ITK/Examples

Warning: The media wiki content on this page is no longer maintained. The examples presented on the https://itk.org/Wiki/* pages likely require ITK version 4.13 or earlier releases. In many cases, the examples on this page no longer conform to the best practices for modern ITK versions. Recent examples that are up to date with ITK version 5 can be found at ITK Examples

CMake Techniques

Example Name	ITK Classes Demonstrated	Description
Check if a specific module is present
Check for ITK4

Visualization

Example Name	ITK Classes Demonstrated	Description
Display an image		QuickView

Simple Operations

Example Name	ITK Classes Demonstrated	Description

Mathematical Operations

Example Name	ITK Classes Demonstrated	Description

Trigonometric Filters

Example Name	ITK Classes Demonstrated	Description

Image Functions

Example Name	ITK Classes Demonstrated	Description

Point Set

Example Name	ITK Classes Demonstrated	Description

Input/Output (IO)

Example Name	ITK Classes Demonstrated	Description
Display an ITK image	ImageToVTKImageFilter
Create a 3D volume from a series of 2D images	ImageSeriesReader	Uses NumericSeriesFileNames to generate a list of file names

DICOM

Example Name	ITK Classes Demonstrated	Description

Blob Detection, Labeling, and Properties

Example Name	ITK Classes Demonstrated	Description

Correlation

Example Name	ITK Classes Demonstrated	Description

Image Processing

Example Name	ITK Classes Demonstrated	Description

Vector Images

Example Name	ITK Classes Demonstrated	Description
Join images, stacking their components	JoinImageFilter	concatenate, channels
Stack scalar images into a VectorImage	ImageToVectorImageFilter
NeighborhoodIterator on a VectorImage	VectorImage NeighborhoodIterator
Cast a VectorImage to another type of VectorImage	VectorImage

Iterating Over (Traversing) An Image

Example Name	ITK Classes Demonstrated	Description
Iterator over an image skipping a specified region	ImageRegionExclusionConstIteratorWithIndex
Randomly select pixels from a region of an image	ImageRandomConstIteratorWithIndex
Randomly select pixels from a region of an image without replacement	ImageRandomNonRepeatingConstIteratorWithIndex
Iterate over a line through an image	LineIterator	Walks a Bresenham line through an image (with write access)
Iterate over a line through an image without write access	LineConstIterator	Walks a Bresenham line through an image (without write access)
Iterate over the central region (non-boundary) separately from the face-regions (boundary)	ImageBoundaryFacesCalculator
Iterate over a region of an image with a neighborhood (with write access)	NeighborhoodIterator
Iterate over a region of an image with a neighborhood (without write access)	ConstNeighborhoodIterator
Iterate over a region of an image (with write access)	ImageRegionIterator
Iterate over a region of an image (without write access)	ImageRegionConstIterator
Make out of bounds pixels return a constant value	ConstantBoundaryCondition
Iterate over a region of an image with efficient access to the current index (with write access)	ImageRegionIteratorWithIndex
Iterate over a region of an image with efficient access to the current index (without write access)	ImageRegionConstIteratorWithIndex

Kernels

Example Name	ITK Classes Demonstrated	Description
Create a Gaussian kernel	GaussianOperator
Create a Gaussian derivative kernel	GaussianDerivativeOperator
Create a Laplacian kernel	LaplacianOperator
Create a derivative kernel	DerivativeOperator
Create the Sobel kernel	SobelOperator
Create a forward difference kernel	ForwardDifferenceOperator

Image Edges, Gradients, and Derivatives

Example Name	ITK Classes Demonstrated	Description
Find higher derivatives of an image	RecursiveGaussianImageFilter
Extract the boundaries of connected regions in a binary image	BinaryContourImageFilter	Blob boundary, border
Extract the inner and outer boundaries of blobs in a binary image	BinaryContourImageFilter
A zero-crossing based edge detecor	ZeroCrossingBasedEdgeDetectionImageFilter

Smoothing

Example Name	ITK Classes Demonstrated	Description
BinaryMinMaxCurvatureFlow a binary image	BinaryMinMaxCurvatureFlowImageFilter
Smooth an image with a discrete Gaussian filter	DiscreteGaussianImageFilter
Bilateral filter an image	BilateralImageFilter	Edge preserving smoothing.
Smooth an image using curvature flow	CurvatureFlowImageFilter
Smooth an RGB image using curvature flow	CurvatureFlowImageFilter	Run curvature flow on each component of the RGB image
Smooth an image using min/max curvature flow	MinMaxCurvatureFlowImageFilter
Smooth an RGB image using min/max curvature flow	MinMaxCurvatureFlowImageFilter	Run mon/max curvature flow on each component of the RGB image
Smooth an image while preserving edges	VectorGradientAnisotropicDiffusionImageFilter	Anisotropic diffusion.
Smooth an image while preserving edges	VectorCurvatureAnisotropicDiffusionImageFilter	Anisotropic diffusion.

