Uses of Class
de.unihalle.informatik.MiToBo.core.operator.MTBOperator

Packages that use MTBOperator
de.unihalle.informatik.MiToBo.apps.actinAnalysis Provides tools and applications for quantifying actin filament structures in microscopy images of cells. 
de.unihalle.informatik.MiToBo.apps.neurites2D   
de.unihalle.informatik.MiToBo.apps.neurons2D   
de.unihalle.informatik.MiToBo.apps.nuclei2D   
de.unihalle.informatik.MiToBo.apps.particles2D   
de.unihalle.informatik.MiToBo.apps.scratchAssay   
de.unihalle.informatik.MiToBo.apps.singleCellTracking2D   
de.unihalle.informatik.MiToBo.apps.xylem   
de.unihalle.informatik.MiToBo.clustering   
de.unihalle.informatik.MiToBo.color.conversion   
de.unihalle.informatik.MiToBo.color.visualization   
de.unihalle.informatik.MiToBo.core.datatypes.images Contains MiToBo image data types. 
de.unihalle.informatik.MiToBo.enhance Provides classes for image preprocessing and improvement (no filters!). 
de.unihalle.informatik.MiToBo.features Provides operators for calculating features from given images, e.g., statistical indicators or texture measures. 
de.unihalle.informatik.MiToBo.features.statistical Provides operators for calculating statistical image features, e.g., average intensities or variances, or moments of the intensity distribution. 
de.unihalle.informatik.MiToBo.features.texture Provides operators for calculating texture features from given images, e.g., Haralick measures. 
de.unihalle.informatik.MiToBo.fields Provides classes for calculating gradient vector flow fields, image gradient fields, potential fields and other possible fields from different data sources. 
de.unihalle.informatik.MiToBo.filters.linear Provides classes implementing linear systems. 
de.unihalle.informatik.MiToBo.filters.linear.anisotropic   
de.unihalle.informatik.MiToBo.filters.nonlinear Provides classes implementing nonlinear image filters. 
de.unihalle.informatik.MiToBo.filters.vesselness Provides various operators for enhancing vessel-like structures in images. 
de.unihalle.informatik.MiToBo.io.images Provides classes for handling image files. 
de.unihalle.informatik.MiToBo.math.images Provides mathematical operations on images. 
de.unihalle.informatik.MiToBo.math.optimization   
de.unihalle.informatik.MiToBo.math.statistics This package contains oeprators for performing statistical analysis of data sets. 
de.unihalle.informatik.MiToBo.morphology Provides classes for morphological processing of binary images. 
de.unihalle.informatik.MiToBo.segmentation.basics   
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.core   
de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE   
de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver   
de.unihalle.informatik.MiToBo.segmentation.regions.convert   
de.unihalle.informatik.MiToBo.segmentation.regions.filling Provides operators for filling wholes in binary 2D/3D regions. 
de.unihalle.informatik.MiToBo.segmentation.regions.labeling Provides classes to perform region labeling to find connected components in binarized images. 
de.unihalle.informatik.MiToBo.segmentation.regions.mser   
de.unihalle.informatik.MiToBo.segmentation.thresholds Provides classes for thresholding grayscale and color images. 
de.unihalle.informatik.MiToBo.tools.image   
de.unihalle.informatik.MiToBo.tracking.multitarget.algo   
de.unihalle.informatik.MiToBo.tracking.multitarget.datatools   
de.unihalle.informatik.MiToBo.tracking.multitarget.eval   
de.unihalle.informatik.MiToBo.visualization.drawing Provides operators to visualize data types. 
de.unihalle.informatik.MiToBo.visualization.plots   
 

Uses of MTBOperator in de.unihalle.informatik.MiToBo.apps.actinAnalysis
 

Subclasses of MTBOperator in de.unihalle.informatik.MiToBo.apps.actinAnalysis
 class ActinAnalyzer2D
          Operator for analyzing actin filament structures in 2D images.
 class ActinFeatureExtractorEigenStructures
          Operator for extracting Eigen structures as features for the ActinAnalyzer2D.
 class ActinFeatureExtractorHaralickMeasures
          Operator for extracting Haralick texture measures from cooccurrence matrices as features for the ActinAnalyzer2D.
 

