All Classes
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All Classes Interface Summary Class Summary Enum Summary Class Description Absolute Author: @haesleinhuepf November 2019AbsoluteDifference Author: @haesleinhuepf June 2020AbstractCLIJ2Plugin AddImageAndScalar Author: @haesleinhuepf December 2018AddImages Author: @haesleinhuepf 12 2018AddImagesWeighted Author: @haesleinhuepf December 2018AdjacencyMatrixToTouchMatrix Author: @haesleinhuepf April 2020AffineTransform Deprecated. AffineTransform2D Author: @haesleinhuepf December 2019AffineTransform3D Author: @haesleinhuepf December 2019ApplyVectorField2D Author: @haesleinhuepf 12 2018ApplyVectorField3D Author: @haesleinhuepf 12 2018ArgMaximumZProjection Author: @haesleinhuepf December 2018AutomaticThreshold AutomaticThresholdAutoThresholderImageJ1 Copied from https://github.com/imagej/imagej1/blob/master/ij/process/AutoThresholder.java To reduce dependencies towards ImageJ1AutoThresholderImageJ1.Method AverageDistanceOfNClosestPoints AverageDistanceOfNFarOffPoints AverageDistanceOfTouchingNeighbors BinaryAnd Author: @haesleinhuepf 12 2018BinaryEdgeDetection Author: @haesleinhuepf September 2019BinaryFillHoles Author: @haesleinhuepf March 2020BinaryIntersection BinaryNot Author: @haesleinhuepf 12 2018BinaryOr Author: @haesleinhuepf 12 2018BinarySubtract Author: @haesleinhuepf September 2019BinaryUnion BinaryXOr Author: @haesleinhuepf 12 2018Blur2D Deprecated. Blur3D Deprecated. Blur3DSliceBySlice Deprecated. BottomHatBox BottomHatSphere BoundingBox Author: @haesleinhuepf December 2018Byte1 Byte1ToClearCLBufferConverter Byte2 Byte2ToClearCLBufferConverter Byte3 Byte3ToClearCLBufferConverter CenterOfMass Author: @haesleinhuepf December 2018CentroidsOfBackgroundAndLabels Author: @haesleinhuepf July 2020CentroidsOfLabels Author: @haesleinhuepf December 2018Char1 Char1ToClearCLBufferConverter Char2 Char2ToClearCLBufferConverter Char3 Char3ToClearCLBufferConverter Clear Author: @haesleinhuepf 12 2018ClearCLBufferToByte2Converter ClearCLBufferToByte3Converter ClearCLBufferToChar2Converter ClearCLBufferToChar3Converter ClearCLBufferToDouble2Converter Todo: Shall we deal with float images differently than with double images?ClearCLBufferToDouble3Converter ClearCLBufferToFloat2Converter Todo: Shall we deal with float images differently than with double images?ClearCLBufferToFloat3Converter CLIJ2 The CLIJ2 gateway Author: @haesleinhuepf December 2019CLIJ2MacroExtensions CLIJ2MacroExtensionsCLIJ2Ops CLIJLegacyMacroExtensions Author: @haesleinhuepf June 2019CLIJUtilities ClInfo Author: @haesleinhuepf 12 2018CloseIndexGapsInLabelMap ConnectedComponentsLabelingClosingBox ClosingDiamond CombineHorizontally Author: @haesleinhuepf May 2020CombineVertically Author: @haesleinhuepf May 2020ConcatenateStacks Author: @haesleinhuepf March 2020ConnectedComponentsLabeling Deprecated. ConnectedComponentsLabelingBox ConnectedComponentsLabelingConnectedComponentsLabelingDiamond ConnectedComponentsLabelingConvertFloat Author: @haesleinhuepf 12 2018ConvertUInt16 Author: @haesleinhuepf 12 2018ConvertUInt8 Author: @haesleinhuepf 12 2018Convolve Author: @haesleinhuepf December 2018Copy Author: @haesleinhuepf 12 2018CopySlice Author: @haesleinhuepf December 2018CountNonZeroPixels Author: @haesleinhuepf June 2019CountNonZeroPixels2DSphere Author: @haesleinhuepf December 