Index

A B C D E F G H I J L N O P Q R S T U W Z
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

AbstractDetections - Class in qupath.ext.braian

This abstract class defines the interface to handle groups of different cell detections groups.

AbstractDetections(String, Collection<PathClass>, PathObjectHierarchy) - Constructor for class qupath.ext.braian.AbstractDetections

Constructs an object that groups together detections of the same kind.

annotations() - Method in record class qupath.ext.braian.PartialClassifier

Returns the value of the annotations record component.

applyClassifiers(List<PartialClassifier>, ImageData<?>) - Method in class qupath.ext.braian.AbstractDetections

applies a list of classifiers in sequence to the detections of the instance kind.

AtlasManager - Class in qupath.ext.braian

This class helps managing and exporting results for each brain region.

AtlasManager(PathObjectHierarchy) - Constructor for class qupath.ext.braian.AtlasManager

AutoThresholdParmameters - Class in qupath.ext.braian.config

AutoThresholdParmameters() - Constructor for class qupath.ext.braian.config.AutoThresholdParmameters

B

BoundingBoxHierarchy - Class in qupath.ext.braian

The class BoundingBoxHierarchy is data structure that helps in searching for specific PathObject based on their shape and in logarithmic time to the total number of object stored.

BoundingBoxHierarchy(Collection<? extends PathObject>) - Constructor for class qupath.ext.braian.BoundingBoxHierarchy

Builds a top-down BVH of maximum 6 levels of hierarchy.

BoundingBoxHierarchy(Collection<? extends PathObject>, int) - Constructor for class qupath.ext.braian.BoundingBoxHierarchy

Builds a top-down BVH

BraiAn - Class in qupath.ext.braian.utils

BraiAn() - Constructor for class qupath.ext.braian.utils.BraiAn

BraiAnExtension - Class in qupath.ext.braian

BraiAnExtension() - Constructor for class qupath.ext.braian.BraiAnExtension

build(ImageChannelTools) - Method in class qupath.ext.braian.config.WatershedCellDetectionConfig

C

ChannelClassifierConfig - Class in qupath.ext.braian.config

ChannelClassifierConfig() - Constructor for class qupath.ext.braian.config.ChannelClassifierConfig

ChannelDetections - Class in qupath.ext.braian

This class allows to manage detections computed with WatershedCellDetection on a given image channel.

ChannelDetections(String, PathObjectHierarchy) - Constructor for class qupath.ext.braian.ChannelDetections

Creates an instance based on pre-computed cell detections.

ChannelDetections(ImageChannelTools, Collection<PathAnnotationObject>, WatershedCellDetectionConfig, PathObjectHierarchy) - Constructor for class qupath.ext.braian.ChannelDetections

Computes the detections using WatershedCellDetection algorithm inside the given annotations

ChannelDetections(ImageChannelTools, PathObjectHierarchy) - Constructor for class qupath.ext.braian.ChannelDetections

Creates an instance based on pre-computed cell detections.

ChannelDetections(ImageChannelTools, PathAnnotationObject, WatershedCellDetectionConfig, PathObjectHierarchy) - Constructor for class qupath.ext.braian.ChannelDetections

Computes the detections using WatershedCellDetection algorithm inside the given annotations

ChannelDetectionsConfig - Class in qupath.ext.braian.config

ChannelDetectionsConfig() - Constructor for class qupath.ext.braian.config.ChannelDetectionsConfig

ChannelHistogram - Class in qupath.ext.braian

ChannelHistogram(String, ImageStatistics) - Constructor for class qupath.ext.braian.ChannelHistogram

Constructs the channel histogram from the ImageStatistics object

classifier() - Method in record class qupath.ext.braian.PartialClassifier

Returns the value of the classifier record component.

classifyObjects(ImageData<T>, Collection<? extends PathObject>, boolean) - Method in class qupath.ext.braian.SingleClassifier

contains(PathObject) - Method in class qupath.ext.braian.BoundingBoxHierarchy

coversFullImage() - Method in record class qupath.ext.braian.PartialClassifier

createAllOverlappingClassNames(List<String>) - Static method in class qupath.ext.braian.OverlappingDetections

Creates all the names of the possible overlaps between the given PathClasses names

createClassification(String) - Static method in class qupath.ext.braian.ChannelDetections

createContainer(PathAnnotationObject, boolean) - Method in class qupath.ext.braian.AbstractDetections

Creates a duplicate child annotation to be used as container

D

DetectionsCheckConfig - Class in qupath.ext.braian.config

DetectionsCheckConfig() - Constructor for class qupath.ext.braian.config.DetectionsCheckConfig

E

equals(Object) - Method in class qupath.ext.braian.AbstractDetections

Two detection objects are functionally the same if they are compatible with each other and they have the same containers

equals(Object) - Method in record class qupath.ext.braian.PartialClassifier

Indicates whether some other object is "equal to" this one.