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

Subclasses of MTBOperator in de.unihalle.informatik.MiToBo.apps.neurites2D
 class NeuriteDetector2D
          The Neurite Detector 2D application offers advanced functionality to detect neurites in 2D fluorescence microscope images of neurons.
 class NeuriteExtractor2D
          The Neurite Extractor 2D application offers advanced functionality to extract neurite regions in 2D binary neuron images of neurons.
 class NeuriteMolProfExtractor2D
          The Neurite Molecular Profile Extractor 2D application offers advanced functionality to extract molecular intensity profiles of multichannel fluorescence images along detected neurite regions.
 class NeuriteParticleDetector2D
          This operator detects particles of a neuron image, for example from FISH analysis.
 

Uses of MTBOperator in de.unihalle.informatik.MiToBo.apps.neurons2D
 

Subclasses of MTBOperator in de.unihalle.informatik.MiToBo.apps.neurons2D
 class NeuronAnalyzer2D
           The Neuron Analyzer 2D application offers advanced functionality to analyze 2D fluorescence microscope images of neurons.
 

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

Subclasses of MTBOperator in de.unihalle.informatik.MiToBo.apps.nuclei2D
 class NuclearParticleDetector2D
           This class detects nuclei and particles inside these nuclei and gives some statistics about particles, like particle number per nuclei, particle size, sum of intensities, etc.
 class NucleusDetector2D
          Operator for segmenting cell nuclei in 2D images.
 class NucleusSeparator2D
          Class provides routines for separating conglomerates of cell nuclei in 2D.
 class NucleusSeparator2DAlgos
          Common super class for all nucleus separators.
 class NucleusSeparator2DBeamCut
          Class provides routines for separating conglomerates of cell nuclei in 2D.
 class NucleusSeparator2DPeakSearch
          Operator for separating merged nuclei regions in images.
 class NucleusSeparator2DPeakSearch_RegionSeparator
          Operator to analyze a given binary image or a set of nuclei regions.
 

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

Subclasses of MTBOperator in de.unihalle.informatik.MiToBo.apps.particles2D
 class MultiChannelParticleAnalyzer2D
          Operator for detecting sub-cellular structures in a given image.
 

Uses of MTBOperator in de.unihalle.informatik.MiToBo.apps.scratchAssay
 

Subclasses of MTBOperator in de.unihalle.informatik.MiToBo.apps.scratchAssay
 class ScratchAssayAnalyzer
          class for analyzing the scratch area in several scratch assay images
 class ScratchAssaySegmenter
          class for segmenting the wound area of a scratch assay image

First the image is smoothed.
 class ScratchAssaySVMTrainer
          class for training and cross validating a support vector machine for classification of scratch assay
images into images containing a scratch and those that don't
 

Uses of MTBOperator in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
 

Subclasses of MTBOperator in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
 class CellMigrationAnalyzer
          Operator for segmenting, tracking and analyzing 2D image sequences of fluorescently labeled cells
 class CellSegmentationPostprocessing
          operator for doing common postprocessing tasks on already segmented cell images
 class CellSegmenter
          base class for cell segmentation
 class CellTrackerBipartite
          This operator assigns unique labels to regions representing individual cells in the input binary image sequence
 class FluorescentCellSegmenter
          This operator is for segmenting images or image sequences containing fluorescently labeled cells
 class MigrationAnalyzer
          Operator for analyzing the movement pattern of cells as well as changes in morphology and fluorescence intensity
 

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

Subclasses of MTBOperator in de.unihalle.informatik.MiToBo.apps.xylem
 class XylemDetector
          This operator implements xylem detection in RGB or HSX images.
 class XylemGrower
          This operators implements region growing for xylem segmentation.
 class XylemInitialSegmentation
          Purpose of this operator is to make an initial segmentation of Xylem Cell Images.
 

