IImageProcessing Interface Reference

import "Imaris.idl";

Public Member Functions
HRESULT	AnisotropicDiffusionFilterChannel ([in] IDataSet *aDataSet,[in] ULONG aChannelIndex,[in] FLOAT aSigma)
HRESULT	AnisotropicDiffusionFilterDataSet ([in] IDataSet aDataSetIn,[in] FLOAT aSigma,[out, retval] IDataSet *aDataSetOut)
HRESULT	BaselineSubtractChannel ([in] IDataSet *aDataSet,[in] ULONG aChannelIndex,[in] FLOAT aBaseline)
HRESULT	BaselineSubtractDataSet ([in] IDataSet aDataSetIn,[in] FLOAT aBaseline,[out, retval] IDataSet *aDataSetOut)
HRESULT	CalculateTracks ([in] VARIANT aPositionsXYZ,[in] VARIANT aIndicesT,[in] VARIANT aRadii,[in] ULONG aAlgorithm,[in] FLOAT aMaximalDistance,[out] VARIANT aEdges,[out] VARIANT aRanges)
HRESULT	ContrastStretchChannel ([in] IDataSet *aDataSet,[in] ULONG aChannelIndex,[in] FLOAT aSourceA,[in] FLOAT aSourceB,[in] FLOAT aDestA,[in] FLOAT aDestB)
HRESULT	ContrastStretchDataSet ([in] IDataSet aDataSetIn,[in] FLOAT aSourceA,[in] FLOAT aSourceB,[in] FLOAT aDestA,[in] FLOAT aDestB,[out, retval] IDataSet *aDataSetOut)
HRESULT	DetectFilament ([in] IDataSet aDataSet,[in] ULONG aChannelIndex,[in] FLOAT aFilamentDiameter,[in] BOOL aPreprocess,[in] BOOL aPreserveEdges,[in] FLOAT aThresholdLow,[in] FLOAT aThresholdHigh,[in] BOOL aConnectiveBaseline,[in] BOOL aFillCavities,[in] FLOAT aMinimalBranchLengthRatio,[in] BOOL aDetectRootPoint,[out] VARIANT aPositionsXYZ,[out] VARIANT aRadii,[out] VARIANT aEdges)
HRESULT	DetectIsoSurface ([in] IDataSet aDataSet,[in] ULONG aChannelIndex,[in] ULONG aTimeIndex,[in] FLOAT aThreshold,[in] FLOAT aUpperThreshold,[in] BOOL aApplyUpperThreshold,[in] ULONG aSizeX,[in] ULONG aSizeY,[in] ULONG aSizeZ,[in] FLOAT aGaussianFilterWidth,[in] BOOL aApplyGaussianFilter,[in] BOOL aCloseObjects,[out] VARIANT aVertices,[out] VARIANT aTriangles,[out] VARIANT aNormals)
HRESULT	DetectSpots ([in] IDataSet aDataSet,[in] ULONG aChannelIndex,[in] FLOAT aSpotDiameter,[in] BOOL aBackgroundSubtraction,[in] BOOL aMultiScale,[in] FLOAT aMaximumDiameter,[in] FLOAT aThreshold,[out] VARIANT aPositionsXYZ,[out] VARIANT aIndicesT,[out] VARIANT aRadii)
HRESULT	DetectSpots2 ([in] IDataSet aDataSet,[in] VARIANT aRegionsOfInterest,[in] ULONG aChannelIndex,[in] FLOAT aEstimateDiameter,[in] BOOL aSubtractBackground,[in] BSTR aSpotFiltersString,[out, retval] ISpots *aSpots)
HRESULT	DetectSpotsRegionGrowing ([in] IDataSet aDataSet,[in] VARIANT aRegionsOfInterest,[in] ULONG aChannelIndex,[in] FLOAT aEstimateDiameter,[in] BOOL aSubtractBackground,[in] BSTR aSpotFiltersString,[in] BOOL aRegionsFromLocalContrast,[in] BOOL aRegionsThresholdAutomatic,[in] FLOAT aRegionsThresholdManual,[in] BOOL aRegionsSpotsDiameterFromVolume,[in] BOOL aRegionsCreateChannel,[out, retval] ISpots *aSpots)
HRESULT	DetectSpotsWithRegions ([in] IDataSet aDataSet,[in] ULONG aChannelIndex,[in] FLOAT aSpotDiameter,[in] BOOL aBackgroundSubtraction,[in] FLOAT aSpotsThreshold,[in] BOOL aInterpolatePositions,[in] ULONG aRegionMethod,[in] FLOAT aRegionsThreshold,[in] BOOL aRemoveOverlappingSpots,[in] ULONG aRadiusFrom,[out] VARIANT aPositionsXYZ,[out] VARIANT aIndicesT,[out] VARIANT aRadii)
HRESULT	DetectSurfaces ([in] IDataSet aDataSet,[in] VARIANT aRegionsOfInterest,[in] ULONG aChannelIndex,[in] FLOAT aSmoothFilterWidth,[in] FLOAT aLocalContrastFilterWidth,[in] BOOL aIntensityThresholdAutomatic,[in] FLOAT aIntensityThresholdManual,[in] BSTR aSurfaceFiltersString,[out, retval] ISurfaces *aSurfaces)
HRESULT	DetectSurfacesRegionGrowing ([in] IDataSet aDataSet,[in] VARIANT aRegionsOfInterest,[in] ULONG aChannelIndex,[in] FLOAT aSmoothFilterWidth,[in] FLOAT aLocalContrastFilterWidth,[in] BOOL aIntensityThresholdAutomatic,[in] FLOAT aIntensityThresholdManual,[in] FLOAT aSeedsEstimateDiameter,[in] BOOL aSeedsSubtractBackground,[in] BSTR aSeedsFiltersString,[in] BSTR aSurfaceFiltersString,[out, retval] ISurfaces *aSurfaces)
HRESULT	DistanceTransformChannel ([in] IDataSet *aDataSet,[in] ULONG aChannelIndex,[in] FLOAT aBaseline,[in] BOOL aInside)
HRESULT	DistanceTransformDataSet ([in] IDataSet aDataSetIn,[in] FLOAT aBaseline,[in] BOOL aInside,[out, retval] IDataSet *aDataSetOut)
HRESULT	EqualizeHistogramChannel ([in] IDataSet *aDataSet,[in] ULONG aChannelIndex,[in] FLOAT aOldValueLow,[in] FLOAT aOldValueHigh,[in] FLOAT aNewValueLow,[in] FLOAT aNewValueHigh)
HRESULT	EqualizeHistogramDataSet ([in] IDataSet aDataSetIn,[in] FLOAT aOldValueLow,[in] FLOAT aOldValueHigh,[in] FLOAT aNewValueLow,[in] FLOAT aNewValueHigh,[out, retval] IDataSet *aDataSetOut)
HRESULT	FastMarchingArrivalTimeChannel ([in] IDataSet *aDataSet,[in] ULONG aChannelIndex,[in] VARIANT aStartPositions)
HRESULT	FastMarchingArrivalTimeDataSet ([in] IDataSet aDataSetIn,[in] VARIANT aStartPositions,[out, retval] IDataSet *aDataSetOut)
HRESULT	Flip3DChannel ([in] IDataSet *aDataSet,[in] ULONG aChannelIndex,[in] ULONG aDimension)
HRESULT	Flip3DDataSet ([in] IDataSet aDataSetIn,[in] ULONG aDimension,[out, retval] IDataSet *aDataSetOut)
HRESULT	GammaCorrectChannel ([in] IDataSet *aDataSet,[in] ULONG aChannelIndex,[in] FLOAT aGammaValue,[in] FLOAT aMaxValue)
HRESULT	GammaCorrectDataSet ([in] IDataSet aDataSetIn,[in] FLOAT aGammaValue,[in] FLOAT aMaxValue,[out, retval] IDataSet *aDataSetOut)
HRESULT	GaussFilterChannel ([in] IDataSet *aDataSet,[in] ULONG aChannelIndex,[in] FLOAT aSigma)
HRESULT	GaussFilterDataSet ([in] IDataSet aDataSetIn,[in] FLOAT aSigma,[out, retval] IDataSet *aDataSetOut)
HRESULT	GaussianDerivativeChannel ([in] IDataSet *aDataSet,[in] ULONG aChannelIndex,[in] FLOAT aSigma,[in] VARIANT aDerivativeOrder)
HRESULT	GaussianDerivativeDataSet ([in] IDataSet aDataSetIn,[in] FLOAT aSigma,[in] VARIANT aDerivativeOrder,[out, retval] IDataSet *aDataSetOut)
HRESULT	InvertChannel ([in] IDataSet *aDataSet,[in] ULONG aChannelIndex)
HRESULT	InvertDataSet ([in] IDataSet aDataSetIn,[out, retval] IDataSet *aDataSetOut)
HRESULT	MedianFilterChannel ([in] IDataSet *aDataSet,[in] ULONG aChannelIndex,[in] VARIANT aSize)
HRESULT	MedianFilterDataSet ([in] IDataSet aDataSetIn,[in] VARIANT aSize,[out, retval] IDataSet *aDataSetOut)
HRESULT	NormalizeLayersChannel ([in] IDataSet *aDataSet,[in] ULONG aChannelIndex)
HRESULT	NormalizeLayersDataSet ([in] IDataSet aDataSetIn,[out, retval] IDataSet *aDataSetOut)
HRESULT	Shift3DChannel ([in] IDataSet *aDataSet,[in] ULONG aChannelIndex,[in] LONG aShiftX,[in] LONG aShiftY,[in] LONG aShiftZ)
HRESULT	Shift3DDataSet ([in] IDataSet aDataSetIn,[in] LONG aShiftX,[in] LONG aShiftY,[in] LONG aShiftZ,[out, retval] IDataSet *aDataSetOut)
HRESULT	ShortestPath ([in] IDataSet aDataSet,[in] ULONG aTimeIndex,[in] ULONG aChannelIndex,[in] VARIANT aStartPositions,[out, retval] VARIANT aPositionsXYZ)
HRESULT	SubtractBackgroundChannel ([in] IDataSet *aDataSet,[in] ULONG aChannelIndex,[in] FLOAT aSigma)
HRESULT	SubtractBackgroundDataSet ([in] IDataSet aDataSetIn,[in] FLOAT aSigma,[out, retval] IDataSet *aDataSetOut)
HRESULT	ThresholdBothChannel ([in] IDataSet *aDataSet,[in] ULONG aChannelIndex,[in] FLOAT aThreshold,[in] FLOAT aNewValueLow,[in] FLOAT aNewValueHigh)
HRESULT	ThresholdBothDataSet ([in] IDataSet aDataSetIn,[in] FLOAT aThreshold,[in] FLOAT aNewValueLow,[in] FLOAT aNewValueHigh,[out, retval] IDataSet *aDataSetOut)
HRESULT	ThresholdChannel ([in] IDataSet *aDataSet,[in] ULONG aChannelIndex,[in] FLOAT aThreshold,[in] FLOAT aNewValue)
HRESULT	ThresholdDataSet ([in] IDataSet aDataSetIn,[in] FLOAT aThreshold,[in] FLOAT aNewValue,[out, retval] IDataSet *aDataSetOut)
HRESULT	ThresholdUpperChannel ([in] IDataSet *aDataSet,[in] ULONG aChannelIndex,[in] FLOAT aThreshold,[in] FLOAT aNewValue)
HRESULT	ThresholdUpperDataSet ([in] IDataSet aDataSetIn,[in] FLOAT aThreshold,[in] FLOAT aNewValue,[out, retval] IDataSet *aDataSetOut)
HRESULT	TrackSpotsAutoregressiveMotion ([in] ISpots aSpots,[in] FLOAT aMaximalDistance,[in] INT aGapSize,[in] BSTR aTrackFiltersString,[out, retval] ISpots *aTrackedSpots)
HRESULT	TrackSpotsAutoregressiveMotionExpert ([in] ISpots aSpots,[in] FLOAT aMaximalDistance,[in] INT aGapSize,[in] FLOAT aIntensityWeight,[in] BSTR aTrackFiltersString,[out, retval] ISpots *aTrackedSpots)
HRESULT	TrackSpotsBrownianMotion ([in] ISpots aSpots,[in] FLOAT aMaximalDistance,[in] INT aGapSize,[in] BSTR aTrackFiltersString,[out, retval] ISpots *aTrackedSpots)
HRESULT	TrackSpotsConnectedComponents ([in] ISpots aSpots,[in] BSTR aTrackFiltersString,[out, retval] ISpots *aTrackedSpots)
HRESULT	TrackSurfacesAutoregressiveMotion ([in] ISurfaces aSurfaces,[in] FLOAT aMaximalDistance,[in] INT aGapSize,[in] BSTR aTrackFiltersString,[out, retval] ISurfaces *aTrackedSurfaces)
HRESULT	TrackSurfacesAutoregressiveMotionExpert ([in] ISurfaces aSurfaces,[in] FLOAT aMaximalDistance,[in] INT aGapSize,[in] FLOAT aIntensityWeight,[in] BSTR aTrackFiltersString,[out, retval] ISurfaces *aTrackedSurfaces)
HRESULT	TrackSurfacesBrownianMotion ([in] ISurfaces aSurfaces,[in] FLOAT aMaximalDistance,[in] INT aGapSize,[in] BSTR aTrackFiltersString,[out, retval] ISurfaces *aTrackedSurfaces)
HRESULT	TrackSurfacesConnectedComponents ([in] ISurfaces aSurfaces,[in] BSTR aTrackFiltersString,[out, retval] ISurfaces *aTrackedSurfaces)

