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

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

averageNeighborDistanceMap

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

B

C

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.

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.

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.

countTouchingNeighbors

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

D

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.

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

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.

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

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.

extendLabelingViaVoronoi

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

extensionRatioMap

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

F

findAndLabelMaxima (Experimental)

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

findMaxima (Experimental)

Finds and labels local maxima with neighboring maxima and background above a given tolerance threshold.

flagLabelsOnEdges (Experimental)

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

G

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.

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.

greyLevelAtttributeFiltering (Experimental)

Inspired by Grayscale attribute filtering from MorpholibJ library by David Legland & Ignacio Arganda-Carreras.

I

imageJ3DSuiteConnectedComponentsLabeling (Experimental)

Apply ImageJ 3D Suite Connected Components Labeling (Segment 3D) to an image in 3D.

imglib2ConnectedComponentsLabeling (Experimental)

Apply imglib2 ConnectedComponents (8-connected) to an image to create a label map.

K

kMeansLabelClusterer (Experimental)

Applies K-Means clustering to an image and a corresponding label map.

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.

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.

labelSurface

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

labelVoronoiOctagon

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

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

maskLabel

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

maskedVoronoiLabeling

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

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.

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.

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.

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.

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: …

medianTouchPortionMap (Experimental)

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

mergeTouchingLabels

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.

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: …

morphoLibJClassicWatershed (Experimental)

Apply MorpholibJs Classic Watershed to an image.

morphoLibJFloodFillComponentsLabeling (Experimental)

Apply MorpholibJ FloodFillComponentsLabeling3D to an image.

morphoLibJMarkerControlledWatershed (Experimental)

Apply MorpholibJs Marker-controlled Watershed to an image.

morphoLibJMorphologicalSegmentationLabelBorderImage (Experimental)

Apply MorpholibJ Morphological Segmentation to an object image to produce a label image.

morphoLibJMorphologicalSegmentationLabelObjectImage (Experimental)

Apply MorpholibJ Morphological Segmentation to an object image to produce a label image.

N

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.

pointlistToLabelledSpots

Takes a pointlist with dimensions n times d with n point coordinates in d dimensions and labels corresponding pixels.

proximalNeighborCountMap

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

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.

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.

reduceLabelsToCentroids

Takes a label map and reduces all labels to their center spots. Label IDs stay and background will be zero.

reduceLabelsToLabelEdges

Takes a label map and reduces all labels to their edges. Label IDs stay the same and background will be zero.

reduceLabelsToLabelledSpots (Experimental)

Takes a label map and reduces all labels to their center spots. Label IDs stay and background will be zero.

S

seededWatershed (Experimental)

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

shrinkLabels (Experimental)

Extend labels with a given radius.

simpleITKConnectedComponent (Experimental)

Apply SimpleITKs ConnectedComponent to an image.

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.

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.

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.

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.

T

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

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.

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.

V

visualizeOutlinesOnOriginal

Combines an intensity image and a label (or binary) image so that you can see segmentation outlines on the intensity image.

voronoiLabeling

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

voronoiOtsuLabeling

Labeles objects directly from grey-value images.

W

wekaLabelClassifier (Experimental)

Applies a pre-trained CLIJx-Weka model to an image and a corresponding label map to classify labeled objects.

wekaRegionalLabelClassifier (Experimental)

Applies a pre-trained CLIJx-Weka model to an image and a corresponding label map to classify labeled objects.

140 methods listed.