View source for Neighborhood Connected CLP

[[File:NeighborhoodConnectedCLP.png | thumb | none| 300px | Neighborhood Connected Threshold Segmentation]]

== General Information ==

* Type: CLP
* Category: Segmentation
* Author: Xavi Planes
* Contributor: Xavi Planes
* Contact: xavier.planes@upf.edu
* Description: Label pixels that are connected to a seed and lie within a neighborhood. NeighborhoodConnectedImageFilter labels pixels with ReplaceValue that are connected to an initial Seed AND whose neighbors all lie within a Lower and Upper threshold range. [http://www.itk.org/Doxygen320/html/classitk_1_1NeighborhoodConnectedImageFilter.html Read More...].

== Usage ==


=== Parameters ===

{| border="1" cellpadding="2" cellspacing="0" style="text-align: left;"
|- style="text-align: center; background-color: #95b3d7;" 
! Label
! Type
! Flag / Index
! Default value / Channel
! Description
|-
! style="text-align: center; background-color: #dce6f1;" colspan="5" | Parameters to denoise the image prior to segmenting
|-
! Smoothing iterations
| integer
| --smoothingIterations
| 5
| Number of smoothing iterations
|-
! Timestep
| double
| --timestep
| 0.0625
| Timestep for curvature flow
|-
! style="text-align: center; background-color: #dce6f1;" colspan="5" | Parameters to prescribe the region growing
|-
! Radius
| integer-vector
| --radius
| 5
| Radius of the neighborhood used for a mask.
|-
! Lower
| double
| --lower
| 0
| Set Upper and Lower Threshold inputs as values
|-
! Upper
| double
| --upper
| 1000
| Set Upper and Lower Threshold inputs as values
|-
! Output Label Value
| integer
| --labelvalue
| 2
| The integer value (0-255) to use for the segmentation results. This will determine the color of the segmentation that will be generated by the Region growing algorithm
|-
! Seeds
| point coordinateSystem="ras" multiple="true"
| --seed
| 0,0,0
| Seed point(s) for region growing
|-
! style="text-align: center; background-color: #dce6f1;" colspan="5" | IO
|-
! Input Volume
| image
| index 0
| input
| Input volume to be filtered
|-
! Output Volume
| image
| index 1
| output
| Output Volume
|}

=== Examples ===

Sample Data:[http://www.gimias.org/download/sampledata/file/30-atrial-fibrillation Atrial Fibrillation]

In this example, the heart is segmented but the regions that are small are not included, because the radius has been set to 15:

[[File:NeighborhoodConnectedCLP.png | thumb | none| 500px | Neighborhood Connected Threshold Segmentation]]

== Development ==

Source code: [{{SVN_GIMIAS_Trunk}}/src/Modules/TpExtLib/Applications/NeighborhoodConnected/NeighborhoodConnected.cxx C++ Source code] and [{{SVN_GIMIAS_Trunk}}/src/Modules/TpExtLib/Applications/NeighborhoodConnected/NeighborhoodConnected.xml XML description]

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