Detailed Description

This class exports the Imaris image processing algorithms to be used through the ImarisXT interface.

Member Function Documentation

HRESULT IImageProcessing::AnisotropicDiffusionFilterChannel	(	[in] IDataSet *	aDataSet,
		[in] ULONG	aChannelIndex,
		[in] FLOAT	aSigma
	)

Apply an anisotropic diffusion filter to the selected channel.

Parameters:

	aDataSet	[in], [out] The dataset
	aChannelIndex	[in] Index of channel to be processed
	aSigma	[in] The width of the filter (float)

 %% The following MATLAB code applies an anisotropic diffusion filter to the selected channel.
 %% Caution: this will directly replace the current dataset with the filtered one in vImarisApplication.mDataSet.
 aDataSetIn=vImarisApplication.mDataSet; %% Current dataset
 aChannelIndex=0;
 aSigma=2.5;
 vImarisApplication.mImageProcessing.AnisotropicDiffusionFilterChannel(aDataSetIn,aChannelIndex,aSigma);

HRESULT IImageProcessing::AnisotropicDiffusionFilterDataSet	(	[in] IDataSet *	aDataSetIn,
		[in] FLOAT	aSigma,
		[out, retval] IDataSet **	aDataSetOut
	)

Apply an anisotropic diffusion filter to the whole dataset.

Parameters:

	aDataSetIn	[in] The source dataset
	aSigma	[in] The width of the filter (float)
	aDataSetOut	[out] The destination dataset

 %% The following MATLAB code applies an anisotropic diffusion filter to the whole dataset.
 aDataSetIn=vImarisApplication.mDataSet; %% Current dataset
 aSigma=2.5;
 aDataSetOut=vImarisApplication.mImageProcessing.AnisotropicDiffusionFilterDataSet(aDataSetIn,aSigma);
 %% To replace current dataset with the filtered one, use the following:
 vImarisApplication.mDataSet=aDataSetOut;

HRESULT IImageProcessing::BaselineSubtractChannel	(	[in] IDataSet *	aDataSet,
		[in] ULONG	aChannelIndex,
		[in] FLOAT	aBaseline
	)

Baseline subtraction. A constant value is subtracted from the selected channel.

Parameters:

	aDataSet	[in], [out] The dataset
	aChannelIndex	[in] Index of channel to be processed.
	aBaseline	[in] The baseline value for each channel.

 %% The following MATLAB code applies in-place baseline subtraction to the selected channel.
 %% Caution: this will directly replace the current dataset with the baseline-subtracted one in vImarisApplication.mDataSet.
 aDataSetIn=vImarisApplication.mDataSet; %% Current dataset
 aChannelIndex=0;
 aBaseline=100;
 vImarisApplication.mImageProcessing.BaselineSubtractChannel(aDataSetIn,aChannelIndex,aBaseline);

HRESULT IImageProcessing::BaselineSubtractDataSet	(	[in] IDataSet *	aDataSetIn,
		[in] FLOAT	aBaseline,
		[out, retval] IDataSet **	aDataSetOut
	)

Baseline subtraction. A constant value is subtracted from the dataset.

