Slicer Wiki - User contributions [en]

File:SlicerAstroIcon1.png

2020-07-28T14:50:34Z

Davide: Davide uploaded a new version of File:SlicerAstroIcon1.png

Documentation/Labs/NrrdReading Writing Optimizations

2018-11-12T09:10:56Z

Davide:

= Overview =

Here we summarize some efforts to optimize the reading and writing of nrrd files (currently done by using the teem library).

== Use Case ==
When reading or writing nrrd files currently Slicer uses a factor x2 of the dimension of the datasets in RAM.
This can already be an issue when loading datasets rather large (~2-3 GB) on systems with limited ram (already 8 GB).
The use of virtual memory can slow down (loading time increases up to 30 minutes instead of few seconds) or freeze completely Slicer (e.g., if using HDD).

== Solution ==
The idea is to stream the data between the Teem library and Slicer:

* For Teem: last four commits in https://github.com/ProxSim/teem/commits/slicer-2015-04-14-r6245
* For Slicer: https://www.slicer.org/w/images/b/b2/Reading_Writing.txt

== Issue ==
Before merging the solution, we still need to address:
* random access for compressed files to allow streaming with good performances in TEEM
* temporal filter as new interface to read/write data in the nrrdReader in SLICER

See https://github.com/SlicerRt/Sequences/pull/59 for more info.

== Current contributors ==
* Davide Punzo (punzodavide@hotmail.it)
* Andras Lasso (lasso@queensu.ca)

Anyone is welcome to contribute.

Documentation/Labs/NrrdReading Writing Optimizations

2018-11-12T09:07:01Z

Davide: Created page with "= Overview = Here we summarize some efforts to optimize the reading and writing of nrrd files (currently done by using the teem library). == Use Case == When reading or wri..."

= Overview =

Here we summarize some efforts to optimize the reading and writing of nrrd files (currently done by using the teem library).

== Use Case ==
When reading or writing nrrd files currently Slicer uses a factor x2 of the dimension of the datasets in RAM.
This can already be an issue when loading datasets rather large (~2-3 GB) on systems with limited ram (already 8 GB).
The use of virtual memory can slow down (loading time increases up to 30 minutes instead of few seconds) or freeze completely Slicer (e.g., if using HDD).

== Solution ==
The idea is to stream the data between the Teem library and Slicer:

A) For Teem: last four commits in https://github.com/ProxSim/teem/commits/slicer-2015-04-14-r6245
B) For Slicer: https://www.slicer.org/w/images/b/b2/Reading_Writing.txt

== Issue ==
Before merging the solution, we still need to address:
1) random access for compressed files to allow streaming with good performances in TEEM
2) temporal filter as new interface to read/write data in the nrrdReader in SLICER

See https://github.com/SlicerRt/Sequences/pull/59 for more info.

== Current contributors ==
-Davide Punzo (punzodavide@hotmail.it)
-Andras Lasso (lasso@queensu.ca)

Anyone is welcome to contribute.

File:Reading Writing.txt

2018-11-12T09:06:16Z

Davide:

Documentation/Labs

2018-11-12T08:44:39Z

Davide: /* Internals */

This is the place where we will keep track of our experiments and projects.

__TOC__

= On-going =

== Internals ==
* [[{{FULLPAGENAME}}/NrrdReading_Writing_Optimizations|NrrdReading_Writing_Optimizations]]
* [[{{FULLPAGENAME}}/OpenGLFilters|OpenGLFilters]]
* [[{{FULLPAGENAME}}/DeprecatedModules|DeprecatedModules extension]]
* [[{{FULLPAGENAME}}/FHSCompliantDirectoryStructure|FHS compliant directory structure]]
* [[{{FULLPAGENAME}}/FiberTractMeasurementAndVisualization|Fiber Tract measurement and visualization]]
* [[{{FULLPAGENAME}}/VTKWidgets|VTK Widgets improvements]]
* [[{{FULLPAGENAME}}/CLIInfrastructureCleanupAndRefactoring|CLI infrastructure cleanup and refactoring]]
* [[{{FULLPAGENAME}}/UpgradingCompilerInfrastructure|Upgrading Compiler Infrastructure]]
* [[{{FULLPAGENAME}}/ViewInfrastructureImprovements| View Infrastructure Improvements]]
* [[{{FULLPAGENAME}}/CDash Improvements|CDash Improvements]]
* [[{{FULLPAGENAME}}/SlicerBridge|SlicerBridge]]

* [[{{FULLPAGENAME}}/CI-and-NightlyPackagesGeneration|Continuous Integration and Nightly packages build infrastructure]]
* [[{{FULLPAGENAME}}/ParameterSerializer|Parameter Serializer support for CLIs]]
* [[{{FULLPAGENAME}}/Augmented Reality and Virtual Reality support|Augmented Reality and Virtual Reality support]]
* [[{{FULLPAGENAME}}/Infrastucture Status|Infrastucture Status]]
* [[{{FULLPAGENAME}}/Improving Slicer Packages Download Experience|Improving Slicer Packages Download experience]]
* [[{{FULLPAGENAME}}/Sequences|Sequences]]
* [[{{FULLPAGENAME}}/Improving Markups|Improving Markups]]

== Libraries ==
* [[{{FULLPAGENAME}}/VTK-Orientation|Design: Addition of orientation to VTK data structures]]

== Python ==
* [[{{FULLPAGENAME}}/CallingPythonMethodsFromCpp|Calling Python methods from Cpp]]
* [[{{FULLPAGENAME}}/IPython|IPython]]
* [[{{FULLPAGENAME}}/PythonCondaBuild|Python conda build]]

== Compilers & IDE ==
*

== Virtual Machines ==
* [[{{FULLPAGENAME}}/GPU Virtualization|GPU Virtualization]]

== Documentation ==
* [[{{FULLPAGENAME}}/DocumentationImprovments|Documentation Improvements (Wiki, website, ...)]]
* [[{{FULLPAGENAME}}/ModulesAndEvents|Intermediate documentation for developers]]

== Tutorials ==
* [[{{FULLPAGENAME}}/IPythonSlicerTutorials|IPython Slicer Tutorials]]

== Source code management ==
* [[{{FULLPAGENAME}}/TransitionToGit|Transition to Git]]

== Extension ==

* [[{{FULLPAGENAME}}/ExtensionsFrameworkRoadmap|Extensions Framework Roadmap]]
* [[{{FULLPAGENAME}}/CustomSlicerGenerator|Custom Slicer Generator]]
* [[{{FULLPAGENAME}}/ExtensionsMetadata|Improving Extensions Metadata]]

== Functionalities ==
* [[{{FULLPAGENAME}}/FlyThroughNavigation|Fly-through Navigation]]
* [[{{FULLPAGENAME}}/AutomaticUpdateAndInstallationFramework|Automatic Update and Installation Framework]]
* [[{{FULLPAGENAME}}/ApplicationUsageAnalytics|Application usage analytics]]

== Packaging ==
* [[{{FULLPAGENAME}}/HomebrewCask|Homebrew Cask]

= Completed =

* [[Slicer4:Developers|Developer Projects]]

== Extension ==
* [[{{FULLPAGENAME}}/EasyExtensionContribution|Easy Extension Contribution]] - See [[Documentation/Nightly/Developers/ExtensionWizard|ExtensionWizard]]

== Internals ==
* [[{{FULLPAGENAME}}/StartupTimeImprovement|Slicer startup time improvement]]
* [[{{FULLPAGENAME}}/CMake-ified Python|CMake-ified Python]] - See [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=21911 r21911], [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=21912 r21912], [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=21913 r21913]
* [[{{FULLPAGENAME}}/NonlinearTransforms|Full support for non-linear transforms]]

== Libraries ==
* [[{{FULLPAGENAME}}/Qt5-and-VTK8|Migration to Qt5 and VTK8]]
* [[{{FULLPAGENAME}}/OpenCV|Integration with OpenCV]]
* [[{{FULLPAGENAME}}/ITKv4|ITKv4]]
* [[{{FULLPAGENAME}}/Qt484|Qt484]]
* [[{{FULLPAGENAME}}/VTK6|VTK6]]
* [[{{FULLPAGENAME}}/VTK7|VTK7]]

== Python ==
* [[{{FULLPAGENAME}}/Pip|Pip]]
* [[{{FULLPAGENAME}}/DevelopmentWithGit|Development with Git]] - See [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=21863 r21863], [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=21867 r21867], [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=21869 r21869], [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=21879 r21879], [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=21891 r21891]
* [[{{FULLPAGENAME}}/PythonObserverCallbacks|Python observer callbacks]]

== Compilers & IDE ==
* [[{{FULLPAGENAME}}/Ninja|Ninja]]
* [[{{FULLPAGENAME}}/VS2012|VS2012]]
* [[{{FULLPAGENAME}}/NUMPY171|Support for Numpy 1.7.1]]

== Modules ==
* [[{{FULLPAGENAME}}/SimpleFilters|Simple Filters]]
* [[{{FULLPAGENAME}}/Editor|Editor]]

== Tutorials testing ==
* [[{{FULLPAGENAME}}/TutorialTesting/4.3-Release|4.3 Release]]

== Debug ==
* [[{{FULLPAGENAME}}/BRAINS_and_ITKv4_issue|BRAINS and ITKv4 issue]]

== Internals ==
* [[{{FULLPAGENAME}}/Segmentations|Segmentations]]
* [[{{FULLPAGENAME}}/MultiDimensional Data Management|MultiDimensional Data Management]]
* [[{{FULLPAGENAME}}/DICOMExport|DICOM Export]]
* [[{{FULLPAGENAME}}/SliceViewAnnotations|Slice View Annotations]]
* [[{{FULLPAGENAME}}/SubjectHierarchy|Subject hierarchy module and plugins]]
* [[{{FULLPAGENAME}}/I18N|Internationalization]]
* [[{{FULLPAGENAME}}/Units|Units]]
* [https://github.com/TubeTK/SlicerExecutionModel/wiki/SlicerExecutionModel-Parameter-Serialization SlicerExecutionModel Parameter Serialization]

= Abandoned =

* [[{{FULLPAGENAME}}/SlicerConfigAndUseSlicerTweaks|SlicerConfig and UseSlicer Tweaks]]

Documentation/Nightly/Developers/Plots

2018-09-19T07:34:14Z

Davide:

<noinclude>{{documentation/versioncheck}}</noinclude>
{{Clear}}{{TOC right}}

= Slicer plotting overview and acknowledgements =

Slicer provides Plotting facilities that include a plot view that can be displayed in the view layout, similarly to slice 3D views. Plot data is stored in table nodes, and plot series, chart, and view nodes define which table column need to be displayed and how. Plot can be serialized with the MRML scene, including the plot data and display properties. Plot series and charts can be created and edited in Plots module and plots can be also generated directly from Tables module by a single click.

Authors: 
Davide Punzo (Kapteyn Astronomical Institute, University of Groningen) 
Andras Lasso (PerkLab, Queen's University) 

Contributors: 
Jean-Christophe Fillion-Robin (Kitware) 
Steve Pieper (Isomics) 

Acknowledgements: 
This work was supported by the European Research Council under the European Union's Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement nr. 291-531. 

[[File:ERCIcon.png|300px|European Research Council]]
[[File:Kapteyn logo1.png|500px|Kapteyn Astronomical Institute]]


Contacts:
* Davide Punzo, <email>punzodavide@hotmail.it</email>; <email>D.Punzo@astro.rug.nl</email>

= Plot capabilities =
* Multiple plots types (Line, Bar, Scatter, Scatter bar), shown in standard view layouts.
* Configurable chart and axis title, legend, grid lines.
* Use indexes (0, 1, 2, ...) or a table column for X axis values.
* Multiple plot series can be added to a single plot chart (even showing data from different tables, with different types - plot, bar), and the same series can be added to multiple charts. The same plot chart can be shown in any plot views (even simultaneously).
* Label can be assigned to each data point (shown in tooltip when hovering over a data point).
* Interactive editing of data points by drag-and-drop (data in referenced table nodes is updated).
* Interactive selection of data points (rectangular or free-hand selection).
* Plot data and display properties are stored in the MRML scene.
* Plot view can be embedded into module user interfaces. Plot views can [[#Signals|emit signals]] back to the application as the user interacts with a plot, which allows modules to perform additional processing on the selected data points.

What is the difference between Slicer Plot and Chart?
[[Documentation/{{documentation/version}}/Developers/FAQ#What_is_the_difference_between_Slicer_Plot_and_Chart_.3F | See FAQ.]]

= Shortcuts and Interactions =
The Plot infrastructure allow the following interaction:

* Left mouse button: depends on interaction mode of the view
** Pan view: pan view
** Select points: select points using rectangular selection
** Freehand select points: select points using free-form selection
** Move points: move data points by drag-and-drop; this changes values in the referenced table node
* Middle mouse button: pan view (except in pan view mode; in that case it zooms to selected rectangular region)
* Right mouse button: zoom in/out along X and Y axes
* S: switch interaction mode (pan/select points/.../move points)
* R: reset view to show all data series
* U: unselect the points selection

=Architecture=

== MRML Nodes ==

; [{{doxygen-class-url|vtkMRMLTableNode}} vtkMRMLTableNode]
: Table node stores values that specify data point positions or bar heights in the plots.

; [{{doxygen-class-url|vtkMRMLPlotSeriesNode}} vtkMRMLPlotSeriesNode]
: Defines a data series by referring to a table node and column name(s) for X and Y axes and labels.
: It also defines display properties, such as plot type, color, line style.
: Line and bar plots only require Y axis (points along X axis are equally spaced), scatter plots require two input data columns, for X and Y axes.

; [{{doxygen-class-url|vtkMRMLPlotChartNode}} vtkMRMLPlotChartNode]
: Specifies which data series need to be shown in the chart.
: Also contains global display properties for the chart, such as titles and font style.

; [{{doxygen-class-url|vtkMRMLPlotViewNode}} vtkMRMLPlotViewNode]
: Specifies which chart is to be displayed in the plot view and how the user can interact with it.
: There has to be exactly one plot view node for each plot view widget. This class can not be created or copied unless is connected with a plot view.

== Widgets ==

; [{{doxygen-class-url|qMRMLPlotView}} qMRMLPlotView]
: Displays a plot. It can be embedded into a module user interface.

; [{{doxygen-class-url|qMRMLPlotWidget}} qMRMLPlotWidget]
: Displays a plot and in a popup window a plot view controller widget [{{doxygen-class-url|qMRMLPlotViewControllerWidget}} plot view controller widget].

; [{{doxygen-class-url|qMRMLPlotSeriesPropertiesWidget}} qMRMLPlotSeriesPropertiesWidget]
: Display/edit properties of a plot series node.

; [{{doxygen-class-url|qMRMLPlotChartPropertiesWidget}} qMRMLPlotChartPropertiesWidget]
: Display/edit properties of a plot series node.

; [{{doxygen-class-url|qMRMLPlotViewControllerWidget}} qMRMLPlotViewControllerWidget]
: Display/edit properties of a plot view node.

= Constructing a plot =
Below is an example in python to construct and display a plot communicating completely at the level of MRML. Note: this functionality is not available in Slicer 4.8, please use a recent SlicerPreview nightly build.

<pre lang="python">
import slicer
import math

# Create table with x, cos, sin columns

tableNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLTableNode")
table = tableNode.GetTable()

arrX = vtk.vtkFloatArray()
arrX.SetName("x")
table.AddColumn(arrX)

arrY1 = vtk.vtkFloatArray()
arrY1.SetName("cos")
table.AddColumn(arrY1)

arrY2 = vtk.vtkFloatArray()
arrY2.SetName("sin")
table.AddColumn(arrY2)

# Fill in the table with some example values

import math
numPoints = 69
inc = 7.5 / (numPoints - 1)
table.SetNumberOfRows(numPoints)
for i in range(numPoints):
table.SetValue(i, 0, i * inc )
table.SetValue(i, 1, math.cos(i * inc))
table.SetValue(i, 2, math.sin(i * inc))

# Create two plot series nodes

plotSeriesNode1 = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLPlotSeriesNode", "My first")
plotSeriesNode1.SetAndObserveTableNodeID(tableNode.GetID())
plotSeriesNode1.SetXColumnName("x")
plotSeriesNode1.SetYColumnName("cos")
plotSeriesNode1.SetPlotType(slicer.vtkMRMLPlotSeriesNode.PlotTypeScatter)
plotSeriesNode1.SetLineStyle(slicer.vtkMRMLPlotSeriesNode.LineStyleNone)
plotSeriesNode1.SetMarkerStyle(slicer.vtkMRMLPlotSeriesNode.MarkerStyleSquare)
plotSeriesNode1.SetUniqueColor()

plotSeriesNode2 = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLPlotSeriesNode", "My second")
plotSeriesNode2.SetAndObserveTableNodeID(tableNode.GetID())
plotSeriesNode2.SetXColumnName("x")
plotSeriesNode2.SetYColumnName("sin")
plotSeriesNode2.SetPlotType(slicer.vtkMRMLPlotSeriesNode.PlotTypeScatter)
plotSeriesNode2.SetUniqueColor()

# Create plot chart node

plotChartNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLPlotChartNode")
plotChartNode.AddAndObservePlotSeriesNodeID(plotSeriesNode1.GetID())
plotChartNode.AddAndObservePlotSeriesNodeID(plotSeriesNode2.GetID())
plotChartNode.SetTitle('A simple plot with 2 curves')
plotChartNode.SetXAxisTitle('Something in x')
plotChartNode.SetYAxisTitle('Something in y')

# Switch to a layout that contains a plot view to create a plot widget

layoutManager = slicer.app.layoutManager()
layoutWithPlot = slicer.modules.plots.logic().GetLayoutWithPlot(layoutManager.layout)
layoutManager.setLayout(layoutWithPlot)

# Select chart in plot view

plotWidget = layoutManager.plotWidget(0)
plotViewNode = plotWidget.mrmlPlotViewNode()
plotViewNode.SetPlotChartNodeID(plotChartNode.GetID())
</pre>

This code produces the plot below.

[[Image:VtkPlot.png|A simple plot.|1200px]]

= Signals =
PlotViews provide signals that allow Slicer to respond to user interactions with the Plot canvas:

;void dataSelected(vtkStringArray* mrmlPlotDataIDs, vtkCollection* selectionCol)
:Signal emitted when a data point or more has been selected. Returns the MRMLPlotDataNodes IDs and the correspective arrays with the data points ids (vtkIdTypeArray).

Python API example:

<pre lang="python">
# Switch to a layout that contains a plot view to create a plot widget
layoutManager = slicer.app.layoutManager()
layoutWithPlot = slicer.modules.plots.logic().GetLayoutWithPlot(layoutManager.layout)
layoutManager.setLayout(layoutWithPlot)

# Select chart in plot view
plotWidget = layoutManager.plotWidget(0)
plotViewNode = plotWidget.mrmlPlotViewNode()

# Add a PlotCharNode
# plotViewNode.SetPlotChartNodeID(''PlotChartNode''.GetID())

# Connect the signal with a slot ''onDataSelected''
plotView = plotWidget.plotView()
plotView.connect("dataSelected(vtkStringArray*, vtkCollection*)", self.onDataSelected)

</pre>

= Future Work =
* Adding to VTKPlots the possibility to plot errorbars.
* Add categorical and date labels to the Bar plotting (analogous to the CHART infrastructure)
* More signals?
* Add 3D Plots (vtkChartXYZ)
* Add Click and Drag action for multiple selected points

Documentation/Nightly/Developers/Plots

2018-09-19T07:33:36Z

Davide:

Documentation/Nightly/Developers/Plots

2018-09-19T07:32:25Z

Davide:

<noinclude>{{documentation/versioncheck}}</noinclude>
{{Clear}}{{TOC right}}

= Slicer plotting overview and acknowledgements =

Slicer provides Plotting facilities that include a plot view that can be displayed in the view layout, similarly to slice 3D views. Plot data is stored in table nodes, and plot series, chart, and view nodes define which table column need to be displayed and how. Plot can be serialized with the MRML scene, including the plot data and display properties. Plot series and charts can be created and edited in Plots module and plots can be also generated directly from Tables module by a single click.

Authors: 
Davide Punzo (Kapteyn Astronomical Institute, University of Groningen) 
Andras Lasso (PerkLab, Queen's University) 

Contributors: 
Jean-Christophe Fillion-Robin (Kitware) 
Steve Pieper (Isomics) 

Acknowledgements: 
This work was supported by the European Research Council under the European Union's Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement nr. 291-531. 

[[File:ERCIcon.png|300px|European Research Council]]
[[File:Kapteyn logo1.png|500px|Kapteyn Astronomical Institute]]


Contacts:
* Davide Punzo, <email>punzodavide@hotmail.it</email>; <email>D.Punzo@astro.rug.nl</email>

= Plot capabilities =
* Multiple plots types (Line, Bar, Scatter, Scatter bar), shown in standard view layouts.
* Configurable chart and axis title, legend, grid lines.
* Use indexes (0, 1, 2, ...) or a table column for X axis values.
* Multiple plot series can be added to a single plot chart (even showing data from different tables, with different types - plot, bar), and the same series can be added to multiple charts. The same plot chart can be shown in any plot views (even simultaneously).
* Label can be assigned to each data point (shown in tooltip when hovering over a data point).
* Interactive editing of data points by drag-and-drop (data in referenced table nodes is updated).
* Interactive selection of data points (rectangular or free-hand selection).
* Plot data and display properties are stored in the MRML scene.
* Plot view can be embedded into module user interfaces. Plot views can [[#Signals|emit signals]] back to the application as the user interacts with a plot, which allows modules to perform additional processing on the selected data points.

What is the difference between Slicer Plot and Chart?
[[Documentation/{{documentation/version}}/Developers/FAQ#What_is_the_difference_between_Slicer_Plot_and_Chart_.3F | See FAQ.]]

= Shortcuts and Interactions =
The Plot infrastructure allow the following interaction:

* Left mouse button: depends on interaction mode of the view
** Pan view: pan view
** Select points: select points using rectangular selection
** Freehand select points: select points using free-form selection
** Move points: move data points by drag-and-drop; this changes values in the referenced table node
* Middle mouse button: pan view (except in pan view mode; in that case it zooms to selected rectangular region)
* Right mouse button: zoom in/out along X and Y axes
* S: switch interaction mode (pan/select points/.../move points)
* R: reset view to show all data series
* U: unselect the points selection

=Architecture=

== MRML Nodes ==

; [{{doxygen-class-url|vtkMRMLTableNode}} vtkMRMLTableNode]
: Table node stores values that specify data point positions or bar heights in the plots.

; [{{doxygen-class-url|vtkMRMLPlotSeriesNode}} vtkMRMLPlotSeriesNode]
: Defines a data series by referring to a table node and column name(s) for X and Y axes and labels.
: It also defines display properties, such as plot type, color, line style.
: Line and bar plots only require Y axis (points along X axis are equally spaced), scatter plots require two input data columns, for X and Y axes.

; [{{doxygen-class-url|vtkMRMLPlotChartNode}} vtkMRMLPlotChartNode]
: Specifies which data series need to be shown in the chart.
: Also contains global display properties for the chart, such as titles and font style.

; [{{doxygen-class-url|vtkMRMLPlotViewNode}} vtkMRMLPlotViewNode]
: Specifies which chart is to be displayed in the plot view and how the user can interact with it.
: There has to be exactly one plot view node for each plot view widget. This class can not be created or copied unless is connected with a plot view.

== Widgets ==

; [{{doxygen-class-url|qMRMLPlotView}} qMRMLPlotView]
: Displays a plot. It can be embedded into a module user interface.

; [{{doxygen-class-url|qMRMLPlotWidget}} qMRMLPlotWidget]
: Displays a plot and in a popup window a plot view controller widget [{{doxygen-class-url|qMRMLPlotViewControllerWidget}} plot view controller widget].

; [{{doxygen-class-url|qMRMLPlotSeriesPropertiesWidget}} qMRMLPlotSeriesPropertiesWidget]
: Display/edit properties of a plot series node.

; [{{doxygen-class-url|qMRMLPlotChartPropertiesWidget}} qMRMLPlotChartPropertiesWidget]
: Display/edit properties of a plot series node.

; [{{doxygen-class-url|qMRMLPlotViewControllerWidget}} qMRMLPlotViewControllerWidget]
: Display/edit properties of a plot view node.

= Constructing a plot =
Below is an example in python to construct and display a plot communicating completely at the level of MRML. Note: this functionality is not available in Slicer 4.8, please use a recent SlicerPreview nightly build.

<pre lang="python">
import slicer
import math

# Create table with x, cos, sin columns

tableNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLTableNode")
table = tableNode.GetTable()

arrX = vtk.vtkFloatArray()
arrX.SetName("x")
table.AddColumn(arrX)

arrY1 = vtk.vtkFloatArray()
arrY1.SetName("cos")
table.AddColumn(arrY1)

arrY2 = vtk.vtkFloatArray()
arrY2.SetName("sin")
table.AddColumn(arrY2)

# Fill in the table with some example values

import math
numPoints = 69
inc = 7.5 / (numPoints - 1)
table.SetNumberOfRows(numPoints)
for i in range(numPoints):
table.SetValue(i, 0, i * inc )
table.SetValue(i, 1, math.cos(i * inc))
table.SetValue(i, 2, math.sin(i * inc))

# Create two plot series nodes

plotSeriesNode1 = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLPlotSeriesNode", "My first")
plotSeriesNode1.SetAndObserveTableNodeID(tableNode.GetID())
plotSeriesNode1.SetXColumnName("x")
plotSeriesNode1.SetYColumnName("cos")
plotSeriesNode1.SetPlotType(slicer.vtkMRMLPlotSeriesNode.PlotTypeScatter)
plotSeriesNode1.SetLineStyle(slicer.vtkMRMLPlotSeriesNode.LineStyleNone)
plotSeriesNode1.SetMarkerStyle(slicer.vtkMRMLPlotSeriesNode.MarkerStyleSquare)
plotSeriesNode1.SetUniqueColor()

plotSeriesNode2 = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLPlotSeriesNode", "My second")
plotSeriesNode2.SetAndObserveTableNodeID(tableNode.GetID())
plotSeriesNode2.SetXColumnName("x")
plotSeriesNode2.SetYColumnName("sin")
plotSeriesNode2.SetPlotType(slicer.vtkMRMLPlotSeriesNode.PlotTypeScatter)
plotSeriesNode2.SetUniqueColor()

# Create plot chart node

plotChartNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLPlotChartNode")
plotChartNode.AddAndObservePlotSeriesNodeID(plotSeriesNode1.GetID())
plotChartNode.AddAndObservePlotSeriesNodeID(plotSeriesNode2.GetID())
plotChartNode.SetTitle('A simple plot with 2 curves')
plotChartNode.SetXAxisTitle('Something in x')
plotChartNode.SetYAxisTitle('Something in y')

# Switch to a layout that contains a plot view to create a plot widget

layoutManager = slicer.app.layoutManager()
layoutWithPlot = slicer.modules.plots.logic().GetLayoutWithPlot(layoutManager.layout)
layoutManager.setLayout(layoutWithPlot)

# Select chart in plot view

plotWidget = layoutManager.plotWidget(0)
plotViewNode = plotWidget.mrmlPlotViewNode()
plotViewNode.SetPlotChartNodeID(plotChartNode.GetID())
</pre>

This code produces the plot below.

[[Image:VtkPlot.png|A simple plot.|1200px]]

= Signals =
PlotViews provide signals that allow Slicer to respond to user interactions with the Plot canvas:

;void dataSelected(vtkStringArray* mrmlPlotDataIDs, vtkCollection* selectionCol)
:Signal emitted when a data point or more has been selected. Returns the MRMLPlotDataNodes IDs and the correspective arrays with the data points ids (vtkIdTypeArray).

Python API example:

<pre lang="python">
# Switch to a layout that contains a plot view to create a plot widget
layoutManager = slicer.app.layoutManager()
layoutWithPlot = slicer.modules.plots.logic().GetLayoutWithPlot(layoutManager.layout)
layoutManager.setLayout(layoutWithPlot)

# Select chart in plot view
plotWidget = layoutManager.plotWidget(0)
plotViewNode = plotWidget.mrmlPlotViewNode()

# Add a PlotCharNode
# plotViewNode.SetPlotChartNodeID(''PlotChartNode''.GetID())

plotView = plotWidget.plotView()
plotView.connect("dataSelected(vtkStringArray*, vtkCollection*)", self.onDataSelected)

def onDataSelected(self):
...
</pre>

= Future Work =
* Adding to VTKPlots the possibility to plot errorbars.
* Add categorical and date labels to the Bar plotting (analogous to the CHART infrastructure)
* More signals?
* Add 3D Plots (vtkChartXYZ)
* Add Click and Drag action for multiple selected points

Documentation/Nightly/Developers/Plots

2018-09-11T07:17:08Z

Davide:

<noinclude>{{documentation/versioncheck}}</noinclude>
{{Clear}}{{TOC right}}

= Slicer plotting overview and acknowledgements =

Slicer provides Plotting facilities that include a plot view that can be displayed in the view layout, similarly to slice 3D views. Plot data is stored in table nodes, and plot series, chart, and view nodes define which table column need to be displayed and how. Plot can be serialized with the MRML scene, including the plot data and display properties. Plot series and charts can be created and edited in Plots module and plots can be also generated directly from Tables module by a single click.

Authors: 
Davide Punzo (Kapteyn Astronomical Institute, University of Groningen) 
Andras Lasso (PerkLab, Queen's University) 

Contributors: 
Jean-Christophe Fillion-Robin (Kitware) 
Steve Pieper (Isomics) 

Acknowledgements: 
This work was supported by the European Research Council under the European Union's Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement nr. 291-531. 

[[File:ERCIcon.png|300px|European Research Council]]
[[File:Kapteyn logo1.png|500px|Kapteyn Astronomical Institute]]


Contacts:
* Davide Punzo, <email>punzodavide@hotmail.it</email>; <email>D.Punzo@astro.rug.nl</email>

= Plot capabilities =
* Multiple plots types (Line, Bar, Scatter, Scatter bar), shown in standard view layouts.
* Configurable chart and axis title, legend, grid lines.
* Use indexes (0, 1, 2, ...) or a table column for X axis values.
* Multiple plot series can be added to a single plot chart (even showing data from different tables, with different types - plot, bar), and the same series can be added to multiple charts. The same plot chart can be shown in any plot views (even simultaneously).
* Label can be assigned to each data point (shown in tooltip when hovering over a data point).
* Interactive editing of data points by drag-and-drop (data in referenced table nodes is updated).
* Interactive selection of data points (rectangular or free-hand selection).
* Plot data and display properties are stored in the MRML scene.
* Plot view can be embedded into module user interfaces. Plot views can [[#Signals|emit signals]] back to the application as the user interacts with a plot, which allows modules to perform additional processing on the selected data points.

What is the difference between Slicer Plot and Chart?
[[Documentation/{{documentation/version}}/Developers/FAQ#What_is_the_difference_between_Slicer_Plot_and_Chart_.3F | See FAQ.]]

= Shortcuts and Interactions =
The Plot infrastructure allow the following interaction:

* Left mouse button: depends on interaction mode of the view
** Pan view: pan view
** Select points: select points using rectangular selection
** Freehand select points: select points using free-form selection
** Move points: move data points by drag-and-drop; this changes values in the referenced table node
* Middle mouse button: pan view (except in pan view mode; in that case it zooms to selected rectangular region)
* Right mouse button: zoom in/out along X and Y axes
* S: switch interaction mode (pan/select points/.../move points)
* R: reset view to show all data series
* U: unselect the points selection

=Architecture=

== MRML Nodes ==

; [{{doxygen-class-url|vtkMRMLTableNode}} vtkMRMLTableNode]
: Table node stores values that specify data point positions or bar heights in the plots.

; [{{doxygen-class-url|vtkMRMLPlotSeriesNode}} vtkMRMLPlotSeriesNode]
: Defines a data series by referring to a table node and column name(s) for X and Y axes and labels.
: It also defines display properties, such as plot type, color, line style.
: Line and bar plots only require Y axis (points along X axis are equally spaced), scatter plots require two input data columns, for X and Y axes.

; [{{doxygen-class-url|vtkMRMLPlotChartNode}} vtkMRMLPlotChartNode]
: Specifies which data series need to be shown in the chart.
: Also contains global display properties for the chart, such as titles and font style.

; [{{doxygen-class-url|vtkMRMLPlotViewNode}} vtkMRMLPlotViewNode]
: Specifies which chart is to be displayed in the plot view and how the user can interact with it.
: There has to be exactly one plot view node for each plot view widget. This class can not be created or copied unless is connected with a plot view.

== Widgets ==

; [{{doxygen-class-url|qMRMLPlotView}} qMRMLPlotView]
: Displays a plot. It can be embedded into a module user interface.

; [{{doxygen-class-url|qMRMLPlotWidget}} qMRMLPlotWidget]
: Displays a plot and in a popup window a plot view controller widget [{{doxygen-class-url|qMRMLPlotViewControllerWidget}} plot view controller widget].

; [{{doxygen-class-url|qMRMLPlotSeriesPropertiesWidget}} qMRMLPlotSeriesPropertiesWidget]
: Display/edit properties of a plot series node.

; [{{doxygen-class-url|qMRMLPlotChartPropertiesWidget}} qMRMLPlotChartPropertiesWidget]
: Display/edit properties of a plot series node.

; [{{doxygen-class-url|qMRMLPlotViewControllerWidget}} qMRMLPlotViewControllerWidget]
: Display/edit properties of a plot view node.

= Constructing a plot =
Below is an example in python to construct and display a plot communicating completely at the level of MRML. Note: this functionality is not available in Slicer 4.8, please use a recent SlicerPreview nightly build.

<pre lang="python">
import slicer
import math

# Create table with x, cos, sin columns

tableNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLTableNode")
table = tableNode.GetTable()

arrX = vtk.vtkFloatArray()
arrX.SetName("x")
table.AddColumn(arrX)

arrY1 = vtk.vtkFloatArray()
arrY1.SetName("cos")
table.AddColumn(arrY1)

arrY2 = vtk.vtkFloatArray()
arrY2.SetName("sin")
table.AddColumn(arrY2)

# Fill in the table with some example values

import math
numPoints = 69
inc = 7.5 / (numPoints - 1)
table.SetNumberOfRows(numPoints)
for i in range(numPoints):
table.SetValue(i, 0, i * inc )
table.SetValue(i, 1, math.cos(i * inc))
table.SetValue(i, 2, math.sin(i * inc))

# Create two plot series nodes

plotSeriesNode1 = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLPlotSeriesNode", "My first")
plotSeriesNode1.SetAndObserveTableNodeID(tableNode.GetID())
plotSeriesNode1.SetXColumnName("x")
plotSeriesNode1.SetYColumnName("cos")
plotSeriesNode1.SetPlotType(slicer.vtkMRMLPlotSeriesNode.PlotTypeScatter)
plotSeriesNode1.SetLineStyle(slicer.vtkMRMLPlotSeriesNode.LineStyleNone)
plotSeriesNode1.SetMarkerStyle(slicer.vtkMRMLPlotSeriesNode.MarkerStyleSquare)
plotSeriesNode1.SetUniqueColor()

plotSeriesNode2 = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLPlotSeriesNode", "My second")
plotSeriesNode2.SetAndObserveTableNodeID(tableNode.GetID())
plotSeriesNode2.SetXColumnName("x")
plotSeriesNode2.SetYColumnName("sin")
plotSeriesNode2.SetPlotType(slicer.vtkMRMLPlotSeriesNode.PlotTypeScatter)
plotSeriesNode2.SetUniqueColor()

# Create plot chart node

plotChartNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLPlotChartNode")
plotChartNode.AddAndObservePlotSeriesNodeID(plotSeriesNode1.GetID())
plotChartNode.AddAndObservePlotSeriesNodeID(plotSeriesNode2.GetID())
plotChartNode.SetTitle('A simple plot with 2 curves')
plotChartNode.SetXAxisTitle('Something in x')
plotChartNode.SetYAxisTitle('Something in y')

# Switch to a layout that contains a plot view to create a plot widget

layoutManager = slicer.app.layoutManager()
layoutWithPlot = slicer.modules.plots.logic().GetLayoutWithPlot(layoutManager.layout)
layoutManager.setLayout(layoutWithPlot)

# Select chart in plot view

plotWidget = layoutManager.plotWidget(0)
plotViewNode = plotWidget.mrmlPlotViewNode()
plotViewNode.SetPlotChartNodeID(plotChartNode.GetID())
</pre>

This code produces the plot below.

