Index

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All Classes and Interfaces|All Packages|Constant Field Values

A

abs(Mat) - Static method in class qupath.opencv.tools.GroovyCV
Compute the absolute value of all elements in an array.
AbstractDnnModel<T> - Class in qupath.opencv.dnn
Wrapper for a deep learning model in a pipeline using OpenCV.
AbstractDnnModel() - Constructor for class qupath.opencv.dnn.AbstractDnnModel
 
add(double...) - Static method in class qupath.opencv.ops.ImageOps.Core
Add a constant to all pixels.
add(T, ImageProcessor...) - Static method in class qupath.imagej.processing.IJProcessing
Pixelwise sum of input images.
addClusterMeasurements() - Method in class qupath.opencv.features.DelaunayTriangulation
Deprecated.
Compute mean measurements from clustering all connected objects.
addDensities(String, PathObjectPredicates.PathObjectPredicate) - Method in class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapBuilder
Add a filter for computing densities.
addIntensityMeasurements(ImageServer<BufferedImage>, PathObject, double, Collection<ObjectMeasurements.Measurements>, Collection<ObjectMeasurements.Compartments>) - Static method in class qupath.lib.analysis.features.ObjectMeasurements
Measure all channels of an image for one individual object or cell.
addMeasurements(Collection<? extends PathObject>, String) - Method in class qupath.opencv.ml.pixel.PixelClassificationMeasurementManager
Add measurements to specified objects
addMeasurements(Collection<? extends PathObject>, PixelClassificationMeasurementManager, String) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools
Add measurements to specified objects from a PixelClassificationMeasurementManager.
addMeasurementsToSelectedObjects(ImageData<BufferedImage>, PixelClassifier, String) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools
Add measurements to selected objects based upon the output of a PixelClassifier.
addNodeMeasurements() - Method in class qupath.opencv.features.DelaunayTriangulation
Deprecated.
Add Delaunay measurements to each pathObject.
addNoise(Mat, double, double) - Static method in class qupath.opencv.tools.OpenCVTools
Add Gaussian noise with specified mean and standard deviation to all channels of a Mat.
addObject(PathObject) - Static method in class qupath.lib.scripting.QP
Add the specified object to the current PathObjectHierarchy.
addObjects(Collection<PathObject>) - Static method in class qupath.lib.scripting.QP
Add the specified collection of objects to the current PathObjectHierarchy.
addObjects(PathObject...) - Static method in class qupath.lib.scripting.QP
Add the specified array of objects to the current PathObjectHierarchy.
addPixelClassifierMeasurements(String, String) - Static method in class qupath.lib.scripting.QP
Add measurements from pixel classification to the selected objects.
addPixelClassifierMeasurements(PixelClassifier, String) - Static method in class qupath.lib.scripting.QP
Add measurements from pixel classification to the selected objects.
addRunnableTasks(ImageData<BufferedImage>, PathObject, List<Runnable>) - Method in class qupath.imagej.detect.cells.SubcellularDetection
 
addRunnableTasks(ImageData<BufferedImage>, PathObject, List<Runnable>) - Method in class qupath.imagej.detect.dearray.TMADearrayerPluginIJ
 
addRunnableTasks(ImageData<BufferedImage>, PathObject, List<Runnable>) - Method in class qupath.imagej.detect.tissue.PositivePixelCounterIJ
 
addRunnableTasks(ImageData<BufferedImage>, PathObject, List<Runnable>) - Method in class qupath.imagej.detect.tissue.SimpleTissueDetection2
 
addRunnableTasks(ImageData<BufferedImage>, PathObject, List<Runnable>) - Method in class qupath.lib.algorithms.CoherenceFeaturePlugin
 
addRunnableTasks(ImageData<BufferedImage>, PathObject, List<Runnable>) - Method in class qupath.lib.algorithms.HaralickFeaturesPlugin
 
addRunnableTasks(ImageData<BufferedImage>, PathObject, List<Runnable>) - Method in class qupath.lib.algorithms.IntensityFeaturesPlugin
 
addRunnableTasks(ImageData<BufferedImage>, PathObject, List<Runnable>) - Method in class qupath.lib.algorithms.LocalBinaryPatternsPlugin
 
addRunnableTasks(ImageData<T>, PathObject, List<Runnable>) - Method in class qupath.lib.algorithms.TilerPlugin
 
addRunnableTasks(ImageData<T>, PathObject, List<Runnable>) - Method in class qupath.lib.plugins.objects.DilateAnnotationPlugin
 
addRunnableTasks(ImageData<T>, PathObject, List<Runnable>) - Method in class qupath.lib.plugins.objects.FillAnnotationHolesPlugin
 
addRunnableTasks(ImageData<T>, PathObject, List<Runnable>) - Method in class qupath.lib.plugins.objects.FindConvexHullDetectionsPlugin
 
addRunnableTasks(ImageData<T>, PathObject, List<Runnable>) - Method in class qupath.lib.plugins.objects.RefineAnnotationsPlugin
 
addRunnableTasks(ImageData<T>, PathObject, List<Runnable>) - Method in class qupath.lib.plugins.objects.ShapeFeaturesPlugin
 
addRunnableTasks(ImageData<T>, PathObject, List<Runnable>) - Method in class qupath.lib.plugins.objects.SmoothFeaturesPlugin
 
addRunnableTasks(ImageData<T>, PathObject, List<Runnable>) - Method in class qupath.lib.plugins.objects.SplitAnnotationsPlugin
 
addRunnableTasks(ImageData<T>, PathObject, List<Runnable>) - Method in class qupath.lib.plugins.objects.TileClassificationsToAnnotationsPlugin
 
addRunnableTasks(ImageData<T>, PathObject, List<Runnable>) - Method in class qupath.opencv.features.DelaunayClusteringPlugin
Deprecated.
 
addShapeMeasurements(String...) - Static method in class qupath.lib.scripting.QP
Add the specified shape measurements to the current selected objects of the current image.
addShapeMeasurements(Collection<? extends PathObject>, PixelCalibration, ObjectMeasurements.ShapeFeatures...) - Static method in class qupath.lib.analysis.features.ObjectMeasurements
Add shape measurements for multiple objects.
addShapeMeasurements(ImageData<?>, Collection<? extends PathObject>, String, String...) - Static method in class qupath.lib.scripting.QP
Add shape measurements to the specified objects.
addShapeMeasurements(ImageData<?>, Collection<? extends PathObject>, ObjectMeasurements.ShapeFeatures...) - Static method in class qupath.lib.scripting.QP
Add shape measurements to the specified objects.
addShapeMeasurements(PathObject, PixelCalibration, ObjectMeasurements.ShapeFeatures...) - Static method in class qupath.lib.analysis.features.ObjectMeasurements
Add shape measurements for one object.
addWorkflowStep(ImageData<BufferedImage>, String) - Method in class qupath.imagej.detect.dearray.TMADearrayerPluginIJ
 
alwaysPromptForObjects() - Method in class qupath.lib.algorithms.IntensityFeaturesPlugin
 
and(Mat, Mat) - Static method in class qupath.opencv.tools.GroovyCV
Compute the bitwise AND of two arrays.
andThen(OutputHandler<S, T, U>) - Method in interface qupath.lib.experimental.pixels.OutputHandler
Append a second output handler to this one.
appendOps(ImageOp...) - Method in interface qupath.opencv.ops.ImageDataOp
Append one or more additional ImageOps sequentially.
apply(Mat) - Method in class qupath.opencv.ml.FeaturePreprocessor
Apply preprocessing in-place.
apply(Mat) - Method in interface qupath.opencv.ops.ImageOp
Apply operation to the image.
apply(Mat) - Method in class qupath.opencv.ops.ImageOps.PaddedOp
 
apply(Mat, boolean) - Method in class qupath.opencv.ml.FeaturePreprocessor
Apply preprocessing in-place.
apply(Mat, DoubleUnaryOperator) - Static method in class qupath.opencv.tools.OpenCVTools
Apply an operation to the pixels of an image.
apply(ImageData<BufferedImage>, RegionRequest) - Method in interface qupath.opencv.ops.ImageDataOp
Apply the operation to the requested region of the image.
applyTiled(Function<Mat, Mat>, Mat, int, int, Padding, int) - Static method in class qupath.opencv.tools.OpenCVTools
Apply a function to a Mat that strictly requires a specific input size.
applyToChannels(Mat, Consumer<Mat>) - Static method in class qupath.opencv.tools.OpenCVTools
Apply a method that modifies a Mat in-place to all channels of the Mat, merging the result and storing the result in-place.
AREA - Enum constant in enum class qupath.lib.analysis.features.ObjectMeasurements.ShapeFeatures
Area of the shape.
ARGS - Static variable in class qupath.lib.scripting.ScriptAttributes
Optional string args passed to the script.
asType(ImagePlus, Class<T>) - Static method in class qupath.opencv.tools.GroovyCV
Helper method to convert an ImagePlus to a Mat or ImageProcessor using Groovy's 'as' syntax.
asType(ImageProcessor, Class<T>) - Static method in class qupath.opencv.tools.GroovyCV
Helper method to convert an ImageProcessor to a Mat using Groovy's 'as' syntax.
asType(BufferedImage, Class<T>) - Static method in class qupath.opencv.tools.GroovyCV
Helper method to convert a BufferedImage to a Mat, ImageProcessor or ImagePlus using Groovy's 'as' syntax.
asType(Number, Class<T>) - Static method in class qupath.opencv.tools.GroovyCV
Helper function to convert a Number to a Mat or Scalar using Groovy's 'as' syntax.
asType(Mat, Class<T>) - Static method in class qupath.opencv.tools.GroovyCV
Helper method to convert a Mat to a BufferedImage, ImagePlus, ImageProcessor, double or float array using Groovy's 'as' syntax.
AutoCompletions - Class in qupath.lib.scripting.languages
Class to deal with script auto-completions.
AutoCompletions() - Constructor for class qupath.lib.scripting.languages.AutoCompletions
 
AutoCompletions.Completion - Interface in qupath.lib.scripting.languages
A single completion.
AutoCompletions.CompletionTokenizer - Interface in qupath.lib.scripting.languages
Functional interface to extract a token from a string needed to determine a completion.
autoThresholdToRoi(ImageProcessor, String) - Static method in class qupath.imagej.processing.IJProcessing
Apply an auto-threshold to an image, and generate a Roi from the result.
autoThresholdToSplitRois(ImageProcessor, String, int) - Static method in class qupath.imagej.processing.IJProcessing
Apply an auto-threshold to an image, and generate a zero or more Rois from the result based on connected components.

B

backend(int) - Method in class qupath.opencv.dnn.OpenCVDnn.Builder
Specify the backend, e.g.
BACKGROUND_DARK - Static variable in class qupath.imagej.tools.IJProperties
Property value for IMAGE_BACKGROUND when an image is known to have a dark background.
BACKGROUND_LIGHT - Static variable in class qupath.imagej.tools.IJProperties
Property value for IMAGE_BACKGROUND when an image is known to have a light background.
BATCH_INDEX - Static variable in class qupath.lib.scripting.ScriptAttributes
Index of the current run when batch processing (starting at 0).
BATCH_LAST - Static variable in class qupath.lib.scripting.ScriptAttributes
Boolean flag to indicate if the current script is the last in a batch.
BATCH_SAVE - Static variable in class qupath.lib.scripting.ScriptAttributes
Boolean flag to indicate whether changes to the image data should automatically be saved.
BATCH_SIZE - Static variable in class qupath.lib.scripting.ScriptAttributes
Size of the current batch processing batch.
batchPredict(List<? extends Mat>) - Method in class qupath.opencv.dnn.AbstractDnnModel
Convenience method to convert one or more image patches to a blob, apply the PredictionFunction, and convert the output to standard Mats.
batchPredict(List<? extends Mat>) - Method in interface qupath.opencv.dnn.DnnModel
Prediction function that can take a batch of inputs and gives a corresponding batch of outputs.
binaryReconstruction(ByteProcessor, ByteProcessor, boolean) - Static method in class qupath.imagej.processing.MorphologicalReconstruction
Alternative morphological reconstruction (based on ImageJ's FloodFiller) suitable for binary images only.
BioimageIoTools - Class in qupath.opencv.ml
Helper class for working with Bioimage Model Zoo model specs, and attempting to replicating the processing within QuPath.
BioimageIoTools() - Constructor for class qupath.opencv.ml.BioimageIoTools
 
bitwiseNegate(Mat) - Static method in class qupath.opencv.tools.GroovyCV
Compute the bitwise NOT of an array.
blackTopHat(ImageProcessor, double) - Static method in class qupath.imagej.processing.IJFilters
Apply a black tophat filter; this is equivalent to subtracting an 'opened' image from the original.
blobFromImage(Mat) - Static method in class qupath.opencv.dnn.DnnTools
Create an OpenCV blob from a single mat.
blobFromImages(Collection<Mat>, double, Size, Scalar, boolean, boolean) - Static method in class qupath.opencv.dnn.DnnTools
Create an OpenCV blob from a batch of Mats with optional scaling, resizing and cropping.
blobFromImages(Mat...) - Static method in class qupath.opencv.dnn.DnnTools
Create an OpenCV blob from one or more mats.
blobFromImages(Mat, double, Size, Scalar, boolean, boolean) - Static method in class qupath.opencv.dnn.DnnTools
Create an OpenCV blob from a Mat with optional scaling, resizing and cropping.
BlobFunction<T> - Interface in qupath.opencv.dnn
Convert OpenCV Mats into blobs (tensors) for use with a deep learning framework.
BRIGHTFIELD_H_DAB - Static variable in class qupath.lib.scripting.QP
Brightfield image type with hematoxylin and DAB staining
BRIGHTFIELD_H_E - Static variable in class qupath.lib.scripting.QP
Brightfield image type with hematoxylin and eosin staining
BRIGHTFIELD_OTHER - Static variable in class qupath.lib.scripting.QP
Brightfield image type
build() - Method in interface qupath.lib.analysis.heatmaps.ColorModels.ColorModelBuilder
Build a ColorModel.
build() - Method in class qupath.lib.experimental.pixels.Parameters.Builder
Build the parameters.
build() - Method in class qupath.lib.experimental.pixels.PixelProcessor.Builder
Build a PixelProcessor from the current state of the builder.
build() - Method in class qupath.lib.scripting.ScriptParameters.Builder
Build the ScriptParameters with the current options.
build() - Method in class qupath.opencv.dnn.DnnModelParams.Builder
Build the params.
build() - Method in class qupath.opencv.dnn.OpenCVDnn.Builder
Build a new OpenCVDnn.
build() - Method in class qupath.opencv.ml.PatchClassifierParams.Builder
Build the patch classifier parameters.
build(List<Mat>) - Method in class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder
Calculate results as a list of maps connecting features and Mats for all slices of a z-stack.
build(List<Mat>, int) - Method in class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder
Calculate results for a map of features and Mats for one slice of a z-stack.
build(Mat) - Method in class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder
Calculate results for a single Mat.
build(Mat, boolean) - Method in class qupath.opencv.ml.FeaturePreprocessor.Builder
buildClassifier(ImageData<BufferedImage>) - Method in class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapBuilder
Build a PixelClassifier for a density map using the current parameters and the specified ImageData.
buildDnnModel(Model) - Static method in class qupath.opencv.ml.BioimageIoTools
Attempt to build a DnnModel that follows this spec as closely as possible.
builder() - Static method in class qupath.lib.experimental.pixels.Parameters
Create a new builder for parameters.
builder() - Static method in class qupath.lib.experimental.pixels.PixelProcessor
Create a new builder to construct a PixelProcessor.
builder() - Static method in class qupath.lib.scripting.ScriptParameters
Create a new builder for ScriptParameters.
builder() - Static method in class qupath.opencv.dnn.DnnModelParams
Create a new params builder, with default values.
builder() - Static method in class qupath.opencv.ml.FeaturePreprocessor
builder() - Static method in class qupath.opencv.ml.PatchClassifierParams
Create a builder to generate new patch classifier params.
builder(String) - Static method in class qupath.opencv.dnn.DnnTools
Initiative building and configuring an OpenCVDnn.
builder(String) - Static method in class qupath.opencv.dnn.OpenCVDnn
Create a new builder.
builder(Collection<? extends MeasurementProcessor.CustomMeasurement<BufferedImage, BufferedImage>>) - Static method in class qupath.lib.experimental.pixels.MeasurementProcessor
Create a new builder for a PixelProcessor that can make custom measurements for an image object.
builder(DensityMaps.DensityMapBuilder) - Static method in class qupath.lib.analysis.heatmaps.DensityMaps
Create a new DensityMaps.DensityMapBuilder initialized with the same properties as an existing builder.
builder(Processor<ImagePlus, ImagePlus, Object>) - Static method in class qupath.lib.experimental.pixels.ImageJProcessor
Create a PixelProcessor.Builder for an ImageJ ImagePlus.
builder(Processor<Mat, Mat, Mat>) - Static method in class qupath.lib.experimental.pixels.OpenCVProcessor
Create a PixelProcessor.Builder for an OpenCV Mat.
builder(PathObjectPredicates.PathObjectPredicate) - Static method in class qupath.lib.analysis.heatmaps.DensityMaps
Create a new DensityMaps.DensityMapBuilder to generate a customized density map.
builder(DnnModelParams) - Static method in class qupath.opencv.dnn.DnnModelParams
Create a new params builder, initialized with the values from existing params.
builder(PatchClassifierParams) - Static method in class qupath.opencv.ml.PatchClassifierParams
Create a builder to generate new patch classifier params, initialized with the values from an existing parameter object.
Builder() - Constructor for class qupath.lib.experimental.pixels.Parameters.Builder
 
Builder() - Constructor for class qupath.lib.experimental.pixels.PixelProcessor.Builder
 
buildFilePath(String, String...) - Static method in class qupath.lib.scripting.QP
Build a file path from multiple components.
buildImageDataOp(Collection<? extends ColorTransforms.ColorTransform>) - Static method in class qupath.opencv.ops.ImageOps
Create an ImageDataOp, optionally using a specified collection of input channels.
buildImageDataOp(ColorTransforms.ColorTransform...) - Static method in class qupath.opencv.ops.ImageOps
Create an ImageDataOp, optionally using a specified array of input channels.
buildModel() - Method in class qupath.opencv.dnn.OpenCVDnn
Build a model.
buildModel(DnnModelParams) - Method in interface qupath.opencv.dnn.DnnModelBuilder
Build a DnnModel if possible, or return null otherwise.
buildModel(DnnModelParams) - Static method in class qupath.opencv.dnn.DnnModels
Build a DnnModel from the given parameters.
buildModel(DnnModelParams) - Method in class qupath.opencv.dnn.OpenCVDnnModelBuilder
 
buildModel(OpenCVDnn.ModelType) - Method in class qupath.opencv.dnn.OpenCVDnn
Build a model, specifying the OpenCVDnn.ModelType.
buildNet() - Method in class qupath.opencv.dnn.OpenCVDnn
Build the OpenCV Net.
buildParameters() - Method in class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapBuilder
Build a DensityMaps.DensityMapParameters object containing the main density map parameters.
buildPatchClassifierParams(Model, int, int, ImageOp...) - Static method in class qupath.opencv.ml.BioimageIoTools
Create an instance of PatchClassifierParams from a model spec.
buildPatchClassifierParams(Model, ImageOp...) - Static method in class qupath.opencv.ml.BioimageIoTools
Create an instance of PatchClassifierParams from a model spec.
buildPathInProject(String...) - Static method in class qupath.lib.scripting.QP
Build a file or directory path relative to the current project, but do not make any changes on the file system.
buildPixelClassifier(PatchClassifierParams) - Static method in class qupath.opencv.ml.PatchClassifierParams
Build a pixel classifier using these parameters
buildServer(String, Class<T>, String...) - Static method in class qupath.lib.scripting.QP
Deprecated.
In the usual case where BufferedImage is the class, use QP.buildServer(String, String...) instead because it handles default args.
buildServer(String, String...) - Static method in class qupath.lib.scripting.QP
Build an ImageServer with the class BufferedImage.
buildServer(URI, String...) - Method in class qupath.imagej.images.servers.ImageJServerBuilder
 
buildServer(URI, String...) - Static method in class qupath.lib.scripting.QP
Build an ImageServer with the class BufferedImage.
buildServer(ImageData<BufferedImage>) - Method in class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapBuilder
Build an ImageServer representing this density map.
buildServer(ImageData<BufferedImage>, ImageDataOp, PixelCalibration) - Static method in class qupath.opencv.ops.ImageOps
Build an ImageServer that generates pixels on demand from an ImageData by applying an ImageDataOp.
buildServer(ImageData<BufferedImage>, ImageDataOp, PixelCalibration, int, int) - Static method in class qupath.opencv.ops.ImageOps
Build an ImageServer that generates pixels on demand from an ImageData by applying an ImageDataOp.

