Uses of Class
de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte

Packages that use MTBImageByte
de.unihalle.informatik.MiToBo.apps.datatypes.cellImages   
de.unihalle.informatik.MiToBo.apps.neurites2D   
de.unihalle.informatik.MiToBo.apps.nuclei2D   
de.unihalle.informatik.MiToBo.apps.particles2D   
de.unihalle.informatik.MiToBo.apps.xylem   
de.unihalle.informatik.MiToBo.core.datatypes Provides basic datatypes for MiToBo. 
de.unihalle.informatik.MiToBo.core.datatypes.images Contains MiToBo image data types. 
de.unihalle.informatik.MiToBo.core.datatypes.neurites   
de.unihalle.informatik.MiToBo.enhance Provides classes for image preprocessing and improvement (no filters!). 
de.unihalle.informatik.MiToBo.filters.linear.anisotropic   
de.unihalle.informatik.MiToBo.filters.vesselness Provides various operators for enhancing vessel-like structures in images. 
de.unihalle.informatik.MiToBo.morphology Provides classes for morphological processing of binary images. 
de.unihalle.informatik.MiToBo.segmentation.contours.extraction Provides classes for performing contour extractions from regions or other image elements. 
de.unihalle.informatik.MiToBo.segmentation.evaluation   
de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE   
de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes   
de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver   
de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes Provides basic datatypes for MiToBo explicit active contours (snakes). 
de.unihalle.informatik.MiToBo.segmentation.snakes.energies Provides classes with energies to be used with MiToBo snakes. 
de.unihalle.informatik.MiToBo.segmentation.thresholds Provides classes for thresholding grayscale and color images. 
 

Uses of MTBImageByte in de.unihalle.informatik.MiToBo.apps.datatypes.cellImages
 

Fields in de.unihalle.informatik.MiToBo.apps.datatypes.cellImages declared as MTBImageByte
protected  MTBImageByte SegResult_Particles.binMask
          Binary segmentation mask.
protected  MTBImageByte SegResult_Nuclei.binMask
          Binary segmentation mask.
protected  MTBImageByte SegResult_Cytoplasm.labelImage
          Label mask.
 

Methods in de.unihalle.informatik.MiToBo.apps.datatypes.cellImages that return MTBImageByte
 MTBImageByte SegResult_Cytoplasm.getLabelImage()
          Returns label mask with segmentation result.
 MTBImageByte SegResult_Particles.getMask()
          Returns binary mask with segmentation result.
 MTBImageByte SegResult_Nuclei.getMask()
          Returns binary mask with segmentation result.
 

Methods in de.unihalle.informatik.MiToBo.apps.datatypes.cellImages with parameters of type MTBImageByte
 void SegResult_Nuclei.setMask(MTBImageByte m)
          Specify binary mask of nuclei.
 

Constructors in de.unihalle.informatik.MiToBo.apps.datatypes.cellImages with parameters of type MTBImageByte
SegResult_Cytoplasm(String imgName, MTBPolygon2DSet conts, MTBImageByte labels, int count, double avgsize)
          Deprecated. 
SegResult_Cytoplasm(String imgName, MTBPolygon2DSet conts, MTBImageByte labels, int count, int[] sizes, double avgsize)
          Default constructor.
SegResult_Nuclei(String imgName, int channel, MTBImageByte mask, MTBImage labels, MTBRegion2DSet regs, int count, double avgsize)
          Default constructor.
SegResult_Particles(String imgName, int ch, MTBRegion2DSet regions, MTBImageByte mask, int count, double avgsize)
          Default constructor.
 

Uses of MTBImageByte in de.unihalle.informatik.MiToBo.apps.neurites2D
 

Methods in de.unihalle.informatik.MiToBo.apps.neurites2D that return MTBImageByte
 MTBImageByte NeuriteExtractor2D.drawLine2D(Line2D.Double line, Point2D.Double point)
          Draws a 2D line into the neuron image.
 MTBImageByte NeuriteExtractor2D.getNeuronImage()
          Get input image of the binary neuron.
 

Methods in de.unihalle.informatik.MiToBo.apps.neurites2D with parameters of type MTBImageByte
 void NeuriteExtractor2D.setNeuronImage(MTBImageByte _neuronImage)
          Set input image of the binary neuron.
 