[[Image:VtkPlot.png|A simple plot.|1200px]]

= Signals =
PlotViews provide signals that allow Slicer to respond to user interactions with the Plot canvas:

;void dataSelected(vtkStringArray* mrmlPlotDataIDs, vtkCollection* selectionCol)
:Signal emitted when a data point or more has been selected. Returns the MRMLPlotDataNodes IDs and the correspective arrays with the data points ids (vtkIdTypeArray).

= Future Work =
* Adding to VTKPlots the possibility to plot errorbars.
* Add categorical and date labels to the Bar plotting (analogous to the CHART infrastructure)
* More signals?
* Add 3D Plots (vtkChartXYZ)
* Add Click and Drag action for multiple selected points

Documentation/Nightly/Extensions/SlicerAstro

2018-08-10T13:59:34Z

Davide:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:ERCIcon.png|300px|European Research Council]]
[[File:Kapteyn logo1.png|500px|Kapteyn Astronomical Institute]]


{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
Authors: 
Davide Punzo (Kapteyn Astronomical Institute, University of Groningen) 
Thijs van der Hulst (Kapteyn Astronomical Institute, University of Groningen) 
Jos Roerdink (Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen) 

Contributors: 
Jean-Christophe Fillion-Robin (Kitware) 
Steve Pieper (Isomics) 
Andras Lasso (PerkLab, Queen's) 

Acknowledgements: 
This work was supported by the European Research Council under the European Union's Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement nr. 291-531. 

Note: 
As of August 2018 financial support for SlicerAstro development has ended. The software will be maintained at the Kapteyn Astronomical Institute of the University of Groningen, but further development is currently on hold. If you have any query, pull request and/or ideas you can still contact [https://github.com/Punzo/SlicerAstro/wiki#contacts us] or submit a [https://github.com/Punzo/SlicerAstro/issues ticket]. 

Contacts:
* Davide Punzo, <email>punzodavide@hotmail.it</email>; <email>D.Punzo@astro.rug.nl</email>
* Thijs van der Hulst, <email>J.M.van.der.Hulst@astro.rug.nl</email>
* Jos Roerdink <email>j.b.t.m.roerdink@rug.nl</email>

Source: [https://github.com/Punzo/SlicerAstro] 
License: [http://www.slicer.org/pages/LicenseText Slicer license] 
'''Download/install:''' install 3D Slicer, start 3D Slicer, open the Extension Manager, install the SlicerAstro extension[https://github.com/Punzo/SlicerAstro/wiki].



{{documentation/{{documentation/version}}/extension-section|Extension Description}}
{|

|
[[Image:SlicerAstroIcon1.png|350px]]
|
Upcoming HI (neutral Hydrogen) surveys will deliver large datasets, and automated processing using the full 3-D information (two positional dimensions and one spectral dimension) to find and characterize HI objects is imperative. In this context, visualization is an essential tool for enabling qualitative and quantitative human control on an automated source finding and analysis pipeline. Visual Analytics, the combination of automated data processing and human reasoning, creativity and intuition, supported by interactive visualization, enables flexible and fast interaction with the 3-D data, helping the astronomer to deal with the analysis of complex sources. 3-D visualization, coupled to modeling, provides additional capabilities helping the discovery and analysis of subtle structures in the 3-D domain.

<h3> Objective: general description</h3>
* 1) proper visualization of astronomical data cubes: using data astronomical data formats, such as FITS, and astronomical world coordinates system (WCS);
* 2) generation of Histogram, flux density profiles, moment maps and position-velocity diagrams linked with the 3-D view;
* 3) enabling interactive smoothing in all three dimensions;
* 4) interactive HI data modeling coupled to visualization;
* 5) introduction of the SAMP protocol to enable interoperability with Topcat, and other VO tools and catalogs.

for more info see [https://github.com/Punzo/SlicerAstro/wiki] and [http://arxiv.org/pdf/1505.06976v2.pdf], [https://arxiv.org/pdf/1703.06651].

|
|}


{{documentation/{{documentation/version}}/extension-section|Modules}}
{||

SlicerAstro development focuses on HI datasets. The [[Documentation/{{documentation/version}}/Modules/AstroVolume|Astro Volume]] component is the core module and handles the loading/saving, color functions and WCS corrdinates.

Tutorials and information can be found in the [[Documentation/{{documentation/version}}/Modules/AstroWelcome|Astro Welcome]] module and sample data are available at the [[Documentation/{{documentation/version}}/Modules/AstroSampleData|Astro Sample Data]] module.

We currently provide additional modules with their own interface widgets for user interaction, which are mainly aimed for the analysis of HI data-cubes:

*[[Documentation/{{documentation/version}}/Modules/SlicerAstroDataProbe|SlicerAstro Data Probe]]
*[[Documentation/{{documentation/version}}/Modules/AstroReproject|Astro Reproject]]
*[[Documentation/{{documentation/version}}/Modules/AstroStatistics|Astro Statistics]]
*[[Documentation/{{documentation/version}}/Modules/AstroMasking|Astro Masking]]
*[[Documentation/{{documentation/version}}/Modules/AstroSmoothing|Astro Smoothing]]
*[[Documentation/{{documentation/version}}/Modules/AstroProfiles|Astro Profiles]]
*[[Documentation/{{documentation/version}}/Modules/AstroMomentMaps|Astro Moment Maps]]
*[[Documentation/{{documentation/version}}/Modules/AstroPVSlice|Astro PV Slice]]
*[[Documentation/{{documentation/version}}/Modules/AstroPVDiagram|Astro PV Diagram]]
*[[Documentation/{{documentation/version}}/Modules/AstroModeling|Astro Modeling]]


{{documentation/{{documentation/version}}/extension-section|Use Case: Visualization of HI dataset}}

3D visualization for the inspection and analysis of complex HI source:
A 3D view gives an immediate overview of the coherence along the spatial and velocity dimensions such as tidal tail, gas stripping and filaments.

NOTE: SlicerAstro can potentially enhance also the inspection of other datasets such as mm/submm molecular line data and optical integral field spectroscopic data. The user is welcome to share any idea and feedback in the issue tracker[https://github.com/Punzo/SlicerAstro/issues].
 
[[File:SlicerAstroScreenshot.png| Slicer Astro Screenshot|1000px]]
 


{{documentation/{{documentation/version}}/extension-section|References}}
==How to cite==
Please cite the following paper when referring to SlicerAstro in your publication: 

<pre>
@MISC{SlicerAstro,
author = {{Punzo}, D. and {van der Hulst}, T. and {Roerdink}, J. and {Fillion-Robin}, J.-C.
},
title = "{SlicerAstro: Astronomy (HI) extension for 3D Slicer}",
keywords = {Software },
howpublished = {Astrophysics Source Code Library},
year = 2016,
month = nov,
archivePrefix = "ascl",
eprint = {1611.021},
}
</pre>

<pre>
@ARTICLE{2017A&C....19...45P,
author = {{Punzo}, D. and {van der Hulst}, J.~M. and {Roerdink}, J.~B.~T.~M. and
{Fillion-Robin}, J.~C. and {Yu}, L.},
title = "{SlicerAstro: A 3-D interactive visual analytics tool for HI data}",
journal = {Astronomy and Computing},
archivePrefix = "arXiv",
eprint = {1703.06651},
primaryClass = "astro-ph.IM",
keywords = {Radio lines: galaxies, Scientific visualization, Visual analytics, Agile software development, Object oriented development, Empirical software validation},
year = 2017,
month = apr,
volume = 19,
pages = {45-59},
doi = {10.1016/j.ascom.2017.03.004},
}
</pre>

<pre>
@ARTICLE{2015A&C....12...86P,
author = {{Punzo}, D. and {van der Hulst}, J.~M. and {Roerdink}, J.~B.~T.~M. and {Oosterloo}, T.~A. and {Ramatsoku}, M. and {Verheijen}, M.~A.~W.},
title = "{The role of 3-D interactive visualization in blind surveys of H I in galaxies}",
journal = {Astronomy and Computing},
archivePrefix = "arXiv",
eprint = {1505.06976},
primaryClass = "astro-ph.IM",
keywords = {Radio lines: galaxies, Galaxies: kinematics and dynamics, Surveys, Scientific visualization, Visual analytics},
year = 2015,
month = sep,
volume = 12,
pages = {86-99},
doi = {10.1016/j.ascom.2015.05.004},
}
</pre>


{{documentation/{{documentation/version}}/extension-footer}}

Documentation/Nightly/Extensions/SlicerAstro

2018-08-10T13:58:24Z

Davide:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:ERCIcon.png|300px|European Research Council]]
[[File:Kapteyn logo1.png|500px|Kapteyn Astronomical Institute]]


{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
Authors: 
Davide Punzo (Kapteyn Astronomical Institute, University of Groningen) 
Thijs van der Hulst (Kapteyn Astronomical Institute, University of Groningen) 
Jos Roerdink (Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen) 

Contributors: 
Jean-Christophe Fillion-Robin (Kitware) 
Steve Pieper (Isomics) 
Andras Lasso (PerkLab, Queen's) 

Acknowledgements: 
This work was supported by the European Research Council under the European Union's Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement nr. 291-531. 

Note: 
As of August 2018 financial support for SlicerAstro development has ended. The software will be maintained at the Kapteyn Astronomical Institute of the University of Groningen, but further development is currently on hold. If you have any query, pull request and/or ideas you can still contact [us](https://github.com/Punzo/SlicerAstro/wiki#contacts) or submit a [ticket](https://github.com/Punzo/SlicerAstro/issues). 

Contacts:
* Davide Punzo, <email>punzodavide@hotmail.it</email>; <email>D.Punzo@astro.rug.nl</email>
* Thijs van der Hulst, <email>J.M.van.der.Hulst@astro.rug.nl</email>
* Jos Roerdink <email>j.b.t.m.roerdink@rug.nl</email>

Source: [https://github.com/Punzo/SlicerAstro] 
License: [http://www.slicer.org/pages/LicenseText Slicer license] 
'''Download/install:''' install 3D Slicer, start 3D Slicer, open the Extension Manager, install the SlicerAstro extension[https://github.com/Punzo/SlicerAstro/wiki].



{{documentation/{{documentation/version}}/extension-section|Extension Description}}
{|

|
[[Image:SlicerAstroIcon1.png|350px]]
|
Upcoming HI (neutral Hydrogen) surveys will deliver large datasets, and automated processing using the full 3-D information (two positional dimensions and one spectral dimension) to find and characterize HI objects is imperative. In this context, visualization is an essential tool for enabling qualitative and quantitative human control on an automated source finding and analysis pipeline. Visual Analytics, the combination of automated data processing and human reasoning, creativity and intuition, supported by interactive visualization, enables flexible and fast interaction with the 3-D data, helping the astronomer to deal with the analysis of complex sources. 3-D visualization, coupled to modeling, provides additional capabilities helping the discovery and analysis of subtle structures in the 3-D domain.

<h3> Objective: general description</h3>
* 1) proper visualization of astronomical data cubes: using data astronomical data formats, such as FITS, and astronomical world coordinates system (WCS);
* 2) generation of Histogram, flux density profiles, moment maps and position-velocity diagrams linked with the 3-D view;
* 3) enabling interactive smoothing in all three dimensions;
* 4) interactive HI data modeling coupled to visualization;
* 5) introduction of the SAMP protocol to enable interoperability with Topcat, and other VO tools and catalogs.

for more info see [https://github.com/Punzo/SlicerAstro/wiki] and [http://arxiv.org/pdf/1505.06976v2.pdf], [https://arxiv.org/pdf/1703.06651].

|
|}


{{documentation/{{documentation/version}}/extension-section|Modules}}
{||

SlicerAstro development focuses on HI datasets. The [[Documentation/{{documentation/version}}/Modules/AstroVolume|Astro Volume]] component is the core module and handles the loading/saving, color functions and WCS corrdinates.

Tutorials and information can be found in the [[Documentation/{{documentation/version}}/Modules/AstroWelcome|Astro Welcome]] module and sample data are available at the [[Documentation/{{documentation/version}}/Modules/AstroSampleData|Astro Sample Data]] module.

We currently provide additional modules with their own interface widgets for user interaction, which are mainly aimed for the analysis of HI data-cubes:

*[[Documentation/{{documentation/version}}/Modules/SlicerAstroDataProbe|SlicerAstro Data Probe]]
*[[Documentation/{{documentation/version}}/Modules/AstroReproject|Astro Reproject]]
*[[Documentation/{{documentation/version}}/Modules/AstroStatistics|Astro Statistics]]
*[[Documentation/{{documentation/version}}/Modules/AstroMasking|Astro Masking]]
*[[Documentation/{{documentation/version}}/Modules/AstroSmoothing|Astro Smoothing]]
*[[Documentation/{{documentation/version}}/Modules/AstroProfiles|Astro Profiles]]
*[[Documentation/{{documentation/version}}/Modules/AstroMomentMaps|Astro Moment Maps]]
*[[Documentation/{{documentation/version}}/Modules/AstroPVSlice|Astro PV Slice]]
*[[Documentation/{{documentation/version}}/Modules/AstroPVDiagram|Astro PV Diagram]]
*[[Documentation/{{documentation/version}}/Modules/AstroModeling|Astro Modeling]]


{{documentation/{{documentation/version}}/extension-section|Use Case: Visualization of HI dataset}}

3D visualization for the inspection and analysis of complex HI source:
A 3D view gives an immediate overview of the coherence along the spatial and velocity dimensions such as tidal tail, gas stripping and filaments.

NOTE: SlicerAstro can potentially enhance also the inspection of other datasets such as mm/submm molecular line data and optical integral field spectroscopic data. The user is welcome to share any idea and feedback in the issue tracker[https://github.com/Punzo/SlicerAstro/issues].
 
[[File:SlicerAstroScreenshot.png| Slicer Astro Screenshot|1000px]]
 


{{documentation/{{documentation/version}}/extension-section|References}}
==How to cite==
Please cite the following paper when referring to SlicerAstro in your publication: 

<pre>
@MISC{SlicerAstro,
author = {{Punzo}, D. and {van der Hulst}, T. and {Roerdink}, J. and {Fillion-Robin}, J.-C.
},
title = "{SlicerAstro: Astronomy (HI) extension for 3D Slicer}",
keywords = {Software },
howpublished = {Astrophysics Source Code Library},
year = 2016,
month = nov,
archivePrefix = "ascl",
eprint = {1611.021},
}
</pre>

<pre>
@ARTICLE{2017A&C....19...45P,
author = {{Punzo}, D. and {van der Hulst}, J.~M. and {Roerdink}, J.~B.~T.~M. and
{Fillion-Robin}, J.~C. and {Yu}, L.},
title = "{SlicerAstro: A 3-D interactive visual analytics tool for HI data}",
journal = {Astronomy and Computing},
archivePrefix = "arXiv",
eprint = {1703.06651},
primaryClass = "astro-ph.IM",
keywords = {Radio lines: galaxies, Scientific visualization, Visual analytics, Agile software development, Object oriented development, Empirical software validation},
year = 2017,
month = apr,
volume = 19,
pages = {45-59},
doi = {10.1016/j.ascom.2017.03.004},
}
</pre>

<pre>
@ARTICLE{2015A&C....12...86P,
author = {{Punzo}, D. and {van der Hulst}, J.~M. and {Roerdink}, J.~B.~T.~M. and {Oosterloo}, T.~A. and {Ramatsoku}, M. and {Verheijen}, M.~A.~W.},
title = "{The role of 3-D interactive visualization in blind surveys of H I in galaxies}",
journal = {Astronomy and Computing},
archivePrefix = "arXiv",
eprint = {1505.06976},
primaryClass = "astro-ph.IM",
keywords = {Radio lines: galaxies, Galaxies: kinematics and dynamics, Surveys, Scientific visualization, Visual analytics},
year = 2015,
month = sep,
volume = 12,
pages = {86-99},
doi = {10.1016/j.ascom.2015.05.004},
}
</pre>


{{documentation/{{documentation/version}}/extension-footer}}

Documentation/Nightly/Extensions/SlicerAstro

2018-08-10T13:58:09Z

Davide:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:ERCIcon.png|300px|European Research Council]]
[[File:Kapteyn logo1.png|500px|Kapteyn Astronomical Institute]]


{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
Authors: 
Davide Punzo (Kapteyn Astronomical Institute, University of Groningen) 
Thijs van der Hulst (Kapteyn Astronomical Institute, University of Groningen) 
Jos Roerdink (Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen) 

Contributors: 
Jean-Christophe Fillion-Robin (Kitware) 
Steve Pieper (Isomics) 
Andras Lasso (PerkLab, Queen's) 

Acknowledgements: 
This work was supported by the European Research Council under the European Union's Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement nr. 291-531. 

Note: 
As of August 2018 financial support for SlicerAstro development has ended. The software will be maintained at the Kapteyn Astronomical Institute of the University of Groningen, but further development is currently on hold. If you have any query, pull request and/or ideas you can still contact [us](https://github.com/Punzo/SlicerAstro/wiki#contacts) or submit a [ticket](https://github.com/Punzo/SlicerAstro/issues).

Contacts:
* Davide Punzo, <email>punzodavide@hotmail.it</email>; <email>D.Punzo@astro.rug.nl</email>
* Thijs van der Hulst, <email>J.M.van.der.Hulst@astro.rug.nl</email>
* Jos Roerdink <email>j.b.t.m.roerdink@rug.nl</email>

Source: [https://github.com/Punzo/SlicerAstro] 
License: [http://www.slicer.org/pages/LicenseText Slicer license] 
'''Download/install:''' install 3D Slicer, start 3D Slicer, open the Extension Manager, install the SlicerAstro extension[https://github.com/Punzo/SlicerAstro/wiki].



{{documentation/{{documentation/version}}/extension-section|Extension Description}}
{|

|
[[Image:SlicerAstroIcon1.png|350px]]
|
Upcoming HI (neutral Hydrogen) surveys will deliver large datasets, and automated processing using the full 3-D information (two positional dimensions and one spectral dimension) to find and characterize HI objects is imperative. In this context, visualization is an essential tool for enabling qualitative and quantitative human control on an automated source finding and analysis pipeline. Visual Analytics, the combination of automated data processing and human reasoning, creativity and intuition, supported by interactive visualization, enables flexible and fast interaction with the 3-D data, helping the astronomer to deal with the analysis of complex sources. 3-D visualization, coupled to modeling, provides additional capabilities helping the discovery and analysis of subtle structures in the 3-D domain.

<h3> Objective: general description</h3>
* 1) proper visualization of astronomical data cubes: using data astronomical data formats, such as FITS, and astronomical world coordinates system (WCS);
* 2) generation of Histogram, flux density profiles, moment maps and position-velocity diagrams linked with the 3-D view;
* 3) enabling interactive smoothing in all three dimensions;
* 4) interactive HI data modeling coupled to visualization;
* 5) introduction of the SAMP protocol to enable interoperability with Topcat, and other VO tools and catalogs.

for more info see [https://github.com/Punzo/SlicerAstro/wiki] and [http://arxiv.org/pdf/1505.06976v2.pdf], [https://arxiv.org/pdf/1703.06651].

|
|}


{{documentation/{{documentation/version}}/extension-section|Modules}}
{||

SlicerAstro development focuses on HI datasets. The [[Documentation/{{documentation/version}}/Modules/AstroVolume|Astro Volume]] component is the core module and handles the loading/saving, color functions and WCS corrdinates.

Tutorials and information can be found in the [[Documentation/{{documentation/version}}/Modules/AstroWelcome|Astro Welcome]] module and sample data are available at the [[Documentation/{{documentation/version}}/Modules/AstroSampleData|Astro Sample Data]] module.

We currently provide additional modules with their own interface widgets for user interaction, which are mainly aimed for the analysis of HI data-cubes:

*[[Documentation/{{documentation/version}}/Modules/SlicerAstroDataProbe|SlicerAstro Data Probe]]
*[[Documentation/{{documentation/version}}/Modules/AstroReproject|Astro Reproject]]
*[[Documentation/{{documentation/version}}/Modules/AstroStatistics|Astro Statistics]]
*[[Documentation/{{documentation/version}}/Modules/AstroMasking|Astro Masking]]
*[[Documentation/{{documentation/version}}/Modules/AstroSmoothing|Astro Smoothing]]
*[[Documentation/{{documentation/version}}/Modules/AstroProfiles|Astro Profiles]]
*[[Documentation/{{documentation/version}}/Modules/AstroMomentMaps|Astro Moment Maps]]
*[[Documentation/{{documentation/version}}/Modules/AstroPVSlice|Astro PV Slice]]
*[[Documentation/{{documentation/version}}/Modules/AstroPVDiagram|Astro PV Diagram]]
*[[Documentation/{{documentation/version}}/Modules/AstroModeling|Astro Modeling]]


{{documentation/{{documentation/version}}/extension-section|Use Case: Visualization of HI dataset}}

3D visualization for the inspection and analysis of complex HI source:
A 3D view gives an immediate overview of the coherence along the spatial and velocity dimensions such as tidal tail, gas stripping and filaments.

NOTE: SlicerAstro can potentially enhance also the inspection of other datasets such as mm/submm molecular line data and optical integral field spectroscopic data. The user is welcome to share any idea and feedback in the issue tracker[https://github.com/Punzo/SlicerAstro/issues].
 
[[File:SlicerAstroScreenshot.png| Slicer Astro Screenshot|1000px]]
 


{{documentation/{{documentation/version}}/extension-section|References}}
==How to cite==
Please cite the following paper when referring to SlicerAstro in your publication: 

<pre>
@MISC{SlicerAstro,
author = {{Punzo}, D. and {van der Hulst}, T. and {Roerdink}, J. and {Fillion-Robin}, J.-C.
},
title = "{SlicerAstro: Astronomy (HI) extension for 3D Slicer}",
keywords = {Software },
howpublished = {Astrophysics Source Code Library},
year = 2016,
month = nov,
archivePrefix = "ascl",
eprint = {1611.021},
}
</pre>

<pre>
@ARTICLE{2017A&C....19...45P,
author = {{Punzo}, D. and {van der Hulst}, J.~M. and {Roerdink}, J.~B.~T.~M. and
{Fillion-Robin}, J.~C. and {Yu}, L.},
title = "{SlicerAstro: A 3-D interactive visual analytics tool for HI data}",
journal = {Astronomy and Computing},
archivePrefix = "arXiv",
eprint = {1703.06651},
primaryClass = "astro-ph.IM",
keywords = {Radio lines: galaxies, Scientific visualization, Visual analytics, Agile software development, Object oriented development, Empirical software validation},
year = 2017,
month = apr,
volume = 19,
pages = {45-59},
doi = {10.1016/j.ascom.2017.03.004},
}
</pre>

<pre>
@ARTICLE{2015A&C....12...86P,
author = {{Punzo}, D. and {van der Hulst}, J.~M. and {Roerdink}, J.~B.~T.~M. and {Oosterloo}, T.~A. and {Ramatsoku}, M. and {Verheijen}, M.~A.~W.},
title = "{The role of 3-D interactive visualization in blind surveys of H I in galaxies}",
journal = {Astronomy and Computing},
archivePrefix = "arXiv",
eprint = {1505.06976},
primaryClass = "astro-ph.IM",
keywords = {Radio lines: galaxies, Galaxies: kinematics and dynamics, Surveys, Scientific visualization, Visual analytics},
year = 2015,
month = sep,
volume = 12,
pages = {86-99},
doi = {10.1016/j.ascom.2015.05.004},
}
</pre>


{{documentation/{{documentation/version}}/extension-footer}}

File:Astro3DColorFunction.png

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Documentation/Nightly/ModuleExtensionListing

2018-05-17T16:30:43Z

Davide: /* Modules by name */

__NOTOC__
<noinclude>{{:Documentation/Nightly/ModuleExtensionListing/TOC}}</noinclude>
= Modules by category =
46 categories:
* [[#Modules_by_category_Astronomy|Astronomy]]
* [[#Modules_by_category_Cardiac|Cardiac]]
* [[#Modules_by_category_Cardiac_MRI_Toolkit|Cardiac MRI Toolkit]]
* [[#Modules_by_category_Chest_Imaging_Platform|Chest Imaging Platform]]
** [[#Modules_by_category_Chest_Imaging_Platform_Toolkit|Toolkit]]
*** [[#Modules_by_category_Toolkit_Particles|Particles]]
*** [[#Modules_by_category_Toolkit_Processing|Processing]]
*** [[#Modules_by_category_Toolkit_Quantification|Quantification]]
*** [[#Modules_by_category_Toolkit_Registration|Registration]]
*** [[#Modules_by_category_Toolkit_Segmentation|Segmentation]]
*** [[#Modules_by_category_Toolkit_Utils|Utils]]
* [[#Modules_by_category_CIP|CIP]]
* [[#Modules_by_category_Converters|Converters]]
* [[#Modules_by_category_Developer_Tools|Developer Tools]]
** [[#Modules_by_category_Developer_Tools_DICOM_Plugins|DICOM Plugins]]
** [[#Modules_by_category_Developer_Tools_Editor_Extensions|Editor Extensions]]
** [[#Modules_by_category_Developer_Tools_Matlab|Matlab]]
** [[#Modules_by_category_Developer_Tools_Segment_Editor_Extensions|Segment Editor Extensions]]
** [[#Modules_by_category_Developer_Tools_Utils|Utils]]
* [[#Modules_by_category_Diffusion|Diffusion]]
** [[#Modules_by_category_Diffusion_Diffusion_Data_Conversion|Diffusion Data Conversion]]
** [[#Modules_by_category_Diffusion_Diffusion_Tensor_Images|Diffusion Tensor Images]]
** [[#Modules_by_category_Diffusion_Diffusion_Weighted_Images|Diffusion Weighted Images]]
** [[#Modules_by_category_Diffusion_Import_and_Export|Import and Export]]
** [[#Modules_by_category_Diffusion_Process|Process]]
** [[#Modules_by_category_Diffusion_Quantify|Quantify]]
** [[#Modules_by_category_Diffusion_Tractography|Tractography]]
*** [[#Modules_by_category_Tractography_Region-based|Region-based]]
** [[#Modules_by_category_Diffusion_Utilities|Utilities]]
* [[#Modules_by_category_Editor_Effects|Editor Effects]]
* [[#Modules_by_category_EditorEffect|EditorEffect]]
* [[#Modules_by_category_Endoscopy|Endoscopy]]
* [[#Modules_by_category_Examples|Examples]]
* [[#Modules_by_category_Exporter|Exporter]]
* [[#Modules_by_category_Filter|Filter]]
* [[#Modules_by_category_Filtering|Filtering]]
** [[#Modules_by_category_Filtering_Arithmetic|Arithmetic]]
** [[#Modules_by_category_Filtering_Denoising|Denoising]]
** [[#Modules_by_category_Filtering_Morphology|Morphology]]
* [[#Modules_by_category_IGT|IGT]]
* [[#Modules_by_category_Informatics|Informatics]]
** [[#Modules_by_category_Informatics_Converters|Converters]]
* [[#Modules_by_category_Legacy|Legacy]]
** [[#Modules_by_category_Legacy_Converters|Converters]]
** [[#Modules_by_category_Legacy_Filtering|Filtering]]
** [[#Modules_by_category_Legacy_Registration|Registration]]
** [[#Modules_by_category_Legacy_Work_in_Progress|Work in Progress]]
*** [[#Modules_by_category_Work_in_Progress_Diffusion_Tensor|Diffusion Tensor]]
**** [[#Modules_by_category_Diffusion_Tensor_Test|Test]]
* [[#Modules_by_category_Libraries|Libraries]]
* [[#Modules_by_category_Machine_Learning|Machine Learning]]
* [[#Modules_by_category_Margin_Calculator|Margin Calculator]]
* [[#Modules_by_category_Mesh_Generation|Mesh Generation]]
* [[#Modules_by_category_MeshGeneration|MeshGeneration]]
* [[#Modules_by_category_Microscopy|Microscopy]]
* [[#Modules_by_category_MultiVolume_Support|MultiVolume Support]]
* [[#Modules_by_category_Pathology|Pathology]]
* [[#Modules_by_category_Perk_Tutor|Perk Tutor]]
* [[#Modules_by_category_Plastimatch|Plastimatch]]
** [[#Modules_by_category_Plastimatch_Registration|Registration]]
** [[#Modules_by_category_Plastimatch_Utilities|Utilities]]
* [[#Modules_by_category_Quantification|Quantification]]
** [[#Modules_by_category_Quantification_ChangeQuantification|ChangeQuantification]]
* [[#Modules_by_category_Radiology|Radiology]]
* [[#Modules_by_category_Radiotherapy|Radiotherapy]]
* [[#Modules_by_category_Registration|Registration]]
** [[#Modules_by_category_Registration_CMF_Registration|CMF Registration]]
*** [[#Modules_by_category_CMF_Registration_Voxelbase_Registration|Voxelbase Registration]]
** [[#Modules_by_category_Registration_Label_Registration|Label Registration]]
** [[#Modules_by_category_Registration_Specialized|Specialized]]
* [[#Modules_by_category_Segmentation|Segmentation]]
** [[#Modules_by_category_Segmentation_Specialized|Specialized]]
* [[#Modules_by_category_Sequences|Sequences]]
* [[#Modules_by_category_Slicelets|Slicelets]]
* [[#Modules_by_category_SlicerProstate|SlicerProstate]]
* [[#Modules_by_category_Surface_Models|Surface Models]]
* [[#Modules_by_category_TestCases|TestCases]]
* [[#Modules_by_category_Testing|Testing]]
** [[#Modules_by_category_Testing_IGT_Tests|IGT Tests]]
** [[#Modules_by_category_Testing_SlicerRT_Tests|SlicerRT Tests]]
** [[#Modules_by_category_Testing_TestCases|TestCases]]
* [[#Modules_by_category_Ultrasound|Ultrasound]]
* [[#Modules_by_category_Uncategorized|Uncategorized]]
* [[#Modules_by_category_Utilities|Utilities]]
** [[#Modules_by_category_Utilities_BRAINS|BRAINS]]
* [[#Modules_by_category_Vascular_Modeling_Toolkit|Vascular Modeling Toolkit]]
* [[#Modules_by_category_Virtual_Reality|Virtual Reality]]
* [[#Modules_by_category_Web_System_Tools|Web System Tools]]
* [[#Modules_by_category_Wizards|Wizards]]
* [[#Modules_by_category_XNATSlicer|XNATSlicer]]

== Astronomy ==
* [[Documentation/Nightly/Modules/AstroVolume|AstroVolume]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/AstroReproject|AstroReproject]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/AstroStatistics|AstroStatistics]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/AstroMasking|AstroMasking]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/AstroSmoothing|AstroSmoothing]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/AstroSampleData|AstroSampleData]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/AstroProfiles|AstroProfiles]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/AstroMomentMaps|AstroMomentMaps]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/AstroPVSlice|AstroPVSlice]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/AstroPVDiagram|AstroPVDiagram]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/AstroModeling|AstroModeling]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/AstroWelcome|AstroWelcome]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/SlicerAstroDataProbe|SlicerAstroDataProbe]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)


== Cardiac ==
* [[Documentation/Nightly/Extensions/SlicerHeart|Philips4dUsDicomPatcher]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerHeart|SlicerHeart]] extension)
* [[Documentation/Nightly/Extensions/SlicerHeart|ValveView]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerHeart|SlicerHeart]] extension)

== Cardiac MRI Toolkit ==
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitPVAntrumCut] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitBooleanREMOVEFilter] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [[Documentation/Nightly/Modules/LASegmentationWorkflow|LASegmentationWorkflow]] (scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitRegistrationBRAINSFit] (scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitAutomaticLeftAtrialScar] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitConnectedThresholdFilter] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitWizard] (scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitIsolatedConnectedFilter] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitInhomogeneityCorrection] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitAxialDilate] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [[Documentation/Nightly/Modules/ScarVisualization|ScarVisualization]] (scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitRegistration] (scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitLASegmentationGraphCuts] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)

== Chest Imaging Platform ==
* [http://www.chestimagingplatform.org CIP_MIPViewer] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CIP_BodyComposition] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CIP_InteractiveLobeSegmentation] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CIP_TracheaStentPlanning] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CIP_LesionModel] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org AirwayInspector] (loadable, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CIP_PAARatio] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CIP_CalciumScoring] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CIP_ParenchymaAnalysis] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CIP_ParenchymaSubtypeTraining] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CIP_PointsLabelling] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)

=== Toolkit ===

==== Particles ====
* [http://www.chestimagingplatform.org ExtractParticlesFromChestRegionChestType] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org FilterVesselParticleData] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org RemoveParticlesFromParticlesDataSet] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org PerturbParticles] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org MergeParticleDataSets] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org FilterAirwayParticleData] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org FitLobeSurfaceModelsToParticleData] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ClassifyFissureParticles] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateStenciledLabelMapFromParticles] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org FilterFissureParticleData] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)

==== Processing ====
* [http://www.chestimagingplatform.org ResampleLabelMap] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org RescaleLabelMap] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateMedianFilteredImage] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org LabelMapFromRegionAndTypePoints] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CropLung] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateNLMFilteredImage] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org RemoveChestTypeFromLabelMapUsingParticles] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateAtlasConvexHull] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org RemapLabelMap] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ComputeFissureFeatureVectors] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateLobeSurfaceModels] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org FilterConnectedComponents] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ExtractChestLabelMap] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org PerformMorphological] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ExtractFissureBoundaryFromLobeMap] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org EnhanceFissuresInImage] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GraphCutsOptimization] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateDistanceMapFromLabelMap] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ResampleCT] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ComputeFeatureStrength] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ComputeDistanceMap] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org QualityControl] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateImageSubVolumes] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)

==== Quantification ====
* [http://www.chestimagingplatform.org EvaluateLungLobeSegmentationResults] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GetTransformationKappa] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ReadWriteImageData] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ComputeIntensityStatistics] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ComputeCrossSectionalArea] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateParenchymaPhenotypes] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org LabelParticlesByChestRegionChestType] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GetTransformationSimilarityMetric] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GetTransformationKappa2D] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)

==== Registration ====
*[[:Category:Documentation/Nightly/Modules/Registration|Introduction to Registration]] (by Dominik Meier)
* [http://www.chestimagingplatform.org RegisterLungAtlas] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org RegisterLabelMaps] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org RegisterCT] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)


==== Segmentation ====
* [http://www.chestimagingplatform.org GenerateOtsuLungCast] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org SegmentLungAirways] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org SegmentLungLobes] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GeneratePartialLungLabelMap] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateSimpleLungMask] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org SplitLeftLungRightLung] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateBinaryThinning3D] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateLesionSegmentation] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)

==== Utils ====
* [http://www.chestimagingplatform.org ConvertDicom] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org RegionTypeLocationsToROIVolume] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ReadVTKWriteNRRDs] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateModel] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateOverlayImages] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ExecuteSystemCommand] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GetStructuresInLabelMap] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org FindPatchMatch] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ConvertChestRegionChestTypeToLabelMapValue] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org MaskOutLabelMapStructures] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ReadNRRDsWriteVTK] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ConvertLabelMapValueToChestRegionChestType] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ReadWriteRegionAndTypePoints] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org MergeChestLabelMaps] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ReadVidaWriteCIP] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ReadDicomWriteTags] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org TransferRegionAndTypeIndicesToFromPoints] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)

== CIP ==
* [http://www.chestimagingplatform.org CIP_] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CIP_Common] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)

== Converters ==
* [[Documentation/Nightly/Modules/QuadEdgeSurfaceMesher|QuadEdgeSurfaceMesher]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerProstate|SlicerProstate]] extension)
* [[Documentation/Nightly/Modules/CropVolume|CropVolume]] (loadable, built-in)
* [[Documentation/Nightly/Modules/OrientScalarVolume|OrientScalarVolume]] (cli, built-in)
* [[Documentation/Nightly/Extensions/UKFTractography|ConvertVTK]] (cli, bundled in [[Documentation/Nightly/Extensions/UKFTractography|UKFTractography]] extension)
* [[Documentation/Nightly/Modules/VectorToScalarVolume|VectorToScalarVolume]] (scripted, built-in)
* [[Documentation/Nightly/Modules/CreateDICOMSeries|CreateDICOMSeries]] (cli, built-in)
* [http://www.chestimagingplatform.org ParticlesDisplay] (loadable, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org RegionType] (loadable, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)