EXCLUDE_CLASSIFICATION - Static variable in class qupath.ext.braian.AtlasManager

F

findHistogramPeaks() - Method in class qupath.ext.braian.ChannelHistogram

Smooths the ChannelHistogram and find the color values that appear the most.

findHistogramPeaks(int, double) - Method in class qupath.ext.braian.ChannelHistogram

Smooths the ChannelHistogram and find the color values that appear the most

findPeaks(double[], double) - Static method in class qupath.ext.braian.ChannelHistogram

Finds the local maxima that peak above the nearby data

findThreshold(ImageChannelTools, AutoThresholdParmameters) - Static method in class qupath.ext.braian.config.WatershedCellDetectionConfig

fireUpdate() - Method in class qupath.ext.braian.AbstractDetections

Updates the internal representation to the current state.

flatten() - Method in class qupath.ext.braian.AtlasManager

Flattens the atlas's ontology into a list of annotations.

flatten(List<AbstractDetections>) - Method in class qupath.ext.braian.AtlasManager

Flattens the atlas ontology into a list of annotations.

FULL_IMAGE_DETECTIONS_NAME - Static variable in class qupath.ext.braian.ChannelDetections

G

getAnnotationsForDetections(PathObjectHierarchy) - Method in class qupath.ext.braian.config.ProjectsConfig

Finds (or creates) the annotations chosen for computing the detections, accordingly to the configuration file.

getAnnotationsToClassify() - Method in class qupath.ext.braian.config.ChannelClassifierConfig

getAnnotationsToClassify(PathObjectHierarchy) - Method in class qupath.ext.braian.config.ChannelClassifierConfig

It searches all annotations specified by their name in the configuration file.

getApply() - Method in class qupath.ext.braian.config.DetectionsCheckConfig

getBackgroundRadiusMicrons() - Method in class qupath.ext.braian.config.WatershedCellDetectionConfig

getBox() - Method in class qupath.ext.braian.BoundingBoxHierarchy

Returns a rectangle in which all objects' ROI are inside

getCellExpansionMicrons() - Method in class qupath.ext.braian.config.WatershedCellDetectionConfig

getChannel() - Method in class qupath.ext.braian.config.ChannelClassifierConfig

getChannelDetections() - Method in class qupath.ext.braian.config.ProjectsConfig

getChannelName() - Method in class qupath.ext.braian.ChannelHistogram

getChannelStats(int) - Method in class qupath.ext.braian.ImageChannelTools

Computes the ImageStatistics of the current channel at the given resolution.

getChildrenDetections(PathAnnotationObject) - Static method in class qupath.ext.braian.AbstractDetections

getClassForDetections() - Method in class qupath.ext.braian.config.ProjectsConfig

getClassifiers() - Method in class qupath.ext.braian.config.ChannelDetectionsConfig

getContainers() - Method in class qupath.ext.braian.AbstractDetections

getContainersName() - Method in class qupath.ext.braian.AbstractDetections

getContainersName() - Method in class qupath.ext.braian.ChannelDetections

getContainersName() - Method in class qupath.ext.braian.OverlappingDetections

getContainersPathClass() - Method in class qupath.ext.braian.AbstractDetections

getControlChannel() - Method in class qupath.ext.braian.config.DetectionsCheckConfig

getControlChannel() - Method in class qupath.ext.braian.config.ProjectsConfig

Retrieves the name of the channel to be used as control in the overlapping

getDepth() - Method in class qupath.ext.braian.BoundingBoxHierarchy

Compute the BoundingBoxHierarchy's maximum depth

getDescription() - Method in class qupath.ext.braian.BraiAnExtension

getDetectionImage() - Method in class qupath.ext.braian.config.WatershedCellDetectionConfig

getDetections(PathObjectHierarchy) - Method in class qupath.ext.braian.ImageChannelTools

