CLIJ2 (BETA test release)

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CLIJ2 (BETA test release)

View the Project on GitHub clij/clij2-docs

CLIJ 1/2/x reference

This reference contains all methods currently available in CLIJ2 and CLIJx. Read more about CLIJs release cycle

Please note: CLIJ2 and CLIJx are under heavy construction. This list may change at any point.

Method is available in CLIJ (stable release)
Method is available in CLIJ2 (alpha release, read more)
Method is available in CLIJx (experimental version)

[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

absolute

Computes the absolute value of every individual pixel x in a given image.

absoluteInplace (Experimental)

Computes the absolute value of every individual pixel x in a given image.

addImageAndScalar

Adds a scalar value s to all pixels x of a given image X.

addImages

Calculates the sum of pairs of pixels x and y of two images X and Y.

addImagesWeighted

Calculates the sum of pairs of pixels x and y from images X and Y weighted with factors a and b.

adjacencyMatrixToTouchMatrix

Converts a adjacency matrix in a touch matrix

affineTransform2D

Applies an affine transform to a 2D image. Individual transforms must be separated by spaces.

affineTransform3D

Applies an affine transform to a 3D image. Individual transforms must be separated by spaces.

applyVectorField2D

Deforms an image according to distances provided in the given vector images. It is recommended to use 32-bit images for input, output and vector images.

applyVectorField3D

Deforms an image stack according to distances provided in the given vector image stacks. It is recommended to use 32-bit image stacks for input, output and vector image stacks.

applyVectorfield

Deforms an image according to distances provided in the given vector images. It is recommended to use 32-bit images for input, output and vector images.

applyWekaModel (Experimental)

Applies a Weka model using functionality of Fijis Trainable Weka Segmentation plugin.

applyWekaToTable (Experimental)

Applies a Weka model using functionality of Fijis Trainable Weka Segmentation plugin.

argMaximumZProjection

Determines the maximum projection of an image stack along Z. Furthermore, another 2D image is generated with pixels containing the z-index where the maximum was found (zero based).

automaticThreshold

The automatic thresholder utilizes the threshold methods from ImageJ on a histogram determined on the GPU to create binary images as similar as possible to ImageJ ‘Apply Threshold’ method. Enter one of these methods in the method text field: [Default, Huang, Intermodes, IsoData, IJ_IsoData, Li, MaxEntropy, Mean, MinError, Minimum, Moments, Otsu, Percentile, RenyiEntropy, Shanbhag, Triangle, Yen]

automaticThresholdInplace (Experimental)

The automatic thresholder utilizes the threshold methods from ImageJ on a histogram determined on the GPU to create binary images as similar as possible to ImageJ ‘Apply Threshold’ method. Enter one of these methods in the method text field: [Default, Huang, Intermodes, IsoData, IJ_IsoData, Li, MaxEntropy, Mean, MinError, Minimum, Moments, Otsu, Percentile, RenyiEntropy, Shanbhag, Triangle, Yen]

averageAngleBetweenAdjacentTriangles (Experimental)

Takes a pointlist and a touch matrix to determine the average angle of adjacent triangles in a surface mesh. For every point, the average angle of adjacent triangles is saved.

averageDistanceOfNClosestPoints

Determines the average of the n closest points for every point in a distance matrix.

averageDistanceOfNFarOffPoints

Determines the average of the n far off (most distant) points for every point in a distance matrix.

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.

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.

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 ! All pixel values except 0 in the input image are interpreted as 1.

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 |. All pixel values except 0 in the input images are interpreted as 1.<pre>f(x, y) = x | y</pre>

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. All pixel values except 0 in the input images are interpreted as 1.

blur2D

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

blur3D

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

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.

boundingBox

Determines the bounding box of all non-zero pixels in a binary image.

C

captureWebcamImage (Experimental)

Acquires an image (in fact an RGB image stack with three slices) of given size using a webcam.

centerOfMass

Determines the center of mass of an image or image stack and writes the result in the results table in the columns MassX, MassY and MassZ.

centroidsOfLabels

Determines the centroids of all labels in a label image or image stack.

closeIndexGapsInLabelMap

Analyses a label map and if there are gaps in the indexing (e.g. label 5 is not present) all subsequent labels will be relabelled.

