Package net.haesleinhuepf.clij2

Interface CLIJ2Ops

  • All Known Implementing Classes:
    CLIJ2
    public interface CLIJ2Ops

    • Method Summary

      All Methods Instance Methods Abstract Methods Default Methods Deprecated Methods 
      Modifier and Type Method Description
      default boolean absolute​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Computes the absolute value of every individual pixel x in a given image.
      default boolean absoluteDifference​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer source2, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
      Determines the absolute difference pixel by pixel between two images.
      default boolean addImageAndScalar​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3)
      Adds a scalar value s to all pixels x of a given image X.
      default boolean addImages​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface summand1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface summand2, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Calculates the sum of pairs of pixels x and y of two images X and Y.
      default boolean addImagesWeighted​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg3, double arg4, double arg5)
      Calculates the sum of pairs of pixels x and y from images X and Y weighted with factors a and b.
      default boolean adjacencyMatrixToTouchMatrix​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer adjacency_matrix, net.haesleinhuepf.clij.clearcl.ClearCLBuffer touch_matrix)
      Converts a adjacency matrix in a touch matrix.
      default boolean affineTransform2D​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, float[] arg3)
      Applies an affine transform to a 2D image.
      default boolean affineTransform2D​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination, String transform)
      Applies an affine transform to a 2D image.
      default boolean affineTransform2D​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, AffineTransform2D arg3)
      Applies an affine transform to a 2D image.
      default boolean affineTransform2D​(net.haesleinhuepf.clij.clearcl.ClearCLImage arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, float[] arg3)
      Applies an affine transform to a 2D image.
      default boolean affineTransform2D​(net.haesleinhuepf.clij.clearcl.ClearCLImage arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, AffineTransform2D arg3)
      Applies an affine transform to a 2D image.
      default boolean affineTransform3D​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, float[] arg3)
      Applies an affine transform to a 3D image.
      default boolean affineTransform3D​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination, String transform)
      Applies an affine transform to a 3D image.
      default boolean affineTransform3D​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, AffineTransform3D arg3)
      Applies an affine transform to a 3D image.
      default boolean affineTransform3D​(net.haesleinhuepf.clij.clearcl.ClearCLImage arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, float[] arg3)
      Applies an affine transform to a 3D image.
      default boolean affineTransform3D​(net.haesleinhuepf.clij.clearcl.ClearCLImage arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, AffineTransform3D arg3)
      Applies an affine transform to a 3D image.
      default boolean applyVectorField​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface vector_x, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface vector_y, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Deforms an image according to distances provided in the given vector images.
      default boolean applyVectorField​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg3, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg4, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg5)
      Deforms an image according to distances provided in the given vector images.
      default boolean applyVectorField2D​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface vector_x, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface vector_y, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Deforms an image according to distances provided in the given vector images.
      default boolean applyVectorField3D​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface vectorX, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface vectorY, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface vectorZ, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Deforms an image stack according to distances provided in the given vector image stacks.
      default boolean argMaximumZProjection​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination_max, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination_arg_max)
      Determines the maximum projection of an image stack along Z.
      default boolean automaticThreshold​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination, String method)
      The automatic thresholder utilizes the threshold methods from ImageJ on a histogram determined on the GPU to create binary images as similar as possible to ImageJ 'Apply Threshold' method.
      default boolean automaticThreshold​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, String arg3, double arg4, double arg5, double arg6)
      The automatic thresholder utilizes the threshold methods from ImageJ on a histogram determined on the GPU to create binary images as similar as possible to ImageJ 'Apply Threshold' method.
      default boolean averageDistanceOfClosestPoints​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3)
      Deprecated.
      default boolean averageDistanceOfNClosestPoints​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3)
      Determines the average of the n closest points for every point in a distance matrix.
      default boolean averageDistanceOfNFarOffPoints​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3)
      Determines the average of the n far off (most distant) points for every point in a distance matrix.
      default boolean averageDistanceOfTouchingNeighbors​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer distance_matrix, net.haesleinhuepf.clij.clearcl.ClearCLBuffer touch_matrix, net.haesleinhuepf.clij.clearcl.ClearCLBuffer average_distancelist_destination)
      Takes a touch matrix and a distance matrix to determine the average distance of touching neighbors for every object.
      default boolean binaryAnd​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface operand1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface operand2, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      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 &.
      default boolean binaryEdgeDetection​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Determines pixels/voxels which are on the surface of binary objects and sets only them to 1 in the destination image.
      default boolean binaryFillHoles​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Fills holes (pixels with value 0 surrounded by pixels with value 1) in a binary image.
      default boolean binaryIntersection​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer operand1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer operand2, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
      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 intersection operator &.
      default boolean binaryNot​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      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 ! All pixel values except 0 in the input image are interpreted as 1.
      default boolean binaryOr​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface operand1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface operand2, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      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 |.
      default boolean binarySubtract​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface minuend, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface subtrahend, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Subtracts one binary image from another.
      default boolean binaryUnion​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer operand1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer operand2, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
      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 union operator |.
      default boolean binaryXOr​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface operand1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface operand2, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      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.
      default boolean blur​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4)
      Deprecated.
      default boolean blur​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4, double arg5)
      Deprecated.
      default boolean blur2D​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4)
      Deprecated.
      default boolean blur3D​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4, double arg5)
      Deprecated.
      default boolean bottomHatBox​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3, double arg4, double arg5)
      Apply a bottom-hat filter for background subtraction to the input image.
      default boolean bottomHatSphere​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3, double arg4, double arg5)
      Applies a bottom-hat filter for background subtraction to the input image.
      default double[] boundingBox​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source)
      Determines the bounding box of all non-zero pixels in a binary image.
      default double[] centerOfMass​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source)
      Determines the center of mass of an image or image stack.
      default boolean centroidsOfBackgroundAndLabels​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source, net.haesleinhuepf.clij.clearcl.ClearCLBuffer pointlist_destination)
      Determines the centroids of the background and all labels in a label image or image stack.
      default boolean centroidsOfLabels​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source, net.haesleinhuepf.clij.clearcl.ClearCLBuffer pointlist_destination)
      Determines the centroids of all labels in a label image or image stack.
      default boolean closeIndexGapsInLabelMap​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer labeling_input, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface labeling_destination)
      Analyses a label map and if there are gaps in the indexing (e.g.
      default boolean closingBox​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3)
      Apply a binary closing to the input image by calling n dilations and n erosions subsequenntly.
      default boolean closingDiamond​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3)
      Apply a binary closing to the input image by calling n dilations and n erosions subsequently.
      default boolean combineHorizontally​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface stack1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface stack2, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Combines two images or stacks in X.
      default boolean combineVertically​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface stack1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface stack2, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Combines two images or stacks in Y.
      default boolean concatenateStacks​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface stack1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface stack2, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Concatenates two stacks in Z.
      default boolean connectedComponentsLabeling​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface binary_input, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface labeling_destination)
      Deprecated.
      default boolean connectedComponentsLabelingBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface binary_input, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface labeling_destination)
      Performs connected components analysis inspecting the box neighborhood of every pixel to a binary image and generates a label map.
      default boolean connectedComponentsLabelingBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, boolean arg3)
      Performs connected components analysis inspecting the box neighborhood of every pixel to a binary image and generates a label map.
      default boolean connectedComponentsLabelingDiamond​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface binary_input, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface labeling_destination)
      Performs connected components analysis inspecting the diamond neighborhood of every pixel to a binary image and generates a label map.
      default boolean connectedComponentsLabelingDiamond​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, boolean arg3)
      Performs connected components analysis inspecting the diamond neighborhood of every pixel to a binary image and generates a label map.
      default boolean convolve​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source, net.haesleinhuepf.clij.clearcl.ClearCLBuffer convolution_kernel, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
      Convolve the image with a given kernel image.
      default boolean copy​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Copies an image.
      default boolean copySlice​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3)
      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.
      default double countNonZeroPixels​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source)
      Determines the number of all pixels in a given image which are not equal to 0.
      default boolean countNonZeroPixels2DSphere​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3, double arg4)
      Counts non-zero pixels in a sphere around every pixel.
      default boolean countNonZeroPixelsLocally​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3, double arg4)
      Deprecated.
      default boolean countNonZeroPixelsLocallySliceBySlice​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3, double arg4)
      Deprecated.
      default boolean countNonZeroPixelsSliceBySliceSphere​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3, double arg4)
      Counts non-zero pixels in a sphere around every pixel slice by slice in a stack.
      default boolean countNonZeroVoxels3DSphere​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3, double arg4, double arg5)
      Counts non-zero voxels in a sphere around every voxel.
      default boolean countNonZeroVoxelsLocally​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3, double arg4, double arg5)
      Deprecated.
      default boolean countTouchingNeighbors​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer touch_matrix, net.haesleinhuepf.clij.clearcl.ClearCLBuffer touching_neighbors_count_destination)
      Takes a touch matrix as input and delivers a vector with number of touching neighbors per label as a vector.
      default boolean crop​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4)
      Crops a given rectangle out of a given image.
      default boolean crop​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4, double arg5)
      Crops a given rectangle out of a given image.
      default boolean crop2D​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4)
      Crops a given rectangle out of a given image.
      default boolean crop3D​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4, double arg5)
      Crops a given sub-stack out of a given image stack.
      default boolean customOperation​(String arg1, String arg2, HashMap arg3)
      Executes a custom operation wirtten in OpenCL on a custom list of images.
      default boolean depthColorProjection​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg3, double arg4, double arg5)
      Determines a maximum projection of an image stack and does a color coding of the determined arg Z (position of the found maximum).
      default boolean detectLabelEdges​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface label_map, net.haesleinhuepf.clij.clearcl.ClearCLBuffer edge_image_destination)
      Takes a labelmap and returns an image where all pixels on label edges are set to 1 and all other pixels to 0.
      default boolean detectMaxima2DBox​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3, double arg4)
      Detects local maxima in a given square/cubic neighborhood.
      default boolean detectMaxima3DBox​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3, double arg4, double arg5)
      Detects local maxima in a given square/cubic neighborhood.
      default boolean detectMaximaBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3)
      Deprecated.
      default boolean detectMaximaBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4, double arg5)
      Detects local maxima in a given square/cubic neighborhood.
      default boolean detectMaximaSliceBySliceBox​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3, double arg4)
      Detects local maxima in a given square neighborhood of an input image stack.
      default boolean detectMinima2DBox​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3, double arg4)
      Detects local minima in a given square/cubic neighborhood.
      default boolean detectMinima3DBox​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3, double arg4, double arg5)
      Detects local minima in a given square/cubic neighborhood.
      default boolean detectMinimaBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3)
      Deprecated.
      default boolean detectMinimaBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4, double arg5)
      Detects local minima in a given square/cubic neighborhood.
      default boolean detectMinimaSliceBySliceBox​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3, double arg4)
      Detects local minima in a given square neighborhood of an input image stack.
      default boolean differenceOfGaussian​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3, double arg4, double arg5, double arg6)
      Applies Gaussian blur to the input image twice with different sigma values resulting in two images which are then subtracted from each other.
      default boolean differenceOfGaussian​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3, double arg4, double arg5, double arg6, double arg7, double arg8)
      Applies Gaussian blur to the input image twice with different sigma values resulting in two images which are then subtracted from each other.
      default boolean differenceOfGaussian2D​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3, double arg4, double arg5, double arg6)
      Applies Gaussian blur to the input image twice with different sigma values resulting in two images which are then subtracted from each other.
      default boolean differenceOfGaussian3D​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3, double arg4, double arg5, double arg6, double arg7, double arg8)
      Applies Gaussian blur to the input image twice with different sigma values resulting in two images which are then subtracted from each other.
      default boolean dilateBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Computes a binary image with pixel values 0 and 1 containing the binary dilation of a given input image.
      default boolean dilateBoxSliceBySlice​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Computes a binary image with pixel values 0 and 1 containing the binary dilation of a given input image.
      default boolean dilateSphere​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Computes a binary image with pixel values 0 and 1 containing the binary dilation of a given input image.
      default boolean dilateSphereSliceBySlice​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Computes a binary image with pixel values 0 and 1 containing the binary dilation of a given input image.
      default boolean distanceMap​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
      Generates a distance map from a binary image.
      default boolean distanceMatrixToMesh​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg3, double arg4)
      Generates a mesh from a distance matric and a list of point coordinates.
      default boolean divideImages​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface divident, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface divisor, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Divides two images X and Y by each other pixel wise.
      boolean doTimeTracing()  
      default boolean downsample​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4)
      Deprecated.
      default boolean downsample​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4, double arg5)
      Deprecated.
      default boolean downsample2D​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4)
      Deprecated.
      default boolean downsample3D​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4, double arg5)
      Deprecated.
      default boolean downsampleSliceBySliceHalfMedian​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Scales an image using scaling factors 0.5 for X and Y dimensions.
      default boolean drawBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, double arg2, double arg3, double arg4, double arg5)
      Draws a box at a given start point with given size.
      default boolean drawBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, double arg2, double arg3, double arg4, double arg5, double arg6, double arg7)
      Draws a box at a given start point with given size.
      default boolean drawBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, double arg2, double arg3, double arg4, double arg5, double arg6, double arg7, double arg8)
      Draws a box at a given start point with given size.
      default boolean drawLine​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, double arg2, double arg3, double arg4, double arg5, double arg6, double arg7, double arg8)
      Draws a line between two points with a given thickness.
      default boolean drawLine​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, double arg2, double arg3, double arg4, double arg5, double arg6, double arg7, double arg8, double arg9)
      Draws a line between two points with a given thickness.
      default boolean drawSphere​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, double arg2, double arg3, double arg4, double arg5)
      Draws a sphere around a given point with given radii in x, y and z (if 3D).
      default boolean drawSphere​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, double arg2, double arg3, double arg4, double arg5, double arg6)
      Draws a sphere around a given point with given radii in x, y and z (if 3D).
      default boolean drawSphere​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, double arg2, double arg3, double arg4, double arg5, double arg6, double arg7)
      Draws a sphere around a given point with given radii in x, y and z (if 3D).
      default boolean drawSphere​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, double arg2, double arg3, double arg4, double arg5, double arg6, double arg7, double arg8)
      Draws a sphere around a given point with given radii in x, y and z (if 3D).
      default boolean entropyBox​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3, double arg4, double arg5)
      Determines the local entropy in a box with a given radius around every pixel.
      default boolean entropyBox​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3, double arg4, double arg5, double arg6, double arg7)
      Determines the local entropy in a box with a given radius around every pixel.
      default boolean equal​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source2, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Determines if two images A and B equal pixel wise.
      default boolean equalConstant​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3)
      Determines if an image A and a constant b are equal.
      default boolean equalizeMeanIntensitiesOfSlices​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3)
      Determines correction factors for each z-slice so that the average intensity in all slices can be made the same and multiplies these factors with the slices.
      default boolean erodeBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Computes a binary image with pixel values 0 and 1 containing the binary erosion of a given input image.
      default boolean erodeBoxSliceBySlice​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Computes a binary image with pixel values 0 and 1 containing the binary erosion of a given input image.
      default boolean erodeSphere​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Computes a binary image with pixel values 0 and 1 containing the binary erosion of a given input image.
      default boolean erodeSphereSliceBySlice​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Computes a binary image with pixel values 0 and 1 containing the binary erosion of a given input image.
      default boolean excludeLabels​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer binary_flaglist, net.haesleinhuepf.clij.clearcl.ClearCLBuffer label_map_input, net.haesleinhuepf.clij.clearcl.ClearCLBuffer label_map_destination)
      This operation removes labels from a labelmap and renumbers the remaining labels.
      default boolean excludeLabelsOnEdges​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer label_map_input, net.haesleinhuepf.clij.clearcl.ClearCLBuffer label_map_destination)
      Removes all labels from a label map which touch the edges of the image (in X, Y and Z if the image is 3D).
      default boolean excludeLabelsOnSurface​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg3, double arg4, double arg5, double arg6)
      This operation follows a ray from a given position towards a label (or opposite direction) and checks if there is another label between the label an the image border.
      default boolean excludeLabelsSubSurface​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg3, double arg4, double arg5, double arg6)
      This operation follows a ray from a given position towards a label (or opposite direction) and checks if there is another label between the label an the image border.
      default boolean excludeLabelsWithValuesOutOfRange​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg3, double arg4, double arg5)
      This operation removes labels from a labelmap and renumbers the remaining labels.
      default boolean excludeLabelsWithValuesWithinRange​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg3, double arg4, double arg5)
      This operation removes labels from a labelmap and renumbers the remaining labels.
      default boolean exponential​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Computes base exponential of all pixels values.
      default boolean extendLabelingViaVoronoi​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Takes a label map image and dilates the regions using a octagon shape until they touch.
      default boolean fillHistogram​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3, double arg4)
      Deprecated.
      default boolean flip​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, boolean arg3, boolean arg4)
      Flips an image in X and/or Y direction depending on if flip_x and/or flip_y are set to true or false.
      default boolean flip​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, boolean arg3, boolean arg4, boolean arg5)
      Flips an image in X and/or Y direction depending on if flip_x and/or flip_y are set to true or false.
      default boolean flip2D​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, boolean arg3, boolean arg4)
      Flips an image in X and/or Y direction depending on if flip_x and/or flip_y are set to true or false.
      default boolean flip3D​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, boolean arg3, boolean arg4, boolean arg5)
      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.
      default boolean floodFillDiamond​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3, double arg4)
      Replaces recursively all pixels of value a with value b if the pixels have a neighbor with value b.
      default boolean gaussianBlur​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4)
      Computes the Gaussian blurred image of an image given two sigma values in X and Y.
      default boolean gaussianBlur​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4, double arg5)
      Computes the Gaussian blurred image of an image given two sigma values in X and Y.
      default boolean gaussianBlur2D​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4)
      Computes the Gaussian blurred image of an image given two sigma values in X and Y.
      default boolean gaussianBlur3D​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4, double arg5)
      Computes the Gaussian blurred image of an image given two sigma values in X, Y and Z.
      default boolean generateBinaryOverlapMatrix​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer label_map1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer label_map2, net.haesleinhuepf.clij.clearcl.ClearCLBuffer binary_overlap_matrix_destination)
      Takes two labelmaps with n and m labels and generates a (n+1)*(m+1) matrix where all pixels are set to 0 exept those where labels overlap between the label maps.
      default boolean generateDistanceMatrix​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer coordinate_list1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer coordinate_list2, net.haesleinhuepf.clij.clearcl.ClearCLBuffer distance_matrix_destination)
      Computes the distance between all point coordinates given in two point lists.
      default boolean generateJaccardIndexMatrix​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer label_map1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer label_map2, net.haesleinhuepf.clij.clearcl.ClearCLBuffer jaccard_index_matrix_destination)
      Takes two labelmaps with n and m labels_2 and generates a (n+1)*(m+1) matrix where all labels_1 are set to 0 exept those where labels_2 overlap between the label maps.
      default boolean generateParametricImage​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface label_map, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface parameter_value_vector, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface parametric_image_destination)
      Take a labelmap and a vector of values to replace label 1 with the 1st value in the vector.
      default boolean generateParametricImageFromResultsTableColumn​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, ResultsTable arg3, String arg4)
      Take a labelmap and a column from the results table to replace label 1 with the 1st value in the vector.
      default boolean generateTouchCountMatrix​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer label_map, net.haesleinhuepf.clij.clearcl.ClearCLBuffer touch_count_matrix_destination)
      Takes a label map with n labels and generates a (n+1)*(n+1) matrix where all pixels are set the number of pixels where labels touch (diamond neighborhood).
      default boolean generateTouchMatrix​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer label_map, net.haesleinhuepf.clij.clearcl.ClearCLBuffer touch_matrix_destination)
      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.
      default double getAutomaticThreshold​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, String arg2)
      Determines a threshold according to a given method and saves it to the threshold_value variable.
      default double getAutomaticThreshold​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, String arg2, double arg3, double arg4, double arg5)
      Determines a threshold according to a given method and saves it to the threshold_value variable.
      default double[] getBoundingBox​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1)
      Determines the bounding box of all non-zero pixels in a binary image.
      default double[] getCenterOfMass​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1)
      Determines the center of mass of an image or image stack.
      net.haesleinhuepf.clij.CLIJ getCLIJ()  
      CLIJ2 getCLIJ2()  
      default long[] getDimensions​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1)
      Reads out the size of an image [stack] and writes it to the variables 'width', 'height' and 'depth'.
      default double getJaccardIndex​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2)
      Determines the overlap of two binary images using the Jaccard index.
      default double getMaximumOfAllPixels​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1)
      Determines the maximum of all pixels in a given image.
      default double getMeanOfAllPixels​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1)
      Determines the mean of all pixels in a given image.
      default double getMeanOfMaskedPixels​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2)
      Determines the mean of all pixels in a given image which have non-zero value in a corresponding mask image.
      default double getMinimumOfAllPixels​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1)
      Determines the minimum of all pixels in a given image.
      default long[] getSize​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source)
      Deprecated.
      default double getSorensenDiceCoefficient​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2)
      Determines the overlap of two binary images using the Sorensen-Dice coefficent.
      default double getSumOfAllPixels​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1)
      Determines the sum of all pixels in a given image.
      default boolean gradientX​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
      Computes the gradient of gray values along X.
      default boolean gradientY​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
      Computes the gradient of gray values along Y.
      default boolean gradientZ​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
      Computes the gradient of gray values along Z.
      default boolean greater​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source2, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Determines if two images A and B greater pixel wise.
      default boolean greaterConstant​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3)
      Determines if two images A and B greater pixel wise.
      default boolean greaterOrEqual​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source2, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Determines if two images A and B greater or equal pixel wise.
      default boolean greaterOrEqualConstant​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3)
      Determines if two images A and B greater or equal pixel wise.
      default net.haesleinhuepf.clij.clearcl.ClearCLBuffer histogram​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1)
      Determines the histogram of a given image.
      default float[] histogram​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, double arg2, double arg3, double arg4)
      Determines the histogram of a given image.
      default boolean histogram​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2)
      Determines the histogram of a given image.
      default boolean histogram​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3, double arg4, double arg5, boolean arg6)
      Determines the histogram of a given image.
      default boolean histogram​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3, double arg4, double arg5, boolean arg6, boolean arg7)
      Determines the histogram of a given image.
      default ResultsTable image2DToResultsTable​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, ResultsTable arg2)
      Deprecated.
      default ResultsTable image2DToResultsTable​(net.haesleinhuepf.clij.clearcl.ClearCLImage arg1, ResultsTable arg2)
      Deprecated.
      default boolean imageToStack​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3)
      Copies a single slice into a stack a given number of times.
      default boolean invert​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Computes the negative value of all pixels in a given image.
      default double jaccardIndex​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer source2)
      Determines the overlap of two binary images using the Jaccard index.
      default boolean labelledSpotsToPointList​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input_labelled_spots, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination_pointlist)
      Generates a coordinate list of points in a labelled spot image.
      default boolean labelSpots​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input_spots, net.haesleinhuepf.clij.clearcl.ClearCLBuffer labelled_spots_destination)
      Transforms a binary image with single pixles set to 1 to a labelled spots image.
      default boolean labelToMask​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3)
      Masks a single label in a label map.
      default boolean labelVoronoiOctagon​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer label_map, net.haesleinhuepf.clij.clearcl.ClearCLBuffer label_voronoi_destination)
      Takes a labelled image and dilates the labels using a octagon shape until they touch.
      default boolean laplaceBox​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
      Applies the Laplace operator (Box neighborhood) to an image.
      default boolean laplaceSphere​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
      Applies the Laplace operator (Diamond neighborhood) to an image.
      default boolean localThreshold​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface localThreshold, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Computes a binary image with pixel values 0 and 1 depending on if a pixel value x in image X was above of equal to the pixel value m in mask image M.
      default boolean logarithm​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Computes base e logarithm of all pixels values.
      default boolean mask​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface mask, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Computes a masked image by applying a binary mask to an image.
      default boolean maskLabel​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg3, double arg4)
      Computes a masked image by applying a label mask to an image.
      default boolean maskStackWithPlane​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface mask, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Computes a masked image by applying a binary 2D mask to an image stack.
      default boolean matrixEqual​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3)
      Checks if all elements of a matrix are different by less than or equal to a given tolerance.
      default boolean maximum2DBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4)
      Computes the local maximum of a pixels rectangular neighborhood.
      default boolean maximum2DSphere​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4)
      Computes the local maximum of a pixels ellipsoidal neighborhood.
      default boolean maximum3DBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4, double arg5)
      Computes the local maximum of a pixels cube neighborhood.
      default boolean maximum3DSliceBySliceSphere​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4)
      Computes the local maximum of a pixels ellipsoidal 2D neighborhood in an image stack slice by slice.
      default boolean maximum3DSphere​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4, double arg5)
      Computes the local maximum of a pixels spherical neighborhood.
      default boolean maximumBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4)
      Computes the local maximum of a pixels rectangular neighborhood.
      default boolean maximumBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4, double arg5)
      Computes the local maximum of a pixels rectangular neighborhood.
      default net.haesleinhuepf.clij.clearcl.ClearCLKernel maximumBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, net.haesleinhuepf.clij.clearcl.ClearCLKernel arg3)
      Deprecated.
      default net.haesleinhuepf.clij.clearcl.ClearCLKernel maximumDiamond​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, net.haesleinhuepf.clij.clearcl.ClearCLKernel arg3)
      Deprecated.
      default boolean maximumImageAndScalar​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3)
      Computes the maximum of a constant scalar s and each pixel value x in a given image X.
      default boolean maximumImages​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source2, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Computes the maximum of a pair of pixel values x, y from two given images X and Y.
      default boolean maximumOctagon​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3)
      Applies a maximum filter with kernel size 3x3 n times to an image iteratively.
      default double maximumOfAllPixels​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source)
      Determines the maximum of all pixels in a given image.
      default double maximumOfMaskedPixels​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source, net.haesleinhuepf.clij.clearcl.ClearCLBuffer mask)
      Determines the maximum intensity in an image, but only in pixels which have non-zero values in another mask image.
      default boolean maximumOfTouchingNeighbors​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer values, net.haesleinhuepf.clij.clearcl.ClearCLBuffer touch_matrix, net.haesleinhuepf.clij.clearcl.ClearCLBuffer maximum_values_destination)
      Takes a touch matrix and a vector of values to determine the maximum value among touching neighbors for every object.
