GPU accelerated image processing for everyone

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

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

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

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

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

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

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

Determines the number of all pixels in a given image which are not equal to 0.

Counts non-zero pixels in a sphere around every pixel.

Counts non-zero pixels in a sphere around every pixel slice by slice in a stack.

Counts non-zero voxels in a sphere around every voxel.

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

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

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

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

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

Determines the maximum of all pixels in a given image.

Determines the mean of all pixels in a given image.

Determines the minimum of all pixels in a given image.

Determines the sum of all pixels in a given image.

Determines the histogram of a given image.

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

Determines the maximum of all pixels in a given image.

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

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

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

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

Determines the mean intensity in a masked image.

Determines the mean intensity in a threshleded image.

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

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

Determines the minimum of all pixels in a given image.

Determines the minimum intensity in a masked image.

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

Determine the n point indices with shortest distance for all points in a distance matrix.

Determine the n point indices with shortest distance for all points in a distance matrix.

Determine the shortest distance from a distance matrix.

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

Determines the standard deviation of all pixels in an image.

Determines the standard deviation of all pixels in an image which have non-zero value in a corresponding mask image.

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

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.

Determines image size (bounding box), area (in pixels/voxels), min, max and mean intensity of all pixels in the original image.

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.

Sums all pixels slice by slice and returns them in an array.

Determines the sum of all pixels in a given image.

Determines the variance of all pixels in an image.

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