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.

combineHorizontally

Combines two images or stacks in X.

combineVertically

Combines two images or stacks in Y.

concatenateStacks

Concatenates two stacks in Z.

connectedComponentsLabeling

Performs connected components analysis to a binary image and generates a label map.

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.

connectedComponentsLabelingInplace (Experimental)

Performs connected components analysis to a binary image and generates a label map.

convertRGBStackToGraySlice (Experimental)

Converts a three channel image (stack with three slices) to a single channel image (2D image) by multiplying with factors 0.299, 0.587, 0.114.

convertToImageJBinary

convolve

Convolve the image with a given kernel image.

copy

Copies an image.

copySlice

This method has two purposes: It copies a 2D image to a given slice z position in a 3D image stack or It copies a given slice at position z in an image stack to a 2D image.

countNonZeroPixels

Determines the number of all pixels in a given image which are not equal to 0.

countNonZeroPixels2DSphere

Counts non-zero pixels in a sphere around every pixel.Put the number in the result image.

countNonZeroPixelsSliceBySliceSphere

Counts non-zero pixels in a sphere around every pixel slice by slice in a stack and puts the resulting number in the destination image stack.

countNonZeroVoxels3DSphere

Counts non-zero voxels in a sphere around every voxel.Put the number in the result image.

countTouchingNeighbors

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

crop2D

Crops a given rectangle out of a given image.

crop3D

Crops a given sub-stack out of a given image stack.

crossCorrelation (Experimental)

Performs cross correlation analysis between two images.

customOperation

Executes a custom operation wirtten in OpenCL on a custom list of images.

D

deformableRegistration2D (Experimental)

Applies particle image velocimetry to two images and registers them afterwards by warping input image 2 with a smoothed vector field.

depthColorProjection

Determines a maximum projection of an image stack and does a color coding of the determined arg Z (position of the found maximum).

detectLabelEdges

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

detectMaximaBox

Detects local maxima in a given square/cubic neighborhood. Pixels in the resulting image are set to 1 if there is no other pixel in a given radius which has a higher intensity, and to 0 otherwise.

detectMaximaSliceBySliceBox

Detects local maxima in a given square neighborhood of an input image stack. The input image stack is processed slice by slice. Pixels in the resulting image are set to 1 if there is no other pixel in a given radius which has a higher intensity, and to 0 otherwise.

detectMinimaBox

Detects local minima in a given square/cubic neighborhood. Pixels in the resulting image are set to 1 if there is no other pixel in a given radius which has a lower intensity, and to 0 otherwise.

detectMinimaSliceBySliceBox

Detects local minima in a given square neighborhood of an input image stack. The input image stack is processed slice by slice. Pixels in the resulting image are set to 1 if there is no other pixel in a given radius which has a lower intensity, and to 0 otherwise.

detectOptima

detectOptimaSliceBySlice

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.

differenceOfGaussianInplace3D (Experimental)

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. The dilation takes the Moore-neighborhood (8 pixels in 2D and 26 pixels in 3d) into account. The pixels in the input image with pixel value not equal to 0 will be interpreted as 1.

dilateBoxSliceBySlice

Computes a binary image with pixel values 0 and 1 containing the binary dilation of a given input image. The dilation takes the Moore-neighborhood (8 pixels in 2D and 26 pixels in 3d) into account. The pixels in the input image with pixel value not equal to 0 will be interpreted as 1.

dilateSphere

Computes a binary image with pixel values 0 and 1 containing the binary dilation of a given input image. The dilation takes the von-Neumann-neighborhood (4 pixels in 2D and 6 pixels in 3d) into account. The pixels in the input image with pixel value not equal to 0 will be interpreted as 1.

dilateSphereSliceBySlice

Computes a binary image with pixel values 0 and 1 containing the binary dilation of a given input image. The dilation takes the von-Neumann-neighborhood (4 pixels in 2D and 6 pixels in 3d) into account. The pixels in the input image with pixel value not equal to 0 will be interpreted as 1.

distanceMap

Generates a distance map from a binary image.

distanceMatrixToMesh

Generates a mesh from a distance matric and a list of point coordinates.

divideImages

Divides two images X and Y by each other pixel wise.

downsample2D

Scales an image using given scaling factors for X and Y dimensions. The nearest-neighbor method is applied. In ImageJ the method which is similar is called ‘Interpolation method: none’.