      default boolean maximumXProjection​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination_max)
      Determines the maximum intensity projection of an image along X.
      default boolean maximumYProjection​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination_max)
      Determines the maximum intensity projection of an image along X.
      default boolean maximumZProjection​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination_max)
      Determines the maximum intensity projection of an image along Z.
      default boolean maximumZProjectionBounded​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4)
      Determines the maximum intensity projection of an image along Z within a given z range.
      default boolean mean2DBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4)
      Computes the local mean average of a pixels rectangular neighborhood.
      default boolean mean2DSphere​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4)
      Computes the local mean average of a pixels ellipsoidal neighborhood.
      default boolean mean3DBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4, double arg5)
      Computes the local mean average of a pixels cube neighborhood.
      default boolean mean3DSphere​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4, double arg5)
      Computes the local mean average of a pixels spherical neighborhood.
      default boolean meanBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4, double arg5)
      Computes the local mean average of a pixels rectangular neighborhood.
      default double meanClosestSpotDistance​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2)
      Determines the distance between pairs of closest spots in two binary images.
      default double[] meanClosestSpotDistance​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, boolean arg3)
      Determines the distance between pairs of closest spots in two binary images.
      default double meanOfAllPixels​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source)
      Determines the mean average of all pixels in a given image.
      default double meanOfMaskedPixels​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source, net.haesleinhuepf.clij.clearcl.ClearCLBuffer mask)
      Determines the mean intensity in a masked image.
      default double meanOfPixelsAboveThreshold​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, double arg2)
      Determines the mean intensity in a threshleded image.
      default boolean meanOfTouchingNeighbors​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer values, net.haesleinhuepf.clij.clearcl.ClearCLBuffer touch_matrix, net.haesleinhuepf.clij.clearcl.ClearCLBuffer mean_values_destination)
      Takes a touch matrix and a vector of values to determine the mean value among touching neighbors for every object.
      default boolean meanSliceBySliceSphere​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4)
      Computes the local mean average of a pixels ellipsoidal 2D neighborhood in an image stack slice by slice.
      default double meanSquaredError​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer source2)
      Determines the mean squared error (MSE) between two images.
      default boolean meanXProjection​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Determines the mean average intensity projection of an image along X.
      default boolean meanYProjection​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Determines the mean average intensity projection of an image along Y.
      default boolean meanZProjection​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Determines the mean average intensity projection of an image along Z.
      default boolean meanZProjectionBounded​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4)
      Determines the mean average intensity projection of an image along Z within a given z range.
      default boolean median2DBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4)
      Computes the local median of a pixels rectangular neighborhood.
      default boolean median2DSphere​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4)
      Computes the local median of a pixels ellipsoidal neighborhood.
      default boolean median3DBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4, double arg5)
      Computes the local median of a pixels cuboid neighborhood.
      default boolean median3DSliceBySliceBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4)
      Computes the local median of a pixels rectangular neighborhood.
      default boolean median3DSliceBySliceSphere​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4)
      Computes the local median of a pixels ellipsoidal neighborhood.
      default boolean median3DSphere​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4, double arg5)
      Computes the local median of a pixels spherical neighborhood.
      default boolean medianOfTouchingNeighbors​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer values, net.haesleinhuepf.clij.clearcl.ClearCLBuffer touch_matrix, net.haesleinhuepf.clij.clearcl.ClearCLBuffer median_values_destination)
      Takes a touch matrix and a vector of values to determine the median value among touching neighbors for every object.
      default boolean medianZProjection​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Determines the median intensity projection of an image stack along Z.
      default boolean minimum2DBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4)
      Computes the local minimum of a pixels rectangular neighborhood.
      default boolean minimum2DSphere​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4)
      Computes the local minimum of a pixels ellipsoidal neighborhood.
      default boolean minimum3DBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4, double arg5)
      Computes the local minimum of a pixels cube neighborhood.
      default boolean minimum3DSliceBySliceSphere​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4)
      Computes the local minimum of a pixels ellipsoidal 2D neighborhood in an image stack slice by slice.
      default boolean minimum3DSphere​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4, double arg5)
      Computes the local minimum of a pixels spherical neighborhood.
      default boolean minimumBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4)
      Computes the local minimum of a pixels rectangular neighborhood.
      default boolean minimumBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4, double arg5)
      Computes the local minimum of a pixels rectangular neighborhood.
      default net.haesleinhuepf.clij.clearcl.ClearCLKernel minimumBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, net.haesleinhuepf.clij.clearcl.ClearCLKernel arg3)
      Deprecated.
      default net.haesleinhuepf.clij.clearcl.ClearCLKernel minimumDiamond​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, net.haesleinhuepf.clij.clearcl.ClearCLKernel arg3)
      Deprecated.
      default boolean minimumDistanceOfTouchingNeighbors​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer distance_matrix, net.haesleinhuepf.clij.clearcl.ClearCLBuffer touch_matrix, net.haesleinhuepf.clij.clearcl.ClearCLBuffer minimum_distancelist_destination)
      Takes a touch matrix and a distance matrix to determine the shortest distance of touching neighbors for every object.
      default boolean minimumImageAndScalar​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3)
      Computes the minimum of a constant scalar s and each pixel value x in a given image X.
      default boolean minimumImages​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source2, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Computes the minimum of a pair of pixel values x, y from two given images X and Y.
      default boolean minimumOctagon​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3)
      Applies a minimum filter with kernel size 3x3 n times to an image iteratively.
      default double minimumOfAllPixels​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source)
      Determines the minimum of all pixels in a given image.
      default double minimumOfMaskedPixels​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source, net.haesleinhuepf.clij.clearcl.ClearCLBuffer mask)
      Determines the minimum intensity in a masked image.
      default boolean minimumOfTouchingNeighbors​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer values, net.haesleinhuepf.clij.clearcl.ClearCLBuffer touch_matrix, net.haesleinhuepf.clij.clearcl.ClearCLBuffer minimum_values_destination)
      Takes a touch matrix and a vector of values to determine the minimum value among touching neighbors for every object.
      default boolean minimumXProjection​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination_min)
      Determines the minimum intensity projection of an image along Y.
      default boolean minimumYProjection​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination_min)
      Determines the minimum intensity projection of an image along Y.
      default boolean minimumZProjection​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination_min)
      Determines the minimum intensity projection of an image along Z.
      default boolean minimumZProjectionBounded​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4)
      Determines the minimum intensity projection of an image along Z within a given z range.
      default boolean minimumZProjectionThresholdedBounded​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3, double arg4, double arg5)
      Determines the minimum intensity projection of all pixels in an image above a given threshold along Z within a given z range.
      default boolean multiplyImageAndCoordinate​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3)
      Multiplies all pixel intensities with the x, y or z coordinate, depending on specified dimension.
      default boolean multiplyImageAndScalar​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3)
      Multiplies all pixels value x in a given image X with a constant scalar s.
      default boolean multiplyImages​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface factor1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface factor2, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Multiplies all pairs of pixel values x and y from two images X and Y.
      default boolean multiplyImageStackWithScalars​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, float[] arg3)
      Multiplies all pixels value x in a given image X with a constant scalar s from a list of scalars.
      default boolean multiplyImageStackWithScalars​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg3)
      Multiplies all pixels value x in a given image X with a constant scalar s from a list of scalars.
      default boolean multiplyMatrix​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer matrix1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer matrix2, net.haesleinhuepf.clij.clearcl.ClearCLBuffer matrix_destination)
      Multiplies two matrices with each other.
      default boolean multiplySliceBySliceWithScalars​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, float[] arg3)
      Deprecated.
      default boolean multiplyStackWithPlane​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface sourceStack, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface sourcePlane, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Multiplies all pairs of pixel values x and y from an image stack X and a 2D image Y.
      default boolean nClosestDistances​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg3)
      Determine the n point indices with shortest distance for all points in a distance matrix.
      default boolean nClosestPoints​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2)
      Determine the n point indices with shortest distance for all points in a distance matrix.
      default boolean neighborsOfNeighbors​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer touch_matrix, net.haesleinhuepf.clij.clearcl.ClearCLBuffer neighbor_matrix_destination)
      Determines neighbors of neigbors from touch matrix and saves the result as a new touch matrix.
      default boolean nonzeroMaximumBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface input, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Apply a maximum filter (box shape) to the input image.
      default boolean nonzeroMaximumBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg3)
      Apply a maximum filter (box shape) to the input image.
      default net.haesleinhuepf.clij.clearcl.ClearCLKernel nonzeroMaximumBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg3, net.haesleinhuepf.clij.clearcl.ClearCLKernel arg4)
      Apply a maximum filter (box shape) to the input image.
      default boolean nonzeroMaximumDiamond​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface input, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Apply a maximum filter (diamond shape) to the input image.
      default boolean nonzeroMaximumDiamond​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg3)
      Apply a maximum filter (diamond shape) to the input image.
      default net.haesleinhuepf.clij.clearcl.ClearCLKernel nonzeroMaximumDiamond​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg3, net.haesleinhuepf.clij.clearcl.ClearCLKernel arg4)
      Apply a maximum filter (diamond shape) to the input image.
      default boolean nonzeroMinimumBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface input, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Apply a minimum filter (box shape) to the input image.
      default boolean nonzeroMinimumBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg3)
      Apply a minimum filter (box shape) to the input image.
      default net.haesleinhuepf.clij.clearcl.ClearCLKernel nonzeroMinimumBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg3, net.haesleinhuepf.clij.clearcl.ClearCLKernel arg4)
      Apply a minimum filter (box shape) to the input image.
      default boolean nonzeroMinimumDiamond​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface input, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Apply a minimum filter (diamond shape) to the input image.
      default boolean nonzeroMinimumDiamond​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg3)
      Apply a minimum filter (diamond shape) to the input image.
      default net.haesleinhuepf.clij.clearcl.ClearCLKernel nonzeroMinimumDiamond​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg3, net.haesleinhuepf.clij.clearcl.ClearCLKernel arg4)
      Apply a minimum filter (diamond shape) to the input image.
      default boolean notEqual​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source2, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
      Determines if two images A and B equal pixel wise.
      default boolean notEqualConstant​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3)
      Determines if two images A and B equal pixel wise.
      default boolean onlyzeroOverwriteMaximumBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface input, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Apply a local maximum filter to an image which only overwrites pixels with value 0.
      default boolean onlyzeroOverwriteMaximumBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg3)
      Apply a local maximum filter to an image which only overwrites pixels with value 0.
      default net.haesleinhuepf.clij.clearcl.ClearCLKernel onlyzeroOverwriteMaximumBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg3, net.haesleinhuepf.clij.clearcl.ClearCLKernel arg4)
      Apply a local maximum filter to an image which only overwrites pixels with value 0.
      default boolean onlyzeroOverwriteMaximumDiamond​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface input, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Apply a local maximum filter to an image which only overwrites pixels with value 0.
      default boolean onlyzeroOverwriteMaximumDiamond​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg3)
      Apply a local maximum filter to an image which only overwrites pixels with value 0.
      default net.haesleinhuepf.clij.clearcl.ClearCLKernel onlyzeroOverwriteMaximumDiamond​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg3, net.haesleinhuepf.clij.clearcl.ClearCLKernel arg4)
      Apply a local maximum filter to an image which only overwrites pixels with value 0.
      default boolean openingBox​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3)
      Apply a binary opening to the input image by calling n erosions and n dilations subsequenntly.
      default boolean openingDiamond​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3)
      Apply a binary opening to the input image by calling n erosions and n dilations subsequenntly.
      default boolean paste​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4)
      Pastes an image into another image at a given position.
      default boolean paste​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4, double arg5)
      Pastes an image into another image at a given position.
      default boolean paste2D​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4)
      Pastes an image into another image at a given position.
      default boolean paste3D​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4, double arg5)
      Pastes an image into another image at a given position.
      default boolean pointIndexListToMesh​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer pointlist, net.haesleinhuepf.clij.clearcl.ClearCLBuffer indexlist, net.haesleinhuepf.clij.clearcl.ClearCLBuffer mesh_destination)
      Meshes all points in a given point list which are indiced in a corresponding index list.
      default boolean pointlistToLabelledSpots​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer pointlist, net.haesleinhuepf.clij.clearcl.ClearCLBuffer spots_destination)
      Takes a pointlist with dimensions n times d with n point coordinates in d dimensions and labels corresponding pixels.
      default boolean power​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3)
      Computes all pixels value x to the power of a given exponent a.
      default boolean powerImages​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input, net.haesleinhuepf.clij.clearcl.ClearCLBuffer exponent, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
      Calculates x to the power of y pixel wise of two images X and Y.
      default boolean print​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface input)
      Visualises an image on standard out (console).
      default Roi pullAsROI​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer binary_input)
      Pulls a binary image from the GPU memory and puts it on the currently active ImageJ window as region of interest.
      default ArrayList pullLabelsToROIList​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer labelmap_input)
      Pulls all labels in a label map as ROIs to a list.
      default boolean pullLabelsToROIList​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, List arg2)
      Pulls all labels in a label map as ROIs to a list.
      default boolean pullLabelsToROIManager​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer labelmap_input)
      Pulls all labels in a label map as ROIs to the ROI manager.
      default boolean pullLabelsToROIManager​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, RoiManager arg2)
      Pulls all labels in a label map as ROIs to the ROI manager.
      default String pullString​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1)
      Writes an image into a string.
      default ResultsTable pullToResultsTable​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, ResultsTable arg2)
      Converts an image into a table.
      default ResultsTable pullToResultsTable​(net.haesleinhuepf.clij.clearcl.ClearCLImage arg1, ResultsTable arg2)
      Converts an image into a table.
      default net.haesleinhuepf.clij.clearcl.ClearCLBuffer pushArray​(float[] arg1, double arg2, double arg3, double arg4)
      Converts an array to an image.
      default boolean pushArray​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, Object arg2)
      Converts an array to an image.
      default boolean pushResultsTable​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, ResultsTable arg2)
      Converts a table to an image.
      default boolean pushResultsTableColumn​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, ResultsTable arg2, String arg3)
      Converts a table column to an image.
      default net.haesleinhuepf.clij.clearcl.ClearCLBuffer pushString​(String arg1)
      Converts an string to an image.
      default boolean pushString​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, String arg2)
      Converts an string to an image.
      default boolean radialProjection​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3)
      Deprecated.
      void recordMethodEnd​(String method)  
      void recordMethodStart​(String method)  
      default boolean reduceStack​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4)
      Reduces the number of slices in a stack by a given factor.
      default boolean replaceIntensities​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface input, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface new_values_vector, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Replaces integer intensities specified in a vector image.
      default boolean replaceIntensity​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4)
      Replaces a specific intensity in an image with a given new value.
      default boolean replacePixelsIfZero​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface input1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface input2, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Replaces pixel values x with y in case x is zero.
      default boolean resample​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4, double arg5, boolean arg6)
      Deprecated.
      default boolean resample2D​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4, boolean arg5)  
      default boolean resample3D​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3, double arg4, double arg5, boolean arg6)  
      default boolean resliceBottom​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Flippes Y and Z axis of an image stack.
      default boolean resliceLeft​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Flippes X, Y and Z axis of an image stack.
      default boolean resliceRadial​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3)
      Computes a radial projection of an image stack.
      default boolean resliceRadial​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3, double arg4, double arg5)
      Computes a radial projection of an image stack.
      default boolean resliceRadial​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3, double arg4, double arg5, double arg6, double arg7, double arg8)
      Computes a radial projection of an image stack.
      default boolean resliceRight​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Flippes X, Y and Z axis of an image stack.
      default boolean resliceTop​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Flippes Y and Z axis of an image stack.
      default boolean resultsTableColumnToImage​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, ResultsTable arg2, String arg3)
      Converts a table column to an image.
      default boolean resultsTableToImage2D​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, ResultsTable arg2)
      Deprecated.
      default boolean rotate2D​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3, boolean arg4)
      Rotates an image in plane.
      default boolean rotate3D​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3, double arg4, double arg5, boolean arg6)
      Rotates an image stack in 3D.
      default boolean rotateClockwise​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Rotates a given input image by 90 degrees clockwise.
      default boolean rotateCounterClockwise​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Rotates a given input image by 90 degrees counter-clockwise.
      default boolean rotateLeft​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Deprecated.
      default boolean rotateRight​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Deprecated.
      default boolean saveAsTIF​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input, String filename)
      Pulls an image from the GPU memory and saves it as TIF to disc.
      default boolean scale​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3)
      Scales an image with a given factor.
      default boolean scale​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3, double arg4)
      Scales an image with a given factor.
      default boolean scale​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3, double arg4, double arg5)
      Deprecated.
      default boolean scale2D​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3, double arg4)
      Scales an image with a given factor.
      default boolean scale2D​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3, double arg4, boolean arg5)
      Scales an image with a given factor.
      default boolean scale3D​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3, double arg4, double arg5)
      Scales an image with a given factor.
      default boolean scale3D​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3, double arg4, double arg5, boolean arg6)
      Scales an image with a given factor.
      default boolean set​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, double arg2)
      Sets all pixel values x of a given image X to a constant value v.
      default boolean setColumn​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, double arg2, double arg3)
      Sets all pixel values x of a given column in X to a constant value v.
      default boolean setImageBorders​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, double arg2)
      Sets all pixel values at the image border to a given value.
      default boolean setNonZeroPixelsToPixelIndex​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Sets all pixels in an image which are not zero to the index of the pixel.
      default boolean setPlane​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, double arg2, double arg3)
      Sets all pixel values x of a given plane in X to a constant value v.
      default boolean setRampX​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source)
      Sets all pixel values to their X coordinate
      default boolean setRampY​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source)
      Sets all pixel values to their Y coordinate
      default boolean setRampZ​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source)
      Sets all pixel values to their Z coordinate
      default boolean setRandom​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, double arg2, double arg3)
      Fills an image or image stack with uniformly distributed random numbers between given minimum and maximum values.
      default boolean setRandom​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, double arg2, double arg3, double arg4)
      Fills an image or image stack with uniformly distributed random numbers between given minimum and maximum values.
      default boolean setRow​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, double arg2, double arg3)
      Sets all pixel values x of a given row in X to a constant value v.
      default boolean setWhereXequalsY​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, double arg2)
      Sets all pixel values a of a given image A to a constant value v in case its coordinates x == y.
      default boolean setWhereXgreaterThanY​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, double arg2)
      Sets all pixel values a of a given image A to a constant value v in case its coordinates x > y.
      default boolean setWhereXsmallerThanY​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, double arg2)
      Sets all pixel values a of a given image A to a constant value v in case its coordinates x < y.
      default boolean shiftIntensitiesToCloseGaps​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2)
      Deprecated.
      default boolean shortestDistances​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer distance_matrix, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination_minimum_distances)
      Determine the shortest distance from a distance matrix.
      default boolean smaller​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer source2, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
      Determines if two images A and B smaller pixel wise.
      default boolean smallerConstant​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3)
      Determines if two images A and B smaller pixel wise.
      default boolean smallerOrEqual​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer source2, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
      Determines if two images A and B smaller or equal pixel wise.
      default boolean smallerOrEqualConstant​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3)
      Determines if two images A and B smaller or equal pixel wise.
      default boolean sobel​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
      Convolve the image with the Sobel kernel.
      default double sorensenDiceCoefficient​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer source2)
      Determines the overlap of two binary images using the Sorensen-Dice coefficent.
      default boolean spotsToPointList​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input_spots, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination_pointlist)
      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.
      default boolean squaredDifference​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer source2, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
      Determines the squared difference pixel by pixel between two images.
      default double standardDeviationOfAllPixels​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source)
      Determines the standard deviation of all pixels in an image.
      default double standardDeviationOfAllPixels​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, double arg2)
      Determines the standard deviation of all pixels in an image.
      default double standardDeviationOfMaskedPixels​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source, net.haesleinhuepf.clij.clearcl.ClearCLBuffer mask)
      Determines the standard deviation of all pixels in an image which have non-zero value in a corresponding mask image.
      default double standardDeviationOfMaskedPixels​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3)
      Determines the standard deviation of all pixels in an image which have non-zero value in a corresponding mask image.
      default boolean standardDeviationOfTouchingNeighbors​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer values, net.haesleinhuepf.clij.clearcl.ClearCLBuffer touch_matrix, net.haesleinhuepf.clij.clearcl.ClearCLBuffer standard_deviation_values_destination)
      Takes a touch matrix and a vector of values to determine the standard deviation value among touching neighbors for every object.
      default boolean standardDeviationZProjection​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Determines the standard deviation intensity projection of an image stack along Z.
      default double[][] statisticsOfBackgroundAndLabelledPixels​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input, net.haesleinhuepf.clij.clearcl.ClearCLBuffer labelmap)
      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.
      default ResultsTable statisticsOfBackgroundAndLabelledPixels​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, ResultsTable arg3)
      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.
      default ResultsTable statisticsOfImage​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, ResultsTable arg2)
      Determines image size (bounding box), area (in pixels/voxels), min, max and mean intensity of all pixels in the original image.
      default double[][] statisticsOfLabelledPixels​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input, net.haesleinhuepf.clij.clearcl.ClearCLBuffer labelmap)
      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.
      default double[] statisticsOfLabelledPixels​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3)
      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.
      default double[][] statisticsOfLabelledPixels​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3, double arg4)
      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.
      default ResultsTable statisticsOfLabelledPixels​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, ResultsTable arg3)
      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.
      default double[][] statisticsOfLabelledPixels_single_threaded​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3, double arg4)  
      default boolean subtract​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface subtrahend, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface minuend, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Deprecated.
      default boolean subtractImageFromScalar​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3)
      Subtracts one image X from a scalar s pixel wise.
      default boolean subtractImages​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface subtrahend, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface minuend, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Subtracts one image X from another image Y pixel wise.
      default double[] sumImageSliceBySlice​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1)
      Sums all pixels slice by slice and returns the sums in a vector.
      default boolean sumImageSliceBySlice​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Sums all pixels slice by slice and returns the sums in a vector.
      default double sumOfAllPixels​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source)
      Determines the sum of all pixels in a given image.
      default double sumPixels​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source)
      Deprecated.
      default double[] sumPixelsSliceByslice​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1)
      Deprecated.
      default boolean sumXProjection​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Determines the sum intensity projection of an image along Z.
      default boolean sumYProjection​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Determines the sum intensity projection of an image along Z.
      default boolean sumZProjection​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination_sum)
      Determines the sum intensity projection of an image along Z.
      default boolean threshold​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2, double arg3)
      Computes a binary image with pixel values 0 and 1.
      default boolean thresholdDefault​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
      The automatic thresholder utilizes the Default 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.
      default boolean thresholdHuang​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
      The automatic thresholder utilizes the Huang 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.
      default boolean thresholdIJ_IsoData​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
      The automatic thresholder utilizes the IJ_IsoData 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.
      default boolean thresholdIntermodes​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
      The automatic thresholder utilizes the Intermodes 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.
      default boolean thresholdIsoData​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
      The automatic thresholder utilizes the IsoData 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.
      default boolean thresholdLi​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
      The automatic thresholder utilizes the Li 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.
      default boolean thresholdMaxEntropy​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
      The automatic thresholder utilizes the MaxEntropy 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.
      default boolean thresholdMean​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
      The automatic thresholder utilizes the Mean 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.
      default boolean thresholdMinError​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
      The automatic thresholder utilizes the MinError 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.
      default boolean thresholdMinimum​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
      The automatic thresholder utilizes the Minimum 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.
      default boolean thresholdMoments​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
      The automatic thresholder utilizes the Moments 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.
      default boolean thresholdOtsu​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
      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.
      default boolean thresholdPercentile​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
      The automatic thresholder utilizes the Percentile 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.
      default boolean thresholdRenyiEntropy​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
      The automatic thresholder utilizes the RenyiEntropy 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.
      default boolean thresholdShanbhag​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
      The automatic thresholder utilizes the Shanbhag 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.
      default boolean thresholdTriangle​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
      The automatic thresholder utilizes the Triangle 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.
      default boolean thresholdYen​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
      The automatic thresholder utilizes the Yen 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.
      default boolean topHatBox​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3, double arg4, double arg5)
      Applies a top-hat filter for background subtraction to the input image.
      default boolean topHatSphere​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3, double arg4, double arg5)
      Applies a top-hat filter for background subtraction to the input image.
      default boolean touchMatrixToAdjacencyMatrix​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer touch_matrix, net.haesleinhuepf.clij.clearcl.ClearCLBuffer adjacency_matrix)
      Converts a touch matrix in an adjacency matrix
      default boolean touchMatrixToMesh​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer pointlist, net.haesleinhuepf.clij.clearcl.ClearCLBuffer touch_matrix, net.haesleinhuepf.clij.clearcl.ClearCLBuffer mesh_destination)
      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.
      default boolean translate2D​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3, double arg4)
      Translate an image stack in X and Y.
      default boolean translate3D​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3, double arg4, double arg5)
      Translate an image stack in X, Y and Z.
      default boolean transposeXY​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
      Transpose X and Y axes of an image.
      default boolean transposeXZ​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
      Transpose X and Z axes of an image.
      default boolean transposeYZ​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
      Transpose Y and Z axes of an image.
      default boolean undefinedToZero​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
      Copies all pixels instead those which are not a number (NaN) or infinity (inf), which are replaced by 0.
      default double varianceOfAllPixels​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source)
      Determines the variance of all pixels in an image.
      default double varianceOfAllPixels​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1, double arg2)
      Determines the variance of all pixels in an image.
      default double varianceOfMaskedPixels​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source, net.haesleinhuepf.clij.clearcl.ClearCLBuffer mask)
      Determines the variance in an image, but only in pixels which have non-zero values in another binary mask image.
      default double varianceOfMaskedPixels​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1, net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2, double arg3)
      Determines the variance in an image, but only in pixels which have non-zero values in another binary mask image.
      default boolean voronoiLabeling​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input, net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
      Takes a binary image, labels connected components and dilates the regions using a octagon shape until they touch.
      default boolean voronoiOctagon​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
      Takes a binary image and dilates the regions using a octagon shape until they touch.
      default boolean watershed​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer binary_source, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
      Apply a binary watershed to a binary image and introduces black pixels between objects.
      default boolean writeValuesToPositions​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer positions_and_values, net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
      Takes an image with three/four rows (2D: height = 3; 3D: height = 4): x, y [, z] and v and target image.