Constructors in de.unihalle.informatik.MiToBo.apps.neurites2D with parameters of type MTBImageByte
NeuriteExtractor2D(MTBImageByte _neuronImage, NeuriteExtractor2D.NeuronColor _neuronColor, int _neuriteMaskSize, int _maxSpineLength, org.rosuda.JRI.Rengine _rEngine, String _outputDir)
          Constructor to create a new neurite extraction object.
 

Uses of MTBImageByte in de.unihalle.informatik.MiToBo.apps.nuclei2D
 

Methods in de.unihalle.informatik.MiToBo.apps.nuclei2D that return MTBImageByte
protected  MTBImageByte NucleusDetector2D.detectWithLocalContrastEnhancement()
          Detect nuclei by first improving image contrast.
protected  MTBImageByte NucleusDetector2D.detectWithNiblack()
          Detects nuclei based on Niblack thresholding.
protected  MTBImageByte NucleusDetector2D.detectWithOtsu_erodedilate()
          Detects nuclei based on Otsu thresholding and a combination of erosion/ dilation.
protected  MTBImageByte NucleusDetector2D.detectWithOtsu_openclose()
          Detects nuclei based on Otsu thresholding and a combination of opening and closing.
 

Methods in de.unihalle.informatik.MiToBo.apps.nuclei2D with parameters of type MTBImageByte
 void NucleusSeparator2DPeakSearch_RegionSeparator.setInImg(MTBImageByte _inImg)
          Specify binary input image.
 void NuclearParticleDetector2D.setInputImage(MTBImageByte _inputImage)
          Set input image.
 

Constructors in de.unihalle.informatik.MiToBo.apps.nuclei2D with parameters of type MTBImageByte
NuclearParticleDetector2D(MTBImageByte _inputImage, Integer _nucChannel, Integer _partChannel, Boolean _correctGamma, Double _gamma, Boolean _filterImage, NucleusDetector2D _nucDetector, ParticleDetectorUWT2D _partDetector)
           
NucleusSeparator2DPeakSearch_RegionSeparator(MTBImageByte image)
          Constructor with input image.
 

Uses of MTBImageByte in de.unihalle.informatik.MiToBo.apps.particles2D
 

Methods in de.unihalle.informatik.MiToBo.apps.particles2D with parameters of type MTBImageByte
 void ParticleDetectorUWT2D.setExcludeMask(MTBImageByte mask)
          Specify exclude mask.
 void MultiChannelParticleAnalyzer2D.setNucleiMask(MTBImageByte mask)
          Specify nuclei mask.
 

Uses of MTBImageByte in de.unihalle.informatik.MiToBo.apps.xylem
 

Methods in de.unihalle.informatik.MiToBo.apps.xylem that return MTBImageByte
 MTBImageByte XylemGrower.getGrownRegions()
          Returns a MTBImageByte image after growing.
 MTBImageByte XylemInitialSegmentation.getInitSegImageByte()
          Return the resulting initial segmentation image.
 MTBImageByte XylemGrower.getResultXylemRegions()
          Return the binary image after the post processing of the grown region image.
 MTBImageByte XylemGrower.getSeedRegions()
           
 

Methods in de.unihalle.informatik.MiToBo.apps.xylem with parameters of type MTBImageByte
 void XylemGrower.setGrownRegions(MTBImageByte imageByte)
           
 void XylemGrower.setInitalSegmentation(MTBImageByte image)
           
 void XylemInitialSegmentation.setInitSegImageByte(MTBImageByte initSegImageByte)
           
 void XylemGrower.setSeedImage(MTBImageByte seedRegions)
           
 void XylemGrower.setXylemImage(MTBImageByte hsxMTBImage)
          Set the Hue/Saturation/{Intensity|Brightness|Value}-MTBImage.
 void XylemGrower.setXylemResultRegions(MTBImageByte regions)
          Set the binary image after the morphological processing on the grown region image.
 

