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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)

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

averageDistanceOfNClosestPoints

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

averageDistanceOfNFarOffPoints

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

averageDistanceOfTouchingNeighbors

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

B

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.

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.

G

getBoundingBox

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

getCenterOfMass

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

getDimensions

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

getJaccardIndex

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

getMaximumOfAllPixels

Determines the maximum of all pixels in a given image.

getMeanOfAllPixels

Determines the mean of all pixels in a given image.

getMinimumOfAllPixels

Determines the minimum of all pixels in a given image.

getSumOfAllPixels

Determines the sum of all pixels in a given image.

H

histogram

Determines the histogram of a given image.

J

jaccardIndex

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

M

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.

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.

medianOfTouchingNeighbors

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

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.

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.

S

shortestDistances

Determine the shortest distance from a distance matrix.

sorensenDiceCoefficient

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

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.

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 them in an array.

sumOfAllPixels

Determines the sum of all pixels in a given image.

V

varianceOfAllPixels

Determines the variance of all pixels in an image.

varianceOfMaskedPixels

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