== Developer Tools ==
* [[Documentation/Nightly/Modules/Cameras|Cameras]] (loadable, built-in)
* [[Documentation/Nightly/Modules/ExecutionModelTour|ExecutionModelTour]] (cli, built-in)
* [[Documentation/Nightly/Extensions/DebuggingTools|NodeModifiedStatistics]] (scripted, bundled in [[Documentation/Nightly/Extensions/DebuggingTools|DebuggingTools]] extension)
* [[Documentation/Nightly/Extensions/DebuggingTools|PyDevRemoteDebug]] (scripted, bundled in [[Documentation/Nightly/Extensions/DebuggingTools|DebuggingTools]] extension)
* [[Documentation/Nightly/Modules/ExtensionWizard|ExtensionWizard]] (scripted, built-in)
* [[Documentation/Nightly/Extensions/DebuggingTools|NodeInfo]] (scripted, bundled in [[Documentation/Nightly/Extensions/DebuggingTools|DebuggingTools]] extension)
* [[Documentation/Nightly/Modules/ImageMaker|ImageMaker]] (cli, bundled in [[Documentation/Nightly/Extensions/ImageMaker|ImageMaker]] extension)
* [[Documentation/Nightly/Modules/ExtensionStats|ExtensionStats]] (scripted, bundled in [[Documentation/Nightly/Extensions/DeveloperToolsForExtensions|DeveloperToolsForExtensions]] extension)
* [[Documentation/Nightly/Modules/DeveloperToolsForExtensions|DeveloperToolsForExtensions]] (scripted, bundled in [[Documentation/Nightly/Extensions/DeveloperToolsForExtensions|DeveloperToolsForExtensions]] extension)
* [[Documentation/Nightly/Modules/EventBroker|EventBroker]]
* DoubleArrays (loadable, built-in)

=== DICOM Plugins ===
* DICOMParametricMapPlugin
* DicomUltrasoundPlugin
* DICOMSegmentationPlugin
* DICOMSlicerDataBundlePlugin
* DICOMTID1500Plugin
* [[Documentation/Nightly/Modules/DICOMPETSUVPlugin|DICOMPETSUVPlugin]]
* DICOMScalarVolumePlugin
* DICOMDiffusionVolumePlugin
* DICOMLongitudinalPETCTPlugin
* DicomSroImportPlugin
* [[Documentation/Nightly/Modules/DICOMRWVMPlugin|DICOMRWVMPlugin]]
* DicomRtImportExportPlugin
* MultiVolumeImporterPlugin

=== Editor Extensions ===
* [https://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/FastGrowCut FastGrowCutEffect] (scripted, bundled in [https://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/FastGrowCut FastGrowCutEffect] extension)
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter CarreraSliceEffect] (scripted, bundled in [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter CarreraSlice] extension)
* [[Documentation/Nightly/Extensions/SlicerPathology|QuickTCGAEffect]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerPathology|SlicerPathology]] extension)
* [[Documentation/Nightly/Modules/PETTumorSegmentationEffect|PETTumorSegmentationEffect]] (scripted, bundled in [[Documentation/Nightly/Extensions/PETTumorSegmentation|PETTumorSegmentation]] extension)
* [[Documentation/Nightly/Extensions/IASEM|BinaryWatershedEffect]] (scripted, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)
* [[Documentation/Nightly/Extensions/IASEM|DoubleThresholdEffect]] (scripted, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)
* [[Documentation/Nightly/Extensions/SlicerPathology|ShortCutEffect]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerPathology|SlicerPathology]] extension)

=== Matlab ===
* [[Documentation/Nightly/Modules/MatlabModuleGenerator|MatlabModuleGenerator]] (loadable, bundled in [[Documentation/Nightly/Extensions/MatlabBridge|MatlabBridge]] extension)
* [[Documentation/Nightly/Modules/MatlabCommander|MatlabCommander]] (cli, bundled in [[Documentation/Nightly/Extensions/MatlabBridge|MatlabBridge]] extension)

=== Segment Editor Extensions ===
* [[Documentation/Nightly/Extensions/PETTumorSegmentation|SegmentEditorPETTumor]] (scripted, bundled in [[Documentation/Nightly/Extensions/PETTumorSegmentation|PETTumorSegmentation]] extension)

=== Utils ===
* [[Documentation/Nightly/Extensions/SlicerProstate|SlicerProstate]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerProstate|SlicerProstate]] extension)

== Diffusion ==
* [[Documentation/Nightly/Modules/DMRIInstall|DMRIInstall]] (scripted, built-in)

=== Diffusion Data Conversion ===
* DWIConvert (cli, built-in)

=== Diffusion Tensor Images ===
* [[Documentation/Nightly/Extensions/ResampleDTIlogEuclidean|ResampleDTIlogEuclidean]] (cli, bundled in [[Documentation/Nightly/Extensions/ResampleDTIlogEuclidean|ResampleDTIlogEuclidean]] extension)

=== Diffusion Weighted Images ===
* BRAINSDWICleanup (cli, built-in)

=== Import and Export ===
* DWIConvert (cli, built-in)
* [[Documentation/Nightly/Extensions/SlicerDMRI|DICOMTract_to_VTK]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)
* [[Documentation/Nightly/Extensions/SlicerDMRI|VTK_to_DICOMTract]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)

=== Process ===
* [[Documentation/Nightly/Modules/DiffusionWeightedVolumeMasking|DiffusionWeightedVolumeMasking]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)
* [[Documentation/Nightly/Modules/DWIToDTIEstimation|DWIToDTIEstimation]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)

=== Quantify ===
* [[Documentation/Nightly/Modules/DiffusionTensorScalarMeasurements|DiffusionTensorScalarMeasurements]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)
* [[Documentation/Nightly/Modules/FiberTractMeasurements|FiberTractMeasurements]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)

=== Tractography ===
* [[Documentation/Nightly/Modules/TractographyInteractiveSeeding|TractographyInteractiveSeeding]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)
* [[Documentation/Nightly/Modules/TractographyDisplay|TractographyDisplay]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)
* [[Documentation/Nightly/Modules/UKFTractography|UKFTractography]] (cli, bundled in [[Documentation/Nightly/Extensions/UKFTractography|UKFTractography]] extension)

==== Region-based ====
* [[Documentation/Nightly/Modules/TractographyLabelMapSeeding|TractographyLabelMapSeeding]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)
* [[Documentation/Nightly/Modules/FiberBundleLabelSelect|FiberBundleLabelSelect]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)

=== Utilities ===
* BRAINSDWICleanup (cli, built-in)
* [[Documentation/Nightly/Modules/ResampleDTIVolume|ResampleDTIVolume]] (cli, built-in)
* [[Documentation/Nightly/Modules/FiberBundleToLabelMap|FiberBundleToLabelMap]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)
* [[Documentation/Nightly/Modules/ResampleScalarVectorDWIVolume|ResampleScalarVectorDWIVolume]] (cli, built-in)
* [[Documentation/Nightly/Extensions/SlicerDMRI|DICOM2FullBrainTractography]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)

== Editor Effects ==
* [[Documentation/Nightly/Extensions/WindowLevelEffect|WindowLevelEffect]] (scripted, bundled in [[Documentation/Nightly/Extensions/WindowLevelEffect|WindowLevelEffect]] extension)

== EditorEffect ==
* [[Documentation/Nightly/Extensions/PETTumorSegmentation|PETTumorSegmentation]] (loadable, bundled in [[Documentation/Nightly/Extensions/PETTumorSegmentation|PETTumorSegmentation]] extension)

== Endoscopy ==
* [[Documentation/Nightly/Modules/Endoscopy|Endoscopy]] (scripted, built-in)

== Examples ==
* [[Documentation/Nightly/Modules/FastGrowCut|FastGrowCut]] (loadable, bundled in [https://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/FastGrowCut FastGrowCutEffect] extension)
* [[Documentation/Nightly/Extensions/SlicerPathology|QuickTCGA]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerPathology|SlicerPathology]] extension)
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter FastGrowCutSegmenter] (loadable, bundled in [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter CarreraSlice] extension)
* [[Documentation/Nightly/Extensions/SlicerPathology|ShortCutCore]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerPathology|SlicerPathology]] extension)
* [http://publish.uwo.ca/~dchen285/GraphCutSegment/GraphCutSegment.html GraphCutInteractiveSegmenter] (loadable, bundled in [http://publish.uwo.ca/~dchen285/GraphCutSegment/GraphCutSegment.html GraphCutSegment] extension)
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter CarreraSlice] (loadable, bundled in [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter CarreraSlice] extension)

== Exporter ==
* [[Documentation/Nightly/Modules/SlicerToKiwiExporter|SlicerToKiwiExporter]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerToKiwiExporter|SlicerToKiwiExporter]] extension)

== Filter ==
* IslandRemoval (cli, built-in)

== Filtering ==
* [[Documentation/Nightly/Modules/SegmentationSmoothing|SegmentationSmoothing]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerProstate|SlicerProstate]] extension)
* [[Documentation/Nightly/Modules/N4ITKBiasFieldCorrection|N4ITKBiasFieldCorrection]] (cli, built-in)
* [[Documentation/Nightly/Modules/ImageLabelCombine|ImageLabelCombine]] (cli, built-in)
* [[Documentation/Nightly/Modules/VotingBinaryHoleFillingImageFilter|VotingBinaryHoleFillingImageFilter]] (cli, built-in)
* [[Documentation/Nightly/Modules/CheckerBoardFilter|CheckerBoardFilter]] (cli, built-in)
* [[Documentation/Nightly/Modules/AstroSmoothing|AstroSmoothing]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/ExtractSkeleton|ExtractSkeleton]] (cli, built-in)
* [[Documentation/Nightly/Modules/SimpleFilters|SimpleFilters]] (scripted, built-in)
* [[Documentation/Nightly/Modules/ThresholdScalarVolume|ThresholdScalarVolume]] (cli, built-in)
* [[Documentation/Nightly/Modules/HistogramMatching|HistogramMatching]] (cli, built-in)

=== Arithmetic ===
* [[Documentation/Nightly/Modules/MultiplyScalarVolumes|MultiplyScalarVolumes]] (cli, built-in)
* [[Documentation/Nightly/Modules/AddScalarVolumes|AddScalarVolumes]] (cli, built-in)
* [[Documentation/Nightly/Modules/MaskScalarVolume|MaskScalarVolume]] (cli, built-in)
* [[Documentation/Nightly/Modules/SubtractScalarVolumes|SubtractScalarVolumes]] (cli, built-in)
* [[Documentation/Nightly/Modules/CastScalarVolume|CastScalarVolume]] (cli, built-in)
* [[Documentation/Nightly/Extensions/OpenCVExample|BlendVectorVolumes]] (cli, bundled in [[Documentation/Nightly/Extensions/OpenCVExample|OpenCVExample]] extension)

=== Denoising ===
* [[Documentation/Nightly/Modules/CurvatureAnisotropicDiffusion|CurvatureAnisotropicDiffusion]] (cli, built-in)
* [[Documentation/Nightly/Modules/GradientAnisotropicDiffusion|GradientAnisotropicDiffusion]] (cli, built-in)
* [[Documentation/Nightly/Modules/MedianImageFilter|MedianImageFilter]] (cli, built-in)
* [[Documentation/Nightly/Modules/GaussianBlurImageFilter|GaussianBlurImageFilter]] (cli, built-in)

=== Morphology ===
* [[Documentation/Nightly/Modules/GrayscaleFillHoleImageFilter|GrayscaleFillHoleImageFilter]] (cli, built-in)
* [[Documentation/Nightly/Modules/GrayscaleGrindPeakImageFilter|GrayscaleGrindPeakImageFilter]] (cli, built-in)

== IGT ==
* [[Documentation/Nightly/Extensions/SlicerIGT|Viewpoint]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Modules/CollectFiducials|CollectFiducials]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Extensions/SlicerIGT|TransformFusion]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Modules/GyroGuide|GyroGuide]] (scripted, bundled in [[Documentation/Nightly/Extensions/GyroGuide|GyroGuide]] extension)
* [[Documentation/Nightly/Extensions/SlicerIGT|PlusModelCatalogBrowser]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Extensions/SlicerIGT|CreateModels]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Extensions/NeedleFinder|NeedleFinder]] (scripted, bundled in [[Documentation/Nightly/Extensions/NeedleFinder|NeedleFinder]] extension)
* [[Documentation/Nightly/Modules/TrackerStabilizer|TrackerStabilizer]] (loadable, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/TrackerStabilizer TrackerStabilizer] extension)
* [[Documentation/Nightly/Modules/PathExplorer|PathExplorer]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Extensions/SlicerIGT|UltrasoundSnapshots]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Extensions/SlicerIGT|BreachWarning]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Extensions/SlicerIGT|FiducialRegistrationWizard]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Extensions/SlicerIGT|ModelRegistration]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Modules/ResectionVolume|ResectionVolume]] (scripted, bundled in [[Documentation/Nightly/Extensions/ResectionPlanner|ResectionPlanner]] extension)
* [[Documentation/Nightly/Extensions/SlicerIGT|PivotCalibration]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Modules/VolumeResliceDriver|VolumeResliceDriver]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Modules/OpenIGTLinkRemote|OpenIGTLinkRemote]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Extensions/SlicerIGT|FiducialsToModelRegistration]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Modules/Watchdog|Watchdog]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Modules/CornerAnnotation|CornerAnnotation]] (scripted, bundled in [[Documentation/Nightly/Extensions/CornerAnnotation|CornerAnnotation]] extension)
* [[Documentation/Nightly/Modules/OpenIGTLinkIF|OpenIGTLinkIF]] (loadable, built-in)
* [[Documentation/Nightly/Extensions/SlicerIGT|MarkupsToModel]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Extensions/iGyne|iGyne]] (scripted, bundled in [[Documentation/Nightly/Extensions/iGyne|iGyne]] extension)
* [[Documentation/Nightly/Modules/PlusRemote|PlusRemote]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)

== Informatics ==
* [[Documentation/Nightly/Extensions/DCMQI|tid1500writer]] (cli, bundled in [[Documentation/Nightly/Extensions/DCMQI|DCMQI]] extension)
* [[Documentation/Nightly/Extensions/mpReview|mpReviewPreprocessor]] (scripted, bundled in [[Documentation/Nightly/Extensions/mpReview|mpReview]] extension)
* [[Documentation/Nightly/Modules/SEG2NRRD|SEG2NRRD]] (cli)
* [[Documentation/Nightly/Extensions/TCIABrowser|TCIABrowser]] (scripted, bundled in [[Documentation/Nightly/Extensions/TCIABrowser|TCIABrowser]] extension)
* [[Documentation/Nightly/Extensions/DCMQI|segimage2itkimage]] (cli, bundled in [[Documentation/Nightly/Extensions/DCMQI|DCMQI]] extension)
* [[Documentation/Nightly/Extensions/mpReview|mpReview]] (scripted, bundled in [[Documentation/Nightly/Extensions/mpReview|mpReview]] extension)
* [[Documentation/Nightly/Modules/Tables|Tables]] (loadable, built-in)
* [[Documentation/Nightly/Modules/Data|Data]] (loadable, built-in)
* DumpSEGFrame (cli)
* [[Documentation/Nightly/Extensions/DCMQI|tid1500reader]] (cli, bundled in [[Documentation/Nightly/Extensions/DCMQI|DCMQI]] extension)
* Terminologies (loadable, built-in)
* [[Documentation/Nightly/Modules/Units|Units]] (loadable, built-in)
* [[Documentation/Nightly/Modules/DICOM|DICOM]] (scripted, built-in)
* [[Documentation/Nightly/Modules/SampleData|SampleData]] (scripted, built-in)
* [[Documentation/Nightly/Modules/Colors|Colors]] (loadable, built-in)
* [[Documentation/Nightly/Extensions/CurveMaker|CurveMaker]] (scripted, bundled in [[Documentation/Nightly/Extensions/CurveMaker|CurveMaker]] extension)
* [[Documentation/Nightly/Modules/Annotations|Annotations]] (loadable, built-in)
* [[Documentation/Nightly/Modules/Markups|Markups]] (loadable, built-in)
* [[Documentation/Nightly/Modules/SubjectHierarchy|SubjectHierarchy]] (loadable, built-in)
* [[Documentation/Nightly/Extensions/QuantitativeReporting|QuantitativeReporting]] (scripted, bundled in [[Documentation/Nightly/Extensions/QuantitativeReporting|QuantitativeReporting]] extension)

=== Converters ===
* [[Documentation/Nightly/Extensions/DCMQI|itkimage2paramap]] (cli, bundled in [[Documentation/Nightly/Extensions/DCMQI|DCMQI]] extension)
* [[Documentation/Nightly/Extensions/DCMQI|paramap2itkimage]] (cli, bundled in [[Documentation/Nightly/Extensions/DCMQI|DCMQI]] extension)
* [[Documentation/Nightly/Extensions/DCMQI|itkimage2segimage]] (cli, bundled in [[Documentation/Nightly/Extensions/DCMQI|DCMQI]] extension)
* [[Documentation/Nightly/Modules/EncodeSEG|EncodeSEG]] (cli)

== Legacy ==

=== Converters ===
* [[Documentation/Nightly/Modules/BSplineToDeformationField|BSplineToDeformationField]] (cli, built-in)

=== Filtering ===
* [[Documentation/Nightly/Modules/OtsuThresholdImageFilter|OtsuThresholdImageFilter]] (cli, built-in)
* [[Documentation/Nightly/Modules/ResampleScalarVolume|ResampleScalarVolume]] (cli, built-in)

=== Registration ===
* TestGridTransformRegistration (cli, built-in)
* [[Documentation/Nightly/Modules/ExpertAutomatedRegistration|ExpertAutomatedRegistration]] (cli, built-in)

=== Work in Progress ===

==== Diffusion Tensor ====

===== Test =====
* DiffusionTensorTest (cli, built-in)

== Libraries ==
* [[Documentation/Nightly/Extensions/SlicerOpenCV|OpenCV]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerOpenCV|SlicerOpenCV]] extension)

== Machine Learning ==
* [[Documentation/Nightly/Modules/DeepInfer|DeepInfer]] (scripted, bundled in [[Documentation/Nightly/Extensions/DeepInfer|DeepInfer]] extension)

== Margin Calculator ==
* [[Documentation/Nightly/Extensions/MarginCalculator|MarginCalculator]] (scripted, bundled in [[Documentation/Nightly/Extensions/MarginCalculator|MarginCalculator]] extension)
* [[Documentation/Nightly/Extensions/MarginCalculator|DoseMorphology]] (loadable, bundled in [[Documentation/Nightly/Extensions/MarginCalculator|MarginCalculator]] extension)
* [[Documentation/Nightly/Extensions/MarginCalculator|SyntheticRTDose]] (scripted, bundled in [[Documentation/Nightly/Extensions/MarginCalculator|MarginCalculator]] extension)

== Mesh Generation ==
* [[Documentation/Nightly/Extensions/CleaverExtension|CleaverCLI]] (cli, bundled in [[Documentation/Nightly/Extensions/CleaverExtension|CleaverExtension]] extension)

== MeshGeneration ==
* [[Documentation/Nightly/Modules/BodyCentricCubicMesh|BodyCentricCubicMesh]] (cli, bundled in [[Documentation/Nightly/Extensions/CBC_3D_I2MConversion|CBC_3D_I2MConversion]] extension)

== Microscopy ==
* [[Documentation/Nightly/Extensions/IASEM|IASEMImportSeries]] (cli, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)
* [[Documentation/Nightly/Extensions/IASEM|IASEMImport]] (cli, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)
* [[Documentation/Nightly/Extensions/IASEM|BinShrink]] (cli, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)
* [[Documentation/Nightly/Extensions/IASEM|LabelObjectStatistics]] (scripted, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)
* [[Documentation/Nightly/Extensions/IASEM|SpacingAwareCurvatureDiffusion]] (cli, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)

== MultiVolume Support ==
* [[Documentation/Nightly/Modules/MultiVolumeImporter|MultiVolumeImporter]] (scripted, built-in)
* [[Documentation/Nightly/Modules/MultiVolumeExplorer|MultiVolumeExplorer]] (loadable, built-in)

== Pathology ==
* [[Documentation/Nightly/Extensions/SlicerPathology|SlicerPathology]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerPathology|SlicerPathology]] extension)

== Perk Tutor ==
* [[Documentation/Nightly/Extensions/PerkTutor|PythonMetricsCalculator]] (scripted, bundled in [[Documentation/Nightly/Extensions/PerkTutor|PerkTutor]] extension)
* [[Documentation/Nightly/Modules/TransformRecorder|TransformRecorder]] (loadable, bundled in [[Documentation/Nightly/Extensions/PerkTutor|PerkTutor]] extension)
* [[Documentation/Nightly/Modules/PerkEvaluator|PerkEvaluator]] (loadable, bundled in [[Documentation/Nightly/Extensions/PerkTutor|PerkTutor]] extension)
* [[Documentation/Nightly/Modules/WorkflowSegmentation|WorkflowSegmentation]] (loadable, bundled in [[Documentation/Nightly/Extensions/PerkTutor|PerkTutor]] extension)

== Plastimatch ==
* [[Documentation/Nightly/Modules/DicomSroExport|DicomSroExport]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Extensions/SlicerRT|PlmRegister]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)

=== Registration ===
* [[Documentation/Nightly/Extensions/SlicerRT|plastimatch_slicer_bspline]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Extensions/SlicerRT|plastimatch_slicer_landwarp]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)

=== Utilities ===
* [[Documentation/Nightly/Extensions/SlicerRT|PlastimatchPy]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)

== Quantification ==
* [http://slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DSC_MRI_Analysis DSCMRIAnalysis] (cli, bundled in [http://slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DSC_MRI_Analysis DSCMRIAnalysis] extension)
* [[Documentation/Nightly/Modules/PETLiverUptakeMeasurement|PETLiverUptakeMeasurement]] (cli, bundled in [[Documentation/Nightly/Extensions/PETLiverUptakeMeasurement|PETLiverUptakeMeasurement]] extension)
* [[Documentation/Nightly/Extensions/PET-IndiC|PETIndiC]] (scripted, bundled in [[Documentation/Nightly/Extensions/PET-IndiC|PET-IndiC]] extension)
* [[Documentation/Nightly/Modules/Q3DC|Q3DC]] (scripted, bundled in [[Documentation/Nightly/Extensions/Q3DC|Q3DC]] extension)
* [[Documentation/Nightly/Modules/HeterogeneityCAD|HeterogeneityCAD]] (scripted, bundled in [[Documentation/Nightly/Extensions/OpenCAD|OpenCAD]] extension)
* [[Documentation/Nightly/Modules/ShapeQuantifier|ShapeQuantifier]] (scripted, bundled in [[Documentation/Nightly/Extensions/ShapeQuantifier|ShapeQuantifier]] extension)
* [[Documentation/Nightly/Modules/QuantitativeIndicesCLI|QuantitativeIndicesCLI]] (cli, bundled in [[Documentation/Nightly/Extensions/PET-IndiC|PET-IndiC]] extension)
* [[Documentation/Nightly/Modules/PETStandardUptakeValueComputation|PETStandardUptakeValueComputation]] (cli, built-in)
* [[Documentation/Nightly/Modules/SUVFactorCalculator|SUVFactorCalculator]] (cli, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PETDICOM PETDICOMExtension] extension)
* [[Documentation/Nightly/Modules/SpinalCurvatureMeasurement|SpinalCurvatureMeasurement]] (scripted, bundled in [[Documentation/Nightly/Extensions/Scoliosis|Scoliosis]] extension)
* [[Documentation/Nightly/Modules/QuantitativeIndicesTool|QuantitativeIndicesTool]] (scripted, bundled in [[Documentation/Nightly/Extensions/PET-IndiC|PET-IndiC]] extension)
* SegmentStatistics (scripted, built-in)
* [[Documentation/Nightly/Modules/LabelStatistics|LabelStatistics]] (scripted, built-in)
* [[Documentation/Nightly/Modules/MeshStatistics|MeshStatistics]] (scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/MeshStatistics MeshStatisticsExtension] extension)
* [[Documentation/Nightly/Modules/DWModeling|DWModeling]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerProstate|SlicerProstate]] extension)
* BRAINSLabelStats (cli, built-in)
* [[Documentation/Nightly/Modules/PkModeling|PkModeling]] (cli, bundled in [[Documentation/Nightly/Extensions/PkModeling|PkModeling]] extension)
* [[Documentation/Nightly/Extensions/LongitudinalPETCT|PETSUVImageMaker]] (cli, bundled in [[Documentation/Nightly/Extensions/LongitudinalPETCT|LongitudinalPETCT]] extension)
* [[Documentation/Nightly/Modules/DataProbe|DataProbe]] (scripted, built-in)
* [[Documentation/Nightly/Extensions/ModelToModelDistance|ModelToModelDistance]] (cli, bundled in [[Documentation/Nightly/Extensions/ModelToModelDistance|ModelToModelDistance]] extension)
* [[Documentation/Nightly/Modules/T1Mapping|T1Mapping]] (cli, bundled in [[Documentation/Nightly/Extensions/T1Mapping|T1Mapping]] extension)
* [[Documentation/Nightly/Modules/SlicerAstroDataProbe|SlicerAstroDataProbe]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/AnglePlanes|AnglePlanes]] (scripted, bundled in [[Documentation/Nightly/Extensions/ShapeQuantifier|ShapeQuantifier]] extension)
* [[Documentation/Nightly/Modules/dPetBrainQuantification|dPetBrainQuantification]] (scripted, bundled in [http://gti-fing.github.io/SlicerPetSpectAnalysis PetSpectAnalysis] extension)
* [[Documentation/Nightly/Modules/PickAndPaint|PickAndPaint]] (scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PickAndPaint PickAndPaintExtension] extension)
* [[Documentation/Nightly/Extensions/QuantitativeReporting|QuantitativeReporting]] (scripted, bundled in [[Documentation/Nightly/Extensions/QuantitativeReporting|QuantitativeReporting]] extension)
* [[Documentation/Nightly/Modules/DiceComputation|DiceComputation]] (loadable, bundled in [[Documentation/Nightly/Extensions/DiceComputation|DiceComputation]] extension)

=== ChangeQuantification ===
* [[Documentation/Nightly/Modules/IntensityDifferenceMetric|IntensityDifferenceMetric]] (cli, bundled in [[Documentation/Nightly/Extensions/ChangeTracker|ChangeTracker]] extension)


== Radiology ==
* [[Documentation/Nightly/Extensions/SliceTracker|SliceTracker]] (scripted, bundled in [[Documentation/Nightly/Extensions/SliceTracker|SliceTracker]] extension)
* [[Documentation/Nightly/Extensions/SliceTracker|SliceTrackerRegistration]] (scripted, bundled in [[Documentation/Nightly/Extensions/SliceTracker|SliceTracker]] extension)
* [[Documentation/Nightly/Extensions/SliceTracker|SliceTrackerZFrameRegistration]] (scripted, bundled in [[Documentation/Nightly/Extensions/SliceTracker|SliceTracker]] extension)

== Radiotherapy ==
* [[Documentation/Nightly/Extensions/SlicerRT|Beams]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Extensions/SlicerRT|DvhComparison]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Modules/DoseVolumeHistogram|DoseVolumeHistogram]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Extensions/SlicerRT|DicomRtImportExport]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Modules/DoseAccumulation|DoseAccumulation]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Extensions/SlicerRT|ExternalBeamPlanning]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Modules/SegmentComparison|SegmentComparison]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Extensions/SlicerRT|PlanarImage]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Modules/Isodose|Isodose]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Modules/DoseComparison|DoseComparison]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Modules/SegmentMorphology|SegmentMorphology]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Modules/DicomSroImport|DicomSroImport]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)

== Registration ==
* [[Documentation/Nightly/Modules/Transforms|Transforms]] (loadable, built-in)
* BRAINSResize (cli, built-in)
* PerformMetricTest (cli, built-in)
* [[Documentation/Nightly/Modules/LandmarkRegistration|LandmarkRegistration]] (scripted, built-in)
* [[Documentation/Nightly/Extensions/PBNRR|PBNRR]] (cli, bundled in [[Documentation/Nightly/Extensions/PBNRR|PBNRR]] extension)
* [[Documentation/Nightly/Modules/BRAINSResample|BRAINSResample]] (cli, built-in)
* [[Documentation/Nightly/Modules/BRAINSFit|BRAINSFit]] (cli, built-in)

=== CMF Registration ===
* [[Documentation/Nightly/Extensions/CMFreg|ApplyMatrix]] (cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)
* [[Documentation/Nightly/Modules/LabelExtraction|LabelExtraction]] (cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)
* [[Documentation/Nightly/Modules/LabelAddition|LabelAddition]] (cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)
* [[Documentation/Nightly/Modules/Downsize|Downsize]] (cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)
* [[Documentation/Nightly/Modules/SurfaceRegistration|SurfaceRegistration]] (scripted, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)

==== Voxelbase Registration ====
* [[Documentation/Nightly/Modules/NonGrowing|NonGrowing]] (cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)
* [[Documentation/Nightly/Modules/Growing|Growing]] (cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)
* [[Documentation/Nightly/Modules/MaskCreation|MaskCreation]] (cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)

=== Label Registration ===
* [[Documentation/Nightly/Modules/DistanceMapBasedRegistration|DistanceMapBasedRegistration]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerProstate|SlicerProstate]] extension)

=== Specialized ===
* [[Documentation/Nightly/Modules/ACPCTransform|ACPCTransform]] (cli, built-in)
* [[Documentation/Nightly/Modules/FiducialRegistration|FiducialRegistration]] (cli, built-in)
* [[Documentation/Nightly/Modules/BRAINSDemonWarp|BRAINSDemonWarp]] (cli, built-in)
* [[Documentation/Nightly/Modules/Reformat|Reformat]] (loadable, built-in)
* [[Documentation/Nightly/Extensions/ScatteredTransform|ScatteredTransform]] (cli, bundled in [[Documentation/Nightly/Extensions/ScatteredTransform|ScatteredTransform]] extension)
* VBRAINSDemonWarp (cli, built-in)

== Segmentation ==
* [[Documentation/Nightly/Modules/ROBEXBrainExtraction|ROBEXBrainExtraction]] (cli, bundled in [[Documentation/Nightly/Extensions/ROBEXBrainExtraction|ROBEXBrainExtraction]] extension)
* EMSegmentQuick (loadable, built-in)
* [[Documentation/Nightly/Extensions/VolumeClip|VolumeClipWithModel]] (scripted, bundled in [[Documentation/Nightly/Extensions/VolumeClip|VolumeClip]] extension)
* [http://www.nitrc.org/projects/abc ABC] (cli, bundled in [http://www.nitrc.org/projects/abc ABC] extension)
* [[Documentation/Nightly/Extensions/SliceTracker|VolumeClipToLabel]] (scripted, bundled in [[Documentation/Nightly/Extensions/SliceTracker|SliceTracker]] extension)
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AirwaySegmentation AirwaySegmentationCLI] (cli, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AirwaySegmentation AirwaySegmentation] extension)
* [[Documentation/Nightly/Modules/LAScarSegmenter|LAScarSegmenter]] (cli, bundled in [[Documentation/Nightly/Extensions/LAScarSegmenter|LAScarSegmenter]] extension)
* [[Documentation/Nightly/Modules/SegmentEditor|SegmentEditor]] (scripted, built-in)
* [[Documentation/Nightly/Modules/AirwaySegmentation|AirwaySegmentation]] (scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AirwaySegmentation AirwaySegmentation] extension)
* [[Documentation/Nightly/Modules/SkullStripper|SkullStripper]] (cli, bundled in [[Documentation/Nightly/Extensions/SkullStripper|SkullStripper]] extension)
* [https://github.com/lassoan/SlicerSegmentEditorExtraEffects SegmentEditorFastMarching] (scripted, bundled in [https://github.com/lassoan/SlicerSegmentEditorExtraEffects SegmentEditorExtraEffects] extension)
* [[Documentation/Nightly/Modules/SobolevSegmenter|SobolevSegmenter]] (cli, bundled in [[Documentation/Nightly/Extensions/SobolevSegmenter|SobolevSegmenter]] extension)
* [[Documentation/Nightly/Extensions/VolumeClip|VolumeClipWithRoi]] (scripted, bundled in [[Documentation/Nightly/Extensions/VolumeClip|VolumeClip]] extension)
* [[Documentation/Nightly/Modules/SegmentCAD|SegmentCAD]] (scripted, bundled in [[Documentation/Nightly/Extensions/OpenCAD|OpenCAD]] extension)
* [[Documentation/Nightly/Modules/SwissSkullStripper|SwissSkullStripper]] (cli, bundled in [[Documentation/Nightly/Extensions/SwissSkullStripper|SwissSkullStripper]] extension)
* [https://github.com/lassoan/SlicerSegmentEditorExtraEffects SegmentEditorFloodFilling] (scripted, bundled in [https://github.com/lassoan/SlicerSegmentEditorExtraEffects SegmentEditorExtraEffects] extension)
* [https://github.com/Tomnl/Slicer-Wasp Wasp] (scripted, bundled in [https://github.com/Tomnl/Slicer-Wasp Wasp] extension)
* [[Documentation/Nightly/Modules/Editor|Editor]] (scripted, built-in)
* [[Documentation/Nightly/Modules/SimpleRegionGrowingSegmentation|SimpleRegionGrowingSegmentation]] (cli, built-in)
* [[Documentation/Nightly/Modules/EMSegment|EMSegment]] (loadable, built-in)
* [[Documentation/Nightly/Extensions/QuantitativeReporting|QuantitativeReporting]] (scripted, bundled in [[Documentation/Nightly/Extensions/QuantitativeReporting|QuantitativeReporting]] extension)
* [[Documentation/Nightly/Extensions/IntensitySegmenter|IntensitySegmenter]] (cli, bundled in [[Documentation/Nightly/Extensions/IntensitySegmenter|IntensitySegmenter]] extension)
* [https://github.com/lassoan/SlicerSegmentEditorExtraEffects SegmentEditorWatershed] (scripted, bundled in [https://github.com/lassoan/SlicerSegmentEditorExtraEffects SegmentEditorExtraEffects] extension)

=== Specialized ===
* BRAINSROIAuto (cli, built-in)
* [[Documentation/Nightly/Modules/RobustStatisticsSegmenter|RobustStatisticsSegmenter]] (cli, built-in)
* EMSegmentCommandLine (cli, built-in)

== Sequences ==
* [[Documentation/Nightly/Extensions/Sequences|Sequences]] (loadable, bundled in [[Documentation/Nightly/Extensions/Sequences|Sequences]] extension)
* [[Documentation/Nightly/Extensions/Sequences|SequenceBrowser]] (loadable, bundled in [[Documentation/Nightly/Extensions/Sequences|Sequences]] extension)
* [[Documentation/Nightly/Extensions/Sequences|MetafileImporter]] (loadable, bundled in [[Documentation/Nightly/Extensions/Sequences|Sequences]] extension)

== Slicelets ==
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/FilmDosimetry FilmDosimetryAnalysis] (scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/FilmDosimetry FilmDosimetryAnalysis] extension)
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry GelDosimetryAnalysis] (scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry GelDosimetryAnalysis] extension)
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry GelDosimetryAnalysisAlgo] (loadable, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry GelDosimetryAnalysis] extension)

== SlicerProstate ==
* [[Documentation/Nightly/Extensions/SliceTracker|ZFrameCalibration]] (cli, bundled in [[Documentation/Nightly/Extensions/SliceTracker|SliceTracker]] extension)