downsample3D

Scales an image using given scaling factors for X and Y dimensions. The nearest-neighbor method is applied. In ImageJ the method which is similar is called ‘Interpolation method: none’.

downsampleSliceBySliceHalfMedian

Scales an image using scaling factors 0.5 for X and Y dimensions. The Z dimension stays untouched. Thus, each slice is processed separately. The median method is applied. Thus, each pixel value in the destination image equals to the median of four corresponding pixels in the source image.

drawBox

Draws a box at a given start point with given size. All pixels other than in the box are untouched. Consider using set(buffer, 0); in advance.

drawLine

Draws a line between two points with a given thickness.

drawSphere

Draws a sphere around a given point with given radii in x, y and z (if 3D).

drawTwoValueLine (Experimental)

Draws a line between two points with a given thickness.

E

entropyBox

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

equal

Determines if two images A and B equal pixel wise.

equalConstant

Determines if an image A and a constant b are equal.

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. The erosion takes the Moore-neighborhood (8 pixels in 2D and 26 pixels in 3d) into account. The pixels in the input image with pixel value not equal to 0 will be interpreted as 1.

erodeBoxSliceBySlice

Computes a binary image with pixel values 0 and 1 containing the binary erosion of a given input image. The erosion takes the Moore-neighborhood (8 pixels in 2D and 26 pixels in 3d) into account. The pixels in the input image with pixel value not equal to 0 will be interpreted as 1.

erodeSphere

Computes a binary image with pixel values 0 and 1 containing the binary erosion of a given input image. The erosion takes the von-Neumann-neighborhood (4 pixels in 2D and 6 pixels in 3d) into account. The pixels in the input image with pixel value not equal to 0 will be interpreted as 1.

erodeSphereSliceBySlice

Computes a binary image with pixel values 0 and 1 containing the binary erosion of a given input image. The erosion takes the von-Neumann-neighborhood (4 pixels in 2D and 6 pixels in 3d) into account. The pixels in the input image with pixel value not equal to 0 will be interpreted as 1.

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.

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.

extrema (Experimental)

Returns an image with pixel values most distant from 0:

F

flip2D

Flips an image in X and/or Y direction depending on boolean flags.

flip3D

Flips an image in X, Y and/or Z direction depending on boolean flags.

floodFillDiamond

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

G

gaussJordan (Experimental)

Gauss Jordan elimination algorithm for solving linear equation systems.

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.

generateBinaryOverlapMatrix

Takes two labelmaps with n and m labels and generates a (n+1)*(m+1) matrix where all pixels are set to 0 exept those where labels overlap between the label maps.

generateDistanceMatrix

Takes two images containing coordinates and builds up a matrix containing distance between the points.

generateFeatureStack (Experimental)

Generates a feature stack for Trainable Weka Segmentation.

generateParametricImage

Take a labelmap and a vector of values to replace label 1 with the 1st value in the vector.

generateParametricImageFromResultsTableColumn

Take a labelmap and a column from the results table to replace label 1 with the 1st value in the vector.

generateTouchMatrix

Takes a labelmap with n labels and generates a (n+1)*(n+1) matrix where all pixels are set to 0 exept those where labels are touching.

getAutomaticThreshold

The automatic thresholder utilizes the threshold methods from ImageJ on a histogram determined on the GPU to determine a threshold value as similar as possible to ImageJ ‘Apply Threshold’ method.

getBoundingBox

Determines the bounding box of all non-zero pixels in a binary image.

getCenterOfMass

Determines the center of mass of an image or image stack.

getDimensions

Reads out the size of an image [stack] and writes it to the variables ‘width’, ‘height’ and ‘depth’.

getJaccardIndex

Determines the overlap of two binary images using the Jaccard index.

getMaximumOfAllPixels

Determines the maximum of all pixels in a given image.

getMeanOfAllPixels

Determines the mean of all pixels in a given image.

getMinimumOfAllPixels

Determines the minimum of all pixels in a given image.

getSize

Reads out the size of an image [stack] and writes it to the results table in the columns ‘Width’, ‘Height’ and ‘Depth’.

getSorensenDiceCoefficient

Determines the overlap of two binary images using the Sorensen-Dice coefficent.

getSumOfAllPixels

Determines the sum of all pixels in a given image.

