Modifier and Type | Class and Description |
---|---|
class |
ArealParameterExtractor
operator for calculating areal parameters from biofilm images as described in
Yang et al., Quantifying biofilm structure using image analysis.
|
class |
TexturalParameterExtractor
operator for calculating textural parameters from biofilm images as described in
Yang et al., Quantifying biofilm structure using image analysis.
|
Modifier and Type | Class and Description |
---|---|
class |
FeatureColorMapper
This operator maps numerical feature values to objects in an indexed image.
|
class |
PaCeQuant
Operator for segmenting and analyzing pavement cell shape.
|
private class |
PaCeQuant.SkeletonPostprocessor
Helper operator to post-process border skeletons.
|
Modifier and Type | Class and Description |
---|---|
class |
CellBoundaryExtractor2D
Operator for segmenting cell boundaries in microtubuli experiments.
|
Modifier and Type | Class and Description |
---|---|
class |
ActinAnalyzer2D
Operator for analyzing actin filament structures in 2D images.
|
class |
CytoskeletonAnalyzer2D
Operator for extracting quantative global features of the cytoskeleton.
|
class |
CytoskeletonFeatureExtractor
Operator for extracting features for the
ActinAnalyzer2D . |
class |
CytoskeletonFeatureExtractorEigenStructures
Operator for extracting Eigen structures as features for the
ActinAnalyzer2D . |
class |
CytoskeletonFeatureExtractorHaralickMeasures
Operator for extracting Haralick texture measures from
co-occurrence matrices as features for the
ActinAnalyzer2D . |
class |
CytoskeletonFeatureExtractorLBPs
Operator for extracting LBP features for the
ActinAnalyzer2D . |
class |
CytoskeletonFeatureExtractorLBPsRIU
Operator for extracting LBP RIU features for the
ActinAnalyzer2D . |
class |
CytoskeletonFeatureExtractorTiles
Operator for extracting features for the
ActinAnalyzer2D . |
Modifier and Type | Class and Description |
---|---|
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.
|
Modifier and Type | Class and Description |
---|---|
class |
NeuronAnalyzer2D
The Neuron Analyzer 2D application offers advanced functionality to analyze
2D fluorescence microscope images of neurons.
|
Modifier and Type | Class and Description |
---|---|
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.
|
Modifier and Type | Class and Description |
---|---|
class |
MultiChannelParticleAnalyzer2D
Operator for detecting sub-cellular structures in a given image.
|
Modifier and Type | Class and Description |
---|---|
class |
PlastidDetector2DParticlesUWT
Operator to detect plastid regions in 2D microscope images.
|
Modifier and Type | Class and Description |
---|---|
class |
StromulesDetector2D
Operator to detect stromules in microscope images of plastids.
|
Modifier and Type | Class and Description |
---|---|
class |
ScratchAssayAnalyzer
class for analyzing the scratch areas in a scratch assay/ gap closure/ wound closure assay
|
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 |
Modifier and Type | Class and Description |
---|---|
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 |
IntensityAnalyzer |
class |
ManualTrackingMigrationAnalyzer |
class |
ManualTrackingTrajectoryExtraction |
class |
MigrationAnalyzer
Operator for analyzing the movement pattern of cells as well as changes in morphology and fluorescence intensity
|
class |
ReportGenerator |
class |
ShapeAnalyzer |
class |
TrackAnalyzer
class for analyzing movement and shape of already tracked objects in a given label image
|
Modifier and Type | Class and Description |
---|---|
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.
|
Modifier and Type | Class and Description |
---|---|
class |
KMeans
Clustering of (feature) vectors with k-means based on Weka library.
|
Modifier and Type | Class and Description |
---|---|
class |
HSIToRGBPixelConverter
Operator to convert a single HSI value to RGB.
|
class |
HSVToRGBArrayConverter
Class to convert a whole array of values from HSV color space 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. |
Modifier and Type | Class and Description |
---|---|
class |
DistinctColorListGenerator
Operator generating a list of N colors with subsequent colors being
significantly different to each other.