Morphology

Example Name	ITK Classes Demonstrated	Description
Prune a binary image	BinaryPruningImageFilter
Opening a binary image	BinaryMorphologicalOpeningImageFilter
Closing a binary image	BinaryMorphologicalClosingImageFilter
Erode a binary image using a flat (box) structuring element	FlatStructuringElement
Generate structuring elements with accurate area	FlatStructuringElement	In itkFlatStructuringElement, setting the foregroundHasAccurateArea flag to true will generate structuring elements with more accurate areas, which can be especially important when morphological operations are intended to remove or retain objects of particular sizes.

Curves

Example Name	ITK Classes Demonstrated	Description
Compute the mean distance between all points of two curves	ContourMeanDistanceImageFilter
A data structure for a piece-wise linear curve	PolyLineParametricPath

Spectral Analysis

Example Name	ITK Classes Demonstrated	Description
Compute the FFT of an image	ForwardFFTImageFilter
Compute the inverse FFT of an image	InverseFFTImageFilter
Compute the FFT of an image	VnlFFTRealToComplexConjugateImageFilter
Compute the cross-correlation of two images in the Fourier domain	VnlFFTRealToComplexConjugateImageFilterVnlFFTComplexConjugateToRealImageFilter
Convert a real image and an imaginary image to a complex image	ComposeImageFilter

Utilities

Example Name	ITK Classes Demonstrated	Description
Add noise to a binary image	ImageRandomNonRepeatingIteratorWithIndex	Add uniform random noise to an image
Sort itk::Index	Image	Lexicographic, ordering
Return an object from a function
Create another instance of an image
Create another instance of the same type of object
Pass an image to a function	Image
Cartesian to AzimuthElevation and vice-versa	AzimuthElevationToCartesianTransform
Deep copy an image
Permute a sequence of indices	ImageRandomNonRepeatingConstIteratorWithIndex
Map scalars into a jet colormap	JetColormapFunctor
Direct itk warnings to the console	TextOutput
Direct itk warnings to a file	FileOutputWindow

Statistics

Example Name	ITK Classes Demonstrated	Description
Compute histograms in a sliding window.	MovingHistogramImageFilter
Compute a histogram from an RGB image.	ImageToHistogramFilterRGB
Compute a histogram from a itk::VectorImage.	ImageToHistogramFilterVectorImage
Compute min, max, variance and mean of an Image.	StatisticsImageFilter
Create a Gaussian distribution	GaussianDistribution
Create a histogram from a list of sample measurements	SampleToHistogramFilter
Create a list of sample measurements	ListSample
Create a list of samples from an image without duplicating the data	ImageToListSampleAdaptor
Create a list of samples with associated class IDs	MembershipSample
2D Gaussian Mixture Model Expectation Maximization	ExpectationMaximizationMixtureModelEstimator	EM
1D KMeans Clustering	KdTreeBasedKMeansClustering
3D KMeans Clustering	KdTreeBasedKMeansClustering
Spatial search	KdTreeGenerator
Cluster the pixels in a greyscale image	ScalarImageKmeansImageFilter
Compute the local noise in an image	NoiseImageFilter
Compute kmeans clusters	KdTreeBasedKmeansEstimator
Extract texture features using GLCM	ScalarImageToCooccurrenceMatrixFilter

Spatial Objects

Example Name	ITK Classes Demonstrated	Description
Convert a spatial object to an image	SpatialObjectToImageFilter
Ellipse	EllipseSpatialObject	Circle, dot
Line spatial object	LineSpatialObject, LineSpatialObjectPoint	Specify a piecewise-linear object by specifying points along the line.
Plane spatial object	PlaneSpatialObject
Blob	BlobSpatialObject

Inspection

Example Name	ITK Classes Demonstrated	Description
Printing a pixel value to the console	GetPixel