Parameters:

	aDataSetIn	The source dataset
	aBaseline	The baseline value for each channel.
	aDataSetOut	The destination dataset

 %% The following MATLAB code applies baseline subtraction to the whole dataset
 aDataSetIn=vImarisApplication.mDataSet; %% Current dataset
 aBaseline=100;
 aDataSetOut=vImarisApplication.mImageProcessing.BaselineSubtractDataSet(aDataSetIn,aBaseline);
 %% To replace current dataset with the baseline-subtracted one, use the following:
 vImarisApplication.mDataSet=aDataSetOut;

HRESULT IImageProcessing::CalculateTracks	(	[in] VARIANT	aPositionsXYZ,
		[in] VARIANT	aIndicesT,
		[in] VARIANT	aRadii,
		[in] ULONG	aAlgorithm,
		[in] FLOAT	aMaximalDistance,
		[out] VARIANT *	aEdges,
		[out] VARIANT *	aRanges
	)

Calculate Tracks. OBSOLETE: Use TrackSpots instead.

Parameters:

	aPositionsXYZ	[in] 2D array of positions [x y z]N
	aIndicesT	[in] 1D array of time points
	aRadii	[in] 1D array of radii
	aAlgorithm	[in] Algorithm index
	aMaximalDistance	[in] Algorithm parameter
	aEdges	[out] 2D array of positions (N x 2)
	aRanges	[out] 2D array of delimiters (N x 2) = N x (number of spots; number of edges) %% The following MATLAB code calculates tracks for the selected spots... --> see CreateTracks.m!! %% ... and adds the tracks to the imaris surpass scene. --> see CreateTracks.m!!

HRESULT IImageProcessing::ContrastStretchChannel	(	[in] IDataSet *	aDataSet,
		[in] ULONG	aChannelIndex,
		[in] FLOAT	aSourceA,
		[in] FLOAT	aSourceB,
		[in] FLOAT	aDestA,
		[in] FLOAT	aDestB
	)

Contrast stretch in the selected channel.

Parameters:

	aDataSet	[in], [out] The dataset (IN/OUT)
	aChannelIndex	[in] Index of channel to be processed.
	aSourceA	[in] Intensity, will be mapped to aDestA (float)
	aSourceB	[in] Intensity, will be mapped to aDestB (float)
	aDestA	[in] Intensity, mapped by aSourceA (float)
	aDestB	[in] Intensity, mapped by aSourceB (float)

 %% The following MATLAB code stretches the intensities in the selected channel.
 %% Caution: this will directly replace the current dataset with the filtered one in vImarisApplication.mDataSet.
 aDataSetIn=vImarisApplication.mDataSet; %% Current dataset
 aChannelIndex=0;
 aSourceA=100;
 aSourceB=175;
 aDestA=0;
 aDestB=255;
 vImarisApplication.mImageProcessing.ContrastStretchChannel(aDataSetIn,aChannelIndex,aSourceA,aSourceB,aDestA,aDestB);

HRESULT IImageProcessing::ContrastStretchDataSet	(	[in] IDataSet *	aDataSetIn,
		[in] FLOAT	aSourceA,
		[in] FLOAT	aSourceB,
		[in] FLOAT	aDestA,
		[in] FLOAT	aDestB,
		[out, retval] IDataSet **	aDataSetOut
	)

Contrast stretch in the whole dataset.

Parameters:

	aDataSetIn	[in] The source dataset
	aSourceA	[in] Intensity, will be mapped to aDestA (float)
	aSourceB	[in] Intensity, will be mapped to aDestB (float)
	aDestA	[in] Intensity, mapped by aSourceA (float)
	aDestB	[in] Intensity, mapped by aSourceB (float)
	aDataSetOut	[out] The destination dataset

 %% The following MATLAB code stretches the intensities in the whole dataset.
 aDataSetIn=vImarisApplication.mDataSet; %% Current dataset
 aSourceA=100;
 aSourceB=175;
 aDestA=0;
 aDestB=255;
 aDataSetOut=vImarisApplication.mImageProcessing.ContrastStretchDataSet(aDataSetIn,aSourceA,aSourceB,aDestA,aDestB);
 %% To replace current dataset with the stretched one, use the following:
 vImarisApplication.mDataSet=aDataSetOut;

HRESULT IImageProcessing::DetectFilament	(	[in] IDataSet *	aDataSet,
		[in] ULONG	aChannelIndex,
		[in] FLOAT	aFilamentDiameter,
		[in] BOOL	aPreprocess,
		[in] BOOL	aPreserveEdges,
		[in] FLOAT	aThresholdLow,
		[in] FLOAT	aThresholdHigh,
		[in] BOOL	aConnectiveBaseline,
		[in] BOOL	aFillCavities,
		[in] FLOAT	aMinimalBranchLengthRatio,
		[in] BOOL	aDetectRootPoint,
		[out] VARIANT *	aPositionsXYZ,
		[out] VARIANT *	aRadii,
		[out] VARIANT *	aEdges
	)

Detect filament: Not yet implemented!

Parameters:

	aDataSet	[in] Not yet implemented!
	aChannelIndex	[in] Not yet implemented!
	aFilamentDiameter	[in] Not yet implemented!
	aPreprocess	[in] Not yet implemented!
	aPreserveEdges	[in] Not yet implemented!
	aThresholdLow	[in] Not yet implemented!
	aThresholdHigh	[in] Not yet implemented!
	aConnectiveBaseline	[in] Not yet implemented!
	aFillCavities	[in] Not yet implemented!
	aMinimalBranchLengthRatio	[in] Not yet implemented!
	aDetectRootPoint	[in] Not yet implemented!
	aPositionsXYZ	[out] Not yet implemented!
	aRadii	[out] Not yet implemented!
	aEdges	[out] Not yet implemented!

HRESULT IImageProcessing::DetectIsoSurface	(	[in] IDataSet *	aDataSet,
		[in] ULONG	aChannelIndex,
		[in] ULONG	aTimeIndex,
		[in] FLOAT	aThreshold,
		[in] FLOAT	aUpperThreshold,
		[in] BOOL	aApplyUpperThreshold,
		[in] ULONG	aSizeX,
		[in] ULONG	aSizeY,
		[in] ULONG	aSizeZ,
		[in] FLOAT	aGaussianFilterWidth,
		[in] BOOL	aApplyGaussianFilter,
		[in] BOOL	aCloseObjects,
		[out] VARIANT *	aVertices,
		[out] VARIANT *	aTriangles,
		[out] VARIANT *	aNormals
	)

Computes an Iso Surface. OBSOLETE: Use DetectSurfaces instead.

Parameters:

	aDataSet	[in] The source dataset
	aChannelIndex	[in] Index of channel to be processed
	aTimeIndex	[in] Time index to be processed
	aThreshold	[in] Intensity threshold (float)
	aUpperThreshold	[in] Upper intensity threshold (float)
	aApplyUpperThreshold	[in] Toggles upper thresholding (boolean)
	aSizeX	[in] Size (X)
	aSizeY	[in] Size (Y)
	aSizeZ	[in] Size (Z)
	aGaussianFilterWidth	[in] Width of the Gaussian filter (float)
	aApplyGaussianFilter	[in] Toggles Gaussian filtering (boolean)
	aCloseObjects	[in] Toggles objects closure boolean)
	aVertices	[out] 2D-array [x y z]N containing positions of vertices
	aTriangles	[out] 2D-array (N x 3) containing indices to the vertices array
	aNormals	[out] 2D-array [x y z]N containing orientations of normals

 %% The following MATLAB code computes an isosurface for the selected channel.
 aDataSet=vImarisApplication.mDataSet; %% Current dataset
 aChannelIndex=0;
 aTimeIndex=0;
 aThreshold=200;
 aUpperThreshold=240;
 aApplyUpperThreshold=1;
 aSizeX=255;
 aSizeY=255;
 aSizeZ=100;
 aGaussianFilterWidth=1.5;
 aApplyGaussianFilter=1;
 aCloseObjects=1;
 [aPositionsXYZ,aIndicesT,aRadii]=vImarisApplication.mImageProcessing.DetectIsoSurface(aDataSet,aChannelIndex,aTimeIndex,aThreshold,aUpperThreshold,aApplyUpperThreshold,aSizeX,aSizeY,aSizeZ,aGaussianFilterWidth,aApplyGaussianFilter,aCloseObjects);

HRESULT IImageProcessing::DetectSpots	(	[in] IDataSet *	aDataSet,
		[in] ULONG	aChannelIndex,
		[in] FLOAT	aSpotDiameter,
		[in] BOOL	aBackgroundSubtraction,
		[in] BOOL	aMultiScale,
		[in] FLOAT	aMaximumDiameter,
		[in] FLOAT	aThreshold,
		[out] VARIANT *	aPositionsXYZ,
		[out] VARIANT *	aIndicesT,
		[out] VARIANT *	aRadii
	)

Computes spots (local intensity maxima). OBSOLETE: Use DetectSpots2 instead.