Constructors in de.unihalle.informatik.MiToBo.apps.xylem with parameters of type MTBImageByte
XylemGrower(MTBImageByte binaryImage, MTBImageByte hsxImage, XylemGrower.GrowingMode linkageMode)
           
XylemInitialSegmentation(MTBImageByte grayScaleXylemImage)
           
 

Uses of MTBImageByte in de.unihalle.informatik.MiToBo.core.datatypes
 

Methods in de.unihalle.informatik.MiToBo.core.datatypes that return MTBImageByte
 MTBImageByte MTBNeuriteSkelGraph.toByteImage()
          Draw the skeleton graph into a binary image.
 MTBImageByte MTBRegion2D.toMTBImageByte(String file, int width, int height)
          Method to save the region on a binary image with specific width and height.
 MTBImageByte MTBBorder2D.toMTBImageByte(String file, int width, int height)
          Draws a border with all inner borders to a binary image with given size.
 MTBImageByte MTBRegion2D.toMTBImageByte(String file, int width, int height, int color)
          Method to save the region on a binary image with specific width, height and color.
 

Methods in de.unihalle.informatik.MiToBo.core.datatypes with parameters of type MTBImageByte
 boolean MTBNeuriteSkelGraph.buildSkeletonGraph(int x, int y, int w, int h, MTBImageByte skeletonImg, int skelColor)
           Build the skeleton graph from a given binary skeleton image and a given starting point to build up the graph.
 MTBTableModel MTBNeuriteSkelGraph.toSWC(String fileName, MTBImageByte neuronImage)
          Method to save neurite skeleton graph as SWC file.
 

Uses of MTBImageByte in de.unihalle.informatik.MiToBo.core.datatypes.images
 

Methods in de.unihalle.informatik.MiToBo.core.datatypes.images that return MTBImageByte
static MTBImageByte MTBImage.createMTBImageByte(int sizeX, int sizeY, int sizeZ, int sizeT, int sizeC, byte[][] data)
          Creates an image of type MTBImage.MTBImageType.MTB_BYTE from the given data array.
 

Uses of MTBImageByte in de.unihalle.informatik.MiToBo.core.datatypes.neurites
 

Methods in de.unihalle.informatik.MiToBo.core.datatypes.neurites that return MTBImageByte
 MTBImageByte MTBNeurite2D.drawLine2D(Line2D.Double line, Point2D.Double point, MTBImageByte tmpNeuronImg)
          Draws a 2D line into the neuron image.
 

Methods in de.unihalle.informatik.MiToBo.core.datatypes.neurites with parameters of type MTBImageByte
 MTBImageByte MTBNeurite2D.drawLine2D(Line2D.Double line, Point2D.Double point, MTBImageByte tmpNeuronImg)
          Draws a 2D line into the neuron image.
 

Uses of MTBImageByte in de.unihalle.informatik.MiToBo.enhance
 

Constructors in de.unihalle.informatik.MiToBo.enhance with parameters of type MTBImageByte
TopHatContrastEnhancement(MTBImageByte _inputImage, Integer _wthMaskSize, Integer _bthMaskSize)
          Constructor to create a new IlluminationCorrection object.
 

Uses of MTBImageByte in de.unihalle.informatik.MiToBo.filters.linear.anisotropic
 

Methods in de.unihalle.informatik.MiToBo.filters.linear.anisotropic that return MTBImageByte
 MTBImageByte OrientedFilter2DBatchAnalyzer.getIndexMap()
          Get map of indices of maximal responses.
 

Uses of MTBImageByte in de.unihalle.informatik.MiToBo.filters.vesselness
 

Fields in de.unihalle.informatik.MiToBo.filters.vesselness declared as MTBImageByte
protected  MTBImageByte MPMFFilter2D.resultVesselMap
          Resulting binary vessel map.
protected  MTBImageByte MFFDOGMultiScaleFilter2D.resultVesselMap
          Resulting binary vessel map.
protected  MTBImageByte MFFDOGFilter2D.resultVesselMap
          Final vessel map.
 

Methods in de.unihalle.informatik.MiToBo.filters.vesselness that return MTBImageByte
 MTBImageByte MPMFFilter2D.getBinaryResultMap()
          Returns the final binary map.
 MTBImageByte MFFDOGFilter2D.getResultVesselMap()
          Get result.
 