2018CountNonZeroPixelsSliceBySliceSphere Author: @haesleinhuepf December 2018CountNonZeroVoxels3DSphere Author: @haesleinhuepf December 2018CountTouchingNeighbors Author: @haesleinhuepf October 2019Create2D ReleaseCreate3D ReleaseCrop2D Author: @haesleinhuepf December 2018Crop3D Author: @haesleinhuepf December 2018CustomOperation Author: @haesleinhuepfDepthColorProjection Author: @haesleinhuepf April 2020DetectLabelEdges Author: @haesleinhuepf October 2019DetectMaxima2DBox Author: @haesleinhuepf May 2020DetectMaxima3DBox Author: @haesleinhuepf May 2020DetectMaximaBox Deprecated. DetectMaximaSliceBySliceBox Author: @haesleinhuepf December 2018DetectMinima2DBox Author: @haesleinhuepf May 2020DetectMinima3DBox Author: @haesleinhuepf May 2020DetectMinimaBox Deprecated. DetectMinimaSliceBySliceBox Author: @haesleinhuepf December 2018DifferenceOfGaussian2D DifferenceOfGaussian3D DilateBox Author: @haesleinhuepf 12 2018DilateBoxSliceBySlice Author: @haesleinhuepf 12 2018DilateSphere Author: @haesleinhuepf 12 2018DilateSphereSliceBySlice Author: @haesleinhuepf 12 2018DistanceMap Author: @haesleinhuepf September 2019DistanceMatrixToMesh Author: @haesleinhuepf December 2019DivideImages Author: @haesleinhuepf 12 2018Double1 Double1ToClearCLBufferConverter Double2 Double2ToClearCLBufferConverter Double3 Double3ToClearCLBufferConverter Downsample2D Author: @haesleinhuepf 12 2018Downsample3D Author: @haesleinhuepf 12 2018DownsampleSliceBySliceHalfMedian Author: @haesleinhuepf 12 2018DrawBox DrawLineDrawLine DrawLineDrawSphere DrawLineEntropyBox Equal Author: @haesleinhuepf August 2019EqualConstant Author: @haesleinhuepf August 2019EqualizeMeanIntensitiesOfSlices ErodeBox Author: @haesleinhuepf 12 2018ErodeBoxSliceBySlice Author: @haesleinhuepf 12 2018ErodeSphere Author: @haesleinhuepf 12 2018ErodeSphereSliceBySlice Author: @haesleinhuepf 12 2018ExcludeLabels Author: @haesleinhuepf April 2020ExcludeLabelsOnEdges Author: @haesleinhuepf June 2019ExcludeLabelsOnSurface Author: @haesleinhuepf June 2019ExcludeLabelsSubSurface Author: @haesleinhuepf June 2019ExcludeLabelsWithValuesOutOfRange Author: @haesleinhuepf May 2020ExcludeLabelsWithValuesWithinRange Author: @haesleinhuepf May 2020Exponential Based on net.haesleinhuepf.clij.macro.modules.Power.java Author: @haesleinhuepf December 2018 modified by: @phaub July 2019ExtendLabelingViaVoronoi Author: @haesleinhuepf June 2020FallBackCLIJMacroPluginService FallBackCLIJMacroPluginServiceInitializer Flip2D Author: @haesleinhuepf 12 2018Flip3D Author: @haesleinhuepf 12 2018Float1 Float1ToClearCLBufferConverter Float2 Float2ToClearCLBufferConverter Float3 Float3ToClearCLBufferConverter FloodFillDiamond Author: @haesleinhuepf March 2020GaussianBlur2D Author: @haesleinhuepf 12 2018GaussianBlur3D Author: @haesleinhuepf 12 2018GenerateBinaryOverlapMatrix Author: @haesleinhuepf October 2019GenerateDistanceMatrix Author: @haesleinhuepf December 2018GenerateJaccardIndexMatrix Author: @haesleinhuepf June 2020GenerateParametricImage GenerateParametricImageFromResultsTableColumn GenerateTouchCountMatrix Author: @haesleinhuepf June 2020GenerateTouchMatrix Author: @haesleinhuepf October 2019GetAutomaticThreshold AutomaticThresholdGetBoundingBox Author: @haesleinhuepf April 2020GetCenterOfMass Author: @haesleinhuepf April 2020GetDimensions Author: @haesleinhuepf June 2019GetGPUProperties Author: @haesleinhuepf September 2019GetJaccardIndex Author: @haesleinhuepf April 2020GetMaximumOfAllPixels Author: @haesleinhuepf April 2020GetMeanOfAllPixels Author: @haesleinhuepf April 2020GetMeanOfMaskedPixels Author: @haesleinhuepf August 2020GetMeanSquaredError Author: @haesleinhuepf April 2020GetMinimumOfAllPixels Author: @haesleinhuepf April 2020GetSize Deprecated. GetSorensenDiceCoefficient Author: @haesleinhuepf April 2020GetSumOfAllPixels Author: @haesleinhuepf April 2020GetTimeTracing Author: @haesleinhuepf April 2020GPUProperties Author: @haesleinhuepf April 2020GradientX Author: @haesleinhuepf 12 2018GradientY Author: @haesleinhuepf 12 2018GradientZ Author: @haesleinhuepf 12 2018Greater Author: @haesleinhuepf August 2019GreaterConstant Author: @haesleinhuepf August 2019GreaterOrEqual Author: @haesleinhuepf August 2019GreaterOrEqualConstant Author: @haesleinhuepf August 2019HasClassifiedInputOutput Help Author: @haesleinhuepf 12 2018Histogram Author: @haesleinhuepf December 2019Image2DToResultsTable Deprecated. ImageToStack Author: @haesleinhuepf February 2020InvalidateKernelCache Author: @haesleinhuepf 12 2018Invert Author: @haesleinhuepf 12 2018JaccardIndex Author: @haesleinhuepf July 2019LabelCentroidsToPointList LabelledSpotsToPointList LabelSpots LabelToMask Author: @haesleinhuepf August 2019LabelVoronoiOctagon Author: @haesleinhuepf April 2020LaplaceBox LaplaceDiamond ListAvailableGPUs Author: @haesleinhuepf September 2019LocalThreshold Author: @haesleinhuepf 12 2018Logarithm Based on net.haesleinhuepf.clij.macro.modules.Power.java Author: @haesleinhuepf December 2018 modified by: @phaub July 2019Mask Author: @haesleinhuepf 12 2018MaskLabel Author: @haesleinhuepf 12 2018MaskStackWithPlane Author: @haesleinhuepf 12 2018MatrixEqual Maximum2DBox Author: @haesleinhuepf 12 2018Maximum2DSphere Author: @haesleinhuepf 12 2018Maximum3DBox Author: @haesleinhuepf 12 2018Maximum3DSphere Author: @haesleinhuepf 12 2018MaximumImageAndScalar Author: @haesleinhuepf 12 2018MaximumImages Author: @haesleinhuepf 12 2018MaximumOctagon Author: @haesleinhuepf December 2019MaximumOfAllPixels Author: @haesleinhuepf December 2018MaximumOfMaskedPixels Author: @haesleinhuepf 12 2018MaximumOfTouchingNeighbors MaximumSliceBySliceSphere Author: @haesleinhuepf 12 2018MaximumXProjection Author: @haesleinhuepf December 2018MaximumYProjection Author: @haesleinhuepf December 2018MaximumZProjection Author: @haesleinhuepf December 2018MaximumZProjectionBounded Author: @haesleinhuepf December 2019Mean2DBox Author: @haesleinhuepf 12 2018Mean2DSphere Author: @haesleinhuepf December 2018Mean3DBox Author: @haesleinhuepf 12 2018Mean3DSphere Author: @haesleinhuepf 12 2018MeanClosestSpotDistance Author: @haesleinhuepf July 2019MeanOfAllPixels Author: @haesleinhuepf December 2018MeanOfMaskedPixels Author: @haesleinhuepf 12 2018MeanOfPixelsAboveThreshold Author: @haesleinhuepf 12 2018MeanOfTouchingNeighbors MeanSliceBySliceSphere Author: @haesleinhuepf 12 2018MeanSquaredError Author: @haesleinhuepf December 2018MeanXProjection Author: @haesleinhuepf June 2020MeanYProjection Author: @haesleinhuepf June 2020MeanZProjection Author: @haesleinhuepf December 2018MeanZProjectionBounded Author: @haesleinhuepf December 2019Median2DBox Author: @haesleinhuepf 12 2018Median2DSphere Author: @haesleinhuepf 12 2018Median3DBox Author: @haesleinhuepf 12 