Parameters:

	aDataSet	[in] The source dataset
	aChannelIndex	[in] Index of channel to be processed.
	aSpotDiameter	[in] Expected spot diameter (float)
	aBackgroundSubtraction	[in] Toggles background substraction (boolean)
	aMultiScale	[in] Toggles multiscale filtering (boolean)
	aMaximumDiameter	[in] Maximum allowed spot diameter (float)
	aThreshold	[in] Intensity threshold (float)
	aPositionsXYZ	[out] 2D array of positions [x y z]N
	aIndicesT	[out] 1D array of time points
	aRadii	[out] 1D array of spot radii

 %% The following MATLAB code detects spots for the selected channel.
 aDataSet=vImarisApplication.mDataSet; %% Current dataset
 aChannelIndex=0;
 aSpotDiameter=0.500;
 aBackgroundSubtraction=1;
 aMultiScale=1;
 aMaximumDiameter=1.500;
 aThreshold=100;
 [aPositionsXYZ,aIndicesT,aRadii]=vImarisApplication.mImageProcessing.DetectSpots(aDataSet,aChannelIndex,aSpotDiameter,aBackgroundSubtraction,aMultiScale,aMaximumDiameter,aThreshold);

HRESULT IImageProcessing::DetectSpots2	(	[in] IDataSet *	aDataSet,
		[in] VARIANT	aRegionsOfInterest,
		[in] ULONG	aChannelIndex,
		[in] FLOAT	aEstimateDiameter,
		[in] BOOL	aSubtractBackground,
		[in] BSTR	aSpotFiltersString,
		[out, retval] ISpots **	aSpots
	)

Replaces DetectSpots, implemented for bpPointsViewer.

aRegionsOfInterest is a Nx8 matrix with the Rois extends [vMinX, vMinY, vMinZ, vMinT, vMaxX, vMaxY, vMaxZ, vMaxT]. Process entire image if aRegionsOfInterest is empty. Example of aSpotFiltersString: '"Position X" above 30.000 um "Intensity Center Ch=1" above automatic threshold'

HRESULT IImageProcessing::DetectSpotsRegionGrowing	(	[in] IDataSet *	aDataSet,
		[in] VARIANT	aRegionsOfInterest,
		[in] ULONG	aChannelIndex,
		[in] FLOAT	aEstimateDiameter,
		[in] BOOL	aSubtractBackground,
		[in] BSTR	aSpotFiltersString,
		[in] BOOL	aRegionsFromLocalContrast,
		[in] BOOL	aRegionsThresholdAutomatic,
		[in] FLOAT	aRegionsThresholdManual,
		[in] BOOL	aRegionsSpotsDiameterFromVolume,
		[in] BOOL	aRegionsCreateChannel,
		[out, retval] ISpots **	aSpots
	)

Replaces DetectSpotsWithRegions, implemented for bpPointsViewer.

aRegionsOfInterest is a Nx8 matrix with the Rois extends. [vMinX, vMinY, vMinZ, vMinT, vMaxX, vMaxY, vMaxZ, vMaxT]. Process entire image if aRegionsOfInterest is empty. Example of aSpotFiltersString: '"Position X" above 30.000 um "Intensity Center Ch=1" above automatic threshold'

If aRegionsFromLocalContrast is false, regions are computed from channel intensity. If aRegionsThresholdAutomatic is true, aRegionsThresholdManual is ignored. If aRegionsSpotsDiameterFromVolume is false, spots diameter is equal to region border distance.

HRESULT IImageProcessing::DetectSpotsWithRegions	(	[in] IDataSet *	aDataSet,
		[in] ULONG	aChannelIndex,
		[in] FLOAT	aSpotDiameter,
		[in] BOOL	aBackgroundSubtraction,
		[in] FLOAT	aSpotsThreshold,
		[in] BOOL	aInterpolatePositions,
		[in] ULONG	aRegionMethod,
		[in] FLOAT	aRegionsThreshold,
		[in] BOOL	aRemoveOverlappingSpots,
		[in] ULONG	aRadiusFrom,
		[out] VARIANT *	aPositionsXYZ,
		[out] VARIANT *	aIndicesT,
		[out] VARIANT *	aRadii
	)

Computes spots (local intensity maxima).

Parameters:

	aDataSet	[in] The source dataset
	aChannelIndex	[in] Index of channel to be processed
	aSpotDiameter	[in] Expected spot diameter (float)
	aBackgroundSubtraction	[in] Toggles background substraction (boolean)
	aSpotsThreshold	[in] Intensity spots threshold (float)
	aInterpolatePositions	[in] Interpolate spots positions (bool)
	aRegionMethod	[in] Region detection method index (int)
	aRegionsThreshold	[in] Intensity regions threshold (float)
	aRemoveOverlappingSpots	[in] Toggles Remove Overlapping Spots
	aRadiusFrom	[in] Spots radii computation method (int)
	aPositionsXYZ	[out] 2D array of positions [x y z]N
	aIndicesT	[out] 1D array of time points
	aRadii	[out] 1D array of spot radii

 %% The following MATLAB code detects spots for the selected channel...
 aDataSet = vImarisApplication.mDataSet; %% Current dataset
 aChannelIndex = 0;
 aSpotDiameter = 2;
 aBackgroundSubtraction = 1;
 aSpotsThreshold = 0.5;
 aInterpolatePositions = 1;
 aRegionMethod = 0;
 aRegionsThreshold = 30;
 aRemoveOverlappingSpots = 1;
 aSpotsModel = 1;
 [aPositionsXYZ,aIndicesT,aRadii] = vImarisApplication.mImageProcessing.DetectSpotsWithRegions( ...
     aDataSet,aChannelIndex,aSpotDiameter,aBackgroundSubtraction,aSpotsThreshold, ...
     aInterpolatePositions,aRegionMethod,aRegionsThreshold,aRemoveOverlappingSpots,aSpotsModel);
 %% ... and adds the detected spots to the imaris surpass scene.
 vSpots = vImarisApplication.mFactory.CreateSpots;
 vSpots.Set(aPositionsXYZ,aIndicesT,aRadii);
 vImarisApplication.mSurpassScene.AddChild(vSpots);

HRESULT IImageProcessing::DetectSurfaces	(	[in] IDataSet *	aDataSet,
		[in] VARIANT	aRegionsOfInterest,
		[in] ULONG	aChannelIndex,
		[in] FLOAT	aSmoothFilterWidth,
		[in] FLOAT	aLocalContrastFilterWidth,
		[in] BOOL	aIntensityThresholdAutomatic,
		[in] FLOAT	aIntensityThresholdManual,
		[in] BSTR	aSurfaceFiltersString,
		[out, retval] ISurfaces **	aSurfaces
	)

Replaces DetectIsoSurface, implemented for bpSurfacesViewer.

aRegionsOfInterest is a Nx8 matrix with the Rois extends [vMinX, vMinY, vMinZ, vMinT, vMaxX, vMaxY, vMaxZ, vMaxT]. Process entire image if aRegionsOfInterest is empty. Example of aSurfaceFiltersString: '"Volume" above automatic threshold' If aSmoothFilterWidth is equal to zero, smoothing is disabled. If aLocalContrastFilterWidth is equal to zero, local contrast is disabled. If aIntensityThresholdAutomatic is true, aIntensityThresholdManual is ignored.