C

calculatePadding() - Method in class qupath.opencv.ops.ImageOps.PaddedOp
Calculate the required padding.
calculatePreferredParallelism() - Method in class qupath.opencv.ml.pixel.PixelClassificationMeasurementManager
Make a semi-educated guess as to an appropriate number of threads to use.
calibrateImagePlus(ImagePlus, RegionRequest, ImageServer<BufferedImage>) - Static method in class qupath.imagej.tools.IJTools
Set an ImagePlus's Calibration and FileInfo properties based on a RegionRequest and PathImageServer.
calibrateObject(PathObject, Roi) - Static method in class qupath.imagej.tools.IJTools
Set the properties of a PathObject based upon an ImageJ Roi.
calibrateRoi(Roi, PathObject) - Static method in class qupath.imagej.tools.IJTools
Set properties of an ImageJ Roi based upon the property of a PathObject.
ceil() - Static method in class qupath.opencv.ops.ImageOps.Core
Create an op that ceils floating point values.
ceil(Mat) - Static method in class qupath.opencv.tools.OpenCVTools
Ceil values in a floating point Mat.
CELL - Enum constant in enum class qupath.lib.analysis.features.ObjectMeasurements.Compartments
Full cell region
CellCountsCV - Class in qupath.opencv
Simple plugin to attempt a very fast cell counting based upon (smoothed) peak detection.
CellCountsCV() - Constructor for class qupath.opencv.CellCountsCV
 
CHANNEL_ALL_OBJECTS - Static variable in class qupath.lib.analysis.heatmaps.DensityMaps
Channel name for the channel with all object counts (not always present).
channelMaximum(Mat) - Static method in class qupath.opencv.tools.OpenCVTools
Get the minimum of an image channel, ignoring NaNs.
channelMean(Mat) - Static method in class qupath.opencv.tools.OpenCVTools
Get the mean of an image channel, ignoring NaNs.
channelMinimum(Mat) - Static method in class qupath.opencv.tools.OpenCVTools
Get the minimum of an image channel, ignoring NaNs.
Channels() - Constructor for class qupath.opencv.ops.ImageOps.Channels
 
channelSoftmax(double) - Static method in class qupath.opencv.ops.ImageOps.Normalize
Apply softmax, with the specified output maxValue.
channelStdDev(Mat) - Static method in class qupath.opencv.tools.OpenCVTools
Get the standard deviation of image channels, ignoring NaNs.
channelSum(double) - Static method in class qupath.opencv.ops.ImageOps.Normalize
Normalize channels so that they sum to the specified value.
channelSum(Mat) - Static method in class qupath.opencv.tools.OpenCVTools
Get the sum of image channels, ignoring NaNs.
checkImageSupport(URI, String...) - Method in class qupath.imagej.images.servers.ImageJServerBuilder
 
checkMinVersion(String) - Static method in class qupath.lib.scripting.QP
Check whether the current QuPath version is ≥ the specified version.
checkVersionRange(String, String) - Static method in class qupath.lib.scripting.QP
Check whether the current QuPath version is ≥ the specified minimum version, and < the specified maximum.
CIRCULARITY - Enum constant in enum class qupath.lib.analysis.features.ObjectMeasurements.ShapeFeatures
Circularity.
classification() - Method in class qupath.opencv.dnn.OpenCVDnn.Builder
Set the model type to be OpenCVDnn.ModelType.CLASSIFICATION.
CLASSIFICATION - Enum constant in enum class qupath.opencv.dnn.OpenCVDnn.ModelType
CLASSIFICATION - Static variable in class qupath.lib.lazy.objects.PathObjectLazyValues
Measurement to extract a string representation of an object's classification.
classify(ClassificationModel, PathObject, Mat, IntFunction<PathClass>, String) - Static method in class qupath.opencv.dnn.DnnTools
Apply a classification model to an existing image patch to classify an object.
classify(ClassificationModel, PathObject, ImageServer<BufferedImage>, double, int, int, IntFunction<PathClass>, String) - Static method in class qupath.opencv.dnn.DnnTools
Apply a classification model to an image patch to classify an object.
classify(ClassificationModel, PathObject, ImageServer<BufferedImage>, double, IntFunction<PathClass>, String) - Static method in class qupath.opencv.dnn.DnnTools
Apply a classification model to an image patch to classify an object.
classifyCellsByCentroid(ImageData<BufferedImage>, PixelClassifier, boolean) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools
Classify cells according to the prediction of the pixel corresponding to the cell centroid using a PixelClassifier.
classifyDetectionsByCentroid(String) - Static method in class qupath.lib.scripting.QP
Classify detections according to the prediction of the pixel corresponding to the detection centroid using a PixelClassifier.
classifyDetectionsByCentroid(PixelClassifier) - Static method in class qupath.lib.scripting.QP
Classify detections according to the prediction of the pixel corresponding to the detection centroid using a PixelClassifier.
classifyDetectionsByCentroid(ImageData<BufferedImage>, PixelClassifier) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools
Classify detections according to the prediction of the pixel corresponding to the detection centroid using a PixelClassifier.
classifyObjects(ImageData<BufferedImage>, Collection<? extends PathObject>, boolean) - Method in class qupath.opencv.dnn.DnnObjectClassifier
 
classifyObjects(ImageData<BufferedImage>, Collection<? extends PathObject>, boolean) - Method in class qupath.opencv.dnn.OpenCVModelObjectClassifier
 
classifyObjects(ImageData<T>, Collection<? extends PathObject>, boolean) - Method in class qupath.opencv.ml.objects.OpenCVMLClassifier
 
classifyObjectsByCentroid(ImageData<BufferedImage>, PixelClassifier, Collection<PathObject>, boolean) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools
Classify objects according to the prediction of the pixel corresponding to the object's ROI centroid using a PixelClassifier.
classifyObjectsByCentroid(ImageServer<BufferedImage>, Collection<PathObject>, boolean) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools
Apply classification from a server to a collection of objects.
classifySelected(String) - Static method in class qupath.lib.scripting.QP
Set the classification of the selected objects in the current hierarchy.
classifySelected(PathObjectHierarchy, String) - Static method in class qupath.lib.scripting.QP
Set the classification of the selected objects.
clearAllObjects() - Static method in class qupath.lib.scripting.QP
Deprecated.
For naming consistency; use #removeAllObjects instead.
clearAllObjects(Class<? extends PathObject>) - Static method in class qupath.lib.scripting.QP
Deprecated.
For naming consistency; use #removeAllObjects instead.
clearAnnotationMeasurements() - Static method in class qupath.lib.scripting.QP
Deprecated.
For consistency in naming; use #removeAnnotationMeasurements instead.
clearAnnotationMeasurements(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP
Deprecated.
For consistency in naming; use #removeMeasurements instead.
clearAnnotations() - Static method in class qupath.lib.scripting.QP
Deprecated.
For naming consistency; use #removeAnnotations instead.
clearCellMeasurements() - Static method in class qupath.lib.scripting.QP
Deprecated.
For consistency in naming; use #removeCellMeasurements instead.
clearCellMeasurements(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP
Deprecated.
For consistency in naming; use #removeCellMeasurements instead.
clearDetectionMeasurements() - Static method in class qupath.lib.scripting.QP
Deprecated.
For consistency in naming; use #removeDetectionMeasurements instead.
clearDetectionMeasurements(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP
Deprecated.
For consistency in naming; use #removeDetectionMeasurements instead.
clearDetections() - Static method in class qupath.lib.scripting.QP
Deprecated.
For naming consistency; use #removeDetections instead.
clearMeasurements() - Static method in class qupath.lib.scripting.QP
Deprecated.
For consistency in naming; use #removeMeasurements instead.
clearMeasurements(Class<? extends PathObject>) - Static method in class qupath.lib.scripting.QP
Deprecated.
For consistency in naming; use #removeMeasurements instead.
clearMeasurements(PathObjectHierarchy, Class<? extends PathObject>) - Static method in class qupath.lib.scripting.QP
Deprecated.
For consistency in naming; use #removeMeasurements instead.
clearMeasurements(PathObjectHierarchy, Collection<? extends PathObject>) - Static method in class qupath.lib.scripting.QP
Deprecated.
For consistency in naming; use #removeMeasurements instead.
clearMeasurements(PathObjectHierarchy, PathObject...) - Static method in class qupath.lib.scripting.QP
Deprecated.
For consistency in naming; use #removeMeasurements instead.
clearOutside(ImageProcessor, Roi) - Static method in class qupath.imagej.processing.RoiLabeling
Clear (i.e.
clearRootMeasurements() - Static method in class qupath.lib.scripting.QP
Deprecated.
For consistency in naming; use #removeRootMeasurements instead.
clearRootMeasurements(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP
Deprecated.
For consistency in naming; use #removeRootMeasurements instead.
clearSelectedObjects() - Static method in class qupath.lib.scripting.QP
Deprecated.
For consistency in naming; use #removeSelectedObjects instead.
clearSelectedObjects(boolean) - Static method in class qupath.lib.scripting.QP
Deprecated.
For consistency in naming; use #removeSelectedObjects instead.
clearTileMeasurements() - Static method in class qupath.lib.scripting.QP
Deprecated.
For consistency in naming; use #removeTileMeasurements instead.
clearTileMeasurements(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP
Deprecated.
For consistency in naming; use #removeTileMeasurements instead.
clearTMACoreMeasurements() - Static method in class qupath.lib.scripting.QP
Deprecated.
For consistency in naming; use #removeTMACoreMeasurements instead.
clearTMACoreMeasurements(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP
Deprecated.
For consistency in naming; use #removeTMACoreMeasurements instead.
clearTMAGrid() - Static method in class qupath.lib.scripting.QP
Deprecated.
For naming consistency; use #removeTMAGrid instead.
clip(double, double) - Static method in class qupath.opencv.ops.ImageOps.Core
Create an op that clips Mat values to the specified minimum and maximum.
clip(Mat, double, double) - Static method in class qupath.opencv.tools.GroovyCV
Clip values of a Mat to be within a specified minimum and maximum.
close() - Method in class qupath.imagej.images.servers.ImageJServer
 
close() - Method in interface qupath.opencv.dnn.DnnModel
Close this model if it will not be needed again.
close() - Method in class qupath.opencv.dnn.OpenCVDnn
 
close() - Method in class qupath.opencv.ml.objects.features.Preprocessing.PCAProjector
 
close() - Method in class qupath.opencv.tools.MultiscaleFeatures.Hessian2D
 
close() - Method in class qupath.opencv.tools.MultiscaleFeatures.Hessian3D
 
close(ImageProcessor, double) - Static method in class qupath.imagej.processing.IJFilters
Apply a morphological closing; this is equivalent to applying a maximum followed by a minimum filter.
closing(int) - Static method in class qupath.opencv.ops.ImageOps.Filters
Apply a 2D morphological closing filter.
closingByReconstruction(ImageProcessor, double) - Static method in class qupath.imagej.processing.IJFilters
Apply a closing by (morphological) reconstruction.
closingByReconstruction(ImageProcessor, double) - Static method in class qupath.imagej.processing.MorphologicalReconstruction
Apply a morphological closing by reconstruction.
closingFilter(Mat, int) - Static method in class qupath.opencv.tools.OpenCVTools
Apply a 2D closing filter (dilation followed by erosion) to all channels of an image.
CoherenceFeaturePlugin - Class in qupath.lib.algorithms
Plugin to calculate coherence features for image tiles.
CoherenceFeaturePlugin() - Constructor for class qupath.lib.algorithms.CoherenceFeaturePlugin
Default constructor.
colorDeconvolve(ColorProcessor, ColorDeconvolutionStains) - Static method in class qupath.imagej.tools.IJTools
Apply color deconvolution to an RGB image, outputting 3 'stain' images in the same order as the stain vectors.
colorDeconvolve(ImageProcessor, ImageProcessor, ImageProcessor, ColorDeconvolutionStains) - Static method in class qupath.imagej.tools.IJTools
Apply color deconvolution to RGB channels, outputting 3 'stain' images in the same order as the stain vectors.
colorModel(ColorModels.ColorModelBuilder) - Method in class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapBuilder
ColorModels - Class in qupath.lib.analysis.heatmaps
Helper class for creating a JSON-serializable way to generate a ColorModel.
ColorModels() - Constructor for class qupath.lib.analysis.heatmaps.ColorModels
 
ColorModels.ColorModelBuilder - Interface in qupath.lib.analysis.heatmaps
Simple builder to create a ColorModel.
ColorModels.DisplayBand - Class in qupath.lib.analysis.heatmaps
Helper class to the display of a single channel (band) in a ColorModel.
computeFeatures() - Method in class qupath.lib.analysis.features.CoocurranceMatrices
Compute features.
computeLocalBinaryPatterns16(SimpleImage, double) - Static method in class qupath.lib.analysis.features.LocalBinaryPatterns
Compute local binary pattern descriptor for a SimpleImage.
config(String) - Method in class qupath.opencv.dnn.OpenCVDnn.Builder
Path to config file (if required).
config(URI) - Method in class qupath.opencv.dnn.OpenCVDnn.Builder
Path to config file (if required).
CONNECTIVITY_4 - Static variable in class qupath.imagej.processing.IJProcessing
Constant for 4-connectivity when tracing Rois.
CONNECTIVITY_8 - Static variable in class qupath.imagej.processing.IJProcessing
Constant for 8-connectivity when tracing Rois.
consumeOutput() - Static method in interface qupath.lib.experimental.pixels.OutputHandler
Create a basic do-nothing output handler that consumes the output with no changes.
containsCentroid(ROI, PathObject) - Static method in class qupath.lib.experimental.pixels.PixelProcessorUtils
Check whether a child object's centroid is contained within a ROI.
containsImageJRois(File) - Static method in class qupath.imagej.tools.IJTools
Check whether a file is likely to contain an ImageJ ROI, based upon its extension or .zip file contents.
containsObject(PathObject) - Method in class qupath.opencv.features.DelaunayTriangulation
Deprecated.
 
convertDetectionsToPoints() - Static method in class qupath.lib.scripting.QP
Convert all detection objects to points, based on the object centroids.
convertLabelsToCells(ImageProcessor, ImageProcessor, double, double, double, ImagePlane) - Static method in class qupath.imagej.tools.IJTools
Convert integer labeled images into cell objects.
convertLabelsToCells(ImageProcessor, ImageProcessor, Calibration, double, ImagePlane) - Static method in class qupath.imagej.tools.IJTools
Convert integer labeled images into cell objects.
convertSelectedObjectsToPoints() - Static method in class qupath.lib.scripting.QP
Convert the selected objects to points, based on the object centroids.
convertSpecifiedObjectsToPoints(PathObjectHierarchy, Collection<? extends PathObject>) - Static method in class qupath.lib.scripting.QP
Convert the selected objects to points, based on the object centroids.
convertToAnnotation(Roi, double, double, double, ImagePlane) - Static method in class qupath.imagej.tools.IJTools
Create an annotation object for a specific ImageJ Roi, using an ImagePlus to help set properties.
convertToAnnotation(Roi, double, ImagePlus) - Static method in class qupath.imagej.tools.IJTools
Create an annotation object for a specific ImageJ Roi.
convertToAnnotation(ImagePlus, ImageServer<?>, Roi, double, ImagePlane) - Static method in class qupath.imagej.tools.IJTools
convertToDetection(Roi, double, double, double, ImagePlane) - Static method in class qupath.imagej.tools.IJTools
Create a detection object for a specific ImageJ Roi, using an ImagePlus to help set properties.
convertToDetection(Roi, double, ImagePlus) - Static method in class qupath.imagej.tools.IJTools
Create a detection object for a specific ImageJ Roi.
convertToDetection(ImagePlus, ImageServer<?>, Roi, double, ImagePlane) - Static method in class qupath.imagej.tools.IJTools
convertToFloatProcessor(SimpleImage) - Static method in class qupath.imagej.tools.IJTools
Convert a SimpleImage to an ImageProcessor.
convertToIJRoi(ROI, double, double, double) - Static method in class qupath.imagej.tools.IJTools
Convert a QuPath ROI to an ImageJ Roi.
convertToIJRoi(ROI, Calibration, double) - Static method in class qupath.imagej.tools.IJTools
Convert a QuPath ROI to an ImageJ Roi for an image with the specified calibration.
convertToIJRoi(ROI, RegionRequest) - Static method in class qupath.imagej.tools.IJTools
Convert a QuPath ROI to an ImageJ Roi.
convertToIJRoi(ROI, T) - Static method in class qupath.imagej.tools.IJTools
Create an ImageJ Roi from a ROI, suitable for displaying on the ImagePlus of an PathImage<ImagePlus>.
convertToImagePlus(String, ImageServer<BufferedImage>, BufferedImage, RegionRequest) - Static method in class qupath.imagej.tools.IJTools
Convert a BufferedImage into a PathImage<ImagePlus>.
convertToImagePlus(ImageServer<BufferedImage>, RegionRequest) - Static method in class qupath.imagej.tools.IJTools
Read a region from an ImageServer<BufferedImage as a PathImage<ImagePlus>.
convertToImageProcessor(BufferedImage, int) - Static method in class qupath.imagej.tools.IJTools
Extract pixels as an an ImageProcessor from a single band of a BufferedImage.
convertToObjects(Parameters<S, T>, U) - Method in interface qupath.lib.experimental.pixels.OutputHandler.OutputToObjectConverter
Convert the output of a pixel processor to a list of PathObjects.
convertToOpticalDensitySum(ColorProcessor, double, double, double) - Static method in class qupath.imagej.tools.IJTools
Calculate optical density values for the red, green and blue channels, then add these all together.
convertToPathObject(Roi, double, double, double, Function<ROI, PathObject>, ImagePlane) - Static method in class qupath.imagej.tools.IJTools
Create a PathObject for a specific ImageJ Roi.
convertToPathObject(Roi, double, Function<ROI, PathObject>, ImagePlus) - Static method in class qupath.imagej.tools.IJTools
Create a PathObject for a specific ImageJ Roi, using an ImagePlus to help set properties.
convertToPathObject(ImagePlus, ImageServer<?>, Roi, double, Function<ROI, PathObject>, ImagePlane) - Static method in class qupath.imagej.tools.IJTools
convertToPolygonROI(PolygonRoi, Calibration, double, ImagePlane) - Static method in class qupath.imagej.tools.IJTools
Convert an ImageJ PolygonRoi to a QuPath PolygonROI.
convertToROI(Roi, double, double, double, ImagePlane) - Static method in class qupath.imagej.tools.IJTools
Create a ROI from an ImageJ Roi.
convertToROI(Roi, Calibration, double, ImagePlane) - Static method in class qupath.imagej.tools.IJTools
Create a ROI from an ImageJ Roi, using the Calibration object of an ImagePlus.
convertToROI(Roi, RegionRequest) - Static method in class qupath.imagej.tools.IJTools
Convert an ImageJ Roi to a QuPath ROI.
convertToROI(Roi, T) - Static method in class qupath.imagej.tools.IJTools
Create a ROI from an ImageJ Roi.
convertToUncalibratedImagePlus(String, BufferedImage) - Static method in class qupath.imagej.tools.IJTools
Convert a BufferedImage to an ImagePlus, without pixel size information or other calibration.
CoocurranceMatrices - Class in qupath.lib.analysis.features
Data structure to hold cooccurrence matrices for computation of Haralick features.
CoocurranceMatrices(int) - Constructor for class qupath.lib.analysis.features.CoocurranceMatrices
Initialize coocurrence matrices.
copySelectedAnnotationsToPlane(int, int) - Static method in class qupath.lib.scripting.QP
Copy the selected annotations in the current hierarchy to the specified z-slice and timepoint.
copySelectedAnnotationsToPlane(PathObjectHierarchy, ImagePlane) - Static method in class qupath.lib.scripting.QP
Copy the selected annotations in the specified hierarchy to the specified image plane.
copySelectedAnnotationsToPlane(ImagePlane) - Static method in class qupath.lib.scripting.QP
Copy the selected annotations in the current hierarchy to the specified image plane.
copySelectedObjectsToPlane(int, int) - Static method in class qupath.lib.scripting.QP
Copy the selected objects in the current hierarchy to the specified z-slice and timepoint.
copySelectedObjectsToPlane(PathObjectHierarchy, ImagePlane) - Static method in class qupath.lib.scripting.QP
Copy the selected objects in the specified hierarchy to the specified image plane.
copySelectedObjectsToPlane(ImagePlane) - Static method in class qupath.lib.scripting.QP
Copy the selected objects in the current hierarchy to the specified image plane.
Core() - Constructor for class qupath.opencv.ops.ImageOps.Core
 
cpu() - Method in class qupath.opencv.dnn.OpenCVDnn.Builder
Request CPU backend and target, if available.
create(Gson, TypeToken<T>) - Method in class qupath.opencv.io.OpenCVTypeAdapters.OpenCVTypeAdaptorFactory
 
create(String, String, Function<S, T>, Class<T>) - Static method in interface qupath.lib.lazy.interfaces.LazyValue
Create a LazyValue with specified name and help text.
create(OpenCVClassifiers.OpenCVStatModel, PathObjectFilter, FeatureExtractor<T>, List<PathClass>) - Static method in class qupath.opencv.ml.objects.OpenCVMLClassifier
Create a new ObjectClassifier that uses an OpenCVClassifiers.OpenCVStatModel for classification.
createAllFullImageAnnotations(boolean) - Static method in class qupath.lib.scripting.QP
Create annotation around the full image for the current image, on all z-slices and timepoints.
createAllFullImageAnnotations(ImageData<?>, boolean) - Static method in class qupath.lib.scripting.QP
Create annotation around the full image for the specified image, on all z-slices and timepoints.
createAllredIntensityMeasurement(ImageData<?>, Supplier<Double>, PathClass...) - Static method in class qupath.lib.lazy.objects.PathObjectLazyValues
 
createAllredMeasurement(ImageData<?>, Supplier<Double>, PathClass...) - Static method in class qupath.lib.lazy.objects.PathObjectLazyValues
 
createAllredProportionMeasurement(ImageData<?>, Supplier<Double>, PathClass...) - Static method in class qupath.lib.lazy.objects.PathObjectLazyValues
 
createAnnotationConverter() - Static method in class qupath.lib.experimental.pixels.ImageJProcessor
Create an OutputHandler.OutputToObjectConverter that attempts to convert the output into annotation objects.
createAnnotationConverter() - Static method in class qupath.lib.experimental.pixels.OpenCVProcessor
Create an OutputHandler.OutputToObjectConverter that attempts to convert the output into annotation objects.
createAnnotationConverter(Map<? extends Number, String>) - Static method in class qupath.lib.experimental.pixels.OpenCVProcessor
Create an OutputHandler.OutputToObjectConverter that attempts to convert the output into annotation objects.
createAnnotationOutputHandler() - Static method in class qupath.lib.experimental.pixels.ImageJProcessor
Create an OutputHandler that attempts to convert the output into annotation objects.
createAnnotationOutputHandler() - Static method in class qupath.lib.experimental.pixels.OpenCVProcessor
Create an OutputHandler that attempts to convert the output into annotation objects.
createAnnotationOutputHandler(Map<? extends Number, String>) - Static method in class qupath.lib.experimental.pixels.OpenCVProcessor
Create an OutputHandler that attempts to convert the output into annotation objects.
createAnnotations(Mat, RegionRequest, int, int) - Static method in class qupath.opencv.tools.OpenCVTools
Create annotation objects by tracing contours in a labelled image.
createAnnotationsFromDensityMap(String, Map<Integer, ? extends Number>, String, String...) - Static method in class qupath.lib.scripting.QP
Create annotations from a density map for the current image.
createAnnotationsFromDensityMap(ImageData<BufferedImage>, String, Map<Integer, ? extends Number>, String, String...) - Static method in class qupath.lib.scripting.QP
Create annotations from a density map for the specified image.
createAnnotationsFromDensityMap(ImageData<BufferedImage>, DensityMaps.DensityMapBuilder, Map<Integer, ? extends Number>, String, PixelClassifierTools.CreateObjectOptions...) - Static method in class qupath.lib.scripting.QP
Create annotations from a density map for the specified image.
createAnnotationsFromPixelClassifier(String, double, double, String...) - Static method in class qupath.lib.scripting.QP
Create annotation objects based upon the output of a pixel classifier, applied to selected objects.
createAnnotationsFromPixelClassifier(PixelClassifier, double, double, String...) - Static method in class qupath.lib.scripting.QP
Create annotation objects based upon the output of a pixel classifier, applied to selected objects.
createAnnotationsFromPixelClassifier(ImageData<BufferedImage>, PixelClassifier, double, double, PixelClassifierTools.CreateObjectOptions...) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools
Create annotation objects based upon the output of a pixel classifier, applied to selected objects.
createAnnotationsFromPixelClassifier(PathObjectHierarchy, ImageServer<BufferedImage>, double, double, PixelClassifierTools.CreateObjectOptions...) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools
Create annotation objects based upon an ImageServer that provides classification or probability output, applied to selected objects.
createBand(String, int, double, double) - Static method in class qupath.lib.analysis.heatmaps.ColorModels
Create a ColorModels.DisplayBand to define the colormap associated with an image band (channel).
createBand(String, int, double, double, double) - Static method in class qupath.lib.analysis.heatmaps.ColorModels
Create a ColorModels.DisplayBand to define the colormap associated with an image band (channel).
createBaseClassCountsMeasurement(ImageData<?>, PathClass) - Static method in class qupath.lib.lazy.objects.PathObjectLazyValues
 
createBinaryMask(Mat, DoublePredicate) - Static method in class qupath.opencv.tools.OpenCVTools
Create a binary mask (0, 255 values) by applying a predicate to pixel values.
createBoolean(String, String, Function<S, Boolean>) - Static method in interface qupath.lib.lazy.interfaces.LazyValue
Create a LazyBooleanValue with specified name and help text.
createBufferedImageMaskSupplier() - Static method in interface qupath.lib.experimental.pixels.MaskSupplier
Create a image supplier that returns a buffered image.
createBufferedImageSupplier() - Static method in interface qupath.lib.experimental.pixels.ImageSupplier
Create a image supplier that returns a buffered image.
createCells(Mat, Mat, RegionRequest, int, int) - Static method in class qupath.opencv.tools.OpenCVTools
Create cell objects by tracing contours in a labelled image.
createClassifier(OpenCVClassifiers.OpenCVStatModel, ImageDataOp, PixelClassifierMetadata, boolean) - Static method in class qupath.opencv.ml.pixel.PixelClassifiers
Create a PixelClassifier based on an OpenCV StatModel and feature calculator.
createClassifier(ImageDataOp, PixelClassifierMetadata) - Static method in class qupath.opencv.ml.pixel.PixelClassifiers
Convert an ImageDataOp into a simple classifier.
createClassifier(ImageDataOp, PixelCalibration, Map<Integer, PathClass>) - Static method in class qupath.opencv.ml.pixel.PixelClassifiers
Convert an ImageDataOp into a simple classifier by adding an interpretation to the output labels.
createColorModelBuilder(ColorModels.DisplayBand, ColorModels.DisplayBand) - Static method in class qupath.lib.analysis.heatmaps.ColorModels
Create a ColorModels.ColorModelBuilder with a main channel and an optional alpha channel.
createDetectionClassDensityMeasurement(ImageData<?>, PathClass) - Static method in class qupath.lib.lazy.objects.PathObjectLazyValues
 