Uses of MTBOperator in de.unihalle.informatik.MiToBo.clustering
 

Subclasses of MTBOperator in de.unihalle.informatik.MiToBo.clustering
 class KMeans
          Clustering of (feature) vectors with k-means based on Weka library.
 

Uses of MTBOperator in de.unihalle.informatik.MiToBo.color.conversion
 

Subclasses of MTBOperator in de.unihalle.informatik.MiToBo.color.conversion
 class HSIToRGBPixelConverter
          Operator to convert a single HSI value to RGB.
 class HSVToRGBPixelConverter
           Class to convert values from HSV color space into other color spaces like RGB or so.
 class RGBToHSXConverter
          Converts an image of type MTBImageRGB ( RGB color space ) into an image with HSX( hue saturation intensity/brightness/value ) color space.
 

Uses of MTBOperator in de.unihalle.informatik.MiToBo.color.visualization
 

Subclasses of MTBOperator in de.unihalle.informatik.MiToBo.color.visualization
 class ArrayToColorMapImage
          This operator visualizes a 2D array using a specified color mapping.
 

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

Subclasses of MTBOperator in de.unihalle.informatik.MiToBo.core.datatypes.images
 class MTBImage.MTBImageFactory
          A class for creating MTBImages which implements the MTBOperator.
 

Methods in de.unihalle.informatik.MiToBo.core.datatypes.images with parameters of type MTBOperator
 MTBImage MTBImage.convertType(MTBOperator callingOperator, MTBImage.MTBImageType type, boolean scaleDown)
          Create an image of given type from this image's values.
 MTBImage MTBImage.duplicate(MTBOperator callingOperator)
          Duplicates the object.
 MTBImage MTBImage.getCurrentSlice(MTBOperator callingOperator)
          Get a copy of the current slice.
 MTBImage MTBImage.getImagePart(MTBOperator callingOperator, int x, int y, int z, int t, int c, int sizeX, int sizeY, int sizeZ, int sizeT, int sizeC)
          Get a copy of a part of this image as new MTBImage.
 MTBImage MTBImage.getSlice(MTBOperator callingOperator, int z, int t, int c)
          Get a copy of the specified slice.
 

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

Subclasses of MTBOperator in de.unihalle.informatik.MiToBo.enhance
 class GammaCorrection2D
          Gamma correction on a 8- oder 16-bit image for one- or multi-channel images.
 class IlluminationCorrection
           This class corrects the uneven illumination (e.g. background gradient) of especially gray value bright filed or DIC images.
 class LocallyAdaptiveContrastEnhancement
          This class implements contrast enhancement for microscopy images.
 class TopHatContrastEnhancement
           This class enhances the contrast by top-hat operations, especially for gray value bright filed or DIC images.
 

Uses of MTBOperator in de.unihalle.informatik.MiToBo.features
 

Subclasses of MTBOperator in de.unihalle.informatik.MiToBo.features
 class FeatureCalculator
          Super class for operators calculating features on images.
 class TileFeatureCalculator
          Calculates features on images tile-wise, based on operators extending FeatureCalculator.
 

Uses of MTBOperator in de.unihalle.informatik.MiToBo.features.statistical
 

Subclasses of MTBOperator in de.unihalle.informatik.MiToBo.features.statistical
 class FeatureCalculatorIntensityStats
          Calculates statistical features on images tile-wise, based on FeatureCalculator.
 

Uses of MTBOperator in de.unihalle.informatik.MiToBo.features.texture
 

Subclasses of MTBOperator in de.unihalle.informatik.MiToBo.features.texture
 class FeatureCalculatorHaralickMeasures
          Calculates set of Haralick co-occurrence texture features from an image.
 

