GPU accelerated image processing for everyone

This reference contains all methods currently available in CLIJ, CLIJ2 and CLIJx compatible with pyclesperanto.. 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

[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

Computes the absolute value of every individual pixel x in a given image.

Determines the absolute difference pixel by pixel between two images.

Adds a scalar value s to all pixels x of a given image X.

Calculates the sum of pairs of pixels x and y from images X and Y weighted with factors a and b.

Computes a binary image (containing pixel values 0 and 1) from two images X and Y by connecting pairs of pixels x and y with the binary AND operator &. All pixel values except 0 in the input images are interpreted as 1.

Determines pixels/voxels which are on the surface of binary objects and sets only them to 1 in the destination image. All other pixels are set to 0.

Computes a binary image (containing pixel values 0 and 1) from an image X by negating its pixel values x using the binary NOT operator !

Computes a binary image (containing pixel values 0 and 1) from two images X and Y by connecting pairs of pixels x and y with the binary OR operator |.

Subtracts one binary image from another.

Computes a binary image (containing pixel values 0 and 1) from two images X and Y by connecting pairs of pixels x and y with the binary operators AND &, OR | and NOT ! implementing the XOR operator.

Apply a bottom-hat filter for background subtraction to the input image.

Applies a bottom-hat filter for background subtraction to the input image.

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

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

Outputs information about available OpenCL devices.

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.

Performs connected components analysis inspecting the box neighborhood of every pixel to a binary image and generates a label map.

Performs connected components analysis inspecting the diamond neighborhood of every pixel to a binary image and generates a label map.

Convolve the image with a given kernel image.

Copies an image.

This method has two purposes: It copies a 2D image to a given slice z position in a 3D image stack or It copies a given slice at position z in an image stack to a 2D image.

Allocated memory for a new 2D image in the GPU memory.

Allocated memory for a new 3D image in the GPU memory.

Crops a given rectangle out of a given image.

Crops a given sub-stack out of a given image stack.

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

Detects local maxima in a given square/cubic neighborhood.

Detects local maxima in a given square/cubic neighborhood.

Detects local maxima in a given square/cubic neighborhood.

Applies Gaussian blur to the input image twice with different sigma values resulting in two images which are then subtracted from each other.

Applies Gaussian blur to the input image twice with different sigma values resulting in two images which are then subtracted from each other.

Computes a binary image with pixel values 0 and 1 containing the binary dilation of a given input image.

Computes a binary image with pixel values 0 and 1 containing the binary dilation of a given input image.

Computes a binary image with pixel values 0 and 1 containing the binary dilation of a given input image.

Divides two images X and Y by each other pixel wise.

Draws a box at a given start point with given size. All pixels other than in the box are untouched. Consider using `set(buffer, 0);`

in advance.

Draws a line between two points with a given thickness.

Draws a sphere around a given point with given radii in x, y and z (if 3D).

Determines if two images A and B equal pixel wise.

Determines if an image A and a constant b are equal.

Computes a binary image with pixel values 0 and 1 containing the binary erosion of a given input image.

Computes a binary image with pixel values 0 and 1 containing the binary erosion of a given input image.

Computes a binary image with pixel values 0 and 1 containing the binary erosion of a given input image.

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

Computes base exponential of all pixels values.

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

Flips an image in X and/or Y direction depending on boolean flags.

Flips an image in X, Y and/or Z direction depending on boolean flags.

Computes the Gaussian blurred image of an image given two sigma values in X and Y.

Computes the Gaussian blurred image of an image given two sigma values in X, Y and Z.

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

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.

Computes the gradient of gray values along X.

Computes the gradient of gray values along Y.

Computes the gradient of gray values along Z.

Determines if two images A and B greater pixel wise.

Determines if two images A and B greater pixel wise.

Determines if two images A and B greater or equal pixel wise.

Determines if two images A and B greater or equal pixel wise.

Determines the histogram of a given image.

Computes the negative value of all pixels in a given image.

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

Applies the Laplace operator (Box neighborhood) to an image.

Computes base e logarithm of all pixels values.

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

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

Computes the local maximum of a pixels rectangular neighborhood.

Computes the local maximum of a pixels ellipsoidal neighborhood.

Computes the local maximum of a pixels cube neighborhood.

Computes the local maximum of a pixels spherical neighborhood.

