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CLIJ 1/2/x reference in category ‘transform’

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)

Categories: Binary, Filter, Graphs, Labels, Math, Matrices, Measurements, 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

adjacencyMatrixToTouchMatrix

Converts a adjacency matrix in a touch matrix

affineTransform

Applies an affine transform to a 3D image. Individual transforms must be separated by spaces.

affineTransform2D

Applies an affine transform to a 2D image. Individual transforms must be separated by spaces.

affineTransform3D

Applies an affine transform to a 3D image. Individual transforms must be separated by spaces.

applyVectorField2D

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

applyVectorField3D

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

applyVectorfield

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

C

combineHorizontally

Combines two images or stacks in X.

combineVertically

Combines two images or stacks in Y.

concatenateStacks

Concatenates two stacks in Z.

copy

Copies an image.

copySlice

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.

crop2D

Crops a given rectangle out of a given image.

crop3D

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

cylinderTransform (Experimental)

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

D

downsample2D

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

downsample3D

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

downsampleSliceBySliceHalfMedian

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

driftCorrectionByCenterOfMassFixation (Experimental)

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

driftCorrectionByCentroidFixation (Experimental)

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.

F

flip2D

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

flip3D

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

I

imageToStack

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

L

labelSpots

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

labelledSpotsToPointList

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

M

P

paste2D

Pastes an image into another image at a given position.

paste3D

Pastes an image into another image at a given position.

R

reduceStack

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.

resample

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

resliceBottom

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

resliceLeft

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.

resliceRadial

Computes a radial projection of an image stack.

resliceRadialTop

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

resliceRight

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.

resliceTop

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

rigidTransform (Experimental)

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

rotate2D

Rotates an image in plane.

rotate3D

Rotates an image stack in 3D.

rotateClockwise

Rotates a given input image by 90 degrees clockwise.

rotateCounterClockwise

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

rotateLeft

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

rotateRight

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

S

scale

Scales an image with a given factor.

scale2D

Scales an image with a given factor.

scale3D

Scales an image with a given factor.

sphereTransform (Experimental)

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

spotsToPointList

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.

T

touchMatrixToAdjacencyMatrix

Converts a touch matrix in an adjacency matrix

translate2D

Translate an image stack in X and Y.

translate3D

Translate an image stack in X, Y and Z.

transposeXY

Transpose X and Y axes of an image.

transposeXZ

Transpose X and Z axes of an image.

transposeYZ

Transpose Y and Z axes of an image.