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

This reference contains all methods currently available in CLIJ, CLIJ2 and CLIJx for performing measurements in images.. Read more about CLIJs release cycle

Please note: CLIJ is deprecated. Make the transition to CLIJ2.

Method is available in CLIJ (deprecated release)
Method is available in CLIJ2 (stable release)
Method is available in CLIJx (experimental release)
Method is available in clEsperanto (experimental)

Categories: Binary, Filter, Graphs, Labels, Math, Matrices, Measurements, Projections, Transformations, Detection, CLIc

[A],[B],[C],[D],[E], F,[G],[H],[I],[J], K,[L],[M],[N], O,[P], Q,[R],[S],[T], U,[V], W, X, Y, Z

A

averageDistanceOfNClosestNeighborsMap

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

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

B

boundingBox

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

C

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.

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.

D

distanceMap

Generates a distance map from a binary image.

drawDistanceMeshBetweenTouchingLabels

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

drawMeshBetweenNClosestLabels

Starting from a label map, draw lines between n closest labels for each label resulting in a mesh.

drawMeshBetweenNNearestLabels

Starting from a label map, draw lines between n closest labels for each label resulting in a mesh.

drawMeshBetweenProximalLabels

Starting from a label map, draw lines between labels that are closer than a given distance resulting in a mesh.

drawMeshBetweenTouchingLabels

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

drawTouchCountMeshBetweenTouchingLabels (Experimental)

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

E

entropyBox

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

euclideanDistanceFromLabelCentroidMap

Takes a label map, determines the centroids of all labels and writes the distance of all labelled pixels to their centroid in the result image. Background pixels stay zero.

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.

extensionRatioMap

Takes a label map, determines for every label the extension ratio and replaces every label with the that number.

G

generateAngleMatrix (Experimental)

Computes the angle in radians between all point coordinates given in two point lists.

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

Computes the distance between all point coordinates given in two point lists.

generateDistanceMatrixAlongAxis (Experimental)

Computes the distance in X, Y or Z (specified with parameter axis) between all point coordinates given in two point lists.

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.

generateNNearestNeighborsMatrix

Produces a touch-matrix where the n nearest neighbors are marked as touching neighbors.

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.

generateProximalNeighborsMatrix

Produces a touch-matrix where the neighbors within a given distance range are marked as touching neighbors.

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

Determines a threshold according to a given method and saves it to the threshold_value variable.

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.

getSorensenDiceCoefficient

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

getSumOfAllPixels

Determines the sum of all pixels in a given image.

H

histogram

Determines the histogram of a given image.

I

imageJ2FrangiVesselness (Experimental)

Apply ImageJ2 / ImageJ Ops Frangi Vesselness filter to an image.

imageJ2Tubeness (Experimental)

Apply ImageJ2 / ImageJ Ops Tubeness filter to an 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 extension ratio and replaces every label with the that number.

labelMaximumIntensityMap (Experimental)

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

labelMeanExtensionMap (Experimental)

Takes a label map, determines for every label the mean 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.

labelMeanOfLaplacianMap (Experimental)

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

labelMinimumIntensityMap (Experimental)

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

labelOverlapCountMap

Takes two label maps, and counts for every label in label map 1 how many labels overlap with it in label map 2.

labelPixelCountMap (Experimental)

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

labelProximalNeighborCountMap

Takes two label maps, and counts for every label in label map 1 how many labels are in a given distance range to it in label map 2.

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.

labelSurface

Takes a label map and excludes all labels which are not on the surface.

labelledSpotsToPointList

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

localMaximumAverageDistanceOfNClosestNeighborsMap (Experimental)

Deprecated: 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)

Deprecated: 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)

Deprecated: 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)

Deprecated: 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)

Deprecated: 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)

Deprecated: 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)

Deprecated: 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)

Deprecated: 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)

localMinimumAverageDistanceOfNClosestNeighborsMap (Experimental)

Deprecated: 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)

Deprecated: 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)

localStandardDeviationAverageDistanceOfNClosestNeighborsMap (Experimental)

Deprecated: 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)

Deprecated: 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)

M

maximumDistanceOfTouchingNeighbors

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

maximumExtensionMap

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.

maximumIntensityMap

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

maximumNeighborDistanceMap (Experimental)

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

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.

maximumOfNNearestNeighborsMap

Takes a label image and a parametric intensity image and will replace each labels value in the parametric image by the maximum value of neighboring labels. The distance number of nearest neighbors can be configured. Note: Values of all pixels in a label each must be identical.

maximumOfProximalNeighborsMap

Takes a label image and a parametric intensity image and will replace each labels value in the parametric image by the maximum value of neighboring labels.

maximumOfTouchingNeighbors

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

maximumOfTouchingNeighborsMap

Takes a label image and a parametric intensity image and will replace each labels value in the parametric image by the maximum value of neighboring labels. The radius of the neighborhood can be configured: * radius 0: Nothing is replaced * radius 1: direct neighbors are taken into account * radius 2: neighbors and neighbors or neighbors are taken into account * radius n: …

maximumTouchingNeighborDistanceMap

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

meanClosestSpotDistance

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

meanExtensionMap

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

meanIntensityMap

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

meanOfAllPixels

Determines the mean average of all pixels in a given image.