gradientX

Computes the gradient of gray values along X. Assuming a, b and c are three adjacent pixels in X direction. In the target image will be saved as: <pre>b’ = c - a;</pre>

gradientY

Computes the gradient of gray values along Y. Assuming a, b and c are three adjacent pixels in Y direction. In the target image will be saved as: <pre>b’ = c - a;</pre>

gradientZ

Computes the gradient of gray values along Z. Assuming a, b and c are three adjacent pixels in Z direction. In the target image will be saved as: <pre>b’ = c - a;</pre>

greater

Determines if two images A and B greater pixel wise.

greaterConstant

Determines if two images A and B greater pixel wise.

greaterOrEqual

Determines if two images A and B greater or equal pixel wise.

greaterOrEqualConstant

Determines if two images A and B greater or equal pixel wise.

H

histogram

Determines the histogram of a given image.

I

image2DToResultsTable

Converts an image into a table.

imageToStack

Copies a single slice into a stack a given number of times.

invert

Computes the negative value of all pixels in a given image. It is recommended to convert images to 32-bit float before applying this operation.

J

jaccardIndex

Determines the overlap of two binary images using the Jaccard index.

L

labelSpots

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

labelToMask

Masks a single label in a label map.

labelVoronoiOctagon

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

labelledSpotsToPointList

Generates a coordinate list of points in a labelled spot image.

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.

localID (Experimental)

local id

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.

logarithm

Computes base e logarithm of all pixels values.

M

mask

Computes a masked image by applying a mask to an image. All pixel values x of image X will be copied to the destination image in case pixel value m at the same position in the mask image is not equal to zero.

maskLabel

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

maskStackWithPlane

Computes a masked image by applying a 2D mask to an image stack. All pixel values x of image X will be copied to the destination image in case pixel value m at the same spatial position in the mask image is not equal to zero.

matrixEqual

Checks if all elements of a matrix are different by less than or equal to a given tolerance.

maximum2DBox

Computes the local maximum of a pixels rectangular neighborhood. The rectangles size is specified by its half-width and half-height (radius).

maximum2DSphere

Computes the local maximum of a pixels ellipsoidal neighborhood. The ellipses size is specified by its half-width and half-height (radius).

maximum3DBox

Computes the local maximum of a pixels cube neighborhood. The cubes size is specified by its half-width, half-height and half-depth (radius).

maximum3DSphere

Computes the local maximum of a pixels spherical neighborhood. The spheres size is specified by its half-width, half-height and half-depth (radius).

maximumImageAndScalar

Computes the maximum of a constant scalar s and each pixel value x in a given image X.

maximumImages

Computes the maximum of a pair of pixel values x, y from two given images X and Y.

maximumOctagon

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

maximumOfAllPixels

Determines the maximum of all pixels in a given image. It will be stored in a new row of ImageJs Results table in the column ‘Max’.

maximumOfMaskedPixels

Determines the maximum intensity in an image, but only in pixels which have non-zero values in another mask image.

maximumOfTouchingNeighbors

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

maximumXProjection

Determines the maximum projection of an image along X.

maximumXYZProjection

Determines the maximum projection of an image along a given dimension. Furthermore, the X and Y dimesions of the resulting image must be specified by the user according to its definition: X = 0 Y = 1 Z = 2

maximumYProjection

Determines the maximum projection of an image along X.

maximumZProjection

Determines the maximum projection of an image along Z.

maximumZProjectionBounded

Determines the maximum projection of an image along Z within a given z range.

mean2DBox

Computes the local mean average of a pixels rectangular neighborhood. The rectangles size is specified by its half-width and half-height (radius).

mean2DSphere

Computes the local mean average of a pixels ellipsoidal neighborhood. The ellipses size is specified by its half-width and half-height (radius).

mean3DBox

Computes the local mean average of a pixels cube neighborhood. The cubes size is specified by its half-width, half-height and half-depth (radius).

mean3DSphere

Computes the local mean average of a pixels spherical neighborhood. The spheres size is specified by its half-width, half-height and half-depth (radius).

meanClosestSpotDistance

Determines the distance between pairs of closest spots in two binary images.

meanOfAllPixels

Determines the mean average of all pixels in a given image. It will be stored in a new row of ImageJs Results table in the column ‘Mean’.

meanOfMaskedPixels

Determines the mean intensity in a masked image.

meanOfPixelsAboveThreshold

Determines the mean intensity in a threshleded image.