2018Median3DSphere Author: @haesleinhuepf 12 2018MedianOfTouchingNeighbors MedianSliceBySliceBox Author: @haesleinhuepf 12 2018MedianSliceBySliceSphere Author: @haesleinhuepf 12 2018MedianZProjection Author: @haesleinhuepf June 2019Minimum2DBox Author: @haesleinhuepf 12 2018Minimum2DSphere Author: @haesleinhuepf 12 2018Minimum3DBox Author: @haesleinhuepf 12 2018Minimum3DSphere Author: @haesleinhuepf 12 2018MinimumDistanceOfTouchingNeighbors MinimumImageAndScalar Author: @haesleinhuepf 12 2018MinimumImages Author: @haesleinhuepf 12 2018MinimumOctagon Author: @haesleinhuepf December 2019MinimumOfAllPixels Author: @haesleinhuepf December 2018MinimumOfMaskedPixels Author: @haesleinhuepf 12 2018MinimumOfTouchingNeighbors MinimumSliceBySliceSphere Author: @haesleinhuepf 12 2018MinimumXProjection Author: @haesleinhuepf June 2020MinimumYProjection Author: @haesleinhuepf June 2020MinimumZProjection Author: @haesleinhuepf December 2018MinimumZProjectionBounded Author: @haesleinhuepf December 2019MinimumZProjectionThresholdedBounded Author: @haesleinhuepf December 2019MultiplyImageAndCoordinate Author: @haesleinhuepf December 2018MultiplyImageAndScalar Author: @haesleinhuepf December 2018MultiplyImages Author: @haesleinhuepf 12 2018MultiplyImageStackWithScalars Author: @haesleinhuepf December 2018MultiplyMatrix Author: @haesleinhuepf August 2019MultiplyStackWithPlane Author: @haesleinhuepf December 2018NClosestDistances NClosestPoints NeighborsOfNeighbors Author: @haesleinhuepf May 2020NonzeroMaximumBox NonzeroMaximumDiamond NonzeroMinimumBox NonzeroMinimumDiamond NotEqual Author: @haesleinhuepf August 2019NotEqualConstant Author: @haesleinhuepf August 2019OnlyzeroOverwriteMaximumBox OnlyzeroOverwriteMaximumDiamond OpeningBox OpeningDiamond Paste2D Author: @haesleinhuepf December 2018Paste3D Author: @haesleinhuepf December 2018PointIndexListToMesh PointIndexListToMeshPointlistToLabelledSpots Author: @haesleinhuepf April 2020Power Author: @haesleinhuepf December 2018PowerImages Author: @haesleinhuepf August 2019Print Author: @haesleinhuepf March 2020 in BordeauxProcessableInTiles Pull ReleasePullAsROI PullBinary PullBinaryPullLabelsToROIList PullLabelsToROIManager PullString Author: @haesleinhuepf April 2020PullToCurrentSlice PullToCurrentSliceSelection PullToResultsTable Author: @haesleinhuepf April 2020PullToROIManager Push ReleasePushArray Author: @haesleinhuepf September 2019PushCurrentSelection ReleasePushCurrentSlice ReleasePushCurrentSliceSelection ReleasePushCurrentZStack ReleasePushResultsTable Author: @haesleinhuepf April 2020PushResultsTableColumn Author: @haesleinhuepf April 2020PushString Author: @haesleinhuepf April 2020ReduceStack Author: @haesleinhuepf May 2020Release ReleaseReplaceIntensities ReplaceIntensity ReplacePixelsIfZero Author: @haesleinhuepf June 2020ReportMemory Author: @haesleinhuepf 12 2018Resample Author: @haesleinhuepf 12 2018ResliceBottom Author: @haesleinhuepf 12 2018ResliceLeft Author: @haesleinhuepf 12 2018ResliceRadial ResliceRadialResliceRadialTop ResliceRadialResliceRight Author: @haesleinhuepf 12 2018ResliceTop Author: @haesleinhuepf 12 2018ResultsTableColumnToImage Author: @haesleinhuepf April 2020ResultsTableToImage2D Deprecated. Rotate2D Author: @haesleinhuepf 12 2018Rotate3D Author: @haesleinhuepf 12 2018RotateClockwise Author: @haesleinhuepf 12 2018RotateCounterClockwise