createDetectionConverter() - Static method in class qupath.lib.experimental.pixels.ImageJProcessor
Create an OutputHandler.OutputToObjectConverter that attempts to convert the output into detection objects.
createDetectionConverter() - Static method in class qupath.lib.experimental.pixels.OpenCVProcessor
Create an OutputHandler.OutputToObjectConverter that attempts to convert the output into detection objects.
createDetectionConverter(Map<? extends Number, String>) - Static method in class qupath.lib.experimental.pixels.OpenCVProcessor
Create an OutputHandler.OutputToObjectConverter that attempts to convert the output into detection objects.
createDetectionCountMeasurement(ImageData<?>) - Static method in class qupath.lib.lazy.objects.PathObjectLazyValues
Create a measurement that counts the number of detections within an object's ROI.
createDetectionOutputHandler() - Static method in class qupath.lib.experimental.pixels.ImageJProcessor
Create an OutputHandler that attempts to convert the output into detection objects.
createDetectionOutputHandler() - Static method in class qupath.lib.experimental.pixels.OpenCVProcessor
Create an OutputHandler that attempts to convert the output into detection objects.
createDetectionOutputHandler(Map<? extends Number, String>) - Static method in class qupath.lib.experimental.pixels.OpenCVProcessor
Create an OutputHandler that attempts to convert the output into detection objects.
createDetections(Mat, RegionRequest, int, int) - Static method in class qupath.opencv.tools.OpenCVTools
Create detection objects by tracing contours in a labelled image.
createDetectionsFromPixelClassifier(String, double, double, String...) - Static method in class qupath.lib.scripting.QP
Create detection objects based upon the output of a pixel classifier, applied to selected objects.
createDetectionsFromPixelClassifier(PixelClassifier, double, double, String...) - Static method in class qupath.lib.scripting.QP
Create detection objects based upon the output of a pixel classifier, applied to selected objects.
createDetectionsFromPixelClassifier(ImageData<BufferedImage>, PixelClassifier, double, double, PixelClassifierTools.CreateObjectOptions...) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools
Create detection objects based upon the output of a pixel classifier, applied to selected objects.
createDetectionsFromPixelClassifier(PathObjectHierarchy, ImageServer<BufferedImage>, double, double, PixelClassifierTools.CreateObjectOptions...) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools
Create detection objects based upon an ImageServer that provides classification or probability output, applied to selected objects.
createDetector(ImageData<BufferedImage>, ParameterList) - Method in class qupath.imagej.detect.cells.PositiveCellDetection
Wrap the detector to apply any required classification.
createDetector(ImageData<BufferedImage>, ParameterList) - Method in class qupath.imagej.detect.cells.WatershedCellDetection
 
createDetector(ImageData<BufferedImage>, ParameterList) - Method in class qupath.imagej.detect.cells.WatershedCellMembraneDetection
 
createDetector(ImageData<BufferedImage>, ParameterList) - Method in class qupath.imagej.superpixels.DoGSuperpixelsPlugin
 
createDetector(ImageData<BufferedImage>, ParameterList) - Method in class qupath.imagej.superpixels.SLICSuperpixelsPlugin
 
createDetector(ImageData<BufferedImage>, ParameterList) - Method in class qupath.opencv.CellCountsCV
 
createDirectory(String, String...) - Static method in class qupath.lib.scripting.QP
Build a path to a directory, and create the directory if it does not already exist.
createDirectoryInProject(String...) - Static method in class qupath.lib.scripting.QP
Build a path to a directory, and create the directory if it does not already exist.
createDisk(int, boolean) - Static method in class qupath.opencv.tools.OpenCVTools
Create a disk filter.
createExactClassCountsMeasurement(ImageData<?>, PathClass) - Static method in class qupath.lib.lazy.objects.PathObjectLazyValues
 
createFullImageAnnotation(boolean) - Static method in class qupath.lib.scripting.QP
Create an annotation around the full image for the current image, on the default (first) z-slice and timepoint.
createFullImageAnnotation(boolean, int, int) - Static method in class qupath.lib.scripting.QP
Create an annotation around the full image for the current image, on the specified z-slice and timepoint.
createFullImageAnnotation(ImageData<?>, boolean) - Static method in class qupath.lib.scripting.QP
Create an annotation around the full image for the specified image, on the default (first) z-slice and timepoint.
createFullImageAnnotation(ImageData<?>, boolean, int, int) - Static method in class qupath.lib.scripting.QP
Create an annotation around the full image for the specified image, on the specified z-slice and timepoint.
createHScoreMeasurement(ImageData<?>, PathClass...) - Static method in class qupath.lib.lazy.objects.PathObjectLazyValues
 
createID() - Method in class qupath.imagej.images.servers.ImageJServer
 
createImageNameMeasurement(ImageData<?>) - Static method in class qupath.lib.lazy.objects.PathObjectLazyValues
Create a measurement that extracts the current name from an ImageData.
createImagePlusImageSupplier() - Static method in class qupath.lib.experimental.pixels.ImageJProcessor
Create an ImageSupplier that returns an ImageJ ImagePlus.
createImagePlusMaskSupplier() - Static method in class qupath.lib.experimental.pixels.ImageJProcessor
Create a MaskSupplier that returns an ImageJ ByteProcessor.
createImageStack(ImageProcessor...) - Static method in class qupath.imagej.tools.IJTools
Create an ImageStack containing the specified ImageProcessors.
createJavaCompletion(Class<?>) - Static method in class qupath.lib.scripting.languages.AutoCompletions
Create a new completion for a class.
createJavaCompletion(Class<?>, Field) - Static method in class qupath.lib.scripting.languages.AutoCompletions
Create a new completion for a field.
createJavaCompletion(Class<?>, Method) - Static method in class qupath.lib.scripting.languages.AutoCompletions
Create a new completion for a method.
createJavaCompletion(Class<?>, String, String) - Static method in class qupath.lib.scripting.languages.AutoCompletions
Create a new completion with fixed display and completion text.
createLivePixelClassificationMeasurement(PixelClassificationMeasurementManager, String) - Static method in class qupath.lib.lazy.objects.PathObjectLazyValues
Create a measurement for displaying live measurements from a pixel classifier.
createLogWriter(Logger, Level) - Static method in class qupath.lib.scripting.LoggingTools
Create a Writer that passes messages to the log at a specified level.
createMask(Mat, DoublePredicate, double, double) - Static method in class qupath.opencv.tools.OpenCVTools
Create a mask by applying a predicate to pixel values.
createMaskAndSplitObjectOutputHandler(OutputHandler.OutputToObjectConverter<S, T, U>) - Static method in interface qupath.lib.experimental.pixels.OutputHandler
Create an output handler that can be used to add objects to the parent object, applying the ROI mask and splitting objects with discontinuous ROIs.
createMatImageSupplier() - Static method in class qupath.lib.experimental.pixels.OpenCVProcessor
Create an ImageSupplier that returns an OpenCV Mat.
createMatMaskSupplier() - Static method in class qupath.lib.experimental.pixels.OpenCVProcessor
Create a MaskSupplier that returns an OpenCV Mat.
createMeasurementListFeatureExtractor(List<String>) - Static method in class qupath.opencv.ml.objects.features.FeatureExtractors
Create a FeatureExtractor that determines features for the MeasurementList of the PathObject.
createMeasurementListMeasurement(String) - Static method in class qupath.lib.lazy.objects.PathObjectLazyValues
 
createMeasurementManager(ImageData<BufferedImage>, PixelClassifier) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools
Create a PixelClassificationMeasurementManager that can be used to generate measurements from applying a pixel classifier to an image.
createMeasurementManager(ImageServer<BufferedImage>) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools
Create a PixelClassificationMeasurementManager that can be used to generate measurements from an ImageServer where pixels provide classification or probability information.
createMetadataMeasurement(String) - Static method in class qupath.lib.lazy.objects.PathObjectLazyValues
 
createNormalizer(double[], double[], double) - Static method in class qupath.opencv.ml.objects.features.Normalizer
Create a Normalizer with the specified parameters.
createNormalizer(Normalization, Mat, double) - Static method in class qupath.opencv.ml.objects.features.Preprocessing
Create a simple normalizer to rescale input data.
createNormalizingFeatureExtractor(FeatureExtractor<T>, Normalizer) - Static method in class qupath.opencv.ml.objects.features.FeatureExtractors
Wrap an existing FeatureExtractor to apply normalization prior to returning the values.
createNumeric(String, String, Function<S, Number>) - Static method in interface qupath.lib.lazy.interfaces.LazyValue
Create a LazyNumericValue with specified name and help text.
createObjectConverter(Class<U>, Function<ROI, PathObject>) - Static method in class qupath.lib.experimental.pixels.ImageJProcessor
Create an OutputHandler.OutputToObjectConverter for one specify type.
createObjectConverter(BiFunction<ROI, Number, PathObject>) - Static method in class qupath.lib.experimental.pixels.OpenCVProcessor
Create an OutputHandler.OutputToObjectConverter to convert Mat binary or labeled images to path objects, optionally using the label number.
createObjectConverter(Function<ROI, PathObject>) - Static method in class qupath.lib.experimental.pixels.ImageJProcessor
Create an OutputHandler.OutputToObjectConverter that attempts to convert a range of output types into objects.
createObjectConverter(Function<ROI, PathObject>) - Static method in class qupath.lib.experimental.pixels.OpenCVProcessor
Create an OutputHandler.OutputToObjectConverter to convert Mat binary or labeled images to path objects.
createObjectConverter(Function<ROI, PathObject>, Map<? extends Number, String>) - Static method in class qupath.lib.experimental.pixels.OpenCVProcessor
Create an OutputHandler.OutputToObjectConverter to convert Mat labeled images to path objects, optionally setting the classification.
createObjectOutputHandler(OutputHandler.OutputToObjectConverter<S, T, U>) - Static method in interface qupath.lib.experimental.pixels.OutputHandler
Create an output handler that can be used to add objects to the parent object, applying the ROI mask.
createObjects(Mat, RegionRequest, int, int, BiFunction<ROI, Number, PathObject>) - Static method in class qupath.opencv.tools.OpenCVTools
Create objects by tracing contours in a labelled image.
createObjectsFromPixelClassifier(ImageServer<BufferedImage>, Map<Integer, PathClass>, ROI, Function<ROI, ? extends PathObject>, double, double, boolean) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools
Create objects based upon an ImageServer that provides classification or probability output.
createObjectsFromPredictions(ImageServer<BufferedImage>, PathObjectHierarchy, Collection<PathObject>, Function<ROI, ? extends PathObject>, double, double, PixelClassifierTools.CreateObjectOptions...) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools
Create objects from an image (usually created with a pixel classifier) where values represent classifications or predictions.
createOverlay(Collection<? extends Roi>) - Static method in class qupath.imagej.processing.IJProcessing
Create an overlay containing all the Rois in the provided collection.
createPathImage(ImageServer<BufferedImage>, ImagePlus, RegionRequest) - Static method in class qupath.imagej.tools.IJTools
Create a PathImage from an ImagePlus and region.
createPCAProjectFeatureExtractor(FeatureExtractor<T>, Preprocessing.PCAProjector) - Static method in class qupath.opencv.ml.objects.features.FeatureExtractors
Wrap an existing FeatureExtractor to apply PCA projection prior to returning the values.
createPCAProjector(Mat, double, boolean) - Static method in class qupath.opencv.ml.objects.features.Preprocessing
Create a principle components analysis projection to reduce features.
createPixelClassificationServer(ImageData<BufferedImage>, PixelClassifier) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools
Create an ImageServer that displays the results of applying a PixelClassifier to an image.
createPixelClassificationServer(ImageData<BufferedImage>, PixelClassifier, String, ColorModel, boolean) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools
Create an ImageServer that displays the results of applying a PixelClassifier to an image.
createPositivePercentageMeasurement(ImageData<?>, PathClass...) - Static method in class qupath.lib.lazy.objects.PathObjectLazyValues
 
createProcessor(Collection<? extends MeasurementProcessor.CustomMeasurement<S, T>>) - Static method in class qupath.lib.experimental.pixels.MeasurementProcessor
Create a processor that can make custom measurements for an image object.
createProcessor(MeasurementProcessor.CustomMeasurement<S, T>...) - Static method in class qupath.lib.experimental.pixels.MeasurementProcessor
Create a processor that can make custom measurements for an image object.
createROIAreaMeasurement(ImageData<?>) - Static method in class qupath.lib.lazy.objects.PathObjectLazyValues
Create a measurement that extracts the area of an object's ROI.
createROICentroidX(ImageData<?>) - Static method in class qupath.lib.lazy.objects.PathObjectLazyValues
Create a measurement that extracts the x-coordinate of the centroid of an object's ROI.
createROICentroidY(ImageData<?>) - Static method in class qupath.lib.lazy.objects.PathObjectLazyValues
Create a measurement that extracts the y-coordinate of the centroid of an object's ROI.
createROILengthMeasurement(ImageData<?>) - Static method in class qupath.lib.lazy.objects.PathObjectLazyValues
Create a measurement that extracts the length of a line ROI.
createROIPerimeterMeasurement(ImageData<?>) - Static method in class qupath.lib.lazy.objects.PathObjectLazyValues
Create a measurement that extracts the perimeter of an object's ROI.
createROIs(Mat, RegionRequest, int, int) - Static method in class qupath.opencv.tools.OpenCVTools
Convert integer labels into ROIs.
createSelectAllObject(boolean) - Static method in class qupath.lib.scripting.QP
Deprecated.
createSelectAllObject(boolean, int, int) - Static method in class qupath.lib.scripting.QP
Deprecated.
createServerBuilder() - Method in class qupath.imagej.images.servers.ImageJServer
 
createStatModel(Class<? extends StatModel>) - Static method in class qupath.opencv.ml.OpenCVClassifiers
Create an OpenCVClassifiers.OpenCVStatModel for a specific class of StatModel.
createString(String, String, Function<S, String>) - Static method in interface qupath.lib.lazy.interfaces.LazyValue
Create a LazyStringValue with specified name and help text.
createThresholdClassifier(PixelCalibration, int, double, PathClass, PathClass) - Static method in class qupath.opencv.ml.pixel.PixelClassifiers
Create a new PixelClassifier that applies a threshold to one channel of an image.
createThresholdClassifier(PixelCalibration, Map<Integer, ? extends Number>, PathClass, PathClass) - Static method in class qupath.opencv.ml.pixel.PixelClassifiers
Create a new PixelClassifier that applies a threshold to one or more channels of an image.
createThresholdServer(ImageServer<BufferedImage>, int, double, PathClass, PathClass) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools
Create a new ImageServer by applying a threshold to one channel of another server.
createThresholdServer(ImageServer<BufferedImage>, Map<Integer, ? extends Number>, PathClass, PathClass) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools
Create a new ImageServer by applying a threshold to one or more channels of another server.
createTMAGrid(String, String, boolean, double) - Static method in class qupath.lib.scripting.QP
Create a new regular TMAGrid and set it as active on the hierarchy for the current image.
createTMAGrid(ImageData<?>, String, String, boolean, double) - Static method in class qupath.lib.scripting.QP
Create a new regular TMAGrid and set it as active on the hierarchy for an image.
createTrainData(Mat, Mat, Mat, boolean) - Method in class qupath.opencv.ml.OpenCVClassifiers.BoostClassifier
 
createTrainData(Mat, Mat, Mat, boolean) - Method in class qupath.opencv.ml.OpenCVClassifiers.DTreesClassifier
 
createTrainData(Mat, Mat, Mat, boolean) - Method in class qupath.opencv.ml.OpenCVClassifiers.EMClusterer
 
createTrainData(Mat, Mat, Mat, boolean) - Method in class qupath.opencv.ml.OpenCVClassifiers.NormalBayesClassifierCV
 
createTrainData(Mat, Mat, Mat, boolean) - Method in class qupath.opencv.ml.OpenCVClassifiers.RTreesClassifier
 
createTrainData(Mat, Mat, Mat, boolean) - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMClassifierCV
 
createTrainData(Mat, Mat, Mat, boolean) - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMSGDClassifierCV
 
createTrainData(Mat, Mat, Mat, boolean) - Method in class qupath.opencv.ml.OpenCVClassifiers.LogisticRegressionClassifier
 
createTrainData(Mat, Mat, Mat, boolean) - Method in class qupath.opencv.ml.OpenCVClassifiers.OpenCVStatModel
Create training data in the format required by this classifier.
createUnmaskedObjectOutputHandler(OutputHandler.OutputToObjectConverter<S, T, U>) - Static method in interface qupath.lib.experimental.pixels.OutputHandler
Create an output handler that can be used to add objects to the parent object.
crop(Mat, int, int, int, int) - Static method in class qupath.opencv.tools.OpenCVTools
Crop a region from a Mat based on its bounding box, returning a new image (not a subregion).
crop(Mat, Padding) - Static method in class qupath.opencv.tools.OpenCVTools
Crop a region from a Mat by stripping off padding, returning a new image (not a subregion).
cuda() - Method in class qupath.opencv.dnn.OpenCVDnn.Builder
Request CUDA backend and target, if available.
cuda16() - Method in class qupath.opencv.dnn.OpenCVDnn.Builder
Request CUDA backend and target, if available, with 16-bit floating point.
CYTOPLASM - Enum constant in enum class qupath.lib.analysis.features.ObjectMeasurements.Compartments
Full cell region, with nucleus removed

D

deconvolve(ColorDeconvolutionStains) - Static method in class qupath.opencv.ops.ImageOps.Channels
Apply the (fixed) color deconvolution stains to an image.
DEFAULT - Enum constant in enum class qupath.opencv.dnn.OpenCVDnn.ModelType
Default Model class.
DEFAULT_DECIMAL_PLACES - Static variable in interface qupath.lib.lazy.interfaces.LazyValue
Constant representing that the default number of decimal places should be used to convert floating point numbers to strings.
DEFAULT_INPUT_NAME - Static variable in interface qupath.opencv.dnn.DnnModel
Default input layer name.
DEFAULT_INPUT_NAME - Static variable in interface qupath.opencv.dnn.PredictionFunction
Default name to use for single input.
DEFAULT_OUTPUT_NAME - Static variable in interface qupath.opencv.dnn.DnnModel
Default output layer name.
DEFAULT_OUTPUT_NAME - Static variable in interface qupath.opencv.dnn.PredictionFunction
Default name to use for single output.
DelaunayClusteringPlugin<T> - Class in qupath.opencv.features
Deprecated.
v0.6.0 to be replaced by DelaunayTools. See https://github.com/qupath/qupath/issues/1590 for discussion of the problems with this command.
DelaunayClusteringPlugin() - Constructor for class qupath.opencv.features.DelaunayClusteringPlugin
Deprecated.
Constructor.
DelaunayTriangulation - Class in qupath.opencv.features
Deprecated.
v0.6.0, to be replaced by DelaunayTools.Subdivision
DelaunayTriangulation(List<PathObject>, double, double, double, boolean) - Constructor for class qupath.opencv.features.DelaunayTriangulation
Deprecated.
Compute Delaunay triangulation - optionally omitting links above a fixed distance.
DELETE_EXISTING - Enum constant in enum class qupath.opencv.ml.pixel.PixelClassifierTools.CreateObjectOptions
Delete existing child objects
DensityMaps - Class in qupath.lib.analysis.heatmaps
Class for constructing and using density maps.
DensityMaps() - Constructor for class qupath.lib.analysis.heatmaps.DensityMaps
 
DensityMaps.DensityMapBuilder - Class in qupath.lib.analysis.heatmaps
Builder for an ImageServer representing a density map or for DensityMaps.DensityMapParameters.
DensityMaps.DensityMapParameters - Class in qupath.lib.analysis.heatmaps
Class for storing parameters to build a ImageServer representing a density map.
DensityMaps.DensityMapType - Enum Class in qupath.lib.analysis.heatmaps
Density map types.
describe(Class<?>) - Static method in class qupath.lib.scripting.QP
List the fields and methods of a specified class.
describe(Object) - Static method in class qupath.lib.scripting.QP
List the fields and methods of a specified object.
deselectAll() - Static method in class qupath.lib.scripting.QP
Reset the selection for the current hierarchy, so that no objects of any kind are selected.
deselectAll(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP
Reset the selection, so that no objects of any kind are selected.
detect(DetectionModel, Mat, RegionRequest, IntFunction<PathClass>, Function<ROI, PathObject>) - Static method in class qupath.opencv.dnn.DnnTools
Apply a detection model to generate rectangles surrounding distinct structures.
detect(DetectionModel, ImageServer<BufferedImage>, RegionRequest, IntFunction<PathClass>, Function<ROI, PathObject>) - Static method in class qupath.opencv.dnn.DnnTools
Apply a detection model to generate rectangles surrounding distinct structures.
detection() - Method in class qupath.opencv.dnn.OpenCVDnn.Builder
Set the model type to be OpenCVDnn.ModelType.DETECTION.
DETECTION - Enum constant in enum class qupath.opencv.dnn.OpenCVDnn.ModelType
Refers to DetectionModel.
detectionCentroidDistances() - Static method in class qupath.lib.scripting.QP
Deprecated.
retained only for compatibility of v0.2.0 milestone releases; use instead #detectionCentroidDistances(boolean)
detectionCentroidDistances(boolean) - Static method in class qupath.lib.scripting.QP
Compute the distance for all detection object centroids to the closest detection with each valid, not-ignored classification and add the result to the detection measurement list for the current ImageData.
detectionCentroidDistances(ImageData<?>, boolean) - Static method in class qupath.lib.scripting.QP
Compute the distance for all detection object centroids to the closest detection with each valid, not-ignored classification and add the result to the detection measurement list.
detectionToAnnotationDistances() - Static method in class qupath.lib.scripting.QP
Deprecated.
retained only for compatibility of v0.2.0 milestone releases; use instead #detectionToAnnotationDistances(boolean)
detectionToAnnotationDistances(boolean) - Static method in class qupath.lib.scripting.QP
Compute the distance for all detection object centroids to the closest annotation with each valid, not-ignored classification and add the result to the detection measurement list for the current ImageData.
detectionToAnnotationDistances(ImageData<?>, boolean) - Static method in class qupath.lib.scripting.QP
Compute the distance for all detection object centroids to the closest annotation with each valid, not-ignored classification and add the result to the detection measurement list.
detectionToAnnotationDistancesSigned(boolean) - Static method in class qupath.lib.scripting.QP
Compute the signed distance for all detection object centroids to the closest annotation with each valid, not-ignored classification and add the result to the detection measurement list for the current ImageData.
detectionToAnnotationDistancesSigned(ImageData<?>, boolean) - Static method in class qupath.lib.scripting.QP
Compute the signed distance for all detection object centroids to the closest annotation with each valid, not-ignored classification and add the result to the detection measurement list.
detectTMACoresFromBinary(ByteProcessor, double, int, int, Roi) - Static method in class qupath.imagej.detect.dearray.TMADearrayer
Detect TMA cores from a (low-resolution) whole slide image that has been thresholded to give a binary image.
differenceOfGaussians(ImageProcessor, double, double) - Static method in class qupath.imagej.processing.IJFilters
Apply a Difference of Gaussians filter to an input image.
dilate(ImageProcessor, double) - Static method in class qupath.imagej.processing.IJFilters
Apply a dilation; this is equivalent to applying a maximum filter.
DilateAnnotationPlugin<T> - Class in qupath.lib.plugins.objects
Plugin to create new annotations by expanding the size of existing annotations.
DilateAnnotationPlugin() - Constructor for class qupath.lib.plugins.objects.DilateAnnotationPlugin
 
DilateAnnotationPlugin.LineCap - Enum Class in qupath.lib.plugins.objects
Line cap to use for annotation expansion.
distanceSq(OpenCVTools.IndexedPixel) - Method in class qupath.opencv.tools.OpenCVTools.IndexedPixel
Get the euclidean distance to another pixel, based upon the inds array and assuming unit spacing for all dimensions.
div(Mat, double) - Static method in class qupath.opencv.tools.GroovyCV
Divide array elements by a constant.
div(Mat, Mat) - Static method in class qupath.opencv.tools.GroovyCV
Per-element division of two arrays.
divide(double...) - Static method in class qupath.opencv.ops.ImageOps.Core
Divide all pixels by a constant.
divide(T, ImageProcessor...) - Static method in class qupath.imagej.processing.IJProcessing
Pixelwise division of the input images.
dnn(DnnModel, int, int, Padding, String...) - Static method in class qupath.opencv.ops.ImageOps.ML
Apply a DnnModel to pixels to generate a prediction.
DnnModel - Interface in qupath.opencv.dnn
General interface for implementing a deep learning model in a pipeline using OpenCV.
DnnModelBuilder - Interface in qupath.opencv.dnn
Builder to create a DnnModel from DnnModelParams.
DnnModelParams - Class in qupath.opencv.dnn
Parameters to build a DnnModel.
DnnModelParams.Builder - Class in qupath.opencv.dnn
Builder for DnnModelParams.
DnnModels - Class in qupath.opencv.dnn
Helper class for building new DnnModels.
DnnModels() - Constructor for class qupath.opencv.dnn.DnnModels
 
DnnObjectClassifier - Class in qupath.opencv.dnn
Initial implementation of a patch-based ObjectClassifier using an OpenCV-compatible DNN.
DnnObjectClassifier(PathObjectFilter, DnnModel, List<PathClass>, int, int, double) - Constructor for class qupath.opencv.dnn.DnnObjectClassifier
Constructor.
DnnShape - Class in qupath.opencv.dnn
Helper class to represent input and output shapes associated with PredictionFunction.
DnnTools - Class in qupath.opencv.dnn
Tools for working with OpenCV's DNN module.
DnnTools() - Constructor for class qupath.opencv.dnn.DnnTools
 
DnnTools.DNNLayer - Class in qupath.opencv.dnn
Helper class to summarize a DNN layer.
doesFeatureTransform() - Method in class qupath.opencv.ml.FeaturePreprocessor
Returns true if this preprocessor transforms the features beyond a simple normalization.
doesSomething() - Method in class qupath.opencv.ml.FeaturePreprocessor
Returns true if this preprocessor has any effect.
DoGSuperpixelsPlugin - Class in qupath.imagej.superpixels
A simple superpixel-generating command based upon applying ImageJ's watershed transform to the absolute values of a Difference-of-Gaussians filtered image.
DoGSuperpixelsPlugin() - Constructor for class qupath.imagej.superpixels.DoGSuperpixelsPlugin
 
doUpdateHierarchy() - Method in class qupath.lib.scripting.ScriptParameters
Request whether to fire an update event for the object hierarchy, if an image data object is available.
doUpdateHierarchy(boolean) - Method in class qupath.lib.scripting.ScriptParameters.Builder
Optionally request a hierarchy update event after running a script (default is true for scripts that operate on image data).
doWatershed(ImageProcessor, ImageProcessor, boolean) - Static method in class qupath.imagej.processing.Watershed
Apply a watershed transform.
doWatershed(ImageProcessor, ImageProcessor, double, boolean) - Static method in class qupath.imagej.processing.Watershed
Apply an intensity-constrained watershed transform, preventing regions from expanding to pixels below a specified minimum threshold
doWatershed(Mat, Mat, boolean) - Static method in class qupath.opencv.tools.ProcessingCV
Apply a watershed transform.
doWatershed(Mat, Mat, double, boolean) - Static method in class qupath.opencv.tools.ProcessingCV
Apply an intensity-constrained watershed transform, preventing regions from expanding to pixels below a specified minimum threshold
doWatershed(SimpleImage, SimpleModifiableImage, boolean) - Static method in class qupath.lib.analysis.algorithms.Watershed
Apply a 2D watershed transform.
doWatershed(SimpleImage, SimpleModifiableImage, double, boolean) - Static method in class qupath.lib.analysis.algorithms.Watershed
Apply a 2D watershed transform, constraining region growing using an intensity threshold.
downsample(double) - Method in class qupath.lib.experimental.pixels.PixelProcessor.Builder
Set the downsample factor to use with requesting image regions.
dumpMetadata() - Method in class qupath.imagej.images.servers.ImageJServer
Get a String representing the image metadata.
duplicateSelectedAnnotations() - Static method in class qupath.lib.scripting.QP
Duplicate the selected annotations in the current hierarchy.
duplicateSelectedAnnotations(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP
Duplicate the selected annotations in the specified hierarchy.