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. The ellipses size is specified by its half-width and half-height (radius).

meanSquaredError

Determines the mean squared error (MSE) between two images.

meanZProjection

Determines the mean average projection of an image along Z.

meanZProjectionBounded

Determines the mean projection of an image along Z within a given z range.

median2DBox

Computes the local median of a pixels rectangular neighborhood. The rectangle is specified by its half-width and half-height (radius).

median2DSphere

Computes the local median of a pixels ellipsoidal neighborhood. The ellipses size is specified by its half-width and half-height (radius).

median3DBox

Computes the local median of a pixels cuboid neighborhood. The cuboid size is specified by its half-width, half-height and half-depth (radius).

median3DSphere

Computes the local median of a pixels spherical neighborhood. The spheres size is specified by its half-width, half-height and half-depth (radius).

medianOfTouchingNeighbors

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

medianZProjection

Determines the median projection of an image stack along Z.

minimum2DBox

Computes the local minimum of a pixels rectangular neighborhood. The rectangles size is specified by its half-width and half-height (radius).

minimum2DSphere

Computes the local minimum of a pixels ellipsoidal neighborhood. The ellipses size is specified by its half-width and half-height (radius).

minimum3DBox

Computes the local minimum of a pixels cube neighborhood. The cubes size is specified by its half-width, half-height and half-depth (radius).

minimum3DSphere

Computes the local minimum of a pixels spherical neighborhood. The spheres size is specified by its half-width, half-height and half-depth (radius).

minimumDistanceOfTouchingNeighbors

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

minimumImageAndScalar

Computes the maximum of a constant scalar s and each pixel value x in a given image X.

minimumImages

Computes the minimum of a pair of pixel values x, y from two given images X and Y.

minimumOctagon

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

minimumOfAllPixels

Determines the minimum of all pixels in a given image. It will be stored in a new row of ImageJs Results table in the column ‘Min’.

minimumOfMaskedPixels

Determines the minimum intensity in a masked image.

minimumOfTouchingNeighbors

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

minimumZProjection

Determines the minimum projection of an image along Z.

minimumZProjectionBounded

Determines the minimum projection of an image along Z within a given z range.

minimumZProjectionThresholdedBounded

Determines the minimum projection of all pixels in an image above a given threshold along Z within a given z range.

multiplyImageAndCoordinate

Multiplies all pixel intensities with the x, y or z coordinate, depending on specified dimension.

multiplyImageAndScalar

Multiplies all pixels value x in a given image X with a constant scalar s.

multiplyImageStackWithScalars

Multiplies all pixels value x in a given image X with a constant scalar s from a list of scalars.

multiplyImages

Multiplies all pairs of pixel values x and y from two image X and Y.

multiplyMatrix

Multiplies two matrices with each other.

multiplySliceBySliceWithScalars

multiplyStackWithPlane

Multiplies all pairs of pixel values x and y from an image stack X and a 2D image Y. x and y are at the same spatial position within a plane.

N

nClosestDistances

Determine the n point indices with shortest distance for all points in a distance matrix.

nClosestPoints

Determine the n point indices with shortest distance for all points in a distance matrix.

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.

notEqual

Determines if two images A and B equal pixel wise.

notEqualConstant

Determines if two images A and B equal pixel wise.

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.

organiseWindows (Experimental)

Organises windows on screen.

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.

particleImageVelocimetryTimelapse (Experimental)

Run particle image velocimetry on a 2D+t timelapse.

paste2D

Pastes an image into another image at a given position.

paste3D

Pastes an image into another image at a given position.

pointIndexListToMesh

Meshes all points in a given point list which are indiced in a corresponding index list.

pointlistToLabelledSpots

Takes a pointlist with dimensions nd with n point coordinates in d dimensions and a touch matrix of size nn to draw lines from all points to points if the corresponding pixel in the touch matrix is 1.

power

Computes all pixels value x to the power of a given exponent a.

powerImages

Calculates x to the power of y pixel wise of two images X and Y.

preloadFromDisc (Experimental)

This plugin takes two image filenames and loads them into RAM. The first image is returned immediately, the second image is loaded in the background and will be returned when the plugin is called again.

presign (Experimental)

Determines the extrema of pixel values:

print

Visualises an image on standard out (console).

