Modifier and Type | Field and Description |
---|---|
private MTBRegion2DSet |
PaCeQuant.inRegions
Input image to process.
|
private MTBRegion2DSet |
PaCeQuant.resultCellRegions
Set of detected cell regions.
|
MTBRegion2DSet |
PaCeQuant.SegmentationResult.resultRegs
Set of segmented regions.
|
Modifier and Type | Method and Description |
---|---|
private MTBRegion2DSet |
PaCeQuant.filterValidCellRegions(MTBImageByte image)
Postprocesses cell regions and applies some filtering.
|
Modifier and Type | Method and Description |
---|---|
private MTBTableModel |
PaCeQuant.calculateRegionFeatures(MTBRegion2DSet regions,
MTBImage labelImg)
Extracts features for all detected and valid cell regions.
|
protected MTBTableModel |
PaCeQuant.runFeatureExtractionPhase(MTBImage img,
MTBRegion2DSet validRegions,
MTBImage labelImg)
Extracts features from given set of regions and corresponding images
|
protected void |
PaCeQuant.saveRegionData(String resultDir,
String fileRoot,
MTBRegion2DSet regions)
Save region set to output file.
|
Modifier and Type | Field and Description |
---|---|
private MTBRegion2DSet |
CellBoundaryExtractor2D.cellContours
Set of extracted regions.
|
private MTBRegion2DSet |
CellBoundaryExtractor2D.resultCellContours
ROI set of detected cell regions.
|
Modifier and Type | Field and Description |
---|---|
protected MTBRegion2DSet |
SegResult_Nuclei.nucleiRegions
Set of detected regions.
|
protected MTBRegion2DSet |
SegResult_Particles.particleRegions
List of detected regions.
|
Modifier and Type | Method and Description |
---|---|
MTBRegion2DSet |
SegResult_Nuclei.getNucleiRegions()
Returns set of detected regions.
|
Modifier and Type | Method and Description |
---|---|
void |
SegResult_Nuclei.setNucleiRegions(MTBRegion2DSet regs)
Specify set of regions.
|
Constructor and Description |
---|
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.
|
Modifier and Type | Field and Description |
---|---|
private MTBRegion2DSet |
NeuriteParticleDetector2D.detectedParticles |
Modifier and Type | Method and Description |
---|---|
private MTBRegion2DSet |
NeuriteExtractor2D.generateNeuriteRegions(Vector<Vector<Vector<Line2D.Double>>> lines,
Vector<Vector<Vector<Point2D.Double>>> points)
Generate neurite region from calculated features.
|
MTBRegion2DSet |
NeuriteParticleDetector2D.getDetectedParticles()
Get regions of detected particles.
|
private MTBRegion2DSet |
NeuriteDetector2DAlgos.getSnakeRegion(MTBPolygon2DSet theSnakes)
Get the region which is included in the snake contour.
|
Modifier and Type | Method and Description |
---|---|
private MTBRegion2DSet |
NeuronAnalyzer2D.extractParticles(MTBImage particleImage,
MTBNeurite2DSet neuriteSet)
Extraction of molecular particles along the detected neurites.
|
Modifier and Type | Field and Description |
---|---|
private MTBRegion2DSet |
NucleusSeparator2DPeakSearch_RegionSeparator.candidates |
private MTBRegion2DSet |
NucleusSeparator2DPeakSearch_RegionSeparator.inputRegions
Optional set of pre-segmented input regions.
|
private MTBRegion2DSet |
NuclearParticleDetector2D.nucleiRegions |
private MTBRegion2DSet |
NuclearParticleDetector2D.particleRegions |
private MTBRegion2DSet[] |
NucleusSeparator2DPeakSearch_RegionSeparator.resultAreas |
private MTBRegion2DSet |
NucleusSeparator2DPeakSearch_RegionSeparator.resultCenters
Set of detected nuclei centers.
|
private MTBRegion2DSet[] |
NucleusSeparator2DPeakSearch_RegionSeparator.resultRegCenters
Nuclei centers sorted according to former regions.
|
Modifier and Type | Method and Description |
---|---|
MTBRegion2DSet |
NucleusSeparator2DPeakSearch_RegionSeparator.getCandidates()
Returns set of detected candidate peaks.
|
MTBRegion2DSet |
NucleusSeparator2DPeakSearch_RegionSeparator.getInputRegs()
Get set of input regions.
