GPU accelerated image processing for everyone

This reference contains all methods currently available in CLIJ, CLIJ2 and CLIJx for transforming images in space.. 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

Converts a adjacency matrix in a touch matrix.

Applies an affine transform to a 3D image.

Applies an affine transform to a 2D image.

Applies an affine transform to a 3D image.

Deforms an image according to distances provided in the given vector images.

Deforms an image stack according to distances provided in the given vector image stacks.

Deforms an image according to distances provided in the given vector images.

Combines two images or stacks in X.

Combines two images or stacks in Y.

Concatenates two stacks in Z.

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.

Crops a given rectangle out of a given image.

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

Applies a cylinder transform to an image stack assuming the center line goes in Y direction in the center of the stack.

Scales an image using given scaling factors for X and Y dimensions.

Scales an image using given scaling factors for X and Y dimensions.

Scales an image using scaling factors 0.5 for X and Y dimensions. The Z dimension stays untouched.

Determines the centerOfMass of the image stack and translates it so that it stays in a defined position.

Threshold the image stack, determines the centroid of the resulting binary image and translates the image stack so that its centroid sits in a defined position.

Flips an image in X and/or Y direction depending on if flip_x and/or flip_y are set to true or false.

Flips an image in X, Y and/or Z direction depending on if flip_x, flip_y and/or flip_z are set to true or false.

Copies a single slice into a stack a given number of times.

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

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

Applies a scaling operation using linear interpolation to generate an image stack with a given isotropic voxel size.

Pastes an image into another image at a given position.

Pastes an image into another image at a given position.

Reduces the number of slices in a stack by a given factor. With the offset you have control which slices stay: * With factor 3 and offset 0, slices 0, 3, 6,… are kept. * With factor 4 and offset 1, slices 1, 5, 9,… are kept.

Resamples an image with given size factors using an affine transform.

Flippes Y and Z axis of an image stack. This operation is similar to ImageJs ‘Reslice [/]’ method but offers less flexibility such as interpolation.

Flippes X, Y and Z axis of an image stack. This operation is similar to ImageJs ‘Reslice [/]’ method but offers less flexibility such as interpolation.

Computes a radial projection of an image stack.

Computes a radial projection of an image stack and reslices it from top.

Flippes X, Y and Z axis of an image stack. This operation is similar to ImageJs ‘Reslice [/]’ method but offers less flexibility such as interpolation.

Flippes Y and Z axis of an image stack. This operation is similar to ImageJs ‘Reslice [/]’ method but offers less flexibility such as interpolation.

Applies a rigid transform using linear interpolation to an image stack.

Rotates an image in plane.

Rotates an image stack in 3D.

Rotates a given input image by 90 degrees clockwise.

Rotates a given input image by 90 degrees counter-clockwise.

Rotates a given input image by 90 degrees counter-clockwise.

Rotates a given input image by 90 degrees counter-clockwise.

Scales an image with a given factor.

Scales an image with a given factor.

Scales an image with a given factor.

Convolve an image with a kernel image using SimpleITK and a fast Fourier transform (FFT).

Turns an image stack in XYZ cartesian coordinate system to an AID polar coordinate system.

Transforms a spots image as resulting from maximum/minimum detection in an image where every column contains d pixels (with d = dimensionality of the original image) with the coordinates of the maxima/minima.

Converts a touch matrix in an adjacency matrix

Translate an image stack in X and Y.

Translate an image stack in X, Y and Z.

Transpose X and Y axes of an image.

Transpose X and Z axes of an image.

Transpose Y and Z axes of an image.

60 methods listed.