pullAsROI

Pulls a binary image from the GPU memory and puts it on the currently active ImageJ window as region of interest.

pullLabelsToROIList

Pulls all labels in a label map as ROIs to a list.

pullLabelsToROIManager

Pulls all labels in a label map as ROIs to the ROI manager.

pullString

Writes an image into a string.

pullTile (Experimental)

Pushes a tile in an image specified by its name, position and size from GPU memory.

pullToResultsTable

Converts an image into a table.

pushArray

Converts an array to an image.

pushResultsTable

Converts a table to an image.

pushResultsTableColumn

Converts a table column to an image.

pushString

Converts an string to an image.

pushTile (Experimental)

Push a tile in an image specified by its name, position and size to GPU memory in order to process it there later.

R

readImageFromDisc (Experimental)

Read an image from disc.

readRawImageFromDisc (Experimental)

Reads a raw file from disc and pushes it immediately to the GPU.

reduceStack

Reduces the number of slices in a stack by a given factor. With the offset you have control which slices stay: * With factor 3 and offset 0, slices 0, 3, 6,… are kept. * With factor 4 and offset 1, slices 1, 5, 9,… are kept.

replaceIntensities

Replaces integer intensities specified in a vector image.

replaceIntensity

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

resample

Resamples an image with given size factors using an affine transform.

resliceBottom

Flippes Y and Z axis of an image stack. This operation is similar to ImageJs ‘Reslice [/]’ method but offers less flexibility such as interpolation.

resliceLeft

Flippes X, Y and Z axis of an image stack. This operation is similar to ImageJs ‘Reslice [/]’ method but offers less flexibility such as interpolation.

resliceRadial

Computes a radial projection of an image stack. Starting point for the line is the center in any X/Y-plane of a given input image stack. This operation is similar to ImageJs ‘Radial Reslice’ method but offers less flexibility.

resliceRight

Flippes X, Y and Z axis of an image stack. This operation is similar to ImageJs ‘Reslice [/]’ method but offers less flexibility such as interpolation.

resliceTop

Flippes Y and Z axis of an image stack. This operation is similar to ImageJs ‘Reslice [/]’ method but offers less flexibility such as interpolation.

resultsTableColumnToImage

Converts a table column to an image.

resultsTableToImage2D

Converts a table to an image.

rotate2D

Rotates an image in plane. All angles are entered in degrees. If the image is not rotated around the center, it is rotated around the coordinate origin.

rotate3D

Rotates an image stack in 3D. All angles are entered in degrees. If the image is not rotated around the center, it is rotated around the coordinate origin.

rotateClockwise

Rotates a given input image by 90 degrees clockwise.

rotateCounterClockwise

Rotates a given input image by 90 degrees counter-clockwise.

rotateLeft

Rotates a given input image by 90 degrees counter-clockwise. For that, X and Y axis of an image stack are flipped. This operation is similar to ImageJs ‘Reslice [/]’ method but offers less flexibility such as interpolation.

rotateRight

Rotates a given input image by 90 degrees clockwise. For that, X and Y axis of an image stack are flipped. This operation is similar to ImageJs ‘Reslice [/]’ method but offers less flexibility such as interpolation.

S

saveAsTIF

Pulls an image from the GPU memory and saves it as TIF to disc.

scale

DEPRECATED: CLIJ scale() is deprecated. Use scale2D or scale3D instead!

scale2D

Scales an image with a given factor.

scale3D

Scales an image with a given factor.

set

Sets all pixel values x of a given image X to a constant value v.

setColumn

Sets all pixel values x of a given column in X to a constant value v.

setImageBorders

Sets all pixel values at the image border to a given value.

setNonZeroPixelsToPixelIndex

Sets all pixels in an image which are not zero to the index of the pixel.

setPlane

Sets all pixel values x of a given plane in X to a constant value v.

setRampX

Sets all pixel values to their X coordinate

setRampY

Sets all pixel values to their Y coordinate

setRampZ

Sets all pixel values to their Z coordinate

setRandom

Fills an image or image stack with uniformly distributed random numbers between given minimum and maximum values.

setRow

Sets all pixel values x of a given row in X to a constant value v.

setWhereXequalsY

Sets all pixel values a of a given image A to a constant value v in case its coordinates x == y.

setWhereXgreaterThanY

Sets all pixel values a of a given image A to a constant value v in case its coordinates x > y.