HRESULT IImageProcessing::DetectSurfacesRegionGrowing	(	[in] IDataSet *	aDataSet,
		[in] VARIANT	aRegionsOfInterest,
		[in] ULONG	aChannelIndex,
		[in] FLOAT	aSmoothFilterWidth,
		[in] FLOAT	aLocalContrastFilterWidth,
		[in] BOOL	aIntensityThresholdAutomatic,
		[in] FLOAT	aIntensityThresholdManual,
		[in] FLOAT	aSeedsEstimateDiameter,
		[in] BOOL	aSeedsSubtractBackground,
		[in] BSTR	aSeedsFiltersString,
		[in] BSTR	aSurfaceFiltersString,
		[out, retval] ISurfaces **	aSurfaces
	)

Implemented for bpSurfacesViewer.

aRegionsOfInterest is a Nx8 matrix with the Rois extends. [vMinX, vMinY, vMinZ, vMinT, vMaxX, vMaxY, vMaxZ, vMaxT]. Process entire image if aRegionsOfInterest is empty. Example of aSurfaceFiltersString: '"Volume" above automatic threshold' If aSmoothFilterWidth is equal to zero, smoothing is disabled. If aLocalContrastFilterWidth is equal to zero, local contrast is disabled. If aIntensityThresholdAutomatic is true, aIntensityThresholdManual is ignored.

Example of aSeedsFiltersString: '"Quality" above 7.000'

HRESULT IImageProcessing::DistanceTransformChannel	(	[in] IDataSet *	aDataSet,
		[in] ULONG	aChannelIndex,
		[in] FLOAT	aBaseline,
		[in] BOOL	aInside
	)

Distance transform.

Within the regions with intensity greater than threshold, the distance of each voxel to the border of the region is computed. The distance is computed using a Chamfer metric (termed "quasi-euclidean" in Matlab). All voxels where original intensity is less than threshold are set to zero.

Parameters:

	aDataSet	The data set (IN/OUT)
	aChannelIndex	The channels to which the baseline subtraction is applied.
	aBaseline	The baseline value for each channel.
	aInside	true for inside, false for outside.

 %% The following MATLAB code applies in-place baseline subtraction to the selected channel.
 %% Caution: this will directly replace the current dataset with the baseline-subtracted one in vImarisApplication.mDataSet.
 aDataSetIn=vImarisApplication.mDataSet; %% Current dataset
 aChannelIndex=0;
 aBaseline=100;
 vImarisApplication.mImageProcessing.DistanceTransformChannel(aDataSetIn,aChannelIndex,aBaseline);

HRESULT IImageProcessing::DistanceTransformDataSet	(	[in] IDataSet *	aDataSetIn,
		[in] FLOAT	aBaseline,
		[in] BOOL	aInside,
		[out, retval] IDataSet **	aDataSetOut
	)

Distance transform.

Within the regions with intensity greater than threshold, the distance of each voxel to the border of the region is computed. The distance is computed using a Chamfer metric (termed "quasi-euclidean" in Matlab). All voxels where original intensity is less than threshold are set to zero.

Parameters:

	aDataSetIn	The data set (IN)
	aBaseline	The baseline value for each channel.
	aInside	true for inside, false for outside.
	aDataSetOut	The data set (OUT)

 %% The following MATLAB code applies baseline subtraction to the whole dataset
 aDataSetIn=vImarisApplication.mDataSet; %% Current dataset
 aBaseline=100;
 aDataSetOut=vImarisApplication.mImageProcessing.DistanceTransformDataSet(aDataSetIn,aBaseline);
 %% To replace current dataset with the baseline-subtracted one, use the following:
 vImarisApplication.mDataSet=aDataSetOut;

HRESULT IImageProcessing::EqualizeHistogramChannel	(	[in] IDataSet *	aDataSet,
		[in] ULONG	aChannelIndex,
		[in] FLOAT	aOldValueLow,
		[in] FLOAT	aOldValueHigh,
		[in] FLOAT	aNewValueLow,
		[in] FLOAT	aNewValueHigh
	)

Apply histogram equalization to the selected channel.

Parameters:

	aDataSet	[in], [out] The dataset
	aChannelIndex	[in] Index of channel to be processed.
	aOldValueLow	[in] Lower bound of intensity window. Intensites below this value will be set to aNewValueLow.
	aOldValueHigh	[in] Upper bound of itensity window. Intensites above this value will be set to aNewValueHigh.
	aNewValueLow	[in] Minimum intensity of output data set.
	aNewValueHigh	[in] Maximum intensity of output data set.

 %% The following MATLAB code applies a user-defined histogram equalization to the selected channel.
 %% Caution: this will directly replace the current dataset with the equalized one in vImarisApplication.mDataSet.
 aDataSetIn=vImarisApplication.mDataSet; %% Current dataset
 aOldValueLow=0;
 aOldValueHigh=194.921005
 aNewValueLow=0;
 aNewValueHigh=255;
 vImarisApplication.mImageProcessing.EqualizeHistogramChannel(aDataSetIn,aChannelIndex,aOldValueLow,aOldValueHigh,aNewValueLow,aNewValueHigh);

HRESULT IImageProcessing::EqualizeHistogramDataSet	(	[in] IDataSet *	aDataSetIn,
		[in] FLOAT	aOldValueLow,
		[in] FLOAT	aOldValueHigh,
		[in] FLOAT	aNewValueLow,
		[in] FLOAT	aNewValueHigh,
		[out, retval] IDataSet **	aDataSetOut
	)

Apply a histogram equalization to the whole dataset.

Parameters:

	aDataSetIn	[in] The source dataset
	aOldValueLow	[in] Lower bound of intensity window. Intensites below this value will be set to aNewValueLow.
	aOldValueHigh	[in] Upper bound of itensity window. Intensites above this value will be set to aNewValueHigh.
	aNewValueLow	[in] Minimum intensity of output data set.
	aNewValueHigh	[in] Maximum intensity of output data set.
	aDataSetOut	[out] The equalized dataset

 %% The following MATLAB code applies user-defined histogram equalization to the selected channel.
 aDataSetIn=vImarisApplication.mDataSet; %% Current dataset
 aOldValueLow=0;
 aOldValueHigh=194.921005;
 aNewValueLow=0;
 aNewValueHigh=255;
 aDataSetOut=vImarisApplication.mImageProcessing.EqualizeHistogramDataSet(aDataSetIn,aOldValueLow,aOldValueHigh,aNewValueLow,aNewValueHigh);
 %% To replace current dataset with the equalized one, use the following:
 vImarisApplication.mDataSet=aDataSetOut;

HRESULT IImageProcessing::FastMarchingArrivalTimeChannel	(	[in] IDataSet *	aDataSet,
		[in] ULONG	aChannelIndex,
		[in] VARIANT	aStartPositions
	)

FastMarchingArrivalTime algorithm

Parameters:

	aDataSet	[in], [out] The dataset (IN/OUT)
	aChannelIndex	[in] Index of channel to be processed.
	aStartPositions	[in] Vector of 3D start positions for expansion of front

 %% The following MATLAB code runs the FastMarchingArrivalTime algorithm for the selected channel.
 %% Caution: this will directly replace the current dataset with the gamma-corrected one in vImarisApplication.mDataSet.
 aDataSetIn=vImarisApplication.mDataSet; %% Current dataset
 aChannelIndex=0;
 aStartPositions=[100 100 100];
 vImarisApplication.mImageProcessing.FastMarchingArrivalTimeChannel(aDataSetIn,aChannelIndex,aStartPositions);

HRESULT IImageProcessing::FastMarchingArrivalTimeDataSet	(	[in] IDataSet *	aDataSetIn,
		[in] VARIANT	aStartPositions,
		[out, retval] IDataSet **	aDataSetOut
	)

FastMarchingArrivalTime algorithm

Parameters:

	aDataSetIn	[in] The source dataset
	aStartPositions	[in] Vector of 3D start positions for expansion of front
	aDataSetOut	[out] The destination dataset

 %% The following MATLAB code runs the FastMarchingArrivalTime algorithm for the whole dataset.
 aDataSetIn=vImarisApplication.mDataSet; %% Current dataset
 aStartPositions=[100 100 100];
 aDataSetOut=vImarisApplication.mImageProcessing.FastMarchingArrivalTimeDataSet(aDataSetIn,aStartPositions);
 %% To replace current dataset with the output one, use the following:
 vImarisApplication.mDataSet=aDataSetOut;

HRESULT IImageProcessing::Flip3DChannel	(	[in] IDataSet *	aDataSet,
		[in] ULONG	aChannelIndex,
		[in] ULONG	aDimension
	)

Flip the selected channel set. The values are swapped along one dimension.

