├── .gitignore ├── README.md ├── _config.yml ├── _layouts └── default.html ├── images ├── clicy_bridge2.gif ├── clij25.gif ├── clij2_logo.png ├── clij_bridge.gif └── curtain.gif ├── install.bat ├── license.txt ├── pom.xml └── src └── main ├── java └── net │ └── haesleinhuepf │ └── clij2 │ ├── AbstractCLIJ2Plugin.java │ ├── CLIJ2.java │ ├── CLIJ2Ops.java │ ├── converters │ ├── helptypes │ │ ├── Byte1.java │ │ ├── Byte2.java │ │ ├── Byte3.java │ │ ├── Char1.java │ │ ├── Char2.java │ │ ├── Char3.java │ │ ├── Double1.java │ │ ├── Double2.java │ │ ├── Double3.java │ │ ├── Float1.java │ │ ├── Float2.java │ │ ├── Float3.java │ │ ├── Integer1.java │ │ ├── Integer2.java │ │ ├── Integer3.java │ │ ├── Short1.java │ │ ├── Short2.java │ │ └── Short3.java │ └── implementations │ │ ├── Byte1ToClearCLBufferConverter.java │ │ ├── Byte2ToClearCLBufferConverter.java │ │ ├── Byte3ToClearCLBufferConverter.java │ │ ├── Char1ToClearCLBufferConverter.java │ │ ├── Char2ToClearCLBufferConverter.java │ │ ├── Char3ToClearCLBufferConverter.java │ │ ├── ClearCLBufferToByte2Converter.java │ │ ├── ClearCLBufferToByte3Converter.java │ │ ├── ClearCLBufferToChar2Converter.java │ │ ├── ClearCLBufferToChar3Converter.java │ │ ├── ClearCLBufferToDouble2Converter.java │ │ ├── ClearCLBufferToDouble3Converter.java │ │ ├── ClearCLBufferToFloat2Converter.java │ │ ├── ClearCLBufferToFloat3Converter.java │ │ ├── ClearCLBufferToInteger2Converter.java │ │ ├── ClearCLBufferToInteger3Converter.java │ │ ├── ClearCLBufferToShort2Converter.java │ │ ├── ClearCLBufferToShort3Converter.java │ │ ├── Double1ToClearCLBufferConverter.java │ │ ├── Double2ToClearCLBufferConverter.java │ │ ├── Double3ToClearCLBufferConverter.java │ │ ├── Float1ToClearCLBufferConverter.java │ │ ├── Float2ToClearCLBufferConverter.java │ │ ├── Float3ToClearCLBufferConverter.java │ │ ├── Integer1ToClearCLBufferConverter.java │ │ ├── Integer2ToClearCLBufferConverter.java │ │ ├── Integer3ToClearCLBufferConverter.java │ │ ├── Short1ToClearCLBufferConverter.java │ │ ├── Short2ToClearCLBufferConverter.java │ │ └── Short3ToClearCLBufferConverter.java │ ├── legacy │ ├── CLIJLegacyMacroExtensions.java │ ├── FallBackCLIJMacroPluginService.java │ └── FallBackCLIJMacroPluginServiceInitializer.java │ ├── plugins │ ├── Absolute.java │ ├── AbsoluteDifference.java │ ├── AddImageAndScalar.java │ ├── AddImages.java │ ├── AddImagesWeighted.java │ ├── AdjacencyMatrixToTouchMatrix.java │ ├── AffineTransform.java │ ├── AffineTransform2D.java │ ├── AffineTransform3D.java │ ├── ApplyVectorField2D.java │ ├── ApplyVectorField3D.java │ ├── ArgMaximumZProjection.java │ ├── AutoThresholderImageJ1.java │ ├── AutomaticThreshold.java │ ├── AverageDistanceOfNClosestNeighborsMap.java │ ├── AverageDistanceOfNClosestPoints.java │ ├── AverageDistanceOfNFarOffPoints.java │ ├── AverageDistanceOfTouchingNeighbors.java │ ├── AverageNeighborDistanceMap.java │ ├── BinaryAnd.java │ ├── BinaryEdgeDetection.java │ ├── BinaryFillHoles.java │ ├── BinaryIntersection.java │ ├── BinaryNot.java │ ├── BinaryOr.java │ ├── BinarySubtract.java │ ├── BinaryUnion.java │ ├── BinaryXOr.java │ ├── Blur2D.java │ ├── Blur3D.java │ ├── Blur3DSliceBySlice.java │ ├── BottomHatBox.java │ ├── BottomHatSphere.java │ ├── BoundingBox.java │ ├── CenterOfMass.java │ ├── CentroidsOfBackgroundAndLabels.java │ ├── CentroidsOfLabels.java │ ├── ClInfo.java │ ├── Clear.java │ ├── CloseIndexGapsInLabelMap.java │ ├── ClosingBox.java │ ├── ClosingDiamond.java │ ├── CombineHorizontally.java │ ├── CombineVertically.java │ ├── ConcatenateStacks.java │ ├── ConnectedComponentsLabeling.java │ ├── ConnectedComponentsLabelingBox.java │ ├── ConnectedComponentsLabelingDiamond.java │ ├── ConvertFloat.java │ ├── ConvertUInt16.java │ ├── ConvertUInt8.java │ ├── Convolve.java │ ├── Copy.java │ ├── CopySlice.java │ ├── Cosinus.java │ ├── CountNonZeroPixels.java │ ├── CountNonZeroPixels2DSphere.java │ ├── CountNonZeroPixelsSliceBySliceSphere.java │ ├── CountNonZeroVoxels3DSphere.java │ ├── CountTouchingNeighbors.java │ ├── Create2D.java │ ├── Create3D.java │ ├── Crop2D.java │ ├── Crop3D.java │ ├── CustomOperation.java │ ├── CylinderTransform.java │ ├── DepthColorProjection.java │ ├── DetectLabelEdges.java │ ├── DetectMaxima2DBox.java │ ├── DetectMaxima3DBox.java │ ├── DetectMaximaBox.java │ ├── DetectMaximaSliceBySliceBox.java │ ├── DetectMinima2DBox.java │ ├── DetectMinima3DBox.java │ ├── DetectMinimaBox.java │ ├── DetectMinimaSliceBySliceBox.java │ ├── DifferenceOfGaussian2D.java │ ├── DifferenceOfGaussian3D.java │ ├── Different.java │ ├── DilateBox.java │ ├── DilateBoxSliceBySlice.java │ ├── DilateLabels.java │ ├── DilateSphere.java │ ├── DilateSphereSliceBySlice.java │ ├── DistanceMap.java │ ├── DistanceMatrixToMesh.java │ ├── DivideByGaussianBackground.java │ ├── DivideImages.java │ ├── DivideScalarByImage.java │ ├── Downsample2D.java │ ├── Downsample3D.java │ ├── DownsampleSliceBySliceHalfMedian.java │ ├── DrawBox.java │ ├── DrawDistanceMeshBetweenTouchingLabels.java │ ├── DrawLine.java │ ├── DrawMeshBetweenNClosestLabels.java │ ├── DrawMeshBetweenNNearestLabels.java │ ├── DrawMeshBetweenProximalLabels.java │ ├── DrawMeshBetweenTouchingLabels.java │ ├── DrawSphere.java │ ├── EntropyBox.java │ ├── Equal.java │ ├── EqualConstant.java │ ├── EqualizeMeanIntensitiesOfSlices.java │ ├── ErodeBox.java │ ├── ErodeBoxSliceBySlice.java │ ├── ErodeLabels.java │ ├── ErodeSphere.java │ ├── ErodeSphereSliceBySlice.java │ ├── EuclideanDistanceFromLabelCentroidMap.java │ ├── ExcludeLabels.java │ ├── ExcludeLabelsOnEdges.java │ ├── ExcludeLabelsOnSurface.java │ ├── ExcludeLabelsOutsideSizeRange.java │ ├── ExcludeLabelsSubSurface.java │ ├── ExcludeLabelsWithValuesOutOfRange.java │ ├── ExcludeLabelsWithValuesWithinRange.java │ ├── Exponential.java │ ├── ExtendLabelingViaVoronoi.java │ ├── ExtendedDepthOfFocusSobelProjection.java │ ├── ExtendedDepthOfFocusTenengradProjection.java │ ├── ExtendedDepthOfFocusVarianceProjection.java │ ├── ExtensionRatioMap.java │ ├── Flip2D.java │ ├── Flip3D.java │ ├── FloodFillDiamond.java │ ├── GPUProperties.java │ ├── GammaCorrection.java │ ├── GaussianBlur2D.java │ ├── GaussianBlur3D.java │ ├── GenerateBinaryOverlapMatrix.java │ ├── GenerateDistanceMatrix.java │ ├── GenerateJaccardIndexMatrix.java │ ├── GenerateNNearestNeighborsMatrix.java │ ├── GenerateParametricImage.java │ ├── GenerateParametricImageFromResultsTableColumn.java │ ├── GenerateProximalNeighborsMatrix.java │ ├── GenerateTouchCountMatrix.java │ ├── GenerateTouchMatrix.java │ ├── GetAutomaticThreshold.java │ ├── GetBoundingBox.java │ ├── GetCenterOfMass.java │ ├── GetDimensions.java │ ├── GetGPUProperties.java │ ├── GetJaccardIndex.java │ ├── GetMaximumOfAllPixels.java │ ├── GetMeanOfAllPixels.java │ ├── GetMeanOfMaskedPixels.java │ ├── GetMeanSquaredError.java │ ├── GetMinimumOfAllPixels.java │ ├── GetSize.java │ ├── GetSorensenDiceCoefficient.java │ ├── GetSumOfAllPixels.java │ ├── GetTimeTracing.java │ ├── GradientX.java │ ├── GradientY.java │ ├── GradientZ.java │ ├── Greater.java │ ├── GreaterConstant.java │ ├── GreaterOrEqual.java │ ├── GreaterOrEqualConstant.java │ ├── GreyscaleClosingBox.java │ ├── GreyscaleClosingSphere.java │ ├── GreyscaleOpeningBox.java │ ├── GreyscaleOpeningSphere.java │ ├── Help.java │ ├── Histogram.java │ ├── Image2DToResultsTable.java │ ├── ImageToStack.java │ ├── InvalidateKernelCache.java │ ├── Invert.java │ ├── JaccardIndex.java │ ├── LabelCentroidsToPointList.java │ ├── LabelOverlapCountMap.java │ ├── LabelProximalNeighborCountMap.java │ ├── LabelSpots.java │ ├── LabelSurface.java │ ├── LabelToMask.java │ ├── LabelVoronoiOctagon.java │ ├── LabelledSpotsToPointList.java │ ├── LaplaceBox.java │ ├── LaplaceDiamond.java │ ├── ListAvailableGPUs.java │ ├── LocalThreshold.java │ ├── Logarithm.java │ ├── MakeIsotropic.java │ ├── Mask.java │ ├── MaskLabel.java │ ├── MaskStackWithPlane.java │ ├── MaskedVoronoiLabeling.java │ ├── MatrixEqual.java │ ├── Maximum2DBox.java │ ├── Maximum2DSphere.java │ ├── Maximum3DBox.java │ ├── Maximum3DSphere.java │ ├── MaximumDistanceOfTouchingNeighbors.java │ ├── MaximumExtensionMap.java │ ├── MaximumImageAndScalar.java │ ├── MaximumImages.java │ ├── MaximumIntensityMap.java │ ├── MaximumOctagon.java │ ├── MaximumOfAllPixels.java │ ├── MaximumOfMaskedPixels.java │ ├── MaximumOfNNearestNeighborsMap.java │ ├── MaximumOfProximalNeighborsMap.java │ ├── MaximumOfTouchingNeighbors.java │ ├── MaximumOfTouchingNeighborsMap.java │ ├── MaximumSliceBySliceSphere.java │ ├── MaximumTouchingNeighborDistanceMap.java │ ├── MaximumXProjection.java │ ├── MaximumYProjection.java │ ├── MaximumZProjection.java │ ├── MaximumZProjectionBounded.java │ ├── Mean2DBox.java │ ├── Mean2DSphere.java │ ├── Mean3DBox.java │ ├── Mean3DSphere.java │ ├── MeanClosestSpotDistance.java │ ├── MeanExtensionMap.java │ ├── MeanIntensityMap.java │ ├── MeanOfAllPixels.java │ ├── MeanOfMaskedPixels.java │ ├── MeanOfNNearestNeighborsMap.java │ ├── MeanOfPixelsAboveThreshold.java │ ├── MeanOfProximalNeighborsMap.java │ ├── MeanOfTouchingNeighbors.java │ ├── MeanOfTouchingNeighborsMap.java │ ├── MeanSliceBySliceSphere.java │ ├── MeanSquaredError.java │ ├── MeanXProjection.java │ ├── MeanYProjection.java │ ├── MeanZProjection.java │ ├── MeanZProjectionBounded.java │ ├── Median2DBox.java │ ├── Median2DSphere.java │ ├── Median3DBox.java │ ├── Median3DSphere.java │ ├── MedianOfTouchingNeighbors.java │ ├── MedianSliceBySliceBox.java │ ├── MedianSliceBySliceSphere.java │ ├── MedianZProjection.java │ ├── MedianZProjectionMasked.java │ ├── MergeTouchingLabels.java │ ├── Minimum2DBox.java │ ├── Minimum2DSphere.java │ ├── Minimum3DBox.java │ ├── Minimum3DSphere.java │ ├── MinimumDistanceOfTouchingNeighbors.java │ ├── MinimumImageAndScalar.java │ ├── MinimumImages.java │ ├── MinimumIntensityMap.java │ ├── MinimumOctagon.java │ ├── MinimumOfAllPixels.java │ ├── MinimumOfMaskedPixels.java │ ├── MinimumOfNNearestNeighborsMap.java │ ├── MinimumOfProximalNeighborsMap.java │ ├── MinimumOfTouchingNeighbors.java │ ├── MinimumOfTouchingNeighborsMap.java │ ├── MinimumSliceBySliceSphere.java │ ├── MinimumTouchingNeighborDistanceMap.java │ ├── MinimumXProjection.java │ ├── MinimumYProjection.java │ ├── MinimumZProjection.java │ ├── MinimumZProjectionBounded.java │ ├── MinimumZProjectionThresholdedBounded.java │ ├── ModeOfNNearestNeighborsMap.java │ ├── ModeOfProximalNeighborsMap.java │ ├── ModeOfTouchingNeighbors.java │ ├── ModeOfTouchingNeighborsMap.java │ ├── MultiplyImageAndCoordinate.java │ ├── MultiplyImageAndScalar.java │ ├── MultiplyImageStackWithScalars.java │ ├── MultiplyImages.java │ ├── MultiplyMatrix.java │ ├── MultiplyStackWithPlane.java │ ├── NClosestDistances.java │ ├── NClosestPoints.java │ ├── NeighborsOfNeighbors.java │ ├── NonzeroMaximumBox.java │ ├── NonzeroMaximumDiamond.java │ ├── NonzeroMinimumBox.java │ ├── NonzeroMinimumDiamond.java │ ├── NotEqual.java │ ├── NotEqualConstant.java │ ├── OnlyzeroOverwriteMaximumBox.java │ ├── OnlyzeroOverwriteMaximumDiamond.java │ ├── OpeningBox.java │ ├── OpeningDiamond.java │ ├── OutOfIntensityRange.java │ ├── Paste2D.java │ ├── Paste3D.java │ ├── PixelCountMap.java │ ├── PointIndexListToMesh.java │ ├── PointIndexListToTouchMatrix.java │ ├── PointlistToLabelledSpots.java │ ├── Power.java │ ├── PowerImages.java │ ├── Print.java │ ├── ProximalNeighborCountMap.java │ ├── Pull.java │ ├── Pull2DPointListAsRoi.java │ ├── PullAsROI.java │ ├── PullBinary.java │ ├── PullLabelsToROIList.java │ ├── PullLabelsToROIManager.java │ ├── PullString.java │ ├── PullTile.java │ ├── PullToCurrentSlice.java │ ├── PullToCurrentSliceSelection.java │ ├── PullToROIManager.java │ ├── PullToResultsTable.java │ ├── PullToResultsTableColumn.java │ ├── Push.java │ ├── PushArray.java │ ├── PushArray2D.java │ ├── PushAs.java │ ├── PushCurrentSelection.java │ ├── PushCurrentSlice.java │ ├── PushCurrentSliceSelection.java │ ├── PushCurrentZStack.java │ ├── PushResultsTable.java │ ├── PushResultsTableColumn.java │ ├── PushString.java │ ├── PushTile.java │ ├── ReadValuesFromMap.java │ ├── ReadValuesFromPositions.java │ ├── ReduceLabelsToCentroids.java │ ├── ReduceLabelsToLabelEdges.java │ ├── ReduceStack.java │ ├── Release.java │ ├── ReplaceIntensities.java │ ├── ReplaceIntensity.java │ ├── ReplacePixelsIfZero.java │ ├── ReportMemory.java │ ├── Resample.java │ ├── ResliceBottom.java │ ├── ResliceLeft.java │ ├── ReslicePolar.java │ ├── ResliceRadial.java │ ├── ResliceRadialTop.java │ ├── ResliceRight.java │ ├── ResliceTop.java │ ├── ResultsTableColumnToImage.java │ ├── ResultsTableToImage2D.java │ ├── RigidTransform.java │ ├── Rotate2D.java │ ├── Rotate3D.java │ ├── RotateClockwise.java │ ├── RotateCounterClockwise.java │ ├── RotateLeft.java │ ├── RotateRight.java │ ├── SaveAsTIF.java │ ├── Scale.java │ ├── Scale2D.java │ ├── Scale3D.java │ ├── Set.java │ ├── SetColumn.java │ ├── SetImageBorders.java │ ├── SetNonZeroPixelsToPixelIndex.java │ ├── SetPlane.java │ ├── SetRampX.java │ ├── SetRampY.java │ ├── SetRampZ.java │ ├── SetRandom.java │ ├── SetRow.java │ ├── SetWhereXequalsY.java │ ├── SetWhereXgreaterThanY.java │ ├── SetWhereXsmallerThanY.java │ ├── ShortestDistances.java │ ├── Similar.java │ ├── Sinus.java │ ├── Smaller.java │ ├── SmallerConstant.java │ ├── SmallerOrEqual.java │ ├── SmallerOrEqualConstant.java │ ├── Sobel.java │ ├── SobelSliceBySlice.java │ ├── SorensenDiceCoefficient.java │ ├── SphereTransform.java │ ├── SpotsToPointList.java │ ├── SquaredDifference.java │ ├── StackToTiles.java │ ├── StandardDeviationBox.java │ ├── StandardDeviationIntensityMap.java │ ├── StandardDeviationOfAllPixels.java │ ├── StandardDeviationOfMaskedPixels.java │ ├── StandardDeviationOfNNearestNeighborsMap.java │ ├── StandardDeviationOfProximalNeighborsMap.java │ ├── StandardDeviationOfTouchingNeighbors.java │ ├── StandardDeviationOfTouchingNeighborsMap.java │ ├── StandardDeviationSphere.java │ ├── StandardDeviationZProjection.java │ ├── StartTimeTracing.java │ ├── StatisticsOfBackgroundAndLabelledPixels.java │ ├── StatisticsOfImage.java │ ├── StatisticsOfLabelledPixels.java │ ├── StopTimeTracing.java │ ├── SubStack.java │ ├── SubtractImageFromScalar.java │ ├── SubtractImages.java │ ├── SumImageSliceBySlice.java │ ├── SumOfAllPixels.java │ ├── SumXProjection.java │ ├── SumYProjection.java │ ├── SumZProjection.java │ ├── Tenengrad.java │ ├── TenengradSliceBySlice.java │ ├── Threshold.java │ ├── ThresholdDefault.java │ ├── ThresholdHuang.java │ ├── ThresholdIJ_IsoData.java │ ├── ThresholdIntermodes.java │ ├── ThresholdIsoData.java │ ├── ThresholdLi.java │ ├── ThresholdMaxEntropy.java │ ├── ThresholdMean.java │ ├── ThresholdMinError.java │ ├── ThresholdMinimum.java │ ├── ThresholdMoments.java │ ├── ThresholdOtsu.java │ ├── ThresholdPercentile.java │ ├── ThresholdRenyiEntropy.java │ ├── ThresholdShanbhag.java │ ├── ThresholdTriangle.java │ ├── ThresholdYen.java │ ├── TopHatBox.java │ ├── TopHatSphere.java │ ├── TouchMatrixToAdjacencyMatrix.java │ ├── TouchMatrixToMesh.java │ ├── TouchingNeighborCountMap.java │ ├── TouchingNeighborDistanceRangeRatioMap.java │ ├── Translate2D.java │ ├── Translate3D.java │ ├── TransposeXY.java │ ├── TransposeXZ.java │ ├── TransposeYZ.java │ ├── UndefinedToZero.java │ ├── VarianceBox.java │ ├── VarianceOfAllPixels.java │ ├── VarianceOfMaskedPixels.java │ ├── VarianceSphere.java │ ├── VisualizeOutlinesOnOriginal.java │ ├── VoronoiLabeling.java │ ├── VoronoiOctagon.java │ ├── VoronoiOtsuLabeling.java │ ├── Watershed.java │ ├── WithinIntensityRange.java │ ├── WriteValuesToPositions.java │ ├── ZPositionOfMaximumZProjection.java │ ├── ZPositionOfMinimumZProjection.java │ ├── ZPositionProjection.java │ ├── ZPositionRangeProjection.java │ ├── absolute_2d_x.cl │ ├── absolute_3d_x.cl │ ├── add_image_and_scalar_2d_x.cl │ ├── add_image_and_scalar_3d_x.cl │ ├── add_images_weighted_2d_x.cl │ ├── add_images_weighted_3d_x.cl │ ├── affine_transform_2d_interpolate_x.cl │ ├── affine_transform_2d_x.cl │ ├── affine_transform_3d_interpolate_x.cl │ ├── affine_transform_3d_x.cl │ ├── apply_vectorfield_2d_interpolate_x.cl │ ├── apply_vectorfield_2d_x.cl │ ├── apply_vectorfield_3d_interpolate_x.cl │ ├── apply_vectorfield_3d_x.cl │ ├── arg_maximum_z_projection_x.cl │ ├── average_distance_of_n_far_off_distances_x.cl │ ├── average_distance_of_n_shortest_distances_x.cl │ ├── average_distance_of_touching_neighbors_x.cl │ ├── binary_and_2d_x.cl │ ├── binary_and_3d_x.cl │ ├── binary_edge_detection_2d_x.cl │ ├── binary_edge_detection_3d_x.cl │ ├── binary_not_2d_x.cl │ ├── binary_not_3d_x.cl │ ├── binary_or_2d_x.cl │ ├── binary_or_3d_x.cl │ ├── binary_subtract_2d_x.cl │ ├── binary_subtract_3d_x.cl │ ├── binary_xor_2d_x.cl │ ├── binary_xor_3d_x.cl │ ├── convolve_2d_x.cl │ ├── convolve_3d_x.cl │ ├── copy_2d_x.cl │ ├── copy_3d_x.cl │ ├── copy_slice_from_3d_x.cl │ ├── copy_slice_to_3d_x.cl │ ├── cosinus_2d_x.cl │ ├── cosinus_3d_x.cl │ ├── count_non_zero_projection_3d_2d_x.cl │ ├── count_nonzero_pixels_slice_by_slice_sphere_3d_x.cl │ ├── count_nonzero_pixels_sphere_2d_x.cl │ ├── count_nonzero_voxels_sphere_3d_x.cl │ ├── count_touching_neighbors_x.cl │ ├── crop_2d_x.cl │ ├── crop_3d_x.cl │ ├── depth_projection_interpolation_x.cl │ ├── depth_projection_x.cl │ ├── detect_label_edges_2d_x.cl │ ├── detect_label_edges_3d_x.cl │ ├── detect_maxima_2d_x.cl │ ├── detect_maxima_3d_slice_by_slice_x.cl │ ├── detect_maxima_3d_x.cl │ ├── detect_minima_2d_x.cl │ ├── detect_minima_3d_slice_by_slice_x.cl │ ├── detect_minima_3d_x.cl │ ├── dilate_box_2d_x.cl │ ├── dilate_box_3d_x.cl │ ├── dilate_box_slice_by_slice_3d_x.cl │ ├── dilate_sphere_2d_x.cl │ ├── dilate_sphere_3d_x.cl │ ├── dilate_sphere_slice_by_slice_3d_x.cl │ ├── distance_matrix_to_mesh_x.cl │ ├── distancemap_localPositiveMinimum_box_2d_x.cl │ ├── distancemap_localPositiveMinimum_box_3d_x.cl │ ├── distancemap_localPositiveMinimum_diamond_2d_x.cl │ ├── distancemap_localPositiveMinimum_diamond_3d_x.cl │ ├── divide_images_2d_x.cl │ ├── divide_images_3d_x.cl │ ├── divide_scalar_by_image_2d_x.cl │ ├── divide_scalar_by_image_3d_x.cl │ ├── downsample_2d_x.cl │ ├── downsample_3d_x.cl │ ├── downsample_xy_by_half_median_3d_x.cl │ ├── draw_box_2d_x.cl │ ├── draw_box_3d_x.cl │ ├── draw_sphere_2d_x.cl │ ├── draw_sphere_3d_x.cl │ ├── drawline_2d_x.cl │ ├── drawline_3d_x.cl │ ├── entropy_2d_x.cl │ ├── entropy_3d_x.cl │ ├── equal_2d_x.cl │ ├── equal_3d_x.cl │ ├── equal_constant_2d_x.cl │ ├── equal_constant_3d_x.cl │ ├── erode_box_2d_x.cl │ ├── erode_box_3d_x.cl │ ├── erode_box_slice_by_slice_3d_x.cl │ ├── erode_sphere_2d_x.cl │ ├── erode_sphere_3d_x.cl │ ├── erode_sphere_slice_by_slice_3d_x.cl │ ├── euclidean_distance_from_label_centroid_map_x.cl │ ├── excludeLabelsOnEdges_3d_x.cl │ ├── exclude_labels_on_surface_2d_x.cl │ ├── exclude_labels_on_surface_3d_x.cl │ ├── exclude_labels_sub_surface_2d_x.cl │ ├── exclude_labels_sub_surface_3d_x.cl │ ├── exponential_2d_x.cl │ ├── exponential_3d_x.cl │ ├── flip_2d_x.cl │ ├── flip_3d_x.cl │ ├── flood_fill_diamond_x.cl │ ├── gaussian_blur_separable_2d_x.cl │ ├── gaussian_blur_separable_3d_x.cl │ ├── generate_binary_overlap_matrix_2d_x.cl │ ├── generate_binary_overlap_matrix_3d_x.cl │ ├── generate_distance_matrix_x.cl │ ├── generate_touch_matrix_2d_x.cl │ ├── generate_touch_matrix_3d_x.cl │ ├── gradient_x_2d_x.cl │ ├── gradient_x_3d_x.cl │ ├── gradient_y_2d_x.cl │ ├── gradient_y_3d_x.cl │ ├── gradient_z_3d_x.cl │ ├── greater_2d_x.cl │ ├── greater_3d_x.cl │ ├── greater_constant_2d_x.cl │ ├── greater_constant_3d_x.cl │ ├── greater_or_equal_2d_x.cl │ ├── greater_or_equal_3d_x.cl │ ├── greater_or_equal_constant_2d_x.cl │ ├── greater_or_equal_constant_3d_x.cl │ ├── histogram_2d_x.cl │ ├── histogram_3d_x.cl │ ├── label_spots_in_x.cl │ ├── labelled_spots_to_point_list_x.cl │ ├── laplace_box_2d_x.cl │ ├── laplace_box_3d_x.cl │ ├── laplace_diamond_2d_x.cl │ ├── laplace_diamond_3d_x.cl │ ├── logarithm_2d_x.cl │ ├── logarithm_3d_x.cl │ ├── mask_2d_x.cl │ ├── mask_3d_x.cl │ ├── mask_label_2d_x.cl │ ├── mask_label_3d_x.cl │ ├── mask_stack_with_plane_3d_x.cl │ ├── matrix_multiply_float_buffer.cl │ ├── maximum_distance_of_touching_neighbors_x.cl │ ├── maximum_image_and_scalar_2d_x.cl │ ├── maximum_image_and_scalar_3d_x.cl │ ├── maximum_images_2d_x.cl │ ├── maximum_images_3d_x.cl │ ├── maximum_octagon_box_2d_x.cl │ ├── maximum_octagon_box_3d_x.cl │ ├── maximum_octagon_diamond_2d_x.cl │ ├── maximum_octagon_diamond_3d_x.cl │ ├── maximum_of_masked_pixels_3d_2d_x.cl │ ├── maximum_of_touching_neighbors_x.cl │ ├── maximum_projection_3d_2d_x.cl │ ├── maximum_separable_2d_x.cl │ ├── maximum_separable_3d_x.cl │ ├── maximum_slice_by_slice_sphere_3d_x.cl │ ├── maximum_sphere_2d_x.cl │ ├── maximum_sphere_3d_x.cl │ ├── maximum_x_projection_x.cl │ ├── maximum_y_projection_x.cl │ ├── maximum_z_projection_bounded_3d_2d_x.cl │ ├── maximum_z_projection_x.cl │ ├── mean_of_touching_neighbors_x.cl │ ├── mean_separable_2d_x.cl │ ├── mean_separable_3d_x.cl │ ├── mean_slice_by_slice_sphere_3d_x.cl │ ├── mean_sphere_2d_x.cl │ ├── mean_sphere_3d_x.cl │ ├── mean_x_projection_x.cl │ ├── mean_y_projection_x.cl │ ├── mean_z_projection_bounded_3d_2d_x.cl │ ├── mean_z_projection_x.cl │ ├── median_box_2d_x.cl │ ├── median_box_3d_x.cl │ ├── median_of_touching_neighbors_x.cl │ ├── median_slice_by_slice_box_3d_x.cl │ ├── median_slice_by_slice_sphere_3d_x.cl │ ├── median_sphere_2d_x.cl │ ├── median_sphere_3d_x.cl │ ├── median_z_projection_masked_x.cl │ ├── median_z_projection_x.cl │ ├── minimum_distance_of_touching_neighbors_x.cl │ ├── minimum_image_and_scalar_2d_x.cl │ ├── minimum_image_and_scalar_3d_x.cl │ ├── minimum_images_2d_x.cl │ ├── minimum_images_3d_x.cl │ ├── minimum_octagon_box_2d_x.cl │ ├── minimum_octagon_box_3d_x.cl │ ├── minimum_octagon_diamond_2d_x.cl │ ├── minimum_octagon_diamond_3d_x.cl │ ├── minimum_of_masked_pixels_3d_2d_x.cl │ ├── minimum_of_touching_neighbors_x.cl │ ├── minimum_projection_3d_2d_x.cl │ ├── minimum_separable_2d_x.cl │ ├── minimum_separable_3d_x.cl │ ├── minimum_slice_by_slice_sphere_3d_x.cl │ ├── minimum_sphere_2d_x.cl │ ├── minimum_sphere_3d_x.cl │ ├── minimum_x_projection_x.cl │ ├── minimum_y_projection_x.cl │ ├── minimum_z_projection_bounded_3d_2d_x.cl │ ├── minimum_z_projection_thresholded_bounded_3d_2d_x.cl │ ├── minimum_z_projection_x.cl │ ├── mode_of_touching_neighbors_x.cl │ ├── multiply_image_and_coordinate_2d_x.cl │ ├── multiply_image_and_coordinate_3d_x.cl │ ├── multiply_image_and_scalar_2d_x.cl │ ├── multiply_image_and_scalar_3d_x.cl │ ├── multiply_images_2d_x.cl │ ├── multiply_images_3d_x.cl │ ├── multiply_matrix_x.cl │ ├── multiply_stack_with_plane_3d_x.cl │ ├── multiply_stack_with_scalars_x.cl │ ├── n_shortest_distances_x.cl │ ├── n_shortest_points_x.cl │ ├── nonzero_maximum_box_2d_x.cl │ ├── nonzero_maximum_box_3d_x.cl │ ├── nonzero_maximum_diamond_2d_x.cl │ ├── nonzero_maximum_diamond_3d_x.cl │ ├── nonzero_minimum_box_2d_x.cl │ ├── nonzero_minimum_box_3d_x.cl │ ├── nonzero_minimum_diamond_2d_x.cl │ ├── nonzero_minimum_diamond_3d_x.cl │ ├── not_equal_2d_x.cl │ ├── not_equal_3d_x.cl │ ├── not_equal_constant_2d_x.cl │ ├── not_equal_constant_3d_x.cl │ ├── onlyzero_overwrite_maximum_box_2d_x.cl │ ├── onlyzero_overwrite_maximum_box_3d_x.cl │ ├── onlyzero_overwrite_maximum_diamond_2d_x.cl │ ├── onlyzero_overwrite_maximum_diamond_3d_x.cl │ ├── paste_2d_x.cl │ ├── paste_3d_x.cl │ ├── point_index_list_to_touch_matrix_x.cl │ ├── pointindexlist_to_mesh_3d_x.cl │ ├── power_2d_x.cl │ ├── power_3d_x.cl │ ├── power_images_2d_x.cl │ ├── power_images_3d_x.cl │ ├── read_values_from_map_x.cl │ ├── read_values_from_positions_x.cl │ ├── replace_intensities_x.cl │ ├── replace_intensity_x.cl │ ├── replace_pixels_if_zero_x.cl │ ├── reslice_bottom_3d_x.cl │ ├── reslice_left_3d_x.cl │ ├── reslice_polar_interpolate_x.cl │ ├── reslice_radial_interpolate_2d_x.cl │ ├── reslice_radial_interpolate_3d_x.cl │ ├── reslice_right_3d_x.cl │ ├── reslice_top_3d_x.cl │ ├── rotate_clockwise_2d_x.cl │ ├── rotate_clockwise_3d_x.cl │ ├── rotate_counter_clockwise_2d_x.cl │ ├── rotate_counter_clockwise_3d_x.cl │ ├── set_2d_x.cl │ ├── set_3d_x.cl │ ├── set_column_2d_x.cl │ ├── set_column_3d_x.cl │ ├── set_image_borders_2d_x.cl │ ├── set_image_borders_3d_x.cl │ ├── set_nonzero_pixels_to_pixelindex_x.cl │ ├── set_plane_2d_x.cl │ ├── set_plane_3d_x.cl │ ├── set_ramp_x_2d_x.cl │ ├── set_ramp_x_3d_x.cl │ ├── set_ramp_y_2d_x.cl │ ├── set_ramp_y_3d_x.cl │ ├── set_ramp_z_2d_x.cl │ ├── set_ramp_z_3d_x.cl │ ├── set_row_2d_x.cl │ ├── set_row_3d_x.cl │ ├── set_where_x_equals_y_2d_x.cl │ ├── set_where_x_equals_y_3d_x.cl │ ├── set_where_x_greater_than_y_2d_x.cl │ ├── set_where_x_greater_than_y_3d_x.cl │ ├── set_where_x_smaller_than_y_2d_x.cl │ ├── set_where_x_smaller_than_y_3d_x.cl │ ├── sinus_2d_x.cl │ ├── sinus_3d_x.cl │ ├── smaller_2d_x.cl │ ├── smaller_3d_x.cl │ ├── smaller_constant_2d_x.cl │ ├── smaller_constant_3d_x.cl │ ├── smaller_or_equal_2d_x.cl │ ├── smaller_or_equal_3d_x.cl │ ├── smaller_or_equal_constant_2d_x.cl │ ├── smaller_or_equal_constant_3d_x.cl │ ├── sobel_2d_x.cl │ ├── sobel_3d_x.cl │ ├── sobel_slice_by_slice_3d_x.cl │ ├── standard_deviation_of_touching_neighbors_x.cl │ ├── standard_deviation_z_projection_x.cl │ ├── subtract_image_from_scalar_2d_x.cl │ ├── subtract_image_from_scalar_3d_x.cl │ ├── sum_x_projection_x.cl │ ├── sum_y_projection_x.cl │ ├── sum_z_projection_x.cl │ ├── tenengrad_slice_by_slice_x.cl │ ├── tenengrad_x.cl │ ├── touch_matrix_to_mesh_3d_x.cl │ ├── transpose_xy_3d_x.cl │ ├── transpose_xz_3d_x.cl │ ├── transpose_yz_3d_x.cl │ ├── undefined_to_zero_x.cl │ ├── variance_2d_x.cl │ ├── variance_box_2d_x.cl │ ├── variance_box_3d_x.cl │ ├── variance_masked_projection_x.cl │ ├── variance_projection_x.cl │ ├── variance_sphere_2d_x.cl │ ├── variance_sphere_3d_x.cl │ ├── watershed_binarize_labelmap_2d_x.cl │ ├── watershed_binarize_labelmap_3d_x.cl │ ├── watershed_detect_maxima_region_box_2d.cl │ ├── watershed_detect_maxima_region_box_3d.cl │ ├── watershed_eliminate_wrong_maxima_2d_x.cl │ ├── watershed_eliminate_wrong_maxima_3d_x.cl │ ├── watershed_local_maximum_2d_x.cl │ ├── watershed_local_maximum_3d_x.cl │ ├── write_values_to_positions_2d_x.cl │ ├── write_values_to_positions_3d_x.cl │ ├── z_position_of_maximum_z_projection_x.cl │ ├── z_position_of_minimum_z_projection_x.cl │ └── z_position_projection_x.cl │ └── utilities │ ├── CLIJ2MacroExtensions.java │ ├── CLIJUtilities.java │ ├── HasClassifiedInputOutput.java │ └── ProcessableInTiles.java └── resources └── plugins.config /.gitignore: -------------------------------------------------------------------------------- 1 | /target/ 2 | /.idea/ 3 | *.iml 4 | CLIJ*.txt 5 | -------------------------------------------------------------------------------- /README.md: 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