E

ensureContinuous(Mat, boolean) - Static method in class qupath.opencv.tools.OpenCVTools
Ensure a Mat is continuous, creating a copy of the data if necessary.
ensureType(PixelType) - Static method in class qupath.opencv.ops.ImageOps.Core
Convert the Mat to match a specified pixel type.
entrySet() - Method in class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder.FeatureMap
 
eq(Mat, double) - Static method in class qupath.opencv.tools.GroovyCV
Create a binary image showing where an array has a specific value.
eq(Mat, Mat) - Static method in class qupath.opencv.tools.GroovyCV
Create a binary image showing where two arrays have matching values.
equals(Object) - Method in class qupath.opencv.tools.LocalNormalization.SmoothingScale
 
erode(ImageProcessor, double) - Static method in class qupath.imagej.processing.IJFilters
Apply an erosion; this is equivalent to applying a minimum filter.
estimateDownsampleFactor(ImagePlus, ImageServer<?>) - Static method in class qupath.imagej.tools.IJTools
Estimate the downsample factor for an image region extracted from an image server, based upon the ratio of pixel sizes if possible or ratio of dimensions if necessary.
estimateStains(float[], float[], float[], ColorDeconvolutionStains, double, double, double, boolean) - Static method in class qupath.lib.analysis.algorithms.EstimateStainVectors
Check colors only currently applies to H&E.
estimateStains(BufferedImage, ColorDeconvolutionStains, boolean) - Static method in class qupath.lib.analysis.algorithms.EstimateStainVectors
Estimate two stains from a BufferedImage, with default parameter settings.
estimateStains(BufferedImage, ColorDeconvolutionStains, double, double, double, boolean) - Static method in class qupath.lib.analysis.algorithms.EstimateStainVectors
Estimate two stains from a BufferedImage.
EstimateStainVectors - Class in qupath.lib.analysis.algorithms
Code for estimating stain vectors automatically from an image, or to launch an editor for visually/interactively modifying stain vectors.
EstimateStainVectors() - Constructor for class qupath.lib.analysis.algorithms.EstimateStainVectors
 
ExecutableLanguage - Interface in qupath.lib.scripting.languages
Functional interface for scripting languages that are runnable (e.g.
execute(ScriptParameters) - Method in interface qupath.lib.scripting.languages.ExecutableLanguage
Execute the given script String.
exp() - Static method in class qupath.opencv.ops.ImageOps.Core
Create an op that returns Euler's number e raise to the power of the Mat values.
exportAllObjectsToGeoJson(String, String, String...) - Static method in class qupath.lib.scripting.QP
Export all objects (excluding root object) to an output file as GeoJSON.
exportAllObjectsToGeoJson(String, PathIO.GeoJsonExportOptions...) - Static method in class qupath.lib.scripting.QP
Export all objects (excluding root object) to an output file as GeoJSON.
exportObjectsToGeoJson(Collection<? extends PathObject>, String, String, String...) - Static method in class qupath.lib.scripting.QP
Export specified objects to an output file as GeoJSON.
exportObjectsToGeoJson(Collection<? extends PathObject>, String, PathIO.GeoJsonExportOptions...) - Static method in class qupath.lib.scripting.QP
Export specified objects to an output file as GeoJSON.
exportSelectedObjectsToGeoJson(String, String, String...) - Static method in class qupath.lib.scripting.QP
Export the selected objects to an output file as GeoJSON.
exportSelectedObjectsToGeoJson(String, PathIO.GeoJsonExportOptions...) - Static method in class qupath.lib.scripting.QP
Export the selected objects to an output file as GeoJSON.
extendedMaxima(ImageProcessor, double) - Static method in class qupath.imagej.processing.IJFilters
Find regional maxima in an image above a defined height.
extendedMinima(ImageProcessor, double) - Static method in class qupath.imagej.processing.IJFilters
Find regional minima in an image above a defined height.
extract(int...) - Static method in class qupath.opencv.ops.ImageOps.Channels
Extract or rearrange channels by index.
extractDoubles(Mat) - Static method in class qupath.opencv.tools.OpenCVTools
Extract pixels as a double array.
extractFeatures(ImageData<T>, Collection<? extends PathObject>, FloatBuffer) - Method in interface qupath.opencv.ml.objects.features.FeatureExtractor
Extract features from a collection of objects, adding the corresponding values to a FloatBuffer.
extractFloats(Mat) - Static method in class qupath.opencv.tools.OpenCVTools
Extract pixels as a float array.
extractHyperstack(ImageServer<BufferedImage>, RegionRequest) - Static method in class qupath.imagej.tools.IJTools
Extract a full ImageJ hyperstack for a specific region, using all z-slices and time points.
extractHyperstack(ImageServer<BufferedImage>, RegionRequest, int, int, int, int) - Static method in class qupath.imagej.tools.IJTools
Extract a full ImageJ hyperstack for a specific region, for specified ranges of z-slices and time points.
extractMaskedDoubles(Mat, Mat, int) - Static method in class qupath.opencv.tools.OpenCVTools
Extract pixels from an image using a mask, limited to the specified channel index.
extractMaskedFloats(Mat, Mat, int) - Static method in class qupath.opencv.tools.OpenCVTools
Extract pixels from an image using a mask, limited to the specified channel index.
extractMaskedPixels(Parameters<BufferedImage, BufferedImage>, int, Function<PathObject, ROI>) - Static method in class qupath.lib.experimental.pixels.PixelProcessorUtils
Extract the pixels from one channel of an image using the specified transform, and applying any ROI mask.
extractMaskedPixels(Parameters<BufferedImage, BufferedImage>, String, Function<PathObject, ROI>) - Static method in class qupath.lib.experimental.pixels.PixelProcessorUtils
Extract the pixels from one channel of an image using the specified transform, and applying any ROI mask.
extractMaskedPixels(Parameters<BufferedImage, BufferedImage>, ColorTransforms.ColorTransform, Function<PathObject, ROI>) - Static method in class qupath.lib.experimental.pixels.PixelProcessorUtils
Extract the pixels from the image using the specified transform, and applying any ROI mask.
extractPixels(Mat, double[]) - Static method in class qupath.opencv.tools.OpenCVTools
Extract pixels as a double array.
extractPixels(Mat, float[]) - Static method in class qupath.opencv.tools.OpenCVTools
Extract pixels as a float[] array.
extractZStack(ImageServer<BufferedImage>, RegionRequest) - Static method in class qupath.opencv.tools.OpenCVTools
Extract a list of Mats, where each Mat corresponds to a z-slice, for all available z-slices of a region.
extractZStack(ImageServer<BufferedImage>, RegionRequest, int, int) - Static method in class qupath.opencv.tools.OpenCVTools
Extract a list of Mats, where each Mat corresponds to a z-slice.

F

FeatureExtractor<T> - Interface in qupath.opencv.ml.objects.features
Interface for extracting features from PathObjects for the purpose of object classification.
FeatureExtractors - Class in qupath.opencv.ml.objects.features
Helper class for extracting features from objects, used along with ObjectClassifiers.
FeatureExtractors() - Constructor for class qupath.opencv.ml.objects.features.FeatureExtractors
 
FeaturePreprocessor - Class in qupath.opencv.ml
Create a preprocessor for an image or training matrix.
FeaturePreprocessor() - Constructor for class qupath.opencv.ml.FeaturePreprocessor
 
FeaturePreprocessor.Builder - Class in qupath.opencv.ml
Builder to create a custom FeaturePreprocessor.
features(Collection<MultiscaleFeatures.MultiscaleFeature>, double, double) - Static method in class qupath.opencv.ops.ImageOps.Filters
Compute one or more MultiscaleFeatures.MultiscaleFeatures for the specified smoothing values (must be > 0).
FILE_PATH - Static variable in class qupath.lib.scripting.ScriptAttributes
File path of the running script file.
fileExists(String) - Static method in class qupath.lib.scripting.QP
Query if a file exists.
files(File...) - Method in class qupath.opencv.dnn.DnnModelParams.Builder
Specify the URIs as files.
fill(Mat, double) - Static method in class qupath.opencv.tools.OpenCVTools
Fill the pixels of an image with a specific value.
fill(Mat, Mat, double) - Static method in class qupath.opencv.tools.OpenCVTools
Fill the pixels of an image with a specific value, corresponding to a mask.
FillAnnotationHolesPlugin<T> - Class in qupath.lib.plugins.objects
Plugin to create new annotations by expanding the size of existing annotations.
FillAnnotationHolesPlugin() - Constructor for class qupath.lib.plugins.objects.FillAnnotationHolesPlugin
 
fillHoles(ByteProcessor) - Static method in class qupath.imagej.processing.RoiLabeling
Fill holes in a binary image.
fillOutside(ImageProcessor, Roi, double) - Static method in class qupath.imagej.processing.RoiLabeling
Fill in a region outside a specified ROI
fillSmallHoles(Mat, double) - Static method in class qupath.opencv.tools.OpenCVTools
Fill holes in a binary image (1-channel, 8-bit unsigned) with an area <= maxArea.
filter2D(Mat) - Static method in class qupath.opencv.ops.ImageOps.Filters
Apply a 2D filter.
filter2D(Mat, Mat) - Static method in class qupath.opencv.tools.OpenCVTools
Apply a 2D filter to all channels of an image, with symmetric boundary padding.
filter2D(Mat, Mat, int) - Static method in class qupath.opencv.tools.OpenCVTools
Apply a 2D filter to all channels of an image.
Filters() - Constructor for class qupath.opencv.ops.ImageOps.Filters
 
filterSingleZ(List<Mat>, double[], int, int) - Static method in class qupath.opencv.tools.OpenCVTools
Apply a filter along the 'list' dimension for a list of Mats, computing the value for a single entry.
filterZ(List<Mat>, Mat, int, int) - Static method in class qupath.opencv.tools.OpenCVTools
Filter filter along entries in the input list.
FindConvexHullDetectionsPlugin<T> - Class in qupath.lib.plugins.objects
Plugin to identify/remove detections from the convex hull of all detections.
FindConvexHullDetectionsPlugin() - Constructor for class qupath.lib.plugins.objects.FindConvexHullDetectionsPlugin
 
findDensityMapHotspots(String, int, int, double, boolean, boolean) - Static method in class qupath.lib.scripting.QP
Find hotspots in a density map for the current image.
findDensityMapHotspots(ImageData<BufferedImage>, String, int, int, double, boolean, boolean) - Static method in class qupath.lib.scripting.QP
Find hotspots in a density map.
findDensityMapHotspots(ImageData<BufferedImage>, DensityMaps.DensityMapBuilder, int, int, double, boolean, boolean) - Static method in class qupath.lib.scripting.QP
Find hotspots in a density map.
findDirectionalMaxima(ImageProcessor) - Static method in class qupath.imagej.processing.RoiLabeling
Create a binary image for pixels that have a higher value than their neighbors.
findDirectionalMinima(ImageProcessor) - Static method in class qupath.imagej.processing.RoiLabeling
Create a binary image for pixels that have a lower value than their neighbors.
findHotspots(PathObjectHierarchy, ImageServer<BufferedImage>, int, int, double, double, PathClass, boolean, boolean) - Static method in class qupath.lib.analysis.heatmaps.DensityMaps
Find hotspots in a density map.
findMaxima(Mat, Mat) - Static method in class qupath.opencv.tools.OpenCVTools
Find maxima within an image.
findRegionalMaxima(ImageProcessor, float, boolean) - Static method in class qupath.imagej.processing.MorphologicalReconstruction
Find regional maxima using morphological reconstruction.
findRegionalMaxima(Mat) - Static method in class qupath.opencv.tools.OpenCVTools
Get the regional maxima within a Mat, providing the output as a labeled image.
fireHierarchyUpdate() - Static method in class qupath.lib.scripting.QP
Trigger an update for the current hierarchy.
fireHierarchyUpdate(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP
Trigger an update for the specified hierarchy.
fitCorePolygonToGrid(Polygon, double, int, int) - Static method in class qupath.imagej.detect.dearray.TMADearrayer
Given a polygon representing TMA core centroids in any order, fit this to a coordinate grid.
FLAT - Enum constant in enum class qupath.lib.plugins.objects.DilateAnnotationPlugin.LineCap
Flat cap
flatten(Mat) - Static method in class qupath.opencv.tools.GroovyCV
Flatten a Mat to give a single column.
floor() - Static method in class qupath.opencv.ops.ImageOps.Core
Create an op that floors floating point values.
floor(Mat) - Static method in class qupath.opencv.tools.OpenCVTools
Floor values in a floating point Mat.
FLUORESCENCE - Static variable in class qupath.lib.scripting.QP
Fluorescence image type
framework(String) - Method in class qupath.opencv.dnn.DnnModelParams.Builder
Specify the deep learning framework that can use the model.
framework(String) - Method in class qupath.opencv.dnn.OpenCVDnn.Builder
Specify the framework (used to identify the appropriate loader for the model).
FRAMEWORK_MXNET - Static variable in class qupath.opencv.dnn.DnnModelParams
Default name to identify MXNet.
FRAMEWORK_ONNX_RUNTIME - Static variable in class qupath.opencv.dnn.DnnModelParams
Default name to identify ONNX Runtime.
FRAMEWORK_OPENCV_DNN - Static variable in class qupath.opencv.dnn.DnnModelParams
Default name to identify OpenCV DNN.
FRAMEWORK_PYTORCH - Static variable in class qupath.opencv.dnn.DnnModelParams
Default name to identify PyTorch.
FRAMEWORK_TENSORFLOW - Static variable in class qupath.opencv.dnn.DnnModelParams
Default name to identify TensorFlow.
FRAMEWORK_TF_LITE - Static variable in class qupath.opencv.dnn.DnnModelParams
Default name to identify TensorFlow Lite.
fromBlob(T) - Method in interface qupath.opencv.dnn.BlobFunction
Convert a blob (generally the result of a prediction) to a list of mats.
Functions() - Constructor for class qupath.lib.experimental.pixels.MeasurementProcessor.Functions
 

G

gaussian(ImageProcessor, double) - Static method in class qupath.imagej.processing.IJFilters
Apply a Gaussian filter to an input image.
GAUSSIAN - Enum constant in enum class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapType
Gaussian-weighted area normalization; maps provide weighted averaged object counts in a defined radius.
GAUSSIAN - Enum constant in enum class qupath.opencv.tools.MultiscaleFeatures.MultiscaleFeature
Gaussian filter
GAUSSIAN_MEAN_ONLY - Enum constant in enum class qupath.opencv.tools.LocalNormalization.NormalizationType
Subtract Gaussian-filtered image
GAUSSIAN_MEAN_VARIANCE - Enum constant in enum class qupath.opencv.tools.LocalNormalization.NormalizationType
Subtract Gaussian-filtered image, then divide by a weighted estimate of the local standard deviation
gaussianBlur(double) - Static method in class qupath.opencv.ops.ImageOps.Filters
Apply a 2D Gaussian filter.
gaussianBlur(double, double) - Static method in class qupath.opencv.ops.ImageOps.Filters
Apply a (possibly anisotropic) 2D Gaussian filter.
gaussianFilter(Mat, double) - Static method in class qupath.opencv.tools.OpenCVTools
Apply a 2D Gaussian filter to all channels of an image, with symmetric boundary padding.
gaussianFilter(Mat, double, int) - Static method in class qupath.opencv.tools.OpenCVTools
Apply a 2D Gaussian filter to all channels of an image.
gaussianNormalize(List<Mat>, LocalNormalization.LocalNormalizationType, PixelCalibration, int) - Static method in class qupath.opencv.tools.LocalNormalization
Apply local normalization to a stack of Mats representing a z-stack.
gaussianNormalize2D(Mat, double, double, int) - Static method in class qupath.opencv.tools.LocalNormalization
Apply local normalization to a 2D Mat.
gaussianNormalize3D(List<Mat>, double, double, double, double, double, double, int) - Static method in class qupath.opencv.tools.LocalNormalization
Apply 3D normalization.
gaussianSmoothed(boolean) - Method in class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder
Calculate the Gaussian-smoothed image.
geq(Mat, double) - Static method in class qupath.opencv.tools.GroovyCV
Apply a greater than or equal to threshold.
geq(Mat, Mat) - Static method in class qupath.opencv.tools.GroovyCV
Apply a greater than or equal to threshold between two arrays.
get(int) - Method in class qupath.opencv.dnn.DnnShape
Get the length of the specified dimension.
get2D(double) - Static method in class qupath.opencv.tools.LocalNormalization.SmoothingScale
Get a 2D Gaussian scale.
get3DAnisotropic(double) - Static method in class qupath.opencv.tools.LocalNormalization.SmoothingScale
Get a 3D anisotropic Gaussian scale.
get3DIsotropic(double) - Static method in class qupath.opencv.tools.LocalNormalization.SmoothingScale
Get a 3D isotropic Gaussian scale.
getAllMeasurements(Roi) - Static method in class qupath.imagej.tools.IJProperties
Get all QuPath object measurements found in the properties of a Roi.
getAllObjects() - Static method in class qupath.lib.scripting.QP
Get all objects in the current hierarchy, including the root object (which represents the entire image).
getAllObjects(boolean) - Static method in class qupath.lib.scripting.QP
Get all objects in the current hierarchy.
getAllObjectsWithoutRoot() - Static method in class qupath.lib.scripting.QP
Get all objects in the current hierarchy, excluding the root object (which represents the entire image).
getAnnotationObjects() - Static method in class qupath.lib.scripting.QP
Get a list of the current annotation objects.
getArgs() - Method in class qupath.lib.scripting.ScriptParameters
Get an optional array of string arguments passed to the script.
getArray(boolean) - Method in class qupath.imagej.tools.PixelImageIJ
 
getAutoCompletor() - Method in class qupath.lib.scripting.languages.ScriptLanguage
Get the ScriptAutoCompletor object that takes care of this language's auto-completion.
getBasePathClass(PathObject) - Static method in class qupath.lib.scripting.QP
Get a base class - which is either a valid PathClass which is *not* an intensity class, or else null.
getBatchIndex() - Method in class qupath.lib.scripting.ScriptParameters
Get the index of the current image for batch processing, where 0 is the first and getBatchSize() - 1 is the last.
getBatchSaveResult() - Method in class qupath.lib.scripting.ScriptParameters
Get whether changes to the image data should be saved.
getBatchSize() - Method in class qupath.lib.scripting.ScriptParameters
Get the number of images being batch processed, or 1 if just a single image is being processed.
getBlobFunction() - Method in class qupath.opencv.dnn.AbstractDnnModel
Get the function that can convert one or more OpenCV Mats into a blob supported by the prediction function for the first (or only) input.
getBlobFunction() - Method in class qupath.opencv.dnn.OpenCVDnn
 
getBlobFunction(String) - Method in class qupath.opencv.dnn.AbstractDnnModel
Get the function that can convert one or more OpenCV Mats into a blob supported by the prediction function for a specified input layer.
getBlobFunction(String) - Method in class qupath.opencv.dnn.OpenCVDnn
 
getC() - Method in class qupath.opencv.tools.OpenCVTools.IndexedPixel
Get channel index.
getCachedMeasurementValue(PathObject, String) - Method in class qupath.opencv.ml.pixel.PixelClassificationMeasurementManager
Get the value of a single measurement for a specified PathObject if all tiles are cached, otherwise return null.
getCachedMeasurementValue(ROI, String) - Method in class qupath.opencv.ml.pixel.PixelClassificationMeasurementManager
Get the value of a single measurement for a specified ROI if all tiles are cached, otherwise return null.
getCellObjects() - Static method in class qupath.lib.scripting.QP
Get a list of the current cell objects.
getChannels(List<ImageChannel>) - Method in interface qupath.opencv.ops.ImageOp
Get appropriate channels to reflect the output of this transform.
getChannels(ImageData<BufferedImage>) - Method in interface qupath.opencv.ops.ImageDataOp
Get appropriate channels to reflect the output of this transform, given the input.
getCircularStructuringElement(int) - Static method in class qupath.opencv.tools.OpenCVTools
Deprecated.
OpenCVTools.createDisk(int, boolean) gives more reliable shapes.
getClassification(Roi) - Static method in class qupath.imagej.tools.IJProperties
Get a QuPath classification, as stored in a roi's properties.
getClassification(ImageServer<BufferedImage>, int, int, int, int) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools
Request the classification for a specific pixel.
getColorRGB(int...) - Static method in class qupath.lib.scripting.QP
getComparator() - Static method in class qupath.lib.scripting.languages.AutoCompletions
Get a comparator to order completions.
getCompletions(String, int) - Method in interface qupath.lib.scripting.languages.ScriptAutoCompletor
Get a list of possible auto-completions for the given text with the caret at the specified position.
getCompletionText() - Method in interface qupath.lib.scripting.languages.AutoCompletions.Completion
Get the text that should be inserted for the full completion.
getConfigUri() - Method in class qupath.opencv.dnn.OpenCVDnn
Get the path to the model configuration, if required.
getConnectedClusters() - Method in class qupath.opencv.features.DelaunayTriangulation
Deprecated.
Get a list of PathObjects that are connected to each other in this triangulation.
getConnectedNodes(Collection<PathObject>, Collection<double[]>) - Method in class qupath.opencv.features.DelaunayTriangulation
Deprecated.
getConnectedNodes(PathObject, Collection<PathObject>) - Method in class qupath.opencv.features.DelaunayTriangulation
Deprecated.
Get all the PathObjects immediately connected to the specified object, adding the points into a collection (or creating a new one).
getConnectedObjects(PathObject) - Method in class qupath.opencv.features.DelaunayTriangulation
Deprecated.
 