setWhereXsmallerThanY

Sets all pixel values a of a given image A to a constant value v in case its coordinates x < y.

shortestDistances

Determine the shortest distance from a distance matrix.

showGlasbeyOnGrey (Experimental)

Visualises two 2D images as one RGB image.

showGrey (Experimental)

Visualises a single 2D image.

showRGB (Experimental)

Visualises three 2D images as one RGB image

skeletonize (Experimental)

Erodes a binary image until just its skeleton is left.

smaller

Determines if two images A and B smaller pixel wise.

smallerConstant

Determines if two images A and B smaller pixel wise.

smallerOrEqual

Determines if two images A and B smaller or equal pixel wise.

smallerOrEqualConstant

Determines if two images A and B smaller or equal pixel wise.

sobel

Convolve the image with the Sobel kernel.

sorensenDiceCoefficient

Determines the overlap of two binary images using the Sorensen-Dice coefficent.

spotsToPointList

Transforms a spots image as resulting from maximum/minimum detection in an image where every column contains d pixels (with d = dimensionality of the original image) with the coordinates of the maxima/minima.

stackToTiles (Experimental)

Stack to tiles.

standardDeviationOfAllPixels

Determines the standard deviation of all pixels in an image.

standardDeviationOfMaskedPixels

Determines the standard deviation of all pixels in an image which have non-zero value in a corresponding mask image.

standardDeviationOfTouchingNeighbors

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

standardDeviationZProjection

Determines the standard deviation projection of an image stack along Z.

startContinuousWebcamAcquisition (Experimental)

Starts acquistion of images from a webcam.

statisticsOfBackgroundAndLabelledPixels

Determines bounding box, area (in pixels/voxels), min, max and mean intensity of background and labelled objects in a label map and corresponding pixels in the original image.

statisticsOfImage

Determines image size (bounding box), area (in pixels/voxels), min, max and mean intensity of all pixels in the original image.

statisticsOfLabelledPixels

Determines bounding box, area (in pixels/voxels), min, max and mean intensity of labelled objects in a label map and corresponding pixels in the original image.

stopContinuousWebcamAcquisition (Experimental)

Stops continous acquistion from a webcam.

stopWatch (Experimental)

Measures time and outputs delay to last call.

subtractBackground2D (Experimental)

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

subtractBackground3D (Experimental)

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

subtractImageFromScalar

Subtracts one image X from a scalar s pixel wise.

subtractImages

Subtracts one image X from another image Y pixel wise.

sumImageSliceBySlice

Sums all pixels slice by slice and returns them in an array.

sumOfAllPixels

Determines the sum of all pixels in a given image. It will be stored in a new row of ImageJs Results table in the column ‘Sum’.

sumPixelsSliceBySlice

sumXProjection

Determines the sum intensity projection of an image along Z.

sumYProjection

Determines the sum intensity projection of an image along Z.

sumZProjection

Determines the sum projection of an image along Z.

T

tenengradFusion (Experimental)

Fuses #n# image stacks using Tenengrads algorithm.

threshold

Computes a binary image with pixel values 0 and 1. All pixel values x of a given input image with value larger or equal to a given threshold t will be set to 1.

thresholdDefault

The automatic thresholder utilizes the Default threshold method implemented in ImageJ using a histogram determined on the GPU to create binary images as similar as possible to ImageJ ‘Apply Threshold’ method.

thresholdHuang

The automatic thresholder utilizes the Huang threshold method implemented in ImageJ using a histogram determined on the GPU to create binary images as similar as possible to ImageJ ‘Apply Threshold’ method.

thresholdIJ_IsoData

The automatic thresholder utilizes the IJ_IsoData threshold method implemented in ImageJ using a histogram determined on the GPU to create binary images as similar as possible to ImageJ ‘Apply Threshold’ method.

thresholdIntermodes

The automatic thresholder utilizes the Intermodes threshold method implemented in ImageJ using a histogram determined on the GPU to create binary images as similar as possible to ImageJ ‘Apply Threshold’ method.

thresholdIsoData

The automatic thresholder utilizes the IsoData threshold method implemented in ImageJ using a histogram determined on the GPU to create binary images as similar as possible to ImageJ ‘Apply Threshold’ method.

thresholdLi

The automatic thresholder utilizes the Li threshold method implemented in ImageJ using a histogram determined on the GPU to create binary images as similar as possible to ImageJ ‘Apply Threshold’ method.

