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

averageDistanceOfNClosestNeighborsMap (Experimental)

Takes a label map, determines distances between all centroids and replaces every label with the average distance to the n closest neighboring labels.

averageDistanceOfTouchingNeighbors

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

averageNeighborDistanceMap (Experimental)

Takes a label map, determines which labels touch and replaces every label with the average distance to their neighboring labels.

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

detectMaxima2DBox

Detects local maxima in a given square/cubic neighborhood.

detectMaxima3DBox

Detects local maxima in a given square/cubic neighborhood.

detectMaximaBox

Detects local maxima in a given square/cubic neighborhood.

detectMaximaSliceBySliceBox

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

detectMinima2DBox

Detects local minima in a given square/cubic neighborhood.

detectMinima3DBox

Detects local minima in a given square/cubic neighborhood.

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.

drawDistanceMeshBetweenTouchingLabels (Experimental)

Starting from a label map, draw lines between touching neighbors resulting in a mesh.

drawMeshBetweenTouchingLabels (Experimental)

Starting from a label map, draw lines between touching neighbors resulting in a mesh.

drawTouchCountMeshBetweenTouchingLabels (Experimental)

Starting from a label map, draw lines between touching neighbors resulting in a mesh.

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

generateGreyValueCooccurrenceMatrixBox (Experimental)

Takes an image and an intensity range to determine a grey value co-occurrence matrix.

generateIntegerGreyValueCooccurrenceCountMatrixHalfBox (Experimental)

Takes an image and assumes its grey values are integers. It builds up a grey-level co-occurrence matrix of neighboring (west, south-west, south, south-east, in 3D 9 pixels on the next plane) pixel intensities.

generateIntegerGreyValueCooccurrenceCountMatrixHalfDiamond (Experimental)

Takes an image and assumes its grey values are integers. It builds up a grey-level co-occurrence matrix of neighboring (left, bottom, back) pixel intensities.

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.

localMaximumAverageDistanceOfNClosestNeighborsMap (Experimental)

Takes a label map, determines distances between all centroids, the mean distance of the n closest points for every point and replaces every label with the maximum distance of touching labels.

localMaximumAverageNeighborDistanceMap (Experimental)

Takes a label map, determines which labels touch, the distance between their centroids and the maximum distancebetween touching neighbors. It then replaces every label with the that value.

localMaximumTouchingNeighborCountMap (Experimental)

Takes a label map, determines which labels touch, determines for every label with the number of touching neighboring labels and replaces the label index with the local maximum of this count.

localMeanAverageDistanceOfNClosestNeighborsMap (Experimental)

Takes a label map, determines distances between all centroids, the mean distance of the n closest points for every point and replaces every label with the mean distance of touching labels.

localMeanAverageNeighborDistanceMap (Experimental)

Takes a label map, determines which labels touch, the distance between their centroids and the mean distancebetween touching neighbors. It then replaces every label with the that value.

localMeanTouchPortionMap (Experimental)

Takes a label map, determines which labels touch and how much, relatively taking the whole outline of each label into account, and determines for every label with the mean of this value and replaces the label index with that value.

localMeanTouchingNeighborCountMap (Experimental)

Takes a label map, determines which labels touch, determines for every label with the number of touching neighboring labels and replaces the label index with the local mean of this count.

localMedianAverageDistanceOfNClosestNeighborsMap (Experimental)

Takes a label map, determines distances between all centroids, the mean distance of the n closest points for every point and replaces every label with the median distance of touching labels.

localMedianAverageNeighborDistanceMap (Experimental)

Takes a label map, determines which labels touch, the distance between their centroids and the median distancebetween touching neighbors. It then replaces every label with the that value.

localMedianTouchingNeighborCountMap (Experimental)

Takes a label map, determines which labels touch, determines for every label with the number of touching neighboring labels and replaces the label index with the local median of this count.

localMinimumAverageDistanceOfNClosestNeighborsMap (Experimental)

Takes a label map, determines distances between all centroids, the mean distance of the n closest points for every point and replaces every label with the minimum distance of touching labels.

localMinimumAverageNeighborDistanceMap (Experimental)

Takes a label map, determines which labels touch, the distance between their centroids and the minimum distancebetween touching neighbors. It then replaces every label with the that value.

localMinimumTouchingNeighborCountMap (Experimental)

Takes a label map, determines which labels touch, determines for every label with the number of touching neighboring labels and replaces the label index with the local minimum of this count.

localStandardDeviationAverageDistanceOfNClosestNeighborsMap (Experimental)

Takes a label map, determines distances between all centroids, the mean distance of the n closest points for every point and replaces every label with the standard deviation distance of touching labels.

localStandardDeviationAverageNeighborDistanceMap (Experimental)

Takes a label map, determines which labels touch, the distance between their centroids and the standard deviation distancebetween touching neighbors. It then replaces every label with the that value.

localStandardDeviationTouchingNeighborCountMap (Experimental)

Takes a label map, determines which labels touch, determines for every label with the number of touching neighboring labels and replaces the label index with the local standard deviation of this count.

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, Y and Z in the three 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.