getCoreClasses() - Static method in class qupath.lib.scripting.QP
Get a list of core classes that are likely to be useful for scripting.
getCurrentHierarchy() - Static method in class qupath.lib.scripting.QP
Get the PathObjectHierarchy of the current ImageData.
getCurrentImageData() - Static method in class qupath.lib.scripting.QP
Get the path to the current ImageData.
getCurrentImageName() - Static method in class qupath.lib.scripting.QP
Get the name of the current image.
getCurrentImageNameWithoutExtension() - Static method in class qupath.lib.scripting.QP
Get the name of the current image, removing any file extension.
getCurrentServer() - Static method in class qupath.lib.scripting.QP
Get the ImageServer of the current ImageData.
getCurrentServerPath() - Static method in class qupath.lib.scripting.QP
Get the path to the ImageServer of the current ImageData.
getDebugMode() - Static method in class qupath.imagej.detect.cells.WatershedCellDetection
Get whether debug mode is on or off.
getDefaultImports() - Method in class qupath.lib.scripting.ScriptParameters
Get default imports that should be included with the script, where possible.
getDefaultParameterList(ImageData<BufferedImage>) - Method in class qupath.imagej.detect.cells.PositiveCellDetection
 
getDefaultParameterList(ImageData<BufferedImage>) - Method in class qupath.imagej.detect.cells.SubcellularDetection
 
getDefaultParameterList(ImageData<BufferedImage>) - Method in class qupath.imagej.detect.cells.WatershedCellDetection
 
getDefaultParameterList(ImageData<BufferedImage>) - Method in class qupath.imagej.detect.cells.WatershedCellMembraneDetection
 
getDefaultParameterList(ImageData<BufferedImage>) - Method in class qupath.imagej.detect.dearray.TMADearrayerPluginIJ
 
getDefaultParameterList(ImageData<BufferedImage>) - Method in class qupath.imagej.detect.tissue.PositivePixelCounterIJ
 
getDefaultParameterList(ImageData<BufferedImage>) - Method in class qupath.imagej.detect.tissue.SimpleTissueDetection2
 
getDefaultParameterList(ImageData<BufferedImage>) - Method in class qupath.imagej.superpixels.DoGSuperpixelsPlugin
 
getDefaultParameterList(ImageData<BufferedImage>) - Method in class qupath.imagej.superpixels.SLICSuperpixelsPlugin
 
getDefaultParameterList(ImageData<BufferedImage>) - Method in class qupath.lib.algorithms.CoherenceFeaturePlugin
 
getDefaultParameterList(ImageData<BufferedImage>) - Method in class qupath.lib.algorithms.HaralickFeaturesPlugin
 
getDefaultParameterList(ImageData<BufferedImage>) - Method in class qupath.lib.algorithms.IntensityFeaturesPlugin
 
getDefaultParameterList(ImageData<BufferedImage>) - Method in class qupath.lib.algorithms.LocalBinaryPatternsPlugin
 
getDefaultParameterList(ImageData<BufferedImage>) - Method in class qupath.opencv.CellCountsCV
 
getDefaultParameterList(ImageData<T>) - Method in class qupath.lib.algorithms.TilerPlugin
 
getDefaultParameterList(ImageData<T>) - Method in class qupath.lib.plugins.objects.DilateAnnotationPlugin
 
getDefaultParameterList(ImageData<T>) - Method in class qupath.lib.plugins.objects.FillAnnotationHolesPlugin
Returns an empty ParameterList.
getDefaultParameterList(ImageData<T>) - Method in class qupath.lib.plugins.objects.FindConvexHullDetectionsPlugin
 
getDefaultParameterList(ImageData<T>) - Method in class qupath.lib.plugins.objects.RefineAnnotationsPlugin
 
getDefaultParameterList(ImageData<T>) - Method in class qupath.lib.plugins.objects.ShapeFeaturesPlugin
 
getDefaultParameterList(ImageData<T>) - Method in class qupath.lib.plugins.objects.SmoothFeaturesPlugin
 
getDefaultParameterList(ImageData<T>) - Method in class qupath.lib.plugins.objects.SplitAnnotationsPlugin
Returns an empty ParameterList.
getDefaultParameterList(ImageData<T>) - Method in class qupath.lib.plugins.objects.TileClassificationsToAnnotationsPlugin
 
getDefaultParameterList(ImageData<T>) - Method in class qupath.opencv.features.DelaunayClusteringPlugin
Deprecated.
 
getDefaultStaticImports() - Method in class qupath.lib.scripting.ScriptParameters
Get default static imports that should be included with the script, where possible.
getDensityType() - Method in class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapParameters
Get the normalization type of the density map.
getDerivedPathClass(PathClass, String) - Static method in class qupath.lib.scripting.QP
Get a PathClass with the specified name, derived from another PathClass.
getDerivedPathClass(PathClass, String, Integer) - Static method in class qupath.lib.scripting.QP
Get a PathClass with the specified name, derived from another PathClass.
getDescription() - Method in class qupath.imagej.detect.cells.SubcellularDetection
 
getDescription() - Method in class qupath.imagej.detect.cells.WatershedCellDetection
 
getDescription() - Method in class qupath.imagej.detect.cells.WatershedCellMembraneDetection
 
getDescription() - Method in class qupath.imagej.detect.dearray.TMADearrayerPluginIJ
 
getDescription() - Method in class qupath.imagej.detect.tissue.PositivePixelCounterIJ
 
getDescription() - Method in class qupath.imagej.detect.tissue.SimpleTissueDetection2
 
getDescription() - Method in class qupath.imagej.images.servers.ImageJServerBuilder
 
getDescription() - Method in class qupath.imagej.superpixels.DoGSuperpixelsPlugin
 
getDescription() - Method in class qupath.imagej.superpixels.SLICSuperpixelsPlugin
 
getDescription() - Method in class qupath.lib.algorithms.CoherenceFeaturePlugin
 
getDescription() - Method in class qupath.lib.algorithms.HaralickFeaturesPlugin
 
getDescription() - Method in class qupath.lib.algorithms.IntensityFeaturesPlugin
 
getDescription() - Method in class qupath.lib.algorithms.LocalBinaryPatternsPlugin
 
getDescription() - Method in class qupath.lib.algorithms.TilerPlugin
 
getDescription() - Method in class qupath.lib.plugins.objects.DilateAnnotationPlugin
 
getDescription() - Method in class qupath.lib.plugins.objects.FillAnnotationHolesPlugin
 
getDescription() - Method in class qupath.lib.plugins.objects.FindConvexHullDetectionsPlugin
 
getDescription() - Method in class qupath.lib.plugins.objects.RefineAnnotationsPlugin
 
getDescription() - Method in class qupath.lib.plugins.objects.ShapeFeaturesPlugin
 
getDescription() - Method in class qupath.lib.plugins.objects.SmoothFeaturesPlugin
 
getDescription() - Method in class qupath.lib.plugins.objects.SplitAnnotationsPlugin
 
getDescription() - Method in class qupath.lib.plugins.objects.TileClassificationsToAnnotationsPlugin
 
getDescription() - Method in class qupath.opencv.CellCountsCV
 
getDescription() - Method in class qupath.opencv.features.DelaunayClusteringPlugin
Deprecated.
 
getDetails() - Method in class qupath.imagej.images.writers.TiffWriterIJ
 
getDetails() - Method in class qupath.imagej.images.writers.ZipWriterIJ
 
getDetectionObjects() - Static method in class qupath.lib.scripting.QP
Get a list of the current detection objects.
getDeterminant() - Method in interface qupath.opencv.tools.MultiscaleFeatures.Hessian
Get the determinant for each pixel.
getDeterminant() - Method in class qupath.opencv.tools.MultiscaleFeatures.Hessian2D
 
getDeterminant() - Method in class qupath.opencv.tools.MultiscaleFeatures.Hessian3D
 
getDisplayText() - Method in interface qupath.lib.scripting.languages.AutoCompletions.Completion
Get the text that should be displayed for this completion.
getEigenvalues(boolean) - Method in interface qupath.opencv.tools.MultiscaleFeatures.Hessian
Get the eigenvalues, ranked from highest to lowest.
getEigenvalues(boolean) - Method in class qupath.opencv.tools.MultiscaleFeatures.Hessian2D
 
getEigenvalues(boolean) - Method in class qupath.opencv.tools.MultiscaleFeatures.Hessian3D
 
getEigenvectors(boolean) - Method in interface qupath.opencv.tools.MultiscaleFeatures.Hessian
Get the eigenvectors, returned in the same order as the eigenvalues.
getEigenvectors(boolean) - Method in class qupath.opencv.tools.MultiscaleFeatures.Hessian2D
 
getEigenvectors(boolean) - Method in class qupath.opencv.tools.MultiscaleFeatures.Hessian3D
 
getErrorWriter() - Method in class qupath.lib.scripting.ScriptParameters
Get the error writer for script output.
getExtensions() - Method in class qupath.imagej.images.writers.TiffWriterIJ
 
getExtensions() - Method in class qupath.imagej.images.writers.ZipWriterIJ
 
getExtensions() - Method in class qupath.lib.scripting.languages.ScriptLanguage
Get an unmodifiable set containing the possible extensions for this language.
getFeature(int) - Method in class qupath.lib.analysis.features.HaralickFeatures
Get the value of the specified feature.
getFeatureImportance() - Method in class qupath.opencv.ml.OpenCVClassifiers.RTreesClassifier
Request the variable importance values from the last trained RTrees classifier, if available.
getFeatureName(int) - Method in class qupath.lib.analysis.features.HaralickFeatures
Get the name of the specified feature.
getFeatureNames() - Method in interface qupath.opencv.ml.objects.features.FeatureExtractor
 
getFile() - Method in class qupath.lib.scripting.ScriptParameters
Get the file where the script is located.
getFilledPolygonROIs(ImageProcessor, int) - Static method in class qupath.imagej.processing.RoiLabeling
Get filled PolygonRois for connected pixels with the same value in an image.
getFilledPolygonROIsFromLabels(ImageProcessor, int) - Static method in class qupath.imagej.processing.RoiLabeling
Get filled Polygon ROIs using distinct labels, creating a map between labels and ROIs.
getFramework() - Method in class qupath.opencv.dnn.DnnModelParams
Get the name of the deep learning framework that may be used.
getFramework() - Method in class qupath.opencv.dnn.OpenCVDnn
Get the framework used to create the model.
getGaussianDeriv(double, int, int) - Static method in class qupath.opencv.tools.OpenCVTools
Get filter coefficients for a 1D Gaussian (derivative) kernel.
getGaussianDerivKernel(double, int, boolean) - Static method in class qupath.opencv.tools.OpenCVTools
Get filter coefficients for a 1D Gaussian (derivative) kernel.
getHalo() - Method in class qupath.opencv.ml.PatchClassifierParams
Get the 'halo' around the output.
getHeight() - Method in class qupath.imagej.tools.PixelImageIJ
 
getHelpText() - Method in interface qupath.lib.lazy.interfaces.LazyValue
Optional help text that explained the value.
getHelpText() - Method in class qupath.lib.lazy.objects.MeasurementListValue
 
getHessian() - Method in class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder.FeatureMap
Get the MultiscaleFeatures.Hessian associated with these features.
getID() - Method in class qupath.opencv.dnn.DnnTools.DNNLayer
Layer ID.
getImage() - Method in class qupath.lib.experimental.pixels.Parameters
Get the image to process.
getImage(Parameters<S, ?>) - Method in interface qupath.lib.experimental.pixels.ImageSupplier
Get the image to process.
getImageBackground(ImagePlus) - Static method in class qupath.imagej.tools.IJProperties
Get the image background property value
getImageClass() - Method in class qupath.imagej.images.writers.TiffWriterIJ
 
getImageClass() - Method in class qupath.imagej.images.writers.ZipWriterIJ
 
getImageData() - Method in class qupath.lib.experimental.pixels.Parameters
Get the image data.
getImageData() - Method in class qupath.lib.scripting.ScriptParameters
Get the current ImageData that should be used with the script.
getImageData() - Method in interface qupath.opencv.ops.ImageDataServer
Get the ImageData wrapped by the ImageDataServer.
getImagePlane(Roi, ImagePlus) - Static method in class qupath.imagej.tools.IJTools
Get the ImagePlane of an ImageJ Roi, based upon its stored positions.
getImageRegion(ImagePlus) - Static method in class qupath.imagej.tools.IJProperties
 
getImageType() - Method in class qupath.imagej.images.servers.ImageJServerBuilder
 
getInds() - Method in class qupath.opencv.tools.OpenCVTools.IndexedPixel
Get the index array.
getInputChannels() - Method in class qupath.opencv.ml.PatchClassifierParams
Get the channels to extract from the image as input to the model.
getInputLength() - Method in class qupath.opencv.ml.FeaturePreprocessor
Get the number of features required of the input.
getInputResolution() - Method in class qupath.opencv.ml.PatchClassifierParams
Get the requested input resolution for the image.
getInputs() - Method in class qupath.opencv.dnn.DnnModelParams
Get the requested inputs and their shapes.
getInputs() - Method in interface qupath.opencv.dnn.PredictionFunction
Get the required inputs.
getInputShapes() - Method in class qupath.opencv.dnn.DnnTools.DNNLayer
Layer input shape.
getInsertion(String, int, String) - Method in interface qupath.lib.scripting.languages.AutoCompletions.Completion
Get the string to insert, given the provided text and position.
getInstance(LocalNormalization.SmoothingScale, double) - Static method in class qupath.opencv.tools.LocalNormalization.LocalNormalizationType
Get an object containing the parameters necessary for normalization.
getInstance(LocalNormalization.SmoothingScale, LocalNormalization.SmoothingScale) - Static method in class qupath.opencv.tools.LocalNormalization.LocalNormalizationType
Get an object containing the parameters necessary for normalization.
getLaplacian() - Method in interface qupath.opencv.tools.MultiscaleFeatures.Hessian
Get Laplacian of Gaussian image (calculated by summation without requiring eigenvalues).
getLaplacian() - Method in class qupath.opencv.tools.MultiscaleFeatures.Hessian2D
 
getLaplacian() - Method in class qupath.opencv.tools.MultiscaleFeatures.Hessian3D
 
getLastResultsDescription() - Method in class qupath.imagej.detect.cells.SubcellularDetection
 
getLastResultsDescription() - Method in class qupath.imagej.detect.cells.WatershedCellDetection
 
getLastResultsDescription() - Method in class qupath.imagej.detect.cells.WatershedCellMembraneDetection
 
getLastResultsDescription() - Method in class qupath.imagej.detect.dearray.TMADearrayerPluginIJ
 
getLastResultsDescription() - Method in class qupath.imagej.detect.tissue.PositivePixelCounterIJ
 
getLastResultsDescription() - Method in class qupath.imagej.detect.tissue.SimpleTissueDetection2
 
getLastResultsDescription() - Method in class qupath.imagej.superpixels.DoGSuperpixelsPlugin
 
getLastResultsDescription() - Method in class qupath.imagej.superpixels.SLICSuperpixelsPlugin
 
getLastResultsDescription() - Method in class qupath.lib.algorithms.CoherenceFeaturePlugin
 
getLastResultsDescription() - Method in class qupath.lib.algorithms.HaralickFeaturesPlugin
 
getLastResultsDescription() - Method in class qupath.lib.algorithms.IntensityFeaturesPlugin
 
getLastResultsDescription() - Method in class qupath.lib.algorithms.LocalBinaryPatternsPlugin
 
getLastResultsDescription() - Method in class qupath.lib.algorithms.TilerPlugin
 
getLastResultsDescription() - Method in class qupath.lib.plugins.objects.DilateAnnotationPlugin
 
getLastResultsDescription() - Method in class qupath.lib.plugins.objects.FillAnnotationHolesPlugin
 
getLastResultsDescription() - Method in class qupath.lib.plugins.objects.FindConvexHullDetectionsPlugin
 
getLastResultsDescription() - Method in class qupath.lib.plugins.objects.RefineAnnotationsPlugin
 
getLastResultsDescription() - Method in class qupath.lib.plugins.objects.ShapeFeaturesPlugin
 
getLastResultsDescription() - Method in class qupath.lib.plugins.objects.SmoothFeaturesPlugin
 
getLastResultsDescription() - Method in class qupath.lib.plugins.objects.SplitAnnotationsPlugin
 
getLastResultsDescription() - Method in class qupath.lib.plugins.objects.TileClassificationsToAnnotationsPlugin
 
getLastResultsDescription() - Method in class qupath.opencv.CellCountsCV
 
getLastResultsDescription() - Method in class qupath.opencv.features.DelaunayClusteringPlugin
Deprecated.
 
getLayout() - Method in class qupath.opencv.dnn.DnnModelParams
Get a string representing the axes layout that the model expects as input.
getLogger() - Static method in class qupath.lib.scripting.QP
Get the logger associated with this class.
getLogger(Class<?>) - Static method in class qupath.lib.scripting.QP
Get a logger associated with a specified class.
getLogger(String) - Static method in class qupath.lib.scripting.QP
Get a logger with a specified name.
getMainObjectFilter() - Method in class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapParameters
Get the primary object filter.
getMask() - Method in class qupath.lib.experimental.pixels.Parameters
Get the mask associated with the main ROI or the parent object, or null if no mask is available.
getMask(Parameters<S, T>, ROI) - Method in interface qupath.lib.experimental.pixels.MaskSupplier
Get a mask corresponding to the image, depicting a specified ROI.
getMask(ROI) - Method in class qupath.lib.experimental.pixels.Parameters
Get the mask associated with any ROI, or null if no mask is available.
getMaskedPixels(Mat, Mat) - Static method in class qupath.opencv.tools.OpenCVTools
Extract all the masked pixels within an image.
getMaxFeatures() - Method in class qupath.lib.analysis.features.CoocurranceMatrices
Compute maximum features from all four rotations
getMaxHeight() - Method in class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapParameters
Get the maximum height of the density map.
getMaxWidth() - Method in class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapParameters
Get the maximum width of the density map.
getMean() - Method in class qupath.opencv.dnn.OpenCVDnn
Get means which should be subtracted for preprocessing.
getMeanFeatures() - Method in class qupath.lib.analysis.features.CoocurranceMatrices
Compute averaged features over all four rotations
getMeasurement(Roi, String) - Static method in class qupath.imagej.tools.IJProperties
Get a measurement stored as a property.
getMeasurementNames() - Method in class qupath.opencv.ml.pixel.PixelClassificationMeasurementManager
Get the names of all measurements that may be returned.
getMeasurementType() - Method in interface qupath.lib.lazy.interfaces.LazyBooleanValue
 
getMeasurementType() - Method in interface qupath.lib.lazy.interfaces.LazyNumericValue
 
getMeasurementType() - Method in interface qupath.lib.lazy.interfaces.LazyStringValue
 
getMeasurementType() - Method in interface qupath.lib.lazy.interfaces.LazyValue
Get the generic type of the measurement.
getMeasurementValue(PathObject, String) - Method in class qupath.opencv.ml.pixel.PixelClassificationMeasurementManager
Get the value of a single measurement for a specified PathObject, computing it if it is unavailable.
getMeasurementValue(PathObject, String, boolean) - Method in class qupath.opencv.ml.pixel.PixelClassificationMeasurementManager
getMeasurementValue(ROI, String) - Method in class qupath.opencv.ml.pixel.PixelClassificationMeasurementManager
Get the value of a single measurement for a specified ROI, computing it if it is unavailable.
getMeasurementValue(ROI, String, boolean) - Method in class qupath.opencv.ml.pixel.PixelClassificationMeasurementManager
getMinFeatures() - Method in class qupath.lib.analysis.features.CoocurranceMatrices
Compute minimum features from all four rotations
getMissingFeatures(ImageData<BufferedImage>, Collection<? extends PathObject>) - Method in class qupath.opencv.dnn.DnnObjectClassifier
 
getMissingFeatures(ImageData<BufferedImage>, Collection<? extends PathObject>) - Method in class qupath.opencv.dnn.OpenCVModelObjectClassifier
 
getMissingFeatures(ImageData<T>, Collection<? extends PathObject>) - Method in class qupath.opencv.ml.objects.OpenCVMLClassifier
 
getMissingFeatures(ImageData<T>, PathObject) - Method in interface qupath.opencv.ml.objects.features.FeatureExtractor
Check for missing features, returning the names.
getMissingValue() - Method in class qupath.opencv.ml.objects.features.Normalizer
Return the value that will be output after normalization if the computed value is not finite.
getMode(float[], int) - Static method in class qupath.lib.analysis.algorithms.EstimateStainVectors
Estimate the mode from an array of floats.
getModelType() - Method in class qupath.opencv.dnn.OpenCVDnn
Get the type of the model that would be built with OpenCVDnn.buildModel().
getModelUri() - Method in class qupath.opencv.dnn.OpenCVDnn
Get the path to the model.
getModeRGB(int[]) - Static method in class qupath.lib.analysis.algorithms.EstimateStainVectors
Get the mode from an array of (packed) RGB pixel values.
getName() - Method in class qupath.imagej.detect.cells.PositiveCellDetection
 
getName() - Method in class qupath.imagej.detect.cells.SubcellularDetection
 
getName() - Method in class qupath.imagej.detect.cells.WatershedCellDetection
 
getName() - Method in class qupath.imagej.detect.cells.WatershedCellMembraneDetection
 
getName() - Method in class qupath.imagej.detect.dearray.TMADearrayerPluginIJ
 
getName() - Method in class qupath.imagej.detect.tissue.PositivePixelCounterIJ
 
getName() - Method in class qupath.imagej.detect.tissue.SimpleTissueDetection2
 
getName() - Method in class qupath.imagej.images.servers.ImageJServerBuilder
 
getName() - Method in class qupath.imagej.images.writers.TiffWriterIJ
 
getName() - Method in class qupath.imagej.images.writers.ZipWriterIJ
 
getName() - Method in class qupath.imagej.superpixels.DoGSuperpixelsPlugin
 
getName() - Method in class qupath.imagej.superpixels.SLICSuperpixelsPlugin
 
getName() - Method in class qupath.lib.algorithms.CoherenceFeaturePlugin
 
getName() - Method in class qupath.lib.algorithms.HaralickFeaturesPlugin
 
getName() - Method in class qupath.lib.algorithms.IntensityFeaturesPlugin
 
getName() - Method in class qupath.lib.algorithms.LocalBinaryPatternsPlugin
 
getName() - Method in class qupath.lib.algorithms.TilerPlugin
 
getName() - Method in interface qupath.lib.experimental.pixels.MeasurementProcessor.CustomMeasurement
 
getName() - Method in interface qupath.lib.lazy.interfaces.LazyValue
The name of the value.
getName() - Method in class qupath.lib.lazy.objects.MeasurementListValue
 
getName() - Method in class qupath.lib.plugins.objects.DilateAnnotationPlugin
 
getName() - Method in class qupath.lib.plugins.objects.FillAnnotationHolesPlugin
 
getName() - Method in class qupath.lib.plugins.objects.FindConvexHullDetectionsPlugin
 
getName() - Method in class qupath.lib.plugins.objects.RefineAnnotationsPlugin
 
getName() - Method in class qupath.lib.plugins.objects.ShapeFeaturesPlugin
 
getName() - Method in class qupath.lib.plugins.objects.SmoothFeaturesPlugin
 
getName() - Method in class qupath.lib.plugins.objects.SplitAnnotationsPlugin
 
getName() - Method in class qupath.lib.plugins.objects.TileClassificationsToAnnotationsPlugin
 
getName() - Method in class qupath.lib.scripting.languages.ScriptLanguage
Get the name of this language
getName() - Method in class qupath.opencv.CellCountsCV
 
getName() - Method in class qupath.opencv.dnn.DnnTools.DNNLayer
Layer name.
getName() - Method in class qupath.opencv.dnn.OpenCVDnn
Get a user-readable name for this model, or null if no name is specified.
getName() - Method in class qupath.opencv.features.DelaunayClusteringPlugin
Deprecated.
 