    • Method Detail

      • getCLIJ

        net.haesleinhuepf.clij.CLIJ getCLIJ()

      • getCLIJ2

        CLIJ2 getCLIJ2()

      • doTimeTracing

        boolean doTimeTracing()

      • recordMethodStart

        void recordMethodStart​(String method)

      • recordMethodEnd

        void recordMethodEnd​(String method)

      • binaryUnion

        default boolean binaryUnion​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer operand1,
                            net.haesleinhuepf.clij.clearcl.ClearCLBuffer operand2,
                            net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
        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 union operator |. All pixel values except 0 in the input images are interpreted as 1.
        f(x, y) = x | y
        Parameters ---------- operand1 : Image The first binary input image to be processed. operand2 : Image The second binary input image to be processed. destination : Image The output image where results are written into.

      • binaryIntersection

        default boolean binaryIntersection​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer operand1,
                                   net.haesleinhuepf.clij.clearcl.ClearCLBuffer operand2,
                                   net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
        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 intersection operator &. All pixel values except 0 in the input images are interpreted as 1. 
        f(x, y) = x & y
        Parameters ---------- operand1 : Image The first binary input image to be processed. operand2 : Image The second binary input image to be processed. destination : Image The output image where results are written into.

      • connectedComponentsLabeling

        @Deprecated
default boolean connectedComponentsLabeling​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface binary_input,
                                            net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface labeling_destination)
        Deprecated.
        Performs connected components analysis to a binary image and generates a label map. DEPRECATED: This method is deprecated. Use ConnectedComponentsLabellingBox (or Diamond) instead.

      • countNonZeroPixels

        default double countNonZeroPixels​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source)
        Determines the number of all pixels in a given image which are not equal to 0. It will be stored in a new row of ImageJs Results table in the column 'CountNonZero'.

      • differenceOfGaussian

        default boolean differenceOfGaussian​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                     net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                                     double arg3,
                                     double arg4,
                                     double arg5,
                                     double arg6)
        Applies Gaussian blur to the input image twice with different sigma values resulting in two images which are then subtracted from each other. It is recommended to apply this operation to images of type Float (32 bit) as results might be negative. Parameters ---------- input : Image The input image to be processed. destination : Image The output image where results are written into. sigma1_x : float Sigma of the first Gaussian filter in x sigma1_y : float Sigma of the first Gaussian filter in y sigma2_x : float Sigma of the second Gaussian filter in x sigma2_y : float Sigma of the second Gaussian filter in y

      • differenceOfGaussian2D

        default boolean differenceOfGaussian2D​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                       net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                                       double arg3,
                                       double arg4,
                                       double arg5,
                                       double arg6)
        Applies Gaussian blur to the input image twice with different sigma values resulting in two images which are then subtracted from each other. It is recommended to apply this operation to images of type Float (32 bit) as results might be negative. Parameters ---------- input : Image The input image to be processed. destination : Image The output image where results are written into. sigma1_x : float Sigma of the first Gaussian filter in x sigma1_y : float Sigma of the first Gaussian filter in y sigma2_x : float Sigma of the second Gaussian filter in x sigma2_y : float Sigma of the second Gaussian filter in y

      • differenceOfGaussian

        default boolean differenceOfGaussian​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                     net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                                     double arg3,
                                     double arg4,
                                     double arg5,
                                     double arg6,
                                     double arg7,
                                     double arg8)
        Applies Gaussian blur to the input image twice with different sigma values resulting in two images which are then subtracted from each other. It is recommended to apply this operation to images of type Float (32 bit) as results might be negative. Parameters ---------- input : Image The input image to be processed. destination : Image The output image where results are written into. sigma1_x : float Sigma of the first Gaussian filter in x sigma1_y : float Sigma of the first Gaussian filter in y sigma2_x : float Sigma of the second Gaussian filter in x sigma2_y : float Sigma of the second Gaussian filter in y

      • differenceOfGaussian3D

        default boolean differenceOfGaussian3D​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                       net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                                       double arg3,
                                       double arg4,
                                       double arg5,
                                       double arg6,
                                       double arg7,
                                       double arg8)
        Applies Gaussian blur to the input image twice with different sigma values resulting in two images which are then subtracted from each other. It is recommended to apply this operation to images of type Float (32 bit) as results might be negative. Parameters ---------- input : Image The input image to be processed. destination : Image The output image where results are written into. sigma1_x : float Sigma of the first Gaussian filter in x sigma1_y : float Sigma of the first Gaussian filter in y sigma1_z : float Sigma of the first Gaussian filter in z sigma2_x : float Sigma of the second Gaussian filter in x sigma2_y : float Sigma of the second Gaussian filter in y sigma2_z : float Sigma of the second Gaussian filter in z

      • maskLabel

        default boolean maskLabel​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                          net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                          net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg3,
                          double arg4)
        Computes a masked image by applying a label mask to an image. All pixel values x of image X will be copied to the destination image in case pixel value m at the same position in the label_map image has the right index value i. f(x,m,i) = (x if (m == i); (0 otherwise))

      • meanClosestSpotDistance

        default double meanClosestSpotDistance​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                       net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2)
        Determines the distance between pairs of closest spots in two binary images. Takes two binary images A and B with marked spots and determines for each spot in image A the closest spot in image B. Afterwards, it saves the average shortest distances from image A to image B as 'mean_closest_spot_distance_A_B' and from image B to image A as 'mean_closest_spot_distance_B_A' to the results table. The distance between B and A is only determined if the `bidirectional` checkbox is checked.

      • meanClosestSpotDistance

        default double[] meanClosestSpotDistance​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                         net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                                         boolean arg3)
        Determines the distance between pairs of closest spots in two binary images. Takes two binary images A and B with marked spots and determines for each spot in image A the closest spot in image B. Afterwards, it saves the average shortest distances from image A to image B as 'mean_closest_spot_distance_A_B' and from image B to image A as 'mean_closest_spot_distance_B_A' to the results table. The distance between B and A is only determined if the `bidirectional` checkbox is checked.

      • meanSquaredError

        default double meanSquaredError​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source1,
                                net.haesleinhuepf.clij.clearcl.ClearCLBuffer source2)
        Determines the mean squared error (MSE) between two images. The MSE will be stored in a new row of ImageJs Results table in the column 'MSE'.

      • medianZProjection

        default boolean medianZProjection​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                                  net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Determines the median intensity projection of an image stack along Z.

      • nonzeroMinimumDiamond

        default boolean nonzeroMinimumDiamond​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface input,
                                      net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Apply a minimum filter (diamond shape) to the input image. The radius is fixed to 1 and pixels with value 0 are ignored.Note: Pixels with 0 value in the input image will not be overwritten in the output image. Thus, the result image should be initialized by copying the original image in advance.

      • nonzeroMinimumDiamond

        default boolean nonzeroMinimumDiamond​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                      net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                      net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg3)
        Apply a minimum filter (diamond shape) to the input image. The radius is fixed to 1 and pixels with value 0 are ignored.Note: Pixels with 0 value in the input image will not be overwritten in the output image. Thus, the result image should be initialized by copying the original image in advance.

      • nonzeroMinimumDiamond

        default net.haesleinhuepf.clij.clearcl.ClearCLKernel nonzeroMinimumDiamond​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                                                           net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                                                           net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg3,
                                                                           net.haesleinhuepf.clij.clearcl.ClearCLKernel arg4)
        Apply a minimum filter (diamond shape) to the input image. The radius is fixed to 1 and pixels with value 0 are ignored.Note: Pixels with 0 value in the input image will not be overwritten in the output image. Thus, the result image should be initialized by copying the original image in advance.

      • paste

        default boolean paste​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                      net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                      double arg3,
                      double arg4)
        Pastes an image into another image at a given position.

      • paste2D

        default boolean paste2D​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                        net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                        double arg3,
                        double arg4)
        Pastes an image into another image at a given position.

      • paste

        default boolean paste​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                      net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                      double arg3,
                      double arg4,
                      double arg5)
        Pastes an image into another image at a given position.

      • paste3D

        default boolean paste3D​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                        net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                        double arg3,
                        double arg4,
                        double arg5)
        Pastes an image into another image at a given position.

      • jaccardIndex

        default double jaccardIndex​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source1,
                            net.haesleinhuepf.clij.clearcl.ClearCLBuffer source2)
        Determines the overlap of two binary images using the Jaccard index. A value of 0 suggests no overlap, 1 means perfect overlap. The resulting Jaccard index is saved to the results table in the 'Jaccard_Index' column. Note that the Sorensen-Dice coefficient can be calculated from the Jaccard index j using this formula: 
        s = f(j) = 2 j / (j + 1)

      • sorensenDiceCoefficient

        default double sorensenDiceCoefficient​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source1,
                                       net.haesleinhuepf.clij.clearcl.ClearCLBuffer source2)
        Determines the overlap of two binary images using the Sorensen-Dice coefficent. A value of 0 suggests no overlap, 1 means perfect overlap. The Sorensen-Dice coefficient is saved in the colum 'Sorensen_Dice_coefficient'. Note that the Sorensen-Dice coefficient s can be calculated from the Jaccard index j using this formula: 
        s = f(j) = 2 j / (j + 1)

      • standardDeviationZProjection

        default boolean standardDeviationZProjection​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                                             net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Determines the standard deviation intensity projection of an image stack along Z.

      • topHatBox

        default boolean topHatBox​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                          net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                          double arg3,
                          double arg4,
                          double arg5)
        Applies a top-hat filter for background subtraction to the input image. Parameters ---------- input : Image The input image where the background is subtracted from. destination : Image The output image where results are written into. radius_x : Image Radius of the background determination region in X. radius_y : Image Radius of the background determination region in Y. radius_z : Image Radius of the background determination region in Z.

      • topHatSphere

        default boolean topHatSphere​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                             net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                             double arg3,
                             double arg4,
                             double arg5)
        Applies a top-hat filter for background subtraction to the input image. Parameters ---------- input : Image The input image where the background is subtracted from. destination : Image The output image where results are written into. radius_x : Image Radius of the background determination region in X. radius_y : Image Radius of the background determination region in Y. radius_z : Image Radius of the background determination region in Z.

      • exponential

        default boolean exponential​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                            net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Computes base exponential of all pixels values. f(x) = exp(x)

      • logarithm

        default boolean logarithm​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                          net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Computes base e logarithm of all pixels values. f(x) = log(x)

      • generateDistanceMatrix

        default boolean generateDistanceMatrix​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer coordinate_list1,
                                       net.haesleinhuepf.clij.clearcl.ClearCLBuffer coordinate_list2,
                                       net.haesleinhuepf.clij.clearcl.ClearCLBuffer distance_matrix_destination)
        Computes the distance between all point coordinates given in two point lists. Takes two images containing pointlists (dimensionality n * d, n: number of points and d: dimensionality) and builds up a matrix containing the distances between these points. Convention: Given two point lists with dimensionality n * d and m * d, the distance matrix will be of size(n + 1) * (m + 1). The first row and column contain zeros. They represent the distance of the objects to a theoretical background object. In that way, distance matrices are of the same size as touch matrices (see generateTouchMatrix). Thus, one can threshold a distance matrix to generate a touch matrix out of it for drawing meshes.

      • shortestDistances

        default boolean shortestDistances​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer distance_matrix,
                                  net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination_minimum_distances)
        Determine the shortest distance from a distance matrix. This corresponds to the minimum for each individial column.

      • spotsToPointList

        default boolean spotsToPointList​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input_spots,
                                 net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination_pointlist)
        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.

      • transposeXY

        default boolean transposeXY​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input,
                            net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
        Transpose X and Y axes of an image. Parameters ---------- input : Image The input image. destination : Image The output image where results are written into.

      • transposeXZ

        default boolean transposeXZ​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input,
                            net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
        Transpose X and Z axes of an image. Parameters ---------- input : Image The input image. destination : Image The output image where results are written into.

      • transposeYZ

        default boolean transposeYZ​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input,
                            net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
        Transpose Y and Z axes of an image. Parameters ---------- input : Image The input image. destination : Image The output image where results are written into.

      • setWhereXequalsY

        default boolean setWhereXequalsY​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                 double arg2)
        Sets all pixel values a of a given image A to a constant value v in case its coordinates x == y. Otherwise the pixel is not overwritten. If you want to initialize an identity transfrom matrix, set all pixels to 0 first.

      • laplaceSphere

        default boolean laplaceSphere​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input,
                              net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
        Applies the Laplace operator (Diamond neighborhood) to an image.

      • image2DToResultsTable

        @Deprecated
default ResultsTable image2DToResultsTable​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                           ResultsTable arg2)
        Deprecated.
        Converts an image into a table.

      • image2DToResultsTable

        @Deprecated
default ResultsTable image2DToResultsTable​(net.haesleinhuepf.clij.clearcl.ClearCLImage arg1,
                                           ResultsTable arg2)
        Deprecated.
        Converts an image into a table.

      • writeValuesToPositions

        default boolean writeValuesToPositions​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer positions_and_values,
                                       net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
        Takes an image with three/four rows (2D: height = 3; 3D: height = 4): x, y [, z] and v and target image. The value v will be written at position x/y[/z] in the target image.

      • getSize

        @Deprecated
default long[] getSize​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source)
        Deprecated.
        Reads out the size of an image [stack] and writes it to the results table in the columns 'Width', 'Height' and 'Depth'. DEPRECATED: Thie method is deprecated. Use getDimensions instead.

      • multiplyMatrix

        default boolean multiplyMatrix​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer matrix1,
                               net.haesleinhuepf.clij.clearcl.ClearCLBuffer matrix2,
                               net.haesleinhuepf.clij.clearcl.ClearCLBuffer matrix_destination)
        Multiplies two matrices with each other.

      • matrixEqual

        default boolean matrixEqual​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                            net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                            double arg3)
        Checks if all elements of a matrix are different by less than or equal to a given tolerance. The result will be put in the results table in column "MatrixEqual" as 1 if yes and 0 otherwise.

      • powerImages

        default boolean powerImages​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input,
                            net.haesleinhuepf.clij.clearcl.ClearCLBuffer exponent,
                            net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
        Calculates x to the power of y pixel wise of two images X and Y.

      • equal

        default boolean equal​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source1,
                      net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source2,
                      net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Determines if two images A and B equal pixel wise. 
        f(a, b) = 1 if a == b; 0 otherwise.
        Parameters ---------- source1 : Image The first image to be compared with. source2 : Image The second image to be compared with the first. destination : Image The resulting binary image where pixels will be 1 only if source1 and source2 equal in the given pixel.

      • greaterOrEqual

        default boolean greaterOrEqual​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source1,
                               net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source2,
                               net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Determines if two images A and B greater or equal pixel wise. f(a, b) = 1 if a >= b; 0 otherwise.

      • greater

        default boolean greater​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source1,
                        net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source2,
                        net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Determines if two images A and B greater pixel wise. f(a, b) = 1 if a > b; 0 otherwise.

      • smaller

        default boolean smaller​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source1,
                        net.haesleinhuepf.clij.clearcl.ClearCLBuffer source2,
                        net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
        Determines if two images A and B smaller pixel wise. f(a, b) = 1 if a < b; 0 otherwise.

      • smallerOrEqual

        default boolean smallerOrEqual​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source1,
                               net.haesleinhuepf.clij.clearcl.ClearCLBuffer source2,
                               net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
        Determines if two images A and B smaller or equal pixel wise. f(a, b) = 1 if a <= b; 0 otherwise.

      • notEqual

        default boolean notEqual​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source1,
                         net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source2,
                         net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
        Determines if two images A and B equal pixel wise. f(a, b) = 1 if a != b; 0 otherwise. Parameters ---------- source1 : Image The first image to be compared with. source2 : Image The second image to be compared with the first. destination : Image The resulting binary image where pixels will be 1 only if source1 and source2 are not equal in the given pixel.

      • equalConstant

        default boolean equalConstant​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                              net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                              double arg3)
        Determines if an image A and a constant b are equal. 
        f(a, b) = 1 if a == b; 0 otherwise.
        Parameters ---------- source : Image The image where every pixel is compared to the constant. destination : Image The resulting binary image where pixels will be 1 only if source1 and source2 equal in the given pixel. constant : float The constant where every pixel is compared to.

      • greaterOrEqualConstant

        default boolean greaterOrEqualConstant​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                       net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                       double arg3)
        Determines if two images A and B greater or equal pixel wise. f(a, b) = 1 if a >= b; 0 otherwise.

      • greaterConstant

        default boolean greaterConstant​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                double arg3)
        Determines if two images A and B greater pixel wise. f(a, b) = 1 if a > b; 0 otherwise.

      • smallerConstant

        default boolean smallerConstant​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                                double arg3)
        Determines if two images A and B smaller pixel wise. f(a, b) = 1 if a < b; 0 otherwise.