Parameters:

	aDataSet	[in], [out] The dataset (IN/OUT)
	aChannelIndex	[in] Index of channel to be processed.
	aDimension	[out] The dimension in which to flip the channel.

 %% The following MATLAB code flips the selected channel along one dimension.
 %% Caution: this will directly replace the current dataset with the flipped one in vImarisApplication.mDataSet.
 aDataSetIn=vImarisApplication.mDataSet; %% Current dataset
 aChannelIndex=0;
 aDimension=1;
 vImarisApplication.mImageProcessing.Flip3DChannel(aDataSetIn,aChannelIndex,aDimension);

HRESULT IImageProcessing::Flip3DDataSet	(	[in] IDataSet *	aDataSetIn,
		[in] ULONG	aDimension,
		[out, retval] IDataSet **	aDataSetOut
	)

Flip the dataset. The values are swapped in one dimension.

Parameters:

	aDataSetIn	The source dataset
	aDimension	The dimension in which to flip the channels.
	aDataSetOut	The destination dataset

 %% The following MATLAB code flips the whole dataset along one dimension
 aDataSetIn=vImarisApplication.mDataSet; %% Current dataset
 aDimension=1;
 aDataSetOut=vImarisApplication.mImageProcessing.Flip3DDataSet(aDataSetIn,aDimension);
 %% To replace current dataset with the flipped one, use the following:
 vImarisApplication.mDataSet=aDataSetOut;

HRESULT IImageProcessing::GammaCorrectChannel	(	[in] IDataSet *	aDataSet,
		[in] ULONG	aChannelIndex,
		[in] FLOAT	aGammaValue,
		[in] FLOAT	aMaxValue
	)

Gamma correction. I_new = (I_old ^ gamma) / (max ^ (gamma - 1)

Parameters:

	aDataSet	[in], [out] The dataset
	aChannelIndex	[in] Index of channel to be processed.
	aGammaValue	[in] The gamma value for each channel.
	aMaxValue	[in] The maximum value (for normalization) for each channel.

 %% The following MATLAB code applies gamma correction to the selected channel.
 %% Caution: this will directly replace the current dataset with the gamma-corrected one in vImarisApplication.mDataSet.
 aDataSetIn=vImarisApplication.mDataSet; %% Current dataset
 aChannelIndex=0;
 aGammaValue=0.75;
 aMaxValue=200;
 vImarisApplication.mImageProcessing.GammaCorrectChannel(aDataSetIn,aChannelIndex,aGammaValue,aMaxValue);

HRESULT IImageProcessing::GammaCorrectDataSet	(	[in] IDataSet *	aDataSetIn,
		[in] FLOAT	aGammaValue,
		[in] FLOAT	aMaxValue,
		[out, retval] IDataSet **	aDataSetOut
	)

Apply gamma correction for the whole dataset. I_new = (I_old ^ gamma) / (max ^ (gamma - 1)

Parameters:

	aDataSetIn	[in] The source dataset
	aGammaValue	[in] The gamma value for each channel (float)
	aMaxValue	[in] The maximum value (for normalization) for each channel (float)
	aDataSetOut	[out] The destination dataset

 %% The following MATLAB code applies gamma correction to the whole dataset.
 aDataSetIn=vImarisApplication.mDataSet; %% Current dataset
 aGammaValue=0.75;
 aMaxValue=200;
 aDataSetOut=vImarisApplication.mImageProcessing.GammaCorrectDataSet(aDataSetIn,aGammaValue,aMaxValue);
 %% To replace current dataset with the gamma-corrected one, use the following:
 vImarisApplication.mDataSet=aDataSetOut;

HRESULT IImageProcessing::GaussFilterChannel	(	[in] IDataSet *	aDataSet,
		[in] ULONG	aChannelIndex,
		[in] FLOAT	aSigma
	)

Apply a Gaussian filter to the selected channel set. The filter is isotropic and given in dataset coordinates. The width of the filter is given in float. Note that in voxel coordinates the filter may be anisotropic, depending on the voxelsize.

Parameters:

	aDataSet	[in], [out] The dataset
	aChannelIndex	[in] Index of channel to be processed.
	aSigma	[in] The width of the filter.

 %% The following MATLAB code applies a Gaussian filter to the selected channel.
 %% Caution: this will directly replace the current dataset with the filtered one in vImarisApplication.mDataSet.
 aDataSetIn=vImarisApplication.mDataSet; %% Current dataset
 aChannelIndex=0;
 aSigma=2.5;
 vImarisApplication.mImageProcessing.GaussFilterChannel(aDataSetIn,aChannelIndex,aSigma);

HRESULT IImageProcessing::GaussFilterDataSet	(	[in] IDataSet *	aDataSetIn,
		[in] FLOAT	aSigma,
		[out, retval] IDataSet **	aDataSetOut
	)

Apply a Gaussian filter to the dataset. The filter is isotropic and given in dataset coordinates. The width of the filter is given in float. Note that in voxel coordinates the filter may be anisotropic, depending on the voxelsize.

Parameters:

	aDataSetIn	[in] The source dataset
	aSigma	[in] The width of the filter (float))
	aDataSetOut	[out] The destination dataset

 %% The following MATLAB code applies a Gaussian filter to the whole dataset.
 aDataSetIn=vImarisApplication.mDataSet; %% Current dataset
 aSigma=2.5;
 aDataSetOut=vImarisApplication.mImageProcessing.GaussFilterDataSet(aDataSetIn,aSigma);
 %% To replace current dataset with the filtered one, use the following:
 vImarisApplication.mDataSet=aDataSetOut;

HRESULT IImageProcessing::GaussianDerivativeChannel	(	[in] IDataSet *	aDataSet,
		[in] ULONG	aChannelIndex,
		[in] FLOAT	aSigma,
		[in] VARIANT	aDerivativeOrder
	)

Apply a GaussianDerivative filter to the selected channnel. The width of the filter is given in float.

Parameters:

	aDataSet	[in], [out] The dataset
	aChannelIndex	[in] Index of channel to be processed.
	aSigma	[in] The width of the filter.
	aDerivativeOrder	[in] Vector containing order of derivative for each data dimension.

 %% The following MATLAB code applies a GaussianDerivative filter to the selected channel.
 %% Caution: this will directly replace the current dataset with the filtered one in vImarisApplication.mDataSet.
 aDataSetIn=vImarisApplication.mDataSet; %% Current dataset
 aChannelIndex=0;
 aSigma=2.5;
 aDerivativeOrder=[2 2 2];
 vImarisApplication.mImageProcessing.GaussianDerivativeChannel(aDataSetIn,aChannelIndex,aSigma,aDerivativeOrder);

HRESULT IImageProcessing::GaussianDerivativeDataSet	(	[in] IDataSet *	aDataSetIn,
		[in] FLOAT	aSigma,
		[in] VARIANT	aDerivativeOrder,
		[out, retval] IDataSet **	aDataSetOut
	)

Apply a GaussianDerivative filter to the whole dataset. The width of the filter is given in float.

Parameters:

	aDataSetIn	[in] The source dataset
	aSigma	[in] The width of the filter.
	aDerivativeOrder	[in] Vector containing order of derivative for each data dimension.
	aDataSetOut	[out] The destination dataset

 %% The following MATLAB code applies a GaussianDerivative filter to the whole dataset.
 aDataSetIn=vImarisApplication.mDataSet; %% Current dataset
 aSigma=2.5;
 aDerivativeOrder=[2 2 2];
 aDataSetOut=vImarisApplication.mImageProcessing.GaussianDerivativeDataSet(aDataSetIn,aSigma,aDerivativeOrder);
 %% To replace current dataset with the filtered one, use the following:
 vImarisApplication.mDataSet=aDataSetOut;

HRESULT IImageProcessing::InvertChannel	(	[in] IDataSet *	aDataSet,
		[in] ULONG	aChannelIndex
	)

Invert all values in the selected channel.