getName() - Method in class qupath.opencv.ml.OpenCVClassifiers.BoostClassifier
 
getName() - Method in class qupath.opencv.ml.OpenCVClassifiers.DTreesClassifier
 
getName() - Method in class qupath.opencv.ml.OpenCVClassifiers.EMClusterer
 
getName() - Method in class qupath.opencv.ml.OpenCVClassifiers.LogisticRegressionClassifier
 
getName() - Method in class qupath.opencv.ml.OpenCVClassifiers.NormalBayesClassifierCV
 
getName() - Method in class qupath.opencv.ml.OpenCVClassifiers.RTreesClassifier
 
getName() - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMClassifierCV
 
getName() - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMSGDClassifierCV
 
getName() - Method in class qupath.opencv.ml.OpenCVClassifiers.OpenCVStatModel
User-friendly, readable name for the classifier
getNonIntensityAncestorPathClass(PathObject) - Static method in class qupath.lib.scripting.QP
Get the first ancestor class of pathObject.getPathClass() that is not an intensity class (i.e.
getObjectId(Roi) - Static method in class qupath.imagej.tools.IJProperties
Get a QuPath object ID from the Roi properties.
getObjectName(Roi) - Static method in class qupath.imagej.tools.IJProperties
Get a QuPath object name, as stored in a roi's properties.
getObjects(Predicate<PathObject>) - Static method in class qupath.lib.scripting.QP
Get a list of all objects in the current hierarchy according to a specified predicate.
getObjects(PathObjectHierarchy, Predicate<PathObject>) - Static method in class qupath.lib.scripting.QP
Get a list of all objects in the specified hierarchy according to a specified predicate.
getOffset(int) - Method in class qupath.opencv.ml.objects.features.Normalizer
Get the offset for the specified feature
getOpenCVPixelType(PixelType) - Static method in class qupath.opencv.tools.OpenCVTools
Get the OpenCV type code corresponding to a PixelType.
getOpenCVTypeAdaptorFactory() - Static method in class qupath.opencv.io.OpenCVTypeAdapters
Get a TypeAdapterFactory to pass to a GsonBuilder to aid with serializing OpenCV objects (e.g.
getOriginalMetadata() - Method in class qupath.imagej.images.servers.ImageJServer
 
getOutputChannelType() - Method in class qupath.opencv.ml.PatchClassifierParams
Get the requested output channel type.
getOutputClasses() - Method in class qupath.opencv.ml.PatchClassifierParams
Get the classifications for the output.
getOutputLayerNames(Net) - Static method in class qupath.opencv.dnn.DnnTools
Get the names of all unconnected output layers.
getOutputLayers(Net, DnnShape...) - Static method in class qupath.opencv.dnn.DnnTools
Get the names of all unconnected output layers.
getOutputLength() - Method in class qupath.opencv.ml.FeaturePreprocessor
Get the number of features expected in the output.
getOutputs() - Method in class qupath.opencv.dnn.DnnModelParams
Get the expected outputs and their shapes.
getOutputs(DnnShape...) - Method in interface qupath.opencv.dnn.PredictionFunction
Get the output names mapped to the output shapes.
getOutputShapes() - Method in class qupath.opencv.dnn.DnnTools.DNNLayer
Layer output shape.
getOutputType(PixelType) - Method in interface qupath.opencv.ops.ImageDataOp
Get the output pixel type.
getOutputType(PixelType) - Method in interface qupath.opencv.ops.ImageOp
Get the output pixel type.
getPadding() - Method in interface qupath.opencv.ops.ImageOp
Get the padding requested for this operation.
getPadding() - Method in class qupath.opencv.ops.ImageOps.PaddedOp
 
getParameterList() - Method in class qupath.opencv.ml.OpenCVClassifiers.BoostClassifier
 
getParameterList() - Method in class qupath.opencv.ml.OpenCVClassifiers.DTreesClassifier
 
getParameterList() - Method in class qupath.opencv.ml.OpenCVClassifiers.EMClusterer
 
getParameterList() - Method in class qupath.opencv.ml.OpenCVClassifiers.LogisticRegressionClassifier
 
getParameterList() - Method in class qupath.opencv.ml.OpenCVClassifiers.NormalBayesClassifierCV
 
getParameterList() - Method in class qupath.opencv.ml.OpenCVClassifiers.RTreesClassifier
 
getParameterList() - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMClassifierCV
 
getParameterList() - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMSGDClassifierCV
 
getParameterList() - Method in class qupath.opencv.ml.OpenCVClassifiers.OpenCVStatModel
Retrieve a list of adjustable parameter that can be used to customize the classifier.
getParent() - Method in class qupath.lib.experimental.pixels.Parameters
Get the parent object.
getParentObjects(ImageData<BufferedImage>) - Method in class qupath.imagej.detect.cells.SubcellularDetection
 
getParentObjects(ImageData<BufferedImage>) - Method in class qupath.imagej.detect.dearray.TMADearrayerPluginIJ
 
getParentObjects(ImageData<BufferedImage>) - Method in class qupath.imagej.detect.tissue.SimpleTissueDetection2
 
getParentObjects(ImageData<BufferedImage>) - Method in class qupath.imagej.superpixels.DoGSuperpixelsPlugin
 
getParentObjects(ImageData<BufferedImage>) - Method in class qupath.imagej.superpixels.SLICSuperpixelsPlugin
 
getParentObjects(ImageData<BufferedImage>) - Method in class qupath.lib.algorithms.CoherenceFeaturePlugin
 
getParentObjects(ImageData<BufferedImage>) - Method in class qupath.lib.algorithms.HaralickFeaturesPlugin
 
getParentObjects(ImageData<BufferedImage>) - Method in class qupath.lib.algorithms.IntensityFeaturesPlugin
 
getParentObjects(ImageData<BufferedImage>) - Method in class qupath.lib.algorithms.LocalBinaryPatternsPlugin
 
getParentObjects(ImageData<T>) - Method in class qupath.lib.plugins.objects.DilateAnnotationPlugin
 
getParentObjects(ImageData<T>) - Method in class qupath.lib.plugins.objects.FillAnnotationHolesPlugin
 
getParentObjects(ImageData<T>) - Method in class qupath.lib.plugins.objects.FindConvexHullDetectionsPlugin
 
getParentObjects(ImageData<T>) - Method in class qupath.lib.plugins.objects.RefineAnnotationsPlugin
 
getParentObjects(ImageData<T>) - Method in class qupath.lib.plugins.objects.ShapeFeaturesPlugin
 
getParentObjects(ImageData<T>) - Method in class qupath.lib.plugins.objects.SmoothFeaturesPlugin
 
getParentObjects(ImageData<T>) - Method in class qupath.lib.plugins.objects.SplitAnnotationsPlugin
 
getParentObjects(ImageData<T>) - Method in class qupath.lib.plugins.objects.TileClassificationsToAnnotationsPlugin
 
getParentObjects(ImageData<T>) - Method in class qupath.opencv.features.DelaunayClusteringPlugin
Deprecated.
 
getParentOrProxy() - Method in class qupath.lib.experimental.pixels.Parameters
Get the parent, or a proxy parent if one has been specified.
getPatchHeight() - Method in class qupath.opencv.ml.PatchClassifierParams
Get the height of a patch, in pixels.
getPatchWidth() - Method in class qupath.opencv.ml.PatchClassifierParams
Get the width of a patch, in pixels.
getPathClass(String) - Static method in class qupath.lib.scripting.QP
Get a PathClass with the specified name.
getPathClass(String, Integer) - Static method in class qupath.lib.scripting.QP
Get a PathClass with the specified name and color.
getPathClasses() - Method in class qupath.opencv.dnn.DnnObjectClassifier
 
getPathClasses() - Method in class qupath.opencv.dnn.OpenCVModelObjectClassifier
 
getPathClasses() - Method in class qupath.opencv.ml.objects.OpenCVMLClassifier
 
getPathObjects() - Method in class qupath.opencv.features.DelaunayTriangulation
Deprecated.
 
getPixelSize() - Method in class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapParameters
Get the requested pixel size for the density map.
getPoolSizeProp() - Method in class qupath.opencv.ml.pixel.PixelClassificationMeasurementManager
 
getPostprocessing() - Method in class qupath.opencv.ml.PatchClassifierParams
Get any postprocessing steps that should be applied after prediction.
getPredictionFunction() - Method in class qupath.opencv.dnn.AbstractDnnModel
Get the prediction function that can apply a prediction with one or more blobs as input.
getPredictionFunction() - Method in class qupath.opencv.dnn.OpenCVDnn
 
getPredictionOp() - Method in class qupath.opencv.ml.PatchClassifierParams
Get the image op used for prediction only.
getPreferredPixelSizeMicrons(ImageData<BufferedImage>, ParameterList) - Method in class qupath.imagej.detect.cells.WatershedCellDetection
 
getPreferredPixelSizeMicrons(ImageData<BufferedImage>, ParameterList) - Method in class qupath.imagej.detect.cells.WatershedCellMembraneDetection
 
getPreferredPixelSizeMicrons(ImageData<BufferedImage>, ParameterList) - Method in class qupath.imagej.superpixels.DoGSuperpixelsPlugin
 
getPreferredPixelSizeMicrons(ImageData<BufferedImage>, ParameterList) - Method in class qupath.imagej.superpixels.SLICSuperpixelsPlugin
 
getPreferredPixelSizeMicrons(ImageData<BufferedImage>, ParameterList) - Method in class qupath.opencv.CellCountsCV
 
getPreprocessing() - Method in class qupath.opencv.ml.PatchClassifierParams
Get any preprocessing steps that should be applied.
getProbabilityThreshold(WritableRaster) - Static method in class qupath.opencv.ml.pixel.PixelClassificationMeasurementManager
Get a suitable threshold assuming a raster contains probability values.
getProject() - Static method in class qupath.lib.scripting.QP
Get the current project.
getProject() - Method in class qupath.lib.scripting.ScriptParameters
Get the current project that should be used with the script.
getProjectEntry() - Static method in class qupath.lib.scripting.QP
Get the project entry for the currently-open image within the current project, or null if no project/image is open.
getProjectEntryMetadataValue(String) - Static method in class qupath.lib.scripting.QP
Get the metadata value from the current project entry for the specified key, or null if no such metadata value exists (or no project entry is open).
getRadius() - Method in class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapParameters
Get the radius for the density map, in calibrated units.
getRegionRequest() - Method in class qupath.lib.experimental.pixels.Parameters
Get the region request.
getRegionRequest(ImagePlus) - Static method in class qupath.imagej.tools.IJProperties
Get a RegionRequest by reading the json representation stored as a property in the image.
getScale() - Method in class qupath.opencv.dnn.OpenCVDnn
Get scale factors to be applied to preprocess input.
getScale(int) - Method in class qupath.opencv.ml.objects.features.Normalizer
Get the scale factor for the specified feature
getScript() - Method in class qupath.lib.scripting.ScriptParameters
Get the text of the script.
getSecondaryObjectFilters() - Method in class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapParameters
Get the secondary object filters.
getSelectedObject() - Static method in class qupath.lib.scripting.QP
Get the primary selected object within the current PathObjectHierarchy.
getSelectedObjects() - Static method in class qupath.lib.scripting.QP
Get the selected objects within the current PathObjectHierarchy.
getSelectedROI() - Static method in class qupath.lib.scripting.QP
Get the ROI for the primary selected object within the current PathObjectHierarchy.
getServer() - Method in class qupath.lib.experimental.pixels.Parameters
Get the server.
getServerType() - Method in class qupath.imagej.images.servers.ImageJServer
 
getShape() - Method in class qupath.opencv.dnn.DnnShape
Get a copy of the internal dimensions array.
getSigma() - Method in class qupath.opencv.tools.LocalNormalization.SmoothingScale
Get the sigma value.
getSigmaZ(PixelCalibration) - Method in class qupath.opencv.tools.LocalNormalization.SmoothingScale
Get the sigma value for the z dimension.
getStringValue(S) - Method in interface qupath.lib.lazy.interfaces.LazyValue
Get a default string representation of an object measurement.
getStringValue(S, int) - Method in interface qupath.lib.lazy.interfaces.LazyValue
Get a default string representation of an object measurement.
getSupportedParentObjectClasses() - Method in class qupath.imagej.detect.cells.SubcellularDetection
 
getSupportedParentObjectClasses() - Method in class qupath.imagej.detect.dearray.TMADearrayerPluginIJ
 
getSupportedParentObjectClasses() - Method in class qupath.imagej.detect.tissue.SimpleTissueDetection2
 
getSupportedParentObjectClasses() - Method in class qupath.lib.algorithms.CoherenceFeaturePlugin
 
getSupportedParentObjectClasses() - Method in class qupath.lib.algorithms.HaralickFeaturesPlugin
 
getSupportedParentObjectClasses() - Method in class qupath.lib.algorithms.IntensityFeaturesPlugin
 
getSupportedParentObjectClasses() - Method in class qupath.lib.algorithms.LocalBinaryPatternsPlugin
 
getSupportedParentObjectClasses() - Method in class qupath.lib.algorithms.TilerPlugin
 
getSupportedParentObjectClasses() - Method in class qupath.lib.plugins.objects.DilateAnnotationPlugin
 
getSupportedParentObjectClasses() - Method in class qupath.lib.plugins.objects.FillAnnotationHolesPlugin
 
getSupportedParentObjectClasses() - Method in class qupath.lib.plugins.objects.FindConvexHullDetectionsPlugin
 
getSupportedParentObjectClasses() - Method in class qupath.lib.plugins.objects.RefineAnnotationsPlugin
 
getSupportedParentObjectClasses() - Method in class qupath.lib.plugins.objects.ShapeFeaturesPlugin
 
getSupportedParentObjectClasses() - Method in class qupath.lib.plugins.objects.SmoothFeaturesPlugin
 
getSupportedParentObjectClasses() - Method in class qupath.lib.plugins.objects.SplitAnnotationsPlugin
 
getSupportedParentObjectClasses() - Method in class qupath.lib.plugins.objects.TileClassificationsToAnnotationsPlugin
 
getSupportedParentObjectClasses() - Method in class qupath.opencv.features.DelaunayClusteringPlugin
Deprecated.
 
getTasks(ImageData<T>) - Method in class qupath.lib.plugins.objects.DilateAnnotationPlugin
 
getTasks(ImageData<T>) - Method in class qupath.lib.plugins.objects.FillAnnotationHolesPlugin
 
getTasks(ImageData<T>) - Method in class qupath.lib.plugins.objects.RefineAnnotationsPlugin
 
getTasks(ImageData<T>) - Method in class qupath.lib.plugins.objects.SplitAnnotationsPlugin
 
getTileObjects() - Static method in class qupath.lib.scripting.QP
Get a list of the current tile objects.
getTileOverlap(ImageData<BufferedImage>, ParameterList) - Method in class qupath.imagej.detect.cells.WatershedCellDetection
 
getTileOverlap(ImageData<BufferedImage>, ParameterList) - Method in class qupath.imagej.detect.cells.WatershedCellMembraneDetection
 
getTileOverlap(ImageData<BufferedImage>, ParameterList) - Method in class qupath.imagej.superpixels.DoGSuperpixelsPlugin
 
getTileOverlap(ImageData<BufferedImage>, ParameterList) - Method in class qupath.imagej.superpixels.SLICSuperpixelsPlugin
 
getTileOverlap(ImageData<BufferedImage>, ParameterList) - Method in class qupath.opencv.CellCountsCV
Returns zero - indicating no overlap...
getTileRequest() - Method in class qupath.lib.experimental.pixels.Parameters
Get the tile request, if available.
getTMACoreList() - Static method in class qupath.lib.scripting.QP
Get the list of TMA core objects for the current hierarchy.
getToken(String, int) - Method in interface qupath.lib.scripting.languages.AutoCompletions.CompletionTokenizer
Get the token needed for the completion.
getTokenizer() - Method in interface qupath.lib.scripting.languages.AutoCompletions.Completion
Get the tokenizer needed to extract the relevant bit of the text to determine the validity and/or insertion for the completion.
getTrainFlags() - Method in class qupath.opencv.ml.OpenCVClassifiers.BoostClassifier
 
getTrainFlags() - Method in class qupath.opencv.ml.OpenCVClassifiers.DTreesClassifier
 
getTrainFlags() - Method in class qupath.opencv.ml.OpenCVClassifiers.EMClusterer
 
getTrainFlags() - Method in class qupath.opencv.ml.OpenCVClassifiers.LogisticRegressionClassifier
 
getTrainFlags() - Method in class qupath.opencv.ml.OpenCVClassifiers.NormalBayesClassifierCV
 
getTrainFlags() - Method in class qupath.opencv.ml.OpenCVClassifiers.RTreesClassifier
 
getTrainFlags() - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMClassifierCV
 
getTrainFlags() - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMSGDClassifierCV
 
getTypeAdapterFactory() - Static method in class qupath.opencv.ml.objects.features.FeatureExtractors
Get the TypeAdapterFactory default used for FeatureExtractor objects.
getTypeAdapterFactory() - Static method in class qupath.opencv.ml.pixel.PixelClassifiers
Get the TypeAdapterFactory default used for PixelClassifier objects.
getTypeAdaptor(Class<T>) - Static method in class qupath.opencv.io.OpenCVTypeAdapters
Get a TypeAdapter to pass to a GsonBuilder for a specific supported OpenCV class, i.e.
getURIs() - Method in class qupath.imagej.images.servers.ImageJServer
 
getURIs() - Method in class qupath.opencv.dnn.DnnModelParams
Get the URIs associated with the model (e.g.
getURIs() - Method in class qupath.opencv.dnn.DnnObjectClassifier
 
getURIs() - Method in class qupath.opencv.dnn.OpenCVDnn
 
getURIs() - Method in class qupath.opencv.dnn.OpenCVModelObjectClassifier
 
getURIs() - Method in interface qupath.opencv.ops.ImageOp
Default implementation returns an empty list; classes should override this if necessary.
getValue() - Method in class qupath.opencv.tools.OpenCVTools.IndexedPixel
Get the value stored internally for this pixel.
getValue(int, int) - Method in class qupath.imagej.tools.PixelImageIJ
 
getValue(Indexer) - Method in class qupath.opencv.tools.OpenCVTools.IndexedPixel
Get the value from another image via its Indexer.
getValue(Parameters<S, T>) - Method in interface qupath.lib.experimental.pixels.MeasurementProcessor.CustomMeasurement
 
getValue(PathObject) - Method in class qupath.lib.lazy.objects.MeasurementListValue
 
getValue(S) - Method in interface qupath.lib.lazy.interfaces.LazyValue
Calculate a value from the input.
getWidth() - Method in class qupath.imagej.tools.PixelImageIJ
 
getWriter() - Method in class qupath.lib.scripting.ScriptParameters
Get the main writer for script output.
getX() - Method in class qupath.opencv.tools.OpenCVTools.IndexedPixel
Get x index.
getY() - Method in class qupath.opencv.tools.OpenCVTools.IndexedPixel
Get y index.
GRADIENT_MAGNITUDE - Enum constant in enum class qupath.opencv.tools.MultiscaleFeatures.MultiscaleFeature
Gradient magnitude
gradientMagnitude(boolean) - Method in class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder
Calculate the gradient magnitude.
greaterThan(ImageProcessor, ImageProcessor) - Static method in class qupath.imagej.processing.SimpleThresholding
Created a binary image by thresholding pixels to find where ip1 > ip2
greaterThanOrEqual(ImageProcessor, ImageProcessor) - Static method in class qupath.imagej.processing.SimpleThresholding
Created a binary image by thresholding pixels to find where ip1 >= ip2
GroovyCV - Class in qupath.opencv.tools
Category class for enhanced Groovy scripting with OpenCV.
GroovyCV() - Constructor for class qupath.opencv.tools.GroovyCV
 
gt(Mat, double) - Static method in class qupath.opencv.tools.GroovyCV
Apply a greater than threshold.
gt(Mat, Mat) - Static method in class qupath.opencv.tools.GroovyCV
Apply a greater than threshold between two arrays.

H

halo(int) - Method in class qupath.opencv.ml.PatchClassifierParams.Builder
Define a halo that is symmetric in x and y.
halo(Padding) - Method in class qupath.opencv.ml.PatchClassifierParams.Builder
Define a halo using a padding object.
handleOutput(Parameters<S, T>, U) - Method in interface qupath.lib.experimental.pixels.OutputHandler
Optional method to handle the output of a Processor.
handleOutput(Parameters<S, T>, U) - Method in class qupath.lib.experimental.pixels.OutputHandler.ObjectOutputHandler
 
handleOutputClassification(Parameters<?, ?>, String) - Static method in interface qupath.lib.experimental.pixels.OutputHandler
Handle the output of a pixel processor by setting a PathClass, given by its name.
handleOutputClassification(Parameters<?, ?>, PathClass) - Static method in interface qupath.lib.experimental.pixels.OutputHandler
Handle the output of a pixel processor by setting a PathClass.
handleOutputMeasurements(Parameters<?, ?>, Map<String, ? extends Number>) - Static method in interface qupath.lib.experimental.pixels.OutputHandler
Handle the output of a pixel processor by adding measurements to the path object.
HaralickFeatureComputer - Class in qupath.lib.analysis.features
Static methods for computing Haralick texture features.
HaralickFeatureComputer() - Constructor for class qupath.lib.analysis.features.HaralickFeatureComputer
 
HaralickFeatures - Class in qupath.lib.analysis.features
Helper class for computing Haralick features given a cooccurrence matrix.
HaralickFeaturesPlugin - Class in qupath.lib.algorithms
Plugin for calculating Haralick texture features, within or around detections or tiles.
HaralickFeaturesPlugin() - Constructor for class qupath.lib.algorithms.HaralickFeaturesPlugin
Default constructor.
hasFeatureImportance() - Method in class qupath.opencv.ml.OpenCVClassifiers.RTreesClassifier
Check if the last time train was called, variable (feature) importance was calculated.
hashCode() - Method in class qupath.opencv.tools.LocalNormalization.SmoothingScale
 
hasMeasurement(PathObject, String) - Static method in class qupath.lib.scripting.QP
Test whether a PathObject has a specified measurement in its measurement list.
hConcat(Collection<? extends Mat>, Mat) - Static method in class qupath.opencv.tools.OpenCVTools
Horizontal concatenation for a Mat.
HESSIAN_DETERMINANT - Enum constant in enum class qupath.opencv.tools.MultiscaleFeatures.MultiscaleFeature
Determinant of the Hessian matrix, calculated per pixel
HESSIAN_EIGENVALUE_MAX - Enum constant in enum class qupath.opencv.tools.MultiscaleFeatures.MultiscaleFeature
Maximum eigenvalue of the 2x2 or 3x3 Hessian matrix, calculated per pixel (by value, not absolute value)
HESSIAN_EIGENVALUE_MIDDLE - Enum constant in enum class qupath.opencv.tools.MultiscaleFeatures.MultiscaleFeature
Middle eigenvalue of the 3x3 Hessian matrix, calculated per pixel (by value, not absolute value)
HESSIAN_EIGENVALUE_MIN - Enum constant in enum class qupath.opencv.tools.MultiscaleFeatures.MultiscaleFeature
Minimum eigenvalue of the 2x2 or 3x3 Hessian matrix, calculated per pixel (by value, not absolute value)
hessianDeterminant(boolean) - Method in class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder
Calculate the determinant of the Hessian matrix per pixel.
hessianEigenvalues(boolean) - Method in class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder
Calculate the eigenvalues of the Hessian matrix per pixel.
hMaxima(ImageProcessor, double) - Static method in class qupath.imagej.processing.IJFilters
Suppress small local maxima in an image using a H-maxima transform.
hMinima(ImageProcessor, double) - Static method in class qupath.imagej.processing.IJFilters
Suppress small local minima in an image using a H-minima transform.