      • smallerOrEqualConstant

        default boolean smallerOrEqualConstant​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                       net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                                       double arg3)
        Determines if two images A and B smaller or equal pixel wise. f(a, b) = 1 if a <= b; 0 otherwise.

      • notEqualConstant

        default boolean notEqualConstant​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                 net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                                 double arg3)
        Determines if two images A and B equal pixel wise. f(a, b) = 1 if a != b; 0 otherwise.Parameters ---------- source : Image The image where every pixel is compared to the constant. destination : Image The resulting binary image where pixels will be 1 only if source1 and source2 equal in the given pixel. constant : float The constant where every pixel is compared to.

      • drawBox

        default boolean drawBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                        double arg2,
                        double arg3,
                        double arg4,
                        double arg5)
        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.

      • drawBox

        default boolean drawBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                        double arg2,
                        double arg3,
                        double arg4,
                        double arg5,
                        double arg6,
                        double arg7)
        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.

      • drawBox

        default boolean drawBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                        double arg2,
                        double arg3,
                        double arg4,
                        double arg5,
                        double arg6,
                        double arg7,
                        double arg8)
        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.

      • drawLine

        default boolean drawLine​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                         double arg2,
                         double arg3,
                         double arg4,
                         double arg5,
                         double arg6,
                         double arg7,
                         double arg8)
        Draws a line between two points with a given thickness. All pixels other than on the line are untouched. Consider using `set(buffer, 0);` in advance.

      • drawLine

        default boolean drawLine​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                         double arg2,
                         double arg3,
                         double arg4,
                         double arg5,
                         double arg6,
                         double arg7,
                         double arg8,
                         double arg9)
        Draws a line between two points with a given thickness. All pixels other than on the line are untouched. Consider using `set(buffer, 0);` in advance.

      • drawSphere

        default boolean drawSphere​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                           double arg2,
                           double arg3,
                           double arg4,
                           double arg5)
        Draws a sphere around a given point with given radii in x, y and z (if 3D). All pixels other than in the sphere are untouched. Consider using `set(buffer, 0);` in advance.

      • drawSphere

        default boolean drawSphere​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                           double arg2,
                           double arg3,
                           double arg4,
                           double arg5,
                           double arg6)
        Draws a sphere around a given point with given radii in x, y and z (if 3D). All pixels other than in the sphere are untouched. Consider using `set(buffer, 0);` in advance.

      • drawSphere

        default boolean drawSphere​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                           double arg2,
                           double arg3,
                           double arg4,
                           double arg5,
                           double arg6,
                           double arg7)
        Draws a sphere around a given point with given radii in x, y and z (if 3D). All pixels other than in the sphere are untouched. Consider using `set(buffer, 0);` in advance.

      • drawSphere

        default boolean drawSphere​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                           double arg2,
                           double arg3,
                           double arg4,
                           double arg5,
                           double arg6,
                           double arg7,
                           double arg8)
        Draws a sphere around a given point with given radii in x, y and z (if 3D). All pixels other than in the sphere are untouched. Consider using `set(buffer, 0);` in advance.

      • replaceIntensity

        default boolean replaceIntensity​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                 net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                 double arg3,
                                 double arg4)
        Replaces a specific intensity in an image with a given new value.

      • boundingBox

        default double[] boundingBox​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source)
        Determines the bounding box of all non-zero pixels in a binary image. If called from macro, the positions will be stored in a new row of ImageJs Results table in the columns 'BoundingBoxX', 'BoundingBoxY', 'BoundingBoxZ', 'BoundingBoxWidth', 'BoundingBoxHeight' 'BoundingBoxDepth'.In case of 2D images Z and depth will be zero.

      • minimumOfMaskedPixels

        default double minimumOfMaskedPixels​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source,
                                     net.haesleinhuepf.clij.clearcl.ClearCLBuffer mask)
        Determines the minimum intensity in a masked image. But only in pixels which have non-zero values in another mask image.

      • maximumOfMaskedPixels

        default double maximumOfMaskedPixels​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source,
                                     net.haesleinhuepf.clij.clearcl.ClearCLBuffer mask)
        Determines the maximum intensity in an image, but only in pixels which have non-zero values in another mask image. Parameters ---------- source : Image The image of which the minimum of all pixels or voxels where mask=1 will be determined. mask : Image A binary image marking all pixels with 1 which should be taken into accout.

      • meanOfMaskedPixels

        default double meanOfMaskedPixels​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source,
                                  net.haesleinhuepf.clij.clearcl.ClearCLBuffer mask)
        Determines the mean intensity in a masked image. Only in pixels which have non-zero values in another binary mask image.

      • labelToMask

        default boolean labelToMask​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                            net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                            double arg3)
        Masks a single label in a label map. Sets all pixels in the target image to 1, where the given label index was present in the label map. Other pixels are set to 0.

      • nClosestPoints

        default boolean nClosestPoints​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                               net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2)
        Determine the n point indices with shortest distance for all points in a distance matrix. This corresponds to the n row indices with minimum values for each column of the distance matrix.

      • statisticsOfLabelledPixels

        default double[] statisticsOfLabelledPixels​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                            net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                                            double arg3)
        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. Instead of a label map, you can also use a binary image as a binary image is a label map with just one label. This method is executed on the CPU and not on the GPU/OpenCL device.

      • statisticsOfLabelledPixels

        default double[][] statisticsOfLabelledPixels​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input,
                                              net.haesleinhuepf.clij.clearcl.ClearCLBuffer labelmap)
        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. Instead of a label map, you can also use a binary image as a binary image is a label map with just one label. This method is executed on the CPU and not on the GPU/OpenCL device.

      • statisticsOfLabelledPixels

        default double[][] statisticsOfLabelledPixels​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                              net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                                              double arg3,
                                              double arg4)
        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. Instead of a label map, you can also use a binary image as a binary image is a label map with just one label. This method is executed on the CPU and not on the GPU/OpenCL device.

      • statisticsOfLabelledPixels_single_threaded

        default double[][] statisticsOfLabelledPixels_single_threaded​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                                              net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                                                              double arg3,
                                                              double arg4)

      • statisticsOfLabelledPixels

        default ResultsTable statisticsOfLabelledPixels​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                                net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                                                ResultsTable arg3)
        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. Instead of a label map, you can also use a binary image as a binary image is a label map with just one label. This method is executed on the CPU and not on the GPU/OpenCL device.

      • varianceOfAllPixels

        default double varianceOfAllPixels​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source)
        Determines the variance of all pixels in an image. The value will be stored in a new row of ImageJs Results table in the column 'Variance'.

      • varianceOfAllPixels

        default double varianceOfAllPixels​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                   double arg2)
        Determines the variance of all pixels in an image. The value will be stored in a new row of ImageJs Results table in the column 'Variance'.

      • standardDeviationOfAllPixels

        default double standardDeviationOfAllPixels​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source)
        Determines the standard deviation of all pixels in an image. The value will be stored in a new row of ImageJs Results table in the column 'Standard_deviation'.

      • standardDeviationOfAllPixels

        default double standardDeviationOfAllPixels​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                            double arg2)
        Determines the standard deviation of all pixels in an image. The value will be stored in a new row of ImageJs Results table in the column 'Standard_deviation'.

      • varianceOfMaskedPixels

        default double varianceOfMaskedPixels​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source,
                                      net.haesleinhuepf.clij.clearcl.ClearCLBuffer mask)
        Determines the variance in an image, but only in pixels which have non-zero values in another binary mask image. The result is put in the results table as new column named 'Masked_variance'.

      • varianceOfMaskedPixels

        default double varianceOfMaskedPixels​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                      net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                                      double arg3)
        Determines the variance in an image, but only in pixels which have non-zero values in another binary mask image. The result is put in the results table as new column named 'Masked_variance'.

      • standardDeviationOfMaskedPixels

        default double standardDeviationOfMaskedPixels​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source,
                                               net.haesleinhuepf.clij.clearcl.ClearCLBuffer mask)
        Determines the standard deviation of all pixels in an image which have non-zero value in a corresponding mask image. The value will be stored in a new row of ImageJs Results table in the column 'Masked_standard_deviation'.

      • standardDeviationOfMaskedPixels

        default double standardDeviationOfMaskedPixels​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                               net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                                               double arg3)
        Determines the standard deviation of all pixels in an image which have non-zero value in a corresponding mask image. The value will be stored in a new row of ImageJs Results table in the column 'Masked_standard_deviation'.

      • excludeLabelsOnEdges

        default boolean excludeLabelsOnEdges​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer label_map_input,
                                     net.haesleinhuepf.clij.clearcl.ClearCLBuffer label_map_destination)
        Removes all labels from a label map which touch the edges of the image (in X, Y and Z if the image is 3D). Remaining label elements are renumbered afterwards.

      • binarySubtract

        default boolean binarySubtract​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface minuend,
                               net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface subtrahend,
                               net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Subtracts one binary image from another. Parameters ---------- minuend : Image The first binary input image to be processed. suubtrahend : Image The second binary input image to be subtracted from the first. destination : Image The output image where results are written into.

      • binaryEdgeDetection

        default boolean binaryEdgeDetection​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                                    net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        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. Parameters ---------- source : Image The binary input image where edges will be searched. destination : Image The output image where edge pixels will be 1.

      • distanceMap

        default boolean distanceMap​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source,
                            net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
        Generates a distance map from a binary image. Pixels with non-zero value in the binary image are set to a number representing the distance to the closest zero-value pixel. Note: This is not a distance matrix. See generateDistanceMatrix for details.

      • pullAsROI

        default Roi pullAsROI​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer binary_input)
        Pulls a binary image from the GPU memory and puts it on the currently active ImageJ window as region of interest.

      • pullLabelsToROIManager

        default boolean pullLabelsToROIManager​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer labelmap_input)
        Pulls all labels in a label map as ROIs to the ROI manager.

      • pullLabelsToROIManager

        default boolean pullLabelsToROIManager​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                       RoiManager arg2)
        Pulls all labels in a label map as ROIs to the ROI manager.

      • nonzeroMaximumDiamond

        default boolean nonzeroMaximumDiamond​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface input,
                                      net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Apply a maximum filter (diamond shape) to the input image. The radius is fixed to 1 and pixels with value 0 are ignored. Note: Pixels with 0 value in the input image will not be overwritten in the output image. Thus, the result image should be initialized by copying the original image in advance.

      • nonzeroMaximumDiamond

        default boolean nonzeroMaximumDiamond​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                      net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                      net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg3)
        Apply a maximum filter (diamond shape) to the input image. The radius is fixed to 1 and pixels with value 0 are ignored. Note: Pixels with 0 value in the input image will not be overwritten in the output image. Thus, the result image should be initialized by copying the original image in advance.

      • nonzeroMaximumDiamond

        default net.haesleinhuepf.clij.clearcl.ClearCLKernel nonzeroMaximumDiamond​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                                                           net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                                                           net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg3,
                                                                           net.haesleinhuepf.clij.clearcl.ClearCLKernel arg4)
        Apply a maximum filter (diamond shape) to the input image. The radius is fixed to 1 and pixels with value 0 are ignored. Note: Pixels with 0 value in the input image will not be overwritten in the output image. Thus, the result image should be initialized by copying the original image in advance.

      • onlyzeroOverwriteMaximumDiamond

        default boolean onlyzeroOverwriteMaximumDiamond​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface input,
                                                net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Apply a local maximum filter to an image which only overwrites pixels with value 0.

      • onlyzeroOverwriteMaximumDiamond

        default boolean onlyzeroOverwriteMaximumDiamond​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                                net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                                net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg3)
        Apply a local maximum filter to an image which only overwrites pixels with value 0.

      • onlyzeroOverwriteMaximumDiamond

        default net.haesleinhuepf.clij.clearcl.ClearCLKernel onlyzeroOverwriteMaximumDiamond​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                                                                     net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                                                                     net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg3,
                                                                                     net.haesleinhuepf.clij.clearcl.ClearCLKernel arg4)
        Apply a local maximum filter to an image which only overwrites pixels with value 0.

      • onlyzeroOverwriteMaximumBox

        default boolean onlyzeroOverwriteMaximumBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface input,
                                            net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Apply a local maximum filter to an image which only overwrites pixels with value 0.

      • onlyzeroOverwriteMaximumBox

        default boolean onlyzeroOverwriteMaximumBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                            net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                            net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg3)
        Apply a local maximum filter to an image which only overwrites pixels with value 0.

      • onlyzeroOverwriteMaximumBox

        default net.haesleinhuepf.clij.clearcl.ClearCLKernel onlyzeroOverwriteMaximumBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                                                                 net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                                                                 net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg3,
                                                                                 net.haesleinhuepf.clij.clearcl.ClearCLKernel arg4)
        Apply a local maximum filter to an image which only overwrites pixels with value 0.

      • generateTouchMatrix

        default boolean generateTouchMatrix​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer label_map,
                                    net.haesleinhuepf.clij.clearcl.ClearCLBuffer touch_matrix_destination)
        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. Only half of the matrix is filled (with x < y). For example, if labels 3 and 4 are touching then the pixel (3,4) in the matrix will be set to 1. The touch matrix is a representation of a region adjacency graph

      • detectLabelEdges

        default boolean detectLabelEdges​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface label_map,
                                 net.haesleinhuepf.clij.clearcl.ClearCLBuffer edge_image_destination)
        Takes a labelmap and returns an image where all pixels on label edges are set to 1 and all other pixels to 0. Parameters ---------- label_map : Image The label image where edges between labels will be detected. edge_image_destination : Number Binary image where edges were marked with value 1 and all other pixels will be set to 0.

      • countTouchingNeighbors

        default boolean countTouchingNeighbors​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer touch_matrix,
                                       net.haesleinhuepf.clij.clearcl.ClearCLBuffer touching_neighbors_count_destination)
        Takes a touch matrix as input and delivers a vector with number of touching neighbors per label as a vector.

      • replaceIntensities

        default boolean replaceIntensities​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface input,
                                   net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface new_values_vector,
                                   net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Replaces integer intensities specified in a vector image. The vector image must be 3D with size (m, 1, 1) where m corresponds to the maximum intensity in the original image. Assuming the vector image contains values (0, 1, 0, 2) means: * All pixels with value 0 (first entry in the vector image) get value 0 * All pixels with value 1 get value 1 * All pixels with value 2 get value 0 * All pixels with value 3 get value 2

      • averageDistanceOfClosestPoints

        @Deprecated
default boolean averageDistanceOfClosestPoints​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                               net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                                               double arg3)
        Deprecated.

      • averageDistanceOfNClosestPoints

        default boolean averageDistanceOfNClosestPoints​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                                net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                                                double arg3)
        Determines the average of the n closest points for every point in a distance matrix. This corresponds to the average of the n minimum values (rows) for each column of the distance matrix. Parameters ---------- distance_matrix : Image The a distance matrix to be processed. distance_list_destination : Image A vector image with the same width as the distance matrix and height=1, depth=1. Determined average distances will be written into this vector. n_closest_points_to_find : Number Number of smallest distances which should be averaged.

      • saveAsTIF

        default boolean saveAsTIF​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input,
                          String filename)
        Pulls an image from the GPU memory and saves it as TIF to disc.

      • touchMatrixToMesh

        default boolean touchMatrixToMesh​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer pointlist,
                                  net.haesleinhuepf.clij.clearcl.ClearCLBuffer touch_matrix,
                                  net.haesleinhuepf.clij.clearcl.ClearCLBuffer mesh_destination)
        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. Parameters ---------- pointlist : Image n*d matrix representing n coordinates with d dimensions. touch_matrix : Image A 2D binary matrix with 1 in pixels (i,j) where label i touches label j. mesh_destination : Image The output image where results are written into.

      • resample

        @Deprecated
default boolean resample​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                         net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                         double arg3,
                         double arg4,
                         double arg5,
                         boolean arg6)
        Deprecated.
        Resamples an image with given size factors using an affine transform.

      • resample2D

        default boolean resample2D​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                           net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                           double arg3,
                           double arg4,
                           boolean arg5)

      • resample3D

        default boolean resample3D​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                           net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                           double arg3,
                           double arg4,
                           double arg5,
                           boolean arg6)

      • equalizeMeanIntensitiesOfSlices

        default boolean equalizeMeanIntensitiesOfSlices​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                                net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                                                double arg3)
        Determines correction factors for each z-slice so that the average intensity in all slices can be made the same and multiplies these factors with the slices. This functionality is similar to the 'Simple Ratio Bleaching Correction' in Fiji.

      • watershed

        default boolean watershed​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer binary_source,
                          net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
        Apply a binary watershed to a binary image and introduces black pixels between objects.

      • radialProjection

        @Deprecated
default boolean radialProjection​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                 net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                                 double arg3)
        Deprecated.

      • resliceRadial

        default boolean resliceRadial​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                              net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                              double arg3)
        Computes a radial projection of an image stack. Starting point for the line is the given point in any X/Y-plane of a given input image stack. Furthermore, radius of the resulting projection must be given and scaling factors in X and Y in case pixels are not isotropic.This operation is similar to ImageJs 'Radial Reslice' method but offers less flexibility.

      • resliceRadial

        default boolean resliceRadial​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                              net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                              double arg3,
                              double arg4,
                              double arg5)
        Computes a radial projection of an image stack. Starting point for the line is the given point in any X/Y-plane of a given input image stack. Furthermore, radius of the resulting projection must be given and scaling factors in X and Y in case pixels are not isotropic.This operation is similar to ImageJs 'Radial Reslice' method but offers less flexibility.

      • resliceRadial

        default boolean resliceRadial​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                              net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                              double arg3,
                              double arg4,
                              double arg5,
                              double arg6,
                              double arg7,
                              double arg8)
        Computes a radial projection of an image stack. Starting point for the line is the given point in any X/Y-plane of a given input image stack. Furthermore, radius of the resulting projection must be given and scaling factors in X and Y in case pixels are not isotropic.This operation is similar to ImageJs 'Radial Reslice' method but offers less flexibility.

      • sobel

        default boolean sobel​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source,
                      net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
        Convolve the image with the Sobel kernel.

      • absolute

        default boolean absolute​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                         net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Computes the absolute value of every individual pixel x in a given image. 
        f(x) = |x|
        Parameters ---------- source : Image The input image to be processed. destination : Image The output image where results are written into.

      • laplaceBox

        default boolean laplaceBox​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input,
                           net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
        Applies the Laplace operator (Box neighborhood) to an image.

      • bottomHatBox

        default boolean bottomHatBox​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                             net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                             double arg3,
                             double arg4,
                             double arg5)
        Apply a bottom-hat filter for background subtraction to the input image. Parameters ---------- input : Image The input image where the background is subtracted from. destination : Image The output image where results are written into. radius_x : Image Radius of the background determination region in X. radius_y : Image Radius of the background determination region in Y. radius_z : Image Radius of the background determination region in Z.

      • bottomHatSphere

        default boolean bottomHatSphere​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                                double arg3,
                                double arg4,
                                double arg5)
        Applies a bottom-hat filter for background subtraction to the input image. Parameters ---------- input : Image The input image where the background is subtracted from. destination : Image The output image where results are written into. radius_x : Image Radius of the background determination region in X. radius_y : Image Radius of the background determination region in Y. radius_z : Image Radius of the background determination region in Z.

      • closingBox

        default boolean closingBox​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                           net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                           double arg3)
        Apply a binary closing to the input image by calling n dilations and n erosions subsequenntly.

      • closingDiamond

        default boolean closingDiamond​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                               net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                               double arg3)
        Apply a binary closing to the input image by calling n dilations and n erosions subsequently.

      • openingBox

        default boolean openingBox​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                           net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                           double arg3)
        Apply a binary opening to the input image by calling n erosions and n dilations subsequenntly.

      • openingDiamond

        default boolean openingDiamond​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                               net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                               double arg3)
        Apply a binary opening to the input image by calling n erosions and n dilations subsequenntly.

      • maximumXProjection

        default boolean maximumXProjection​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                                   net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination_max)
        Determines the maximum intensity projection of an image along X.

      • maximumYProjection

        default boolean maximumYProjection​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                                   net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination_max)
        Determines the maximum intensity projection of an image along X.

      • maximumZProjectionBounded

        default boolean maximumZProjectionBounded​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                          net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                          double arg3,
                                          double arg4)
        Determines the maximum intensity projection of an image along Z within a given z range.

      • minimumZProjectionBounded

        default boolean minimumZProjectionBounded​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                          net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                          double arg3,
                                          double arg4)
        Determines the minimum intensity projection of an image along Z within a given z range.

      • meanZProjectionBounded

        default boolean meanZProjectionBounded​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                       net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                       double arg3,
                                       double arg4)
        Determines the mean average intensity projection of an image along Z within a given z range.

      • nonzeroMaximumBox

        default boolean nonzeroMaximumBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface input,
                                  net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Apply a maximum filter (box shape) to the input image. The radius is fixed to 1 and pixels with value 0 are ignored. Note: Pixels with 0 value in the input image will not be overwritten in the output image. Thus, the result image should be initialized by copying the original image in advance.

      • nonzeroMaximumBox

        default boolean nonzeroMaximumBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                  net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                  net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg3)
        Apply a maximum filter (box shape) to the input image. The radius is fixed to 1 and pixels with value 0 are ignored. Note: Pixels with 0 value in the input image will not be overwritten in the output image. Thus, the result image should be initialized by copying the original image in advance.

      • nonzeroMaximumBox

        default net.haesleinhuepf.clij.clearcl.ClearCLKernel nonzeroMaximumBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                                                       net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                                                       net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg3,
                                                                       net.haesleinhuepf.clij.clearcl.ClearCLKernel arg4)
        Apply a maximum filter (box shape) to the input image. The radius is fixed to 1 and pixels with value 0 are ignored. Note: Pixels with 0 value in the input image will not be overwritten in the output image. Thus, the result image should be initialized by copying the original image in advance.

      • nonzeroMinimumBox

        default boolean nonzeroMinimumBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface input,
                                  net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Apply a minimum filter (box shape) to the input image. The radius is fixed to 1 and pixels with value 0 are ignored. Note: Pixels with 0 value in the input image will not be overwritten in the output image. Thus, the result image should be initialized by copying the original image in advance.

      • nonzeroMinimumBox

        default boolean nonzeroMinimumBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                  net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                  net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg3)
        Apply a minimum filter (box shape) to the input image. The radius is fixed to 1 and pixels with value 0 are ignored. Note: Pixels with 0 value in the input image will not be overwritten in the output image. Thus, the result image should be initialized by copying the original image in advance.

      • nonzeroMinimumBox

        default net.haesleinhuepf.clij.clearcl.ClearCLKernel nonzeroMinimumBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                                                       net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                                                       net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg3,
                                                                       net.haesleinhuepf.clij.clearcl.ClearCLKernel arg4)
        Apply a minimum filter (box shape) to the input image. The radius is fixed to 1 and pixels with value 0 are ignored. Note: Pixels with 0 value in the input image will not be overwritten in the output image. Thus, the result image should be initialized by copying the original image in advance.

      • minimumZProjectionThresholdedBounded

        default boolean minimumZProjectionThresholdedBounded​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                                     net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                                                     double arg3,
                                                     double arg4,
                                                     double arg5)
        Determines the minimum intensity projection of all pixels in an image above a given threshold along Z within a given z range.