|
MTBRegion2DSet |
NucleusSeparator2DPeakSearch.getNRSCandidates()
Returns possible peak locations from NucleusRegionSeperator.
|
MTBRegion2DSet[] |
NucleusSeparator2DPeakSearch.getNRSResultAreas()
Returns set of result regions from region separator.
|
MTBRegion2DSet |
NucleusSeparator2DPeakSearch.getNRSResultCenters()
Returns set of detected region centers from region separator.
|
MTBRegion2DSet |
NuclearParticleDetector2D.getNucleiRegions()
Get detected nuclei regions.
|
MTBRegion2DSet |
NucleusSeparator2DPeakSearch.getOtsuRegs()
Returns set of regions resulting from Otsu thresholding.
|
MTBRegion2DSet |
NuclearParticleDetector2D.getParticleRegions()
Get detected particle regions.
|
MTBRegion2DSet[] |
NucleusSeparator2DPeakSearch_RegionSeparator.getRegCenters()
Returns the centers of the nuclei sorted to their original regions.
|
MTBRegion2DSet[] |
NucleusSeparator2DPeakSearch_RegionSeparator.getResultAreas()
Returns separated regions sorted according to original regions.
|
MTBRegion2DSet |
NucleusSeparator2DPeakSearch_RegionSeparator.getResultCenters()
Returns centers of result regions.
|
Modifier and Type | Method and Description |
---|---|
private Vector<Vector<Integer>> |
NuclearParticleDetector2D.matchParticles(MTBRegion2DSet tmpPartRegions)
Match particle regions to nuclei regions.
|
void |
NucleusSeparator2DPeakSearch_RegionSeparator.setInputRegs(MTBRegion2DSet _inputRegions)
Specify set of input regions.
|
Constructor and Description |
---|
NucleusSeparator2DPeakSearch_RegionSeparator(MTBRegion2DSet oset)
Constructor with region set.
|
Modifier and Type | Field and Description |
---|---|
private MTBRegion2DSet |
ParticleDetectorUWT2D.resultingRegions
Set of detected particle regions.
|
Modifier and Type | Method and Description |
---|---|
MTBRegion2DSet |
ParticleDetectorUWT2D.getResults()
Get resulting regions (each detetection corresponds to a region)
|
Modifier and Type | Method and Description |
---|---|
protected MTBImage |
ParticleDetectorUWT2D.labelImage(MTBImage img,
MTBRegion2DSet regs) |
protected MTBImage |
ParticleDetectorUWT2D.processedRegionsToBinImage(MTBImage img,
MTBRegion2DSet regs,
int _minRegionSize)
Create a binary image from given regions.
|
protected void |
ParticleDetectorUWT2D.setResults(MTBRegion2DSet detectedRegions)
Set detected regions
|
Modifier and Type | Field and Description |
---|---|
private MTBRegion2DSet |
PlastidDetector2DParticlesUWT.plastidRegions
Set of detected plastid regions with stromuli.
|
Modifier and Type | Method and Description |
---|---|
MTBRegion2DSet |
PlastidDetector2DParticlesUWT.getPlastidRegions()
Access detected plastid regions.
|
Modifier and Type | Field and Description |
---|---|
private MTBRegion2DSet |
StromulesDetector2D.candidateRegions
List of stromule candidate regions.
|
private MTBRegion2DSet |
StromulesDetector2D.plastidRegions
(Optional) set of detected plastid regions.
|
private MTBRegion2DSet |
StromulesDetector2D.stromuliRegions
Set of detected plastid regions with stromuli.
|
Modifier and Type | Method and Description |
---|---|
private MTBRegion2DSet |
StromulesDetector2D.preprocessPlastidRegions()
Pre-filtering of plastid regions to find regions accidentally including
already a stromule.
|
Modifier and Type | Method and Description |
---|---|
private void |
StromulesDetector2D.detectStromuliRidgeModel(MTBImageShort roiImgDilated,
MTBRegion2DSet dilatedROIs)
Detect stromule candidates applying Steger operator.