I

identity() - Static method in class qupath.opencv.ops.ImageOps.Core
Create an op that returns its input unchanged.
IJFilters - Class in qupath.imagej.processing
Helper class for filtering ImageJ images.
IJFilters() - Constructor for class qupath.imagej.processing.IJFilters
 
IJProcessing - Class in qupath.imagej.processing
Helper class for working with ImageJ.
IJProcessing() - Constructor for class qupath.imagej.processing.IJProcessing
 
IJProperties - Class in qupath.imagej.tools
Store QuPath-related information within the properties of ImageJ objects.
IJProperties() - Constructor for class qupath.imagej.tools.IJProperties
 
IJTools - Class in qupath.imagej.tools
Collection of static methods to help with using ImageJ with QuPath.
IJTools() - Constructor for class qupath.imagej.tools.IJTools
 
IMAGE_BACKGROUND - Static variable in class qupath.imagej.tools.IJProperties
Key for an ImagePlus property storing either "light" or "dark depending upon whether an image is known to be brightfield of fluorescence respectively.
IMAGE_REGION_ROOT - Static variable in class qupath.imagej.tools.IJProperties
Key for a ImagePlus properties to store the bounding box of a QuPath ImageRegion.
IMAGE_REQUEST - Static variable in class qupath.imagej.tools.IJProperties
Key for an ImagePlus property to store a json representation of a RegionRequest used to request the image.
IMAGE_TYPE - Static variable in class qupath.imagej.tools.IJProperties
Key for an ImagePlus property to store a string representing a QuPath ImageData.ImageType.
imageData(ImageData<BufferedImage>) - Method in class qupath.lib.experimental.pixels.Parameters.Builder
Set the image data.
ImageDataOp - Interface in qupath.opencv.ops
Request pixels from an image, potentially applying further transforms.
ImageDataServer<T> - Interface in qupath.opencv.ops
An ImageServer that wraps an ImageData.
imageFunction(ImageSupplier<S>) - Method in class qupath.lib.experimental.pixels.Parameters.Builder
Function used ot lazily read the image.
ImageJProcessor - Class in qupath.lib.experimental.pixels
Class to generate a PixelProcessor when using ImageJ for the primary image representation.
ImageJProcessor() - Constructor for class qupath.lib.experimental.pixels.ImageJProcessor
 
ImageJServer - Class in qupath.imagej.images.servers
ImageServer that uses ImageJ's image-reading capabilities.
ImageJServer(URI, String...) - Constructor for class qupath.imagej.images.servers.ImageJServer
Constructor.
ImageJServerBuilder - Class in qupath.imagej.images.servers
Builder for ImageServers that use ImageJ to read images.
ImageJServerBuilder() - Constructor for class qupath.imagej.images.servers.ImageJServerBuilder
 
ImageOp - Interface in qupath.opencv.ops
An operation that may be applied to a Mat.
ImageOps - Class in qupath.opencv.ops
Create and use ImageOp and ImageDataOp objects.
ImageOps() - Constructor for class qupath.opencv.ops.ImageOps
 
ImageOps.Channels - Class in qupath.opencv.ops
Channel and color operations.
ImageOps.Core - Class in qupath.opencv.ops
Core operations.
ImageOps.Filters - Class in qupath.opencv.ops
Filtering operations.
ImageOps.ML - Class in qupath.opencv.ops
Machine learning operations.
ImageOps.Normalize - Class in qupath.opencv.ops
Normalization operations.
ImageOps.PaddedOp - Class in qupath.opencv.ops
Abstract ImageOp to simplify the process of handling padding.
ImageOps.Threshold - Class in qupath.opencv.ops
Thresholding operations.
imagesEqual(ImageProcessor, ImageProcessor) - Static method in class qupath.imagej.processing.SimpleThresholding
Created a binary image by identifying pixels where ip1 == ip2
imagesFromBlob(Mat) - Static method in class qupath.opencv.dnn.DnnTools
Extract images from an OpenCV blob.
imageSupplier(ImageSupplier<S>) - Method in class qupath.lib.experimental.pixels.PixelProcessor.Builder
Set the image supplier.
ImageSupplier<S> - Interface in qupath.lib.experimental.pixels
A functional interface for supplying an image region for processing.
imageToMat(BufferedImage) - Static method in class qupath.opencv.tools.OpenCVTools
Convert a BufferedImage to an OpenCV Mat.
imageToMatBGR(BufferedImage, boolean) - Static method in class qupath.opencv.tools.OpenCVTools
Extract 8-bit unsigned pixels from a BufferedImage as a multichannel BGR(A) Mat.
imageToMatRGB(BufferedImage, boolean) - Static method in class qupath.opencv.tools.OpenCVTools
Extract 8-bit unsigned pixels from a BufferedImage as a multichannel RGB(A) Mat.
importObjectsFromFile(String) - Static method in class qupath.lib.scripting.QP
Import all PathObjects from the given file.
imposeMaxima(FloatProcessor, Roi) - Static method in class qupath.imagej.processing.MorphologicalReconstruction
Ensure that a FloatProcessor only has region maxima within a specified Roi, using morphological reconstruction.
imposeMaxima(FloatProcessor, ImageProcessor) - Static method in class qupath.imagej.processing.MorphologicalReconstruction
Ensure that a FloatProcessor only has region maxima within a specified mask, using morphological reconstruction.
imposeMinima(FloatProcessor, Roi) - Static method in class qupath.imagej.processing.MorphologicalReconstruction
Ensure that a FloatProcessor only has region minima within a specified Roi, using morphological reconstruction.
INCLUDE_IGNORED - Enum constant in enum class qupath.opencv.ml.pixel.PixelClassifierTools.CreateObjectOptions
Generate objects for ignored classes (default is not to)
initializeModel(Model) - Method in class qupath.opencv.dnn.OpenCVDnn
Initialize the model with the same preprocessing defined here (i.e.
input(String, long...) - Method in class qupath.opencv.dnn.DnnModelParams.Builder
Specify the shape as a long array for a single input with a specified name.
input(String, DnnShape) - Method in class qupath.opencv.dnn.DnnModelParams.Builder
Specify the shape for a single input with a specified name.
inputChannels(int...) - Method in class qupath.opencv.ml.PatchClassifierParams.Builder
Define the input channels using (zero-based) channel numbers.
inputChannels(String...) - Method in class qupath.opencv.ml.PatchClassifierParams.Builder
Define the input channels using channel names.
inputChannels(Collection<? extends ColorTransforms.ColorTransform>) - Method in class qupath.opencv.ml.PatchClassifierParams.Builder
Define the input channels from a collection of color transforms.
inputResolution(PixelCalibration) - Method in class qupath.opencv.ml.PatchClassifierParams.Builder
Define the input resolution using a pixel calibration object.
inputResolution(PixelCalibration, double) - Method in class qupath.opencv.ml.PatchClassifierParams.Builder
Define the input resolution using a pixel calibration and a scaling factor.
inputs(Map<String, DnnShape>) - Method in class qupath.opencv.dnn.DnnModelParams.Builder
Specify the shapes for one or more inputs.
inputShape(long...) - Method in class qupath.opencv.dnn.DnnModelParams.Builder
Specify the shape for a single input, with the default input name.
insertObjects(Collection<? extends PathObject>) - Static method in class qupath.lib.scripting.QP
Insert objects into the hierarchy, resolving their location and setting parent/child relationships.
insertObjects(PathObject) - Static method in class qupath.lib.scripting.QP
Insert object into the hierarchy, resolving its location and setting parent/child relationships.
IntensityFeaturesPlugin - Class in qupath.lib.algorithms
Plugin for calculating intensity-based features, including Haralick textures, within or around detections or tiles.
IntensityFeaturesPlugin() - Constructor for class qupath.lib.algorithms.IntensityFeaturesPlugin
 
interp2D(Indexer, double, double) - Static method in class qupath.opencv.tools.Interpolation
Request a value from an Indexer using bilinear interpolation.
interp3D(Indexer, double, double, double) - Static method in class qupath.opencv.tools.Interpolation
Request a value from an Indexer using trilinear interpolation.
Interpolation - Class in qupath.opencv.tools
Methods to help with requesting interpolated values.
Interpolation() - Constructor for class qupath.opencv.tools.Interpolation
 
invertBinary(Mat, Mat) - Static method in class qupath.opencv.tools.OpenCVTools
Invert a binary image.
isBoolean() - Method in interface qupath.lib.lazy.interfaces.LazyValue
Check whether the value returned by this measurement is an instance of Boolean.
isCompatible(String, int, String) - Method in interface qupath.lib.scripting.languages.AutoCompletions.Completion
Test if this completion is compatible with the provided text.
isCudaAvailable() - Static method in class qupath.opencv.dnn.DnnTools
Query whether CUDA is reported as available by OpenCV.
isDirectory(String) - Static method in class qupath.lib.scripting.QP
Query if a file path corresponds to a directory.
isFloat(Mat) - Static method in class qupath.opencv.tools.OpenCVTools
Returns true if a Mat is a floating point (rather than int) type.
isIdentity() - Method in class qupath.opencv.ml.objects.features.Normalizer
Returns true if this normalizer does not actually do anything.
isMemorySufficient(RegionRequest, ImageData<BufferedImage>) - Static method in class qupath.imagej.tools.IJTools
Check if sufficient memory is available to request pixels for a specific region, and the number of pixels is less than the maximum length of a Java array.
isNumeric() - Method in interface qupath.lib.lazy.interfaces.LazyValue
Check whether the value returned by this measurement is an instance of Number.
isString() - Method in interface qupath.lib.lazy.interfaces.LazyValue
Check whether the value returned by this measurement is an instance of String.
isTMADearrayed() - Static method in class qupath.lib.scripting.QP
Returns true if TMA cores are available.
isTrained() - Method in class qupath.opencv.ml.OpenCVClassifiers.BoostClassifier
 
isTrained() - Method in class qupath.opencv.ml.OpenCVClassifiers.DTreesClassifier
 
isTrained() - Method in class qupath.opencv.ml.OpenCVClassifiers.EMClusterer
 
isTrained() - Method in class qupath.opencv.ml.OpenCVClassifiers.LogisticRegressionClassifier
 
isTrained() - Method in class qupath.opencv.ml.OpenCVClassifiers.NormalBayesClassifierCV
 
isTrained() - Method in class qupath.opencv.ml.OpenCVClassifiers.RTreesClassifier
 
isTrained() - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMClassifierCV
 
isTrained() - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMSGDClassifierCV
 
isTrained() - Method in class qupath.opencv.ml.OpenCVClassifiers.OpenCVStatModel
Classifier has already been trained and is ready to predict.
isUnknown() - Method in class qupath.opencv.dnn.DnnShape
Returns true if the shape is unknown.

J

JAVA_TOKENIZER - Static variable in class qupath.lib.scripting.languages.AutoCompletions
A completion tokenizer that extracts a token used to determine Java completions.

K

KEYPOINTS - Enum constant in enum class qupath.opencv.dnn.OpenCVDnn.ModelType
Refers to KeypointsModel.

L

label(Mat, int) - Static method in class qupath.opencv.tools.OpenCVTools
Label connected components for non-zero pixels in an image.
label(Mat, Mat, int) - Static method in class qupath.opencv.tools.OpenCVTools
Label connected components for non-zero pixels in an image.
labelImage(ImageProcessor, float, boolean) - Static method in class qupath.imagej.processing.RoiLabeling
Create a labelled image from above-threshold pixels for an image.
labelImage(ImageProcessor, int) - Static method in class qupath.imagej.processing.IJProcessing
Create a labeled image using the thresholds set on an ImageProcessor (inclusive).
labelImage(ImageProcessor, int, DoublePredicate) - Static method in class qupath.imagej.processing.IJProcessing
Create a labeled image using the thresholds set on an ImageProcessor.
labelImage(Mat, Mat, int) - Static method in class qupath.opencv.tools.OpenCVTools
Deprecated.
labelROIs(ImageProcessor, List<? extends Roi>) - Static method in class qupath.imagej.processing.RoiLabeling
Label ROIs by filling each pixel with an integer value corresponding to the index of the Roi in the list + 1.
labelsToConnectedROIs(ImageProcessor, int) - Static method in class qupath.imagej.processing.RoiLabeling
labelsToFilledRoiList(ImageProcessor, boolean) - Static method in class qupath.imagej.processing.RoiLabeling
Convert a labelled image into a list of PolygonRois by tracing.
labelsToFilledROIs(ImageProcessor, int) - Static method in class qupath.imagej.processing.RoiLabeling
Convert a labelled image into a list of PolygonRois by tracing.
labelsToRois(ImageProcessor) - Static method in class qupath.imagej.processing.IJProcessing
Create ImageJ Rois from labels in an image.
labelsToRoisArray(ImageProcessor) - Static method in class qupath.imagej.processing.IJProcessing
Create ImageJ Rois from labels in an image.
LAPLACIAN - Enum constant in enum class qupath.opencv.tools.MultiscaleFeatures.MultiscaleFeature
Laplacian of Gaussian filter
laplacianOfGaussian(boolean) - Method in class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder
Calculate the Laplacian of Gaussian image.
layout(String) - Method in class qupath.opencv.dnn.DnnModelParams.Builder
Specify a string representing the axes layout that the model expects as input.
LazyBooleanValue<S> - Interface in qupath.lib.lazy.interfaces
Interface for a LazyValue that gives a Boolean output.
lazyInitialize(boolean) - Method in class qupath.opencv.dnn.DnnModelParams.Builder
Optionally request lazy initialization.
LazyNumericValue<S> - Interface in qupath.lib.lazy.interfaces
Interface for a LazyValue that gives a Number output.
LazyStringValue<S> - Interface in qupath.lib.lazy.interfaces
Interface for a LazyValue that gives a String output.
LazyValue<S,T> - Interface in qupath.lib.lazy.interfaces
Interface that can generate a 'lazy' value from an object.
LENGTH - Enum constant in enum class qupath.lib.analysis.features.ObjectMeasurements.ShapeFeatures
Length of the shape; for area geometries, this provides the perimeter.
leq(Mat, double) - Static method in class qupath.opencv.tools.GroovyCV
Apply a less than or equal to threshold.
leq(Mat, Mat) - Static method in class qupath.opencv.tools.GroovyCV
Apply a less than or equal to threshold between two arrays.
loadDensityMap(String) - Static method in class qupath.lib.scripting.QP
Load a density map for a project or file path.
loadDensityMap(Path) - Static method in class qupath.lib.analysis.heatmaps.DensityMaps
Load a DensityMaps.DensityMapBuilder from the specified path.
loadImageData(String, boolean) - Static method in class qupath.lib.scripting.QP
Deprecated.
loadObjectClassifier(String...) - Static method in class qupath.lib.scripting.QP
Load an object classifier for a project or file path.
loadPixelClassifier(String) - Static method in class qupath.lib.scripting.QP
Load a pixel classifier for a project or file path.
LocalBinaryPatterns - Class in qupath.lib.analysis.features
Initial test implementation of Local Binary Patterns.
LocalBinaryPatterns() - Constructor for class qupath.lib.analysis.features.LocalBinaryPatterns
 
LocalBinaryPatternsPlugin - Class in qupath.lib.algorithms
Calculate local binary pattern features.
LocalBinaryPatternsPlugin() - Constructor for class qupath.lib.algorithms.LocalBinaryPatternsPlugin
Default constructor.
localNormalization(double, double) - Static method in class qupath.opencv.ops.ImageOps.Normalize
Apply local 2D normalization using Gaussian-weighted mean subtraction and (optionally) variance estimation.
LocalNormalization - Class in qupath.opencv.tools
Methods to normalize the local image intensity within an image, to have (approximately) zero mean and unit variance.
LocalNormalization() - Constructor for class qupath.opencv.tools.LocalNormalization
 
LocalNormalization.LocalNormalizationType - Class in qupath.opencv.tools
Helper class to store local normalization parameters.
LocalNormalization.NormalizationType - Enum Class in qupath.opencv.tools
Local normalization type.
LocalNormalization.SmoothingScale - Class in qupath.opencv.tools
2D or 3D Gaussian scale.
localNormalizationMinMax(int, double) - Static method in class qupath.opencv.ops.ImageOps.Normalize
Apply local 2D normalization using local min and max values, optionally smoothing with a Gaussian filter to reduce sharp edges.
locateFile(String) - Static method in class qupath.lib.scripting.QP
Locate a specified file based upon its name or path, with a search depth of 4.
locateFile(String, int) - Static method in class qupath.lib.scripting.QP
Locate a specified file based upon its name or path.
log() - Static method in class qupath.opencv.ops.ImageOps.Core
Create an op that returns the natural logarithm of values.
LoggingTools - Class in qupath.lib.scripting
 
LoggingTools() - Constructor for class qupath.lib.scripting.LoggingTools
 
lt(Mat, double) - Static method in class qupath.opencv.tools.GroovyCV
Apply a less than threshold.
lt(Mat, Mat) - Static method in class qupath.opencv.tools.GroovyCV
Apply a less than threshold between two arrays.

M

makeARGB(int, int, int, int) - Static method in class qupath.lib.scripting.QP
Make a packed int representation of an ARGB color.
makeBinaryImage(ImageProcessor, double, Roi, boolean) - Static method in class qupath.imagej.detect.dearray.TMADearrayer
Make a binary image depicting (hopefully) the TMA cores.
makeFileInProject(String...) - Static method in class qupath.lib.scripting.QP
Build a file path relative to the current project, and create a File object.
makeInverseAnnotation() - Static method in class qupath.lib.scripting.QP
Make an inverse annotation using the current ImageData and its current selected objects.
makeInverseAnnotation(ImageData<?>) - Static method in class qupath.lib.scripting.QP
Make an inverse annotation using the specified ImageData and current selected objects.
makeInverseAnnotation(ImageData<?>, Collection<PathObject>) - Static method in class qupath.lib.scripting.QP
Make an annotation, for which the ROI is obtained by subtracting the ROIs of the specified objects from the closest common ancestor ROI (or entire image if the closest ancestor is the root).
makeInverseAnnotation(ImageData<?>, PathObject) - Static method in class qupath.lib.scripting.QP
Make an annotation for the specified ImageData, for which the ROI is obtained by subtracting the existing ROI from the ROI of its parent object (or entire image if no suitable parent object is available).
makeInverseAnnotation(PathObject) - Static method in class qupath.lib.scripting.QP
Make an annotation for the current ImageData, for which the ROI is obtained by subtracting the existing ROI from the ROI of its parent object (or entire image if no suitable parent object is available).
makePathInProject(String...) - Static method in class qupath.lib.scripting.QP
Deprecated.
makeRGB(int, int, int) - Static method in class qupath.lib.scripting.QP
Make a packed int representation of an RGB color.
maskFunction(MaskSupplier<S, T>) - Method in class qupath.lib.experimental.pixels.Parameters.Builder
Function used to lazily create a mask corresponding to the image for a specified ROI.
maskObject(ROI, PathObject) - Static method in class qupath.lib.experimental.pixels.PixelProcessorUtils
Apply a ROI mask to an object, ensuring that the child object's ROI does not extend beyond the mask.
maskObjectAndSplit(ROI, PathObject) - Static method in class qupath.lib.experimental.pixels.PixelProcessorUtils
Apply a ROI mask to an object, ensuring that the child object's ROI does not extend beyond the mask, and splitting the child object's ROI to create multiple objects if it contains disjoint regions.
maskSupplier(MaskSupplier<S, T>) - Method in class qupath.lib.experimental.pixels.PixelProcessor.Builder
Set the mask supplier.
MaskSupplier<S,T> - Interface in qupath.lib.experimental.pixels
A functional interface for supplying a mask corresponding to an image.
matchClassName(String...) - Method in class qupath.imagej.images.servers.ImageJServerBuilder
 
matToBufferedImage(Mat) - Static method in class qupath.opencv.tools.OpenCVTools
Convert a Mat to a BufferedImage.
matToBufferedImage(Mat, ColorModel) - Static method in class qupath.opencv.tools.OpenCVTools
Convert a Mat to a BufferedImage.
matToImagePlus(String, Mat...) - Static method in class qupath.opencv.tools.OpenCVTools
Convert an OpenCV MatVector into an ImageJ ImagePlus.
matToImagePlus(Mat, String) - Static method in class qupath.opencv.tools.OpenCVTools
Convert an OpenCV Mat into an ImageJ ImagePlus.
matToImageProcessor(Mat) - Static method in class qupath.opencv.tools.OpenCVTools
Convert a single-channel OpenCV Mat into an ImageJ ImageProcessor.
matToSimpleImage(Mat, int) - Static method in class qupath.opencv.tools.OpenCVTools
Convert a Mat to a SimpleImage.
max() - Static method in class qupath.lib.experimental.pixels.MeasurementProcessor.Functions
Create a function to calculate the maximum value of an array.
max(Mat) - Static method in class qupath.opencv.tools.GroovyCV
Find the maximum of all elements in a Mat, ignoring NaNs.
max(T, ImageProcessor...) - Static method in class qupath.imagej.processing.IJProcessing
Pixelwise maximum of the input images.
MAX - Enum constant in enum class qupath.lib.analysis.features.ObjectMeasurements.Measurements
Maximum value
MAX_DIAMETER - Enum constant in enum class qupath.lib.analysis.features.ObjectMeasurements.ShapeFeatures
Maximum diameter; this is equivalent to the diameter of the minimum bounding circle.
maximum() - Static method in class qupath.opencv.ops.ImageOps.Channels
Calculate the maximum value along all channels, to give a single-channel output.
maximum(int) - Static method in class qupath.opencv.ops.ImageOps.Filters
Apply a 2D maximum filter.
maximum(ImageProcessor, double) - Static method in class qupath.imagej.processing.IJFilters
Apply a maximum filter.
maximum(Mat) - Static method in class qupath.opencv.tools.OpenCVTools
Get the maximum value in an image, across all pixels (regardless of channels), ignoring NaNs.
maximum(Mat, double) - Static method in class qupath.opencv.tools.GroovyCV
Get the per-element maximum value between an array and a scalar.
maximum(Mat, Mat) - Static method in class qupath.opencv.tools.GroovyCV
Get the per-element maximum value for two arrays.
maximumFilter(Mat, int) - Static method in class qupath.opencv.tools.OpenCVTools
Apply a 2D maximum filter (dilation) to all channels of an image.
mean() - Static method in class qupath.lib.experimental.pixels.MeasurementProcessor.Functions
Create a function to calculate the mean (average) value of an array.
mean() - Static method in class qupath.opencv.ops.ImageOps.Channels
Average all channels together using the mean, to give a single-channel output.
mean(int) - Static method in class qupath.opencv.ops.ImageOps.Filters
Apply a 2D circular mean filter.
mean(ImageProcessor, double) - Static method in class qupath.imagej.processing.IJFilters
Apply a mean (average) filter.
mean(Mat) - Static method in class qupath.opencv.tools.GroovyCV
Calculate the mean of all elements in a Mat, ignoring NaNs.
mean(Mat) - Static method in class qupath.opencv.tools.OpenCVTools
Get the mean of an image, across all pixels (regardless of channels), ignoring NaNs.
mean(Scalar) - Method in class qupath.opencv.dnn.OpenCVDnn.Builder
Mean values which should be subtracted from the image channels before input to the Net.
MEAN - Enum constant in enum class qupath.lib.analysis.features.ObjectMeasurements.Measurements
Arithmetic mean
meanFilter(Mat, int) - Static method in class qupath.opencv.tools.OpenCVTools
Apply a circular 2D mean filter to all channels of an image, with symmetric boundary padding.
meanFilter(Mat, int, int) - Static method in class qupath.opencv.tools.OpenCVTools
Apply a circular 2D mean filter to all channels of an image.
measureHaralick(SimpleImage, SimpleImage, int, double, double, int) - Static method in class qupath.lib.analysis.features.HaralickFeatureComputer
Compute mean Haralick features from a SimpleImage, with optional masking.
measurement(PathObject, String) - Static method in class qupath.lib.scripting.QP
Extract the specified measurement from a PathObject.
MeasurementListValue - Class in qupath.lib.lazy.objects
Value extracted from an object's measurement list.
MeasurementProcessor - Class in qupath.lib.experimental.pixels
Create PixelProcessor instances that make measurements from objects.
MeasurementProcessor() - Constructor for class qupath.lib.experimental.pixels.MeasurementProcessor
 
