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CLIJ 1/2/x reference

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

absolute

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

absoluteDifference

Determines the absolute difference pixel by pixel between two images.

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

affineTransform

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

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.

applyVectorField3D

Deforms an image stack according to distances provided in the given vector image stacks.

applyVectorfield

Deforms an image according to distances provided in the given 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.

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.

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]

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.

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.

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.

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 !

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.

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.

centroidsOfBackgroundAndLabels

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

centroidsOfLabels

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

clInfo

Outputs information about available OpenCL devices.

clear

Resets the GPUs memory by deleting all cached images.

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.

convertFloat

Convert the input image to a float image with 32 bits per pixel.

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

convertUInt16

Convert the input image to a unsigned integer image with 16 bits per pixel.

convertUInt8

Convert the input image to a unsigned integer image with 8 bits per pixel.

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.

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.

countTouchingNeighbors

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

create2D

Allocated memory for a new 2D image in the GPU memory.

create3D

Allocated memory for a new 3D image in the GPU memory.

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.

cylinderTransform (Experimental)

Applies a cylinder transform to an image stack assuming the center line goes in Y direction in the center of the stack.

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).

detectAndLabelMaxima (Experimental)

Determines maximum regions in a Gaussian blurred version of the original image.

detectLabelEdges

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

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.

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.

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.

distanceMatrixToMesh

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

divideByGaussianBackground (Experimental)

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

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.

downsample3D

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

downsampleSliceBySliceHalfMedian

Scales an image using scaling factors 0.5 for X and Y dimensions. The Z dimension stays untouched.

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.

drawDistanceMeshBetweenTouchingLabels (Experimental)

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

drawLine

Draws a line between two points with a given thickness.

drawMeshBetweenTouchingLabels (Experimental)

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

drawSphere

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

drawTouchCountMeshBetweenTouchingLabels (Experimental)

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

drawTwoValueLine (Experimental)

Draws a line between two points with a given thickness.

driftCorrectionByCenterOfMassFixation (Experimental)

Determines the centerOfMass of the image stack and translates it so that it stays in a defined position.

driftCorrectionByCentroidFixation (Experimental)

Threshold the image stack, determines the centroid of the resulting binary image and translates the image stack so that its centroid sits in a defined position.

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.

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.

extrema (Experimental)

Returns an image with pixel values most distant from 0:

F

findAndLabelMaxima (Experimental)

Determine maxima with a given tolerance to surrounding maxima and background and label them.

findMaxima (Experimental)

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.

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.

generateJaccardIndexMatrix

Takes two labelmaps with n and m labels_2 and generates a (n+1)*(m+1) matrix where all labels_1 are set to 0 exept those where labels_2 overlap between the label maps.

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.

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).

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’.

getGPUProperties

Reads out properties of the currently active GPU and write it in the variables ‘GPU_name’, ‘global_memory_in_bytes’ and ‘OpenCL_Version’.

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.

getMeanOfMaskedPixels

Determines the mean of all pixels in a given image which have non-zero value in a corresponding mask 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.

gradientY

Computes the gradient of gray values along Y.

gradientZ

Computes the gradient of gray values along Z.

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.

greyLevelAtttributeFiltering (Experimental)

Todo.

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.

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.

invalidateKernelCache

Invalidates all cached OpenCL programs and kernels.

invert

Computes the negative value of all pixels in a given image.

J

jaccardIndex

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

L

labelMaximumExtensionMap (Experimental)

Takes a label map, determines for every label the maximum distance of any pixel to the centroid and replaces every label with the that number.

labelMaximumExtensionRatioMap (Experimental)

Takes a label map, determines for every label the maximum distance of any pixel to the centroid and replaces every label with the that number.

labelMeanIntensityMap (Experimental)

Takes an image and a corresponding label map, determines the mean intensity per label and replaces every label with the that number.

labelPixelCountMap (Experimental)

Takes a label map, determines the number of pixels per label and replaces every label with the that number.

labelSpots

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

labelStandardDeviationIntensityMap (Experimental)

Takes an image and a corresponding label map, determines the standard deviation of the intensity per label and replaces every label with the that number.

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

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.

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 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.

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.

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.

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.

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 intensity projection of an image along X.

maximumXYZProjection

maximumYProjection

Determines the maximum intensity projection of an image along X.

maximumZProjection

Determines the maximum intensity projection of an image along Z.

maximumZProjectionBounded

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

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.

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.

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.

meanSquaredError

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

meanXProjection

Determines the mean average intensity projection of an image along X.

meanYProjection

Determines the mean average intensity projection of an image along Y.

meanZProjection

Determines the mean average intensity projection of an image along Z.

meanZProjectionAboveThreshold (Experimental)

Determines the mean average intensity projection of an image along Z but only for pixels above a given threshold.

meanZProjectionBounded

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

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.

medianZProjection

Determines the median intensity projection of an image stack along Z.

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.

minimumImageAndScalar

Computes the minimum 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.

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.

minimumXProjection

Determines the minimum intensity projection of an image along Y.

minimumYProjection

Determines the minimum intensity projection of an image along Y.

minimumZProjection

Determines the minimum intensity projection of an image along Z.

minimumZProjectionBounded

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

minimumZProjectionThresholdedBounded

Determines the minimum intensity 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.

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

parametricWatershed (Experimental)

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

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.

popMetaData (Experimental)

Takes meta data from a stack and assigns it to the current image. The stack implements the Last-In-First-Out (LIFO) principle.

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).

pull

Copies an image specified by its name from GPU memory back to ImageJ and shows it.

pullAsROI

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

pullBinary

Copies a binary image specified by its name from GPU memory back to ImageJ and shows it. This binary image will have 0 and 255 pixel intensities as needed for ImageJ to interpret it as binary.

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.

push

Copies an image specified by its name to GPU memory in order to process it there later.

pushArray

Converts an array to an image.

pushCurrentSelection

Copies an image specified by its name to GPU memory in order to process it there later.

pushCurrentSlice

Copies an image specified by its name to GPU memory in order to process it there later.

pushCurrentSliceSelection

Copies an image specified by its name to GPU memory in order to process it there later.

pushCurrentZStack

Copies an image specified by its name to GPU memory in order to process it there later.

pushMetaData (Experimental)

Stores meta data in a stack. The stack implements the Last-In-First-Out (LIFO) principle.

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.

release

Frees memory of a specified image in GPU memory.

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.

reportMemory

Prints a list of all images cached in the GPU to ImageJs log window together with a sum of memory consumption.

resample

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

resetMetaData (Experimental)

Resets the meta data stack.

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.

resliceRadialTop

Computes a radial projection of an image stack and reslices it from top.

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.

rigidTransform (Experimental)

Applies a rigid transform using linear interpolation to an image stack.

rotate2D

Rotates an image in plane.

rotate3D

Rotates an image stack in 3D.

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.

rotateRight

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

S

saveAsTIF

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

scale

Scales an image with a given factor.

scale2D

Scales an image with a given factor.

scale3D

Scales an image with a given factor.

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.

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.

sphereTransform (Experimental)

Turns an image stack in XYZ cartesian coordinate system to an AID polar coordinate system.

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.

squaredDifference

Determines the squared difference pixel by pixel between two images.

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 intensity 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.

subtractGaussianBackground (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.

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 intensity 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.

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.

touchingNeighborCountMap (Experimental)

Takes a label map, determines which labels touch and replaces every label with the number of touching neighboring labels.

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.

U

undefinedToZero

Copies all pixels instead those which are not a number (NaN) or infinity (inf), which are replaced by 0.

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.

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.

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.