Uses of MTBOperator in de.unihalle.informatik.MiToBo.fields
 

Subclasses of MTBOperator in de.unihalle.informatik.MiToBo.fields
 class FieldOperations2D
          Class implements several operations on a 2D vector field.
 class GradientFieldCalculator2D
          Class to calculate a gradient vector field of a given image.
 class GVFFieldCalculator2D
          Class to calculate a special 2D vector field, a Gradient Vector Flow Field (GVF) with its x- and y-flows from the given image.
 

Uses of MTBOperator in de.unihalle.informatik.MiToBo.filters.linear
 

Subclasses of MTBOperator in de.unihalle.informatik.MiToBo.filters.linear
 class GaussFilter
          Multidimensional Gauss filter class.
 class LinearFilter
          Generic linear filter operation class
 class MeanFilter
          Multidimensional mean filter
 

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

Subclasses of MTBOperator in de.unihalle.informatik.MiToBo.filters.linear.anisotropic
 class ChaudhuriMatchedFilter2D
          2D Matched filter.
 class GaborFilter2D
          2D Gabor filter.
 class GaussPDxFilter2D
          2D linear filter implementing first partial derivative of a Gaussian in x.
 class GaussPDxxFilter2D
          2D filter implementing second partial derivative of Gaussian in x.
 class OrientedFilter2D
          Base class for anisotropic linear filters in 2D.
 class OrientedFilter2DBatchAnalyzer
          Base class for applying oriented filters in different orientations.
 

Uses of MTBOperator in de.unihalle.informatik.MiToBo.filters.nonlinear
 

Subclasses of MTBOperator in de.unihalle.informatik.MiToBo.filters.nonlinear
 class RankOperator
          Rank operator class to compute Median, Minimum or Maximum filter for hyperstack, stack and plain images.
 class StatisticsFilter
          class for calculating several statistical values for the neighborhood of the pixels
in an image
 

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

Subclasses of MTBOperator in de.unihalle.informatik.MiToBo.filters.vesselness
 class MedialnessMultiScaleFilter2D
           2D multi-scale medialness filter for vessel segmentation.
 class MFFDOGFilter2D
          MF-FDOG filter for vessel segmentation.
 class MFFDOGMultiScaleFilter2D
          MF-FDOG multi-scale filter for vessel segmentation.
 class MPMFFilter2D
          Multiscale Production of the Matched Filter (MPMF) implementation.
 

Uses of MTBOperator in de.unihalle.informatik.MiToBo.io.images
 

Subclasses of MTBOperator in de.unihalle.informatik.MiToBo.io.images
 class ImageReaderMTB
          Image reader operator to create MTBImage or ImagePlus objects from image files while reading and restoring image history from corresponding history files (.mph).
 class ImageWriterMTB
          Image writer operator to store MTBImage or ImagePlus to disk along with the image history (.mph) file.
 

Uses of MTBOperator in de.unihalle.informatik.MiToBo.math.images
 

Subclasses of MTBOperator in de.unihalle.informatik.MiToBo.math.images
 class ImageArithmetics
          Image arithmetics class for MTBImage objects.
 class ImageStatistics
          Class offering statistical calculations on objects of type MTBImage.
 

Constructors in de.unihalle.informatik.MiToBo.math.images with parameters of type MTBOperator
MTBImageArithmetics(MTBOperator callingOperator)
          Constructor with calling operator.
 

Uses of MTBOperator in de.unihalle.informatik.MiToBo.math.optimization
 

Subclasses of MTBOperator in de.unihalle.informatik.MiToBo.math.optimization
 class MatchingBipartite
          Base class for bipartite matching algorithms.
 class MatchingBipartite_HungarianAlgorithm
          Bipartite matching with Hungarian algorithm.
 