|
Modifier and Type | Class and Description |
---|---|
private class |
MTBRegion2DSet.RegionSelector |
Modifier and Type | Class and Description |
---|---|
class |
MTBImage.MTBImageFactory
A class for creating MTBImages which implements the MTBOperator.
|
Modifier and Type | Method and Description |
---|---|
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)
Deprecated.
|
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.
|
Modifier and Type | Class and Description |
---|---|
class |
RoiFileToCSVConverter
Operator to convert contours of ImageJ ROIs to CSV format.
|
private static class |
RoiManagerAdapter.RoiReader
Class for parsing ImageJ roi files and zip archives.
|
class |
RoiWriter
Operator to save data objects to native ImageJ ROIs.
|
Modifier and Type | Class and Description |
---|---|
class |
GammaCorrection2D
Gamma correction on a 8- oder 16-bit image for one- or multi-channel images.
|
class |
GlobalContrastStretching
Global contrast stretching.
|
class |
HistogramEqualization
Histogram linearization by entropy maximization.
|
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.
|
Modifier and Type | Class and Description |
---|---|
class |
FeatureCalculator
Super class for operators calculating features on images.
|
class |
MorphologyAnalyzer2D
Operator to extract shape and region features for given regions.
|
class |
MorphologyAnalyzer3D |
class |
SurfaceExtraction
Operator for extracting the surface areas of 3D-objects.
|
class |
TileFeatureCalculator
Calculates features on images tile-wise, based on operators extending
FeatureCalculator . |
Modifier and Type | Class and Description |
---|---|
class |
Contour2DConcavityCalculator
class for calculating concaveness of contour pixels according to the method proposed in:
Fernandez, G., Kunt, M. & Zryd, J.P. (1995) A new plant image segmentation algorithm.
|
class |
Contour2DCurvatureCalculator
Implementation of curvature estimating algorithm's for discrete curved lines
in a 2D space.
|
Modifier and Type | Class and Description |
---|---|
class |
Region2DSkeletonAnalyzer
Operator to analyze skeletons of a given set of regions.
|
Modifier and Type | Class and Description |
---|---|
class |
FeatureCalculatorIntensityStats
Calculates statistical features on images tile-wise,
based on
FeatureCalculator . |
Modifier and Type | Class and Description |
---|---|
class |
FeatureCalculatorHaralickMeasures
Calculates set of Haralick co-occurrence texture features from an image.
|
Modifier and Type | Class and Description |
---|---|
class |
FeatureCalculatorLBP
Implements an extended version of local binary patterns (LBPs).
|
class |
FeatureCalculatorLBPJFeatureLib
Abstract super class for LBP operators building on the JFeatureLib.
|
class |
FeatureCalculatorLBPOriginal
Operator for extracting Local Binary Patterns (LBPs).
|
class |
FeatureCalculatorLBPRIU
Implements rotation invariant uniform local binary patterns (LBP-RIU).
|
Modifier and Type | Class and Description |
---|---|
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 |
GradientFieldNonMaxSuppression
Non-Maximum-Suppression and (optional) hysteresis thresholding on
gradient fields.
|
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.
|
Modifier and Type | Class and Description |
---|---|
class |
GaussFilter
Multidimensional Gauss filter class.
|
class |
LinearFilter
Generic linear filter operation class
|
class |
MeanFilter
Multidimensional mean filter
|
Modifier and Type | Class and Description |
---|---|
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.
|
Modifier and Type | Class and Description |
---|---|
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
|
Modifier and Type | Class and Description |
---|---|
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.
|
class |
StegerRidgeDetection2DWrapper
Wrapper for Ridge Detection plugin by Carsten Steger (and Thorsten Wagner).
|
Modifier and Type | Class and Description |
---|---|
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.
|
Modifier and Type | Class and Description |
---|---|
class |
GetMTBContour2DSetFromXSVFiles
Read a
MTBContour2DSet from a list of ASCII xSV files. |
Modifier and Type | Class and Description |
---|---|
class |
ArrayFilterDouble1D
This class defines a superclass for filters for 1D arrays.
|
class |
GaussFilterDouble1D
This class implements a Gaussian filter for 1D arrays.