== Surface Models ==
* [[Documentation/Nightly/Modules/SurfaceToolbox|SurfaceToolbox]] (scripted, built-in)
* [[Documentation/Nightly/Modules/GrayscaleModelMaker|GrayscaleModelMaker]] (cli, built-in)
* [[Documentation/Nightly/Modules/ModelMaker|ModelMaker]] (cli, built-in)
* [[Documentation/Nightly/Modules/ModelToLabelMap|ModelToLabelMap]] (cli, built-in)
* [[Documentation/Nightly/Modules/MergeModels|MergeModels]] (cli, built-in)
* [[Documentation/Nightly/Modules/EasyClip|EasyClip]] (scripted, bundled in [[Documentation/Nightly/Extensions/EasyClip|EasyClip]] extension)
* [[Documentation/Nightly/Modules/LabelMapSmoothing|LabelMapSmoothing]] (cli, built-in)
* [[Documentation/Nightly/Extensions/MeshToLabelMap|MeshToLabelMap]] (cli, bundled in [[Documentation/Nightly/Extensions/MeshToLabelMap|MeshToLabelMap]] extension)
* [[Documentation/Nightly/Modules/ProbeVolumeWithModel|ProbeVolumeWithModel]] (cli, built-in)
* [[Documentation/Nightly/Extensions/SlicerIGT|TextureModel]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)

== TestCases ==
* SEGExporterSelfTest

== Testing ==
* CLI4Test
* ThresholdThreadingTest
* [[Documentation/Nightly/Extensions/Scoliosis|ScoliosisMonitoring]] (scripted, bundled in [[Documentation/Nightly/Extensions/Scoliosis|Scoliosis]] extension)
* SlicerMRBSaveRestoreCheckPathsTest
* CLIROITest (cli, built-in)
* PerformanceTests
* SlicerMRBMultipleSaveRestoreTest
* SlicerMRBTest
* SEGExporterSelfTest
* SelfTests
* SlicerMRBMultipleSaveRestoreLoopTest

=== IGT Tests ===
* BreachWarningSelfTest
* WatchdogSelfTest

=== SlicerRT Tests ===
* IGRTWorkflow_SelfTest
* [[Documentation/Nightly/Extensions/SlicerRT|BatchStructureSetConversion]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)

=== TestCases ===
* AtlasTests
* AddStorableDataAfterSceneViewTest
* test_tractography_display
* SlicerTransformInteractionTest1
* RSNAQuantTutorial
* NeurosurgicalPlanningTutorialMarkupsSelfTest
* ChangeTrackerSelfTest
* FiducialLayoutSwitchBug1914
* GraphCutSegmentSelfTest
* SlicerBoundsTest
* UtilTest
* Charting (scripted, built-in)
* [http://brainsia.github.io/CardiacAgatstonMeasures/ CardiacAgatstonMeasures] (scripted, bundled in [http://brainsia.github.io/CardiacAgatstonMeasures/ CardiacAgatstonMeasures] extension)
* fiber_visibility_crash2438
* RSNAVisTutorial
* JRC2013Vis
* AddManyMarkupsFiducialTest
* CropVolumeSelfTest
* SliceLinkLogic (scripted, built-in)
* VolumeRenderingSceneClose (scripted, built-in)
* slicerCloseCrashBug2590
* CLIEventTest
* [[Documentation/Nightly/Extensions/SlicerDMRI|NsgPlanTracto]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)
* MarkupsWidgetsSelfTest
* TablesSelfTest
* SlicerOrientationSelectorTest
* MarkupsInViewsSelfTest
* TwoCLIsInParallelTest
* SubjectHierarchyCorePluginsSelfTest
* SubjectHierarchyGenericSelfTest
* ScenePerformance (scripted, built-in)
* MarkupsInCompareViewersSelfTest
* sceneImport2428
* RSNA2012ProstateDemo
* DTINotReproducibleIssue3977
* TwoCLIsInARowTest
* ColorsScalarBarSelfTest
* BRAINSFitRigidRegistrationCrashIssue4139
* Slicer4Minute (scripted, built-in)
* ViewControllersSliceInterpolationBug1926

== Ultrasound ==
* [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ ScanConvertCurvilinearArray] (cli, bundled in [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ SlicerITKUltrasound] extension)
* [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ ScanConvertPhasedArray3D] (cli, bundled in [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ SlicerITKUltrasound] extension)
* [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ ScanConvertSliceSeries] (cli, bundled in [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ SlicerITKUltrasound] extension)

== Uncategorized ==
* [[Documentation/Nightly/Extensions/ShapeQuantifier|ShapeQuantifierCore]] (scripted, bundled in [[Documentation/Nightly/Extensions/ShapeQuantifier|ShapeQuantifier]] extension)
* [[Documentation/Nightly/Extensions/DatabaseInteractor|DatabaseInteractorLib]] (scripted, bundled in [[Documentation/Nightly/Extensions/DatabaseInteractor|DatabaseInteractor]] extension)

== Utilities ==
* [[Documentation/Nightly/Modules/ScreenCapture|ScreenCapture]] (scripted, built-in)
* [[Documentation/Nightly/Modules/DataStore|DataStore]] (loadable, built-in)
* DICOMPatcher (scripted, built-in)
* BRAINSStripRotation (cli, built-in)
* EMSegmentTransformToNewFormat (cli, built-in)

=== BRAINS ===
* BRAINSTransformConvert (cli, built-in)

== Vascular Modeling Toolkit ==
* [http://slicer.vmtk.org/ CenterlineComputation] (scripted, bundled in [http://slicer.vmtk.org/ VMTK] extension)
* [http://slicer.vmtk.org/ LevelSetSegmentation] (scripted, bundled in [http://slicer.vmtk.org/ VMTK] extension)
* [http://slicer.vmtk.org/ VesselnessFiltering] (scripted, bundled in [http://slicer.vmtk.org/ VMTK] extension)

== Virtual Reality ==
* [[Documentation/Nightly/Modules/VirtualReality|VirtualReality]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerVirtualReality|SlicerVirtualReality]] extension)

== Web System Tools ==
* [[Documentation/Nightly/Modules/DatabaseInteractor|DatabaseInteractor]] (scripted, bundled in [[Documentation/Nightly/Extensions/DatabaseInteractor|DatabaseInteractor]] extension)

== Wizards ==
* [[Documentation/Nightly/Modules/CompareVolumes|CompareVolumes]] (scripted, built-in)
* [[Documentation/Nightly/Modules/ChangeTracker|ChangeTracker]] (scripted, bundled in [[Documentation/Nightly/Extensions/ChangeTracker|ChangeTracker]] extension)

== XNATSlicer ==
* [[Documentation/Nightly/Extensions/XNATSlicer|XnatSlicer]] (scripted, bundled in [[Documentation/Nightly/Extensions/XNATSlicer|XNATSlicer]] extension)

= Modules by name =
367 modules:
* [http://www.nitrc.org/projects/abc ABC] (cli, bundled in [http://www.nitrc.org/projects/abc ABC] extension)
* [[Documentation/Nightly/Modules/ACPCTransform|ACPCTransform]] (cli, built-in)
* [[Documentation/Nightly/Modules/AddScalarVolumes|AddScalarVolumes]] (cli, built-in)
* [http://www.chestimagingplatform.org AirwayInspector] (loadable, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Modules/AirwaySegmentation|AirwaySegmentation]] (scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AirwaySegmentation AirwaySegmentation] extension)
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AirwaySegmentation AirwaySegmentationCLI] (cli, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AirwaySegmentation AirwaySegmentation] extension)
* [[Documentation/Nightly/Modules/AnglePlanes|AnglePlanes]] (scripted, bundled in [[Documentation/Nightly/Extensions/ShapeQuantifier|ShapeQuantifier]] extension)
* [[Documentation/Nightly/Modules/Annotations|Annotations]] (loadable, built-in)
* [[Documentation/Nightly/Extensions/CMFreg|ApplyMatrix]] (cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)
* [[Documentation/Nightly/Modules/AstroMasking|AstroMasking]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/AstroModeling|AstroModeling]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/AstroMomentMaps|AstroMomentMaps]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/AstroProfiles|AstroProfiles]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/AstroPVDiagram|AstroPVDiagram]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/AstroPVSlice|AstroPVSlice]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/AstroReproject|AstroReproject]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Extensions/SlicerAstro|AstroSampleData]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/AstroSmoothing|AstroSmoothing]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/AstroStatistics|AstroStatistics]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/AstroVolume|AstroVolume]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Extensions/SlicerAstro|AstroWelcome]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Extensions/SlicerRT|Beams]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Extensions/IASEM|BinShrink]] (cli, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)
* [[Documentation/Nightly/Extensions/OpenCVExample|BlendVectorVolumes]] (cli, bundled in [[Documentation/Nightly/Extensions/OpenCVExample|OpenCVExample]] extension)
* [[Documentation/Nightly/Modules/BodyCentricCubicMesh|BodyCentricCubicMesh]] (cli, bundled in [[Documentation/Nightly/Extensions/CBC_3D_I2MConversion|CBC_3D_I2MConversion]] extension)
* [[Documentation/Nightly/Modules/BRAINSDemonWarp|BRAINSDemonWarp]] (cli, built-in)
* BRAINSDWICleanup (cli, built-in)
* [[Documentation/Nightly/Modules/BRAINSFit|BRAINSFit]] (cli, built-in)
* BRAINSLabelStats (cli, built-in)
* [[Documentation/Nightly/Modules/BRAINSResample|BRAINSResample]] (cli, built-in)
* BRAINSResize (cli, built-in)
* BRAINSROIAuto (cli, built-in)
* BRAINSStripRotation (cli, built-in)
* BRAINSTransformConvert (cli, built-in)
* [[Documentation/Nightly/Extensions/SlicerIGT|BreachWarning]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter CarreraSlice] (loadable, bundled in [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter CarreraSlice] extension)
* [[Documentation/Nightly/Modules/CastScalarVolume|CastScalarVolume]] (cli, built-in)
* [http://slicer.vmtk.org/ CenterlineComputation] (scripted, bundled in [http://slicer.vmtk.org/ VMTK] extension)
* [[Documentation/Nightly/Modules/ChangeTracker|ChangeTracker]] (scripted, bundled in [[Documentation/Nightly/Extensions/ChangeTracker|ChangeTracker]] extension)
* [[Documentation/Nightly/Modules/CheckerBoardFilter|CheckerBoardFilter]] (cli, built-in)
* [http://www.chestimagingplatform.org CIP_] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CIP_BodyComposition] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CIP_CalciumScoring] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CIP_Common] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CIP_InteractiveLobeSegmentation] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CIP_LesionModel] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CIP_MIPViewer] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CIP_PAARatio] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CIP_ParenchymaAnalysis] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CIP_ParenchymaSubtypeTraining] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CIP_PointsLabelling] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CIP_TracheaStentPlanning] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ClassifyFissureParticles] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Extensions/CleaverExtension|CleaverCLI]] (cli, bundled in [[Documentation/Nightly/Extensions/CleaverExtension|CleaverExtension]] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitAutomaticLeftAtrialScar] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitAxialDilate] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitBooleanREMOVEFilter] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitConnectedThresholdFilter] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitInhomogeneityCorrection] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitIsolatedConnectedFilter] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitLASegmentationGraphCuts] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitPVAntrumCut] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitRegistration] (scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitRegistrationBRAINSFit] (scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitWizard] (scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [[Documentation/Nightly/Modules/CollectFiducials|CollectFiducials]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Modules/Colors|Colors]] (loadable, built-in)
* [[Documentation/Nightly/Modules/CompareVolumes|CompareVolumes]] (scripted, built-in)
* [http://www.chestimagingplatform.org ComputeCrossSectionalArea] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ComputeDistanceMap] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ComputeFeatureStrength] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ComputeFissureFeatureVectors] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ComputeIntensityStatistics] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ConvertChestRegionChestTypeToLabelMapValue] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ConvertDicom] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ConvertLabelMapValueToChestRegionChestType] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Extensions/UKFTractography|ConvertVTK]] (cli, bundled in [[Documentation/Nightly/Extensions/UKFTractography|UKFTractography]] extension)
* [[Documentation/Nightly/Modules/CornerAnnotation|CornerAnnotation]] (scripted, bundled in [[Documentation/Nightly/Extensions/CornerAnnotation|CornerAnnotation]] extension)
* [[Documentation/Nightly/Modules/CreateDICOMSeries|CreateDICOMSeries]] (cli, built-in)
* [[Documentation/Nightly/Extensions/SlicerIGT|CreateModels]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [http://www.chestimagingplatform.org CropLung] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Modules/CropVolume|CropVolume]] (loadable, built-in)
* [[Documentation/Nightly/Modules/CurvatureAnisotropicDiffusion|CurvatureAnisotropicDiffusion]] (cli, built-in)
* [[Documentation/Nightly/Extensions/CurveMaker|CurveMaker]] (scripted, bundled in [[Documentation/Nightly/Extensions/CurveMaker|CurveMaker]] extension)
* [[Documentation/Nightly/Modules/Data|Data]] (loadable, built-in)
* [[Documentation/Nightly/Modules/DatabaseInteractor|DatabaseInteractor]] (scripted, bundled in [[Documentation/Nightly/Extensions/DatabaseInteractor|DatabaseInteractor]] extension)
* [[Documentation/Nightly/Extensions/DatabaseInteractor|DatabaseInteractorLib]] (scripted, bundled in [[Documentation/Nightly/Extensions/DatabaseInteractor|DatabaseInteractor]] extension)
* [[Documentation/Nightly/Modules/DataProbe|DataProbe]] (scripted, built-in)
* [[Documentation/Nightly/Modules/DataStore|DataStore]] (loadable, built-in)
* [[Documentation/Nightly/Modules/DeepInfer|DeepInfer]] (scripted, bundled in [[Documentation/Nightly/Extensions/DeepInfer|DeepInfer]] extension)
* [[Documentation/Nightly/Modules/DiceComputation|DiceComputation]] (loadable, bundled in [[Documentation/Nightly/Extensions/DiceComputation|DiceComputation]] extension)
* [[Documentation/Nightly/Modules/DICOM|DICOM]] (scripted, built-in)
* [[Documentation/Nightly/Extensions/SlicerDMRI|DICOM2FullBrainTractography]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)
* DICOMPatcher (scripted, built-in)
* [[Documentation/Nightly/Extensions/SlicerRT|DicomRtImportExport]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Modules/DicomSroExport|DicomSroExport]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Modules/DicomSroImport|DicomSroImport]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Extensions/SlicerDMRI|DICOMTract_to_VTK]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)
* [[Documentation/Nightly/Modules/DiffusionTensorScalarMeasurements|DiffusionTensorScalarMeasurements]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)
* [[Documentation/Nightly/Modules/DiffusionWeightedVolumeMasking|DiffusionWeightedVolumeMasking]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)
* [[Documentation/Nightly/Modules/DistanceMapBasedRegistration|DistanceMapBasedRegistration]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerProstate|SlicerProstate]] extension)
* [[Documentation/Nightly/Modules/DMRIInstall|DMRIInstall]] (scripted, built-in)
* [[Documentation/Nightly/Modules/DoseAccumulation|DoseAccumulation]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Modules/DoseComparison|DoseComparison]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Extensions/MarginCalculator|DoseMorphology]] (loadable, bundled in [[Documentation/Nightly/Extensions/MarginCalculator|MarginCalculator]] extension)
* [[Documentation/Nightly/Modules/DoseVolumeHistogram|DoseVolumeHistogram]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Modules/Downsize|Downsize]] (cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)
* [[Documentation/Nightly/Modules/dPetBrainQuantification|dPetBrainQuantification]] (scripted, bundled in [http://gti-fing.github.io/SlicerPetSpectAnalysis PetSpectAnalysis] extension)
* [http://slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DSC_MRI_Analysis DSCMRIAnalysis] (cli, bundled in [http://slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DSC_MRI_Analysis DSCMRIAnalysis] extension)
* DumpSEGFrame (cli)
* [[Documentation/Nightly/Extensions/SlicerRT|DvhComparison]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* DWIConvert (cli, built-in)
* [[Documentation/Nightly/Modules/DWIToDTIEstimation|DWIToDTIEstimation]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)
* [[Documentation/Nightly/Modules/DWModeling|DWModeling]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerProstate|SlicerProstate]] extension)
* [[Documentation/Nightly/Modules/EasyClip|EasyClip]] (scripted, bundled in [[Documentation/Nightly/Extensions/EasyClip|EasyClip]] extension)
* [[Documentation/Nightly/Modules/Editor|Editor]] (scripted, built-in)
* [[Documentation/Nightly/Modules/EMSegment|EMSegment]] (loadable, built-in)
* EMSegmentCommandLine (cli, built-in)
* EMSegmentQuick (loadable, built-in)
* EMSegmentTransformToNewFormat (cli, built-in)
* [[Documentation/Nightly/Modules/EncodeSEG|EncodeSEG]] (cli)
* [[Documentation/Nightly/Modules/Endoscopy|Endoscopy]] (scripted, built-in)
* [http://www.chestimagingplatform.org EnhanceFissuresInImage] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org EvaluateLungLobeSegmentationResults] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ExecuteSystemCommand] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Extensions/SlicerRT|ExternalBeamPlanning]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [http://www.chestimagingplatform.org ExtractChestLabelMap] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ExtractFissureBoundaryFromLobeMap] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ExtractParticlesFromChestRegionChestType] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Modules/ExtractSkeleton|ExtractSkeleton]] (cli, built-in)
* [[Documentation/Nightly/Modules/FastGrowCut|FastGrowCut]] (loadable, bundled in [https://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/FastGrowCut FastGrowCutEffect] extension)
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter FastGrowCutSegmenter] (loadable, bundled in [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter CarreraSlice] extension)
* [[Documentation/Nightly/Modules/FiberBundleLabelSelect|FiberBundleLabelSelect]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)
* [[Documentation/Nightly/Modules/FiberBundleToLabelMap|FiberBundleToLabelMap]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)
* [[Documentation/Nightly/Modules/FiberTractMeasurements|FiberTractMeasurements]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)
* [[Documentation/Nightly/Modules/FiducialRegistration|FiducialRegistration]] (cli, built-in)
* [[Documentation/Nightly/Extensions/SlicerIGT|FiducialRegistrationWizard]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Extensions/SlicerIGT|FiducialsToModelRegistration]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/FilmDosimetry FilmDosimetryAnalysis] (scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/FilmDosimetry FilmDosimetryAnalysis] extension)
* [http://www.chestimagingplatform.org FilterAirwayParticleData] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org FilterConnectedComponents] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org FilterFissureParticleData] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org FilterVesselParticleData] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org FindPatchMatch] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org FitLobeSurfaceModelsToParticleData] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Modules/GaussianBlurImageFilter|GaussianBlurImageFilter]] (cli, built-in)
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry GelDosimetryAnalysis] (scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry GelDosimetryAnalysis] extension)
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry GelDosimetryAnalysisAlgo] (loadable, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry GelDosimetryAnalysis] extension)
* [http://www.chestimagingplatform.org GenerateAtlasConvexHull] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateBinaryThinning3D] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateDistanceMapFromLabelMap] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateImageSubVolumes] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateLesionSegmentation] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateLobeSurfaceModels] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateMedianFilteredImage] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateModel] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateNLMFilteredImage] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateOtsuLungCast] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateOverlayImages] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateParenchymaPhenotypes] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GeneratePartialLungLabelMap] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateSimpleLungMask] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateStenciledLabelMapFromParticles] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GetStructuresInLabelMap] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GetTransformationKappa] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GetTransformationKappa2D] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GetTransformationSimilarityMetric] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Modules/GradientAnisotropicDiffusion|GradientAnisotropicDiffusion]] (cli, built-in)
* [http://publish.uwo.ca/~dchen285/GraphCutSegment/GraphCutSegment.html GraphCutInteractiveSegmenter] (loadable, bundled in [http://publish.uwo.ca/~dchen285/GraphCutSegment/GraphCutSegment.html GraphCutSegment] extension)
* [http://www.chestimagingplatform.org GraphCutsOptimization] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Modules/GrayscaleFillHoleImageFilter|GrayscaleFillHoleImageFilter]] (cli, built-in)
* [[Documentation/Nightly/Modules/GrayscaleGrindPeakImageFilter|GrayscaleGrindPeakImageFilter]] (cli, built-in)
* [[Documentation/Nightly/Modules/GrayscaleModelMaker|GrayscaleModelMaker]] (cli, built-in)
* [[Documentation/Nightly/Modules/Growing|Growing]] (cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)
* [[Documentation/Nightly/Modules/GyroGuide|GyroGuide]] (scripted, bundled in [[Documentation/Nightly/Extensions/GyroGuide|GyroGuide]] extension)
* [[Documentation/Nightly/Modules/HeterogeneityCAD|HeterogeneityCAD]] (scripted, bundled in [[Documentation/Nightly/Extensions/OpenCAD|OpenCAD]] extension)
* [[Documentation/Nightly/Modules/HistogramMatching|HistogramMatching]] (cli, built-in)
* [[Documentation/Nightly/Extensions/IASEM|IASEMImport]] (cli, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)
* [[Documentation/Nightly/Extensions/IASEM|IASEMImportSeries]] (cli, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)
* [[Documentation/Nightly/Extensions/iGyne|iGyne]] (scripted, bundled in [[Documentation/Nightly/Extensions/iGyne|iGyne]] extension)
* [[Documentation/Nightly/Modules/ImageLabelCombine|ImageLabelCombine]] (cli, built-in)
* [[Documentation/Nightly/Modules/IntensityDifferenceMetric|IntensityDifferenceMetric]] (cli, bundled in [[Documentation/Nightly/Extensions/ChangeTracker|ChangeTracker]] extension)
* [[Documentation/Nightly/Extensions/IntensitySegmenter|IntensitySegmenter]] (cli, bundled in [[Documentation/Nightly/Extensions/IntensitySegmenter|IntensitySegmenter]] extension)
* IslandRemoval (cli, built-in)
* [[Documentation/Nightly/Modules/Isodose|Isodose]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Extensions/DCMQI|itkimage2paramap]] (cli, bundled in [[Documentation/Nightly/Extensions/DCMQI|DCMQI]] extension)
* [[Documentation/Nightly/Extensions/DCMQI|itkimage2segimage]] (cli, bundled in [[Documentation/Nightly/Extensions/DCMQI|DCMQI]] extension)
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter KUtil] (scripted, bundled in [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter CarreraSlice] extension)
* [[Documentation/Nightly/Modules/LabelAddition|LabelAddition]] (cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)
* [[Documentation/Nightly/Modules/LabelExtraction|LabelExtraction]] (cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)
* [http://www.chestimagingplatform.org LabelMapFromRegionAndTypePoints] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Modules/LabelMapSmoothing|LabelMapSmoothing]] (cli, built-in)
* [[Documentation/Nightly/Extensions/IASEM|LabelObjectStatistics]] (scripted, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)
* [http://www.chestimagingplatform.org LabelParticlesByChestRegionChestType] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Modules/LabelStatistics|LabelStatistics]] (scripted, built-in)
* [[Documentation/Nightly/Modules/LandmarkRegistration|LandmarkRegistration]] (scripted, built-in)
* [[Documentation/Nightly/Modules/LAScarSegmenter|LAScarSegmenter]] (cli, bundled in [[Documentation/Nightly/Extensions/LAScarSegmenter|LAScarSegmenter]] extension)
* [[Documentation/Nightly/Modules/LASegmentationWorkflow|LASegmentationWorkflow]] (scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [http://slicer.vmtk.org/ LevelSetSegmentation] (scripted, bundled in [http://slicer.vmtk.org/ VMTK] extension)
* [[Documentation/Nightly/Extensions/MarginCalculator|MarginCalculator]] (scripted, bundled in [[Documentation/Nightly/Extensions/MarginCalculator|MarginCalculator]] extension)
* [[Documentation/Nightly/Modules/Markups|Markups]] (loadable, built-in)
* [[Documentation/Nightly/Extensions/SlicerIGT|MarkupsToModel]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Modules/MaskCreation|MaskCreation]] (cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)
* [http://www.chestimagingplatform.org MaskOutLabelMapStructures] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Modules/MaskScalarVolume|MaskScalarVolume]] (cli, built-in)
* [[Documentation/Nightly/Modules/MedianImageFilter|MedianImageFilter]] (cli, built-in)
* [http://www.chestimagingplatform.org MergeChestLabelMaps] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Modules/MergeModels|MergeModels]] (cli, built-in)
* [http://www.chestimagingplatform.org MergeParticleDataSets] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Modules/MeshStatistics|MeshStatistics]] (scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/MeshStatistics MeshStatisticsExtension] extension)
* [[Documentation/Nightly/Extensions/MeshToLabelMap|MeshToLabelMap]] (cli, bundled in [[Documentation/Nightly/Extensions/MeshToLabelMap|MeshToLabelMap]] extension)
* [[Documentation/Nightly/Extensions/Sequences|MetafileImporter]] (loadable, bundled in [[Documentation/Nightly/Extensions/Sequences|Sequences]] extension)
* [[Documentation/Nightly/Modules/ModelMaker|ModelMaker]] (cli, built-in)
* [[Documentation/Nightly/Extensions/SlicerIGT|ModelRegistration]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Modules/Models|Models]] (loadable, built-in)
* [[Documentation/Nightly/Modules/ModelToLabelMap|ModelToLabelMap]] (cli, built-in)
* [[Documentation/Nightly/Extensions/ModelToModelDistance|ModelToModelDistance]] (cli, bundled in [[Documentation/Nightly/Extensions/ModelToModelDistance|ModelToModelDistance]] extension)
* [[Documentation/Nightly/Extensions/mpReview|mpReview]] (scripted, bundled in [[Documentation/Nightly/Extensions/mpReview|mpReview]] extension)
* [[Documentation/Nightly/Extensions/mpReview|mpReviewPreprocessor]] (scripted, bundled in [[Documentation/Nightly/Extensions/mpReview|mpReview]] extension)
* [[Documentation/Nightly/Modules/MultiplyScalarVolumes|MultiplyScalarVolumes]] (cli, built-in)
* [[Documentation/Nightly/Modules/MultiVolumeExplorer|MultiVolumeExplorer]] (loadable, built-in)
* [[Documentation/Nightly/Modules/MultiVolumeImporter|MultiVolumeImporter]] (scripted, built-in)
* [[Documentation/Nightly/Modules/N4ITKBiasFieldCorrection|N4ITKBiasFieldCorrection]] (cli, built-in)
* [[Documentation/Nightly/Extensions/NeedleFinder|NeedleFinder]] (scripted, bundled in [[Documentation/Nightly/Extensions/NeedleFinder|NeedleFinder]] extension)
* [[Documentation/Nightly/Modules/NonGrowing|NonGrowing]] (cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)
* [[Documentation/Nightly/Extensions/SlicerOpenCV|OpenCV]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerOpenCV|SlicerOpenCV]] extension)
* [[Documentation/Nightly/Modules/OpenIGTLinkIF|OpenIGTLinkIF]] (loadable, built-in)
* [[Documentation/Nightly/Modules/OpenIGTLinkRemote|OpenIGTLinkRemote]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Modules/OrientScalarVolume|OrientScalarVolume]] (cli, built-in)
* [[Documentation/Nightly/Extensions/DCMQI|paramap2itkimage]] (cli, bundled in [[Documentation/Nightly/Extensions/DCMQI|DCMQI]] extension)
* [http://www.chestimagingplatform.org ParticlesDisplay] (loadable, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Modules/PathExplorer|PathExplorer]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Extensions/PBNRR|PBNRR]] (cli, bundled in [[Documentation/Nightly/Extensions/PBNRR|PBNRR]] extension)
* PerformMetricTest (cli, built-in)
* [http://www.chestimagingplatform.org PerformMorphological] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Modules/PerkEvaluator|PerkEvaluator]] (loadable, bundled in [[Documentation/Nightly/Extensions/PerkTutor|PerkTutor]] extension)
* [http://www.chestimagingplatform.org PerturbParticles] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Extensions/PET-IndiC|PETIndiC]] (scripted, bundled in [[Documentation/Nightly/Extensions/PET-IndiC|PET-IndiC]] extension)
* [[Documentation/Nightly/Modules/PETLiverUptakeMeasurement|PETLiverUptakeMeasurement]] (cli, bundled in [[Documentation/Nightly/Extensions/PETLiverUptakeMeasurement|PETLiverUptakeMeasurement]] extension)
* [[Documentation/Nightly/Modules/PETStandardUptakeValueComputation|PETStandardUptakeValueComputation]] (cli, built-in)
* [[Documentation/Nightly/Extensions/LongitudinalPETCT|PETSUVImageMaker]] (cli, bundled in [[Documentation/Nightly/Extensions/LongitudinalPETCT|LongitudinalPETCT]] extension)
* [[Documentation/Nightly/Extensions/PETTumorSegmentation|PETTumorSegmentation]] (loadable, bundled in [[Documentation/Nightly/Extensions/PETTumorSegmentation|PETTumorSegmentation]] extension)
* [[Documentation/Nightly/Extensions/SlicerHeart|Philips4dUsDicomPatcher]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerHeart|SlicerHeart]] extension)
* [[Documentation/Nightly/Modules/PickAndPaint|PickAndPaint]] (scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PickAndPaint PickAndPaintExtension] extension)
* [[Documentation/Nightly/Extensions/SlicerIGT|PivotCalibration]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Modules/PkModeling|PkModeling]] (cli, bundled in [[Documentation/Nightly/Extensions/PkModeling|PkModeling]] extension)
* [[Documentation/Nightly/Extensions/SlicerRT|PlanarImage]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Extensions/SlicerRT|plastimatch_slicer_bspline]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Extensions/SlicerRT|plastimatch_slicer_landwarp]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Extensions/SlicerRT|PlastimatchPy]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Extensions/SlicerRT|PlmRegister]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Extensions/SlicerIGT|PlusModelCatalogBrowser]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Modules/PlusRemote|PlusRemote]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Modules/ProbeVolumeWithModel|ProbeVolumeWithModel]] (cli, built-in)
* [[Documentation/Nightly/Extensions/PerkTutor|PythonMetricsCalculator]] (scripted, bundled in [[Documentation/Nightly/Extensions/PerkTutor|PerkTutor]] extension)
* [[Documentation/Nightly/Modules/Q3DC|Q3DC]] (scripted, bundled in [[Documentation/Nightly/Extensions/Q3DC|Q3DC]] extension)
* [[Documentation/Nightly/Modules/QuadEdgeSurfaceMesher|QuadEdgeSurfaceMesher]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerProstate|SlicerProstate]] extension)
* [http://www.chestimagingplatform.org QualityControl] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Modules/QuantitativeIndicesCLI|QuantitativeIndicesCLI]] (cli, bundled in [[Documentation/Nightly/Extensions/PET-IndiC|PET-IndiC]] extension)
* [[Documentation/Nightly/Modules/QuantitativeIndicesTool|QuantitativeIndicesTool]] (scripted, bundled in [[Documentation/Nightly/Extensions/PET-IndiC|PET-IndiC]] extension)
* [[Documentation/Nightly/Extensions/QuantitativeReporting|QuantitativeReporting]] (scripted, bundled in [[Documentation/Nightly/Extensions/QuantitativeReporting|QuantitativeReporting]] extension)
* [[Documentation/Nightly/Extensions/SlicerPathology|QuickTCGA]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerPathology|SlicerPathology]] extension)
* [http://www.chestimagingplatform.org ReadDicomWriteTags] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ReadNRRDsWriteVTK] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ReadVidaWriteCIP] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ReadVTKWriteNRRDs] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ReadWriteImageData] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ReadWriteRegionAndTypePoints] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Modules/Reformat|Reformat]] (loadable, built-in)
* [http://www.chestimagingplatform.org RegionType] (loadable, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org RegionTypeLocationsToROIVolume] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org RegisterCT] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org RegisterLabelMaps] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org RegisterLungAtlas] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org RemapLabelMap] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org RemoveChestTypeFromLabelMapUsingParticles] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org RemoveParticlesFromParticlesDataSet] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ResampleCT] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Extensions/ResampleDTIlogEuclidean|ResampleDTIlogEuclidean]] (cli, bundled in [[Documentation/Nightly/Extensions/ResampleDTIlogEuclidean|ResampleDTIlogEuclidean]] extension)
* [[Documentation/Nightly/Modules/ResampleDTIVolume|ResampleDTIVolume]] (cli, built-in)
* [http://www.chestimagingplatform.org ResampleLabelMap] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Modules/ResampleScalarVectorDWIVolume|ResampleScalarVectorDWIVolume]] (cli, built-in)
* [http://www.chestimagingplatform.org RescaleLabelMap] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Modules/ResectionVolume|ResectionVolume]] (scripted, bundled in [[Documentation/Nightly/Extensions/ResectionPlanner|ResectionPlanner]] extension)
* [[Documentation/Nightly/Modules/ROBEXBrainExtraction|ROBEXBrainExtraction]] (cli, bundled in [[Documentation/Nightly/Extensions/ROBEXBrainExtraction|ROBEXBrainExtraction]] extension)
* [[Documentation/Nightly/Modules/RobustStatisticsSegmenter|RobustStatisticsSegmenter]] (cli, built-in)
* [[Documentation/Nightly/Modules/SampleData|SampleData]] (scripted, built-in)
* [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ ScanConvertCurvilinearArray] (cli, bundled in [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ SlicerITKUltrasound] extension)
* [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ ScanConvertPhasedArray3D] (cli, bundled in [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ SlicerITKUltrasound] extension)
* [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ ScanConvertSliceSeries] (cli, bundled in [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ SlicerITKUltrasound] extension)
* [[Documentation/Nightly/Modules/ScarVisualization|ScarVisualization]] (scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [[Documentation/Nightly/Extensions/ScatteredTransform|ScatteredTransform]] (cli, bundled in [[Documentation/Nightly/Extensions/ScatteredTransform|ScatteredTransform]] extension)
* [[Documentation/Nightly/Modules/SceneViews|SceneViews]] (loadable, built-in)
* [[Documentation/Nightly/Modules/ScreenCapture|ScreenCapture]] (scripted, built-in)
* [[Documentation/Nightly/Modules/SEG2NRRD|SEG2NRRD]] (cli)
* [[Documentation/Nightly/Extensions/DCMQI|segimage2itkimage]] (cli, bundled in [[Documentation/Nightly/Extensions/DCMQI|DCMQI]] extension)
* [[Documentation/Nightly/Modules/Segmentations|Segmentations]] (loadable, built-in)
* [[Documentation/Nightly/Modules/SegmentationSmoothing|SegmentationSmoothing]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerProstate|SlicerProstate]] extension)
* [[Documentation/Nightly/Modules/SegmentCAD|SegmentCAD]] (scripted, bundled in [[Documentation/Nightly/Extensions/OpenCAD|OpenCAD]] extension)
* [[Documentation/Nightly/Modules/SegmentComparison|SegmentComparison]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Modules/SegmentEditor|SegmentEditor]] (scripted, built-in)
* [https://github.com/lassoan/SlicerSegmentEditorExtraEffects SegmentEditorFastMarching] (scripted, bundled in [https://github.com/lassoan/SlicerSegmentEditorExtraEffects SegmentEditorExtraEffects] extension)
* [https://github.com/lassoan/SlicerSegmentEditorExtraEffects SegmentEditorFloodFilling] (scripted, bundled in [https://github.com/lassoan/SlicerSegmentEditorExtraEffects SegmentEditorExtraEffects] extension)
* [https://github.com/lassoan/SlicerSegmentEditorExtraEffects SegmentEditorWatershed] (scripted, bundled in [https://github.com/lassoan/SlicerSegmentEditorExtraEffects SegmentEditorExtraEffects] extension)
* [http://www.chestimagingplatform.org SegmentLungAirways] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org SegmentLungLobes] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Modules/SegmentMorphology|SegmentMorphology]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* SegmentStatistics (scripted, built-in)
* [[Documentation/Nightly/Extensions/Sequences|SequenceBrowser]] (loadable, bundled in [[Documentation/Nightly/Extensions/Sequences|Sequences]] extension)
* [[Documentation/Nightly/Extensions/Sequences|Sequences]] (loadable, bundled in [[Documentation/Nightly/Extensions/Sequences|Sequences]] extension)
* [[Documentation/Nightly/Modules/ShapeQuantifier|ShapeQuantifier]] (scripted, bundled in [[Documentation/Nightly/Extensions/ShapeQuantifier|ShapeQuantifier]] extension)
* [[Documentation/Nightly/Extensions/ShapeQuantifier|ShapeQuantifierCore]] (scripted, bundled in [[Documentation/Nightly/Extensions/ShapeQuantifier|ShapeQuantifier]] extension)
* [[Documentation/Nightly/Extensions/SlicerPathology|ShortCutCore]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerPathology|SlicerPathology]] extension)
* [[Documentation/Nightly/Modules/SimpleFilters|SimpleFilters]] (scripted, built-in)
* [[Documentation/Nightly/Modules/SimpleRegionGrowingSegmentation|SimpleRegionGrowingSegmentation]] (cli, built-in)
* [[Documentation/Nightly/Modules/SkullStripper|SkullStripper]] (cli, bundled in [[Documentation/Nightly/Extensions/SkullStripper|SkullStripper]] extension)
* [[Documentation/Nightly/Modules/SlicerAstroDataProbe|SlicerAstroDataProbe]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Extensions/SlicerPathology|SlicerPathology]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerPathology|SlicerPathology]] extension)
* [[Documentation/Nightly/Modules/SlicerToKiwiExporter|SlicerToKiwiExporter]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerToKiwiExporter|SlicerToKiwiExporter]] extension)
* [[Documentation/Nightly/Extensions/SliceTracker|SliceTracker]] (scripted, bundled in [[Documentation/Nightly/Extensions/SliceTracker|SliceTracker]] extension)
* [[Documentation/Nightly/Extensions/SliceTracker|SliceTrackerRegistration]] (scripted, bundled in [[Documentation/Nightly/Extensions/SliceTracker|SliceTracker]] extension)
* [[Documentation/Nightly/Extensions/SliceTracker|SliceTrackerZFrameRegistration]] (scripted, bundled in [[Documentation/Nightly/Extensions/SliceTracker|SliceTracker]] extension)
* [[Documentation/Nightly/Modules/SobolevSegmenter|SobolevSegmenter]] (cli, bundled in [[Documentation/Nightly/Extensions/SobolevSegmenter|SobolevSegmenter]] extension)
* [[Documentation/Nightly/Extensions/IASEM|SpacingAwareCurvatureDiffusion]] (cli, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)
* [[Documentation/Nightly/Modules/SpinalCurvatureMeasurement|SpinalCurvatureMeasurement]] (scripted, bundled in [[Documentation/Nightly/Extensions/Scoliosis|Scoliosis]] extension)
* [http://www.chestimagingplatform.org SplitLeftLungRightLung] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Modules/SubjectHierarchy|SubjectHierarchy]] (loadable, built-in)
* [[Documentation/Nightly/Modules/SubtractScalarVolumes|SubtractScalarVolumes]] (cli, built-in)
* [[Documentation/Nightly/Modules/SurfaceRegistration|SurfaceRegistration]] (scripted, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)
* [[Documentation/Nightly/Modules/SurfaceToolbox|SurfaceToolbox]] (scripted, built-in)
* [[Documentation/Nightly/Modules/SUVFactorCalculator|SUVFactorCalculator]] (cli, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PETDICOM PETDICOMExtension] extension)
* [[Documentation/Nightly/Modules/SwissSkullStripper|SwissSkullStripper]] (cli, bundled in [[Documentation/Nightly/Extensions/SwissSkullStripper|SwissSkullStripper]] extension)
* [[Documentation/Nightly/Extensions/MarginCalculator|SyntheticRTDose]] (scripted, bundled in [[Documentation/Nightly/Extensions/MarginCalculator|MarginCalculator]] extension)
* [[Documentation/Nightly/Modules/T1Mapping|T1Mapping]] (cli, bundled in [[Documentation/Nightly/Extensions/T1Mapping|T1Mapping]] extension)
* [[Documentation/Nightly/Modules/Tables|Tables]] (loadable, built-in)
* [[Documentation/Nightly/Extensions/TCIABrowser|TCIABrowser]] (scripted, bundled in [[Documentation/Nightly/Extensions/TCIABrowser|TCIABrowser]] extension)
* Terminologies (loadable, built-in)
* [[Documentation/Nightly/Extensions/SlicerIGT|TextureModel]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Modules/ThresholdScalarVolume|ThresholdScalarVolume]] (cli, built-in)
* [[Documentation/Nightly/Extensions/DCMQI|tid1500reader]] (cli, bundled in [[Documentation/Nightly/Extensions/DCMQI|DCMQI]] extension)
* [[Documentation/Nightly/Extensions/DCMQI|tid1500writer]] (cli, bundled in [[Documentation/Nightly/Extensions/DCMQI|DCMQI]] extension)
* [[Documentation/Nightly/Modules/TrackerStabilizer|TrackerStabilizer]] (loadable, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/TrackerStabilizer TrackerStabilizer] extension)
* [[Documentation/Nightly/Modules/TractographyDisplay|TractographyDisplay]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)
* [[Documentation/Nightly/Modules/TractographyInteractiveSeeding|TractographyInteractiveSeeding]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)
* [[Documentation/Nightly/Modules/TractographyLabelMapSeeding|TractographyLabelMapSeeding]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)
* [http://www.chestimagingplatform.org TransferRegionAndTypeIndicesToFromPoints] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Extensions/SlicerIGT|TransformFusion]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Modules/TransformRecorder|TransformRecorder]] (loadable, bundled in [[Documentation/Nightly/Extensions/PerkTutor|PerkTutor]] extension)
* [[Documentation/Nightly/Modules/Transforms|Transforms]] (loadable, built-in)
* [[Documentation/Nightly/Modules/UKFTractography|UKFTractography]] (cli, bundled in [[Documentation/Nightly/Extensions/UKFTractography|UKFTractography]] extension)
* [[Documentation/Nightly/Extensions/SlicerIGT|UltrasoundSnapshots]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Modules/Units|Units]] (loadable, built-in)
* [[Documentation/Nightly/Extensions/SlicerHeart|ValveView]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerHeart|SlicerHeart]] extension)
* VBRAINSDemonWarp (cli, built-in)
* [[Documentation/Nightly/Modules/VectorToScalarVolume|VectorToScalarVolume]] (scripted, built-in)
* [http://slicer.vmtk.org/ VesselnessFiltering] (scripted, bundled in [http://slicer.vmtk.org/ VMTK] extension)
* [[Documentation/Nightly/Extensions/SlicerRT|VffFileReader]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Modules/ViewControllers|ViewControllers]] (loadable, built-in)
* [[Documentation/Nightly/Extensions/SlicerIGT|Viewpoint]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Modules/VirtualReality|VirtualReality]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerVirtualReality|SlicerVirtualReality]] extension)
* [[Documentation/Nightly/Extensions/SliceTracker|VolumeClipToLabel]] (scripted, bundled in [[Documentation/Nightly/Extensions/SliceTracker|SliceTracker]] extension)
* [[Documentation/Nightly/Extensions/VolumeClip|VolumeClipWithModel]] (scripted, bundled in [[Documentation/Nightly/Extensions/VolumeClip|VolumeClip]] extension)
* [[Documentation/Nightly/Extensions/VolumeClip|VolumeClipWithRoi]] (scripted, bundled in [[Documentation/Nightly/Extensions/VolumeClip|VolumeClip]] extension)
* [[Documentation/Nightly/Modules/VolumeRendering|VolumeRendering]] (loadable, built-in)
* [[Documentation/Nightly/Modules/VolumeResliceDriver|VolumeResliceDriver]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Modules/Volumes|Volumes]] (loadable, built-in)
* [[Documentation/Nightly/Modules/VotingBinaryHoleFillingImageFilter|VotingBinaryHoleFillingImageFilter]] (cli, built-in)
* [[Documentation/Nightly/Extensions/SlicerDMRI|VTK_to_DICOMTract]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)
* [https://github.com/Tomnl/Slicer-Wasp Wasp] (scripted, bundled in [https://github.com/Tomnl/Slicer-Wasp Wasp] extension)
* [[Documentation/Nightly/Modules/Watchdog|Watchdog]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Modules/Welcome|Welcome]] (loadable, built-in)
* [[Documentation/Nightly/Extensions/WindowLevelEffect|WindowLevelEffect]] (scripted, bundled in [[Documentation/Nightly/Extensions/WindowLevelEffect|WindowLevelEffect]] extension)
* [[Documentation/Nightly/Modules/WorkflowSegmentation|WorkflowSegmentation]] (loadable, bundled in [[Documentation/Nightly/Extensions/PerkTutor|PerkTutor]] extension)
* [[Documentation/Nightly/Extensions/XNATSlicer|XnatSlicer]] (scripted, bundled in [[Documentation/Nightly/Extensions/XNATSlicer|XNATSlicer]] extension)
* [[Documentation/Nightly/Extensions/SliceTracker|ZFrameCalibration]] (cli, bundled in [[Documentation/Nightly/Extensions/SliceTracker|SliceTracker]] extension)