returns an instance of ChannelDetections, if existing in the current hierarchy

getDetectionsCheck() - Method in class qupath.ext.braian.config.ProjectsConfig

getDetectionsInside(PathAnnotationObject, PathObjectHierarchy) - Static method in class qupath.ext.braian.AbstractDetections

returns the detections inside the given annotation

getDetectionsInside(ROI, PathObjectHierarchy) - Static method in class qupath.ext.braian.AbstractDetections

returns the detections inside the given ROI

getDetectionsPathClasses() - Method in class qupath.ext.braian.AbstractDetections

getDiscardedDetectionsPathClass() - Method in class qupath.ext.braian.AbstractDetections

getExcludedBrainRegions() - Method in class qupath.ext.braian.AtlasManager

Gets all the brain regions that should be excluded from further analysis due to being missing or badly aligned to the image.

getFullImageDetectionAnnotation(PathObjectHierarchy) - Static method in class qupath.ext.braian.ChannelDetections

Returns the annotation used when working with detections on the whole image

getHierarchy() - Method in class qupath.ext.braian.AbstractDetections

getHistogram(int) - Method in class qupath.ext.braian.ImageChannelTools

Computes the ChannelHistogram of the current channel at the given resolution.

getHistogramThreshold() - Method in class qupath.ext.braian.config.WatershedCellDetectionConfig

getId() - Method in class qupath.ext.braian.AbstractDetections

getLogger() - Static method in class qupath.ext.braian.BraiAnExtension

getMaxAreaMicrons() - Method in class qupath.ext.braian.config.WatershedCellDetectionConfig

getMaxValue() - Method in class qupath.ext.braian.ChannelHistogram

getMedianRadiusMicrons() - Method in class qupath.ext.braian.config.WatershedCellDetectionConfig

getMinAreaMicrons() - Method in class qupath.ext.braian.config.WatershedCellDetectionConfig

getMissingFeatures(ImageData<T>, Collection<? extends PathObject>) - Method in class qupath.ext.braian.SingleClassifier

getName() - Method in class qupath.ext.braian.BraiAnExtension

getName() - Method in class qupath.ext.braian.config.ChannelClassifierConfig

getName() - Method in class qupath.ext.braian.config.ChannelDetectionsConfig

getName() - Method in class qupath.ext.braian.ImageChannelTools

getnChannel() - Method in class qupath.ext.braian.ImageChannelTools

getnPeak() - Method in class qupath.ext.braian.config.AutoThresholdParmameters

getOverlappingObject(PathObject) - Method in class qupath.ext.braian.BoundingBoxHierarchy

Retrieves the object in the hierarchy whose centroid: is inside the specified object is the closest to the specified object's centroid It follows ROI.contains(double, double) definition of insideness for determining the overlap.

getOverlappingObjectIfPresent(PathObject) - Method in class qupath.ext.braian.AbstractDetections

getOverlappingObjectIfPresent(PathObject) - Method in class qupath.ext.braian.BoundingBoxHierarchy

Retrieves the object in the hierarchy whose centroid: is inside the specified object is the closest to the specified object's centroid It follows ROI.contains(double, double) definition of insideness for determining the overlap.

getParameters() - Method in class qupath.ext.braian.config.ChannelDetectionsConfig

getPathClasses() - Method in class qupath.ext.braian.SingleClassifier

getPeakProminence() - Method in class qupath.ext.braian.config.AutoThresholdParmameters

getRepository() - Method in class qupath.ext.braian.BraiAnExtension

getRequestedPixelSizeMicrons() - Method in class qupath.ext.braian.config.WatershedCellDetectionConfig

getResolutionLevel() - Method in class qupath.ext.braian.config.AutoThresholdParmameters

getSigmaMicrons() - Method in class qupath.ext.braian.config.WatershedCellDetectionConfig

getSmoothWindowSize() - Method in class qupath.ext.braian.config.AutoThresholdParmameters

getThreshold() - Method in class qupath.ext.braian.config.WatershedCellDetectionConfig

H

hashCode() - Method in record class qupath.ext.braian.PartialClassifier

Returns a hash code value for this object.