Uses of MTBImageByte in de.unihalle.informatik.MiToBo.morphology
 

Methods in de.unihalle.informatik.MiToBo.morphology that return MTBImageByte
protected  MTBImageByte ComponentPostprocess.EraseLargeComponents(MTBImageByte binIP, int maxComponentSize)
          Function to remove large components from a binary image.
protected  MTBImageByte ComponentPostprocess.eraseNonCompactComponents(MTBImageByte binImage, double threshold)
          Function to remove all non compact/circular components of a binary image.
protected  MTBImageByte ComponentPostprocess.EraseRoundComponents(MTBImageByte binImage, double threshold)
          Remove components with small eccentricity.
protected  MTBImageByte ComponentPostprocess.EraseSmallComponents(MTBImageByte binIP, int minComponentSize)
          Function to remove small components from a binary image.
 MTBImageByte DistanceTransform.getInImg()
          Get the input image.
 MTBImageByte ComponentPostprocess.getResultImage()
          Get the result image after applying operator.
protected  MTBImageByte ComponentPostprocess.LinkAdjacentComponents(MTBImageByte binIP)
          Function for linking adjacent components/regions in a binary image.
protected  MTBImageByte ComponentPostprocess.LinkAdjacentPixels(MTBImageByte binIP, int maxDist)
          Function for linking adjacent pixels in a binary image.
protected  MTBImageByte ComponentPostprocess.VoronoiExpandComponents(MTBImageByte binImg, int maxDist)
          Dilate components, but avoid merges.
 

Methods in de.unihalle.informatik.MiToBo.morphology with parameters of type MTBImageByte
protected  MTBImageByte ComponentPostprocess.EraseLargeComponents(MTBImageByte binIP, int maxComponentSize)
          Function to remove large components from a binary image.
protected  MTBImageByte ComponentPostprocess.eraseNonCompactComponents(MTBImageByte binImage, double threshold)
          Function to remove all non compact/circular components of a binary image.
protected  MTBImageByte ComponentPostprocess.EraseRoundComponents(MTBImageByte binImage, double threshold)
          Remove components with small eccentricity.
protected  MTBImageByte ComponentPostprocess.EraseSmallComponents(MTBImageByte binIP, int minComponentSize)
          Function to remove small components from a binary image.
protected  MTBImageByte ComponentPostprocess.LinkAdjacentComponents(MTBImageByte binIP)
          Function for linking adjacent components/regions in a binary image.
protected  MTBImageByte ComponentPostprocess.LinkAdjacentPixels(MTBImageByte binIP, int maxDist)
          Function for linking adjacent pixels in a binary image.
 void DistanceTransform.setInImg(MTBImageByte inImg)
          Set the input image.
protected  MTBImageByte ComponentPostprocess.VoronoiExpandComponents(MTBImageByte binImg, int maxDist)
          Dilate components, but avoid merges.
 

Constructors in de.unihalle.informatik.MiToBo.morphology with parameters of type MTBImageByte
DistanceTransform(MTBImageByte image, DistanceTransform.DistanceMetric dm, DistanceTransform.ForegroundColor fg)
          Constructor to create a new DistanceTransform object.
 

Uses of MTBImageByte in de.unihalle.informatik.MiToBo.segmentation.contours.extraction
 

Methods in de.unihalle.informatik.MiToBo.segmentation.contours.extraction that return MTBImageByte
protected  MTBImageByte ContourOnLabeledComponents.calcContours()
          Get all inner- and outer-contours for the given regions.
 MTBImageByte ContourOnLabeledComponents.getInputImage()
          Get reference to the current input image.
 MTBImageByte ContourOnLabeledComponents.getResultImage()
          Get reference to the binary image with the calculated contours.
protected  MTBImageByte ContourOnLabeledComponents.toMTBImageByte()
          Method to save all contours from the regions on a binary image with specific width and height.
 

Methods in de.unihalle.informatik.MiToBo.segmentation.contours.extraction with parameters of type MTBImageByte
protected  int ContourOnLabeledComponents.findNextPoint(Point2D.Double Xc, int dir, MTBImageByte theImage)
          Find direction to next pixel in specific direction from the last pixel.
protected  MTBContour2DSet ContourOnLabeledComponents.getOuterContours(MTBRegion2DSet theRegions, MTBImageByte theImage)
          Calculate the outer contours of the given regions in a image.
 void ContourOnLabeledComponents.setInputImage(MTBImageByte inImg)
          Set reference to the current input image.
 void BordersOnLabeledComponents.setInputImage(MTBImageByte inImg)
          Set input image.
protected  MTBContour2D ContourOnLabeledComponents.traceContour(int xS, int yS, MTBImageByte theImage)
          Trace contour, starting at (xS, yS) in direction dS.
 