Documentation/Nightly/ModuleExtensionListing

2018-05-17T16:29:05Z

Davide: /* Astronomy */

__NOTOC__
<noinclude>{{:Documentation/Nightly/ModuleExtensionListing/TOC}}</noinclude>
= Modules by category =
46 categories:
* [[#Modules_by_category_Astronomy|Astronomy]]
* [[#Modules_by_category_Cardiac|Cardiac]]
* [[#Modules_by_category_Cardiac_MRI_Toolkit|Cardiac MRI Toolkit]]
* [[#Modules_by_category_Chest_Imaging_Platform|Chest Imaging Platform]]
** [[#Modules_by_category_Chest_Imaging_Platform_Toolkit|Toolkit]]
*** [[#Modules_by_category_Toolkit_Particles|Particles]]
*** [[#Modules_by_category_Toolkit_Processing|Processing]]
*** [[#Modules_by_category_Toolkit_Quantification|Quantification]]
*** [[#Modules_by_category_Toolkit_Registration|Registration]]
*** [[#Modules_by_category_Toolkit_Segmentation|Segmentation]]
*** [[#Modules_by_category_Toolkit_Utils|Utils]]
* [[#Modules_by_category_CIP|CIP]]
* [[#Modules_by_category_Converters|Converters]]
* [[#Modules_by_category_Developer_Tools|Developer Tools]]
** [[#Modules_by_category_Developer_Tools_DICOM_Plugins|DICOM Plugins]]
** [[#Modules_by_category_Developer_Tools_Editor_Extensions|Editor Extensions]]
** [[#Modules_by_category_Developer_Tools_Matlab|Matlab]]
** [[#Modules_by_category_Developer_Tools_Segment_Editor_Extensions|Segment Editor Extensions]]
** [[#Modules_by_category_Developer_Tools_Utils|Utils]]
* [[#Modules_by_category_Diffusion|Diffusion]]
** [[#Modules_by_category_Diffusion_Diffusion_Data_Conversion|Diffusion Data Conversion]]
** [[#Modules_by_category_Diffusion_Diffusion_Tensor_Images|Diffusion Tensor Images]]
** [[#Modules_by_category_Diffusion_Diffusion_Weighted_Images|Diffusion Weighted Images]]
** [[#Modules_by_category_Diffusion_Import_and_Export|Import and Export]]
** [[#Modules_by_category_Diffusion_Process|Process]]
** [[#Modules_by_category_Diffusion_Quantify|Quantify]]
** [[#Modules_by_category_Diffusion_Tractography|Tractography]]
*** [[#Modules_by_category_Tractography_Region-based|Region-based]]
** [[#Modules_by_category_Diffusion_Utilities|Utilities]]
* [[#Modules_by_category_Editor_Effects|Editor Effects]]
* [[#Modules_by_category_EditorEffect|EditorEffect]]
* [[#Modules_by_category_Endoscopy|Endoscopy]]
* [[#Modules_by_category_Examples|Examples]]
* [[#Modules_by_category_Exporter|Exporter]]
* [[#Modules_by_category_Filter|Filter]]
* [[#Modules_by_category_Filtering|Filtering]]
** [[#Modules_by_category_Filtering_Arithmetic|Arithmetic]]
** [[#Modules_by_category_Filtering_Denoising|Denoising]]
** [[#Modules_by_category_Filtering_Morphology|Morphology]]
* [[#Modules_by_category_IGT|IGT]]
* [[#Modules_by_category_Informatics|Informatics]]
** [[#Modules_by_category_Informatics_Converters|Converters]]
* [[#Modules_by_category_Legacy|Legacy]]
** [[#Modules_by_category_Legacy_Converters|Converters]]
** [[#Modules_by_category_Legacy_Filtering|Filtering]]
** [[#Modules_by_category_Legacy_Registration|Registration]]
** [[#Modules_by_category_Legacy_Work_in_Progress|Work in Progress]]
*** [[#Modules_by_category_Work_in_Progress_Diffusion_Tensor|Diffusion Tensor]]
**** [[#Modules_by_category_Diffusion_Tensor_Test|Test]]
* [[#Modules_by_category_Libraries|Libraries]]
* [[#Modules_by_category_Machine_Learning|Machine Learning]]
* [[#Modules_by_category_Margin_Calculator|Margin Calculator]]
* [[#Modules_by_category_Mesh_Generation|Mesh Generation]]
* [[#Modules_by_category_MeshGeneration|MeshGeneration]]
* [[#Modules_by_category_Microscopy|Microscopy]]
* [[#Modules_by_category_MultiVolume_Support|MultiVolume Support]]
* [[#Modules_by_category_Pathology|Pathology]]
* [[#Modules_by_category_Perk_Tutor|Perk Tutor]]
* [[#Modules_by_category_Plastimatch|Plastimatch]]
** [[#Modules_by_category_Plastimatch_Registration|Registration]]
** [[#Modules_by_category_Plastimatch_Utilities|Utilities]]
* [[#Modules_by_category_Quantification|Quantification]]
** [[#Modules_by_category_Quantification_ChangeQuantification|ChangeQuantification]]
* [[#Modules_by_category_Radiology|Radiology]]
* [[#Modules_by_category_Radiotherapy|Radiotherapy]]
* [[#Modules_by_category_Registration|Registration]]
** [[#Modules_by_category_Registration_CMF_Registration|CMF Registration]]
*** [[#Modules_by_category_CMF_Registration_Voxelbase_Registration|Voxelbase Registration]]
** [[#Modules_by_category_Registration_Label_Registration|Label Registration]]
** [[#Modules_by_category_Registration_Specialized|Specialized]]
* [[#Modules_by_category_Segmentation|Segmentation]]
** [[#Modules_by_category_Segmentation_Specialized|Specialized]]
* [[#Modules_by_category_Sequences|Sequences]]
* [[#Modules_by_category_Slicelets|Slicelets]]
* [[#Modules_by_category_SlicerProstate|SlicerProstate]]
* [[#Modules_by_category_Surface_Models|Surface Models]]
* [[#Modules_by_category_TestCases|TestCases]]
* [[#Modules_by_category_Testing|Testing]]
** [[#Modules_by_category_Testing_IGT_Tests|IGT Tests]]
** [[#Modules_by_category_Testing_SlicerRT_Tests|SlicerRT Tests]]
** [[#Modules_by_category_Testing_TestCases|TestCases]]
* [[#Modules_by_category_Ultrasound|Ultrasound]]
* [[#Modules_by_category_Uncategorized|Uncategorized]]
* [[#Modules_by_category_Utilities|Utilities]]
** [[#Modules_by_category_Utilities_BRAINS|BRAINS]]
* [[#Modules_by_category_Vascular_Modeling_Toolkit|Vascular Modeling Toolkit]]
* [[#Modules_by_category_Virtual_Reality|Virtual Reality]]
* [[#Modules_by_category_Web_System_Tools|Web System Tools]]
* [[#Modules_by_category_Wizards|Wizards]]
* [[#Modules_by_category_XNATSlicer|XNATSlicer]]

== Astronomy ==
* [[Documentation/Nightly/Modules/AstroVolume|AstroVolume]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/AstroReproject|AstroReproject]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/AstroStatistics|AstroStatistics]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/AstroMasking|AstroMasking]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/AstroSmoothing|AstroSmoothing]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/AstroSampleData|AstroSampleData]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/AstroProfiles|AstroProfiles]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/AstroMomentMaps|AstroMomentMaps]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/AstroPVSlice|AstroPVSlice]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/AstroPVDiagram|AstroPVDiagram]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/AstroModeling|AstroModeling]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/AstroWelcome|AstroWelcome]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/SlicerAstroDataProbe|SlicerAstroDataProbe]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)


== Cardiac ==
* [[Documentation/Nightly/Extensions/SlicerHeart|Philips4dUsDicomPatcher]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerHeart|SlicerHeart]] extension)
* [[Documentation/Nightly/Extensions/SlicerHeart|ValveView]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerHeart|SlicerHeart]] extension)

== Cardiac MRI Toolkit ==
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitPVAntrumCut] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitBooleanREMOVEFilter] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [[Documentation/Nightly/Modules/LASegmentationWorkflow|LASegmentationWorkflow]] (scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitRegistrationBRAINSFit] (scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitAutomaticLeftAtrialScar] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitConnectedThresholdFilter] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitWizard] (scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitIsolatedConnectedFilter] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitInhomogeneityCorrection] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitAxialDilate] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [[Documentation/Nightly/Modules/ScarVisualization|ScarVisualization]] (scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitRegistration] (scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitLASegmentationGraphCuts] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)

== Chest Imaging Platform ==
* [http://www.chestimagingplatform.org CIP_MIPViewer] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CIP_BodyComposition] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CIP_InteractiveLobeSegmentation] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CIP_TracheaStentPlanning] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CIP_LesionModel] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org AirwayInspector] (loadable, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CIP_PAARatio] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CIP_CalciumScoring] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CIP_ParenchymaAnalysis] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CIP_ParenchymaSubtypeTraining] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CIP_PointsLabelling] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)

=== Toolkit ===

==== Particles ====
* [http://www.chestimagingplatform.org ExtractParticlesFromChestRegionChestType] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org FilterVesselParticleData] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org RemoveParticlesFromParticlesDataSet] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org PerturbParticles] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org MergeParticleDataSets] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org FilterAirwayParticleData] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org FitLobeSurfaceModelsToParticleData] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ClassifyFissureParticles] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateStenciledLabelMapFromParticles] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org FilterFissureParticleData] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)

==== Processing ====
* [http://www.chestimagingplatform.org ResampleLabelMap] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org RescaleLabelMap] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateMedianFilteredImage] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org LabelMapFromRegionAndTypePoints] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CropLung] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateNLMFilteredImage] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org RemoveChestTypeFromLabelMapUsingParticles] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateAtlasConvexHull] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org RemapLabelMap] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ComputeFissureFeatureVectors] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateLobeSurfaceModels] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org FilterConnectedComponents] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ExtractChestLabelMap] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org PerformMorphological] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ExtractFissureBoundaryFromLobeMap] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org EnhanceFissuresInImage] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GraphCutsOptimization] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateDistanceMapFromLabelMap] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ResampleCT] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ComputeFeatureStrength] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ComputeDistanceMap] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org QualityControl] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateImageSubVolumes] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)

==== Quantification ====
* [http://www.chestimagingplatform.org EvaluateLungLobeSegmentationResults] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GetTransformationKappa] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ReadWriteImageData] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ComputeIntensityStatistics] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ComputeCrossSectionalArea] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateParenchymaPhenotypes] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org LabelParticlesByChestRegionChestType] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GetTransformationSimilarityMetric] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GetTransformationKappa2D] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)

==== Registration ====
*[[:Category:Documentation/Nightly/Modules/Registration|Introduction to Registration]] (by Dominik Meier)
* [http://www.chestimagingplatform.org RegisterLungAtlas] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org RegisterLabelMaps] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org RegisterCT] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)


==== Segmentation ====
* [http://www.chestimagingplatform.org GenerateOtsuLungCast] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org SegmentLungAirways] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org SegmentLungLobes] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GeneratePartialLungLabelMap] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateSimpleLungMask] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org SplitLeftLungRightLung] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateBinaryThinning3D] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateLesionSegmentation] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)

==== Utils ====
* [http://www.chestimagingplatform.org ConvertDicom] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org RegionTypeLocationsToROIVolume] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ReadVTKWriteNRRDs] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateModel] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateOverlayImages] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ExecuteSystemCommand] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GetStructuresInLabelMap] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org FindPatchMatch] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ConvertChestRegionChestTypeToLabelMapValue] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org MaskOutLabelMapStructures] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ReadNRRDsWriteVTK] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ConvertLabelMapValueToChestRegionChestType] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ReadWriteRegionAndTypePoints] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org MergeChestLabelMaps] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ReadVidaWriteCIP] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ReadDicomWriteTags] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org TransferRegionAndTypeIndicesToFromPoints] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)

== CIP ==
* [http://www.chestimagingplatform.org CIP_] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CIP_Common] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)

== Converters ==
* [[Documentation/Nightly/Modules/QuadEdgeSurfaceMesher|QuadEdgeSurfaceMesher]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerProstate|SlicerProstate]] extension)
* [[Documentation/Nightly/Modules/CropVolume|CropVolume]] (loadable, built-in)
* [[Documentation/Nightly/Modules/OrientScalarVolume|OrientScalarVolume]] (cli, built-in)
* [[Documentation/Nightly/Extensions/UKFTractography|ConvertVTK]] (cli, bundled in [[Documentation/Nightly/Extensions/UKFTractography|UKFTractography]] extension)
* [[Documentation/Nightly/Modules/VectorToScalarVolume|VectorToScalarVolume]] (scripted, built-in)
* [[Documentation/Nightly/Modules/CreateDICOMSeries|CreateDICOMSeries]] (cli, built-in)
* [http://www.chestimagingplatform.org ParticlesDisplay] (loadable, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org RegionType] (loadable, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)

== Developer Tools ==
* [[Documentation/Nightly/Modules/Cameras|Cameras]] (loadable, built-in)
* [[Documentation/Nightly/Modules/ExecutionModelTour|ExecutionModelTour]] (cli, built-in)
* [[Documentation/Nightly/Extensions/DebuggingTools|NodeModifiedStatistics]] (scripted, bundled in [[Documentation/Nightly/Extensions/DebuggingTools|DebuggingTools]] extension)
* [[Documentation/Nightly/Extensions/DebuggingTools|PyDevRemoteDebug]] (scripted, bundled in [[Documentation/Nightly/Extensions/DebuggingTools|DebuggingTools]] extension)
* [[Documentation/Nightly/Modules/ExtensionWizard|ExtensionWizard]] (scripted, built-in)
* [[Documentation/Nightly/Extensions/DebuggingTools|NodeInfo]] (scripted, bundled in [[Documentation/Nightly/Extensions/DebuggingTools|DebuggingTools]] extension)
* [[Documentation/Nightly/Modules/ImageMaker|ImageMaker]] (cli, bundled in [[Documentation/Nightly/Extensions/ImageMaker|ImageMaker]] extension)
* [[Documentation/Nightly/Modules/ExtensionStats|ExtensionStats]] (scripted, bundled in [[Documentation/Nightly/Extensions/DeveloperToolsForExtensions|DeveloperToolsForExtensions]] extension)
* [[Documentation/Nightly/Modules/DeveloperToolsForExtensions|DeveloperToolsForExtensions]] (scripted, bundled in [[Documentation/Nightly/Extensions/DeveloperToolsForExtensions|DeveloperToolsForExtensions]] extension)
* [[Documentation/Nightly/Modules/EventBroker|EventBroker]]
* DoubleArrays (loadable, built-in)

=== DICOM Plugins ===
* DICOMParametricMapPlugin
* DicomUltrasoundPlugin
* DICOMSegmentationPlugin
* DICOMSlicerDataBundlePlugin
* DICOMTID1500Plugin
* [[Documentation/Nightly/Modules/DICOMPETSUVPlugin|DICOMPETSUVPlugin]]
* DICOMScalarVolumePlugin
* DICOMDiffusionVolumePlugin
* DICOMLongitudinalPETCTPlugin
* DicomSroImportPlugin
* [[Documentation/Nightly/Modules/DICOMRWVMPlugin|DICOMRWVMPlugin]]
* DicomRtImportExportPlugin
* MultiVolumeImporterPlugin

=== Editor Extensions ===
* [https://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/FastGrowCut FastGrowCutEffect] (scripted, bundled in [https://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/FastGrowCut FastGrowCutEffect] extension)
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter CarreraSliceEffect] (scripted, bundled in [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter CarreraSlice] extension)
* [[Documentation/Nightly/Extensions/SlicerPathology|QuickTCGAEffect]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerPathology|SlicerPathology]] extension)
* [[Documentation/Nightly/Modules/PETTumorSegmentationEffect|PETTumorSegmentationEffect]] (scripted, bundled in [[Documentation/Nightly/Extensions/PETTumorSegmentation|PETTumorSegmentation]] extension)
* [[Documentation/Nightly/Extensions/IASEM|BinaryWatershedEffect]] (scripted, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)
* [[Documentation/Nightly/Extensions/IASEM|DoubleThresholdEffect]] (scripted, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)
* [[Documentation/Nightly/Extensions/SlicerPathology|ShortCutEffect]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerPathology|SlicerPathology]] extension)

=== Matlab ===
* [[Documentation/Nightly/Modules/MatlabModuleGenerator|MatlabModuleGenerator]] (loadable, bundled in [[Documentation/Nightly/Extensions/MatlabBridge|MatlabBridge]] extension)
* [[Documentation/Nightly/Modules/MatlabCommander|MatlabCommander]] (cli, bundled in [[Documentation/Nightly/Extensions/MatlabBridge|MatlabBridge]] extension)

=== Segment Editor Extensions ===
* [[Documentation/Nightly/Extensions/PETTumorSegmentation|SegmentEditorPETTumor]] (scripted, bundled in [[Documentation/Nightly/Extensions/PETTumorSegmentation|PETTumorSegmentation]] extension)

=== Utils ===
* [[Documentation/Nightly/Extensions/SlicerProstate|SlicerProstate]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerProstate|SlicerProstate]] extension)

== Diffusion ==
* [[Documentation/Nightly/Modules/DMRIInstall|DMRIInstall]] (scripted, built-in)

=== Diffusion Data Conversion ===
* DWIConvert (cli, built-in)

=== Diffusion Tensor Images ===
* [[Documentation/Nightly/Extensions/ResampleDTIlogEuclidean|ResampleDTIlogEuclidean]] (cli, bundled in [[Documentation/Nightly/Extensions/ResampleDTIlogEuclidean|ResampleDTIlogEuclidean]] extension)

=== Diffusion Weighted Images ===
* BRAINSDWICleanup (cli, built-in)

=== Import and Export ===
* DWIConvert (cli, built-in)
* [[Documentation/Nightly/Extensions/SlicerDMRI|DICOMTract_to_VTK]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)
* [[Documentation/Nightly/Extensions/SlicerDMRI|VTK_to_DICOMTract]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)

=== Process ===
* [[Documentation/Nightly/Modules/DiffusionWeightedVolumeMasking|DiffusionWeightedVolumeMasking]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)
* [[Documentation/Nightly/Modules/DWIToDTIEstimation|DWIToDTIEstimation]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)

=== Quantify ===
* [[Documentation/Nightly/Modules/DiffusionTensorScalarMeasurements|DiffusionTensorScalarMeasurements]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)
* [[Documentation/Nightly/Modules/FiberTractMeasurements|FiberTractMeasurements]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)

=== Tractography ===
* [[Documentation/Nightly/Modules/TractographyInteractiveSeeding|TractographyInteractiveSeeding]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)
* [[Documentation/Nightly/Modules/TractographyDisplay|TractographyDisplay]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)
* [[Documentation/Nightly/Modules/UKFTractography|UKFTractography]] (cli, bundled in [[Documentation/Nightly/Extensions/UKFTractography|UKFTractography]] extension)

==== Region-based ====
* [[Documentation/Nightly/Modules/TractographyLabelMapSeeding|TractographyLabelMapSeeding]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)
* [[Documentation/Nightly/Modules/FiberBundleLabelSelect|FiberBundleLabelSelect]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)

=== Utilities ===
* BRAINSDWICleanup (cli, built-in)
* [[Documentation/Nightly/Modules/ResampleDTIVolume|ResampleDTIVolume]] (cli, built-in)
* [[Documentation/Nightly/Modules/FiberBundleToLabelMap|FiberBundleToLabelMap]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)
* [[Documentation/Nightly/Modules/ResampleScalarVectorDWIVolume|ResampleScalarVectorDWIVolume]] (cli, built-in)
* [[Documentation/Nightly/Extensions/SlicerDMRI|DICOM2FullBrainTractography]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)

== Editor Effects ==
* [[Documentation/Nightly/Extensions/WindowLevelEffect|WindowLevelEffect]] (scripted, bundled in [[Documentation/Nightly/Extensions/WindowLevelEffect|WindowLevelEffect]] extension)

== EditorEffect ==
* [[Documentation/Nightly/Extensions/PETTumorSegmentation|PETTumorSegmentation]] (loadable, bundled in [[Documentation/Nightly/Extensions/PETTumorSegmentation|PETTumorSegmentation]] extension)

== Endoscopy ==
* [[Documentation/Nightly/Modules/Endoscopy|Endoscopy]] (scripted, built-in)

== Examples ==
* [[Documentation/Nightly/Modules/FastGrowCut|FastGrowCut]] (loadable, bundled in [https://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/FastGrowCut FastGrowCutEffect] extension)
* [[Documentation/Nightly/Extensions/SlicerPathology|QuickTCGA]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerPathology|SlicerPathology]] extension)
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter FastGrowCutSegmenter] (loadable, bundled in [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter CarreraSlice] extension)
* [[Documentation/Nightly/Extensions/SlicerPathology|ShortCutCore]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerPathology|SlicerPathology]] extension)
* [http://publish.uwo.ca/~dchen285/GraphCutSegment/GraphCutSegment.html GraphCutInteractiveSegmenter] (loadable, bundled in [http://publish.uwo.ca/~dchen285/GraphCutSegment/GraphCutSegment.html GraphCutSegment] extension)
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter CarreraSlice] (loadable, bundled in [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter CarreraSlice] extension)

== Exporter ==
* [[Documentation/Nightly/Modules/SlicerToKiwiExporter|SlicerToKiwiExporter]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerToKiwiExporter|SlicerToKiwiExporter]] extension)

== Filter ==
* IslandRemoval (cli, built-in)

== Filtering ==
* [[Documentation/Nightly/Modules/SegmentationSmoothing|SegmentationSmoothing]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerProstate|SlicerProstate]] extension)
* [[Documentation/Nightly/Modules/N4ITKBiasFieldCorrection|N4ITKBiasFieldCorrection]] (cli, built-in)
* [[Documentation/Nightly/Modules/ImageLabelCombine|ImageLabelCombine]] (cli, built-in)
* [[Documentation/Nightly/Modules/VotingBinaryHoleFillingImageFilter|VotingBinaryHoleFillingImageFilter]] (cli, built-in)
* [[Documentation/Nightly/Modules/CheckerBoardFilter|CheckerBoardFilter]] (cli, built-in)
* [[Documentation/Nightly/Modules/AstroSmoothing|AstroSmoothing]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/ExtractSkeleton|ExtractSkeleton]] (cli, built-in)
* [[Documentation/Nightly/Modules/SimpleFilters|SimpleFilters]] (scripted, built-in)
* [[Documentation/Nightly/Modules/ThresholdScalarVolume|ThresholdScalarVolume]] (cli, built-in)
* [[Documentation/Nightly/Modules/HistogramMatching|HistogramMatching]] (cli, built-in)

=== Arithmetic ===
* [[Documentation/Nightly/Modules/MultiplyScalarVolumes|MultiplyScalarVolumes]] (cli, built-in)
* [[Documentation/Nightly/Modules/AddScalarVolumes|AddScalarVolumes]] (cli, built-in)
* [[Documentation/Nightly/Modules/MaskScalarVolume|MaskScalarVolume]] (cli, built-in)
* [[Documentation/Nightly/Modules/SubtractScalarVolumes|SubtractScalarVolumes]] (cli, built-in)
* [[Documentation/Nightly/Modules/CastScalarVolume|CastScalarVolume]] (cli, built-in)
* [[Documentation/Nightly/Extensions/OpenCVExample|BlendVectorVolumes]] (cli, bundled in [[Documentation/Nightly/Extensions/OpenCVExample|OpenCVExample]] extension)

=== Denoising ===
* [[Documentation/Nightly/Modules/CurvatureAnisotropicDiffusion|CurvatureAnisotropicDiffusion]] (cli, built-in)
* [[Documentation/Nightly/Modules/GradientAnisotropicDiffusion|GradientAnisotropicDiffusion]] (cli, built-in)
* [[Documentation/Nightly/Modules/MedianImageFilter|MedianImageFilter]] (cli, built-in)
* [[Documentation/Nightly/Modules/GaussianBlurImageFilter|GaussianBlurImageFilter]] (cli, built-in)

=== Morphology ===
* [[Documentation/Nightly/Modules/GrayscaleFillHoleImageFilter|GrayscaleFillHoleImageFilter]] (cli, built-in)
* [[Documentation/Nightly/Modules/GrayscaleGrindPeakImageFilter|GrayscaleGrindPeakImageFilter]] (cli, built-in)

== IGT ==
* [[Documentation/Nightly/Extensions/SlicerIGT|Viewpoint]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Modules/CollectFiducials|CollectFiducials]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Extensions/SlicerIGT|TransformFusion]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Modules/GyroGuide|GyroGuide]] (scripted, bundled in [[Documentation/Nightly/Extensions/GyroGuide|GyroGuide]] extension)
* [[Documentation/Nightly/Extensions/SlicerIGT|PlusModelCatalogBrowser]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Extensions/SlicerIGT|CreateModels]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Extensions/NeedleFinder|NeedleFinder]] (scripted, bundled in [[Documentation/Nightly/Extensions/NeedleFinder|NeedleFinder]] extension)
* [[Documentation/Nightly/Modules/TrackerStabilizer|TrackerStabilizer]] (loadable, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/TrackerStabilizer TrackerStabilizer] extension)
* [[Documentation/Nightly/Modules/PathExplorer|PathExplorer]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Extensions/SlicerIGT|UltrasoundSnapshots]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Extensions/SlicerIGT|BreachWarning]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Extensions/SlicerIGT|FiducialRegistrationWizard]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Extensions/SlicerIGT|ModelRegistration]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Modules/ResectionVolume|ResectionVolume]] (scripted, bundled in [[Documentation/Nightly/Extensions/ResectionPlanner|ResectionPlanner]] extension)
* [[Documentation/Nightly/Extensions/SlicerIGT|PivotCalibration]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Modules/VolumeResliceDriver|VolumeResliceDriver]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Modules/OpenIGTLinkRemote|OpenIGTLinkRemote]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Extensions/SlicerIGT|FiducialsToModelRegistration]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Modules/Watchdog|Watchdog]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Modules/CornerAnnotation|CornerAnnotation]] (scripted, bundled in [[Documentation/Nightly/Extensions/CornerAnnotation|CornerAnnotation]] extension)
* [[Documentation/Nightly/Modules/OpenIGTLinkIF|OpenIGTLinkIF]] (loadable, built-in)
* [[Documentation/Nightly/Extensions/SlicerIGT|MarkupsToModel]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Extensions/iGyne|iGyne]] (scripted, bundled in [[Documentation/Nightly/Extensions/iGyne|iGyne]] extension)
* [[Documentation/Nightly/Modules/PlusRemote|PlusRemote]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)