Computes the maximum of a constant scalar s and each pixel value x in a given image X.

Computes the maximum of a pair of pixel values x, y from two given images X and Y.

Determines the maximum of all pixels in a given image.

Determines the maximum intensity projection of an image along X.

Determines the maximum intensity projection of an image along X.

Determines the maximum intensity projection of an image along Z.

Computes the local mean average of a pixels rectangular neighborhood.

Computes the local mean average of a pixels ellipsoidal neighborhood.

Computes the local mean average of a pixels cube neighborhood.

Computes the local mean average of a pixels spherical neighborhood.

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

Determines the mean squared error (MSE) between two images.

Determines the mean average intensity projection of an image along X.

Determines the mean average intensity projection of an image along Y.

Determines the mean average intensity projection of an image along Z.

Computes the local minimum of a pixels rectangular neighborhood.

Computes the local minimum of a pixels ellipsoidal neighborhood.

Computes the local minimum of a pixels cube neighborhood.

Computes the local minimum of a pixels spherical neighborhood.

Computes the minimum of a constant scalar s and each pixel value x in a given image X.

Computes the minimum of a pair of pixel values x, y from two given images X and Y.

Determines the minimum of all pixels in a given image.

Determines the minimum intensity in a masked image.

Determines the minimum intensity projection of an image along Y.

Determines the minimum intensity projection of an image along Y.

Determines the minimum intensity projection of an image along Z.

Multiplies all pixel intensities with the x, y or z coordinate, depending on specified dimension.

Multiplies all pixels value x in a given image X with a constant scalar s.

Multiplies all pairs of pixel values x and y from two image X and Y.

Multiplies two matrices with each other.

Apply a maximum filter (box shape) to the input image.

Apply a maximum filter (diamond shape) to the input image.

Apply a minimum filter (box shape) to the input image.

Apply a minimum filter (diamond shape) to the input image.

Determines if two images A and B equal pixel wise.

Determines if two images A and B equal pixel wise.

Apply a local maximum filter to an image which only overwrites pixels with value 0.

Apply a local maximum filter to an image which only overwrites pixels with value 0.

Pastes an image into another image at a given position.

Pastes an image into another image at a given position.

Computes all pixels value x to the power of a given exponent a.

Calculates x to the power of y pixel wise of two images X and Y.

Copies an image specified by its name from GPU memory back to ImageJ and shows it.

Copies an image specified by its name to GPU memory in order to process it there later.

Replaces integer intensities specified in a vector image.

Replaces a specific intensity in an image with a given new value.

Sets all pixel values x of a given image X to a constant value v.

Sets all pixel values x of a given column in X to a constant value v.

Sets all pixel values at the image border to a given value.

Sets all pixel values x of a given plane in X to a constant value v.

Sets all pixel values to their X coordinate

Sets all pixel values to their Y coordinate

Sets all pixel values to their Z coordinate

Sets all pixel values x of a given row in X to a constant value v.

Determines if two images A and B smaller pixel wise.

Determines if two images A and B smaller pixel wise.

Determines if two images A and B smaller or equal pixel wise.

Determines if two images A and B smaller or equal pixel wise.

Convolve the image with the Sobel kernel.

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

Determines the squared difference pixel by pixel between two images.

Determines the standard deviation intensity projection of an image stack along Z.

Subtracts one image X from a scalar s pixel wise.

Subtracts one image X from another image Y pixel wise.

Determines the sum of all pixels in a given image.

Determines the sum intensity projection of an image along Z.

Determines the sum intensity projection of an image along Z.

Determines the sum intensity projection of an image along Z.

The automatic thresholder utilizes the Otsu threshold method implemented in ImageJ using a histogram determined on the GPU to create binary images as similar as possible to ImageJ ‘Apply Threshold’ method.

Applies a top-hat filter for background subtraction to the input image.

Applies a top-hat filter for background subtraction to the input image.

Takes a pointlist with dimensions n*d with n point coordinates in d dimensions and a touch matrix of size n*n to draw lines from all points to points if the corresponding pixel in the touch matrix is 1.

Transpose X and Y axes of an image.

Transpose X and Z axes of an image.

Transpose Y and Z axes of an image.

Copies all pixels instead those which are not a number (NaN) or infinity (inf), which are replaced by 0.

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

157 methods listed.