Metrics

Example Name	ITK Classes Demonstrated	Description
Compute the mean squares metric between two images	MeanSquaresImageToImageMetric

Image Registration

Example Name	ITK Classes Demonstrated	Description
Rigidly register one image to another using manually specified landmarks	LandmarkBasedTransformInitializer
Register one image to another using manually specified landmarks	DeformationFieldTransform
A basic global registration of two images	ImageRegistrationMethod, TranslationTransform	Translation only transform.
A global registration of two images	ImageRegistrationMethod, AffineTransform	Full affine transform.
A global registration of two images	ImageRegistrationMethod, BSplineDeformableTransform	BSpline transform.
Mutual Information	MutualInformationImageToImageMetric, TranslationTransform	Global registration by maximizing the mutual information and using a translation only transform
Mutual Information Affine	MutualInformationImageToImageMetric, AffineTransform	Global registration by maximizing the mutual information and using an affine transform
ExhaustiveOptimizer	ExhaustiveOptimizer	An optimizer that fully samples a grid on the parametric space
WatchRegistration	MattesMutualInformationImageToImageMetric	Watch the iterations of a registration using VTK.

Image Segmentation

Example Name	ITK Classes Demonstrated	Description
Extract contours from an image	ContourExtractor2DImageFilter
Morphological Watershed segmentation	MorphologicalWatershedImageFilter
Mean shift clustering	SampleMeanShiftClusteringFilter
Voronoi diagram	VoronoiDiagram2DGenerator, VoronoiDiagram2D
Label connected components in a binary image	ConnectedComponentImageFilter
Label connected components in a grayscale image	ScalarConnectedComponentImageFilter
Assign contiguous labels to connected regions of an image	RelabelComponentImageFilter
Label the contours of connected components	LabelContourImageFilter
Segment pixels with similar statistics using connectivity	ConfidenceConnectedImageFilter
Convert an itk::Image consisting of labeled regions to a LabelMap	LabelImageToLabelMapFilter ||
Extract the largest connected component from a Binary Image
Simple implementation of Snakes
Extract the largest connected component from a Binary Image
Demonstrate available threshold algorithms
Demonstrate connected component algorithm using available threshold algorithms

Meshes

Example Name	ITK Classes Demonstrated	Description
Decimation
Add points and edges
Subdivide an itk::QuadEdgeMesh	LoopTriangleCellSubdivisionQuadEdgeMeshFilter	Perform a loop triangle cell subdivision on a spherical quad edge mesh.
Calculate Area and Volume of an itk::SimplexMesh	SimplexMeshVolumeCalculator	Calculate the area and volume of an itk::SimplexMesh.
Convert an itk::Mesh to a vtkUnstructuredGrid
Write an itk::Mesh to a vtp (vtkPolyData) file	VTKPolyDataWriter
Working with PointData and CellData	Mesh	Associate point and cell data with a mesh.

Need Demo

This section consists of examples which compile and work, but a good demonstration image must be selected and added.

Example Name	ITK Classes Demonstrated	Description

Wish List

Example Name	ITK Classes Demonstrated	Description
Match feature points (hierarchically?)	BlockMatchingImageFilter	Segfault.
Uses a custom user matrix to align the image with DICOM physical space	ImageToVTKImageFilter	Need demo image.
Compute a PCA shape model from a training sample	ImagePCAShapeModelEstimator	Estimate the principal modes of variation of a shape from a training sample. Useful for shape guide segmentation. Need example input files and arguments.
Multiphase Chan And Vese Sparse Field Level Set Segmentation	ScalarChanAndVeseSparseLevelSetImageFilter, ScalarChanAndVeseLevelSetFunction	Need example input files and arguments.
Single-phase Chan And Vese Sparse Field Level Set Segmentation	ScalarChanAndVeseSparseLevelSetImageFilter, ScalarChanAndVeseLevelSetFunction	Need example input files and arguments.
KMeans Clustering		Need example input files and arguments.
Single-phase Chan And Vese Dense Field Level Set Segmentation	ScalarChanAndVeseDenseLevelSetImageFilter, ScalarChanAndVeseLevelSetFunction	Need example input files and arguments.
DisconnectPipeline
ConditionalConstIterator	ConditionalConstIterator
Compute texture features	ScalarImageToTextureFeaturesFilter	How to interpret the output?
Resample an itk::VectorImage
Compute the histogram of a masked region of an image	MaskedImageToHistogramFilter
Fit a spline to a point set	BSplineScatteredDataPointSetToImageFilter
BinaryPruningImageFilter	BinaryPruningImageFilter
Compute distributions of image pixels using GMM EM	GaussianMixtureModelComponent
LevenbergMarquart
IterativeClosestPoints
Demonstrate all operators	NeighborhoodOperator
Color Normalized Correlation	NormalizedCorrelationImageFilter
ContourSpatialObject	ContourSpatialObject
Store non-pixel associated data in an image	MetaDataDictionary
Level Sets
Region Growing
Separate foreground and background using Otsu's method	OtsuThresholdImageFilter
Extract contours from an image	SimpleContourExtractorImageFilter
Present an image of RGBPixel pixels as an image of vectors	RGBToVectorImageAdaptor
HoughTransform2DCirclesImageFilter	HoughTransform2DCirclesImageFilter
HoughTransform2DLinesImageFilter	HoughTransform2DLinesImageFilter
Write data from Matlab in a format readable by ITK
Write data from ITK in a format readable by Matlab
Compute edge potential	EdgePotentialImageFilter