      • meanOfPixelsAboveThreshold

        default double meanOfPixelsAboveThreshold​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                          double arg2)
        Determines the mean intensity in a threshleded image. But only in pixels which are above a given threshold.

      • distanceMatrixToMesh

        default boolean distanceMatrixToMesh​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                     net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                                     net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg3,
                                     double arg4)
        Generates a mesh from a distance matric and a list of point coordinates. Takes a pointlist with dimensions n*d with n point coordinates in d dimensions and a distance matrix of size n*n to draw lines from all points to points if the corresponding pixel in the distance matrix is smaller than a given distance threshold.

      • pointIndexListToMesh

        default boolean pointIndexListToMesh​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer pointlist,
                                     net.haesleinhuepf.clij.clearcl.ClearCLBuffer indexlist,
                                     net.haesleinhuepf.clij.clearcl.ClearCLBuffer mesh_destination)
        Meshes all points in a given point list which are indiced in a corresponding index list.

      • minimumOctagon

        default boolean minimumOctagon​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                               net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                               double arg3)
        Applies a minimum filter with kernel size 3x3 n times to an image iteratively. Odd iterations are done with box neighborhood, even iterations with a diamond. Thus, with n > 2, the filter shape is an octagon. The given number of iterations makes the filter result very similar to minimum sphere. Approximately:radius = iterations - 2

      • minimumBox

        @Deprecated
default net.haesleinhuepf.clij.clearcl.ClearCLKernel minimumBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                                                net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                                                net.haesleinhuepf.clij.clearcl.ClearCLKernel arg3)
        Deprecated.
        Computes the local minimum of a pixels rectangular neighborhood. The rectangles size is specified by its half-width and half-height (radius).

      • minimumDiamond

        @Deprecated
default net.haesleinhuepf.clij.clearcl.ClearCLKernel minimumDiamond​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                                                    net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                                                    net.haesleinhuepf.clij.clearcl.ClearCLKernel arg3)
        Deprecated.

      • maximumOctagon

        default boolean maximumOctagon​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                               net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                               double arg3)
        Applies a maximum filter with kernel size 3x3 n times to an image iteratively. Odd iterations are done with box neighborhood, even iterations with a diamond. Thus, with n > 2, the filter shape is an octagon. The given number of iterations makes the filter result very similar to minimum sphere. Approximately:radius = iterations - 2

      • maximumBox

        @Deprecated
default net.haesleinhuepf.clij.clearcl.ClearCLKernel maximumBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                                                net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                                                net.haesleinhuepf.clij.clearcl.ClearCLKernel arg3)
        Deprecated.
        Computes the local maximum of a pixels rectangular neighborhood. The rectangles size is specified by its half-width and half-height (radius).

      • maximumDiamond

        @Deprecated
default net.haesleinhuepf.clij.clearcl.ClearCLKernel maximumDiamond​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                                                    net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                                                    net.haesleinhuepf.clij.clearcl.ClearCLKernel arg3)
        Deprecated.

      • addImages

        default boolean addImages​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface summand1,
                          net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface summand2,
                          net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Calculates the sum of pairs of pixels x and y of two images X and Y. 
        f(x, y) = x + y
        Parameters ---------- summand1 : Image The first input image to added. summand2 : Image The second image to be added. destination : Image The output image where results are written into.

      • addImagesWeighted

        default boolean addImagesWeighted​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                  net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                  net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg3,
                                  double arg4,
                                  double arg5)
        Calculates the sum of pairs of pixels x and y from images X and Y weighted with factors a and b. 
        f(x, y, a, b) = x * a + y * b
        Parameters ---------- summand1 : Image The first input image to added. summand2 : Image The second image to be added. destination : Image The output image where results are written into. factor1 : float The constant number which will be multiplied with each pixel of summand1 before adding it. factor2 : float The constant number which will be multiplied with each pixel of summand2 before adding it.

      • subtract

        @Deprecated
default boolean subtract​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface subtrahend,
                         net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface minuend,
                         net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Deprecated.
        Subtracts one image X from another image Y pixel wise. 
        f(x, y) = x - y

      • subtractImages

        default boolean subtractImages​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface subtrahend,
                               net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface minuend,
                               net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Subtracts one image X from another image Y pixel wise. 
        f(x, y) = x - y

      • affineTransform2D

        default boolean affineTransform2D​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                  net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                  float[] arg3)
        Applies an affine transform to a 2D image. The transform describes how coordinates in the target image are transformed to coordinates in the source image. This may appear unintuitive and will be changed in the next major release. The replacement affineTransform (currently part of CLIJx) will apply inverted transforms compared to this operation. Individual transforms must be separated by spaces. Parameters ---------- source : Image The input image to be processed. destination : Image The output image where results are written into. transform : String A space-separated list of individual transforms. Syntrax see below. Supported transforms: * -center: translate the coordinate origin to the center of the image * center: translate the coordinate origin back to the initial origin * rotate=[angle]: rotate in X/Y plane (around Z-axis) by the given angle in degrees * scale=[factor]: isotropic scaling according to given zoom factor * scaleX=[factor]: scaling along X-axis according to given zoom factor * scaleY=[factor]: scaling along Y-axis according to given zoom factor * shearXY=[factor]: shearing along X-axis in XY plane according to given factor * translateX=[distance]: translate along X-axis by distance given in pixels * translateY=[distance]: translate along X-axis by distance given in pixels Example transform: transform = "-center scale=2 rotate=45 center";

      • affineTransform2D

        default boolean affineTransform2D​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source,
                                  net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination,
                                  String transform)
        Applies an affine transform to a 2D image. The transform describes how coordinates in the target image are transformed to coordinates in the source image. This may appear unintuitive and will be changed in the next major release. The replacement affineTransform (currently part of CLIJx) will apply inverted transforms compared to this operation. Individual transforms must be separated by spaces. Parameters ---------- source : Image The input image to be processed. destination : Image The output image where results are written into. transform : String A space-separated list of individual transforms. Syntrax see below. Supported transforms: * -center: translate the coordinate origin to the center of the image * center: translate the coordinate origin back to the initial origin * rotate=[angle]: rotate in X/Y plane (around Z-axis) by the given angle in degrees * scale=[factor]: isotropic scaling according to given zoom factor * scaleX=[factor]: scaling along X-axis according to given zoom factor * scaleY=[factor]: scaling along Y-axis according to given zoom factor * shearXY=[factor]: shearing along X-axis in XY plane according to given factor * translateX=[distance]: translate along X-axis by distance given in pixels * translateY=[distance]: translate along X-axis by distance given in pixels Example transform: transform = "-center scale=2 rotate=45 center";

      • affineTransform2D

        default boolean affineTransform2D​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                  net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                  AffineTransform2D arg3)
        Applies an affine transform to a 2D image. The transform describes how coordinates in the target image are transformed to coordinates in the source image. This may appear unintuitive and will be changed in the next major release. The replacement affineTransform (currently part of CLIJx) will apply inverted transforms compared to this operation. Individual transforms must be separated by spaces. Parameters ---------- source : Image The input image to be processed. destination : Image The output image where results are written into. transform : String A space-separated list of individual transforms. Syntrax see below. Supported transforms: * -center: translate the coordinate origin to the center of the image * center: translate the coordinate origin back to the initial origin * rotate=[angle]: rotate in X/Y plane (around Z-axis) by the given angle in degrees * scale=[factor]: isotropic scaling according to given zoom factor * scaleX=[factor]: scaling along X-axis according to given zoom factor * scaleY=[factor]: scaling along Y-axis according to given zoom factor * shearXY=[factor]: shearing along X-axis in XY plane according to given factor * translateX=[distance]: translate along X-axis by distance given in pixels * translateY=[distance]: translate along X-axis by distance given in pixels Example transform: transform = "-center scale=2 rotate=45 center";

      • affineTransform2D

        default boolean affineTransform2D​(net.haesleinhuepf.clij.clearcl.ClearCLImage arg1,
                                  net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                  float[] arg3)
        Applies an affine transform to a 2D image. The transform describes how coordinates in the target image are transformed to coordinates in the source image. This may appear unintuitive and will be changed in the next major release. The replacement affineTransform (currently part of CLIJx) will apply inverted transforms compared to this operation. Individual transforms must be separated by spaces. Parameters ---------- source : Image The input image to be processed. destination : Image The output image where results are written into. transform : String A space-separated list of individual transforms. Syntrax see below. Supported transforms: * -center: translate the coordinate origin to the center of the image * center: translate the coordinate origin back to the initial origin * rotate=[angle]: rotate in X/Y plane (around Z-axis) by the given angle in degrees * scale=[factor]: isotropic scaling according to given zoom factor * scaleX=[factor]: scaling along X-axis according to given zoom factor * scaleY=[factor]: scaling along Y-axis according to given zoom factor * shearXY=[factor]: shearing along X-axis in XY plane according to given factor * translateX=[distance]: translate along X-axis by distance given in pixels * translateY=[distance]: translate along X-axis by distance given in pixels Example transform: transform = "-center scale=2 rotate=45 center";

      • affineTransform2D

        default boolean affineTransform2D​(net.haesleinhuepf.clij.clearcl.ClearCLImage arg1,
                                  net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                  AffineTransform2D arg3)
        Applies an affine transform to a 2D image. The transform describes how coordinates in the target image are transformed to coordinates in the source image. This may appear unintuitive and will be changed in the next major release. The replacement affineTransform (currently part of CLIJx) will apply inverted transforms compared to this operation. Individual transforms must be separated by spaces. Parameters ---------- source : Image The input image to be processed. destination : Image The output image where results are written into. transform : String A space-separated list of individual transforms. Syntrax see below. Supported transforms: * -center: translate the coordinate origin to the center of the image * center: translate the coordinate origin back to the initial origin * rotate=[angle]: rotate in X/Y plane (around Z-axis) by the given angle in degrees * scale=[factor]: isotropic scaling according to given zoom factor * scaleX=[factor]: scaling along X-axis according to given zoom factor * scaleY=[factor]: scaling along Y-axis according to given zoom factor * shearXY=[factor]: shearing along X-axis in XY plane according to given factor * translateX=[distance]: translate along X-axis by distance given in pixels * translateY=[distance]: translate along X-axis by distance given in pixels Example transform: transform = "-center scale=2 rotate=45 center";

      • affineTransform3D

        default boolean affineTransform3D​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                  net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                  float[] arg3)
        Applies an affine transform to a 3D image. The transform describes how coordinates in the target image are transformed to coordinates in the source image. This may appear unintuitive and will be changed in the next major release. The replacement affineTransform (currently part of CLIJx) will apply inverted transforms compared to this operation. Individual transforms must be separated by spaces. Parameters ---------- source : Image The input image to be processed. destination : Image The output image where results are written into. transform : String A space-separated list of individual transforms. Syntrax see below. Supported transforms: * -center: translate the coordinate origin to the center of the image * center: translate the coordinate origin back to the initial origin * rotate=[angle]: rotate in X/Y plane (around Z-axis) by the given angle in degrees * rotateX=[angle]: rotate in Y/Z plane (around X-axis) by the given angle in degrees * rotateY=[angle]: rotate in X/Z plane (around Y-axis) by the given angle in degrees * rotateZ=[angle]: rotate in X/Y plane (around Z-axis) by the given angle in degrees * scale=[factor]: isotropic scaling according to given zoom factor * scaleX=[factor]: scaling along X-axis according to given zoom factor * scaleY=[factor]: scaling along Y-axis according to given zoom factor * scaleZ=[factor]: scaling along Z-axis according to given zoom factor * shearXY=[factor]: shearing along X-axis in XY plane according to given factor * shearXZ=[factor]: shearing along X-axis in XZ plane according to given factor * shearYX=[factor]: shearing along Y-axis in XY plane according to given factor * shearYZ=[factor]: shearing along Y-axis in YZ plane according to given factor * shearZX=[factor]: shearing along Z-axis in XZ plane according to given factor * shearZY=[factor]: shearing along Z-axis in YZ plane according to given factor * translateX=[distance]: translate along X-axis by distance given in pixels * translateY=[distance]: translate along X-axis by distance given in pixels * translateZ=[distance]: translate along X-axis by distance given in pixels Example transform: transform = "-center scale=2 rotate=45 center";

      • affineTransform3D

        default boolean affineTransform3D​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source,
                                  net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination,
                                  String transform)
        Applies an affine transform to a 3D image. The transform describes how coordinates in the target image are transformed to coordinates in the source image. This may appear unintuitive and will be changed in the next major release. The replacement affineTransform (currently part of CLIJx) will apply inverted transforms compared to this operation. Individual transforms must be separated by spaces. Parameters ---------- source : Image The input image to be processed. destination : Image The output image where results are written into. transform : String A space-separated list of individual transforms. Syntrax see below. Supported transforms: * -center: translate the coordinate origin to the center of the image * center: translate the coordinate origin back to the initial origin * rotate=[angle]: rotate in X/Y plane (around Z-axis) by the given angle in degrees * rotateX=[angle]: rotate in Y/Z plane (around X-axis) by the given angle in degrees * rotateY=[angle]: rotate in X/Z plane (around Y-axis) by the given angle in degrees * rotateZ=[angle]: rotate in X/Y plane (around Z-axis) by the given angle in degrees * scale=[factor]: isotropic scaling according to given zoom factor * scaleX=[factor]: scaling along X-axis according to given zoom factor * scaleY=[factor]: scaling along Y-axis according to given zoom factor * scaleZ=[factor]: scaling along Z-axis according to given zoom factor * shearXY=[factor]: shearing along X-axis in XY plane according to given factor * shearXZ=[factor]: shearing along X-axis in XZ plane according to given factor * shearYX=[factor]: shearing along Y-axis in XY plane according to given factor * shearYZ=[factor]: shearing along Y-axis in YZ plane according to given factor * shearZX=[factor]: shearing along Z-axis in XZ plane according to given factor * shearZY=[factor]: shearing along Z-axis in YZ plane according to given factor * translateX=[distance]: translate along X-axis by distance given in pixels * translateY=[distance]: translate along X-axis by distance given in pixels * translateZ=[distance]: translate along X-axis by distance given in pixels Example transform: transform = "-center scale=2 rotate=45 center";

      • affineTransform3D

        default boolean affineTransform3D​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                  net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                  AffineTransform3D arg3)
        Applies an affine transform to a 3D image. The transform describes how coordinates in the target image are transformed to coordinates in the source image. This may appear unintuitive and will be changed in the next major release. The replacement affineTransform (currently part of CLIJx) will apply inverted transforms compared to this operation. Individual transforms must be separated by spaces. Parameters ---------- source : Image The input image to be processed. destination : Image The output image where results are written into. transform : String A space-separated list of individual transforms. Syntrax see below. Supported transforms: * -center: translate the coordinate origin to the center of the image * center: translate the coordinate origin back to the initial origin * rotate=[angle]: rotate in X/Y plane (around Z-axis) by the given angle in degrees * rotateX=[angle]: rotate in Y/Z plane (around X-axis) by the given angle in degrees * rotateY=[angle]: rotate in X/Z plane (around Y-axis) by the given angle in degrees * rotateZ=[angle]: rotate in X/Y plane (around Z-axis) by the given angle in degrees * scale=[factor]: isotropic scaling according to given zoom factor * scaleX=[factor]: scaling along X-axis according to given zoom factor * scaleY=[factor]: scaling along Y-axis according to given zoom factor * scaleZ=[factor]: scaling along Z-axis according to given zoom factor * shearXY=[factor]: shearing along X-axis in XY plane according to given factor * shearXZ=[factor]: shearing along X-axis in XZ plane according to given factor * shearYX=[factor]: shearing along Y-axis in XY plane according to given factor * shearYZ=[factor]: shearing along Y-axis in YZ plane according to given factor * shearZX=[factor]: shearing along Z-axis in XZ plane according to given factor * shearZY=[factor]: shearing along Z-axis in YZ plane according to given factor * translateX=[distance]: translate along X-axis by distance given in pixels * translateY=[distance]: translate along X-axis by distance given in pixels * translateZ=[distance]: translate along X-axis by distance given in pixels Example transform: transform = "-center scale=2 rotate=45 center";

      • affineTransform3D

        default boolean affineTransform3D​(net.haesleinhuepf.clij.clearcl.ClearCLImage arg1,
                                  net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                  float[] arg3)
        Applies an affine transform to a 3D image. The transform describes how coordinates in the target image are transformed to coordinates in the source image. This may appear unintuitive and will be changed in the next major release. The replacement affineTransform (currently part of CLIJx) will apply inverted transforms compared to this operation. Individual transforms must be separated by spaces. Parameters ---------- source : Image The input image to be processed. destination : Image The output image where results are written into. transform : String A space-separated list of individual transforms. Syntrax see below. Supported transforms: * -center: translate the coordinate origin to the center of the image * center: translate the coordinate origin back to the initial origin * rotate=[angle]: rotate in X/Y plane (around Z-axis) by the given angle in degrees * rotateX=[angle]: rotate in Y/Z plane (around X-axis) by the given angle in degrees * rotateY=[angle]: rotate in X/Z plane (around Y-axis) by the given angle in degrees * rotateZ=[angle]: rotate in X/Y plane (around Z-axis) by the given angle in degrees * scale=[factor]: isotropic scaling according to given zoom factor * scaleX=[factor]: scaling along X-axis according to given zoom factor * scaleY=[factor]: scaling along Y-axis according to given zoom factor * scaleZ=[factor]: scaling along Z-axis according to given zoom factor * shearXY=[factor]: shearing along X-axis in XY plane according to given factor * shearXZ=[factor]: shearing along X-axis in XZ plane according to given factor * shearYX=[factor]: shearing along Y-axis in XY plane according to given factor * shearYZ=[factor]: shearing along Y-axis in YZ plane according to given factor * shearZX=[factor]: shearing along Z-axis in XZ plane according to given factor * shearZY=[factor]: shearing along Z-axis in YZ plane according to given factor * translateX=[distance]: translate along X-axis by distance given in pixels * translateY=[distance]: translate along X-axis by distance given in pixels * translateZ=[distance]: translate along X-axis by distance given in pixels Example transform: transform = "-center scale=2 rotate=45 center";

      • affineTransform3D

        default boolean affineTransform3D​(net.haesleinhuepf.clij.clearcl.ClearCLImage arg1,
                                  net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                  AffineTransform3D arg3)
        Applies an affine transform to a 3D image. The transform describes how coordinates in the target image are transformed to coordinates in the source image. This may appear unintuitive and will be changed in the next major release. The replacement affineTransform (currently part of CLIJx) will apply inverted transforms compared to this operation. Individual transforms must be separated by spaces. Parameters ---------- source : Image The input image to be processed. destination : Image The output image where results are written into. transform : String A space-separated list of individual transforms. Syntrax see below. Supported transforms: * -center: translate the coordinate origin to the center of the image * center: translate the coordinate origin back to the initial origin * rotate=[angle]: rotate in X/Y plane (around Z-axis) by the given angle in degrees * rotateX=[angle]: rotate in Y/Z plane (around X-axis) by the given angle in degrees * rotateY=[angle]: rotate in X/Z plane (around Y-axis) by the given angle in degrees * rotateZ=[angle]: rotate in X/Y plane (around Z-axis) by the given angle in degrees * scale=[factor]: isotropic scaling according to given zoom factor * scaleX=[factor]: scaling along X-axis according to given zoom factor * scaleY=[factor]: scaling along Y-axis according to given zoom factor * scaleZ=[factor]: scaling along Z-axis according to given zoom factor * shearXY=[factor]: shearing along X-axis in XY plane according to given factor * shearXZ=[factor]: shearing along X-axis in XZ plane according to given factor * shearYX=[factor]: shearing along Y-axis in XY plane according to given factor * shearYZ=[factor]: shearing along Y-axis in YZ plane according to given factor * shearZX=[factor]: shearing along Z-axis in XZ plane according to given factor * shearZY=[factor]: shearing along Z-axis in YZ plane according to given factor * translateX=[distance]: translate along X-axis by distance given in pixels * translateY=[distance]: translate along X-axis by distance given in pixels * translateZ=[distance]: translate along X-axis by distance given in pixels Example transform: transform = "-center scale=2 rotate=45 center";

      • applyVectorField

        default boolean applyVectorField​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                                 net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface vector_x,
                                 net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface vector_y,
                                 net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Deforms an image according to distances provided in the given vector images. It is recommended to use 32-bit images for input, output and vector images. Parameters ---------- source : Image The input image to be processed. vector_x : Image Pixels in this image describe the distance in X direction pixels should be shifted during warping. vector_y : Image Pixels in this image describe the distance in Y direction pixels should be shifted during warping. destination : Image The output image where results are written into.

      • applyVectorField2D

        default boolean applyVectorField2D​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                                   net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface vector_x,
                                   net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface vector_y,
                                   net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Deforms an image according to distances provided in the given vector images. It is recommended to use 32-bit images for input, output and vector images. Parameters ---------- source : Image The input image to be processed. vector_x : Image Pixels in this image describe the distance in X direction pixels should be shifted during warping. vector_y : Image Pixels in this image describe the distance in Y direction pixels should be shifted during warping. destination : Image The output image where results are written into.

      • applyVectorField

        default boolean applyVectorField​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                 net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                 net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg3,
                                 net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg4,
                                 net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg5)
        Deforms an image according to distances provided in the given vector images. It is recommended to use 32-bit images for input, output and vector images. Parameters ---------- source : Image The input image to be processed. vector_x : Image Pixels in this image describe the distance in X direction pixels should be shifted during warping. vector_y : Image Pixels in this image describe the distance in Y direction pixels should be shifted during warping. destination : Image The output image where results are written into.

      • applyVectorField3D

        default boolean applyVectorField3D​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                                   net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface vectorX,
                                   net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface vectorY,
                                   net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface vectorZ,
                                   net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Deforms an image stack according to distances provided in the given vector image stacks. It is recommended to use 32-bit image stacks for input, output and vector image stacks. Parameters ---------- source : Image The input image to be processed. vector_x : Image Pixels in this image describe the distance in X direction pixels should be shifted during warping. vector_y : Image Pixels in this image describe the distance in Y direction pixels should be shifted during warping. vector_z : Image Pixels in this image describe the distance in Z direction pixels should be shifted during warping. destination : Image The output image where results are written into.

      • argMaximumZProjection

        default boolean argMaximumZProjection​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                                      net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination_max,
                                      net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination_arg_max)
        Determines the maximum projection of an image stack along Z. Furthermore, another 2D image is generated with pixels containing the z-index where the maximum was found (zero based).

      • fillHistogram

        @Deprecated
default boolean fillHistogram​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                              net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                              double arg3,
                              double arg4)
        Deprecated.

      • histogram

        default boolean histogram​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                          net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2)
        Determines the histogram of a given image. The histogram image is of dimensions number_of_bins/1/1; a 3D image with height=1 and depth=1. Histogram bins contain the number of pixels with intensity in this corresponding bin. The histogram bins are uniformly distributed between given minimum and maximum grey value intensity. If the flag determine_min_max is set, minimum and maximum intensity will be determined. When calling this operation many times, it is recommended to determine minimum and maximum intensity once at the beginning and handing over these values.