Uses of MTBOperator in de.unihalle.informatik.MiToBo.math.statistics
 

Subclasses of MTBOperator in de.unihalle.informatik.MiToBo.math.statistics
 class PCA
          This class implements the Karhunen-Loeve transformation, also known as PCA.
 

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

Subclasses of MTBOperator in de.unihalle.informatik.MiToBo.morphology
 class BasicMorphology
          class implementing basic morphological operations (for use with grayscale as well as with binary images)
 class ComponentPostprocess
          Methods for post-processing components/pixels in binary images.
 class DistanceTransform
           Class to calculate a distance map / field from a binary image using the Champfer-algorithm from G.
 class HDomeTransform3D
          H-dome transform in 3D (straightforward use with 2D-images).
 class ImgClose
          This class implements morphological closing on 2D binary/grayscale images.
 class ImgDilate
          This class implements morphological dilation on 2D binary/grayscale images.
 class ImgErode
          This class implements morphological erosion on 2D binary/grayscale images.
 class ImgOpen
          This class implements morphological opening on 2D binary/grayscale images.
 class ImgTophat
          This class implements the tophat operator.
 

Uses of MTBOperator in de.unihalle.informatik.MiToBo.segmentation.basics
 

Subclasses of MTBOperator in de.unihalle.informatik.MiToBo.segmentation.basics
 class CalcSegmentationStatistics
          Operator for doing statistical calculations on segmentations of images.
 class SegmentationInitializer
          Operator for initializing objects of type MTBSegmentationInterface.
 

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

Subclasses of MTBOperator in de.unihalle.informatik.MiToBo.segmentation.contours.extraction
 class BordersOnLabeledComponents
          Class to extract borders from connected components.
 class ContourOnLabeledComponents
          Class to segment contours from a binary image using the contour following algorithm.
 

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

Subclasses of MTBOperator in de.unihalle.informatik.MiToBo.segmentation.evaluation
 class CalcStructureStatistics
          Extracts statistics from cell and structure segmentation results.
 

Uses of MTBOperator in de.unihalle.informatik.MiToBo.segmentation.levelset.core
 

Subclasses of MTBOperator in de.unihalle.informatik.MiToBo.segmentation.levelset.core
 class LevelsetSolver
          Generic super class for level set solvers.
 class LevelsetSolverDerivatives
          Level set solver using variational calculus.
 

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

Subclasses of MTBOperator in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
 class LevelsetSegmentationNonPDE
          Operator intended as user interface for level set segmentation using nonPDE optimization and optionally topology preserving.
 class LevelsetSolveNonPDE
          Implements a level set solver which may optionally perserve the topology using non PDE optimization.
 

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

Subclasses of MTBOperator in de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver
 class LevelsetSolverPDE
          Solver for level set segmentation problems based on PDEs.
 

Uses of MTBOperator in de.unihalle.informatik.MiToBo.segmentation.regions.convert
 

Subclasses of MTBOperator in de.unihalle.informatik.MiToBo.segmentation.regions.convert
 class Region2DSetFromLabelimage
          Operator to convert 2D label image to a MTBRegionsSet2D.
 

Uses of MTBOperator in de.unihalle.informatik.MiToBo.segmentation.regions.filling
 

Subclasses of MTBOperator in de.unihalle.informatik.MiToBo.segmentation.regions.filling
 class FillHoles2D
          Operator to fill holes in connected components of binary or label image.
 

Uses of MTBOperator in de.unihalle.informatik.MiToBo.segmentation.regions.labeling
 

Subclasses of MTBOperator in de.unihalle.informatik.MiToBo.segmentation.regions.labeling
 class LabelComponentsSequential
          Sequential component labeling for binarized 2D images to find connected components.
 

Uses of MTBOperator in de.unihalle.informatik.MiToBo.segmentation.regions.mser
 

Subclasses of MTBOperator in de.unihalle.informatik.MiToBo.segmentation.regions.mser
 class DetectMSERs
          Implementation of maximally stable extremal regions based on ImgLib2.
 