Parameters:

	aDataSet	[in], [out] The dataset
	aChannelIndex	[in] Index of channel to be processed

 %% The following MATLAB code inverts all values in the selected channel.
 %% Caution: this will directly replace the current dataset with the filtered one in vImarisApplication.mDataSet.
 aDataSetIn=vImarisApplication.mDataSet; %% Current dataset
 aChannelIndex=0;
 vImarisApplication.mImageProcessing.InvertChannel(aDataSetIn,aChannelIndex);

HRESULT IImageProcessing::InvertDataSet	(	[in] IDataSet *	aDataSetIn,
		[out, retval] IDataSet **	aDataSetOut
	)

Invert all values in the whole dataset.

Parameters:

	aDataSetIn	[in] The source dataset
	aDataSetOut	[out] The destination dataset

 %% The following MATLAB code inverts all values in the whole dataset.
 aDataSetIn=vImarisApplication.mDataSet; %% Current dataset
 aDataSetOut=vImarisApplication.mImageProcessing.InvertDataSet(aDataSetIn);
 %% To replace current dataset with the inverted one, use the following:
 vImarisApplication.mDataSet=aDataSetOut;

HRESULT IImageProcessing::MedianFilterChannel	(	[in] IDataSet *	aDataSet,
		[in] ULONG	aChannelIndex,
		[in] VARIANT	aSize
	)

Apply a median filter to the selected channel.

Parameters:

	aDataSet	[in], [out] The dataset
	aChannelIndex	[in] Index of channel to be processed.
	aSize	[in] The size in x, y and z

 %% The following MATLAB code applies a median to the selected channel.
 %% Caution: this will directly replace the current dataset with the filtered one in vImarisApplication.mDataSet.
 aDataSetIn=vImarisApplication.mDataSet; %% Current dataset
 aChannelIndex=0;
 aSize=[5 5 5];
 vImarisApplication.mImageProcessing.MedianFilterChannel(aDataSetIn,aChannelIndex,aSize);

HRESULT IImageProcessing::MedianFilterDataSet	(	[in] IDataSet *	aDataSetIn,
		[in] VARIANT	aSize,
		[out, retval] IDataSet **	aDataSetOut
	)

Apply a median filter to the whole dataset.

Parameters:

	aDataSetIn	[in] The source dataset
	aSize	[in] The size in x, y and z
	aDataSetOut	[out] The destination dataset

 %% The following MATLAB code applies a median filter to the whole dataset.
 aDataSetIn=vImarisApplication.mDataSet; %% Current dataset
 aSize=[5 5 5];
 aDataSetOut=vImarisApplication.mImageProcessing.MedianFilterDataSet(aDataSetIn,aSize);
 %% To replace current dataset with the filtered one, use the following:
 vImarisApplication.mDataSet=aDataSetOut;

HRESULT IImageProcessing::NormalizeLayersChannel	(	[in] IDataSet *	aDataSet,
		[in] ULONG	aChannelIndex
	)

Normalize layers for the selected channel.

Parameters:

	aDataSet	[in], [out] The dataset
	aChannelIndex	[in] Index of channel to be processed

 %% The following MATLAB code normalizes layers for the selected channel.
 %% Caution: this will directly replace the current dataset with the normalized one in vImarisApplication.mDataSet.
 aDataSetIn=vImarisApplication.mDataSet; %% Current dataset
 aChannelIndex=0;
 vImarisApplication.mImageProcessing.NormalizeLayersChannel(aDataSetIn,aChannelIndex);

HRESULT IImageProcessing::NormalizeLayersDataSet	(	[in] IDataSet *	aDataSetIn,
		[out, retval] IDataSet **	aDataSetOut
	)

Normalize layers for the whole dataset.

Parameters:

	aDataSetIn	[in] The source dataset
	aDataSetOut	[out] The destination dataset

 %% The following MATLAB code normalizes layers for the whole dataset.
 aDataSetIn=vImarisApplication.mDataSet; %% Current dataset
 aDataSetOut=vImarisApplication.mImageProcessing.NormalizeLayersDataSet(aDataSetIn);
 %% To replace current dataset with the normalized one, use the following:
 vImarisApplication.mDataSet=aDataSetOut;

HRESULT IImageProcessing::Shift3DChannel	(	[in] IDataSet *	aDataSet,
		[in] ULONG	aChannelIndex,
		[in] LONG	aShiftX,
		[in] LONG	aShiftY,
		[in] LONG	aShiftZ
	)

Shift selected channel along a Shift Vector.

Parameters:

	aDataSet	[in], [out] The dataset (IN/OUT)
	aChannelIndex	[in] Index of channel to be processed.
	aShiftX	[in] Shift the shift in pixel in +/- X direction
	aShiftY	[in] Shift the shift in pixel in +/- Y direction
	aShiftZ	[in] Shift the shift in pixel in +/- Z direction

 %% The following MATLAB code shifts the selected channel along a Shift vector
 %% Caution: this will directly replace the current dataset with the shifted one in vImarisApplication.mDataSet.
 aDataSetIn=vImarisApplication.mDataSet; %% Current dataset
 aChannelIndex=1;
 aShiftX=1;
 aShiftY=2;
 aShiftZ=-1;
 vImarisApplication.mImageProcessing.Shift3DChannel(aDataSetIn,aChannelIndex,aShiftX,aShiftY,aShiftZ);

HRESULT IImageProcessing::Shift3DDataSet	(	[in] IDataSet *	aDataSetIn,
		[in] LONG	aShiftX,
		[in] LONG	aShiftY,
		[in] LONG	aShiftZ,
		[out, retval] IDataSet **	aDataSetOut
	)

Shift the whole dataset along a Shift Vector.

Parameters:

	aDataSetIn	The source dataset
	aShiftX	[in] Shift the shift in pixel in +/- X direction
	aShiftY	[in] Shift the shift in pixel in +/- Y direction
	aShiftZ	[in] Shift the shift in pixel in +/- Z direction
	aDataSetOut	[out] The destination dataset

 %% The following MATLAB code shifts the whole dataset along a Shift vector
 aDataSetIn=vImarisApplication.mDataSet; %% Current dataset
 aShiftX=1;
 aShiftY=2;
 aShiftZ=-1;
 aDataSetOut=vImarisApplication.mImageProcessing.Shift3DDataSet(aDataSetIn,aShiftX,aShiftY,aShiftZ);
 %% To replace current dataset with the shifted one, use the following:
 vImarisApplication.mDataSet=aDataSetOut;

HRESULT IImageProcessing::ShortestPath	(	[in] IDataSet *	aDataSet,
		[in] ULONG	aTimeIndex,
		[in] ULONG	aChannelIndex,
		[in] VARIANT	aStartPositions,
		[out, retval] VARIANT *	aPositionsXYZ
	)

Compute a gradient descent path from the starting positions "aStartPositions" until a local minimum or an intensity value of zero is reached. The result "aPositionsXYZ" contains a path (list of vertices) for each starting position.

Parameters:

	aDataSet	[in] The source dataset
	aTimeIndex	[in] Time index to be processed.
	aChannelIndex	[in] Index of channel to be processed.
	aStartPositions	[in] Vector of 3D start positions
	aPositionsXYZ	[out]

 %% The following MATLAB code computes a gradient descent path for the selected channel and time point.
 aDataSet=vImarisApplication.mDataSet; %% Current dataset
 aTimeIndex=0;
 aChannelIndex=0;
 aStartPositions=[100 100 100];
 aPositionsXYZ=vImarisApplication.mImageProcessing.ShortestPath(aDataSet,aTimePosition,aChannelIndex,aStartPositions);

HRESULT IImageProcessing::SubtractBackgroundChannel	(	[in] IDataSet *	aDataSet,
		[in] ULONG	aChannelIndex,
		[in] FLOAT	aSigma
	)

Filter the selected channel with a Gaussian of width sigma and subtract that from the original

Parameters:

	aDataSet	[in], [out] The dataset
	aChannelIndex	[in] Index of channel to be processed.
	aSigma	[in] The width of the filter.

