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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, Graphs, Labels, Math, Matrices, Measurements, 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.

binaryAnd

Computes a binary image (containing pixel values 0 and 1) from two images X and Y by connecting pairs of pixels x and y with the binary AND operator &. All pixel values except 0 in the input images are interpreted as 1.

binaryEdgeDetection

Determines pixels/voxels which are on the surface of binary objects and sets only them to 1 in the destination image. All other pixels are set to 0.

binaryFillHoles

Fills holes (pixels with value 0 surrounded by pixels with value 1) in a binary image.

binaryFillHolesSliceBySlice (Experimental)

Fills holes (pixels with value 0 surrounded by pixels with value 1) in a binary image stack slice by slice.

binaryIntersection

Computes a binary image (containing pixel values 0 and 1) from two images X and Y by connecting pairs of pixels x and y with the binary intersection operator &. All pixel values except 0 in the input images are interpreted as 1.

binaryNot

Computes a binary image (containing pixel values 0 and 1) from an image X by negating its pixel values x using the binary NOT operator !

binaryOr

Computes a binary image (containing pixel values 0 and 1) from two images X and Y by connecting pairs of pixels x and y with the binary OR operator |.

binarySubtract

Subtracts one binary image from another.

binaryUnion

Computes a binary image (containing pixel values 0 and 1) from two images X and Y by connecting pairs of pixels x and y with the binary union operator |.

binaryXOr

Computes a binary image (containing pixel values 0 and 1) from two images X and Y by connecting pairs of pixels x and y with the binary operators AND &, OR | and NOT ! implementing the XOR operator.

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

closingBox

Apply a binary closing to the input image by calling n dilations and n erosions subsequenntly.

closingDiamond

Apply a binary closing to the input image by calling n dilations and n erosions subsequently.

convolve

Convolve the image with a given kernel image.

countNonZeroPixels2DSphere

Counts non-zero pixels in a sphere around every pixel.

countNonZeroPixelsSliceBySliceSphere

Counts non-zero pixels in a sphere around every pixel slice by slice in a stack.

countNonZeroVoxels3DSphere

Counts non-zero voxels in a sphere around every voxel.

crossCorrelation (Experimental)

Performs cross correlation analysis between two images.

D

detectLabelEdges

Takes a labelmap and returns an image where all pixels on label edges are set to 1 and all other pixels to 0.

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.

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.

distanceMap

Generates a distance map from a binary image.

divideByGaussianBackground (Experimental)

Applies Gaussian blur to the input image and divides the original by the result.

E

entropyBox

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

equalizeMeanIntensitiesOfSlices

Determines correction factors for each z-slice so that the average intensity in all slices can be made the same and multiplies these factors with the slices.

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.

excludeLabels

This operation removes labels from a labelmap and renumbers the remaining labels.

excludeLabelsOnEdges

Removes all labels from a label map which touch the edges of the image (in X, Y and Z if the image is 3D).

excludeLabelsOnSurface

This operation follows a ray from a given position towards a label (or opposite direction) and checks if there is another label between the label an the image border.

excludeLabelsOutsideSizeRange (Experimental)

Removes labels from a label map which are not within a certain size range.

excludeLabelsSubSurface

This operation follows a ray from a given position towards a label (or opposite direction) and checks if there is another label between the label an the image border.

excludeLabelsWithValuesOutOfRange

This operation removes labels from a labelmap and renumbers the remaining labels.

excludeLabelsWithValuesWithinRange

This operation removes labels from a labelmap and renumbers the remaining labels.

exponential

Computes base exponential of all pixels values.

extendLabelingViaVoronoi

Takes a label map image and dilates the regions using a octagon shape until they touch.

extendLabelsWithMaximumRadius (Experimental)

Extend labels with a given radius.

F

floodFillDiamond

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

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.

greyLevelAtttributeFiltering (Experimental)

Inspired by Grayscale attribute filtering from MorpholibJ library by David Legland & Ignacio Arganda-Carreras. This plugin will remove components in a grayscale image based on user-specified area (for 2D: pixels) or volume (3D: voxels). For each gray level specified in the number of bins, binary images will be generated, followed by exclusion of objects (labels) below a minimum pixel count. All the binary images for each gray level are combined to form the final image. The output is a grayscale image, where bright objects below pixel count are removed. It is recommended that low values be used for number of bins, especially for large 3D images, or it may take long time.

I

intensityCorrection (Experimental)

Determines the mean intensity of the image stack and multiplies it with a factor so that the mean intensity becomes equal to a given value.

intensityCorrectionAboveThresholdOtsu (Experimental)

Determines the mean intensity of all pixel the image stack which are above a determined Threshold (Otsu et al. 1979) and multiplies it with a factor so that the mean intensity becomes equal to a given value.

L

labelSpots

Transforms a binary image with single pixles set to 1 to a labelled spots image.

labelVoronoiOctagon

Takes a labelled image and dilates the labels using a octagon shape until they touch.

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.

localThreshold

Computes a binary image with pixel values 0 and 1 depending on if a pixel value x in image X was above of equal to the pixel value m in mask image M.

M

mask

Computes a masked image by applying a binary mask to an image.

maskLabel

Computes a masked image by applying a label mask to an image.

maskStackWithPlane

Computes a masked image by applying a binary 2D mask to an image stack.

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.

mergeTouchingLabels (Experimental)

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

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.

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.

openingBox

Apply a binary opening to the input image by calling n erosions and n dilations subsequenntly.

openingDiamond

Apply a binary opening to the input image by calling n erosions and n dilations subsequenntly.

P

parametricWatershed (Experimental)

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

R

replaceIntensities

Replaces integer intensities specified in a vector image.

replaceIntensity

Replaces a specific intensity in an image with a given new value.

replacePixelsIfZero

Replaces pixel values x with y in case x is zero.

S

seededWatershed (Experimental)

Takes a label map (seeds) and an input image with gray values to apply the watershed algorithm and split the image above a given threshold in labels.

skeletonize (Experimental)

Erodes a binary image until just its skeleton is left.

sobel

Convolve the image with the Sobel kernel.

squaredDifference

Determines the squared difference pixel by pixel between two images.

subtractGaussianBackground (Experimental)

Applies Gaussian blur to the input image and subtracts the result from the original image.

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.

V

voronoiLabeling

Takes a binary image, labels connected components and dilates the regions using a octagon shape until they touch.

voronoiOctagon

Takes a binary image and dilates the regions using a octagon shape until they touch.

W

watershed

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