      • histogram

        default boolean histogram​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                          net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                          double arg3,
                          double arg4,
                          double arg5,
                          boolean arg6)
        Determines the histogram of a given image. The histogram image is of dimensions number_of_bins/1/1; a 3D image with height=1 and depth=1. Histogram bins contain the number of pixels with intensity in this corresponding bin. The histogram bins are uniformly distributed between given minimum and maximum grey value intensity. If the flag determine_min_max is set, minimum and maximum intensity will be determined. When calling this operation many times, it is recommended to determine minimum and maximum intensity once at the beginning and handing over these values.

      • histogram

        default boolean histogram​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                          net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                          double arg3,
                          double arg4,
                          double arg5,
                          boolean arg6,
                          boolean arg7)
        Determines the histogram of a given image. The histogram image is of dimensions number_of_bins/1/1; a 3D image with height=1 and depth=1. Histogram bins contain the number of pixels with intensity in this corresponding bin. The histogram bins are uniformly distributed between given minimum and maximum grey value intensity. If the flag determine_min_max is set, minimum and maximum intensity will be determined. When calling this operation many times, it is recommended to determine minimum and maximum intensity once at the beginning and handing over these values.

      • histogram

        default float[] histogram​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                          double arg2,
                          double arg3,
                          double arg4)
        Determines the histogram of a given image. The histogram image is of dimensions number_of_bins/1/1; a 3D image with height=1 and depth=1. Histogram bins contain the number of pixels with intensity in this corresponding bin. The histogram bins are uniformly distributed between given minimum and maximum grey value intensity. If the flag determine_min_max is set, minimum and maximum intensity will be determined. When calling this operation many times, it is recommended to determine minimum and maximum intensity once at the beginning and handing over these values.

      • histogram

        default net.haesleinhuepf.clij.clearcl.ClearCLBuffer histogram​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1)
        Determines the histogram of a given image. The histogram image is of dimensions number_of_bins/1/1; a 3D image with height=1 and depth=1. Histogram bins contain the number of pixels with intensity in this corresponding bin. The histogram bins are uniformly distributed between given minimum and maximum grey value intensity. If the flag determine_min_max is set, minimum and maximum intensity will be determined. When calling this operation many times, it is recommended to determine minimum and maximum intensity once at the beginning and handing over these values.

      • automaticThreshold

        default boolean automaticThreshold​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input,
                                   net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination,
                                   String method)
        The automatic thresholder utilizes the threshold methods from ImageJ on a histogram determined on the GPU to create binary images as similar as possible to ImageJ 'Apply Threshold' method. Enter one of these methods in the method text field: [Default, Huang, Intermodes, IsoData, IJ_IsoData, Li, MaxEntropy, Mean, MinError, Minimum, Moments, Otsu, Percentile, RenyiEntropy, Shanbhag, Triangle, Yen]

      • automaticThreshold

        default boolean automaticThreshold​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                   net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                                   String arg3,
                                   double arg4,
                                   double arg5,
                                   double arg6)
        The automatic thresholder utilizes the threshold methods from ImageJ on a histogram determined on the GPU to create binary images as similar as possible to ImageJ 'Apply Threshold' method. Enter one of these methods in the method text field: [Default, Huang, Intermodes, IsoData, IJ_IsoData, Li, MaxEntropy, Mean, MinError, Minimum, Moments, Otsu, Percentile, RenyiEntropy, Shanbhag, Triangle, Yen]

      • threshold

        default boolean threshold​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                          net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                          double arg3)
        Computes a binary image with pixel values 0 and 1. All pixel values x of a given input image with value larger or equal to a given threshold t will be set to 1. f(x,t) = (1 if (x >= t); (0 otherwise)) This plugin is comparable to setting a raw threshold in ImageJ and using the 'Convert to Mask' menu.

      • binaryOr

        default boolean binaryOr​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface operand1,
                         net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface operand2,
                         net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        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 |. All pixel values except 0 in the input images are interpreted as 1.
        f(x, y) = x | y
        Parameters ---------- operand1 : Image The first binary input image to be processed. operand2 : Image The second binary input image to be processed. destination : Image The output image where results are written into.

      • binaryAnd

        default boolean binaryAnd​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface operand1,
                          net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface operand2,
                          net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        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. 
        f(x, y) = x & y
        Parameters ---------- operand1 : Image The first binary input image to be processed. operand2 : Image The second binary input image to be processed. destination : Image The output image where results are written into.

      • binaryXOr

        default boolean binaryXOr​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface operand1,
                          net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface operand2,
                          net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        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. All pixel values except 0 in the input images are interpreted as 1. 
        f(x, y) = (x & !y) | (!x & y)
        Parameters ---------- operand1 : Image The first binary input image to be processed. operand2 : Image The second binary input image to be processed. destination : Image The output image where results are written into.

      • binaryNot

        default boolean binaryNot​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                          net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        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 ! All pixel values except 0 in the input image are interpreted as 1. 
        f(x) = !x
        Parameters ---------- source : Image The binary input image to be inverted. destination : Image The output image where results are written into.

      • erodeSphere

        default boolean erodeSphere​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                            net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Computes a binary image with pixel values 0 and 1 containing the binary erosion of a given input image. The erosion takes the von-Neumann-neighborhood (4 pixels in 2D and 6 pixels in 3d) into account. The pixels in the input image with pixel value not equal to 0 will be interpreted as 1.

      • erodeBox

        default boolean erodeBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                         net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Computes a binary image with pixel values 0 and 1 containing the binary erosion of a given input image. The erosion takes the Moore-neighborhood (8 pixels in 2D and 26 pixels in 3d) into account. The pixels in the input image with pixel value not equal to 0 will be interpreted as 1. This method is comparable to the 'Erode' menu in ImageJ in case it is applied to a 2D image. The only difference is that the output image contains values 0 and 1 instead of 0 and 255.

      • erodeSphereSliceBySlice

        default boolean erodeSphereSliceBySlice​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                                        net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Computes a binary image with pixel values 0 and 1 containing the binary erosion of a given input image. The erosion takes the von-Neumann-neighborhood (4 pixels in 2D and 6 pixels in 3d) into account. The pixels in the input image with pixel value not equal to 0 will be interpreted as 1. This filter is applied slice by slice in 2D.

      • erodeBoxSliceBySlice

        default boolean erodeBoxSliceBySlice​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                                     net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Computes a binary image with pixel values 0 and 1 containing the binary erosion of a given input image. The erosion takes the Moore-neighborhood (8 pixels in 2D and 26 pixels in 3d) into account. The pixels in the input image with pixel value not equal to 0 will be interpreted as 1. This method is comparable to the 'Erode' menu in ImageJ in case it is applied to a 2D image. The only difference is that the output image contains values 0 and 1 instead of 0 and 255. This filter is applied slice by slice in 2D.

      • dilateSphere

        default boolean dilateSphere​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                             net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Computes a binary image with pixel values 0 and 1 containing the binary dilation of a given input image. The dilation takes the von-Neumann-neighborhood (4 pixels in 2D and 6 pixels in 3d) into account. The pixels in the input image with pixel value not equal to 0 will be interpreted as 1.

      • dilateBox

        default boolean dilateBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                          net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Computes a binary image with pixel values 0 and 1 containing the binary dilation of a given input image. The dilation takes the Moore-neighborhood (8 pixels in 2D and 26 pixels in 3d) into account. The pixels in the input image with pixel value not equal to 0 will be interpreted as 1. This method is comparable to the 'Dilate' menu in ImageJ in case it is applied to a 2D image. The only difference is that the output image contains values 0 and 1 instead of 0 and 255.

      • dilateSphereSliceBySlice

        default boolean dilateSphereSliceBySlice​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                                         net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Computes a binary image with pixel values 0 and 1 containing the binary dilation of a given input image. The dilation takes the von-Neumann-neighborhood (4 pixels in 2D and 6 pixels in 3d) into account. The pixels in the input image with pixel value not equal to 0 will be interpreted as 1. This filter is applied slice by slice in 2D.

      • dilateBoxSliceBySlice

        default boolean dilateBoxSliceBySlice​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                                      net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Computes a binary image with pixel values 0 and 1 containing the binary dilation of a given input image. The dilation takes the Moore-neighborhood (8 pixels in 2D and 26 pixels in 3d) into account. The pixels in the input image with pixel value not equal to 0 will be interpreted as 1. This method is comparable to the 'Dilate' menu in ImageJ in case it is applied to a 2D image. The only difference is that the output image contains values 0 and 1 instead of 0 and 255. This filter is applied slice by slice in 2D.

      • copy

        default boolean copy​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                     net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Copies an image. 
        f(x) = x

      • copySlice

        default boolean copySlice​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                          net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                          double arg3)
        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. The first case is only available via ImageJ macro. If you are using it, it is recommended that the target 3D image already pre-exists in GPU memory before calling this method. Otherwise, CLIJ create the image stack with z planes.

      • crop

        default boolean crop​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                     net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                     double arg3,
                     double arg4)
        Crops a given rectangle out of a given image. Note: If the destination image pre-exists already, it will be overwritten and keep it's dimensions. Parameters ---------- source : Image The image where a part will be cropped out. destination : Image The cropped image will be stored in this variable. start_x : Number The horizontal position of the region to crop in the source image. start_y : Number The vertical position of the region to crop in the source image. width : Number The width of the region to crop in the source image. height : Number The height of the region to crop in the source image.

      • crop2D

        default boolean crop2D​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                       net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                       double arg3,
                       double arg4)
        Crops a given rectangle out of a given image. Note: If the destination image pre-exists already, it will be overwritten and keep it's dimensions. Parameters ---------- source : Image The image where a part will be cropped out. destination : Image The cropped image will be stored in this variable. start_x : Number The horizontal position of the region to crop in the source image. start_y : Number The vertical position of the region to crop in the source image. width : Number The width of the region to crop in the source image. height : Number The height of the region to crop in the source image.

      • crop

        default boolean crop​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                     net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                     double arg3,
                     double arg4,
                     double arg5)
        Crops a given rectangle out of a given image. Note: If the destination image pre-exists already, it will be overwritten and keep it's dimensions. Parameters ---------- source : Image The image where a part will be cropped out. destination : Image The cropped image will be stored in this variable. start_x : Number The horizontal position of the region to crop in the source image. start_y : Number The vertical position of the region to crop in the source image. width : Number The width of the region to crop in the source image. height : Number The height of the region to crop in the source image.

      • crop3D

        default boolean crop3D​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                       net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                       double arg3,
                       double arg4,
                       double arg5)
        Crops a given sub-stack out of a given image stack. Note: If the destination image pre-exists already, it will be overwritten and keep it's dimensions. Parameters ---------- source : Image The image where a part will be cropped out. destination : Image The cropped image will be stored in this variable. start_x : Number The horizontal position of the region to crop in the source image. start_y : Number The vertical position of the region to crop in the source image. start_z : Number The slice position of the region to crop in the source image. Slices are counted 0-based; the first slice is z=0. width : Number The width of the region to crop in the source image. height : Number The height of the region to crop in the source image. depth : Number The depth of the region to crop in the source image.

      • set

        default boolean set​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                    double arg2)
        Sets all pixel values x of a given image X to a constant value v. 
        f(x) = v

      • flip

        default boolean flip​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                     net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                     boolean arg3,
                     boolean arg4)
        Flips an image in X and/or Y direction depending on if flip_x and/or flip_y are set to true or false.

      • flip2D

        default boolean flip2D​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                       net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                       boolean arg3,
                       boolean arg4)
        Flips an image in X and/or Y direction depending on if flip_x and/or flip_y are set to true or false.

      • flip

        default boolean flip​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                     net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                     boolean arg3,
                     boolean arg4,
                     boolean arg5)
        Flips an image in X and/or Y direction depending on if flip_x and/or flip_y are set to true or false.

      • flip3D

        default boolean flip3D​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                       net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                       boolean arg3,
                       boolean arg4,
                       boolean arg5)
        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.

      • rotateCounterClockwise

        default boolean rotateCounterClockwise​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                                       net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Rotates a given input image by 90 degrees counter-clockwise. For that, X and Y axis of an image stack are flipped. This operation is similar to ImageJs 'Reslice [/]' method but offers less flexibility such as interpolation.

      • rotateLeft

        @Deprecated
default boolean rotateLeft​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                           net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Deprecated.
        Rotates a given input image by 90 degrees counter-clockwise. For that, X and Y axis of an image stack are flipped. This operation is similar to ImageJs 'Reslice [/]' method but offers less flexibility such as interpolation.

      • rotateClockwise

        default boolean rotateClockwise​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                                net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Rotates a given input image by 90 degrees clockwise. For that, X and Y axis of an image stack are flipped. This operation is similar to ImageJs 'Reslice [/]' method but offers less flexibility such as interpolation.

      • rotateRight

        @Deprecated
default boolean rotateRight​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                            net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Deprecated.
        Rotates a given input image by 90 degrees counter-clockwise. For that, X and Y axis of an image stack are flipped. This operation is similar to ImageJs 'Reslice [/]' method but offers less flexibility such as interpolation.

      • mask

        default boolean mask​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                     net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface mask,
                     net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Computes a masked image by applying a binary mask to an image. All pixel values x of image X will be copied to the destination image in case pixel value m at the same position in the mask image is not equal to zero. 
        f(x,m) = (x if (m != 0); (0 otherwise))

      • maskStackWithPlane

        default boolean maskStackWithPlane​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                                   net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface mask,
                                   net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Computes a masked image by applying a binary 2D mask to an image stack. All pixel values x of image X will be copied to the destination image in case pixel value m at the same spatial position in the mask image is not equal to zero. 
        f(x,m) = (x if (m != 0); (0 otherwise))

      • maximumZProjection

        default boolean maximumZProjection​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                                   net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination_max)
        Determines the maximum intensity projection of an image along Z.

      • meanZProjection

        default boolean meanZProjection​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                                net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Determines the mean average intensity projection of an image along Z.

      • minimumZProjection

        default boolean minimumZProjection​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                                   net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination_min)
        Determines the minimum intensity projection of an image along Z.

      • power

        default boolean power​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                      net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                      double arg3)
        Computes all pixels value x to the power of a given exponent a. 
        f(x, a) = x ^ a

      • divideImages

        default boolean divideImages​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface divident,
                             net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface divisor,
                             net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Divides two images X and Y by each other pixel wise. 
        f(x, y) = x / y

      • maximumImages

        default boolean maximumImages​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source1,
                              net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source2,
                              net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Computes the maximum of a pair of pixel values x, y from two given images X and Y. 
        f(x, y) = max(x, y)

      • maximumImageAndScalar

        default boolean maximumImageAndScalar​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                      net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                      double arg3)
        Computes the maximum of a constant scalar s and each pixel value x in a given image X. 
        f(x, s) = max(x, s)

      • minimumImages

        default boolean minimumImages​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source1,
                              net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source2,
                              net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Computes the minimum of a pair of pixel values x, y from two given images X and Y. 
        f(x, y) = min(x, y)

      • minimumImageAndScalar

        default boolean minimumImageAndScalar​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                      net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                      double arg3)
        Computes the minimum of a constant scalar s and each pixel value x in a given image X. 
        f(x, s) = min(x, s)

      • multiplyImageAndScalar

        default boolean multiplyImageAndScalar​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                       net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                       double arg3)
        Multiplies all pixels value x in a given image X with a constant scalar s. 
        f(x, s) = x * s
        Parameters ---------- source : Image The input image to be multiplied with a constant. destination : Image The output image where results are written into. scalar : float The number with which every pixel will be multiplied with.

      • multiplyStackWithPlane

        default boolean multiplyStackWithPlane​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface sourceStack,
                                       net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface sourcePlane,
                                       net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Multiplies all pairs of pixel values x and y from an image stack X and a 2D image Y. x and y are at the same spatial position within a plane. 
        f(x, y) = x * y

      • countNonZeroPixels2DSphere

        default boolean countNonZeroPixels2DSphere​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                           net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                                           double arg3,
                                           double arg4)
        Counts non-zero pixels in a sphere around every pixel. Put the number in the result image.

      • countNonZeroPixelsLocally

        @Deprecated
default boolean countNonZeroPixelsLocally​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                          net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                                          double arg3,
                                          double arg4)
        Deprecated.

      • countNonZeroPixelsLocallySliceBySlice

        @Deprecated
default boolean countNonZeroPixelsLocallySliceBySlice​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                                      net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                                                      double arg3,
                                                      double arg4)
        Deprecated.

      • countNonZeroPixelsSliceBySliceSphere

        default boolean countNonZeroPixelsSliceBySliceSphere​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                                     net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                                                     double arg3,
                                                     double arg4)
        Counts non-zero pixels in a sphere around every pixel slice by slice in a stack. It puts the resulting number in the destination image stack.

      • countNonZeroVoxels3DSphere

        default boolean countNonZeroVoxels3DSphere​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                           net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                                           double arg3,
                                           double arg4,
                                           double arg5)
        Counts non-zero voxels in a sphere around every voxel. Put the number in the result image.

      • countNonZeroVoxelsLocally

        @Deprecated
default boolean countNonZeroVoxelsLocally​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                          net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                                          double arg3,
                                          double arg4,
                                          double arg5)
        Deprecated.

      • sumZProjection

        default boolean sumZProjection​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                               net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination_sum)
        Determines the sum intensity projection of an image along Z.

      • sumOfAllPixels

        default double sumOfAllPixels​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source)
        Determines the sum of all pixels in a given image. It will be stored in a new row of ImageJs Results table in the column 'Sum'. Parameters ---------- source : Image The image of which all pixels or voxels will be summed.

      • sumPixels

        @Deprecated
default double sumPixels​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source)
        Deprecated.
        Determines the sum of all pixels in a given image. It will be stored in a new row of ImageJs Results table in the column 'Sum'. Parameters ---------- source : Image The image of which all pixels or voxels will be summed.

      • centerOfMass

        default double[] centerOfMass​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source)
        Determines the center of mass of an image or image stack. It writes the result in the results table in the columns MassX, MassY and MassZ.

      • invert

        default boolean invert​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                       net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Computes the negative value of all pixels in a given image. It is recommended to convert images to 32-bit float before applying this operation. 
        f(x) = - x
        For binary images, use binaryNot.

      • downsample

        @Deprecated
default boolean downsample​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                           net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                           double arg3,
                           double arg4)
        Deprecated.
        Scales an image using given scaling factors for X and Y dimensions. The nearest-neighbor method is applied. In ImageJ the method which is similar is called 'Interpolation method: none'.

      • downsample2D

        @Deprecated
default boolean downsample2D​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                             net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                             double arg3,
                             double arg4)
        Deprecated.
        Scales an image using given scaling factors for X and Y dimensions. The nearest-neighbor method is applied. In ImageJ the method which is similar is called 'Interpolation method: none'.

      • downsample

        @Deprecated
default boolean downsample​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                           net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                           double arg3,
                           double arg4,
                           double arg5)
        Deprecated.
        Scales an image using given scaling factors for X and Y dimensions. The nearest-neighbor method is applied. In ImageJ the method which is similar is called 'Interpolation method: none'.

      • downsample3D

        @Deprecated
default boolean downsample3D​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                             net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                             double arg3,
                             double arg4,
                             double arg5)
        Deprecated.
        Scales an image using given scaling factors for X and Y dimensions. The nearest-neighbor method is applied. In ImageJ the method which is similar is called 'Interpolation method: none'.

      • downsampleSliceBySliceHalfMedian

        default boolean downsampleSliceBySliceHalfMedian​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                                                 net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Scales an image using scaling factors 0.5 for X and Y dimensions. The Z dimension stays untouched. Thus, each slice is processed separately. The median method is applied. Thus, each pixel value in the destination image equals to the median of four corresponding pixels in the source image.

      • localThreshold

        default boolean localThreshold​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                               net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface localThreshold,
                               net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Computes a binary image with pixel values 0 and 1 depending on if a pixel value x in image X was above of equal to the pixel value m in mask image M. 
        f(x) = (1 if (x >=  m)); (0 otherwise)

      • gradientX

        default boolean gradientX​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source,
                          net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
        Computes the gradient of gray values along X. Assuming a, b and c are three adjacent pixels in X direction. In the target image will be saved as: 
        b' = c - a;

      • gradientY

        default boolean gradientY​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source,
                          net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
        Computes the gradient of gray values along Y. Assuming a, b and c are three adjacent pixels in Y direction. In the target image will be saved as: 
        b' = c - a;

      • gradientZ

        default boolean gradientZ​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source,
                          net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
        Computes the gradient of gray values along Z. Assuming a, b and c are three adjacent pixels in Z direction. In the target image will be saved as: 
        b' = c - a;

      • multiplyImageAndCoordinate

        default boolean multiplyImageAndCoordinate​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                           net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                           double arg3)
        Multiplies all pixel intensities with the x, y or z coordinate, depending on specified dimension.

      • mean2DBox

        default boolean mean2DBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                          net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                          double arg3,
                          double arg4)
        Computes the local mean average of a pixels rectangular neighborhood. The rectangles size is specified by its half-width and half-height (radius).

      • mean2DSphere

        default boolean mean2DSphere​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                             net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                             double arg3,
                             double arg4)
        Computes the local mean average of a pixels ellipsoidal neighborhood. The ellipses size is specified by its half-width and half-height (radius).

      • mean3DBox

        default boolean mean3DBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                          net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                          double arg3,
                          double arg4,
                          double arg5)
        Computes the local mean average of a pixels cube neighborhood. The cubes size is specified by its half-width, half-height and half-depth (radius).

      • meanBox

        default boolean meanBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                        net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                        double arg3,
                        double arg4,
                        double arg5)
        Computes the local mean average of a pixels rectangular neighborhood. The rectangles size is specified by its half-width and half-height (radius).

      • mean3DSphere

        default boolean mean3DSphere​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                             net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                             double arg3,
                             double arg4,
                             double arg5)
        Computes the local mean average of a pixels spherical neighborhood. The spheres size is specified by its half-width, half-height and half-depth (radius).

      • meanSliceBySliceSphere

        default boolean meanSliceBySliceSphere​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                       net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                       double arg3,
                                       double arg4)
        Computes the local mean average of a pixels ellipsoidal 2D neighborhood in an image stack slice by slice. The ellipses size is specified by its half-width and half-height (radius). This filter is applied slice by slice in 2D.

      • meanOfAllPixels

        default double meanOfAllPixels​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source)
        Determines the mean average of all pixels in a given image. It will be stored in a new row of ImageJs Results table in the column 'Mean'.Parameters ---------- source : Image The image of which the mean average of all pixels or voxels will be determined.

      • median2DBox

        default boolean median2DBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                            net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                            double arg3,
                            double arg4)
        Computes the local median of a pixels rectangular neighborhood. The rectangle is specified by its half-width and half-height (radius). For technical reasons, the area of the rectangle must have less than 1000 pixels.

      • median2DSphere

        default boolean median2DSphere​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                               net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                               double arg3,
                               double arg4)
        Computes the local median of a pixels ellipsoidal neighborhood. The ellipses size is specified by its half-width and half-height (radius). For technical reasons, the area of the ellipse must have less than 1000 pixels.