 %% The following MATLAB code subtracts a filtered version of the selected channel from the selected channel itself.
 %% Caution: this will directly replace the current dataset with the filtered one in vImarisApplication.mDataSet.
 aDataSetIn=vImarisApplication.mDataSet; %% Current dataset
 aChannelIndex=0;
 aSigma=2.5;
 vImarisApplication.mImageProcessing.SubtractBackgroundChannel(aDataSetIn,aChannelIndex,aSigma);

HRESULT IImageProcessing::SubtractBackgroundDataSet	(	[in] IDataSet *	aDataSetIn,
		[in] FLOAT	aSigma,
		[out, retval] IDataSet **	aDataSetOut
	)

Filter the whole dataset with a Gaussian of width sigma and subtract the filtered image from the original

Parameters:

	aDataSetIn	[in] The source dataset
	aSigma	[in] The width of the filter (float)
	aDataSetOut	[out] The destination dataset

 %% The following MATLAB code subtracts a filtered version of the dataset from the dataset itself
 aDataSetIn=vImarisApplication.mDataSet; %% Current dataset
 aSigma=2.5;
 aDataSetOut=vImarisApplication.mImageProcessing.SubtractBackgroundDataSet(aDataSetIn,aSigma);
 %% To replace current dataset with the subtracted one, use the following:
 vImarisApplication.mDataSet=aDataSetOut;

HRESULT IImageProcessing::ThresholdBothChannel	(	[in] IDataSet *	aDataSet,
		[in] ULONG	aChannelIndex,
		[in] FLOAT	aThreshold,
		[in] FLOAT	aNewValueLow,
		[in] FLOAT	aNewValueHigh
	)

Apply a threshold to the selected channel. Values below the threshold are set to newValueLow, values abover or equal to the threshold are set to newValueHigh.

Parameters:

	aDataSet	[in], [out] The dataset
	aChannelIndex	[in] Index of channel to be processed.
	aThreshold	[in] The threshold value for each channel.
	aNewValueLow	[in] All values below or equal the threshold are set to this value.
	aNewValueHigh	[in] All values above the threshold are set to this value.

 %% The following MATLAB code applies a user-defined lower and upper threshold to the selected channel.
 %% Caution: this will directly replace the current dataset with the thresholded one in vImarisApplication.mDataSet.
 aDataSetIn=vImarisApplication.mDataSet; %% Current dataset
 aChannelIndex=0;
 aNewValueLow=0;
 aNewValueHigh=1;
 vImarisApplication.mImageProcessing.ThresholdBothChannel(aDataSetIn,aChannelIndex,aThreshold,aNewValueLow,aNewValueHigh);

HRESULT IImageProcessing::ThresholdBothDataSet	(	[in] IDataSet *	aDataSetIn,
		[in] FLOAT	aThreshold,
		[in] FLOAT	aNewValueLow,
		[in] FLOAT	aNewValueHigh,
		[out, retval] IDataSet **	aDataSetOut
	)

Apply a threshold to the whole dataset: values below the threshold are set to newValueLow, values above or equal to the threshold are set to newValueHigh.

Parameters:

	aDataSetIn	[in] The source dataset
	aThreshold	[in] The threshold value for each channel.
	aNewValueLow	[in] All values below or equal the threshold are set to this value.
	aNewValueHigh	[in] All values above the threshold are set to this value.
	aDataSetOut	[out] The thresholded dataset

 %% The following MATLAB code applies user-defined threshold to the selected channel.
 aDataSetIn=vImarisApplication.mDataSet; %% Current dataset
 aThreshold=128;
 aNewValueLow=0;
 aNewValueHigh=1;
 aDataSetOut=vImarisApplication.mImageProcessing.ThresholdBothDataSet(aDataSetIn,aThreshold,aNewValueLow,aNewValueHigh);
 %% To replace current dataset with the thresholded one, use the following:
 vImarisApplication.mDataSet=aDataSetOut;

HRESULT IImageProcessing::ThresholdChannel	(	[in] IDataSet *	aDataSet,
		[in] ULONG	aChannelIndex,
		[in] FLOAT	aThreshold,
		[in] FLOAT	aNewValue
	)

Apply a lower threshold to the selected channel. Values below the threshold are set to aNewValue.

Parameters:

	aDataSet	[In], [out] The dataset (is modified in place)
	aChannelIndex	[in] Index of channel to be processed.
	aThreshold	[in] The threshold value.
	aNewValue	[in] All values below the threshold are set to this value.

 %% The following MATLAB code applies a user-defined lower threshold to the selected channel.
 %% Caution: this will directly replace the current dataset with the thresholded one in vImarisApplication.mDataSet.
 aDataSetIn=vImarisApplication.mDataSet; %% Current dataset
 aChannelIndex=0;
 aThreshold=128;
 vImarisApplication.mImageProcessing.ThresholdChannel(aDataSetIn,aChannelIndex,aThreshold,aNewValue);

HRESULT IImageProcessing::ThresholdDataSet	(	[in] IDataSet *	aDataSetIn,
		[in] FLOAT	aThreshold,
		[in] FLOAT	aNewValue,
		[out, retval] IDataSet **	aDataSetOut
	)

Apply a lower threshold to the whole dataset. Values below the threshold are set to aNewValue.

Parameters:

	aDataSetIn	[In] The source dataset
	aThreshold	[In] The threshold value.
	aNewValue	[In] All values below the threshold are set to this value.
	aDataSetOut	[out] The thresholded dataset

 %% The following MATLAB code applies a user-defined lower threshold to the whole dataset.
 aDataSetIn=vImarisApplication.mDataSet; %% Current dataset
 aThreshold=128;
 aNewValue=0;
 aDataSetOut=vImarisApplication.mImageProcessing.ThresholdDataSet(aDataSetIn,aThreshold,aNewValue);
 %% To replace current dataset with the thresholded one, use the following:
 vImarisApplication.mDataSet=aDataSetOut;

HRESULT IImageProcessing::ThresholdUpperChannel	(	[in] IDataSet *	aDataSet,
		[in] ULONG	aChannelIndex,
		[in] FLOAT	aThreshold,
		[in] FLOAT	aNewValue
	)

Apply a upper threshold to the selected channel. Values above or equal the threshold are set to newValue.

Parameters:

	aDataSet	[in], [out] The dataset (IN/OUT)
	aChannelIndex	[in] Index of channel to be processed.
	aThreshold	[in] The threshold value.
	aNewValue	[in] All values above or equal the threshold are set to this value.

 %% The following MATLAB code applies a user-defined upper threshold to the selected channel.
 %% Caution: this will directly replace the current dataset with the thresholded one in vImarisApplication.mDataSet.
 aDataSetIn=vImarisApplication.mDataSet; %% Current dataset
 aChannelIndex=0;
 aThreshold=128;
 vImarisApplication.mImageProcessing.ThresholdUpperChannel(aDataSetIn,aChannelIndex,aThreshold,aNewValue);

HRESULT IImageProcessing::ThresholdUpperDataSet	(	[in] IDataSet *	aDataSetIn,
		[in] FLOAT	aThreshold,
		[in] FLOAT	aNewValue,
		[out, retval] IDataSet **	aDataSetOut
	)

Apply a upper threshold to the whole dataset. Values above or equal to the threshold are set to newValue.

Parameters:

	aDataSetIn	[in] The dource dataset
	aThreshold	[in] The threshold value.
	aNewValue	[in] All values above or equal the threshold are set to this value.
	aDataSetOut	[out] The thresholded dataset

 %% The following MATLAB code applies a user-defined upper threshold to the whole dataset.
 aDataSetIn=vImarisApplication.mDataSet; %% Current dataset
 aThreshold=128;
 aNewValue=0;
 aDataSetOut=vImarisApplication.mImageProcessing.ThresholdUpperDataSet(aDataSetIn,aThreshold,aNewValue);
 %% To replace current dataset with the thresholded one, use the following:
 vImarisApplication.mDataSet=aDataSetOut;

HRESULT IImageProcessing::TrackSpotsAutoregressiveMotion	(	[in] ISpots *	aSpots,
		[in] FLOAT	aMaximalDistance,
		[in] INT	aGapSize,
		[in] BSTR	aTrackFiltersString,
		[out, retval] ISpots **	aTrackedSpots
	)

TrackSpotsBrownianMotion, TrackSpotsAutoregressiveMotion, TrackSpotsAutoregressiveMotionExpert, TrackSpotsConnectedComponents replaces CalculateTracks, implemented for bpPointsViewer.