I

ImageChannelTools - Class in qupath.ext.braian

ImageChannelTools(String, ImageServer<BufferedImage>) - Constructor for class qupath.ext.braian.ImageChannelTools

Creates an ImageChannelTools from the given channel name and ImageServer

installExtension(QuPathGUI) - Method in class qupath.ext.braian.BraiAnExtension

integrate the extension in QuPath GUI

is16bit() - Method in class qupath.ext.braian.ChannelHistogram

is8bit() - Method in class qupath.ext.braian.ChannelHistogram

isBackgroundByReconstruction() - Method in class qupath.ext.braian.config.WatershedCellDetectionConfig

isChannelDetection(PathObject, boolean) - Method in class qupath.ext.braian.AbstractDetections

checks whether the given object is a detection belonging to the instance kind

isCompatibleClassifier(ObjectClassifier<T>) - Method in class qupath.ext.braian.AbstractDetections

isCompatibleWith(AbstractDetections) - Method in class qupath.ext.braian.AbstractDetections

Check whether two AbstractDetections are compatible.

isContainer(PathObject) - Method in class qupath.ext.braian.AbstractDetections

isEmpty() - Method in class qupath.ext.braian.AbstractDetections

If there are no detections within the current instance.

isEmpty() - Method in class qupath.ext.braian.BoundingBoxHierarchy

isImported(PathObjectHierarchy) - Static method in class qupath.ext.braian.AtlasManager

Checks whether an ABBA atlas was previously imported.

isIncludeNuclei() - Method in class qupath.ext.braian.config.WatershedCellDetectionConfig

isMakeMeasurements() - Method in class qupath.ext.braian.config.WatershedCellDetectionConfig

isSmoothBoundaries() - Method in class qupath.ext.braian.config.WatershedCellDetectionConfig

isWatershedPostProcess() - Method in class qupath.ext.braian.config.WatershedCellDetectionConfig

J

join(Collection<T>, String) - Static method in class qupath.ext.braian.utils.BraiAn

L

loadClassifier() - Method in class qupath.ext.braian.config.ChannelClassifierConfig

Loads the object classifier specified in the configuration file.

N

NoCellContainersFoundException - Exception in qupath.ext.braian

NoCellContainersFoundException(Class<? extends AbstractDetections>) - Constructor for exception qupath.ext.braian.NoCellContainersFoundException

O

OVERLAP_DELIMITER - Static variable in class qupath.ext.braian.OverlappingDetections

OverlappingDetections - Class in qupath.ext.braian

This class allows to compute and manage double/triple/multiple positive detections.

OverlappingDetections(AbstractDetections, Collection<AbstractDetections>, boolean, PathObjectHierarchy) - Constructor for class qupath.ext.braian.OverlappingDetections

Creates an instance of overlapping detections

OverlappingDetections(AbstractDetections, Collection<AbstractDetections>, PathObjectHierarchy) - Constructor for class qupath.ext.braian.OverlappingDetections

Creates an instance based on pre-computed overlapping detections

P

PartialClassifier - Record Class in qupath.ext.braian

Creates a classifier to apply to an instance of AbstractDetections

PartialClassifier(ObjectClassifier<?>, Collection<PathAnnotationObject>) - Constructor for record class qupath.ext.braian.PartialClassifier

Creates an instance of a PartialClassifier record class.

populatePathClassGUI(PathClass...) - Static method in class qupath.ext.braian.utils.BraiAn

ProjectsConfig - Class in qupath.ext.braian.config

This class reads a YAML file and can be used to apply the given parameters to the computation offered by BraiAn extension For more information, read this config file example.

ProjectsConfig() - Constructor for class qupath.ext.braian.config.ProjectsConfig

Q

qupath.ext.braian - package qupath.ext.braian

qupath.ext.braian.config - package qupath.ext.braian.config

qupath.ext.braian.utils - package qupath.ext.braian.utils

R

read(String) - Static method in class qupath.ext.braian.config.ProjectsConfig

Reads a BraiAn configuration file

resolvePath(String) - Static method in class qupath.ext.braian.utils.BraiAn

It searches for a file accordingly to BraiAn specifics: it first searches it in the project's path; if it is not present, it searches it in the parent directory, were supposedly other QuPath projects of the same experiment reside.

resolvePathIfPresent(String) - Static method in class qupath.ext.braian.utils.BraiAn

S

saveExcludedRegions(File) - Method in class qupath.ext.braian.AtlasManager

Saves a file containing, on each line, the name and hemisphere of the regions to be excluded.

saveResults(List<AbstractDetections>, File) - Method in class qupath.ext.braian.AtlasManager

Saves a TSV file containing data for each brain region of the atlas.