      • median3DBox

        default boolean median3DBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                            net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                            double arg3,
                            double arg4,
                            double arg5)
        Computes the local median of a pixels cuboid neighborhood. The cuboid size is specified by its half-width, half-height and half-depth (radius). For technical reasons, the volume of the cuboid must contain less than 1000 voxels.

      • median3DSphere

        default boolean median3DSphere​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                               net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                               double arg3,
                               double arg4,
                               double arg5)
        Computes the local median of a pixels spherical neighborhood. The spheres size is specified by its half-width, half-height and half-depth (radius). For technical reasons, the volume of the sphere must contain less than 1000 voxels.

      • median3DSliceBySliceBox

        default boolean median3DSliceBySliceBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                        net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                        double arg3,
                                        double arg4)
        Computes the local median of a pixels rectangular neighborhood. This is done slice-by-slice in a 3D image stack. The rectangle is specified by its half-width and half-height (radius). For technical reasons, the area of the rectangle must have less than 1000 pixels.

      • median3DSliceBySliceSphere

        default boolean median3DSliceBySliceSphere​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                           net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                           double arg3,
                                           double arg4)
        Computes the local median of a pixels ellipsoidal neighborhood. This is done slice-by-slice in a 3D image stack. The ellipses size is specified by its half-width and half-height (radius). For technical reasons, the area of the ellipse must have less than 1000 pixels.

      • maximum2DSphere

        default boolean maximum2DSphere​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                double arg3,
                                double arg4)
        Computes the local maximum of a pixels ellipsoidal neighborhood. The ellipses size is specified by its half-width and half-height (radius).

      • maximum3DSphere

        default boolean maximum3DSphere​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                double arg3,
                                double arg4,
                                double arg5)
        Computes the local maximum of a pixels spherical neighborhood. The spheres size is specified by its half-width, half-height and half-depth (radius).

      • maximum2DBox

        default boolean maximum2DBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                             net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                             double arg3,
                             double arg4)
        Computes the local maximum of a pixels rectangular neighborhood. The rectangles size is specified by its half-width and half-height (radius).

      • maximumBox

        default boolean maximumBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                           net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                           double arg3,
                           double arg4)
        Computes the local maximum of a pixels rectangular neighborhood. The rectangles size is specified by its half-width and half-height (radius).

      • maximum3DBox

        default boolean maximum3DBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                             net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                             double arg3,
                             double arg4,
                             double arg5)
        Computes the local maximum of a pixels cube neighborhood. The cubes size is specified by its half-width, half-height and half-depth (radius).

      • maximumBox

        default boolean maximumBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                           net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                           double arg3,
                           double arg4,
                           double arg5)
        Computes the local maximum of a pixels rectangular neighborhood. The rectangles size is specified by its half-width and half-height (radius).

      • maximum3DSliceBySliceSphere

        default boolean maximum3DSliceBySliceSphere​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                            net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                            double arg3,
                                            double arg4)
        Computes the local maximum of a pixels ellipsoidal 2D neighborhood in an image stack slice by slice. The ellipses size is specified by its half-width and half-height (radius). This filter is applied slice by slice in 2D.

      • minimum2DSphere

        default boolean minimum2DSphere​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                double arg3,
                                double arg4)
        Computes the local minimum of a pixels ellipsoidal neighborhood. The ellipses size is specified by its half-width and half-height (radius).

      • minimum3DSphere

        default boolean minimum3DSphere​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                double arg3,
                                double arg4,
                                double arg5)
        Computes the local minimum of a pixels spherical neighborhood. The spheres size is specified by its half-width, half-height and half-depth (radius).

      • minimum2DBox

        default boolean minimum2DBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                             net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                             double arg3,
                             double arg4)
        Computes the local minimum of a pixels rectangular neighborhood. The rectangles size is specified by its half-width and half-height (radius).

      • minimumBox

        default boolean minimumBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                           net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                           double arg3,
                           double arg4)
        Computes the local minimum of a pixels rectangular neighborhood. The rectangles size is specified by its half-width and half-height (radius).

      • minimum3DBox

        default boolean minimum3DBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                             net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                             double arg3,
                             double arg4,
                             double arg5)
        Computes the local minimum of a pixels cube neighborhood. The cubes size is specified by its half-width, half-height and half-depth (radius).

      • minimumBox

        default boolean minimumBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                           net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                           double arg3,
                           double arg4,
                           double arg5)
        Computes the local minimum of a pixels rectangular neighborhood. The rectangles size is specified by its half-width and half-height (radius).

      • minimum3DSliceBySliceSphere

        default boolean minimum3DSliceBySliceSphere​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                            net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                            double arg3,
                                            double arg4)
        Computes the local minimum of a pixels ellipsoidal 2D neighborhood in an image stack slice by slice. The ellipses size is specified by its half-width and half-height (radius). This filter is applied slice by slice in 2D.

      • multiplyImages

        default boolean multiplyImages​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface factor1,
                               net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface factor2,
                               net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Multiplies all pairs of pixel values x and y from two images X and Y. 
        f(x, y) = x * y
        Parameters ---------- factor1 : Image The first input image to be multiplied. factor2 : Image The second image to be multiplied. destination : Image The output image where results are written into.

      • blur

        @Deprecated
default boolean blur​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                     net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                     double arg3,
                     double arg4)
        Deprecated.
        Computes the Gaussian blurred image of an image given two sigma values in X and Y. Thus, the filterkernel can have non-isotropic shape. The implementation is done separable. In case a sigma equals zero, the direction is not blurred. DEPRECATED: This method is deprecated. Use gaussianBlur2D instead.

      • blur2D

        @Deprecated
default boolean blur2D​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                       net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                       double arg3,
                       double arg4)
        Deprecated.
        Computes the Gaussian blurred image of an image given two sigma values in X and Y. Thus, the filterkernel can have non-isotropic shape. The implementation is done separable. In case a sigma equals zero, the direction is not blurred. DEPRECATED: This method is deprecated. Use gaussianBlur2D instead.

      • gaussianBlur

        default boolean gaussianBlur​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                             net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                             double arg3,
                             double arg4)
        Computes the Gaussian blurred image of an image given two sigma values in X and Y. Thus, the filterkernel can have non-isotropic shape. The implementation is done separable. In case a sigma equals zero, the direction is not blurred.

      • gaussianBlur2D

        default boolean gaussianBlur2D​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                               net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                               double arg3,
                               double arg4)
        Computes the Gaussian blurred image of an image given two sigma values in X and Y. Thus, the filterkernel can have non-isotropic shape. The implementation is done separable. In case a sigma equals zero, the direction is not blurred.

      • blur

        @Deprecated
default boolean blur​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                     net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                     double arg3,
                     double arg4,
                     double arg5)
        Deprecated.
        Computes the Gaussian blurred image of an image given two sigma values in X and Y. Thus, the filterkernel can have non-isotropic shape. The implementation is done separable. In case a sigma equals zero, the direction is not blurred. DEPRECATED: This method is deprecated. Use gaussianBlur2D instead.

      • blur3D

        @Deprecated
default boolean blur3D​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                       net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                       double arg3,
                       double arg4,
                       double arg5)
        Deprecated.
        Computes the Gaussian blurred image of an image given two sigma values in X, Y and Z. Thus, the filterkernel can have non-isotropic shape. The implementation is done separable. In case a sigma equals zero, the direction is not blurred. DEPRECATED: This method is deprecated. Use gaussianBlur3D instead.

      • gaussianBlur

        default boolean gaussianBlur​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                             net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                             double arg3,
                             double arg4,
                             double arg5)
        Computes the Gaussian blurred image of an image given two sigma values in X and Y. Thus, the filterkernel can have non-isotropic shape. The implementation is done separable. In case a sigma equals zero, the direction is not blurred.

      • gaussianBlur3D

        default boolean gaussianBlur3D​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                               net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                               double arg3,
                               double arg4,
                               double arg5)
        Computes the Gaussian blurred image of an image given two sigma values in X, Y and Z. Thus, the filterkernel can have non-isotropic shape. The implementation is done separable. In case a sigma equals zero, the direction is not blurred.

      • resliceBottom

        default boolean resliceBottom​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                              net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Flippes Y and Z axis of an image stack. This operation is similar to ImageJs 'Reslice [/]' method but offers less flexibility such as interpolation.

      • resliceTop

        default boolean resliceTop​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                           net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        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

        default boolean resliceLeft​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                            net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        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.

      • resliceRight

        default boolean resliceRight​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                             net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        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.

      • rotate2D

        default boolean rotate2D​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                         net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                         double arg3,
                         boolean arg4)
        Rotates an image in plane. All angles are entered in degrees. If the image is not rotated around the center, it is rotated around the coordinate origin. It is recommended to apply the rotation to an isotropic image.

      • rotate3D

        default boolean rotate3D​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                         net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                         double arg3,
                         double arg4,
                         double arg5,
                         boolean arg6)
        Rotates an image stack in 3D. All angles are entered in degrees. If the image is not rotated around the center, it is rotated around the coordinate origin. It is recommended to apply the rotation to an isotropic image stack.

      • scale

        default boolean scale​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                      net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                      double arg3)
        Scales an image with a given factor.

      • scale

        default boolean scale​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                      net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                      double arg3,
                      double arg4)
        Scales an image with a given factor.

      • scale2D

        default boolean scale2D​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                        net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                        double arg3,
                        double arg4)
        Scales an image with a given factor.

      • scale2D

        default boolean scale2D​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                        net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                        double arg3,
                        double arg4,
                        boolean arg5)
        Scales an image with a given factor.

      • scale3D

        default boolean scale3D​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                        net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                        double arg3,
                        double arg4,
                        double arg5)
        Scales an image with a given factor.

      • scale3D

        default boolean scale3D​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                        net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                        double arg3,
                        double arg4,
                        double arg5,
                        boolean arg6)
        Scales an image with a given factor.

      • translate2D

        default boolean translate2D​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                            net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                            double arg3,
                            double arg4)
        Translate an image stack in X and Y.

      • translate3D

        default boolean translate3D​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                            net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                            double arg3,
                            double arg4,
                            double arg5)
        Translate an image stack in X, Y and Z.

      • addImageAndScalar

        default boolean addImageAndScalar​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                  net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                  double arg3)
        Adds a scalar value s to all pixels x of a given image X. 
        f(x, s) = x + s
        Parameters ---------- source : Image The input image where scalare should be added. destination : Image The output image where results are written into. scalar : float The constant number which will be added to all pixels.

      • detectMinimaBox

        @Deprecated
default boolean detectMinimaBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                double arg3)
        Deprecated.
        Detects local minima in a given square/cubic neighborhood. Pixels in the resulting image are set to 1 if there is no other pixel in a given radius which has a lower intensity, and to 0 otherwise.

      • detectMinimaBox

        default boolean detectMinimaBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                double arg3,
                                double arg4,
                                double arg5)
        Detects local minima in a given square/cubic neighborhood. Pixels in the resulting image are set to 1 if there is no other pixel in a given radius which has a lower intensity, and to 0 otherwise.

      • detectMaximaBox

        @Deprecated
default boolean detectMaximaBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                double arg3)
        Deprecated.
        Detects local maxima in a given square/cubic neighborhood. Pixels in the resulting image are set to 1 if there is no other pixel in a given radius which has a higher intensity, and to 0 otherwise.

      • detectMaximaBox

        default boolean detectMaximaBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                double arg3,
                                double arg4,
                                double arg5)
        Detects local maxima in a given square/cubic neighborhood. Pixels in the resulting image are set to 1 if there is no other pixel in a given radius which has a higher intensity, and to 0 otherwise.

      • detectMaximaSliceBySliceBox

        default boolean detectMaximaSliceBySliceBox​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                            net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                                            double arg3,
                                            double arg4)
        Detects local maxima in a given square neighborhood of an input image stack. The input image stack is processed slice by slice. Pixels in the resulting image are set to 1 if there is no other pixel in a given radius which has a higher intensity, and to 0 otherwise.

      • detectMinimaSliceBySliceBox

        default boolean detectMinimaSliceBySliceBox​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                            net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                                            double arg3,
                                            double arg4)
        Detects local minima in a given square neighborhood of an input image stack. The input image stack is processed slice by slice. Pixels in the resulting image are set to 1 if there is no other pixel in a given radius which has a lower intensity, and to 0 otherwise.

      • maximumOfAllPixels

        default double maximumOfAllPixels​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source)
        Determines the maximum of all pixels in a given image. It will be stored in a new row of ImageJs Results table in the column 'Max'. Parameters ---------- source : Image The image of which the maximum of all pixels or voxels will be determined.

      • minimumOfAllPixels

        default double minimumOfAllPixels​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source)
        Determines the minimum of all pixels in a given image. It will be stored in a new row of ImageJs Results table in the column 'Min'. Parameters ---------- source : Image The image of which the minimum of all pixels or voxels will be determined.

      • setColumn

        default boolean setColumn​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                          double arg2,
                          double arg3)
        Sets all pixel values x of a given column in X to a constant value v.

      • setRow

        default boolean setRow​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                       double arg2,
                       double arg3)
        Sets all pixel values x of a given row in X to a constant value v.

      • sumYProjection

        default boolean sumYProjection​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                               net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Determines the sum intensity projection of an image along Z.

      • averageDistanceOfTouchingNeighbors

        default boolean averageDistanceOfTouchingNeighbors​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer distance_matrix,
                                                   net.haesleinhuepf.clij.clearcl.ClearCLBuffer touch_matrix,
                                                   net.haesleinhuepf.clij.clearcl.ClearCLBuffer average_distancelist_destination)
        Takes a touch matrix and a distance matrix to determine the average distance of touching neighbors for every object. Parameters ---------- distance_matrix : Image The a distance matrix to be processed. touch_matrix : Image The binary touch matrix describing which distances should be taken into account. distance_list_destination : Image A vector image with the same width as the distance matrix and height=1, depth=1. Determined average distances will be written into this vector.

      • labelledSpotsToPointList

        default boolean labelledSpotsToPointList​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input_labelled_spots,
                                         net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination_pointlist)
        Generates a coordinate list of points in a labelled spot image. Transforms a labelmap of spots (single pixels with values 1, 2, ..., n for n spots) as resulting from connected components analysis in an image where every column contains d pixels (with d = dimensionality of the original image) with the coordinates of the maxima/minima.

      • labelSpots

        default boolean labelSpots​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input_spots,
                           net.haesleinhuepf.clij.clearcl.ClearCLBuffer labelled_spots_destination)
        Transforms a binary image with single pixles set to 1 to a labelled spots image. Transforms a spots image as resulting from maximum/minimum detection in an image of the same size where every spot has a number 1, 2, ... n.

      • minimumDistanceOfTouchingNeighbors

        default boolean minimumDistanceOfTouchingNeighbors​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer distance_matrix,
                                                   net.haesleinhuepf.clij.clearcl.ClearCLBuffer touch_matrix,
                                                   net.haesleinhuepf.clij.clearcl.ClearCLBuffer minimum_distancelist_destination)
        Takes a touch matrix and a distance matrix to determine the shortest distance of touching neighbors for every object.

      • setWhereXgreaterThanY

        default boolean setWhereXgreaterThanY​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                      double arg2)
        Sets all pixel values a of a given image A to a constant value v in case its coordinates x > y. Otherwise the pixel is not overwritten. If you want to initialize an identity transfrom matrix, set all pixels to 0 first.

      • setWhereXsmallerThanY

        default boolean setWhereXsmallerThanY​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                      double arg2)
        Sets all pixel values a of a given image A to a constant value v in case its coordinates x < y. Otherwise the pixel is not overwritten. If you want to initialize an identity transfrom matrix, set all pixels to 0 first.

      • setNonZeroPixelsToPixelIndex

        default boolean setNonZeroPixelsToPixelIndex​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                                             net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Sets all pixels in an image which are not zero to the index of the pixel. This can be used for Connected Components Analysis.

      • closeIndexGapsInLabelMap

        default boolean closeIndexGapsInLabelMap​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer labeling_input,
                                         net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface labeling_destination)
        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. Thus, afterwards number of labels and maximum label index are equal. This operation is mostly performed on the CPU.

      • shiftIntensitiesToCloseGaps

        @Deprecated
default boolean shiftIntensitiesToCloseGaps​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                            net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2)
        Deprecated.

      • scale

        @Deprecated
default boolean scale​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                      net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                      double arg3,
                      double arg4,
                      double arg5)
        Deprecated.
        Scales an image with a given factor.

      • centroidsOfLabels

        default boolean centroidsOfLabels​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source,
                                  net.haesleinhuepf.clij.clearcl.ClearCLBuffer pointlist_destination)
        Determines the centroids of all labels in a label image or image stack. It writes the resulting coordinates in a pointlist image. Depending on the dimensionality d of the labelmap and the number of labels n, the pointlist image will have n*d pixels.

      • setRampX

        default boolean setRampX​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source)
        Sets all pixel values to their X coordinate

      • setRampY

        default boolean setRampY​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source)
        Sets all pixel values to their Y coordinate

      • setRampZ

        default boolean setRampZ​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source)
        Sets all pixel values to their Z coordinate

      • subtractImageFromScalar

        default boolean subtractImageFromScalar​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                        net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                        double arg3)
        Subtracts one image X from a scalar s pixel wise. 
        f(x, s) = s - x

      • thresholdDefault

        default boolean thresholdDefault​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input,
                                 net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
        The automatic thresholder utilizes the Default 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.

      • thresholdOtsu

        default boolean thresholdOtsu​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input,
                              net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
        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.

      • thresholdHuang

        default boolean thresholdHuang​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input,
                               net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
        The automatic thresholder utilizes the Huang 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.

      • thresholdIntermodes

        default boolean thresholdIntermodes​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input,
                                    net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
        The automatic thresholder utilizes the Intermodes 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.

      • thresholdIsoData

        default boolean thresholdIsoData​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input,
                                 net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
        The automatic thresholder utilizes the IsoData 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.

      • thresholdIJ_IsoData

        default boolean thresholdIJ_IsoData​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input,
                                    net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
        The automatic thresholder utilizes the IJ_IsoData 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.

      • thresholdLi

        default boolean thresholdLi​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input,
                            net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
        The automatic thresholder utilizes the Li 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.

      • thresholdMaxEntropy

        default boolean thresholdMaxEntropy​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input,
                                    net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
        The automatic thresholder utilizes the MaxEntropy 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.

      • thresholdMean

        default boolean thresholdMean​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input,
                              net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
        The automatic thresholder utilizes the Mean 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.

      • thresholdMinError

        default boolean thresholdMinError​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input,
                                  net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
        The automatic thresholder utilizes the MinError 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.

      • thresholdMinimum

        default boolean thresholdMinimum​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input,
                                 net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
        The automatic thresholder utilizes the Minimum 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.

      • thresholdMoments

        default boolean thresholdMoments​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input,
                                 net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
        The automatic thresholder utilizes the Moments 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.

      • thresholdPercentile

        default boolean thresholdPercentile​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input,
                                    net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
        The automatic thresholder utilizes the Percentile 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.

      • thresholdRenyiEntropy

        default boolean thresholdRenyiEntropy​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input,
                                      net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
        The automatic thresholder utilizes the RenyiEntropy 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.

      • thresholdShanbhag

        default boolean thresholdShanbhag​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input,
                                  net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
        The automatic thresholder utilizes the Shanbhag 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.

      • thresholdTriangle

        default boolean thresholdTriangle​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input,
                                  net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
        The automatic thresholder utilizes the Triangle 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.

      • thresholdYen

        default boolean thresholdYen​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input,
                             net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
        The automatic thresholder utilizes the Yen 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.

      • excludeLabelsSubSurface

        default boolean excludeLabelsSubSurface​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                        net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                                        net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg3,
                                        double arg4,
                                        double arg5,
                                        double arg6)
        This operation follows a ray from a given position towards a label (or opposite direction) and checks if there is another label between the label an the image border. If yes, this label is eliminated from the label map.

      • excludeLabelsOnSurface

        default boolean excludeLabelsOnSurface​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                       net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                                       net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg3,
                                       double arg4,
                                       double arg5,
                                       double arg6)
        This operation follows a ray from a given position towards a label (or opposite direction) and checks if there is another label between the label an the image border. If yes, this label is eliminated from the label map.

      • setPlane

        default boolean setPlane​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                         double arg2,
                         double arg3)
        Sets all pixel values x of a given plane in X to a constant value v.

      • imageToStack

        default boolean imageToStack​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                             net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                             double arg3)
        Copies a single slice into a stack a given number of times.

      • sumXProjection

        default boolean sumXProjection​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                               net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Determines the sum intensity projection of an image along Z.

      • sumImageSliceBySlice

        default boolean sumImageSliceBySlice​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                                     net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Sums all pixels slice by slice and returns the sums in a vector.

      • sumImageSliceBySlice

        default double[] sumImageSliceBySlice​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1)
        Sums all pixels slice by slice and returns the sums in a vector.

      • sumPixelsSliceByslice

        @Deprecated
default double[] sumPixelsSliceByslice​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1)
        Deprecated.

      • multiplyImageStackWithScalars

        default boolean multiplyImageStackWithScalars​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                              net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                              float[] arg3)
        Multiplies all pixels value x in a given image X with a constant scalar s from a list of scalars. 
        f(x, s) = x * s

      • multiplyImageStackWithScalars

        default boolean multiplyImageStackWithScalars​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                              net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                              net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg3)
        Multiplies all pixels value x in a given image X with a constant scalar s from a list of scalars. 
        f(x, s) = x * s

      • multiplySliceBySliceWithScalars

        @Deprecated
default boolean multiplySliceBySliceWithScalars​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                                net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                                float[] arg3)
        Deprecated.

      • print

        default boolean print​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface input)
        Visualises an image on standard out (console).

      • voronoiOctagon

        default boolean voronoiOctagon​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input,
                               net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
        Takes a binary image and dilates the regions using a octagon shape until they touch. The pixels where the regions touched are afterwards returned as binary image which corresponds to the Voronoi diagram.

      • setImageBorders

        default boolean setImageBorders​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                double arg2)
        Sets all pixel values at the image border to a given value.

      • floodFillDiamond

        default boolean floodFillDiamond​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                 net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                                 double arg3,
                                 double arg4)
        Replaces recursively all pixels of value a with value b if the pixels have a neighbor with value b.

      • binaryFillHoles

        default boolean binaryFillHoles​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                                net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Fills holes (pixels with value 0 surrounded by pixels with value 1) in a binary image. Note: This function is known to perform slowly on large images. Consider using the extension CLIJx_morphoLibJFillHoles(input, destination) instead. Read more: http://clij.github.io/assistant/installation#extensions Parameters ---------- source : Image The binary input image where holes will be filled. destination : Image The output image where true pixels will be 1.

      • connectedComponentsLabelingDiamond

        default boolean connectedComponentsLabelingDiamond​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface binary_input,
                                                   net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface labeling_destination)
        Performs connected components analysis inspecting the diamond neighborhood of every pixel to a binary image and generates a label map.

      • connectedComponentsLabelingDiamond

        default boolean connectedComponentsLabelingDiamond​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                                   net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                                   boolean arg3)
        Performs connected components analysis inspecting the diamond neighborhood of every pixel to a binary image and generates a label map.