Constructors in de.unihalle.informatik.MiToBo.segmentation.contours.extraction with parameters of type MTBImageByte
BordersOnLabeledComponents(MTBImageByte inImg, MTBRegion2DSet inRegions, MTBBorder2D.BorderConnectivity con, BordersOnLabeledComponents.BorderType type, int minLength)
          Constructor.
ContourOnLabeledComponents(MTBImageByte inImg, MTBRegion2DSet inRegions, ContourOnLabeledComponents.ContourType type, int length)
          Constructor.
 

Uses of MTBImageByte in de.unihalle.informatik.MiToBo.segmentation.evaluation
 

Constructors in de.unihalle.informatik.MiToBo.segmentation.evaluation with parameters of type MTBImageByte
CalcStructureStatistics(MTBImageByte sMask, MTBImageByte nMask, MTBImageByte labelImg)
          Default constructor.
CalcStructureStatistics(MTBImageByte sMask, MTBImageByte nMask, MTBImageByte labelImg, boolean ignoreNuclei)
          Deprecated. 
 

Uses of MTBImageByte in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
 

Methods in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE that return MTBImageByte
 MTBImageByte MTBLevelsetMembership.getMTBImage()
          Creates a bi-level MTBImageByte of the level set function.
 MTBImageByte MTBLevelsetMembership.getMTBImageLabel()
          Creates a MTBImageByte of the level set function.
 MTBImageByte LevelsetSolveNonPDE.getResultImage()
          Get value of resultImage.
 

Methods in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE that return types with arguments of type MTBImageByte
 Vector<MTBImageByte> LevelsetSolveNonPDE.getIntermediateLS()
          Get value of intermediateLS.
 

Uses of MTBImageByte in de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes
 

Methods in de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes that return MTBImageByte
 MTBImageByte MTBLevelsetFunctionPDE.getBinaryMask()
          Get a binary mask of the represented segmentation.
 

Uses of MTBImageByte in de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver
 

Fields in de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver declared as MTBImageByte
protected  MTBImageByte LevelsetSolverPDE.intermediateResultStack
           
protected  MTBImageByte LevelsetSolverPDE.resultMask
           
 

Fields in de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver with type parameters of type MTBImageByte
protected  Vector<MTBImageByte> LevelsetSolverPDE.intermediateResults
          List of intermediate result segmentations.
 

Methods in de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver that return MTBImageByte
 MTBImageByte LevelsetSolverPDE.getResultMask()
          Get binary mask of segmentation result.
 

Uses of MTBImageByte in de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes
 

Methods in de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes that return MTBImageByte
 MTBImageByte MTBSnake.toMTBImageByte(String file, int w, int h)
          Method to draw and save the snake in a binary image.
 

Uses of MTBImageByte in de.unihalle.informatik.MiToBo.segmentation.snakes.energies
 

Constructors in de.unihalle.informatik.MiToBo.segmentation.snakes.energies with parameters of type MTBImageByte
MTBSnakeEnergyCDIB_Distance(MTBImageByte image, DistanceTransform.DistanceMetric d, DistanceTransform.ForegroundColor f)
          Constructor to create a new SnakeExternalEnergyDistance object.
 

Uses of MTBImageByte in de.unihalle.informatik.MiToBo.segmentation.thresholds
 

Fields in de.unihalle.informatik.MiToBo.segmentation.thresholds declared as MTBImageByte
protected  MTBImageByte HysteresisThresholding.resultImage
          Resulting binarized image.
 

Methods in de.unihalle.informatik.MiToBo.segmentation.thresholds that return MTBImageByte
 MTBImageByte ImgThreshNiblack.getResultImage()
          Get the resulting thresholded image.
 MTBImageByte HysteresisThresholding.getResultImage()
          Returns the result image.
 

Constructors in de.unihalle.informatik.MiToBo.segmentation.thresholds with parameters of type MTBImageByte
ImgThreshNiblack(MTBImage _inImg, ImgThreshNiblack.Mode mode, double k, double R, int wSize, int vcNB, double vcThresh, MTBImageByte _mask)
          Constructor.
 



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