|
Modifier and Type | Class and Description |
---|---|
class |
FitEllipseToPointSet
Operator that fits an ellipse to a given set of 2D points.
|
class |
FitQuadraticCurveToPointSet
Operator that fits a quadratic curve or conic to a given set of 2D points.
|
Modifier and Type | Class and Description |
---|---|
class |
DijkstraShortestPixelPathFinder
Search shortest path between two pixels in an image using Dijkstra.
|
Modifier and Type | Class and Description |
---|---|
class |
ImageArithmetics
Image arithmetics class for
MTBImage objects. |
class |
ImageStatistics
Class offering statistical calculations on objects of type
MTBImage . |
Modifier and Type | Field and Description |
---|---|
private MTBOperator |
MTBImageArithmetics.callingOperator |
Modifier and Type | Method and Description |
---|---|
private MTBImage |
MTBImageArithmetics.runOperation(MTBOperator callingOperator,
ImageArithmetics.ArithOp op,
MTBImage img,
double constant)
Run an operation with one input image and one input constant
|
private MTBImage |
MTBImageArithmetics.runOperation(MTBOperator callingOperator,
ImageArithmetics.ArithOp op,
MTBImage img1,
MTBImage img2)
Run an operation with two input images
|
Constructor and Description |
---|
MTBImageArithmetics(MTBOperator callingOperator)
Constructor with calling operator.
|
Modifier and Type | Class and Description |
---|---|
class |
MatchingBipartite
Base class for bipartite matching algorithms.
|
class |
MatchingBipartite_HungarianAlgorithm
Bipartite matching with Hungarian algorithm.
|
Modifier and Type | Class and Description |
---|---|
class |
PCA
This class implements the Karhunen-Loeve transformation, also known as PCA.
|
Modifier and Type | Class and Description |
---|---|
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 |
ConvexHullExtraction
operator for calculating the convex hulls of binary connected components
in a given image or of a set of regions using the Jarvis march algorithm |
class |
DistanceTransform
Calculate Champfer distance transform with optional precursor infos.
|
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.
|
class |
SkeletonExtractor
Extracts skeleton of foreground region.
|
class |
SkeletonPostprocessor
Helper operator to post-process binary region skeletons.
|
class |
WatershedBinary
Watershed transformation on binary images.
|
Modifier and Type | Class and Description |
---|---|
class |
CalcSegmentationStatistics
Operator for doing statistical calculations on segmentations of images.
|
class |
SegmentationInitializer
Operator for initializing objects of type
MTBSegmentationInterface . |
Modifier and Type | Class and Description |
---|---|
class |
BordersOnLabeledComponents
Class to extract borders from connected components.
|
class |
ContourOnLabeledComponents
Class to segment contours from a binary image using the contour following
algorithm.
|
Modifier and Type | Class and Description |
---|---|
private static class |
CalcQualityMeasures.PrecisionCalc
Internal operator for precision calculation.
|
private static class |
CalcQualityMeasures.RecallCalc
Internal operator for recall calculation.
|
class |
CalcStructureStatistics
Extracts statistics from cell and structure segmentation results.
|
class |
GroundtruthEvaluation
Implementation of segmentation evaluation measures.
|
Modifier and Type | Class and Description |
---|---|
class |
EvaluationMeasure
Base class for evaluation measures comparing a segmentation result
against a groundtruth segmentation.
|
class |
EvaluationMeasureContours
Class implements the super class for contour detection evaluation operators.
|
class |
Measure_DetectionErrors
This class implements 3 detection errors for contour detection evaluation.
|
class |
Measure_HausdorffDistance
The class implements the Hausdorff Distance for contour detection evaluation.
|
class |
Measure_OdetsCriteria
This class implements Odet's contour detection evaluation criteria for
oversegmentation (OCO) and undersegmentation (OCU).
|
class |
Measure_PrattsFigureOfMerit
This class implements Pratt's figure of merit for contour detection evaluation.
|
class |
Measure_RecallPrecisionF
Class for evaluating recalls, precisions, F1-scores and Jaccard indices.
|
class |
PreprocessLabelImages
Helper class to preprocess label images for segmentation evaluation.