Included in the ITK Repository

Example Name	ITK Classes Demonstrated	Description
Image registration

Matlab

Example Name	ITK Classes Demonstrated	Description

Developer Examples

Example Name	ITK Classes Demonstrated	Description
Throw an exception
Produce an image programmatically.	ImageSource	Nothing in, image out.
Filter an image	ImageToImageFilter	Image in, same type of image out.
Filter an image without copying its data	InPlaceImageFilter
Filter an image using multiple threads	ImageToImageFilter
Multi-threaded oil painting image filter	ImageToImageFilter and MinimumMaximumImageCalculator	A simple multi-threaded scenario (oil painting artistic filter). You can also use this class as-is (copy .h and .txx files into your project and use them).
Write a filter with multiple inputs of the same type.	ImageToImageFilter	Two images in (same type), same type of image out.
Write a filter with multiple inputs of different types.	ImageToImageFilter	Two images in (different type), image (same type as first input) out.
Write a filter with multiple outputs of the same type.	ImageToImageFilter	Images in, two images out (same type as first input).
Write a filter with multiple outputs of different types.	ImageToImageFilter	Images in, two images out (different types).
Get or set a member variable of an ITK class.		SetMacro, GetMacro
Output an error, a warning, or debug information.		DebugMacro, ErrorMacro, WarningMacro
MiniPipeline

Problems

Small Problems

Example Name	ITK Classes Demonstrated	Description
Compute kmeans clusters of pixels in an image	ImageKmeansModelEstimator	Segfault.
Iterate over an image starting at a seed and following a rule for connectivity decisions	FloodFilledImageFunctionConditionalIterator
Traverse a region using a flood fill iterator	FloodFilledSpatialFunctionConditionalIterator	How to do this?
Compute the gradient of a vector image	GradientImageFilter	How to do this?
Compute distributions of image pixels using GMM EM	ExpectationMaximizationMixtureModelEstimator
Compute distributions of samples using GMM EM	ExpectationMaximizationMixtureModelEstimator	Someone please confirm that this outputs the mean and the variance (i.e. I used a standard deviation of 30 to create the samples and the second estimated parameter is near 1000 (~30^2) . Is this correct?)
Compute the histogram of an image	Statistics_1_1ImageToHistogramFilter	The last entry of the red histogram should contain several values, but it is 0?
Classifying pixels using KMeans	KmeansModelEstimator	How to apply the labels of the filter to the input image?
Basic region growing	RegionGrowImageFilter	Just getting started with demo...
Find connected components in an image	ConnectedThresholdImageFilter	Just need to finish it.
Convert an image from one type to another	ConvertPixelBuffer
In-place filtering of an image	InPlaceImageFilter	This only works for filters which derive from itkInPlaceImageFilter
Convert a VTK image to an ITK image	VTKImageToImageFilter	Seems to expect an input image with only 1 component? (i.e. greyscale)

Big Problems

Example Name	ITK Classes Demonstrated	Description
Find the best position of the moving image in the fixed image.	MeanSquaresImageToImageMetric	Output (0,0) is incorrect.
Compute and display the gradient of an image	GradientImageFilter	Blank output on the screen (the filter works fine). There should be a "DisplayVectorImage" added to itkQuickView that draws vector glyphs at specified pixels of an image.