|
Modifier and Type | Method and Description |
---|---|
private MTBRegion2DSet |
CellSegmentationPostprocessing.excludeBorderRegions(MTBRegion2DSet regions)
exclude regions that are adjacent to the image borders
|
private MTBRegion2DSet |
CellSegmentationPostprocessing.excludeLargeRegions(MTBRegion2DSet regions)
exclude regions that are larger than the predefined (Parameter maxArea) maximum
|
private MTBRegion2DSet |
CellSegmentationPostprocessing.excludeSmallRegions(MTBRegion2DSet regions)
exclude regions that are smaller than the predefined (Parameter minArea) minimum
|
private MTBRegion2DSet |
CellTrackerBipartite.label(MTBImage img) |
Modifier and Type | Method and Description |
---|---|
private byte[][] |
CellTrackerBipartite.assign(MTBRegion2DSet currentRegions,
MTBRegion2DSet nextRegions)
assign regions from one frame to regions from another frame
|
private MTBImage |
CellTrackerBipartite.drawRegions(MTBRegion2DSet regions) |
private void |
CellSegmentationPostprocessing.drawRegions(MTBRegion2DSet keepRegions,
int z,
int t,
int c)
draw regions to the output image
|
private MTBRegion2DSet |
CellSegmentationPostprocessing.excludeBorderRegions(MTBRegion2DSet regions)
exclude regions that are adjacent to the image borders
|
private MTBRegion2DSet |
CellSegmentationPostprocessing.excludeLargeRegions(MTBRegion2DSet regions)
exclude regions that are larger than the predefined (Parameter maxArea) maximum
|
private MTBRegion2DSet |
CellSegmentationPostprocessing.excludeSmallRegions(MTBRegion2DSet regions)
exclude regions that are smaller than the predefined (Parameter minArea) minimum
|
private double[][] |
CellTrackerBipartite.getAreaFracMatrix(MTBRegion2DSet currRegions,
MTBRegion2DSet nextRegions) |
private double[][] |
CellTrackerBipartite.getDistMatrix(MTBRegion2DSet currRegions,
MTBRegion2DSet nextRegions) |
private MTBImage |
CellTrackerBipartite.relabel(byte[][] a,
int n,
int m,
MTBRegion2DSet nextRegions)
find and assign object labels to segmented objects in two frames
|
Modifier and Type | Method and Description |
---|---|
(package private) static MTBRegion2DSet |
XylemGrower.labelComponentsOfImage(MTBImage image)
Label a MTBImage.
|
Modifier and Type | Method and Description |
---|---|
private MTBTableModel |
XylemGrower.makeTable(MTBRegion2DSet regionSet,
MTBImage labelImg,
int imgWidth,
int imgHeight)
create results table
|
private static Collection<MTBRegion2D> |
XylemGrower.sortRegionSetBy(MTBRegion2DSet regionSet,
XylemGrower.SortMode sortMode) |
Modifier and Type | Field and Description |
---|---|
(package private) MTBRegion2DSet |
MTBRegion2DSet.RegionSelector.inRegs |
(package private) MTBRegion2DSet |
MTBRegion2DSet.RegionSelector.outRegs |
Modifier and Type | Field and Description |
---|---|
(package private) Vector<MTBRegion2DSet> |
MTBRegion2DSetBag.regionsets
the container of the region sets
|
Modifier and Type | Method and Description |
---|---|
MTBRegion2DSet |
MTBRegion2DSet.clone() |
MTBRegion2DSet |
MTBRegion2DSetBag.get(int idx) |
MTBRegion2DSet |
MTBRegion2DSetBag.remove(int idx)
Remove a region set from this bag by its index
|
MTBRegion2DSet |
MTBRegion2DSet.selectLargeRegions(int minSize) |
Modifier and Type | Method and Description |
---|---|
Iterator<MTBRegion2DSet> |
MTBRegion2DSetBag.iterator() |
Modifier and Type | Method and Description |
---|---|
void |
MTBRegion2DSetBag.add(MTBRegion2DSet regionset)
Add a region set to this bag
|
boolean |
MTBRegion2DSetBag.remove(MTBRegion2DSet regionset)
Remove a region set from this bag
|
void |
MTBRegion2DSetBag.set(int idx,
MTBRegion2DSet regionset) |
Constructor and Description |
---|
RegionSelector(MTBRegion2DSet input,
int msize) |
Modifier and Type | Field and Description |
---|---|
private MTBRegion2DSet |
MTBNeurite2D.growthCones
Neurite corresponding growth cone regions as MTBRegion2D objects.