|
Modifier and Type | Class and Description |
---|---|
class |
LabelImageConverter
Converts (pseudo-) colored RGB labels to unique gray-scale labels.
|
Modifier and Type | Class and Description |
---|---|
class |
LevelsetSolver
Generic super class for level set solvers.
|
class |
LevelsetSolverDerivatives
Level set solver using variational calculus.
|
Modifier and Type | Class and Description |
---|---|
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.
|
Modifier and Type | Class and Description |
---|---|
class |
LevelsetSolverPDE
Solver for level set segmentation problems based on PDEs.
|
Modifier and Type | Class and Description |
---|---|
class |
Region2DSetFromLabelimage
Operator to convert 2D label image to a MTBRegionsSet2D.
|
Modifier and Type | Class and Description |
---|---|
class |
FillHoles2D
Operator to fill holes in connected components of binary or label images.
|
Modifier and Type | Class and Description |
---|---|
class |
LabelComponentsSequential
Sequential component labeling for binarized 2D images to find
connected components.
|
Modifier and Type | Class and Description |
---|---|
class |
DetectMSERs
Implementation of maximally stable extremal regions based on ImgLib2.
|
Modifier and Type | Class and Description |
---|---|
private class |
MTBSnake.SnakeCloner
Operator class to construct new snake object from a given one.
|
protected class |
SnakeHelperOperators.ContourConverter
Operator class to convert a contour into a snake.
|
protected class |
SnakeHelperOperators.ImageMaker
Operator class to draw snake to an image.
|
protected class |
SnakeHelperOperators.MaskMaker
Operator class to generate 2D array mask for snake interior.
|
protected class |
SnakeHelperOperators.RegionConverter
Operator class to convert a region into a snake.
|
protected class |
SnakeHelperOperators.RegionImageConverter
Operator class to extract snakes from a region image.
|
Modifier and Type | Class and Description |
---|---|
class |
CalcGlobalThreshOtsu
This class implements Otsu's method for calculating an optimal
threshold for a 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.
|
Modifier and Type | Class and Description |
---|---|
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
Operator to reduce image dimension by projecting multi-dimensional
images along selected dimensions.
|
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.
|
Modifier and Type | Method and Description |
---|---|
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].
|
Modifier and Type | Class and Description |
---|---|
class |
LabelImageEditor
A small interactive tool for editing label images by mouse-clicks.
|
Modifier and Type | Class and Description |
---|---|
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.
|
Modifier and Type | Class and Description |
---|---|
class |
DataConverter<S,T>
An operator class to convert between data types.
|
Modifier and Type | Class and Description |
---|---|
class |
TrackEvaluator |
Modifier and Type | Class and Description |
---|---|
class |
ArrayToColorMapImage
This operator visualizes a 2D array using a specified color mapping.
|
class |
GrayscaleImageToHeatmap
This operator converts a gray-scale image to a heat map image.
|
class |
GrayscaleToGrayscaleMapping
This operator transforms the intensity values of a gray-scale image
according to a given intensity mapping.
|
Modifier and Type | Class and Description |
---|---|
class |
DrawContour2DSet
A class to visualize 2D contours.
|
class |
DrawEllipse
Operator to draw an ellipse to a given image.
|
class |
DrawLine
Implementation of the Bresenham line drawing algorithm according to
Wikipedia.
|
class |
DrawMask2D
Operator for drawing a mask into an image.
|
class |
DrawPolygon2DSet
A class to visualize 2D polygons.
|
class |
DrawRegion2DSet
A class to visualize 2D regions.
|
class |
DrawStringToImage
Operator to draw a given string into a given image.
|
class |
DrawTracks2D
Draw trajectories of tracked observations over time.
|
class |
MTBPlotHistogram
A class to visualize 2D polygons.
|
Modifier and Type | Class and Description |
---|---|
class |
BoxWhiskerChartPlotter
Operator that generates box-whisker plots using JFreeChart.
|
class |
StackedBarChartPlotter
Operator that generates stacked bar plots using JFreeChart.
|
Copyright © 2010–2020 Martin Luther University Halle-Wittenberg, Institute of Computer Science, Pattern Recognition and Bioinformatics. All rights reserved.