meanOfMaskedPixels

Determines the mean intensity in a masked image.

meanOfNNearestNeighborsMap

Takes a label image and a parametric intensity image and will replace each labels value in the parametric image by the minimum value of neighboring labels. The distance number of nearest neighbors can be configured. Note: Values of all pixels in a label each must be identical.

meanOfPixelsAboveThreshold

Determines the mean intensity in a threshleded image.

meanOfProximalNeighborsMap

Takes a label image and a parametric intensity image and will replace each labels value in the parametric image by the mean average value of neighboring labels.

meanOfTouchingNeighbors

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

meanOfTouchingNeighborsMap

Takes a label image and a parametric intensity image and will replace each labels value in the parametric image by the mean average value of neighboring labels. The radius of the neighborhood can be configured: * radius 0: Nothing is replaced * radius 1: direct neighbors are taken into account * radius 2: neighbors and neighbors or neighbors are taken into account * radius n: …

medianOfTouchingNeighbors

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

medianTouchPortionMap (Experimental)

Starts from a label map, determines median touch portion to neighbors (between 0 and 1) and draws a map.

minimumDistanceOfTouchingNeighbors

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

minimumIntensityMap

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

minimumNeighborDistanceMap (Experimental)

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

minimumOfAllPixels

Determines the minimum of all pixels in a given image.

minimumOfMaskedPixels

Determines the minimum intensity in a masked image.

minimumOfNNearestNeighborsMap

minimumOfProximalNeighborsMap

Takes a label image and a parametric intensity image and will replace each labels value in the parametric image by the minimum value of neighboring labels.

minimumOfTouchingNeighbors

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

minimumOfTouchingNeighborsMap

Takes a label image and a parametric intensity image and will replace each labels value in the parametric image by the minimum value of neighboring labels. The radius of the neighborhood can be configured: * radius 0: Nothing is replaced * radius 1: direct neighbors are taken into account * radius 2: neighbors and neighbors or neighbors are taken into account * radius n: …

minimumTouchingNeighborDistanceMap

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

modeOfNNearestNeighborsMap

Takes a label image and a parametric intensity image and will replace each labels value in the parametric image by the mode value of neighboring labels. The distance number of nearest neighbors can be configured. Note: Values of all pixels in a label each must be identical.

modeOfProximalNeighborsMap

Takes a label image and a parametric intensity image and will replace each labels value in the parametric image by the most popular value of neighboring labels.

modeOfTouchingNeighborsMap

Takes a label image and a parametric intensity image and will replace each labels value in the parametric image by the most popular value of neighboring labels. The radius of the neighborhood can be configured: * radius 0: Nothing is replaced * radius 1: direct neighbors are taken into account * radius 2: neighbors and neighbors or neighbors are taken into account * radius n: …

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.

neighborCountWithTouchPortionAboveThresholdMap (Experimental)

Starts from a label map, determines touch portion to neighbors, counts those above a given value (between 0 and 1) and draws a map.

neighborDistanceRangeRatioMap (Experimental)

Takes a label map, determines which labels touch and replaces every label with the distance range ratio (maximum distance divided by minimum distance) to their neighboring labels.

P

pixelCountMap

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

proximalNeighborCountMap

Takes a label map, determines which labels are within a given distance range and replaces every label with the number of neighboring labels.

pullToResultsTable

Converts an image into a table.

R

readIntensitiesFromMap (Experimental)

Takes a label image and an parametric image and reads parametric values from the labels positions.

readValuesFromMap

Takes a label image and an parametric image and reads parametric values from the labels positions.

readValuesFromPositions

Takes a pointlist and a parametric image and reads parametric values from the positions.

S

shortestDistances

Determine the shortest distance from a distance matrix.

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.

standardDeviationIntensityMap

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.

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.

standardDeviationOfNNearestNeighborsMap

Takes a label image and a parametric intensity image and will replace each labels value in the parametric image by the standard deviation value of neighboring labels. The distance number of nearest neighbors can be configured. Note: Values of all pixels in a label each must be identical.

standardDeviationOfProximalNeighborsMap

Takes a label image and a parametric intensity image and will replace each labels value in the parametric image by the standard deviation value of neighboring labels.

standardDeviationOfTouchingNeighbors

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

standardDeviationOfTouchingNeighborsMap

Takes a label image and a parametric intensity image and will replace each labels value in the parametric image by the standard deviation value of touching neighbor labels. The radius of the neighborhood can be configured: * radius 0: Nothing is replaced * radius 1: direct neighbors are taken into account * radius 2: neighbors and neighbors or neighbors are taken into account * radius n: …

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.

sumImageSliceBySlice

Sums all pixels slice by slice and returns the sums in a vector.

sumOfAllPixels

Determines the sum of all pixels in a given image.

T

touchingNeighborCountMap

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

touchingNeighborDistanceRangeRatioMap

Takes a label map, determines which labels touch and replaces every label with the distance range ratio (maximum distance divided by minimum distance) to their neighboring labels.

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.

151 methods listed.