|
Modifier and Type | Method and Description |
---|---|
MTBRegion2DSet |
MTBNeurite2D.getGrowthConeRegions()
Get regions of the separated growth cones.
|
Modifier and Type | Field and Description |
---|---|
private MTBRegion2DSet |
RoiManagerAdapter.RoiReader.regions
Result region set, if target format are regions.
|
private MTBRegion2DSet |
MTBRegion2DSetROI.regionSet
Set of 2D regions.
|
Modifier and Type | Method and Description |
---|---|
MTBRegion2DSet |
RoiManagerAdapter.RoiReader.getRegionSet()
Get the region set.
|
MTBRegion2DSet |
MTBRegion2DSetROI.getRegionSet()
Get 2D region set from Roi.
|
MTBRegion2DSet |
RoiManagerAdapter.getRegionSetFromRoiFile(String file)
Reads an ImageJ roi file into a set of regions.
|
MTBRegion2DSet |
RoiManagerAdapter.getRegionSetFromRoiFile(String file,
double xMin,
double yMin,
double xMax,
double yMax)
Reads an ImageJ roi file into a set of regions.
|
MTBRegion2DSet |
RoiManagerAdapter.getRegionSetFromRoiManager()
Reads a ROI manager selection into a set of regions.
|
Modifier and Type | Method and Description |
---|---|
void |
RoiManagerAdapter.addRegionsToRoiManager(MTBRegion2DSet regs)
Adds a set of 2D regions to the ROI manager.
|
Constructor and Description |
---|
MTBRegion2DSetROI(MTBRegion2DSet regSet,
String roiLabel)
Constructor to create a new Roi-Manager-Object, based on a MTBRegion2DSet.
|
Modifier and Type | Method and Description |
---|---|
private MTBRegion2DSet |
LocallyAdaptiveContrastEnhancement.extractLocalComponents()
Extracts list of connected components from Otsu thresholded input image.
|
Modifier and Type | Field and Description |
---|---|
private MTBRegion2DSet |
MorphologyAnalyzer2D.inRegions |
private MTBRegion2DSet |
MorphologyAnalyzer2D.regions |
Modifier and Type | Method and Description |
---|---|
void |
MorphologyAnalyzer2D.setRegionSet(MTBRegion2DSet regs)
Set regions.
|
Constructor and Description |
---|
MorphologyAnalyzer2D(MTBRegion2DSet rs) |
Modifier and Type | Field and Description |
---|---|
private MTBRegion2DSet |
CellCntrSegResultRegions.detectedRegions
Set of pre-segmented regions.
|
Modifier and Type | Method and Description |
---|---|
MTBRegion2DSet |
CellCntrSegResultRegions.getRegions()
Get set of segmented regions.
|
Constructor and Description |
---|
CellCntrSegResultRegions(MTBImage img,
MTBRegion2DSet regs)
Constructor.
|
CellCntrSegResultRegions(MTBImage img,
MTBRegion2DSet regs,
MTBBorder2DSet borders,
Vector<Double> avgIntensities)
Constructor.
|
Modifier and Type | Field and Description |
---|---|
private MTBRegion2DSet |
ConvexHullExtraction.inRegions
Set of input regions.
|
Modifier and Type | Method and Description |
---|---|
private void |
ConvexHullExtraction.extractHullsOnRegions(MTBRegion2DSet regs) |
void |
ConvexHullExtraction.setInputRegions(MTBRegion2DSet regs)
Set input regions (if
ConvexHullExtraction.inType is InputType.REGIONS ). |
Modifier and Type | Field and Description |
---|---|
protected MTBRegion2DSet |
SegmentationInitializer.regionSet |
Modifier and Type | Method and Description |
---|---|
MTBRegion2DSet |
SegmentationInitializer.getRegionSet()
Get the region set.
|
Modifier and Type | Method and Description |
---|---|
void |
SegmentationInitializer.setRegionSet(MTBRegion2DSet _regionSet)
Set the region set.
|
Modifier and Type | Field and Description |
---|---|
private MTBRegion2DSet |
BordersOnLabeledComponents.inputRegions
(Optional) region set where the borders should be extracted from.
|
private MTBRegion2DSet |
ContourOnLabeledComponents.inputRegions
The input regions where the contours should be calculated from.
|
Modifier and Type | Method and Description |
---|---|
MTBRegion2DSet |
ContourOnLabeledComponents.getInputRegions()
Get reference to the input regions.