== Informatics ==
* [[Documentation/Nightly/Extensions/DCMQI|tid1500writer]] (cli, bundled in [[Documentation/Nightly/Extensions/DCMQI|DCMQI]] extension)
* [[Documentation/Nightly/Extensions/mpReview|mpReviewPreprocessor]] (scripted, bundled in [[Documentation/Nightly/Extensions/mpReview|mpReview]] extension)
* [[Documentation/Nightly/Modules/SEG2NRRD|SEG2NRRD]] (cli)
* [[Documentation/Nightly/Extensions/TCIABrowser|TCIABrowser]] (scripted, bundled in [[Documentation/Nightly/Extensions/TCIABrowser|TCIABrowser]] extension)
* [[Documentation/Nightly/Extensions/DCMQI|segimage2itkimage]] (cli, bundled in [[Documentation/Nightly/Extensions/DCMQI|DCMQI]] extension)
* [[Documentation/Nightly/Extensions/mpReview|mpReview]] (scripted, bundled in [[Documentation/Nightly/Extensions/mpReview|mpReview]] extension)
* [[Documentation/Nightly/Modules/Tables|Tables]] (loadable, built-in)
* [[Documentation/Nightly/Modules/Data|Data]] (loadable, built-in)
* DumpSEGFrame (cli)
* [[Documentation/Nightly/Extensions/DCMQI|tid1500reader]] (cli, bundled in [[Documentation/Nightly/Extensions/DCMQI|DCMQI]] extension)
* Terminologies (loadable, built-in)
* [[Documentation/Nightly/Modules/Units|Units]] (loadable, built-in)
* [[Documentation/Nightly/Modules/DICOM|DICOM]] (scripted, built-in)
* [[Documentation/Nightly/Modules/SampleData|SampleData]] (scripted, built-in)
* [[Documentation/Nightly/Modules/Colors|Colors]] (loadable, built-in)
* [[Documentation/Nightly/Extensions/CurveMaker|CurveMaker]] (scripted, bundled in [[Documentation/Nightly/Extensions/CurveMaker|CurveMaker]] extension)
* [[Documentation/Nightly/Modules/Annotations|Annotations]] (loadable, built-in)
* [[Documentation/Nightly/Modules/Markups|Markups]] (loadable, built-in)
* [[Documentation/Nightly/Modules/SubjectHierarchy|SubjectHierarchy]] (loadable, built-in)
* [[Documentation/Nightly/Extensions/QuantitativeReporting|QuantitativeReporting]] (scripted, bundled in [[Documentation/Nightly/Extensions/QuantitativeReporting|QuantitativeReporting]] extension)

=== Converters ===
* [[Documentation/Nightly/Extensions/DCMQI|itkimage2paramap]] (cli, bundled in [[Documentation/Nightly/Extensions/DCMQI|DCMQI]] extension)
* [[Documentation/Nightly/Extensions/DCMQI|paramap2itkimage]] (cli, bundled in [[Documentation/Nightly/Extensions/DCMQI|DCMQI]] extension)
* [[Documentation/Nightly/Extensions/DCMQI|itkimage2segimage]] (cli, bundled in [[Documentation/Nightly/Extensions/DCMQI|DCMQI]] extension)
* [[Documentation/Nightly/Modules/EncodeSEG|EncodeSEG]] (cli)

== Legacy ==

=== Converters ===
* [[Documentation/Nightly/Modules/BSplineToDeformationField|BSplineToDeformationField]] (cli, built-in)

=== Filtering ===
* [[Documentation/Nightly/Modules/OtsuThresholdImageFilter|OtsuThresholdImageFilter]] (cli, built-in)
* [[Documentation/Nightly/Modules/ResampleScalarVolume|ResampleScalarVolume]] (cli, built-in)

=== Registration ===
* TestGridTransformRegistration (cli, built-in)
* [[Documentation/Nightly/Modules/ExpertAutomatedRegistration|ExpertAutomatedRegistration]] (cli, built-in)

=== Work in Progress ===

==== Diffusion Tensor ====

===== Test =====
* DiffusionTensorTest (cli, built-in)

== Libraries ==
* [[Documentation/Nightly/Extensions/SlicerOpenCV|OpenCV]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerOpenCV|SlicerOpenCV]] extension)

== Machine Learning ==
* [[Documentation/Nightly/Modules/DeepInfer|DeepInfer]] (scripted, bundled in [[Documentation/Nightly/Extensions/DeepInfer|DeepInfer]] extension)

== Margin Calculator ==
* [[Documentation/Nightly/Extensions/MarginCalculator|MarginCalculator]] (scripted, bundled in [[Documentation/Nightly/Extensions/MarginCalculator|MarginCalculator]] extension)
* [[Documentation/Nightly/Extensions/MarginCalculator|DoseMorphology]] (loadable, bundled in [[Documentation/Nightly/Extensions/MarginCalculator|MarginCalculator]] extension)
* [[Documentation/Nightly/Extensions/MarginCalculator|SyntheticRTDose]] (scripted, bundled in [[Documentation/Nightly/Extensions/MarginCalculator|MarginCalculator]] extension)

== Mesh Generation ==
* [[Documentation/Nightly/Extensions/CleaverExtension|CleaverCLI]] (cli, bundled in [[Documentation/Nightly/Extensions/CleaverExtension|CleaverExtension]] extension)

== MeshGeneration ==
* [[Documentation/Nightly/Modules/BodyCentricCubicMesh|BodyCentricCubicMesh]] (cli, bundled in [[Documentation/Nightly/Extensions/CBC_3D_I2MConversion|CBC_3D_I2MConversion]] extension)

== Microscopy ==
* [[Documentation/Nightly/Extensions/IASEM|IASEMImportSeries]] (cli, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)
* [[Documentation/Nightly/Extensions/IASEM|IASEMImport]] (cli, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)
* [[Documentation/Nightly/Extensions/IASEM|BinShrink]] (cli, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)
* [[Documentation/Nightly/Extensions/IASEM|LabelObjectStatistics]] (scripted, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)
* [[Documentation/Nightly/Extensions/IASEM|SpacingAwareCurvatureDiffusion]] (cli, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)

== MultiVolume Support ==
* [[Documentation/Nightly/Modules/MultiVolumeImporter|MultiVolumeImporter]] (scripted, built-in)
* [[Documentation/Nightly/Modules/MultiVolumeExplorer|MultiVolumeExplorer]] (loadable, built-in)

== Pathology ==
* [[Documentation/Nightly/Extensions/SlicerPathology|SlicerPathology]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerPathology|SlicerPathology]] extension)

== Perk Tutor ==
* [[Documentation/Nightly/Extensions/PerkTutor|PythonMetricsCalculator]] (scripted, bundled in [[Documentation/Nightly/Extensions/PerkTutor|PerkTutor]] extension)
* [[Documentation/Nightly/Modules/TransformRecorder|TransformRecorder]] (loadable, bundled in [[Documentation/Nightly/Extensions/PerkTutor|PerkTutor]] extension)
* [[Documentation/Nightly/Modules/PerkEvaluator|PerkEvaluator]] (loadable, bundled in [[Documentation/Nightly/Extensions/PerkTutor|PerkTutor]] extension)
* [[Documentation/Nightly/Modules/WorkflowSegmentation|WorkflowSegmentation]] (loadable, bundled in [[Documentation/Nightly/Extensions/PerkTutor|PerkTutor]] extension)

== Plastimatch ==
* [[Documentation/Nightly/Modules/DicomSroExport|DicomSroExport]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Extensions/SlicerRT|PlmRegister]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)

=== Registration ===
* [[Documentation/Nightly/Extensions/SlicerRT|plastimatch_slicer_bspline]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Extensions/SlicerRT|plastimatch_slicer_landwarp]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)

=== Utilities ===
* [[Documentation/Nightly/Extensions/SlicerRT|PlastimatchPy]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)

== Quantification ==
* [http://slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DSC_MRI_Analysis DSCMRIAnalysis] (cli, bundled in [http://slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DSC_MRI_Analysis DSCMRIAnalysis] extension)
* [[Documentation/Nightly/Modules/PETLiverUptakeMeasurement|PETLiverUptakeMeasurement]] (cli, bundled in [[Documentation/Nightly/Extensions/PETLiverUptakeMeasurement|PETLiverUptakeMeasurement]] extension)
* [[Documentation/Nightly/Extensions/PET-IndiC|PETIndiC]] (scripted, bundled in [[Documentation/Nightly/Extensions/PET-IndiC|PET-IndiC]] extension)
* [[Documentation/Nightly/Modules/Q3DC|Q3DC]] (scripted, bundled in [[Documentation/Nightly/Extensions/Q3DC|Q3DC]] extension)
* [[Documentation/Nightly/Modules/HeterogeneityCAD|HeterogeneityCAD]] (scripted, bundled in [[Documentation/Nightly/Extensions/OpenCAD|OpenCAD]] extension)
* [[Documentation/Nightly/Modules/ShapeQuantifier|ShapeQuantifier]] (scripted, bundled in [[Documentation/Nightly/Extensions/ShapeQuantifier|ShapeQuantifier]] extension)
* [[Documentation/Nightly/Modules/QuantitativeIndicesCLI|QuantitativeIndicesCLI]] (cli, bundled in [[Documentation/Nightly/Extensions/PET-IndiC|PET-IndiC]] extension)
* [[Documentation/Nightly/Modules/PETStandardUptakeValueComputation|PETStandardUptakeValueComputation]] (cli, built-in)
* [[Documentation/Nightly/Modules/SUVFactorCalculator|SUVFactorCalculator]] (cli, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PETDICOM PETDICOMExtension] extension)
* [[Documentation/Nightly/Modules/SpinalCurvatureMeasurement|SpinalCurvatureMeasurement]] (scripted, bundled in [[Documentation/Nightly/Extensions/Scoliosis|Scoliosis]] extension)
* [[Documentation/Nightly/Modules/QuantitativeIndicesTool|QuantitativeIndicesTool]] (scripted, bundled in [[Documentation/Nightly/Extensions/PET-IndiC|PET-IndiC]] extension)
* SegmentStatistics (scripted, built-in)
* [[Documentation/Nightly/Modules/LabelStatistics|LabelStatistics]] (scripted, built-in)
* [[Documentation/Nightly/Modules/MeshStatistics|MeshStatistics]] (scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/MeshStatistics MeshStatisticsExtension] extension)
* [[Documentation/Nightly/Modules/DWModeling|DWModeling]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerProstate|SlicerProstate]] extension)
* BRAINSLabelStats (cli, built-in)
* [[Documentation/Nightly/Modules/PkModeling|PkModeling]] (cli, bundled in [[Documentation/Nightly/Extensions/PkModeling|PkModeling]] extension)
* [[Documentation/Nightly/Extensions/LongitudinalPETCT|PETSUVImageMaker]] (cli, bundled in [[Documentation/Nightly/Extensions/LongitudinalPETCT|LongitudinalPETCT]] extension)
* [[Documentation/Nightly/Modules/DataProbe|DataProbe]] (scripted, built-in)
* [[Documentation/Nightly/Extensions/ModelToModelDistance|ModelToModelDistance]] (cli, bundled in [[Documentation/Nightly/Extensions/ModelToModelDistance|ModelToModelDistance]] extension)
* [[Documentation/Nightly/Modules/T1Mapping|T1Mapping]] (cli, bundled in [[Documentation/Nightly/Extensions/T1Mapping|T1Mapping]] extension)
* [[Documentation/Nightly/Modules/SlicerAstroDataProbe|SlicerAstroDataProbe]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/AnglePlanes|AnglePlanes]] (scripted, bundled in [[Documentation/Nightly/Extensions/ShapeQuantifier|ShapeQuantifier]] extension)
* [[Documentation/Nightly/Modules/dPetBrainQuantification|dPetBrainQuantification]] (scripted, bundled in [http://gti-fing.github.io/SlicerPetSpectAnalysis PetSpectAnalysis] extension)
* [[Documentation/Nightly/Modules/PickAndPaint|PickAndPaint]] (scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PickAndPaint PickAndPaintExtension] extension)
* [[Documentation/Nightly/Extensions/QuantitativeReporting|QuantitativeReporting]] (scripted, bundled in [[Documentation/Nightly/Extensions/QuantitativeReporting|QuantitativeReporting]] extension)
* [[Documentation/Nightly/Modules/DiceComputation|DiceComputation]] (loadable, bundled in [[Documentation/Nightly/Extensions/DiceComputation|DiceComputation]] extension)

=== ChangeQuantification ===
* [[Documentation/Nightly/Modules/IntensityDifferenceMetric|IntensityDifferenceMetric]] (cli, bundled in [[Documentation/Nightly/Extensions/ChangeTracker|ChangeTracker]] extension)


== Radiology ==
* [[Documentation/Nightly/Extensions/SliceTracker|SliceTracker]] (scripted, bundled in [[Documentation/Nightly/Extensions/SliceTracker|SliceTracker]] extension)
* [[Documentation/Nightly/Extensions/SliceTracker|SliceTrackerRegistration]] (scripted, bundled in [[Documentation/Nightly/Extensions/SliceTracker|SliceTracker]] extension)
* [[Documentation/Nightly/Extensions/SliceTracker|SliceTrackerZFrameRegistration]] (scripted, bundled in [[Documentation/Nightly/Extensions/SliceTracker|SliceTracker]] extension)

== Radiotherapy ==
* [[Documentation/Nightly/Extensions/SlicerRT|Beams]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Extensions/SlicerRT|DvhComparison]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Modules/DoseVolumeHistogram|DoseVolumeHistogram]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Extensions/SlicerRT|DicomRtImportExport]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Modules/DoseAccumulation|DoseAccumulation]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Extensions/SlicerRT|ExternalBeamPlanning]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Modules/SegmentComparison|SegmentComparison]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Extensions/SlicerRT|PlanarImage]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Modules/Isodose|Isodose]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Modules/DoseComparison|DoseComparison]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Modules/SegmentMorphology|SegmentMorphology]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Modules/DicomSroImport|DicomSroImport]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)

== Registration ==
* [[Documentation/Nightly/Modules/Transforms|Transforms]] (loadable, built-in)
* BRAINSResize (cli, built-in)
* PerformMetricTest (cli, built-in)
* [[Documentation/Nightly/Modules/LandmarkRegistration|LandmarkRegistration]] (scripted, built-in)
* [[Documentation/Nightly/Extensions/PBNRR|PBNRR]] (cli, bundled in [[Documentation/Nightly/Extensions/PBNRR|PBNRR]] extension)
* [[Documentation/Nightly/Modules/BRAINSResample|BRAINSResample]] (cli, built-in)
* [[Documentation/Nightly/Modules/BRAINSFit|BRAINSFit]] (cli, built-in)

=== CMF Registration ===
* [[Documentation/Nightly/Extensions/CMFreg|ApplyMatrix]] (cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)
* [[Documentation/Nightly/Modules/LabelExtraction|LabelExtraction]] (cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)
* [[Documentation/Nightly/Modules/LabelAddition|LabelAddition]] (cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)
* [[Documentation/Nightly/Modules/Downsize|Downsize]] (cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)
* [[Documentation/Nightly/Modules/SurfaceRegistration|SurfaceRegistration]] (scripted, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)

==== Voxelbase Registration ====
* [[Documentation/Nightly/Modules/NonGrowing|NonGrowing]] (cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)
* [[Documentation/Nightly/Modules/Growing|Growing]] (cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)
* [[Documentation/Nightly/Modules/MaskCreation|MaskCreation]] (cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)

=== Label Registration ===
* [[Documentation/Nightly/Modules/DistanceMapBasedRegistration|DistanceMapBasedRegistration]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerProstate|SlicerProstate]] extension)

=== Specialized ===
* [[Documentation/Nightly/Modules/ACPCTransform|ACPCTransform]] (cli, built-in)
* [[Documentation/Nightly/Modules/FiducialRegistration|FiducialRegistration]] (cli, built-in)
* [[Documentation/Nightly/Modules/BRAINSDemonWarp|BRAINSDemonWarp]] (cli, built-in)
* [[Documentation/Nightly/Modules/Reformat|Reformat]] (loadable, built-in)
* [[Documentation/Nightly/Extensions/ScatteredTransform|ScatteredTransform]] (cli, bundled in [[Documentation/Nightly/Extensions/ScatteredTransform|ScatteredTransform]] extension)
* VBRAINSDemonWarp (cli, built-in)

== Segmentation ==
* [[Documentation/Nightly/Modules/ROBEXBrainExtraction|ROBEXBrainExtraction]] (cli, bundled in [[Documentation/Nightly/Extensions/ROBEXBrainExtraction|ROBEXBrainExtraction]] extension)
* EMSegmentQuick (loadable, built-in)
* [[Documentation/Nightly/Extensions/VolumeClip|VolumeClipWithModel]] (scripted, bundled in [[Documentation/Nightly/Extensions/VolumeClip|VolumeClip]] extension)
* [http://www.nitrc.org/projects/abc ABC] (cli, bundled in [http://www.nitrc.org/projects/abc ABC] extension)
* [[Documentation/Nightly/Extensions/SliceTracker|VolumeClipToLabel]] (scripted, bundled in [[Documentation/Nightly/Extensions/SliceTracker|SliceTracker]] extension)
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AirwaySegmentation AirwaySegmentationCLI] (cli, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AirwaySegmentation AirwaySegmentation] extension)
* [[Documentation/Nightly/Modules/LAScarSegmenter|LAScarSegmenter]] (cli, bundled in [[Documentation/Nightly/Extensions/LAScarSegmenter|LAScarSegmenter]] extension)
* [[Documentation/Nightly/Modules/SegmentEditor|SegmentEditor]] (scripted, built-in)
* [[Documentation/Nightly/Modules/AirwaySegmentation|AirwaySegmentation]] (scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AirwaySegmentation AirwaySegmentation] extension)
* [[Documentation/Nightly/Modules/SkullStripper|SkullStripper]] (cli, bundled in [[Documentation/Nightly/Extensions/SkullStripper|SkullStripper]] extension)
* [https://github.com/lassoan/SlicerSegmentEditorExtraEffects SegmentEditorFastMarching] (scripted, bundled in [https://github.com/lassoan/SlicerSegmentEditorExtraEffects SegmentEditorExtraEffects] extension)
* [[Documentation/Nightly/Modules/SobolevSegmenter|SobolevSegmenter]] (cli, bundled in [[Documentation/Nightly/Extensions/SobolevSegmenter|SobolevSegmenter]] extension)
* [[Documentation/Nightly/Extensions/VolumeClip|VolumeClipWithRoi]] (scripted, bundled in [[Documentation/Nightly/Extensions/VolumeClip|VolumeClip]] extension)
* [[Documentation/Nightly/Modules/SegmentCAD|SegmentCAD]] (scripted, bundled in [[Documentation/Nightly/Extensions/OpenCAD|OpenCAD]] extension)
* [[Documentation/Nightly/Modules/SwissSkullStripper|SwissSkullStripper]] (cli, bundled in [[Documentation/Nightly/Extensions/SwissSkullStripper|SwissSkullStripper]] extension)
* [https://github.com/lassoan/SlicerSegmentEditorExtraEffects SegmentEditorFloodFilling] (scripted, bundled in [https://github.com/lassoan/SlicerSegmentEditorExtraEffects SegmentEditorExtraEffects] extension)
* [https://github.com/Tomnl/Slicer-Wasp Wasp] (scripted, bundled in [https://github.com/Tomnl/Slicer-Wasp Wasp] extension)
* [[Documentation/Nightly/Modules/Editor|Editor]] (scripted, built-in)
* [[Documentation/Nightly/Modules/SimpleRegionGrowingSegmentation|SimpleRegionGrowingSegmentation]] (cli, built-in)
* [[Documentation/Nightly/Modules/EMSegment|EMSegment]] (loadable, built-in)
* [[Documentation/Nightly/Extensions/QuantitativeReporting|QuantitativeReporting]] (scripted, bundled in [[Documentation/Nightly/Extensions/QuantitativeReporting|QuantitativeReporting]] extension)
* [[Documentation/Nightly/Extensions/IntensitySegmenter|IntensitySegmenter]] (cli, bundled in [[Documentation/Nightly/Extensions/IntensitySegmenter|IntensitySegmenter]] extension)
* [https://github.com/lassoan/SlicerSegmentEditorExtraEffects SegmentEditorWatershed] (scripted, bundled in [https://github.com/lassoan/SlicerSegmentEditorExtraEffects SegmentEditorExtraEffects] extension)

=== Specialized ===
* BRAINSROIAuto (cli, built-in)
* [[Documentation/Nightly/Modules/RobustStatisticsSegmenter|RobustStatisticsSegmenter]] (cli, built-in)
* EMSegmentCommandLine (cli, built-in)

== Sequences ==
* [[Documentation/Nightly/Extensions/Sequences|Sequences]] (loadable, bundled in [[Documentation/Nightly/Extensions/Sequences|Sequences]] extension)
* [[Documentation/Nightly/Extensions/Sequences|SequenceBrowser]] (loadable, bundled in [[Documentation/Nightly/Extensions/Sequences|Sequences]] extension)
* [[Documentation/Nightly/Extensions/Sequences|MetafileImporter]] (loadable, bundled in [[Documentation/Nightly/Extensions/Sequences|Sequences]] extension)

== Slicelets ==
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/FilmDosimetry FilmDosimetryAnalysis] (scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/FilmDosimetry FilmDosimetryAnalysis] extension)
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry GelDosimetryAnalysis] (scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry GelDosimetryAnalysis] extension)
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry GelDosimetryAnalysisAlgo] (loadable, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry GelDosimetryAnalysis] extension)

== SlicerProstate ==
* [[Documentation/Nightly/Extensions/SliceTracker|ZFrameCalibration]] (cli, bundled in [[Documentation/Nightly/Extensions/SliceTracker|SliceTracker]] extension)

== Surface Models ==
* [[Documentation/Nightly/Modules/SurfaceToolbox|SurfaceToolbox]] (scripted, built-in)
* [[Documentation/Nightly/Modules/GrayscaleModelMaker|GrayscaleModelMaker]] (cli, built-in)
* [[Documentation/Nightly/Modules/ModelMaker|ModelMaker]] (cli, built-in)
* [[Documentation/Nightly/Modules/ModelToLabelMap|ModelToLabelMap]] (cli, built-in)
* [[Documentation/Nightly/Modules/MergeModels|MergeModels]] (cli, built-in)
* [[Documentation/Nightly/Modules/EasyClip|EasyClip]] (scripted, bundled in [[Documentation/Nightly/Extensions/EasyClip|EasyClip]] extension)
* [[Documentation/Nightly/Modules/LabelMapSmoothing|LabelMapSmoothing]] (cli, built-in)
* [[Documentation/Nightly/Extensions/MeshToLabelMap|MeshToLabelMap]] (cli, bundled in [[Documentation/Nightly/Extensions/MeshToLabelMap|MeshToLabelMap]] extension)
* [[Documentation/Nightly/Modules/ProbeVolumeWithModel|ProbeVolumeWithModel]] (cli, built-in)
* [[Documentation/Nightly/Extensions/SlicerIGT|TextureModel]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)

== TestCases ==
* SEGExporterSelfTest

== Testing ==
* CLI4Test
* ThresholdThreadingTest
* [[Documentation/Nightly/Extensions/Scoliosis|ScoliosisMonitoring]] (scripted, bundled in [[Documentation/Nightly/Extensions/Scoliosis|Scoliosis]] extension)
* SlicerMRBSaveRestoreCheckPathsTest
* CLIROITest (cli, built-in)
* PerformanceTests
* SlicerMRBMultipleSaveRestoreTest
* SlicerMRBTest
* SEGExporterSelfTest
* SelfTests
* SlicerMRBMultipleSaveRestoreLoopTest

=== IGT Tests ===
* BreachWarningSelfTest
* WatchdogSelfTest

=== SlicerRT Tests ===
* IGRTWorkflow_SelfTest
* [[Documentation/Nightly/Extensions/SlicerRT|BatchStructureSetConversion]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)

=== TestCases ===
* AtlasTests
* AddStorableDataAfterSceneViewTest
* test_tractography_display
* SlicerTransformInteractionTest1
* RSNAQuantTutorial
* NeurosurgicalPlanningTutorialMarkupsSelfTest
* ChangeTrackerSelfTest
* FiducialLayoutSwitchBug1914
* GraphCutSegmentSelfTest
* SlicerBoundsTest
* UtilTest
* Charting (scripted, built-in)
* [http://brainsia.github.io/CardiacAgatstonMeasures/ CardiacAgatstonMeasures] (scripted, bundled in [http://brainsia.github.io/CardiacAgatstonMeasures/ CardiacAgatstonMeasures] extension)
* fiber_visibility_crash2438
* RSNAVisTutorial
* JRC2013Vis
* AddManyMarkupsFiducialTest
* CropVolumeSelfTest
* SliceLinkLogic (scripted, built-in)
* VolumeRenderingSceneClose (scripted, built-in)
* slicerCloseCrashBug2590
* CLIEventTest
* [[Documentation/Nightly/Extensions/SlicerDMRI|NsgPlanTracto]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)
* MarkupsWidgetsSelfTest
* TablesSelfTest
* SlicerOrientationSelectorTest
* MarkupsInViewsSelfTest
* TwoCLIsInParallelTest
* SubjectHierarchyCorePluginsSelfTest
* SubjectHierarchyGenericSelfTest
* ScenePerformance (scripted, built-in)
* MarkupsInCompareViewersSelfTest
* sceneImport2428
* RSNA2012ProstateDemo
* DTINotReproducibleIssue3977
* TwoCLIsInARowTest
* ColorsScalarBarSelfTest
* BRAINSFitRigidRegistrationCrashIssue4139
* Slicer4Minute (scripted, built-in)
* ViewControllersSliceInterpolationBug1926

== Ultrasound ==
* [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ ScanConvertCurvilinearArray] (cli, bundled in [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ SlicerITKUltrasound] extension)
* [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ ScanConvertPhasedArray3D] (cli, bundled in [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ SlicerITKUltrasound] extension)
* [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ ScanConvertSliceSeries] (cli, bundled in [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ SlicerITKUltrasound] extension)

== Uncategorized ==
* [[Documentation/Nightly/Extensions/ShapeQuantifier|ShapeQuantifierCore]] (scripted, bundled in [[Documentation/Nightly/Extensions/ShapeQuantifier|ShapeQuantifier]] extension)
* [[Documentation/Nightly/Extensions/DatabaseInteractor|DatabaseInteractorLib]] (scripted, bundled in [[Documentation/Nightly/Extensions/DatabaseInteractor|DatabaseInteractor]] extension)

== Utilities ==
* [[Documentation/Nightly/Modules/ScreenCapture|ScreenCapture]] (scripted, built-in)
* [[Documentation/Nightly/Modules/DataStore|DataStore]] (loadable, built-in)
* DICOMPatcher (scripted, built-in)
* BRAINSStripRotation (cli, built-in)
* EMSegmentTransformToNewFormat (cli, built-in)

=== BRAINS ===
* BRAINSTransformConvert (cli, built-in)

== Vascular Modeling Toolkit ==
* [http://slicer.vmtk.org/ CenterlineComputation] (scripted, bundled in [http://slicer.vmtk.org/ VMTK] extension)
* [http://slicer.vmtk.org/ LevelSetSegmentation] (scripted, bundled in [http://slicer.vmtk.org/ VMTK] extension)
* [http://slicer.vmtk.org/ VesselnessFiltering] (scripted, bundled in [http://slicer.vmtk.org/ VMTK] extension)

== Virtual Reality ==
* [[Documentation/Nightly/Modules/VirtualReality|VirtualReality]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerVirtualReality|SlicerVirtualReality]] extension)

== Web System Tools ==
* [[Documentation/Nightly/Modules/DatabaseInteractor|DatabaseInteractor]] (scripted, bundled in [[Documentation/Nightly/Extensions/DatabaseInteractor|DatabaseInteractor]] extension)

== Wizards ==
* [[Documentation/Nightly/Modules/CompareVolumes|CompareVolumes]] (scripted, built-in)
* [[Documentation/Nightly/Modules/ChangeTracker|ChangeTracker]] (scripted, bundled in [[Documentation/Nightly/Extensions/ChangeTracker|ChangeTracker]] extension)

== XNATSlicer ==
* [[Documentation/Nightly/Extensions/XNATSlicer|XnatSlicer]] (scripted, bundled in [[Documentation/Nightly/Extensions/XNATSlicer|XNATSlicer]] extension)

