this link to the Slicer3 bug tracker. Please select the usability issue category when browsing or contributing.

Source code & documentation

Source code:

• vtkSlicerColorGUI.cxx
• vtkSlicerColorGUI.h
• vtkSlicerColorLogic.cxx
• vtkSlicerColorLogic.h
• vtkSlicerColorDisplayWidget.cxx
• vtkSlicerColorDisplayWidget.h
• vtkSlicerColorEditWidget.cxx
• vtkSlicerColorEditWidget.h
• vtkMRMLColorNode.cxx
• vtkMRMLColorNode.h

Documentation generated by doxygen.

• Color GUI
• Color Logic
• Color Display Widget
• Color Edit Widget
• MRML Color Node (superclass from which other color nodes are derived)

More Information

Acknowledgment

This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.