|
Modifier and Type | Method and Description |
---|---|
protected MTBContour2DSet |
ContourOnLabeledComponents.getOuterContours(MTBRegion2DSet theRegions,
MTBImageByte theImage)
Calculate the outer contours of the given regions in a image.
|
void |
BordersOnLabeledComponents.setInputRegions(MTBRegion2DSet inRegions)
Set input regions.
|
void |
ContourOnLabeledComponents.setInputRegions(MTBRegion2DSet inRegions)
Set reference to the the input regions.
|
Constructor and Description |
---|
BordersOnLabeledComponents(MTBImage inImg,
MTBRegion2DSet inRegions,
MTBBorder2D.BorderConnectivity con,
BordersOnLabeledComponents.BorderType type,
int minLength)
Constructor.
|
ContourOnLabeledComponents(MTBImageByte inImg,
MTBRegion2DSet inRegions,
ContourOnLabeledComponents.ContourType type,
int length)
Constructor.
|
ContourOnLabeledComponents(MTBRegion2DSet inRegions,
ContourOnLabeledComponents.ContourType type,
int length)
Constructor.
|
Modifier and Type | Field and Description |
---|---|
private HashMap<Integer,MTBRegion2DSet> |
CalcStructureStatistics.cparticles |
Modifier and Type | Method and Description |
---|---|
private void |
CalcStructureStatistics.assignStructsToCell_com(MTBRegion2DSet regs)
Assigns the given set of structure regions to individual cells.
|
private void |
CalcStructureStatistics.assignStructsToCell_overlap(MTBRegion2DSet regions)
Assigns the given set of structure regions to individual cells.
|
Modifier and Type | Field and Description |
---|---|
private MTBRegion2DSet |
LevelsetSegmentationNonPDE.initRegions |
Constructor and Description |
---|
MTBLevelsetMembership(int sizeX,
int sizeY,
MTBRegion2DSet regions,
MTBImage invalidImg,
boolean multiphase)
Constructor for given size which is initialized from a MTBRegion2DSet for a 2D level set function.
|
Modifier and Type | Field and Description |
---|---|
private MTBRegion2DSet |
Region2DSetFromLabelimage.regionSet
Resulting region set.
|
Modifier and Type | Method and Description |
---|---|
MTBRegion2DSet |
Region2DSetFromLabelimage.getRegionSet() |
Modifier and Type | Field and Description |
---|---|
private MTBRegion2DSet |
LabelComponentsSequential.resultingRegions
Resulting set of labeled regions.
|
Modifier and Type | Method and Description |
---|---|
static MTBRegion2DSet |
LabelAreasToRegions.getRegions(MTBImage frame) |
static MTBRegion2DSet |
LabelAreasToRegions.getRegions(MTBImage frame,
int bgLabel) |
MTBRegion2DSet |
LabelComponentsSequential.getResultingRegions()
Get the resulting regions.
|
protected MTBRegion2DSet |
LabelComponentsSequential.labelComponents(MTBImage img,
boolean diagonalNeighbors)
Sequential component labeling
|
Modifier and Type | Method and Description |
---|---|
protected void |
LabelComponentsSequential.setResultingRegions(MTBRegion2DSet regions)
Attach the vector of resulting regions.
|
Modifier and Type | Field and Description |
---|---|
private MTBRegion2DSet |
DrawRegion2DSet.inputRegions
Set of regions to draw.
|
Modifier and Type | Method and Description |
---|---|
MTBRegion2DSet |
DrawRegion2DSet.getInputRegions()
Get the regions that have to be drawn
|
Modifier and Type | Method and Description |
---|---|
void |
DrawRegion2DSet.setInputRegions(MTBRegion2DSet regions)
Set the input regions to be drawn.
|
Constructor and Description |
---|
DrawRegion2DSet(DrawRegion2DSet.DrawType dtype,
MTBRegion2DSet regions)
Simple constructor to create the most common region image types.
|
DrawRegion2DSet(DrawRegion2DSet.DrawType dtype,
MTBRegion2DSet regions,
MTBImage tImage,
boolean cloneTImage)
Simple constructor to draw the most common region image types to
a given image.
|
Copyright © 2010–2020 Martin Luther University Halle-Wittenberg, Institute of Computer Science, Pattern Recognition and Bioinformatics. All rights reserved.