Author: @haesleinhuepf 12 2018RotateLeft Deprecated. RotateRight Deprecated. SaveAsTIF Scale Deprecated. Scale2D Author: @haesleinhuepf 12 2018Scale3D Author: @haesleinhuepf 12 2018Set Author: @haesleinhuepf December 2018SetColumn Author: @haesleinhuepf December 2018SetImageBorders Author: @haesleinhuepf March 2020SetNonZeroPixelsToPixelIndex Author: @haesleinhuepf 12 2018SetPlane Author: @haesleinhuepf December 2018SetRampX Author: @haesleinhuepf February 2020SetRampY Author: @haesleinhuepf February 2020SetRampZ Author: @haesleinhuepf February 2020SetRandom Author: @haesleinhuepf March 2020SetRow Author: @haesleinhuepf December 2018SetWhereXequalsY Author: @haesleinhuepf December 2018SetWhereXgreaterThanY Author: @haesleinhuepf December 2018SetWhereXsmallerThanY Author: @haesleinhuepf December 2018ShortestDistances Smaller Author: @haesleinhuepf August 2019SmallerConstant Author: @haesleinhuepf August 2019SmallerOrEqual Author: @haesleinhuepf August 2019SmallerOrEqualConstant Author: @haesleinhuepf August 2019Sobel Author: @ruthhwj, @haesleinhuepf November 2019SorensenDiceCoefficient Author: @haesleinhuepf July 2019SpotsToPointList SquaredDifference Author: @haesleinhuepf June 2020StandardDeviationOfAllPixels Author: @haesleinhuepf September 2019StandardDeviationOfMaskedPixels Author: @haesleinhuepf September 2019StandardDeviationOfTouchingNeighbors StandardDeviationZProjection Author: @haesleinhuepf June 2019StartTimeTracing Author: @haesleinhuepf April 2020StatisticsOfBackgroundAndLabelledPixels Author: @haesleinhuepf April 2020StatisticsOfImage Author: @haesleinhuepf April 2020StatisticsOfLabelledPixels Author: @haesleinhuepf September 2019 in PragueStatisticsOfLabelledPixels.STATISTICS_ENTRY StopTimeTracing Author: @haesleinhuepf April 2020SubtractImageFromScalar Author: @haesleinhuepf 12 2018SubtractImages Author: @haesleinhuepf 12 2018SumImageSliceBySlice Author: @haesleinhuepf December 2018SumOfAllPixels Author: @haesleinhuepf December 2018SumXProjection Author: @haesleinhuepf December 2018SumYProjection Author: @haesleinhuepf December 2018SumZProjection Author: @haesleinhuepf December 2018Threshold Author: @haesleinhuepf December 2018ThresholdDefault ThresholdDefaultThresholdHuang ThresholdHuangThresholdIJ_IsoData ThresholdIJ_IsoDataThresholdIntermodes ThresholdIntermodesThresholdIsoData ThresholdIsoDataThresholdLi ThresholdLiThresholdMaxEntropy ThresholdMaxEntropyThresholdMean ThresholdMeanThresholdMinError ThresholdMinErrorThresholdMinimum ThresholdMinimumThresholdMoments ThresholdMomentsThresholdOtsu ThresholdOtsuThresholdPercentile ThresholdPercentileThresholdRenyiEntropy ThresholdRenyiEntropyThresholdShanbhag ThresholdShanbhagThresholdTriangle ThresholdTriangleThresholdYen ThresholdYenTopHatBox TopHatSphere TouchMatrixToAdjacencyMatrix Author: @haesleinhuepf April 2020TouchMatrixToMesh Author: @haesleinhuepf November 2019Translate2D Author: @haesleinhuepf 12 2018Translate3D Author: @haesleinhuepf 12 2018TransposeXY TransposeXZ TransposeYZ UndefinedToZero Author: @haesleinhuepf June 2020VarianceOfAllPixels Author: @haesleinhuepf September 2019VarianceOfMaskedPixels Author: @haesleinhuepf 12 2018VoronoiLabeling Author: @haesleinhuepf March 2020VoronoiOctagon Author: @haesleinhuepf March 2020Watershed Author: @haesleinhuepf December 2018WriteValuesToPositions Author: @haesleinhuepf June 2019