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

This reference contains all methods currently available in CLIJ, CLIJ2 and CLIJx for filtering images.. 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

B

bilateral (Experimental)

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

blur2D

Computes the Gaussian blurred image of an image given two sigma values in X and Y.

blur3D

Computes the Gaussian blurred image of an image given two sigma values in X, Y and Z.

blurSliceBySlice (Experimental)

Computes the Gaussian blurred image of an image given two sigma values in X and Y. Thus, the filterkernel can have non-isotropic shape.

bottomHatBox

Apply a bottom-hat filter for background subtraction to the input image.

bottomHatSphere

Applies a bottom-hat filter for background subtraction to the input image.

C

convolve

Convolve the image with a given kernel image.

crossCorrelation (Experimental)

Performs cross correlation analysis between two images.

D

differenceOfGaussian2D

Applies Gaussian blur to the input image twice with different sigma values resulting in two images which are then subtracted from each other.

differenceOfGaussian3D

Applies Gaussian blur to the input image twice with different sigma values resulting in two images which are then subtracted from each other.

dilateBoxSliceBySlice

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.

E

entropyBox

Determines the local entropy in a box with a given radius around every pixel.

erodeBoxSliceBySlice

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.

G

gaussianBlur2D

Computes the Gaussian blurred image of an image given two sigma values in X and Y.

gaussianBlur3D

Computes the Gaussian blurred image of an image given two sigma values in X, Y and Z.

generateFeatureStack (Experimental)

Generates a feature stack for Trainable Weka Segmentation.

gradientX

Computes the gradient of gray values along X.

gradientY

Computes the gradient of gray values along Y.

gradientZ

Computes the gradient of gray values along Z.

L

laplaceBox

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

laplaceSphere (Experimental)

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

localExtremaBox (Experimental)

Applies a local minimum and maximum filter.

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.

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.

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.

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.

minimumOctagon

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

N

nonLocalMeans (Experimental)

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

nonzeroMaximumBox

Apply a maximum filter (box shape) to the input image.

nonzeroMaximumDiamond

Apply a maximum filter (diamond shape) to the input image.

nonzeroMinimumBox

Apply a minimum filter (box shape) to the input image.

nonzeroMinimumDiamond

Apply a minimum filter (diamond shape) to the input image.

O

onlyzeroOverwriteMaximumBox

Apply a local maximum filter to an image which only overwrites pixels with value 0.

onlyzeroOverwriteMaximumDiamond

Apply a local maximum filter to an image which only overwrites pixels with value 0.

S

sobel

Convolve the image with the Sobel kernel.

T

topHatBox

Applies a top-hat filter for background subtraction to the input image.

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.

topHatSphere

Applies a top-hat filter for background subtraction to the input image.

W

watershed

Apply a binary watershed to a binary image and introduces black pixels between objects.