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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)

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

C

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

detectLabelEdges

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

E

excludeLabels

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

excludeLabelsOnEdges

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

excludeLabelsOnSurface

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

excludeLabelsSubSurface

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

excludeLabelsWithValuesOutOfRange

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

excludeLabelsWithValuesWithinRange

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

extendLabelingViaVoronoi

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

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.

L

labelSpots

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

labelToMask

Masks a single label in a label map.

labelVoronoiOctagon

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

labelledSpotsToPointList

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

M

maskLabel

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

P

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.

S

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

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

voronoiLabeling

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