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

Subclasses of MTBOperator in de.unihalle.informatik.MiToBo.segmentation.thresholds
 class CalcGlobalThreshOtsu
          This class implements routines to calculate Otsu's threshold from given grayscale images.
 class HysteresisThresholding
          Hysteresis thresholding on gray-scale images.
 class ImgThresh
          Image thresholding operator with lower threshold (threshold and upper threshold (upperThreshold.
 class ImgThreshNiblack
          Image binarization based on local Niblack thresholding.
 

Uses of MTBOperator in de.unihalle.informatik.MiToBo.tools.image
 

Subclasses of MTBOperator in de.unihalle.informatik.MiToBo.tools.image
 class CropImage
          Crop an image part.
 class ImageContrastReducer
          Contrast-reduction of images by reducing number of gray-scale values.
 class ImageConverter
          Plugin to convert images that are represented by MTBImage.
 class ImageDimensionReducer
           
 class ImageToTilesSplitter
          Operator to split an image into tiles and save them to disk.
 class ImageValueTools
          An operator class for different simple operations on the values of an image like inversion, filling with a constant value, etc.
 

Methods in de.unihalle.informatik.MiToBo.tools.image with parameters of type MTBOperator
static void ImageValueTools.fillImage(MTBImage img, Color rgbvalue, MTBOperator callingOperator)
          Fill the image with a RGB color value.
static void ImageValueTools.fillImage(MTBImage img, double grayvalue, MTBOperator callingOperator)
          Fill the specified image with a gray value.
static void ImageValueTools.invertImage(MTBImage img, MTBOperator callingOperator)
          Invert the specified image.
static void ImageValueTools.normImageFromTo(MTBImage img, double oldMinVal, double oldMaxVal, double newMinVal, double newMaxVal, MTBOperator callingOperator)
          Normalize the image values to range [lowerBound, upperBound].
static void ImageValueTools.normImageTo(MTBImage img, double lowerBound, double upperBound, MTBOperator callingOperator)
          Normalize the image values to range [lowerBound, upperBound].
 

Uses of MTBOperator in de.unihalle.informatik.MiToBo.tracking.multitarget.algo
 

Subclasses of MTBOperator in de.unihalle.informatik.MiToBo.tracking.multitarget.algo
 class MultiObservationTrackerRBMCDAIMM
          Tracking of multiple targets using Rao-Blackwellized Monte Carlo Data Association (RBMCDA) for observation-to-target association and Interacting Multiple Models (IMM) filters for target state estimation.
 

Uses of MTBOperator in de.unihalle.informatik.MiToBo.tracking.multitarget.datatools
 

Subclasses of MTBOperator in de.unihalle.informatik.MiToBo.tracking.multitarget.datatools
 class DataConverter<S,T>
          An operator class to convert between data types.
 

Uses of MTBOperator in de.unihalle.informatik.MiToBo.tracking.multitarget.eval
 

Subclasses of MTBOperator in de.unihalle.informatik.MiToBo.tracking.multitarget.eval
 class TrackEvaluator
           
 

Uses of MTBOperator in de.unihalle.informatik.MiToBo.visualization.drawing
 

Subclasses of MTBOperator in de.unihalle.informatik.MiToBo.visualization.drawing
 class DrawPolygon2DSet
          A class to visualize 2D polygons.
 class DrawRegion2DSet
          A class to visualize 2D regions.
 class DrawTracks2D
          Draw trajectories of tracked observations over time.
 class MTBPlotHistogram
          A class to visualize 2D polygons.
 

Uses of MTBOperator in de.unihalle.informatik.MiToBo.visualization.plots
 

Subclasses of MTBOperator in de.unihalle.informatik.MiToBo.visualization.plots
 class BoxWhiskerChartPlotter
          Operator that generates box-whisker plots using JFreeChart.
 class StackedBarChartPlotter
          Operator that generates stacked bar plots using JFreeChart.
 



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