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CLIJ 1/2/x reference in category ‘neighbor’

This reference contains all methods currently available in CLIJ, CLIJ2 and CLIJx for processing neighboring objects.. Read more about CLIJs release cycle

Please note: CLIJ is deprecated. Make the transition to CLIJ2.

Method is available in CLIJ (deprecated release)
Method is available in CLIJ2 (stable release)
Method is available in CLIJx (experimental release)

Categories: Binary, Filter, Labels, Math, Matrices, Measurements, Neighbors, Projections, Transformations

[A],[B],[C],[D],[E],[F],[G], H, I, J, K,[L],[M],[N], O,[P], Q, R,[S],[T], U, V, W, X, Y, Z

A

averageDistanceOfTouchingNeighbors

Takes a touch matrix and a distance matrix to determine the average distance of touching neighbors for every object.

B

bilateral (Experimental)

Applies a bilateral filter using a box neighborhood with sigma weights for space and intensity to the input image.

C

connectedComponentsLabelingBox

Performs connected components analysis inspecting the box neighborhood of every pixel to a binary image and generates a label map.

connectedComponentsLabelingDiamond

Performs connected components analysis inspecting the diamond neighborhood of every pixel to a binary image and generates a label map.

countTouchingNeighbors

Takes a touch matrix as input and delivers a vector with number of touching neighbors per label as a vector.

D

detectMaximaBox

Detects local maxima in a given square/cubic neighborhood.

detectMaximaSliceBySliceBox

Detects local maxima in a given square neighborhood of an input image stack.

detectMinimaBox

Detects local minima in a given square/cubic neighborhood.

detectMinimaSliceBySliceBox

Detects local minima in a given square neighborhood of an input image stack.

dilateBox

Computes a binary image with pixel values 0 and 1 containing the binary dilation of a given input image.

dilateBoxSliceBySlice

Computes a binary image with pixel values 0 and 1 containing the binary dilation of a given input image.

dilateSphere

Computes a binary image with pixel values 0 and 1 containing the binary dilation of a given input image.

dilateSphereSliceBySlice

Computes a binary image with pixel values 0 and 1 containing the binary dilation of a given input image.

downsample2D

Scales an image using given scaling factors for X and Y dimensions.

downsample3D

Scales an image using given scaling factors for X and Y dimensions.

E

erodeBox

Computes a binary image with pixel values 0 and 1 containing the binary erosion of a given input image.

erodeBoxSliceBySlice

Computes a binary image with pixel values 0 and 1 containing the binary erosion of a given input image.

erodeSphere

Computes a binary image with pixel values 0 and 1 containing the binary erosion of a given input image.

erodeSphereSliceBySlice

Computes a binary image with pixel values 0 and 1 containing the binary erosion of a given input image.

F

floodFillDiamond

Replaces recursively all pixels of value a with value b if the pixels have a neighbor with value b.

G

generateTouchCountMatrix

Takes a label map with n labels and generates a (n+1)*(n+1) matrix where all pixels are set the number of pixels where labels touch (diamond neighborhood).

L

laplaceBox

Applies the Laplace operator (Box neighborhood) to an image.

laplaceSphere (Experimental)

Applies the Laplace operator (Diamond neighborhood) to an image.

M

maximum2DBox

Computes the local maximum of a pixels rectangular neighborhood.

maximum2DSphere

Computes the local maximum of a pixels ellipsoidal neighborhood.

maximum3DBox

Computes the local maximum of a pixels cube neighborhood.

maximum3DSphere

Computes the local maximum of a pixels spherical neighborhood.

maximumOctagon

Applies a maximum filter with kernel size 3x3 n times to an image iteratively.

maximumOfTouchingNeighbors

Takes a touch matrix and a vector of values to determine the maximum value among touching neighbors for every object.

mean2DBox

Computes the local mean average of a pixels rectangular neighborhood.

mean2DSphere

Computes the local mean average of a pixels ellipsoidal neighborhood.

mean3DBox

Computes the local mean average of a pixels cube neighborhood.

mean3DSphere

Computes the local mean average of a pixels spherical neighborhood.

meanOfTouchingNeighbors

Takes a touch matrix and a vector of values to determine the mean value among touching neighbors for every object.

meanSliceBySliceSphere

Computes the local mean average of a pixels ellipsoidal 2D neighborhood in an image stack slice by slice.

median2DBox

Computes the local median of a pixels rectangular neighborhood.

median2DSphere

Computes the local median of a pixels ellipsoidal neighborhood.

median3DBox

Computes the local median of a pixels cuboid neighborhood.

median3DSphere

Computes the local median of a pixels spherical neighborhood.

medianOfTouchingNeighbors

Takes a touch matrix and a vector of values to determine the median value among touching neighbors for every object.

minimum2DBox

Computes the local minimum of a pixels rectangular neighborhood.

minimum2DSphere

Computes the local minimum of a pixels ellipsoidal neighborhood.

minimum3DBox

Computes the local minimum of a pixels cube neighborhood.

minimum3DSphere

Computes the local minimum of a pixels spherical neighborhood.

minimumDistanceOfTouchingNeighbors

Takes a touch matrix and a distance matrix to determine the shortest distance of touching neighbors for every object.

minimumOctagon

Applies a minimum filter with kernel size 3x3 n times to an image iteratively.

minimumOfTouchingNeighbors

Takes a touch matrix and a vector of values to determine the minimum value among touching neighbors for every object.

N

neighborsOfNeighbors

Determines neighbors of neigbors from touch matrix and saves the result as a new touch matrix.

nonLocalMeans (Experimental)

Applies a non-local means filter using a box neighborhood with a Gaussian weight specified with sigma to the input image.

P

particleImageVelocimetry (Experimental)

For every pixel in source image 1, determine the pixel with the most similar intensity in the local neighborhood with a given radius in source image 2. Write the distance in X and Y in the two corresponding destination images.

S

standardDeviationOfTouchingNeighbors

Takes a touch matrix and a vector of values to determine the standard deviation value among touching neighbors for every object.

T

topHatOctagon (Experimental)

Applies a minimum filter with kernel size 3x3 n times to an image iteratively.

topHatOctagonSliceBySlice (Experimental)

Applies a minimum filter with kernel size 3x3 n times to an image iteratively.