setAnnotationsToClassify(List<String>) - Method in class qupath.ext.braian.config.ChannelClassifierConfig

setApply(boolean) - Method in class qupath.ext.braian.config.DetectionsCheckConfig

setBackgroundByReconstruction(boolean) - Method in class qupath.ext.braian.config.WatershedCellDetectionConfig

setBackgroundRadiusMicrons(double) - Method in class qupath.ext.braian.config.WatershedCellDetectionConfig

setCellExpansionMicrons(double) - Method in class qupath.ext.braian.config.WatershedCellDetectionConfig

setChannel(String) - Method in class qupath.ext.braian.config.ChannelClassifierConfig

setChannelDetections(List<ChannelDetectionsConfig>) - Method in class qupath.ext.braian.config.ProjectsConfig

setClassForDetections(String) - Method in class qupath.ext.braian.config.ProjectsConfig

setClassifiers(List<ChannelClassifierConfig>) - Method in class qupath.ext.braian.config.ChannelDetectionsConfig

setControlChannel(String) - Method in class qupath.ext.braian.config.DetectionsCheckConfig

setDetectionImage(String) - Method in class qupath.ext.braian.config.WatershedCellDetectionConfig

setDetectionsCheck(DetectionsCheckConfig) - Method in class qupath.ext.braian.config.ProjectsConfig

setHistogramThreshold(AutoThresholdParmameters) - Method in class qupath.ext.braian.config.WatershedCellDetectionConfig

setIncludeNuclei(boolean) - Method in class qupath.ext.braian.config.WatershedCellDetectionConfig

setMakeMeasurements(boolean) - Method in class qupath.ext.braian.config.WatershedCellDetectionConfig

setMaxAreaMicrons(double) - Method in class qupath.ext.braian.config.WatershedCellDetectionConfig

setMedianRadiusMicrons(double) - Method in class qupath.ext.braian.config.WatershedCellDetectionConfig

setMinAreaMicrons(double) - Method in class qupath.ext.braian.config.WatershedCellDetectionConfig

setName(String) - Method in class qupath.ext.braian.config.ChannelClassifierConfig

setName(String) - Method in class qupath.ext.braian.config.ChannelDetectionsConfig

setnPeak(int) - Method in class qupath.ext.braian.config.AutoThresholdParmameters

setParameters(WatershedCellDetectionConfig) - Method in class qupath.ext.braian.config.ChannelDetectionsConfig

setPeakProminence(double) - Method in class qupath.ext.braian.config.AutoThresholdParmameters

setRequestedPixelSizeMicrons(double) - Method in class qupath.ext.braian.config.WatershedCellDetectionConfig

setResolutionLevel(int) - Method in class qupath.ext.braian.config.AutoThresholdParmameters

setSigmaMicrons(double) - Method in class qupath.ext.braian.config.WatershedCellDetectionConfig

setSmoothBoundaries(boolean) - Method in class qupath.ext.braian.config.WatershedCellDetectionConfig

setSmoothWindowSize(int) - Method in class qupath.ext.braian.config.AutoThresholdParmameters

setThreshold(double) - Method in class qupath.ext.braian.config.WatershedCellDetectionConfig

setWatershedPostProcess(boolean) - Method in class qupath.ext.braian.config.WatershedCellDetectionConfig

SingleClassifier<T> - Class in qupath.ext.braian

SingleClassifier(PathClass) - Constructor for class qupath.ext.braian.SingleClassifier

T

toPartialClassifier(PathObjectHierarchy) - Method in class qupath.ext.braian.config.ChannelClassifierConfig

Loads the classifier and associates it to the annotations whose name is listed in the configuration file.

toStream() - Method in class qupath.ext.braian.AbstractDetections

toStream() - Method in class qupath.ext.braian.BoundingBoxHierarchy

Visits each element of the hierarchy and outputs all the objects contained as Stream.

toString() - Method in record class qupath.ext.braian.PartialClassifier

Returns a string representation of this record class.

U

um - Static variable in class qupath.ext.braian.AtlasManager

W

WatershedCellDetectionConfig - Class in qupath.ext.braian.config

WatershedCellDetectionConfig() - Constructor for class qupath.ext.braian.config.WatershedCellDetectionConfig

Z

zeroPhaseFilter(double[], double[]) - Static method in class qupath.ext.braian.ChannelHistogram

Applies Applies a linear digital filter twice, once forward and once backwards.

A B C D E F G H I J L N O P Q R S T U W Z
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form