= Modules by name =
367 modules:
* [http://www.nitrc.org/projects/abc ABC] (cli, bundled in [http://www.nitrc.org/projects/abc ABC] extension)
* [[Documentation/Nightly/Modules/ACPCTransform|ACPCTransform]] (cli, built-in)
* [[Documentation/Nightly/Modules/AddScalarVolumes|AddScalarVolumes]] (cli, built-in)
* [http://www.chestimagingplatform.org AirwayInspector] (loadable, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Modules/AirwaySegmentation|AirwaySegmentation]] (scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AirwaySegmentation AirwaySegmentation] extension)
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AirwaySegmentation AirwaySegmentationCLI] (cli, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AirwaySegmentation AirwaySegmentation] extension)
* [[Documentation/Nightly/Modules/AnglePlanes|AnglePlanes]] (scripted, bundled in [[Documentation/Nightly/Extensions/ShapeQuantifier|ShapeQuantifier]] extension)
* [[Documentation/Nightly/Modules/Annotations|Annotations]] (loadable, built-in)
* [[Documentation/Nightly/Extensions/CMFreg|ApplyMatrix]] (cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)
* [[Documentation/Nightly/Modules/AstroMasking|AstroMasking]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/AstroModeling|AstroModeling]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/AstroMomentMaps|AstroMomentMaps]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/AstroProfiles|AstroProfiles]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/AstroPVDiagram|AstroPVDiagram]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/AstroPVSlice|AstroPVSlice]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Extensions/SlicerAstro|AstroSampleData]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/AstroSmoothing|AstroSmoothing]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/AstroStatistics|AstroStatistics]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Modules/AstroVolume|AstroVolume]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Extensions/SlicerAstro|AstroWelcome]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Extensions/SlicerRT|Beams]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Extensions/IASEM|BinShrink]] (cli, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)
* [[Documentation/Nightly/Extensions/OpenCVExample|BlendVectorVolumes]] (cli, bundled in [[Documentation/Nightly/Extensions/OpenCVExample|OpenCVExample]] extension)
* [[Documentation/Nightly/Modules/BodyCentricCubicMesh|BodyCentricCubicMesh]] (cli, bundled in [[Documentation/Nightly/Extensions/CBC_3D_I2MConversion|CBC_3D_I2MConversion]] extension)
* [[Documentation/Nightly/Modules/BRAINSDemonWarp|BRAINSDemonWarp]] (cli, built-in)
* BRAINSDWICleanup (cli, built-in)
* [[Documentation/Nightly/Modules/BRAINSFit|BRAINSFit]] (cli, built-in)
* BRAINSLabelStats (cli, built-in)
* [[Documentation/Nightly/Modules/BRAINSResample|BRAINSResample]] (cli, built-in)
* BRAINSResize (cli, built-in)
* BRAINSROIAuto (cli, built-in)
* BRAINSStripRotation (cli, built-in)
* BRAINSTransformConvert (cli, built-in)
* [[Documentation/Nightly/Extensions/SlicerIGT|BreachWarning]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter CarreraSlice] (loadable, bundled in [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter CarreraSlice] extension)
* [[Documentation/Nightly/Modules/CastScalarVolume|CastScalarVolume]] (cli, built-in)
* [http://slicer.vmtk.org/ CenterlineComputation] (scripted, bundled in [http://slicer.vmtk.org/ VMTK] extension)
* [[Documentation/Nightly/Modules/ChangeTracker|ChangeTracker]] (scripted, bundled in [[Documentation/Nightly/Extensions/ChangeTracker|ChangeTracker]] extension)
* [[Documentation/Nightly/Modules/CheckerBoardFilter|CheckerBoardFilter]] (cli, built-in)
* [http://www.chestimagingplatform.org CIP_] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CIP_BodyComposition] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CIP_CalciumScoring] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CIP_Common] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CIP_InteractiveLobeSegmentation] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CIP_LesionModel] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CIP_MIPViewer] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CIP_PAARatio] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CIP_ParenchymaAnalysis] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CIP_ParenchymaSubtypeTraining] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CIP_PointsLabelling] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org CIP_TracheaStentPlanning] (scripted, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ClassifyFissureParticles] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Extensions/CleaverExtension|CleaverCLI]] (cli, bundled in [[Documentation/Nightly/Extensions/CleaverExtension|CleaverExtension]] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitAutomaticLeftAtrialScar] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitAxialDilate] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitBooleanREMOVEFilter] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitConnectedThresholdFilter] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitInhomogeneityCorrection] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitIsolatedConnectedFilter] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitLASegmentationGraphCuts] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitPVAntrumCut] (cli, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitRegistration] (scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitRegistrationBRAINSFit] (scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [http://capulet.med.utah.edu/namic/cmrslicer/ CMRToolkitWizard] (scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [[Documentation/Nightly/Modules/CollectFiducials|CollectFiducials]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Modules/Colors|Colors]] (loadable, built-in)
* [[Documentation/Nightly/Modules/CompareVolumes|CompareVolumes]] (scripted, built-in)
* [http://www.chestimagingplatform.org ComputeCrossSectionalArea] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ComputeDistanceMap] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ComputeFeatureStrength] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ComputeFissureFeatureVectors] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ComputeIntensityStatistics] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ConvertChestRegionChestTypeToLabelMapValue] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ConvertDicom] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ConvertLabelMapValueToChestRegionChestType] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Extensions/UKFTractography|ConvertVTK]] (cli, bundled in [[Documentation/Nightly/Extensions/UKFTractography|UKFTractography]] extension)
* [[Documentation/Nightly/Modules/CornerAnnotation|CornerAnnotation]] (scripted, bundled in [[Documentation/Nightly/Extensions/CornerAnnotation|CornerAnnotation]] extension)
* [[Documentation/Nightly/Modules/CreateDICOMSeries|CreateDICOMSeries]] (cli, built-in)
* [[Documentation/Nightly/Extensions/SlicerIGT|CreateModels]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [http://www.chestimagingplatform.org CropLung] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Modules/CropVolume|CropVolume]] (loadable, built-in)
* [[Documentation/Nightly/Modules/CurvatureAnisotropicDiffusion|CurvatureAnisotropicDiffusion]] (cli, built-in)
* [[Documentation/Nightly/Extensions/CurveMaker|CurveMaker]] (scripted, bundled in [[Documentation/Nightly/Extensions/CurveMaker|CurveMaker]] extension)
* [[Documentation/Nightly/Modules/Data|Data]] (loadable, built-in)
* [[Documentation/Nightly/Modules/DatabaseInteractor|DatabaseInteractor]] (scripted, bundled in [[Documentation/Nightly/Extensions/DatabaseInteractor|DatabaseInteractor]] extension)
* [[Documentation/Nightly/Extensions/DatabaseInteractor|DatabaseInteractorLib]] (scripted, bundled in [[Documentation/Nightly/Extensions/DatabaseInteractor|DatabaseInteractor]] extension)
* [[Documentation/Nightly/Modules/DataProbe|DataProbe]] (scripted, built-in)
* [[Documentation/Nightly/Modules/DataStore|DataStore]] (loadable, built-in)
* [[Documentation/Nightly/Modules/DeepInfer|DeepInfer]] (scripted, bundled in [[Documentation/Nightly/Extensions/DeepInfer|DeepInfer]] extension)
* [[Documentation/Nightly/Modules/DiceComputation|DiceComputation]] (loadable, bundled in [[Documentation/Nightly/Extensions/DiceComputation|DiceComputation]] extension)
* [[Documentation/Nightly/Modules/DICOM|DICOM]] (scripted, built-in)
* [[Documentation/Nightly/Extensions/SlicerDMRI|DICOM2FullBrainTractography]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)
* DICOMPatcher (scripted, built-in)
* [[Documentation/Nightly/Extensions/SlicerRT|DicomRtImportExport]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Modules/DicomSroExport|DicomSroExport]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Modules/DicomSroImport|DicomSroImport]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Extensions/SlicerDMRI|DICOMTract_to_VTK]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)
* [[Documentation/Nightly/Modules/DiffusionTensorScalarMeasurements|DiffusionTensorScalarMeasurements]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)
* [[Documentation/Nightly/Modules/DiffusionWeightedVolumeMasking|DiffusionWeightedVolumeMasking]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)
* [[Documentation/Nightly/Modules/DistanceMapBasedRegistration|DistanceMapBasedRegistration]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerProstate|SlicerProstate]] extension)
* [[Documentation/Nightly/Modules/DMRIInstall|DMRIInstall]] (scripted, built-in)
* [[Documentation/Nightly/Modules/DoseAccumulation|DoseAccumulation]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Modules/DoseComparison|DoseComparison]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Extensions/MarginCalculator|DoseMorphology]] (loadable, bundled in [[Documentation/Nightly/Extensions/MarginCalculator|MarginCalculator]] extension)
* [[Documentation/Nightly/Modules/DoseVolumeHistogram|DoseVolumeHistogram]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Modules/Downsize|Downsize]] (cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)
* [[Documentation/Nightly/Modules/dPetBrainQuantification|dPetBrainQuantification]] (scripted, bundled in [http://gti-fing.github.io/SlicerPetSpectAnalysis PetSpectAnalysis] extension)
* [http://slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DSC_MRI_Analysis DSCMRIAnalysis] (cli, bundled in [http://slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DSC_MRI_Analysis DSCMRIAnalysis] extension)
* DumpSEGFrame (cli)
* [[Documentation/Nightly/Extensions/SlicerRT|DvhComparison]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* DWIConvert (cli, built-in)
* [[Documentation/Nightly/Modules/DWIToDTIEstimation|DWIToDTIEstimation]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)
* [[Documentation/Nightly/Modules/DWModeling|DWModeling]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerProstate|SlicerProstate]] extension)
* [[Documentation/Nightly/Modules/EasyClip|EasyClip]] (scripted, bundled in [[Documentation/Nightly/Extensions/EasyClip|EasyClip]] extension)
* [[Documentation/Nightly/Modules/Editor|Editor]] (scripted, built-in)
* [[Documentation/Nightly/Modules/EMSegment|EMSegment]] (loadable, built-in)
* EMSegmentCommandLine (cli, built-in)
* EMSegmentQuick (loadable, built-in)
* EMSegmentTransformToNewFormat (cli, built-in)
* [[Documentation/Nightly/Modules/EncodeSEG|EncodeSEG]] (cli)
* [[Documentation/Nightly/Modules/Endoscopy|Endoscopy]] (scripted, built-in)
* [http://www.chestimagingplatform.org EnhanceFissuresInImage] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org EvaluateLungLobeSegmentationResults] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ExecuteSystemCommand] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Extensions/SlicerRT|ExternalBeamPlanning]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [http://www.chestimagingplatform.org ExtractChestLabelMap] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ExtractFissureBoundaryFromLobeMap] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ExtractParticlesFromChestRegionChestType] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Modules/ExtractSkeleton|ExtractSkeleton]] (cli, built-in)
* [[Documentation/Nightly/Modules/FastGrowCut|FastGrowCut]] (loadable, bundled in [https://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/FastGrowCut FastGrowCutEffect] extension)
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter FastGrowCutSegmenter] (loadable, bundled in [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter CarreraSlice] extension)
* [[Documentation/Nightly/Modules/FiberBundleLabelSelect|FiberBundleLabelSelect]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)
* [[Documentation/Nightly/Modules/FiberBundleToLabelMap|FiberBundleToLabelMap]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)
* [[Documentation/Nightly/Modules/FiberTractMeasurements|FiberTractMeasurements]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)
* [[Documentation/Nightly/Modules/FiducialRegistration|FiducialRegistration]] (cli, built-in)
* [[Documentation/Nightly/Extensions/SlicerIGT|FiducialRegistrationWizard]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Extensions/SlicerIGT|FiducialsToModelRegistration]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/FilmDosimetry FilmDosimetryAnalysis] (scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/FilmDosimetry FilmDosimetryAnalysis] extension)
* [http://www.chestimagingplatform.org FilterAirwayParticleData] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org FilterConnectedComponents] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org FilterFissureParticleData] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org FilterVesselParticleData] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org FindPatchMatch] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org FitLobeSurfaceModelsToParticleData] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Modules/GaussianBlurImageFilter|GaussianBlurImageFilter]] (cli, built-in)
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry GelDosimetryAnalysis] (scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry GelDosimetryAnalysis] extension)
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry GelDosimetryAnalysisAlgo] (loadable, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry GelDosimetryAnalysis] extension)
* [http://www.chestimagingplatform.org GenerateAtlasConvexHull] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateBinaryThinning3D] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateDistanceMapFromLabelMap] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateImageSubVolumes] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateLesionSegmentation] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateLobeSurfaceModels] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateMedianFilteredImage] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateModel] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateNLMFilteredImage] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateOtsuLungCast] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateOverlayImages] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateParenchymaPhenotypes] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GeneratePartialLungLabelMap] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateSimpleLungMask] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GenerateStenciledLabelMapFromParticles] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GetStructuresInLabelMap] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GetTransformationKappa] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GetTransformationKappa2D] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org GetTransformationSimilarityMetric] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Modules/GradientAnisotropicDiffusion|GradientAnisotropicDiffusion]] (cli, built-in)
* [http://publish.uwo.ca/~dchen285/GraphCutSegment/GraphCutSegment.html GraphCutInteractiveSegmenter] (loadable, bundled in [http://publish.uwo.ca/~dchen285/GraphCutSegment/GraphCutSegment.html GraphCutSegment] extension)
* [http://www.chestimagingplatform.org GraphCutsOptimization] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Modules/GrayscaleFillHoleImageFilter|GrayscaleFillHoleImageFilter]] (cli, built-in)
* [[Documentation/Nightly/Modules/GrayscaleGrindPeakImageFilter|GrayscaleGrindPeakImageFilter]] (cli, built-in)
* [[Documentation/Nightly/Modules/GrayscaleModelMaker|GrayscaleModelMaker]] (cli, built-in)
* [[Documentation/Nightly/Modules/Growing|Growing]] (cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)
* [[Documentation/Nightly/Modules/GyroGuide|GyroGuide]] (scripted, bundled in [[Documentation/Nightly/Extensions/GyroGuide|GyroGuide]] extension)
* [[Documentation/Nightly/Modules/HeterogeneityCAD|HeterogeneityCAD]] (scripted, bundled in [[Documentation/Nightly/Extensions/OpenCAD|OpenCAD]] extension)
* [[Documentation/Nightly/Modules/HistogramMatching|HistogramMatching]] (cli, built-in)
* [[Documentation/Nightly/Extensions/IASEM|IASEMImport]] (cli, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)
* [[Documentation/Nightly/Extensions/IASEM|IASEMImportSeries]] (cli, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)
* [[Documentation/Nightly/Extensions/iGyne|iGyne]] (scripted, bundled in [[Documentation/Nightly/Extensions/iGyne|iGyne]] extension)
* [[Documentation/Nightly/Modules/ImageLabelCombine|ImageLabelCombine]] (cli, built-in)
* [[Documentation/Nightly/Modules/IntensityDifferenceMetric|IntensityDifferenceMetric]] (cli, bundled in [[Documentation/Nightly/Extensions/ChangeTracker|ChangeTracker]] extension)
* [[Documentation/Nightly/Extensions/IntensitySegmenter|IntensitySegmenter]] (cli, bundled in [[Documentation/Nightly/Extensions/IntensitySegmenter|IntensitySegmenter]] extension)
* IslandRemoval (cli, built-in)
* [[Documentation/Nightly/Modules/Isodose|Isodose]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Extensions/DCMQI|itkimage2paramap]] (cli, bundled in [[Documentation/Nightly/Extensions/DCMQI|DCMQI]] extension)
* [[Documentation/Nightly/Extensions/DCMQI|itkimage2segimage]] (cli, bundled in [[Documentation/Nightly/Extensions/DCMQI|DCMQI]] extension)
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter KUtil] (scripted, bundled in [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter CarreraSlice] extension)
* [[Documentation/Nightly/Modules/LabelAddition|LabelAddition]] (cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)
* [[Documentation/Nightly/Modules/LabelExtraction|LabelExtraction]] (cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)
* [http://www.chestimagingplatform.org LabelMapFromRegionAndTypePoints] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Modules/LabelMapSmoothing|LabelMapSmoothing]] (cli, built-in)
* [[Documentation/Nightly/Extensions/IASEM|LabelObjectStatistics]] (scripted, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)
* [http://www.chestimagingplatform.org LabelParticlesByChestRegionChestType] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Modules/LabelStatistics|LabelStatistics]] (scripted, built-in)
* [[Documentation/Nightly/Modules/LandmarkRegistration|LandmarkRegistration]] (scripted, built-in)
* [[Documentation/Nightly/Modules/LAScarSegmenter|LAScarSegmenter]] (cli, bundled in [[Documentation/Nightly/Extensions/LAScarSegmenter|LAScarSegmenter]] extension)
* [[Documentation/Nightly/Modules/LASegmentationWorkflow|LASegmentationWorkflow]] (scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [http://slicer.vmtk.org/ LevelSetSegmentation] (scripted, bundled in [http://slicer.vmtk.org/ VMTK] extension)
* [[Documentation/Nightly/Extensions/MarginCalculator|MarginCalculator]] (scripted, bundled in [[Documentation/Nightly/Extensions/MarginCalculator|MarginCalculator]] extension)
* [[Documentation/Nightly/Modules/Markups|Markups]] (loadable, built-in)
* [[Documentation/Nightly/Extensions/SlicerIGT|MarkupsToModel]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Modules/MaskCreation|MaskCreation]] (cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)
* [http://www.chestimagingplatform.org MaskOutLabelMapStructures] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Modules/MaskScalarVolume|MaskScalarVolume]] (cli, built-in)
* [[Documentation/Nightly/Modules/MedianImageFilter|MedianImageFilter]] (cli, built-in)
* [http://www.chestimagingplatform.org MergeChestLabelMaps] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Modules/MergeModels|MergeModels]] (cli, built-in)
* [http://www.chestimagingplatform.org MergeParticleDataSets] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Modules/MeshStatistics|MeshStatistics]] (scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/MeshStatistics MeshStatisticsExtension] extension)
* [[Documentation/Nightly/Extensions/MeshToLabelMap|MeshToLabelMap]] (cli, bundled in [[Documentation/Nightly/Extensions/MeshToLabelMap|MeshToLabelMap]] extension)
* [[Documentation/Nightly/Extensions/Sequences|MetafileImporter]] (loadable, bundled in [[Documentation/Nightly/Extensions/Sequences|Sequences]] extension)
* [[Documentation/Nightly/Modules/ModelMaker|ModelMaker]] (cli, built-in)
* [[Documentation/Nightly/Extensions/SlicerIGT|ModelRegistration]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Modules/Models|Models]] (loadable, built-in)
* [[Documentation/Nightly/Modules/ModelToLabelMap|ModelToLabelMap]] (cli, built-in)
* [[Documentation/Nightly/Extensions/ModelToModelDistance|ModelToModelDistance]] (cli, bundled in [[Documentation/Nightly/Extensions/ModelToModelDistance|ModelToModelDistance]] extension)
* [[Documentation/Nightly/Extensions/mpReview|mpReview]] (scripted, bundled in [[Documentation/Nightly/Extensions/mpReview|mpReview]] extension)
* [[Documentation/Nightly/Extensions/mpReview|mpReviewPreprocessor]] (scripted, bundled in [[Documentation/Nightly/Extensions/mpReview|mpReview]] extension)
* [[Documentation/Nightly/Modules/MultiplyScalarVolumes|MultiplyScalarVolumes]] (cli, built-in)
* [[Documentation/Nightly/Modules/MultiVolumeExplorer|MultiVolumeExplorer]] (loadable, built-in)
* [[Documentation/Nightly/Modules/MultiVolumeImporter|MultiVolumeImporter]] (scripted, built-in)
* [[Documentation/Nightly/Modules/N4ITKBiasFieldCorrection|N4ITKBiasFieldCorrection]] (cli, built-in)
* [[Documentation/Nightly/Extensions/NeedleFinder|NeedleFinder]] (scripted, bundled in [[Documentation/Nightly/Extensions/NeedleFinder|NeedleFinder]] extension)
* [[Documentation/Nightly/Modules/NonGrowing|NonGrowing]] (cli, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)
* [[Documentation/Nightly/Extensions/SlicerOpenCV|OpenCV]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerOpenCV|SlicerOpenCV]] extension)
* [[Documentation/Nightly/Modules/OpenIGTLinkIF|OpenIGTLinkIF]] (loadable, built-in)
* [[Documentation/Nightly/Modules/OpenIGTLinkRemote|OpenIGTLinkRemote]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Modules/OrientScalarVolume|OrientScalarVolume]] (cli, built-in)
* [[Documentation/Nightly/Extensions/DCMQI|paramap2itkimage]] (cli, bundled in [[Documentation/Nightly/Extensions/DCMQI|DCMQI]] extension)
* [http://www.chestimagingplatform.org ParticlesDisplay] (loadable, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Modules/PathExplorer|PathExplorer]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Extensions/PBNRR|PBNRR]] (cli, bundled in [[Documentation/Nightly/Extensions/PBNRR|PBNRR]] extension)
* PerformMetricTest (cli, built-in)
* [http://www.chestimagingplatform.org PerformMorphological] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Modules/PerkEvaluator|PerkEvaluator]] (loadable, bundled in [[Documentation/Nightly/Extensions/PerkTutor|PerkTutor]] extension)
* [http://www.chestimagingplatform.org PerturbParticles] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Extensions/PET-IndiC|PETIndiC]] (scripted, bundled in [[Documentation/Nightly/Extensions/PET-IndiC|PET-IndiC]] extension)
* [[Documentation/Nightly/Modules/PETLiverUptakeMeasurement|PETLiverUptakeMeasurement]] (cli, bundled in [[Documentation/Nightly/Extensions/PETLiverUptakeMeasurement|PETLiverUptakeMeasurement]] extension)
* [[Documentation/Nightly/Modules/PETStandardUptakeValueComputation|PETStandardUptakeValueComputation]] (cli, built-in)
* [[Documentation/Nightly/Extensions/LongitudinalPETCT|PETSUVImageMaker]] (cli, bundled in [[Documentation/Nightly/Extensions/LongitudinalPETCT|LongitudinalPETCT]] extension)
* [[Documentation/Nightly/Extensions/PETTumorSegmentation|PETTumorSegmentation]] (loadable, bundled in [[Documentation/Nightly/Extensions/PETTumorSegmentation|PETTumorSegmentation]] extension)
* [[Documentation/Nightly/Extensions/SlicerHeart|Philips4dUsDicomPatcher]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerHeart|SlicerHeart]] extension)
* [[Documentation/Nightly/Modules/PickAndPaint|PickAndPaint]] (scripted, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PickAndPaint PickAndPaintExtension] extension)
* [[Documentation/Nightly/Extensions/SlicerIGT|PivotCalibration]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Modules/PkModeling|PkModeling]] (cli, bundled in [[Documentation/Nightly/Extensions/PkModeling|PkModeling]] extension)
* [[Documentation/Nightly/Extensions/SlicerRT|PlanarImage]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Extensions/SlicerRT|plastimatch_slicer_bspline]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Extensions/SlicerRT|plastimatch_slicer_landwarp]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Extensions/SlicerRT|PlastimatchPy]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Extensions/SlicerRT|PlmRegister]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Extensions/SlicerIGT|PlusModelCatalogBrowser]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Modules/PlusRemote|PlusRemote]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Modules/ProbeVolumeWithModel|ProbeVolumeWithModel]] (cli, built-in)
* [[Documentation/Nightly/Extensions/PerkTutor|PythonMetricsCalculator]] (scripted, bundled in [[Documentation/Nightly/Extensions/PerkTutor|PerkTutor]] extension)
* [[Documentation/Nightly/Modules/Q3DC|Q3DC]] (scripted, bundled in [[Documentation/Nightly/Extensions/Q3DC|Q3DC]] extension)
* [[Documentation/Nightly/Modules/QuadEdgeSurfaceMesher|QuadEdgeSurfaceMesher]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerProstate|SlicerProstate]] extension)
* [http://www.chestimagingplatform.org QualityControl] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Modules/QuantitativeIndicesCLI|QuantitativeIndicesCLI]] (cli, bundled in [[Documentation/Nightly/Extensions/PET-IndiC|PET-IndiC]] extension)
* [[Documentation/Nightly/Modules/QuantitativeIndicesTool|QuantitativeIndicesTool]] (scripted, bundled in [[Documentation/Nightly/Extensions/PET-IndiC|PET-IndiC]] extension)
* [[Documentation/Nightly/Extensions/QuantitativeReporting|QuantitativeReporting]] (scripted, bundled in [[Documentation/Nightly/Extensions/QuantitativeReporting|QuantitativeReporting]] extension)
* [[Documentation/Nightly/Extensions/SlicerPathology|QuickTCGA]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerPathology|SlicerPathology]] extension)
* [http://www.chestimagingplatform.org ReadDicomWriteTags] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ReadNRRDsWriteVTK] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ReadVidaWriteCIP] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ReadVTKWriteNRRDs] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ReadWriteImageData] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ReadWriteRegionAndTypePoints] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Modules/Reformat|Reformat]] (loadable, built-in)
* [http://www.chestimagingplatform.org RegionType] (loadable, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org RegionTypeLocationsToROIVolume] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org RegisterCT] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org RegisterLabelMaps] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org RegisterLungAtlas] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org RemapLabelMap] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org RemoveChestTypeFromLabelMapUsingParticles] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org RemoveParticlesFromParticlesDataSet] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org ResampleCT] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Extensions/ResampleDTIlogEuclidean|ResampleDTIlogEuclidean]] (cli, bundled in [[Documentation/Nightly/Extensions/ResampleDTIlogEuclidean|ResampleDTIlogEuclidean]] extension)
* [[Documentation/Nightly/Modules/ResampleDTIVolume|ResampleDTIVolume]] (cli, built-in)
* [http://www.chestimagingplatform.org ResampleLabelMap] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Modules/ResampleScalarVectorDWIVolume|ResampleScalarVectorDWIVolume]] (cli, built-in)
* [http://www.chestimagingplatform.org RescaleLabelMap] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Modules/ResectionVolume|ResectionVolume]] (scripted, bundled in [[Documentation/Nightly/Extensions/ResectionPlanner|ResectionPlanner]] extension)
* [[Documentation/Nightly/Modules/ROBEXBrainExtraction|ROBEXBrainExtraction]] (cli, bundled in [[Documentation/Nightly/Extensions/ROBEXBrainExtraction|ROBEXBrainExtraction]] extension)
* [[Documentation/Nightly/Modules/RobustStatisticsSegmenter|RobustStatisticsSegmenter]] (cli, built-in)
* [[Documentation/Nightly/Modules/SampleData|SampleData]] (scripted, built-in)
* [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ ScanConvertCurvilinearArray] (cli, bundled in [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ SlicerITKUltrasound] extension)
* [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ ScanConvertPhasedArray3D] (cli, bundled in [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ SlicerITKUltrasound] extension)
* [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ ScanConvertSliceSeries] (cli, bundled in [https://kitwaremedical.github.io/SlicerITKUltrasoundDoc/ SlicerITKUltrasound] extension)
* [[Documentation/Nightly/Modules/ScarVisualization|ScarVisualization]] (scripted, bundled in [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac_MRI_Toolkit] extension)
* [[Documentation/Nightly/Extensions/ScatteredTransform|ScatteredTransform]] (cli, bundled in [[Documentation/Nightly/Extensions/ScatteredTransform|ScatteredTransform]] extension)
* [[Documentation/Nightly/Modules/SceneViews|SceneViews]] (loadable, built-in)
* [[Documentation/Nightly/Modules/ScreenCapture|ScreenCapture]] (scripted, built-in)
* [[Documentation/Nightly/Modules/SEG2NRRD|SEG2NRRD]] (cli)
* [[Documentation/Nightly/Extensions/DCMQI|segimage2itkimage]] (cli, bundled in [[Documentation/Nightly/Extensions/DCMQI|DCMQI]] extension)
* [[Documentation/Nightly/Modules/Segmentations|Segmentations]] (loadable, built-in)
* [[Documentation/Nightly/Modules/SegmentationSmoothing|SegmentationSmoothing]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerProstate|SlicerProstate]] extension)
* [[Documentation/Nightly/Modules/SegmentCAD|SegmentCAD]] (scripted, bundled in [[Documentation/Nightly/Extensions/OpenCAD|OpenCAD]] extension)
* [[Documentation/Nightly/Modules/SegmentComparison|SegmentComparison]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Modules/SegmentEditor|SegmentEditor]] (scripted, built-in)
* [https://github.com/lassoan/SlicerSegmentEditorExtraEffects SegmentEditorFastMarching] (scripted, bundled in [https://github.com/lassoan/SlicerSegmentEditorExtraEffects SegmentEditorExtraEffects] extension)
* [https://github.com/lassoan/SlicerSegmentEditorExtraEffects SegmentEditorFloodFilling] (scripted, bundled in [https://github.com/lassoan/SlicerSegmentEditorExtraEffects SegmentEditorExtraEffects] extension)
* [https://github.com/lassoan/SlicerSegmentEditorExtraEffects SegmentEditorWatershed] (scripted, bundled in [https://github.com/lassoan/SlicerSegmentEditorExtraEffects SegmentEditorExtraEffects] extension)
* [http://www.chestimagingplatform.org SegmentLungAirways] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [http://www.chestimagingplatform.org SegmentLungLobes] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Modules/SegmentMorphology|SegmentMorphology]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* SegmentStatistics (scripted, built-in)
* [[Documentation/Nightly/Extensions/Sequences|SequenceBrowser]] (loadable, bundled in [[Documentation/Nightly/Extensions/Sequences|Sequences]] extension)
* [[Documentation/Nightly/Extensions/Sequences|Sequences]] (loadable, bundled in [[Documentation/Nightly/Extensions/Sequences|Sequences]] extension)
* [[Documentation/Nightly/Modules/ShapeQuantifier|ShapeQuantifier]] (scripted, bundled in [[Documentation/Nightly/Extensions/ShapeQuantifier|ShapeQuantifier]] extension)
* [[Documentation/Nightly/Extensions/ShapeQuantifier|ShapeQuantifierCore]] (scripted, bundled in [[Documentation/Nightly/Extensions/ShapeQuantifier|ShapeQuantifier]] extension)
* [[Documentation/Nightly/Extensions/SlicerPathology|ShortCutCore]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerPathology|SlicerPathology]] extension)
* [[Documentation/Nightly/Modules/SimpleFilters|SimpleFilters]] (scripted, built-in)
* [[Documentation/Nightly/Modules/SimpleRegionGrowingSegmentation|SimpleRegionGrowingSegmentation]] (cli, built-in)
* [[Documentation/Nightly/Modules/SkullStripper|SkullStripper]] (cli, bundled in [[Documentation/Nightly/Extensions/SkullStripper|SkullStripper]] extension)
* [[Documentation/Nightly/Modules/SlicerAstroDataProbe|SlicerAstroDataProbe]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerAstro|SlicerAstro]] extension)
* [[Documentation/Nightly/Extensions/SlicerPathology|SlicerPathology]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerPathology|SlicerPathology]] extension)
* [[Documentation/Nightly/Modules/SlicerToKiwiExporter|SlicerToKiwiExporter]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerToKiwiExporter|SlicerToKiwiExporter]] extension)
* [[Documentation/Nightly/Extensions/SliceTracker|SliceTracker]] (scripted, bundled in [[Documentation/Nightly/Extensions/SliceTracker|SliceTracker]] extension)
* [[Documentation/Nightly/Extensions/SliceTracker|SliceTrackerRegistration]] (scripted, bundled in [[Documentation/Nightly/Extensions/SliceTracker|SliceTracker]] extension)
* [[Documentation/Nightly/Extensions/SliceTracker|SliceTrackerZFrameRegistration]] (scripted, bundled in [[Documentation/Nightly/Extensions/SliceTracker|SliceTracker]] extension)
* [[Documentation/Nightly/Modules/SobolevSegmenter|SobolevSegmenter]] (cli, bundled in [[Documentation/Nightly/Extensions/SobolevSegmenter|SobolevSegmenter]] extension)
* [[Documentation/Nightly/Extensions/IASEM|SpacingAwareCurvatureDiffusion]] (cli, bundled in [[Documentation/Nightly/Extensions/IASEM|IASEM]] extension)
* [[Documentation/Nightly/Modules/SpinalCurvatureMeasurement|SpinalCurvatureMeasurement]] (scripted, bundled in [[Documentation/Nightly/Extensions/Scoliosis|Scoliosis]] extension)
* [http://www.chestimagingplatform.org SplitLeftLungRightLung] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Modules/SubjectHierarchy|SubjectHierarchy]] (loadable, built-in)
* [[Documentation/Nightly/Modules/SubtractScalarVolumes|SubtractScalarVolumes]] (cli, built-in)
* [[Documentation/Nightly/Modules/SurfaceRegistration|SurfaceRegistration]] (scripted, bundled in [[Documentation/Nightly/Extensions/CMFreg|CMFreg]] extension)
* [[Documentation/Nightly/Modules/SurfaceToolbox|SurfaceToolbox]] (scripted, built-in)
* [[Documentation/Nightly/Modules/SUVFactorCalculator|SUVFactorCalculator]] (cli, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PETDICOM PETDICOMExtension] extension)
* [[Documentation/Nightly/Modules/SwissSkullStripper|SwissSkullStripper]] (cli, bundled in [[Documentation/Nightly/Extensions/SwissSkullStripper|SwissSkullStripper]] extension)
* [[Documentation/Nightly/Extensions/MarginCalculator|SyntheticRTDose]] (scripted, bundled in [[Documentation/Nightly/Extensions/MarginCalculator|MarginCalculator]] extension)
* [[Documentation/Nightly/Modules/T1Mapping|T1Mapping]] (cli, bundled in [[Documentation/Nightly/Extensions/T1Mapping|T1Mapping]] extension)
* [[Documentation/Nightly/Modules/Tables|Tables]] (loadable, built-in)
* [[Documentation/Nightly/Extensions/TCIABrowser|TCIABrowser]] (scripted, bundled in [[Documentation/Nightly/Extensions/TCIABrowser|TCIABrowser]] extension)
* Terminologies (loadable, built-in)
* [[Documentation/Nightly/Extensions/SlicerIGT|TextureModel]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Modules/ThresholdScalarVolume|ThresholdScalarVolume]] (cli, built-in)
* [[Documentation/Nightly/Extensions/DCMQI|tid1500reader]] (cli, bundled in [[Documentation/Nightly/Extensions/DCMQI|DCMQI]] extension)
* [[Documentation/Nightly/Extensions/DCMQI|tid1500writer]] (cli, bundled in [[Documentation/Nightly/Extensions/DCMQI|DCMQI]] extension)
* [[Documentation/Nightly/Modules/TrackerStabilizer|TrackerStabilizer]] (loadable, bundled in [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/TrackerStabilizer TrackerStabilizer] extension)
* [[Documentation/Nightly/Modules/TractographyDisplay|TractographyDisplay]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)
* [[Documentation/Nightly/Modules/TractographyInteractiveSeeding|TractographyInteractiveSeeding]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)
* [[Documentation/Nightly/Modules/TractographyLabelMapSeeding|TractographyLabelMapSeeding]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)
* [http://www.chestimagingplatform.org TransferRegionAndTypeIndicesToFromPoints] (cli, bundled in [http://www.chestimagingplatform.org Chest_Imaging_Platform] extension)
* [[Documentation/Nightly/Extensions/SlicerIGT|TransformFusion]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Modules/TransformRecorder|TransformRecorder]] (loadable, bundled in [[Documentation/Nightly/Extensions/PerkTutor|PerkTutor]] extension)
* [[Documentation/Nightly/Modules/Transforms|Transforms]] (loadable, built-in)
* [[Documentation/Nightly/Modules/UKFTractography|UKFTractography]] (cli, bundled in [[Documentation/Nightly/Extensions/UKFTractography|UKFTractography]] extension)
* [[Documentation/Nightly/Extensions/SlicerIGT|UltrasoundSnapshots]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Modules/Units|Units]] (loadable, built-in)
* [[Documentation/Nightly/Extensions/SlicerHeart|ValveView]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerHeart|SlicerHeart]] extension)
* VBRAINSDemonWarp (cli, built-in)
* [[Documentation/Nightly/Modules/VectorToScalarVolume|VectorToScalarVolume]] (scripted, built-in)
* [http://slicer.vmtk.org/ VesselnessFiltering] (scripted, bundled in [http://slicer.vmtk.org/ VMTK] extension)
* [[Documentation/Nightly/Extensions/SlicerRT|VffFileReader]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerRT|SlicerRT]] extension)
* [[Documentation/Nightly/Modules/ViewControllers|ViewControllers]] (loadable, built-in)
* [[Documentation/Nightly/Extensions/SlicerIGT|Viewpoint]] (scripted, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Modules/VirtualReality|VirtualReality]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerVirtualReality|SlicerVirtualReality]] extension)
* [[Documentation/Nightly/Extensions/SliceTracker|VolumeClipToLabel]] (scripted, bundled in [[Documentation/Nightly/Extensions/SliceTracker|SliceTracker]] extension)
* [[Documentation/Nightly/Extensions/VolumeClip|VolumeClipWithModel]] (scripted, bundled in [[Documentation/Nightly/Extensions/VolumeClip|VolumeClip]] extension)
* [[Documentation/Nightly/Extensions/VolumeClip|VolumeClipWithRoi]] (scripted, bundled in [[Documentation/Nightly/Extensions/VolumeClip|VolumeClip]] extension)
* [[Documentation/Nightly/Modules/VolumeRendering|VolumeRendering]] (loadable, built-in)
* [[Documentation/Nightly/Modules/VolumeResliceDriver|VolumeResliceDriver]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Modules/Volumes|Volumes]] (loadable, built-in)
* [[Documentation/Nightly/Modules/VotingBinaryHoleFillingImageFilter|VotingBinaryHoleFillingImageFilter]] (cli, built-in)
* [[Documentation/Nightly/Extensions/SlicerDMRI|VTK_to_DICOMTract]] (cli, bundled in [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension)
* [https://github.com/Tomnl/Slicer-Wasp Wasp] (scripted, bundled in [https://github.com/Tomnl/Slicer-Wasp Wasp] extension)
* [[Documentation/Nightly/Modules/Watchdog|Watchdog]] (loadable, bundled in [[Documentation/Nightly/Extensions/SlicerIGT|SlicerIGT]] extension)
* [[Documentation/Nightly/Modules/Welcome|Welcome]] (loadable, built-in)
* [[Documentation/Nightly/Extensions/WindowLevelEffect|WindowLevelEffect]] (scripted, bundled in [[Documentation/Nightly/Extensions/WindowLevelEffect|WindowLevelEffect]] extension)
* [[Documentation/Nightly/Modules/WorkflowSegmentation|WorkflowSegmentation]] (loadable, bundled in [[Documentation/Nightly/Extensions/PerkTutor|PerkTutor]] extension)
* [[Documentation/Nightly/Extensions/XNATSlicer|XnatSlicer]] (scripted, bundled in [[Documentation/Nightly/Extensions/XNATSlicer|XNATSlicer]] extension)
* [[Documentation/Nightly/Extensions/SliceTracker|ZFrameCalibration]] (cli, bundled in [[Documentation/Nightly/Extensions/SliceTracker|SliceTracker]] extension)

Documentation/Nightly/Modules/AstroReproject

2018-05-17T16:27:59Z

Davide: Created page with "<noinclude>{{documentation/versioncheck}}</noinclude>  {{documentation/{{documentation/version}}/module-header}} <!-- --------------------..."

Documentation/Nightly/Extensions/SlicerAstro

2018-05-17T16:27:21Z

Davide:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:ERCIcon.png|300px|European Research Council]]
[[File:Kapteyn logo1.png|500px|Kapteyn Astronomical Institute]]


{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
Authors: 
Davide Punzo (Kapteyn Astronomical Institute, University of Groningen) 
Thijs van der Hulst (Kapteyn Astronomical Institute, University of Groningen) 
Jos Roerdink (Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen) 

Contributors: 
Jean-Christophe Fillion-Robin (Kitware) 
Steve Pieper (Isomics) 
Andras Lasso (PerkLab, Queen's) 

Acknowledgements: 
This work was supported by the European Research Council under the European Union's Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement nr. 291-531. 

Contacts:
* Davide Punzo, <email>punzodavide@hotmail.it</email>; <email>D.Punzo@astro.rug.nl</email>
* Thijs van der Hulst, <email>J.M.van.der.Hulst@astro.rug.nl</email>
* Jos Roerdink <email>j.b.t.m.roerdink@rug.nl</email>

Source: [https://github.com/Punzo/SlicerAstro] 
License: [http://www.slicer.org/pages/LicenseText Slicer license] 
'''Download/install:''' install 3D Slicer, start 3D Slicer, open the Extension Manager, install the SlicerAstro extension[https://github.com/Punzo/SlicerAstro/wiki].



{{documentation/{{documentation/version}}/extension-section|Extension Description}}
{|

|
[[Image:SlicerAstroIcon1.png|350px]]
|
Upcoming HI (neutral Hydrogen) surveys will deliver large datasets, and automated processing using the full 3-D information (two positional dimensions and one spectral dimension) to find and characterize HI objects is imperative. In this context, visualization is an essential tool for enabling qualitative and quantitative human control on an automated source finding and analysis pipeline. Visual Analytics, the combination of automated data processing and human reasoning, creativity and intuition, supported by interactive visualization, enables flexible and fast interaction with the 3-D data, helping the astronomer to deal with the analysis of complex sources. 3-D visualization, coupled to modeling, provides additional capabilities helping the discovery and analysis of subtle structures in the 3-D domain.

<h3> Objective: general description</h3>
* 1) proper visualization of astronomical data cubes: using data astronomical data formats, such as FITS, and astronomical world coordinates system (WCS);
* 2) generation of Histogram, flux density profiles, moment maps and position-velocity diagrams linked with the 3-D view;
* 3) enabling interactive smoothing in all three dimensions;
* 4) interactive HI data modeling coupled to visualization;
* 5) introduction of the SAMP protocol to enable interoperability with Topcat, and other VO tools and catalogs.

for more info see [https://github.com/Punzo/SlicerAstro/wiki] and [http://arxiv.org/pdf/1505.06976v2.pdf], [https://arxiv.org/pdf/1703.06651].

|
|}


{{documentation/{{documentation/version}}/extension-section|Modules}}
{||

SlicerAstro development focuses on HI datasets. The [[Documentation/{{documentation/version}}/Modules/AstroVolume|Astro Volume]] component is the core module and handles the loading/saving, color functions and WCS corrdinates.

Tutorials and information can be found in the [[Documentation/{{documentation/version}}/Modules/AstroWelcome|Astro Welcome]] module and sample data are available at the [[Documentation/{{documentation/version}}/Modules/AstroSampleData|Astro Sample Data]] module.

We currently provide additional modules with their own interface widgets for user interaction, which are mainly aimed for the analysis of HI data-cubes:

*[[Documentation/{{documentation/version}}/Modules/SlicerAstroDataProbe|SlicerAstro Data Probe]]
*[[Documentation/{{documentation/version}}/Modules/AstroReproject|Astro Reproject]]
*[[Documentation/{{documentation/version}}/Modules/AstroStatistics|Astro Statistics]]
*[[Documentation/{{documentation/version}}/Modules/AstroMasking|Astro Masking]]
*[[Documentation/{{documentation/version}}/Modules/AstroSmoothing|Astro Smoothing]]
*[[Documentation/{{documentation/version}}/Modules/AstroProfiles|Astro Profiles]]
*[[Documentation/{{documentation/version}}/Modules/AstroMomentMaps|Astro Moment Maps]]
*[[Documentation/{{documentation/version}}/Modules/AstroPVSlice|Astro PV Slice]]
*[[Documentation/{{documentation/version}}/Modules/AstroPVDiagram|Astro PV Diagram]]
*[[Documentation/{{documentation/version}}/Modules/AstroModeling|Astro Modeling]]


{{documentation/{{documentation/version}}/extension-section|Use Case: Visualization of HI dataset}}

3D visualization for the inspection and analysis of complex HI source:
A 3D view gives an immediate overview of the coherence along the spatial and velocity dimensions such as tidal tail, gas stripping and filaments.

NOTE: SlicerAstro can potentially enhance also the inspection of other datasets such as mm/submm molecular line data and optical integral field spectroscopic data. The user is welcome to share any idea and feedback in the issue tracker[https://github.com/Punzo/SlicerAstro/issues].
 