thresholdMaxEntropy

The automatic thresholder utilizes the MaxEntropy threshold method implemented in ImageJ using a histogram determined on the GPU to create binary images as similar as possible to ImageJ ‘Apply Threshold’ method.

thresholdMean

The automatic thresholder utilizes the Mean threshold method implemented in ImageJ using a histogram determined on the GPU to create binary images as similar as possible to ImageJ ‘Apply Threshold’ method.

thresholdMinError

The automatic thresholder utilizes the MinError threshold method implemented in ImageJ using a histogram determined on the GPU to create binary images as similar as possible to ImageJ ‘Apply Threshold’ method.

thresholdMinimum

The automatic thresholder utilizes the Minimum threshold method implemented in ImageJ using a histogram determined on the GPU to create binary images as similar as possible to ImageJ ‘Apply Threshold’ method.

thresholdMoments

The automatic thresholder utilizes the Moments threshold method implemented in ImageJ using a histogram determined on the GPU to create binary images as similar as possible to ImageJ ‘Apply Threshold’ method.

thresholdOtsu

The automatic thresholder utilizes the Otsu threshold method implemented in ImageJ using a histogram determined on the GPU to create binary images as similar as possible to ImageJ ‘Apply Threshold’ method.

thresholdPercentile

The automatic thresholder utilizes the Percentile threshold method implemented in ImageJ using a histogram determined on the GPU to create binary images as similar as possible to ImageJ ‘Apply Threshold’ method.

thresholdRenyiEntropy

The automatic thresholder utilizes the RenyiEntropy threshold method implemented in ImageJ using a histogram determined on the GPU to create binary images as similar as possible to ImageJ ‘Apply Threshold’ method.

thresholdShanbhag

The automatic thresholder utilizes the Shanbhag threshold method implemented in ImageJ using a histogram determined on the GPU to create binary images as similar as possible to ImageJ ‘Apply Threshold’ method.

thresholdTriangle

The automatic thresholder utilizes the Triangle threshold method implemented in ImageJ using a histogram determined on the GPU to create binary images as similar as possible to ImageJ ‘Apply Threshold’ method.

thresholdYen

The automatic thresholder utilizes the Yen threshold method implemented in ImageJ using a histogram determined on the GPU to create binary images as similar as possible to ImageJ ‘Apply Threshold’ method.

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.

touchMatrixToAdjacencyMatrix

Converts a touch matrix in an adjacency matrix

touchMatrixToMesh

Takes a pointlist with dimensions nd with n point coordinates in d dimensions and a touch matrix of size nn to draw lines from all points to points if the corresponding pixel in the touch matrix is 1.

trainWekaFromTable (Experimental)

Trains a Weka model using functionality of Fijis Trainable Weka Segmentation plugin.

trainWekaModel (Experimental)

Trains a Weka model using functionality of Fijis Trainable Weka Segmentation plugin.

trainWekaModelWithOptions (Experimental)

Trains a Weka model using functionality of Fijis Trainable Weka Segmentation plugin.

translate2D

Translate an image stack in X and Y.

translate3D

Translate an image stack in X, Y and Z.

translationRegistration (Experimental)

Measures center of mass of thresholded objects in the two input images and translates the second image so that it better fits to the first image.

translationTimelapseRegistration (Experimental)

Applies 2D translation registration to every pair of t, t+1 slices of a 2D+t image stack.

transposeXY

Transpose X and Y axes of an image.

transposeXZ

Transpose X and Z axes of an image.

transposeYZ

Transpose Y and Z axes of an image.

V

varianceOfAllPixels

Determines the variance of all pixels in an image.

varianceOfMaskedPixels

Determines the variance in an image, but only in pixels which have non-zero values in another binary mask image.

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.

writeVTKLineListToDisc (Experimental)

Takes a point list image representing n points (n2 for 2D points, n3 for 3D points) and a corresponding touch matrix , sized (n+1)*(n+1), and exports them in VTK format.

writeValuesToPositions

Takes an image with three/four rows (2D: height = 3; 3D: height = 4): x, y [, z] and v and target image.

writeXYZPointListToDisc (Experimental)

Takes a point list image representing n points (n2 for 2D points, n3 for 3D points) and exports them in XYZ format.