      • connectedComponentsLabelingBox

        default boolean connectedComponentsLabelingBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface binary_input,
                                               net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface labeling_destination)
        Performs connected components analysis inspecting the box neighborhood of every pixel to a binary image and generates a label map.

      • connectedComponentsLabelingBox

        default boolean connectedComponentsLabelingBox​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                               net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                               boolean arg3)
        Performs connected components analysis inspecting the box neighborhood of every pixel to a binary image and generates a label map.

      • setRandom

        default boolean setRandom​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                          double arg2,
                          double arg3)
        Fills an image or image stack with uniformly distributed random numbers between given minimum and maximum values. Recommendation: For the seed, use getTime().

      • setRandom

        default boolean setRandom​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                          double arg2,
                          double arg3,
                          double arg4)
        Fills an image or image stack with uniformly distributed random numbers between given minimum and maximum values. Recommendation: For the seed, use getTime().

      • entropyBox

        default boolean entropyBox​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                           net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                           double arg3,
                           double arg4,
                           double arg5)
        Determines the local entropy in a box with a given radius around every pixel.

      • entropyBox

        default boolean entropyBox​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                           net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                           double arg3,
                           double arg4,
                           double arg5,
                           double arg6,
                           double arg7)
        Determines the local entropy in a box with a given radius around every pixel.

      • concatenateStacks

        default boolean concatenateStacks​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface stack1,
                                  net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface stack2,
                                  net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Concatenates two stacks in Z.

      • resultsTableToImage2D

        @Deprecated
default boolean resultsTableToImage2D​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                      ResultsTable arg2)
        Deprecated.
        Converts a table to an image. Rows stay rows, columns stay columns.

      • getAutomaticThreshold

        default double getAutomaticThreshold​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                     String arg2)
        Determines a threshold according to a given method and saves it to the threshold_value variable. The automatic thresholder utilizes the threshold methods from ImageJ on a histogram determined on the GPU to determine a threshold value as similar as possible to ImageJ 'Apply Threshold' method. Enter one of these methods in the method text field: [Default, Huang, Intermodes, IsoData, IJ_IsoData, Li, MaxEntropy, Mean, MinError, Minimum, Moments, Otsu, Percentile, RenyiEntropy, Shanbhag, Triangle, Yen]

      • getAutomaticThreshold

        default double getAutomaticThreshold​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                     String arg2,
                                     double arg3,
                                     double arg4,
                                     double arg5)
        Determines a threshold according to a given method and saves it to the threshold_value variable. The automatic thresholder utilizes the threshold methods from ImageJ on a histogram determined on the GPU to determine a threshold value as similar as possible to ImageJ 'Apply Threshold' method. Enter one of these methods in the method text field: [Default, Huang, Intermodes, IsoData, IJ_IsoData, Li, MaxEntropy, Mean, MinError, Minimum, Moments, Otsu, Percentile, RenyiEntropy, Shanbhag, Triangle, Yen]

      • getDimensions

        default long[] getDimensions​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1)
        Reads out the size of an image [stack] and writes it to the variables 'width', 'height' and 'depth'.

      • customOperation

        default boolean customOperation​(String arg1,
                                String arg2,
                                HashMap arg3)
        Executes a custom operation wirtten in OpenCL on a custom list of images. All images must be created before calling this method. Image parameters should be handed over as an array with parameter names and image names alternating, e.g. Ext.CLIJ2_customOperation(..., ..., newArray("image1", "blobs.gif", "image2", "Processed_blobs.gif")) In the custom code, you can use the predefined variables x, y and z to deal with coordinates. You can for example use it to access pixel intensities like this: float value = READ_IMAGE(image, sampler, POS_image_INSTANCE(x, y, z, 0)).x; WRITE_IMAGE(image, POS_image_INSTANCE(x, y, z, 0), CONVERT_image_PIXEL_TYPE(value)); Note: replace `image` with the given image parameter name. You can furthermore use custom function to organise code in the global_code parameter. In OpenCL they may look like this: inline float sum(float a, float b) { return a + b; }

      • pullLabelsToROIList

        default boolean pullLabelsToROIList​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                    List arg2)
        Pulls all labels in a label map as ROIs to a list. From ImageJ macro this list is written to the log window. From ImageJ macro conside using pullLabelsToROIManager.

      • pullLabelsToROIList

        default ArrayList pullLabelsToROIList​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer labelmap_input)
        Pulls all labels in a label map as ROIs to a list. From ImageJ macro this list is written to the log window. From ImageJ macro conside using pullLabelsToROIManager.

      • meanOfTouchingNeighbors

        default boolean meanOfTouchingNeighbors​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer values,
                                        net.haesleinhuepf.clij.clearcl.ClearCLBuffer touch_matrix,
                                        net.haesleinhuepf.clij.clearcl.ClearCLBuffer mean_values_destination)
        Takes a touch matrix and a vector of values to determine the mean value among touching neighbors for every object. Parameters ---------- values : Image A vector of values corresponding to the labels of which the mean average should be determined. touch_matrix : Image A touch_matrix specifying which labels are taken into account for neighborhood relationships. mean_values_destination : Image A the resulting vector of mean average values in the neighborhood.

      • minimumOfTouchingNeighbors

        default boolean minimumOfTouchingNeighbors​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer values,
                                           net.haesleinhuepf.clij.clearcl.ClearCLBuffer touch_matrix,
                                           net.haesleinhuepf.clij.clearcl.ClearCLBuffer minimum_values_destination)
        Takes a touch matrix and a vector of values to determine the minimum value among touching neighbors for every object. Parameters ---------- values : Image A vector of values corresponding to the labels of which the minimum should be determined. touch_matrix : Image A touch_matrix specifying which labels are taken into account for neighborhood relationships. minimum_values_destination : Image A the resulting vector of minimum values in the neighborhood.

      • maximumOfTouchingNeighbors

        default boolean maximumOfTouchingNeighbors​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer values,
                                           net.haesleinhuepf.clij.clearcl.ClearCLBuffer touch_matrix,
                                           net.haesleinhuepf.clij.clearcl.ClearCLBuffer maximum_values_destination)
        Takes a touch matrix and a vector of values to determine the maximum value among touching neighbors for every object. Parameters ---------- values : Image A vector of values corresponding to the labels of which the maximum should be determined. touch_matrix : Image A touch_matrix specifying which labels are taken into account for neighborhood relationships. maximum_values_destination : Image A the resulting vector of maximum values in the neighborhood.

      • resultsTableColumnToImage

        default boolean resultsTableColumnToImage​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                          ResultsTable arg2,
                                          String arg3)
        Converts a table column to an image. The values are stored in x dimension.

      • statisticsOfBackgroundAndLabelledPixels

        default double[][] statisticsOfBackgroundAndLabelledPixels​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input,
                                                           net.haesleinhuepf.clij.clearcl.ClearCLBuffer labelmap)
        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. Instead of a label map, you can also use a binary image as a binary image is a label map with just one label. This method is executed on the CPU and not on the GPU/OpenCL device.

      • statisticsOfBackgroundAndLabelledPixels

        default ResultsTable statisticsOfBackgroundAndLabelledPixels​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                                             net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                                                             ResultsTable arg3)
        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. Instead of a label map, you can also use a binary image as a binary image is a label map with just one label. This method is executed on the CPU and not on the GPU/OpenCL device.

      • getSumOfAllPixels

        default double getSumOfAllPixels​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1)
        Determines the sum of all pixels in a given image. It will be stored in the variable sum_of_all_pixels.

      • getSorensenDiceCoefficient

        default double getSorensenDiceCoefficient​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                          net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2)
        Determines the overlap of two binary images using the Sorensen-Dice coefficent. A value of 0 suggests no overlap, 1 means perfect overlap. The Sorensen-Dice coefficient is saved in the colum 'Sorensen_Dice_coefficient'. Note that the Sorensen-Dice coefficient s can be calculated from the Jaccard index j using this formula: 
        s = f(j) = 2 j / (j + 1)

      • getMinimumOfAllPixels

        default double getMinimumOfAllPixels​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1)
        Determines the minimum of all pixels in a given image. It will be stored in the variable minimum_of_all_pixels.

      • getMaximumOfAllPixels

        default double getMaximumOfAllPixels​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1)
        Determines the maximum of all pixels in a given image. It will be stored in the variable maximum_of_all_pixels.

      • getMeanOfAllPixels

        default double getMeanOfAllPixels​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1)
        Determines the mean of all pixels in a given image. It will be stored in the variable mean_of_all_pixels.

      • getJaccardIndex

        default double getJaccardIndex​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                               net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2)
        Determines the overlap of two binary images using the Jaccard index. A value of 0 suggests no overlap, 1 means perfect overlap. The resulting Jaccard index is saved to the results table in the 'Jaccard_Index' column. Note that the Sorensen-Dice coefficient can be calculated from the Jaccard index j using this formula: 
        s = f(j) = 2 j / (j + 1)

      • getCenterOfMass

        default double[] getCenterOfMass​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1)
        Determines the center of mass of an image or image stack. It writes the result in the variables centerOfMassX, centerOfMassY and centerOfMassZ.

      • getBoundingBox

        default double[] getBoundingBox​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1)
        Determines the bounding box of all non-zero pixels in a binary image. If called from macro, the positions will be stored in the variables 'boundingBoxX', 'boundingBoxY', 'boundingBoxZ', 'boundingBoxWidth', 'boundingBoxHeight' and 'boundingBoxDepth'.In case of 2D images Z and depth will be zero.

      • pushArray

        default boolean pushArray​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                          Object arg2)
        Converts an array to an image.

      • pushArray

        default net.haesleinhuepf.clij.clearcl.ClearCLBuffer pushArray​(float[] arg1,
                                                               double arg2,
                                                               double arg3,
                                                               double arg4)
        Converts an array to an image.

      • pullString

        default String pullString​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1)
        Writes an image into a string.

      • pushString

        default boolean pushString​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                           String arg2)
        Converts an string to an image. The formatting works with double line breaks for slice switches, single line breaks for y swithces and spaces for x. For example this string is converted to an image with width=4, height=3 and depth=2: 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4

      • pushString

        default net.haesleinhuepf.clij.clearcl.ClearCLBuffer pushString​(String arg1)
        Converts an string to an image. The formatting works with double line breaks for slice switches, single line breaks for y swithces and spaces for x. For example this string is converted to an image with width=4, height=3 and depth=2: 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4

      • medianOfTouchingNeighbors

        default boolean medianOfTouchingNeighbors​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer values,
                                          net.haesleinhuepf.clij.clearcl.ClearCLBuffer touch_matrix,
                                          net.haesleinhuepf.clij.clearcl.ClearCLBuffer median_values_destination)
        Takes a touch matrix and a vector of values to determine the median value among touching neighbors for every object.

      • pushResultsTableColumn

        default boolean pushResultsTableColumn​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                       ResultsTable arg2,
                                       String arg3)
        Converts a table column to an image. The values are stored in x dimension.

      • pushResultsTable

        default boolean pushResultsTable​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                 ResultsTable arg2)
        Converts a table to an image. Rows stay rows, columns stay columns.

      • pullToResultsTable

        default ResultsTable pullToResultsTable​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                        ResultsTable arg2)
        Converts an image into a table.

      • pullToResultsTable

        default ResultsTable pullToResultsTable​(net.haesleinhuepf.clij.clearcl.ClearCLImage arg1,
                                        ResultsTable arg2)
        Converts an image into a table.

      • labelVoronoiOctagon

        default boolean labelVoronoiOctagon​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer label_map,
                                    net.haesleinhuepf.clij.clearcl.ClearCLBuffer label_voronoi_destination)
        Takes a labelled image and dilates the labels using a octagon shape until they touch. The pixels where the regions touched are afterwards returned as binary image which corresponds to the Voronoi diagram.

      • touchMatrixToAdjacencyMatrix

        default boolean touchMatrixToAdjacencyMatrix​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer touch_matrix,
                                             net.haesleinhuepf.clij.clearcl.ClearCLBuffer adjacency_matrix)
        Converts a touch matrix in an adjacency matrix

      • adjacencyMatrixToTouchMatrix

        default boolean adjacencyMatrixToTouchMatrix​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer adjacency_matrix,
                                             net.haesleinhuepf.clij.clearcl.ClearCLBuffer touch_matrix)
        Converts a adjacency matrix in a touch matrix. An adjacency matrix is symmetric while a touch matrix is typically not. Parameters ---------- adjacency_matrix : Image The input adjacency matrix to be read from. touch_matrix : Image The output touch matrix to be written into.

      • pointlistToLabelledSpots

        default boolean pointlistToLabelledSpots​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer pointlist,
                                         net.haesleinhuepf.clij.clearcl.ClearCLBuffer spots_destination)
        Takes a pointlist with dimensions n times d with n point coordinates in d dimensions and labels corresponding pixels.

      • statisticsOfImage

        default ResultsTable statisticsOfImage​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                       ResultsTable arg2)
        Determines image size (bounding box), area (in pixels/voxels), min, max and mean intensity of all pixels in the original image. This method is executed on the CPU and not on the GPU/OpenCL device.

      • nClosestDistances

        default boolean nClosestDistances​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                  net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                                  net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg3)
        Determine the n point indices with shortest distance for all points in a distance matrix. This corresponds to the n row indices with minimum values for each column of the distance matrix.Returns the n shortest distances in one image and the point indices in another image.

      • excludeLabels

        default boolean excludeLabels​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer binary_flaglist,
                              net.haesleinhuepf.clij.clearcl.ClearCLBuffer label_map_input,
                              net.haesleinhuepf.clij.clearcl.ClearCLBuffer label_map_destination)
        This operation removes labels from a labelmap and renumbers the remaining labels. Hand over a binary flag list vector starting with a flag for the background, continuing with label1, label2, ... For example if you pass 0,1,0,0,1: Labels 1 and 4 will be removed (those with a 1 in the vector will be excluded). Labels 2 and 3 will be kept and renumbered to 1 and 2.

      • averageDistanceOfNFarOffPoints

        default boolean averageDistanceOfNFarOffPoints​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                               net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                                               double arg3)
        Determines the average of the n far off (most distant) points for every point in a distance matrix. This corresponds to the average of the n maximum values (rows) for each column of the distance matrix. Parameters ---------- distance_matrix : Image The a distance matrix to be processed. distance_list_destination : Image A vector image with the same width as the distance matrix and height=1, depth=1. Determined average distances will be written into this vector. n_far_off_points_to_find : Number Number of largest distances which should be averaged.

      • standardDeviationOfTouchingNeighbors

        default boolean standardDeviationOfTouchingNeighbors​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer values,
                                                     net.haesleinhuepf.clij.clearcl.ClearCLBuffer touch_matrix,
                                                     net.haesleinhuepf.clij.clearcl.ClearCLBuffer standard_deviation_values_destination)
        Takes a touch matrix and a vector of values to determine the standard deviation value among touching neighbors for every object.

      • neighborsOfNeighbors

        default boolean neighborsOfNeighbors​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer touch_matrix,
                                     net.haesleinhuepf.clij.clearcl.ClearCLBuffer neighbor_matrix_destination)
        Determines neighbors of neigbors from touch matrix and saves the result as a new touch matrix.

      • generateParametricImage

        default boolean generateParametricImage​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface label_map,
                                        net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface parameter_value_vector,
                                        net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface parametric_image_destination)
        Take a labelmap and a vector of values to replace label 1 with the 1st value in the vector. Note that indexing in the vector starts at zero. The 0th entry corresponds to background in the label map.Internally this method just calls ReplaceIntensities.

      • generateParametricImageFromResultsTableColumn

        default boolean generateParametricImageFromResultsTableColumn​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                                              net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                                                              ResultsTable arg3,
                                                              String arg4)
        Take a labelmap and a column from the results table to replace label 1 with the 1st value in the vector. Note that indexing in the table column starts at zero. The results table should contain a line at the beginningrepresenting the background.

      • excludeLabelsWithValuesOutOfRange

        default boolean excludeLabelsWithValuesOutOfRange​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                                  net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                                                  net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg3,
                                                  double arg4,
                                                  double arg5)
        This operation removes labels from a labelmap and renumbers the remaining labels. Hand over a vector of values and a range specifying which labels with which values are eliminated.

      • excludeLabelsWithValuesWithinRange

        default boolean excludeLabelsWithValuesWithinRange​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                                   net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                                                   net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg3,
                                                   double arg4,
                                                   double arg5)
        This operation removes labels from a labelmap and renumbers the remaining labels. Hand over a vector of values and a range specifying which labels with which values are eliminated.

      • combineVertically

        default boolean combineVertically​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface stack1,
                                  net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface stack2,
                                  net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Combines two images or stacks in Y.

      • combineHorizontally

        default boolean combineHorizontally​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface stack1,
                                    net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface stack2,
                                    net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Combines two images or stacks in X.

      • reduceStack

        default boolean reduceStack​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                            net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg2,
                            double arg3,
                            double arg4)
        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.

      • detectMinima2DBox

        default boolean detectMinima2DBox​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                  net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                                  double arg3,
                                  double arg4)
        Detects local minima in a given square/cubic neighborhood. Pixels in the resulting image are set to 1 if there is no other pixel in a given radius which has a lower intensity, and to 0 otherwise.

      • detectMaxima2DBox

        default boolean detectMaxima2DBox​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                  net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                                  double arg3,
                                  double arg4)
        Detects local maxima in a given square/cubic neighborhood. Pixels in the resulting image are set to 1 if there is no other pixel in a given radius which has a higher intensity, and to 0 otherwise.

      • detectMinima3DBox

        default boolean detectMinima3DBox​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                  net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                                  double arg3,
                                  double arg4,
                                  double arg5)
        Detects local minima in a given square/cubic neighborhood. Pixels in the resulting image are set to 1 if there is no other pixel in a given radius which has a lower intensity, and to 0 otherwise.

      • detectMaxima3DBox

        default boolean detectMaxima3DBox​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                  net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                                  double arg3,
                                  double arg4,
                                  double arg5)
        Detects local maxima in a given square/cubic neighborhood. Pixels in the resulting image are set to 1 if there is no other pixel in a given radius which has a higher intensity, and to 0 otherwise.

      • depthColorProjection

        default boolean depthColorProjection​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface arg1,
                                     net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2,
                                     net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg3,
                                     double arg4,
                                     double arg5)
        Determines a maximum projection of an image stack and does a color coding of the determined arg Z (position of the found maximum). Second parameter is a Lookup-Table in the form of an 8-bit image stack 255 pixels wide, 1 pixel high with 3 planes representing red, green and blue intensities. Resulting image is a 3D image with three Z-planes representing red, green and blue channels.

      • generateBinaryOverlapMatrix

        default boolean generateBinaryOverlapMatrix​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer label_map1,
                                            net.haesleinhuepf.clij.clearcl.ClearCLBuffer label_map2,
                                            net.haesleinhuepf.clij.clearcl.ClearCLBuffer binary_overlap_matrix_destination)
        Takes two labelmaps with n and m labels and generates a (n+1)*(m+1) matrix where all pixels are set to 0 exept those where labels overlap between the label maps. For example, if labels 3 in labelmap1 and 4 in labelmap2 are touching then the pixel (3,4) in the matrix will be set to 1.

      • convolve

        default boolean convolve​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source,
                         net.haesleinhuepf.clij.clearcl.ClearCLBuffer convolution_kernel,
                         net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
        Convolve the image with a given kernel image. It is recommended that the kernel image has an odd size in X, Y and Z.

      • undefinedToZero

        default boolean undefinedToZero​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source,
                                net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
        Copies all pixels instead those which are not a number (NaN) or infinity (inf), which are replaced by 0.

      • generateJaccardIndexMatrix

        default boolean generateJaccardIndexMatrix​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer label_map1,
                                           net.haesleinhuepf.clij.clearcl.ClearCLBuffer label_map2,
                                           net.haesleinhuepf.clij.clearcl.ClearCLBuffer jaccard_index_matrix_destination)
        Takes two labelmaps with n and m labels_2 and generates a (n+1)*(m+1) matrix where all labels_1 are set to 0 exept those where labels_2 overlap between the label maps. For the remaining labels_1, the value will be between 0 and 1 indicating the overlap as measured by the Jaccard Index. Major parts of this operation run on the CPU.

      • generateTouchCountMatrix

        default boolean generateTouchCountMatrix​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer label_map,
                                         net.haesleinhuepf.clij.clearcl.ClearCLBuffer touch_count_matrix_destination)
        Takes a label map with n labels and generates a (n+1)*(n+1) matrix where all pixels are set the number of pixels where labels touch (diamond neighborhood). Major parts of this operation run on the CPU.

      • minimumXProjection

        default boolean minimumXProjection​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                                   net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination_min)
        Determines the minimum intensity projection of an image along Y.

      • minimumYProjection

        default boolean minimumYProjection​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                                   net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination_min)
        Determines the minimum intensity projection of an image along Y.

      • meanXProjection

        default boolean meanXProjection​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                                net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Determines the mean average intensity projection of an image along X.

      • meanYProjection

        default boolean meanYProjection​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface source,
                                net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Determines the mean average intensity projection of an image along Y.

      • squaredDifference

        default boolean squaredDifference​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source1,
                                  net.haesleinhuepf.clij.clearcl.ClearCLBuffer source2,
                                  net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
        Determines the squared difference pixel by pixel between two images.

      • absoluteDifference

        default boolean absoluteDifference​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source1,
                                   net.haesleinhuepf.clij.clearcl.ClearCLBuffer source2,
                                   net.haesleinhuepf.clij.clearcl.ClearCLBuffer destination)
        Determines the absolute difference pixel by pixel between two images. 
        f(x, y) = |x - y|
        Parameters ---------- source1 : Image The input image to be subtracted from. source2 : Image The input image which is subtracted. destination : Image The output image where results are written into.

      • replacePixelsIfZero

        default boolean replacePixelsIfZero​(net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface input1,
                                    net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface input2,
                                    net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Replaces pixel values x with y in case x is zero. This functionality is comparable to ImageJs image calculator operator 'transparent zero'.

      • voronoiLabeling

        default boolean voronoiLabeling​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input,
                                net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Takes a binary image, labels connected components and dilates the regions using a octagon shape until they touch. The resulting label map is written to the output.

      • extendLabelingViaVoronoi

        default boolean extendLabelingViaVoronoi​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer input,
                                         net.haesleinhuepf.clij.clearcl.interfaces.ClearCLImageInterface destination)
        Takes a label map image and dilates the regions using a octagon shape until they touch. The resulting label map is written to the output.

      • centroidsOfBackgroundAndLabels

        default boolean centroidsOfBackgroundAndLabels​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer source,
                                               net.haesleinhuepf.clij.clearcl.ClearCLBuffer pointlist_destination)
        Determines the centroids of the background and all labels in a label image or image stack. It writes the resulting coordinates in a pointlist image. Depending on the dimensionality d of the labelmap and the number of labels n, the pointlist image will have n*d pixels.

      • getMeanOfMaskedPixels

        default double getMeanOfMaskedPixels​(net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg1,
                                     net.haesleinhuepf.clij.clearcl.ClearCLBuffer arg2)
        Determines the mean of all pixels in a given image which have non-zero value in a corresponding mask image. It will be stored in the variable mean_of_masked_pixels.