[[File:SlicerAstroScreenshot.png| Slicer Astro Screenshot|1000px]]
 


{{documentation/{{documentation/version}}/extension-section|References}}
==How to cite==
Please cite the following paper when referring to SlicerAstro in your publication: 

<pre>
@MISC{SlicerAstro,
author = {{Punzo}, D. and {van der Hulst}, T. and {Roerdink}, J. and {Fillion-Robin}, J.-C.
},
title = "{SlicerAstro: Astronomy (HI) extension for 3D Slicer}",
keywords = {Software },
howpublished = {Astrophysics Source Code Library},
year = 2016,
month = nov,
archivePrefix = "ascl",
eprint = {1611.021},
}
</pre>

<pre>
@ARTICLE{2017A&C....19...45P,
author = {{Punzo}, D. and {van der Hulst}, J.~M. and {Roerdink}, J.~B.~T.~M. and
{Fillion-Robin}, J.~C. and {Yu}, L.},
title = "{SlicerAstro: A 3-D interactive visual analytics tool for HI data}",
journal = {Astronomy and Computing},
archivePrefix = "arXiv",
eprint = {1703.06651},
primaryClass = "astro-ph.IM",
keywords = {Radio lines: galaxies, Scientific visualization, Visual analytics, Agile software development, Object oriented development, Empirical software validation},
year = 2017,
month = apr,
volume = 19,
pages = {45-59},
doi = {10.1016/j.ascom.2017.03.004},
}
</pre>

<pre>
@ARTICLE{2015A&C....12...86P,
author = {{Punzo}, D. and {van der Hulst}, J.~M. and {Roerdink}, J.~B.~T.~M. and {Oosterloo}, T.~A. and {Ramatsoku}, M. and {Verheijen}, M.~A.~W.},
title = "{The role of 3-D interactive visualization in blind surveys of H I in galaxies}",
journal = {Astronomy and Computing},
archivePrefix = "arXiv",
eprint = {1505.06976},
primaryClass = "astro-ph.IM",
keywords = {Radio lines: galaxies, Galaxies: kinematics and dynamics, Surveys, Scientific visualization, Visual analytics},
year = 2015,
month = sep,
volume = 12,
pages = {86-99},
doi = {10.1016/j.ascom.2015.05.004},
}
</pre>


{{documentation/{{documentation/version}}/extension-footer}}

Documentation/Nightly/Modules/AstroReprojection

2018-05-17T16:26:37Z

Davide:

Documentation/Nightly/Modules/AstroReprojection

2018-05-17T16:26:20Z

Davide:

File:AstroReprojectContours.png

2018-05-17T16:25:33Z

Davide:

File:AstroReproject.png

2018-05-17T16:25:17Z

Davide:

Documentation/Nightly/Modules/AstroReprojection

2018-05-17T16:24:57Z

Documentation/Nightly/Modules/AstroVolume

2018-05-17T16:23:06Z

Davide:

Documentation/Nightly/Extensions/SlicerAstro

2018-05-17T16:21:56Z

Davide:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:ERCIcon.png|300px|European Research Council]]
[[File:Kapteyn logo1.png|500px|Kapteyn Astronomical Institute]]


{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
Authors: 
Davide Punzo (Kapteyn Astronomical Institute, University of Groningen) 
Thijs van der Hulst (Kapteyn Astronomical Institute, University of Groningen) 
Jos Roerdink (Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen) 

Contributors: 
Jean-Christophe Fillion-Robin (Kitware) 
Steve Pieper (Isomics) 
Andras Lasso (PerkLab, Queen's) 

Acknowledgements: 
This work was supported by the European Research Council under the European Union's Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement nr. 291-531. 

Contacts:
* Davide Punzo, <email>punzodavide@hotmail.it</email>; <email>D.Punzo@astro.rug.nl</email>
* Thijs van der Hulst, <email>J.M.van.der.Hulst@astro.rug.nl</email>
* Jos Roerdink <email>j.b.t.m.roerdink@rug.nl</email>

Source: [https://github.com/Punzo/SlicerAstro] 
License: [http://www.slicer.org/pages/LicenseText Slicer license] 
'''Download/install:''' install 3D Slicer, start 3D Slicer, open the Extension Manager, install the SlicerAstro extension[https://github.com/Punzo/SlicerAstro/wiki].



{{documentation/{{documentation/version}}/extension-section|Extension Description}}
{|

|
[[Image:SlicerAstroIcon1.png|350px]]
|
Upcoming HI (neutral Hydrogen) surveys will deliver large datasets, and automated processing using the full 3-D information (two positional dimensions and one spectral dimension) to find and characterize HI objects is imperative. In this context, visualization is an essential tool for enabling qualitative and quantitative human control on an automated source finding and analysis pipeline. Visual Analytics, the combination of automated data processing and human reasoning, creativity and intuition, supported by interactive visualization, enables flexible and fast interaction with the 3-D data, helping the astronomer to deal with the analysis of complex sources. 3-D visualization, coupled to modeling, provides additional capabilities helping the discovery and analysis of subtle structures in the 3-D domain.

<h3> Objective: general description</h3>
* 1) proper visualization of astronomical data cubes: using data astronomical data formats, such as FITS, and astronomical world coordinates system (WCS);
* 2) generation of Histogram, flux density profiles, moment maps and position-velocity diagrams linked with the 3-D view;
* 3) enabling interactive smoothing in all three dimensions;
* 4) interactive HI data modeling coupled to visualization;
* 5) introduction of the SAMP protocol to enable interoperability with Topcat, and other VO tools and catalogs.

for more info see [https://github.com/Punzo/SlicerAstro/wiki] and [http://arxiv.org/pdf/1505.06976v2.pdf], [https://arxiv.org/pdf/1703.06651].

|
|}


{{documentation/{{documentation/version}}/extension-section|Modules}}
{||

SlicerAstro development focuses on HI datasets. The [[Documentation/{{documentation/version}}/Modules/AstroVolume|Astro Volume]] component is the core module and handles the loading/saving, color functions and WCS corrdinates.

Tutorials and information can be found in the [[Documentation/{{documentation/version}}/Modules/AstroWelcome|Astro Welcome]] module and sample data are available at the [[Documentation/{{documentation/version}}/Modules/AstroSampleData|Astro Sample Data]] module.

We currently provide additional modules with their own interface widgets for user interaction, which are mainly aimed for the analysis of HI data-cubes:

*[[Documentation/{{documentation/version}}/Modules/SlicerAstroDataProbe|SlicerAstro Data Probe]]
*[[Documentation/{{documentation/version}}/Modules/AstroReprojection|Astro Reprojection]]
*[[Documentation/{{documentation/version}}/Modules/AstroStatistics|Astro Statistics]]
*[[Documentation/{{documentation/version}}/Modules/AstroMasking|Astro Masking]]
*[[Documentation/{{documentation/version}}/Modules/AstroSmoothing|Astro Smoothing]]
*[[Documentation/{{documentation/version}}/Modules/AstroProfiles|Astro Profiles]]
*[[Documentation/{{documentation/version}}/Modules/AstroMomentMaps|Astro Moment Maps]]
*[[Documentation/{{documentation/version}}/Modules/AstroPVSlice|Astro PV Slice]]
*[[Documentation/{{documentation/version}}/Modules/AstroPVDiagram|Astro PV Diagram]]
*[[Documentation/{{documentation/version}}/Modules/AstroModeling|Astro Modeling]]


{{documentation/{{documentation/version}}/extension-section|Use Case: Visualization of HI dataset}}

3D visualization for the inspection and analysis of complex HI source:
A 3D view gives an immediate overview of the coherence along the spatial and velocity dimensions such as tidal tail, gas stripping and filaments.

NOTE: SlicerAstro can potentially enhance also the inspection of other datasets such as mm/submm molecular line data and optical integral field spectroscopic data. The user is welcome to share any idea and feedback in the issue tracker[https://github.com/Punzo/SlicerAstro/issues].
 
[[File:SlicerAstroScreenshot.png| Slicer Astro Screenshot|1000px]]
 


{{documentation/{{documentation/version}}/extension-section|References}}
==How to cite==
Please cite the following paper when referring to SlicerAstro in your publication: 

<pre>
@MISC{SlicerAstro,
author = {{Punzo}, D. and {van der Hulst}, T. and {Roerdink}, J. and {Fillion-Robin}, J.-C.
},
title = "{SlicerAstro: Astronomy (HI) extension for 3D Slicer}",
keywords = {Software },
howpublished = {Astrophysics Source Code Library},
year = 2016,
month = nov,
archivePrefix = "ascl",
eprint = {1611.021},
}
</pre>

<pre>
@ARTICLE{2017A&C....19...45P,
author = {{Punzo}, D. and {van der Hulst}, J.~M. and {Roerdink}, J.~B.~T.~M. and
{Fillion-Robin}, J.~C. and {Yu}, L.},
title = "{SlicerAstro: A 3-D interactive visual analytics tool for HI data}",
journal = {Astronomy and Computing},
archivePrefix = "arXiv",
eprint = {1703.06651},
primaryClass = "astro-ph.IM",
keywords = {Radio lines: galaxies, Scientific visualization, Visual analytics, Agile software development, Object oriented development, Empirical software validation},
year = 2017,
month = apr,
volume = 19,
pages = {45-59},
doi = {10.1016/j.ascom.2017.03.004},
}
</pre>

<pre>
@ARTICLE{2015A&C....12...86P,
author = {{Punzo}, D. and {van der Hulst}, J.~M. and {Roerdink}, J.~B.~T.~M. and {Oosterloo}, T.~A. and {Ramatsoku}, M. and {Verheijen}, M.~A.~W.},
title = "{The role of 3-D interactive visualization in blind surveys of H I in galaxies}",
journal = {Astronomy and Computing},
archivePrefix = "arXiv",
eprint = {1505.06976},
primaryClass = "astro-ph.IM",
keywords = {Radio lines: galaxies, Galaxies: kinematics and dynamics, Surveys, Scientific visualization, Visual analytics},
year = 2015,
month = sep,
volume = 12,
pages = {86-99},
doi = {10.1016/j.ascom.2015.05.004},
}
</pre>


{{documentation/{{documentation/version}}/extension-footer}}

File:AstroMask6.png

2018-03-22T16:17:36Z

Davide: Davide uploaded a new version of File:AstroMask6.png

File:AstroMask6.png

2018-03-22T14:50:04Z

Davide: Davide uploaded a new version of File:AstroMask6.png

File:AstroMask2.png

2018-03-22T14:49:51Z

Davide: Davide uploaded a new version of File:AstroMask2.png

File:AstroPVDiagram.png

2018-03-07T18:34:41Z

Davide: Davide uploaded a new version of File:AstroPVDiagram.png

File:AstroPVDiagram.png

2018-03-07T18:32:57Z

Davide:

Documentation/Nightly/Modules/AstroPVDiagram

2018-03-07T17:56:41Z

Davide:

noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:ERCIcon.png|300px|European Research Council]]
[[File:Kapteyn logo1.png|500px|Kapteyn Astronomical Institute]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Authors: 
Davide Punzo (Kapteyn Astronomical Institute, University of Groningen) 
Thijs van der Hulst (Kapteyn Astronomical Institute, University of Groningen) 

Acknowledgements: 
This work was supported by the European Research Council under the European Union's Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement nr. 291-531. 

Contacts:
* Davide Punzo, <email>punzodavide@hotmail.it</email>; <email>D.Punzo@astro.rug.nl</email>
* Thijs van der Hulst, <email>J.M.van.der.Hulst@astro.rug.nl</email>
[http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerAstro Back to SlicerAstro home]
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
The AstroPVDiagram module generates a Position Velocity (PV) diagram. The user can manually place fiducials in the 3D view or on a moment map in the red 2D view. Such fiducials will be connected and a PV Diagram from this selection will be generated.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}
[[File:AstroPVDiagram.png | 1000px]]




{{documentation/{{documentation/version}}/module-section|References}}
<pre>
@ARTICLE{2017A&C....19...45P,
author = {{Punzo}, D. and {van der Hulst}, J.~M. and {Roerdink}, J.~B.~T.~M. and
{Fillion-Robin}, J.~C. and {Yu}, L.},
title = "{SlicerAstro: A 3-D interactive visual analytics tool for HI data}",
journal = {Astronomy and Computing},
archivePrefix = "arXiv",
eprint = {1703.06651},
primaryClass = "astro-ph.IM",
keywords = {Radio lines: galaxies, Scientific visualization, Visual analytics, Agile software development, Object oriented development, Empirical software validation},
year = 2017,
month = apr,
volume = 19,
pages = {45-59},
doi = {10.1016/j.ascom.2017.03.004},
}
</pre>




{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Modules/AstroPVDiagram

2018-03-07T17:45:49Z

Davide:

noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:ERCIcon.png|300px|European Research Council]]
[[File:Kapteyn logo1.png|500px|Kapteyn Astronomical Institute]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Authors: 
Davide Punzo (Kapteyn Astronomical Institute, University of Groningen) 
Thijs van der Hulst (Kapteyn Astronomical Institute, University of Groningen) 

Acknowledgements: 
This work was supported by the European Research Council under the European Union's Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement nr. 291-531. 

Contacts:
* Davide Punzo, <email>punzodavide@hotmail.it</email>; <email>D.Punzo@astro.rug.nl</email>
* Thijs van der Hulst, <email>J.M.van.der.Hulst@astro.rug.nl</email>
[http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerAstro Back to SlicerAstro home]
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
The AstroPVDiagram module generates a Position Velocity (PV) diagram. The user can manually place fiducials in the 3D view or on a moment map in the red 2D view. Such fiducials will be connected and a PV Diagram from this selection will be generated.


{{documentation/{{documentation/version}}/module-section|Panels and their use}}
working...




{{documentation/{{documentation/version}}/module-section|References}}
<pre>
@ARTICLE{2017A&C....19...45P,
author = {{Punzo}, D. and {van der Hulst}, J.~M. and {Roerdink}, J.~B.~T.~M. and
{Fillion-Robin}, J.~C. and {Yu}, L.},
title = "{SlicerAstro: A 3-D interactive visual analytics tool for HI data}",
journal = {Astronomy and Computing},
archivePrefix = "arXiv",
eprint = {1703.06651},
primaryClass = "astro-ph.IM",
keywords = {Radio lines: galaxies, Scientific visualization, Visual analytics, Agile software development, Object oriented development, Empirical software validation},
year = 2017,
month = apr,
volume = 19,
pages = {45-59},
doi = {10.1016/j.ascom.2017.03.004},
}
</pre>




{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Modules/AstroPVSlice

2018-02-26T18:14:50Z

Davide:

Documentation/Nightly/Modules/AstroPVSlice

2018-02-26T18:13:50Z

Davide:

Documentation/Nightly/Modules/AstroVolume

2018-02-23T16:09:25Z

Davide:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:ERCIcon.png|300px|European Research Council]]
[[File:Kapteyn logo1.png|500px|Kapteyn Astronomical Institute]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Authors: 
Davide Punzo (Kapteyn Astronomical Institute, University of Groningen) 
Thijs van der Hulst (Kapteyn Astronomical Institute, University of Groningen) 
Jos Roerdink (Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen) 

Contributors: 
Jean-Christophe Fillion-Robin (Kitware) 
Steve Pieper (Isomics) 
Andras Lasso (PerkLab, Queen's) 

Acknowledgements: 
This work was supported by the European Research Council under the European Union's Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement nr. 291-531. 

Contacts:
* Davide Punzo, <email>punzodavide@hotmail.it</email>; <email>D.Punzo@astro.rug.nl</email>
* Thijs van der Hulst, <email>J.M.van.der.Hulst@astro.rug.nl</email>
* Jos Roerdink <email>j.b.t.m.roerdink@rug.nl</email>
[http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerAstro Back to SlicerAstro home]
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
The {{documentation/modulename}} can read/write FITS file (astronomical data format) and handle the color function and display of Astro Volumes. 



{{documentation/{{documentation/version}}/module-section|Panels and their use}}
 
<h4>Handling the loading and writing of FITS files</h4> 
[[File:AstroLoading.png|750 px]]

 

<h4> MRML nodes that store the data-cube and the FITS keywords in the 3DSlicer object-tree (Data module) </h4> 

[[File:AstroData.png|500 px]]

 
<h4>The control of the display coordinates</h4> 
[[File:AstroVolumeInformation.png|1000 px]]

 
<h4> The display of Beam information in the XY view </h4> 

[[File:AstroHistogram.png|1000 px]]

 
<h4>The control of the 2D color transfer function</h4> 
[[File:Astro2DColorFunction1.png|1000 px]]
[[File:Astro2DColorFunction2.png|1000 px]]
[[File:Astro2DColorFunction3.png|1000 px]]
[[File:Astro2DColorFunction4.png|1000 px]]

 
<h4> The display of the Astronomical World Coordinate (WCS) and Data Probing for 2D views </h4> 

[[File:Astro2DAxes1.png|1000 px]]

 
<h4> The display of Beam information in the XY view </h4> 

[[File:AstroBeam.png|1000 px]]

 
<h4>The control of the 3D color transfer function</h4> 
[[File:Astro3DColorFunction.png|1000 px]]

 
<h4>Tools to convert mask from FITS files (e.g., generated by SoFiA) into segmentations objects and viceversa</h4> 
[[File:AstroMask2.png|1000 px]]
[[File:AstroMask6.png|1000 px]]



{{documentation/{{documentation/version}}/module-section|Astro segmentation editor effect}}


 
<h4>AstroContours Effect</h4> 
This editor effect can create multiple segmentation (3D contours) of the input volume.
 

[[File:AstroContourEffect.png|1000 px]]

 
 
The Contour Levels can be specified using the following format:
 
 
'FISRT:LAST+SPACING' for linear spacing or 'FISRT:LAST*SPACING' for non linear spacing.
 
 
The levels can also be specified as a list (e.g., 'VALUE1;VALUE2;VALUE3'). In the case of a list, it is possible also to specify for each contour
both the MIN and MAX intensity values of the level (e.g., 'CONTOUR1MIN,CONTOUR1MAX;CONTOUR2MIN,CONTOUR2MAX').
 
 
If the string is preceded by '3DDisplayThreshold', the levels are evaluated in units of the value of 3DDisplayThreshold of the dataset.
 
 
If the Histogram is active in the plot view and a selection is made, by typing the string 'Histogram' will create a segmentation around the selection.
 
 
The contours in SlicerAstro are a full 3D segmentation. Therefore it can be computationally heavy to segment
(marching cubes algorithm) and visualize around the noise range [-2, 2] RMS for large datacubes.
 
 

 
<h4>AstroCloudLasso Effect</h4> 
The AstroCloudLasso segmentation editor effect is a tool to interactively perform a 3D selection.
This 3D selection (the segmentation) can be used either for:

1. changing an imported mask generated by automated algorithms (e.g., source finders); 
2. providing an input mask to a variety of tools in SlicerAstro (e.g., MomentMaps module and Modeling module). 

[[File:AstroMask3.png|1000 px]]
[[File:AstroMask4.png|1000 px]]


{{documentation/{{documentation/version}}/module-section|References}}
<pre>
@ARTICLE{2017A&C....19...45P,
author = {{Punzo}, D. and {van der Hulst}, J.~M. and {Roerdink}, J.~B.~T.~M. and
{Fillion-Robin}, J.~C. and {Yu}, L.},
title = "{SlicerAstro: A 3-D interactive visual analytics tool for HI data}",
journal = {Astronomy and Computing},
archivePrefix = "arXiv",
eprint = {1703.06651},
primaryClass = "astro-ph.IM",
keywords = {Radio lines: galaxies, Scientific visualization, Visual analytics, Agile software development, Object oriented development, Empirical software validation},
year = 2017,
month = apr,
volume = 19,
pages = {45-59},
doi = {10.1016/j.ascom.2017.03.004},
}
</pre>




{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Modules/AstroVolume

2018-02-23T16:08:49Z

Davide:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:ERCIcon.png|300px|European Research Council]]
[[File:Kapteyn logo1.png|500px|Kapteyn Astronomical Institute]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Authors: 
Davide Punzo (Kapteyn Astronomical Institute, University of Groningen) 
Thijs van der Hulst (Kapteyn Astronomical Institute, University of Groningen) 
Jos Roerdink (Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen) 

Contributors: 
Jean-Christophe Fillion-Robin (Kitware) 
Steve Pieper (Isomics) 
Andras Lasso (PerkLab, Queen's) 

Acknowledgements: 
This work was supported by the European Research Council under the European Union's Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement nr. 291-531. 

Contacts:
* Davide Punzo, <email>punzodavide@hotmail.it</email>; <email>D.Punzo@astro.rug.nl</email>
* Thijs van der Hulst, <email>J.M.van.der.Hulst@astro.rug.nl</email>
* Jos Roerdink <email>j.b.t.m.roerdink@rug.nl</email>
[http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerAstro Back to SlicerAstro home]
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
The {{documentation/modulename}} can read/write FITS file (astronomical data format) and handle the color function and display of Astro Volumes. 



{{documentation/{{documentation/version}}/module-section|Panels and their use}}
 
<h4>Handling the loading and writing of FITS files</h4> 
[[File:AstroLoading.png|750 px]]

 

<h4> MRML nodes that store the data-cube and the FITS keywords in the 3DSlicer object-tree (Data module) </h4> 

[[File:AstroData.png|500 px]]

 
<h4>The control of the display coordinates</h4> 
[[File:AstroVolumeInformation.png|1000 px]]

 
<h4> The display of Beam information in the XY view </h4> 

[[File:AstroHistogram.png|1000 px]]

 
<h4>The control of the 2D color transfer function</h4> 
[[File:Astro2DColorFunction1.png|1000 px]]
[[File:Astro2DColorFunction2.png|1000 px]]
[[File:Astro2DColorFunction3.png|1000 px]]
[[File:Astro2DColorFunction4.png|1000 px]]

 
<h4> The display of the Astronomical World Coordinate (WCS) and Data Probing for 2D views </h4> 

[[File:Astro2Daxes1.png|1000 px]]

 
<h4> The display of Beam information in the XY view </h4> 

[[File:AstroBeam.png|1000 px]]

 
<h4>The control of the 3D color transfer function</h4> 
[[File:Astro3DColorFunction.png|1000 px]]

 
<h4>Tools to convert mask from FITS files (e.g., generated by SoFiA) into segmentations objects and viceversa</h4> 
[[File:AstroMask2.png|1000 px]]
[[File:AstroMask6.png|1000 px]]



{{documentation/{{documentation/version}}/module-section|Astro segmentation editor effect}}


 
<h4>AstroContours Effect</h4> 
This editor effect can create multiple segmentation (3D contours) of the input volume.
 

[[File:AstroContourEffect.png|1000 px]]

 
 
The Contour Levels can be specified using the following format:
 
 
'FISRT:LAST+SPACING' for linear spacing or 'FISRT:LAST*SPACING' for non linear spacing.
 
 
The levels can also be specified as a list (e.g., 'VALUE1;VALUE2;VALUE3'). In the case of a list, it is possible also to specify for each contour
both the MIN and MAX intensity values of the level (e.g., 'CONTOUR1MIN,CONTOUR1MAX;CONTOUR2MIN,CONTOUR2MAX').
 
 
If the string is preceded by '3DDisplayThreshold', the levels are evaluated in units of the value of 3DDisplayThreshold of the dataset.
 
 
If the Histogram is active in the plot view and a selection is made, by typing the string 'Histogram' will create a segmentation around the selection.
 
 
The contours in SlicerAstro are a full 3D segmentation. Therefore it can be computationally heavy to segment
(marching cubes algorithm) and visualize around the noise range [-2, 2] RMS for large datacubes.
 
 

 
<h4>AstroCloudLasso Effect</h4> 
The AstroCloudLasso segmentation editor effect is a tool to interactively perform a 3D selection.
This 3D selection (the segmentation) can be used either for:

1. changing an imported mask generated by automated algorithms (e.g., source finders); 
2. providing an input mask to a variety of tools in SlicerAstro (e.g., MomentMaps module and Modeling module). 

[[File:AstroMask3.png|1000 px]]
[[File:AstroMask4.png|1000 px]]


{{documentation/{{documentation/version}}/module-section|References}}
<pre>
@ARTICLE{2017A&C....19...45P,
author = {{Punzo}, D. and {van der Hulst}, J.~M. and {Roerdink}, J.~B.~T.~M. and
{Fillion-Robin}, J.~C. and {Yu}, L.},
title = "{SlicerAstro: A 3-D interactive visual analytics tool for HI data}",
journal = {Astronomy and Computing},
archivePrefix = "arXiv",
eprint = {1703.06651},
primaryClass = "astro-ph.IM",
keywords = {Radio lines: galaxies, Scientific visualization, Visual analytics, Agile software development, Object oriented development, Empirical software validation},
year = 2017,
month = apr,
volume = 19,
pages = {45-59},
doi = {10.1016/j.ascom.2017.03.004},
}
</pre>




{{documentation/{{documentation/version}}/module-footer}}

File:Astro2DAxes1.png

2018-02-23T16:08:33Z

Davide:

Documentation/Nightly/Modules/AstroVolume

2018-02-23T16:08:09Z

Davide:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:ERCIcon.png|300px|European Research Council]]
[[File:Kapteyn logo1.png|500px|Kapteyn Astronomical Institute]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Authors: 
Davide Punzo (Kapteyn Astronomical Institute, University of Groningen) 
Thijs van der Hulst (Kapteyn Astronomical Institute, University of Groningen) 
Jos Roerdink (Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen) 

Contributors: 
Jean-Christophe Fillion-Robin (Kitware) 
Steve Pieper (Isomics) 
Andras Lasso (PerkLab, Queen's) 

Acknowledgements: 
This work was supported by the European Research Council under the European Union's Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement nr. 291-531. 

Contacts:
* Davide Punzo, <email>punzodavide@hotmail.it</email>; <email>D.Punzo@astro.rug.nl</email>
* Thijs van der Hulst, <email>J.M.van.der.Hulst@astro.rug.nl</email>
* Jos Roerdink <email>j.b.t.m.roerdink@rug.nl</email>
[http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerAstro Back to SlicerAstro home]
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
The {{documentation/modulename}} can read/write FITS file (astronomical data format) and handle the color function and display of Astro Volumes. 



{{documentation/{{documentation/version}}/module-section|Panels and their use}}
 
<h4>Handling the loading and writing of FITS files</h4> 
[[File:AstroLoading.png|750 px]]

 

<h4> MRML nodes that store the data-cube and the FITS keywords in the 3DSlicer object-tree (Data module) </h4> 

[[File:AstroData.png|500 px]]

 
<h4>The control of the display coordinates</h4> 
[[File:AstroVolumeInformation.png|1000 px]]

 
<h4> The display of Beam information in the XY view </h4> 

[[File:AstroHistogram.png|1000 px]]

 
<h4>The control of the 2D color transfer function</h4> 
[[File:Astro2DColorFunction1.png|1000 px]]
[[File:Astro2DColorFunction2.png|1000 px]]
[[File:Astro2DColorFunction3.png|1000 px]]
[[File:Astro2DColorFunction4.png|1000 px]]

 
<h4> The display of the Astronomical World Coordinate (WCS) and Data Probing for 2D views </h4> 

[[File:Astro2Daxes.png|1000 px]]

 
<h4> The display of Beam information in the XY view </h4> 

[[File:AstroBeam.png|1000 px]]

 
<h4>The control of the 3D color transfer function</h4> 
[[File:Astro3DColorFunction.png|1000 px]]

 
<h4>Tools to convert mask from FITS files (e.g., generated by SoFiA) into segmentations objects and viceversa</h4> 
[[File:AstroMask2.png|1000 px]]
[[File:AstroMask6.png|1000 px]]



{{documentation/{{documentation/version}}/module-section|Astro segmentation editor effect}}


 
<h4>AstroContours Effect</h4> 
This editor effect can create multiple segmentation (3D contours) of the input volume.
 

[[File:AstroContourEffect.png|1000 px]]

 
 
The Contour Levels can be specified using the following format:
 
 
'FISRT:LAST+SPACING' for linear spacing or 'FISRT:LAST*SPACING' for non linear spacing.
 
 
The levels can also be specified as a list (e.g., 'VALUE1;VALUE2;VALUE3'). In the case of a list, it is possible also to specify for each contour
both the MIN and MAX intensity values of the level (e.g., 'CONTOUR1MIN,CONTOUR1MAX;CONTOUR2MIN,CONTOUR2MAX').
 
 
If the string is preceded by '3DDisplayThreshold', the levels are evaluated in units of the value of 3DDisplayThreshold of the dataset.
 
 
If the Histogram is active in the plot view and a selection is made, by typing the string 'Histogram' will create a segmentation around the selection.
 
 
The contours in SlicerAstro are a full 3D segmentation. Therefore it can be computationally heavy to segment
(marching cubes algorithm) and visualize around the noise range [-2, 2] RMS for large datacubes.
 
 

 
<h4>AstroCloudLasso Effect</h4> 
The AstroCloudLasso segmentation editor effect is a tool to interactively perform a 3D selection.
This 3D selection (the segmentation) can be used either for:

1. changing an imported mask generated by automated algorithms (e.g., source finders); 
2. providing an input mask to a variety of tools in SlicerAstro (e.g., MomentMaps module and Modeling module). 

[[File:AstroMask3.png|1000 px]]
[[File:AstroMask4.png|1000 px]]


{{documentation/{{documentation/version}}/module-section|References}}
<pre>
@ARTICLE{2017A&C....19...45P,
author = {{Punzo}, D. and {van der Hulst}, J.~M. and {Roerdink}, J.~B.~T.~M. and
{Fillion-Robin}, J.~C. and {Yu}, L.},
title = "{SlicerAstro: A 3-D interactive visual analytics tool for HI data}",
journal = {Astronomy and Computing},
archivePrefix = "arXiv",
eprint = {1703.06651},
primaryClass = "astro-ph.IM",
keywords = {Radio lines: galaxies, Scientific visualization, Visual analytics, Agile software development, Object oriented development, Empirical software validation},
year = 2017,
month = apr,
volume = 19,
pages = {45-59},
doi = {10.1016/j.ascom.2017.03.004},
}
</pre>




{{documentation/{{documentation/version}}/module-footer}}

Documentation/Nightly/Modules/AstroVolume

2018-02-23T16:08:00Z

Davide:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[File:ERCIcon.png|300px|European Research Council]]
[[File:Kapteyn logo1.png|500px|Kapteyn Astronomical Institute]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Authors: 
Davide Punzo (Kapteyn Astronomical Institute, University of Groningen) 
Thijs van der Hulst (Kapteyn Astronomical Institute, University of Groningen) 
Jos Roerdink (Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen) 

Contributors: 
Jean-Christophe Fillion-Robin (Kitware) 
Steve Pieper (Isomics) 
Andras Lasso (PerkLab, Queen's) 

Acknowledgements: 
This work was supported by the European Research Council under the European Union's Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement nr. 291-531. 

Contacts:
* Davide Punzo, <email>punzodavide@hotmail.it</email>; <email>D.Punzo@astro.rug.nl</email>
* Thijs van der Hulst, <email>J.M.van.der.Hulst@astro.rug.nl</email>
* Jos Roerdink <email>j.b.t.m.roerdink@rug.nl</email>
[http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerAstro Back to SlicerAstro home]
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
The {{documentation/modulename}} can read/write FITS file (astronomical data format) and handle the color function and display of Astro Volumes. 



{{documentation/{{documentation/version}}/module-section|Panels and their use}}
 
<h4>Handling the loading and writing of FITS files</h4> 
[[File:AstroLoading.png|750 px]]

 

<h4> MRML nodes that store the data-cube and the FITS keywords in the 3DSlicer object-tree (Data module) </h4> 

[[File:AstroData.png|500 px]]

 
<h4>The control of the display coordinates</h4> 
[[File:AstroVolumeInformation.png|1000 px]]

 
<h4> The display of Beam information in the XY view </h4> 

[[File:AstroHistogram.png|1000 px]]

 
<h4>The control of the 2D color transfer function</h4> 
[[File:Astro2DColorFunction1.png|1000 px]]
[[File:Astro2DColorFunction2.png|1000 px]]
[[File:Astro2DColorFunction3.png|1000 px]]
[[File:Astro2DColorFunction4.png|1000 px]]

 
<h4> The display of the Astronomical World Coordinate (WCS) and Data Probing for 2D views </h4> 

 
<h4> The display of Beam information in the XY view </h4> 

[[File:AstroBeam.png|1000 px]]

 
<h4>The control of the 3D color transfer function</h4> 
[[File:Astro3DColorFunction.png|1000 px]]

 
<h4>Tools to convert mask from FITS files (e.g., generated by SoFiA) into segmentations objects and viceversa</h4> 
[[File:AstroMask2.png|1000 px]]
[[File:AstroMask6.png|1000 px]]



{{documentation/{{documentation/version}}/module-section|Astro segmentation editor effect}}


 
<h4>AstroContours Effect</h4> 
This editor effect can create multiple segmentation (3D contours) of the input volume.
 

[[File:AstroContourEffect.png|1000 px]]

 
 
The Contour Levels can be specified using the following format:
 
 
'FISRT:LAST+SPACING' for linear spacing or 'FISRT:LAST*SPACING' for non linear spacing.
 
 
The levels can also be specified as a list (e.g., 'VALUE1;VALUE2;VALUE3'). In the case of a list, it is possible also to specify for each contour
both the MIN and MAX intensity values of the level (e.g., 'CONTOUR1MIN,CONTOUR1MAX;CONTOUR2MIN,CONTOUR2MAX').
 
 
If the string is preceded by '3DDisplayThreshold', the levels are evaluated in units of the value of 3DDisplayThreshold of the dataset.
 
 
If the Histogram is active in the plot view and a selection is made, by typing the string 'Histogram' will create a segmentation around the selection.
 
 
The contours in SlicerAstro are a full 3D segmentation. Therefore it can be computationally heavy to segment
(marching cubes algorithm) and visualize around the noise range [-2, 2] RMS for large datacubes.
 
 

 
<h4>AstroCloudLasso Effect</h4> 
The AstroCloudLasso segmentation editor effect is a tool to interactively perform a 3D selection.
This 3D selection (the segmentation) can be used either for:

1. changing an imported mask generated by automated algorithms (e.g., source finders); 
2. providing an input mask to a variety of tools in SlicerAstro (e.g., MomentMaps module and Modeling module). 

[[File:AstroMask3.png|1000 px]]
[[File:AstroMask4.png|1000 px]]


{{documentation/{{documentation/version}}/module-section|References}}
<pre>
@ARTICLE{2017A&C....19...45P,
author = {{Punzo}, D. and {van der Hulst}, J.~M. and {Roerdink}, J.~B.~T.~M. and
{Fillion-Robin}, J.~C. and {Yu}, L.},
title = "{SlicerAstro: A 3-D interactive visual analytics tool for HI data}",
journal = {Astronomy and Computing},
archivePrefix = "arXiv",
eprint = {1703.06651},
primaryClass = "astro-ph.IM",
keywords = {Radio lines: galaxies, Scientific visualization, Visual analytics, Agile software development, Object oriented development, Empirical software validation},
year = 2017,
month = apr,
volume = 19,
pages = {45-59},
doi = {10.1016/j.ascom.2017.03.004},
}
</pre>




{{documentation/{{documentation/version}}/module-footer}}

File:SlicerAstroDataProbe1.png

2018-02-23T16:07:03Z

Davide:

Documentation/Nightly/Modules/SlicerAstroDataProbe

2018-02-23T16:06:56Z

Davide:

File:SlicerAstroDataProbe.png

2018-02-23T16:05:58Z

Davide: Davide uploaded a new version of File:SlicerAstroDataProbe.png

File:SlicerAstroDataProbe.png

2018-02-23T16:05:17Z

Davide: Davide uploaded a new version of File:SlicerAstroDataProbe.png

File:SlicerAstroDataProbe.png

2018-02-23T16:04:27Z

Davide: Davide uploaded a new version of File:SlicerAstroDataProbe.png

File:SlicerAstroDataProbe.png

2018-02-23T16:02:42Z

Davide: Davide uploaded a new version of File:SlicerAstroDataProbe.png

File:Astro2Daxes.png

2018-02-23T16:02:31Z

Davide: Davide uploaded a new version of File:Astro2Daxes.png