MeasurementProcessor.CustomMeasurement<S,T> - Interface in qupath.lib.experimental.pixels
Interface for calculating one custom measurement from an image, using Parameters.
MeasurementProcessor.Functions - Class in qupath.lib.experimental.pixels
Functions for calculating measurements from an array of pixels.
MeasurementProcessor.Measurements - Class in qupath.lib.experimental.pixels
Methods to create custom measurements.
Measurements() - Constructor for class qupath.lib.experimental.pixels.MeasurementProcessor.Measurements
 
median(int) - Static method in class qupath.opencv.ops.ImageOps.Filters
Apply a 2D median filter
median(ImageProcessor, double) - Static method in class qupath.imagej.processing.IJFilters
Apply a median filter.
median(Mat) - Static method in class qupath.opencv.tools.OpenCVTools
Get the median pixel value in a Mat, ignoring NaNs.
MEDIAN - Enum constant in enum class qupath.lib.analysis.features.ObjectMeasurements.Measurements
Median value
MEMBRANE - Enum constant in enum class qupath.lib.analysis.features.ObjectMeasurements.Compartments
Cell boundary, with interior removed
memoryReport(CharSequence) - Static method in class qupath.opencv.tools.OpenCVTools
Create a brief report on memory use, based on JavaCPP's Pointer class.
mergeAnnotations(Collection<PathObject>) - Static method in class qupath.lib.scripting.QP
Merge annotations for the current hierarchy.
mergeAnnotations(PathObjectHierarchy, Collection<PathObject>) - Static method in class qupath.lib.scripting.QP
Merge the specified annotations to create a new annotation containing the union of their ROIs.
mergeChannels(Collection<? extends Mat>, Mat) - Static method in class qupath.opencv.tools.OpenCVTools
Merge channels from a multichannel Mat.
mergePointsForAllClasses() - Static method in class qupath.lib.scripting.QP
Merge point annotations sharing the same PathClass and ImagePlane as the selected annotations of the current hierarchy, creating multi-point annotations for all matching points and removing the (previously-separated) annotations.
mergePointsForSelectedObjectClasses() - Static method in class qupath.lib.scripting.QP
Merge point annotations sharing the same PathClass and ImagePlane for the current hierarchy, creating multi-point annotations for all matching points and removing the (previously-separated) annotations.
merger(ObjectMerger) - Method in class qupath.lib.experimental.pixels.PixelProcessor.Builder
mergeSelectedAnnotations() - Static method in class qupath.lib.scripting.QP
Merge the currently-selected annotations of the current hierarchy to create a new annotation containing the union of their ROIs.
mergeSelectedAnnotations(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP
Merge the currently-selected annotations to create a new annotation containing the union of their ROIs.
mergeSharedBoundaries(double) - Method in class qupath.lib.experimental.pixels.PixelProcessor.Builder
Convenience method to set a merger that merges objects based on their shared boundary.
min() - Static method in class qupath.lib.experimental.pixels.MeasurementProcessor.Functions
Create a function to calculate the minimum value of an array.
min(Mat) - Static method in class qupath.opencv.tools.GroovyCV
Find the minimum of all elements in a Mat, ignoring NaNs.
min(T, ImageProcessor...) - Static method in class qupath.imagej.processing.IJProcessing
Pixelwise minimum of the input images.
MIN - Enum constant in enum class qupath.lib.analysis.features.ObjectMeasurements.Measurements
Minimum value
MIN_DIAMETER - Enum constant in enum class qupath.lib.analysis.features.ObjectMeasurements.ShapeFeatures
Minimum diameter.
minimum() - Static method in class qupath.opencv.ops.ImageOps.Channels
Calculate the minimum value along all channels, to give a single-channel output.
minimum(int) - Static method in class qupath.opencv.ops.ImageOps.Filters
Apply a 2D minimum filter.
minimum(ImageProcessor, double) - Static method in class qupath.imagej.processing.IJFilters
Apply a minimum filter.
minimum(Mat) - Static method in class qupath.opencv.tools.OpenCVTools
Get the minimum value in an image, across all pixels (regardless of channels), ignoring NaNs.
minimum(Mat, double) - Static method in class qupath.opencv.tools.GroovyCV
Get the per-element minimum value between an array and a scalar.
minimum(Mat, Mat) - Static method in class qupath.opencv.tools.GroovyCV
Get the per-element minimum value for two arrays.
minimumFilter(Mat, int) - Static method in class qupath.opencv.tools.OpenCVTools
Apply a 2D minimum filter (erosion) to all channels of an image.
minMax() - Static method in class qupath.opencv.ops.ImageOps.Normalize
Normalize the minimum and maximum values of the image to fall into the range 0 - 1.
minMax(double, double) - Static method in class qupath.opencv.ops.ImageOps.Normalize
Normalize the minimum and maximum values of the image to fall into the range 'outputMin - outputMax'.
minus(Mat, Number) - Static method in class qupath.opencv.tools.GroovyCV
Subtract a constant from an array.
minus(Mat, Mat) - Static method in class qupath.opencv.tools.GroovyCV
Subtract one array from another.
minus(Mat, Scalar) - Static method in class qupath.opencv.tools.GroovyCV
Subtract a scalar from an array.
missingValue(double) - Method in class qupath.opencv.ml.FeaturePreprocessor.Builder
 
mkdirs(String) - Static method in class qupath.lib.scripting.QP
Ensure directories exist for the specified path, calling file.mkdirs() if not.
ML() - Constructor for class qupath.opencv.ops.ImageOps.ML
 
modelType(OpenCVDnn.ModelType) - Method in class qupath.opencv.dnn.OpenCVDnn.Builder
Set the model type, used by OpenCVDnn.buildModel().
morphologicalReconstruction(ImageProcessor, ImageProcessor) - Static method in class qupath.imagej.processing.MorphologicalReconstruction
Apply morphological operation using marker and mask images.
morphologicalReconstruction(Mat, Mat) - Static method in class qupath.opencv.tools.ProcessingCV
Compute morphological reconstruction.
morphologicalReconstruction(SimpleModifiableImage, SimpleImage) - Static method in class qupath.lib.analysis.algorithms.MorphologicalReconstruction
Apply morphological reconstruction with the specified marker and mask images.
MorphologicalReconstruction - Class in qupath.imagej.processing
Implementation of morphological reconstruction for ImageJ.
MorphologicalReconstruction - Class in qupath.lib.analysis.algorithms
Implementation of 2D morphological reconstruction, using 8-connectivity & a hybrid method.
MorphologicalReconstruction() - Constructor for class qupath.imagej.processing.MorphologicalReconstruction
 
MorphologicalReconstruction() - Constructor for class qupath.lib.analysis.algorithms.MorphologicalReconstruction
 
multiChannel(String, List<ColorTransforms.ColorTransform>, Function<double[][], Double>) - Static method in class qupath.lib.experimental.pixels.MeasurementProcessor.Measurements
Create a new object measurement that requires multiple channels as input, using the main ROI of the object as a mask.
multiChannel(String, List<ColorTransforms.ColorTransform>, Function<double[][], Double>, Function<PathObject, ROI>) - Static method in class qupath.lib.experimental.pixels.MeasurementProcessor.Measurements
Create a new object measurement that requires multiple channels as input.
multiply(double...) - Static method in class qupath.opencv.ops.ImageOps.Core
Multiply all pixels by a constant.
multiply(Mat, double) - Static method in class qupath.opencv.tools.GroovyCV
Multiply array elements by a constant.
multiply(Mat, Mat) - Static method in class qupath.opencv.tools.GroovyCV
Per-element multiplication of two arrays (not matrix multiplication).
multiply(T, ImageProcessor...) - Static method in class qupath.imagej.processing.IJProcessing
Pixelwise multiplication of the input images.
MultiscaleFeatures - Class in qupath.opencv.tools
Calculate pixel-based features in both 2D and 3D.
MultiscaleFeatures() - Constructor for class qupath.opencv.tools.MultiscaleFeatures
 
MultiscaleFeatures.Hessian - Interface in qupath.opencv.tools
Helper class for storing and computing pixel features from Hessian matrices.
MultiscaleFeatures.Hessian2D - Class in qupath.opencv.tools
Hessian matrix values for 2D images.
MultiscaleFeatures.Hessian3D - Class in qupath.opencv.tools
Hessian matrix values for 3D images (z-stacks).
MultiscaleFeatures.MultiscaleFeature - Enum Class in qupath.opencv.tools
Image features, dependent on Gaussian scale.
MultiscaleFeatures.MultiscaleResultsBuilder - Class in qupath.opencv.tools
Helper-class for computing pixel-features at a specified scale.
MultiscaleFeatures.MultiscaleResultsBuilder.FeatureMap - Class in qupath.opencv.tools
Helper map implementation that provides access to MultiscaleFeatures.Hessian if needed.
MultiscaleResultsBuilder() - Constructor for class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder
Default constructor.
MultiscaleResultsBuilder(Collection<MultiscaleFeatures.MultiscaleFeature>) - Constructor for class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder
Constructor prepared to calculate specified features.

N

name(String) - Method in class qupath.opencv.dnn.OpenCVDnn.Builder
User-friendly name to use with this model.
nComponents() - Method in class qupath.opencv.ml.objects.features.Preprocessing.PCAProjector
Number of output components.
negative(Mat) - Static method in class qupath.opencv.tools.GroovyCV
Multiply elements of an array by -1.
nFeatures() - Method in class qupath.lib.analysis.features.HaralickFeatures
Total number of Haralick features.
nFeatures() - Method in interface qupath.opencv.ml.objects.features.FeatureExtractor
 
nFeatures() - Method in class qupath.opencv.ml.objects.features.Normalizer
The total number of features supported by this Normalizer
nObjects() - Static method in class qupath.lib.scripting.QP
Get a count of the total number of objects in the current hierarchy.
NONE - Enum constant in enum class qupath.opencv.tools.LocalNormalization.NormalizationType
No local normalization
normalize(Mat, Normalizer) - Static method in class qupath.opencv.ml.objects.features.Preprocessing
Apply a Normalizer to new training data samples.
normalize(Normalization) - Method in class qupath.opencv.ml.FeaturePreprocessor.Builder
Define normalization type.
Normalize() - Constructor for class qupath.opencv.ops.ImageOps.Normalize
 
normalizeFeature(int, double) - Method in class qupath.opencv.ml.objects.features.Normalizer
Normalize a single feature.
Normalizer - Class in qupath.opencv.ml.objects.features
Class to help with simple feature normalization, by adding an offset and then multiplying by a scaling factor.
NUCLEUS - Enum constant in enum class qupath.lib.analysis.features.ObjectMeasurements.Compartments
Nucleus only
NUCLEUS_CELL_RATIO - Enum constant in enum class qupath.lib.analysis.features.ObjectMeasurements.ShapeFeatures
Nucleus/cell area ratio (only relevant to cell objects).
numDimensions() - Method in class qupath.opencv.dnn.DnnShape
The total number of dimensions, i.e.
NumpyTools - Class in qupath.opencv.tools
Read .npy and .npz files from NumPy.
NumpyTools() - Constructor for class qupath.opencv.tools.NumpyTools
 

O

OBJECT_CLASSIFICATION - Static variable in class qupath.imagej.tools.IJProperties
Set property for PathObject.getClassification() ()}
OBJECT_ID - Static variable in class qupath.imagej.tools.IJProperties
Set property for PathObject.getID() ()}
OBJECT_ID - Static variable in class qupath.lib.lazy.objects.PathObjectLazyValues
Measurement to extract the unique ID of an object, as a string.
OBJECT_MEASUREMENT_ROOT - Static variable in class qupath.imagej.tools.IJProperties
Base for property names that store measurements to be added to PathObject.getMeasurements().
OBJECT_NAME - Static variable in class qupath.imagej.tools.IJProperties
Set property for PathObject.getName()
OBJECT_NAME - Static variable in class qupath.lib.lazy.objects.PathObjectLazyValues
Measurement to extract the name of an object.
OBJECT_TYPE - Static variable in class qupath.lib.lazy.objects.PathObjectLazyValues
Measurement to extract the type of an object (e.g.
ObjectMeasurements - Class in qupath.lib.analysis.features
Experimental class to generate object measurements.
ObjectMeasurements() - Constructor for class qupath.lib.analysis.features.ObjectMeasurements
 
ObjectMeasurements.Compartments - Enum Class in qupath.lib.analysis.features
Cell compartments.
ObjectMeasurements.Measurements - Enum Class in qupath.lib.analysis.features
Requested intensity measurements.
ObjectMeasurements.ShapeFeatures - Enum Class in qupath.lib.analysis.features
Standard measurements that may be computed from shapes.
of(long...) - Static method in class qupath.opencv.dnn.DnnShape
Create a new DnnShape with the specified dimension lengths.
open(ImageProcessor, double) - Static method in class qupath.imagej.processing.IJFilters
Apply a morphological opening; this is equivalent to applying a minimum followed by a maximum filter.
opencl() - Method in class qupath.opencv.dnn.OpenCVDnn.Builder
Specify OpenCL target.
opencl16() - Method in class qupath.opencv.dnn.OpenCVDnn.Builder
Specify OpenCL target with 16-bit floating point.
OpenCVClassifiers - Class in qupath.opencv.ml
QuPath wrappers for OpenCV classifiers, which are instances of StatModel.
OpenCVClassifiers() - Constructor for class qupath.opencv.ml.OpenCVClassifiers
 
OpenCVClassifiers.BoostClassifier - Class in qupath.opencv.ml
Classifier based on Boost.
OpenCVClassifiers.DTreesClassifier - Class in qupath.opencv.ml
Classifier based on DTrees.
OpenCVClassifiers.EMClusterer - Class in qupath.opencv.ml
Clusterer based on EM.
OpenCVClassifiers.LogisticRegressionClassifier - Class in qupath.opencv.ml
Classifier based on LogisticRegression.
OpenCVClassifiers.NormalBayesClassifierCV - Class in qupath.opencv.ml
Classifier based on NormalBayesClassifier.
OpenCVClassifiers.OpenCVStatModel - Class in qupath.opencv.ml
Wrapper class for a StatModel, which standardizes how training may be performed and parameters can be set.
OpenCVClassifiers.RTreesClassifier - Class in qupath.opencv.ml
Classifier based on RTrees.
OpenCVClassifiers.SVMClassifierCV - Class in qupath.opencv.ml
Classifier based on SVM.
OpenCVClassifiers.SVMSGDClassifierCV - Class in qupath.opencv.ml
Classifier based on SVMSGD.
OpenCVDnn - Class in qupath.opencv.dnn
Wrapper for an OpenCV Net, including essential metadata about how it should be used.
OpenCVDnn() - Constructor for class qupath.opencv.dnn.OpenCVDnn
 
OpenCVDnn.Builder - Class in qupath.opencv.dnn
Helper class to build an OpenCVDnn.
OpenCVDnn.ModelType - Enum Class in qupath.opencv.dnn
Enum representing different classes of Model supported by OpenCV.
OpenCVDnnModelBuilder - Class in qupath.opencv.dnn
A DnnModelBuilder implementation that uses OpenCV's DNN module to build a Net.
OpenCVDnnModelBuilder() - Constructor for class qupath.opencv.dnn.OpenCVDnnModelBuilder
 
OpenCVMLClassifier<T> - Class in qupath.opencv.ml.objects
An ObjectClassifier that uses an OpenCVClassifiers.OpenCVStatModel for classification.
OpenCVModelObjectClassifier - Class in qupath.opencv.dnn
Initial implementation of a patch-based ObjectClassifier using an OpenCV-compatible DNN.
OpenCVModelObjectClassifier(PathObjectFilter, OpenCVDnn, List<PathClass>, int, int, double) - Constructor for class qupath.opencv.dnn.OpenCVModelObjectClassifier
Constructor.
OpenCVProcessor - Class in qupath.lib.experimental.pixels
Class to generate a PixelProcessor when using OpenCV for the primary image representation.
OpenCVProcessor() - Constructor for class qupath.lib.experimental.pixels.OpenCVProcessor
 
OpenCVStatModel() - Constructor for class qupath.opencv.ml.OpenCVClassifiers.OpenCVStatModel
 
OpenCVTools - Class in qupath.opencv.tools
Collection of static methods to help with using OpenCV from Java.
OpenCVTools() - Constructor for class qupath.opencv.tools.OpenCVTools
 
OpenCVTools.IndexedPixel - Class in qupath.opencv.tools
Class representing the indices of a pixel and its value.
OpenCVTypeAdapter() - Constructor for class qupath.opencv.io.OpenCVTypeAdapters.OpenCVTypeAdapter
 
OpenCVTypeAdapters - Class in qupath.opencv.io
Helper classes for combining OpenCV's JSON serialization with Gson's.
OpenCVTypeAdapters() - Constructor for class qupath.opencv.io.OpenCVTypeAdapters
 
OpenCVTypeAdapters.OpenCVTypeAdapter<T> - Class in qupath.opencv.io
TypeAdapter that helps include OpenCV-based objects within a Java object being serialized to JSON.
OpenCVTypeAdapters.OpenCVTypeAdaptorFactory - Class in qupath.opencv.io
TypeAdapterFactory that helps make OpenCV's serialization methods more compatible with custom JSON/Gson serialization.
OpenCVTypeAdaptorFactory() - Constructor for class qupath.opencv.io.OpenCVTypeAdapters.OpenCVTypeAdaptorFactory
 
opening(int) - Static method in class qupath.opencv.ops.ImageOps.Filters
Apply a 2D morphological opening filter.
openingByReconstruction(ImageProcessor, double) - Static method in class qupath.imagej.processing.IJFilters
Apply an opening by (morphological) reconstruction.
openingByReconstruction(ImageProcessor, double) - Static method in class qupath.imagej.processing.MorphologicalReconstruction
Apply opening by reconstruction, with the specified minimum filter radius.
openingFilter(Mat, int) - Static method in class qupath.opencv.tools.OpenCVTools
Apply a 2D opening filter (erosion followed by dilation) to all channels of an image.
or(Mat, Mat) - Static method in class qupath.opencv.tools.GroovyCV
Compute the bitwise OR of two arrays.
orElse(OutputHandler<S, T, U>) - Method in interface qupath.lib.experimental.pixels.OutputHandler
Append a second output handler to this one, but only call it if this one returns false.
OTHER - Static variable in class qupath.lib.scripting.QP
Any other image type (neither brightfield nor fluorescence)
output(String, long...) - Method in class qupath.opencv.dnn.DnnModelParams.Builder
Specify the shape as a long array for a single named output.
output(String, DnnShape) - Method in class qupath.opencv.dnn.DnnModelParams.Builder
Specify the shape for a single named output.
outputChannelType(ImageServerMetadata.ChannelType) - Method in class qupath.opencv.ml.PatchClassifierParams.Builder
Define the channel type for the output.
outputClasses(Map<Integer, PathClass>) - Method in class qupath.opencv.ml.PatchClassifierParams.Builder
Define the classifications for the output as a map.
outputClasses(PathClass...) - Method in class qupath.opencv.ml.PatchClassifierParams.Builder
Define the classifications for the output as an array.
outputClassNames(String...) - Method in class qupath.opencv.ml.PatchClassifierParams.Builder
Define the classifications for the output as an array of classification names.
outputClassNames(Map<Integer, String>) - Method in class qupath.opencv.ml.PatchClassifierParams.Builder
Define the classifications for the output as a map with string values.
outputHandler(OutputHandler<S, T, U>) - Method in class qupath.lib.experimental.pixels.PixelProcessor.Builder
Set the output handler.
OutputHandler<S,T,U> - Interface in qupath.lib.experimental.pixels
A functional interface for handling the output of a Processor.
OutputHandler.ObjectOutputHandler<S,T,U> - Class in qupath.lib.experimental.pixels
 
OutputHandler.OutputToObjectConverter<S,T,U> - Interface in qupath.lib.experimental.pixels
 
outputs(String...) - Method in class qupath.opencv.dnn.OpenCVDnn.Builder
Set the layer outputs.
outputs(Map<String, DnnShape>) - Method in class qupath.opencv.dnn.DnnModelParams.Builder
Specify the shapes for one or more outputs.
outputs(Map<String, DnnShape>) - Method in class qupath.opencv.dnn.OpenCVDnn.Builder
Set the layer outputs and shapes.
outputShape(long...) - Method in class qupath.opencv.dnn.DnnModelParams.Builder
Specify the shape for a single output, with the default output name.

P

padAndApply(ImageOp, Mat) - Static method in class qupath.opencv.ops.ImageOps
Apply an op after adding symmetric (reflection) padding.
padAndApply(ImageOp, Mat, int) - Static method in class qupath.opencv.ops.ImageOps
Apply an op after adding specified padding.
PaddedOp() - Constructor for class qupath.opencv.ops.ImageOps.PaddedOp
 
padding(int) - Method in class qupath.lib.experimental.pixels.PixelProcessor.Builder
Set the padding to use when extracting regions, using a symmetric padding.
padding(Padding) - Method in class qupath.lib.experimental.pixels.PixelProcessor.Builder
Set the padding to use when extracting regions.
paddingXY(int) - Method in class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder
Specify the number of pixels that the input image is padded (left, right, above, below).
Parameters<S,T> - Class in qupath.lib.experimental.pixels
Parameters for use with a PixelProcessor.
Parameters.Builder<S,T> - Class in qupath.lib.experimental.pixels
Builder class for Parameters.
parametersInitialized - Variable in class qupath.imagej.detect.cells.WatershedCellDetection
 
parent(PathObject) - Method in class qupath.lib.experimental.pixels.Parameters.Builder
Set the parent object.
PARENT_DISPLAYED_NAME - Static variable in class qupath.lib.lazy.objects.PathObjectLazyValues
Measurement to extract the displayed name of an object's parent.
parentProxy(PathObject) - Method in class qupath.lib.experimental.pixels.Parameters.Builder
Optionally set a temporary object to use as a parent.
parseArgument(ImageData<BufferedImage>, String) - Method in class qupath.imagej.detect.cells.WatershedCellDetection
 
parseArgument(ImageData<BufferedImage>, String) - Method in class qupath.opencv.CellCountsCV
 
parseLayers(Net, int, int, int, int) - Static method in class qupath.opencv.dnn.DnnTools
Parse the layers for a Net, which allows inspection of names and sizes.
parseShape(MatShapeVector) - Static method in class qupath.opencv.dnn.DnnTools
Extract Mat dimensions from a MatShapeVector.
parseStrings(StringVector) - Static method in class qupath.opencv.dnn.DnnTools
Extract Strings from a StringVector.
PatchClassifierParams - Class in qupath.opencv.ml
Parameters required to build a classifier that operates on an image patch.
PatchClassifierParams.Builder - Class in qupath.opencv.ml
Builder class to create PatchClassifierParams.
patchSize(int) - Method in class qupath.opencv.ml.PatchClassifierParams.Builder
Define the requested square patch size.
patchSize(int, int) - Method in class qupath.opencv.ml.PatchClassifierParams.Builder
Define the requested patch size.
PathObjectLazyValues - Class in qupath.lib.lazy.objects
Helper class to create or access different LazyValue instances.
PathObjectLazyValues() - Constructor for class qupath.lib.lazy.objects.PathObjectLazyValues
 
paths(Path...) - Method in class qupath.opencv.dnn.DnnModelParams.Builder
Specify the URIs as path objects.
pca(double, boolean) - Method in class qupath.opencv.ml.FeaturePreprocessor.Builder
Perform PCA to reduce features.
pearsonsCorrelation() - Static method in class qupath.lib.experimental.pixels.MeasurementProcessor.Functions
Create a function to calculate Pearson's correlation coefficient.
PERCENT - Enum constant in enum class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapType
Maps contain at least two channels.
percentile(double) - Static method in class qupath.lib.experimental.pixels.MeasurementProcessor.Functions
Create a function to calculate a percentile.
percentile(double, double) - Static method in class qupath.opencv.ops.ImageOps.Normalize
Normalize the image, per channel, using low and high percentiles.
percentile(double, double, boolean, double) - Static method in class qupath.opencv.ops.ImageOps.Normalize
Normalize the image using low and high percentiles.
percentiles(Mat, double...) - Static method in class qupath.opencv.tools.OpenCVTools
Get percentile values for all pixels in a Mat, ignoring NaNs.
physicalMemory() - Static method in class qupath.opencv.tools.OpenCVTools
Get a brief, one-line report on current physical memory use, based on JavaCPP's Pointer class.
pixelCalibration(PixelCalibration, double) - Method in class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder
Set the pixel calibration, with optional x,y scaling.
PixelClassificationMeasurementManager - Class in qupath.opencv.ml.pixel
Helper class to compute area-based measurements for regions of interest based on pixel classification.
PixelClassificationMeasurementManager(ImageServer<BufferedImage>) - Constructor for class qupath.opencv.ml.pixel.PixelClassificationMeasurementManager
Constructor.
PixelClassifiers - Class in qupath.opencv.ml.pixel
Static methods and classes for working with pixel classifiers.
PixelClassifiers() - Constructor for class qupath.opencv.ml.pixel.PixelClassifiers
 
PixelClassifierTools - Class in qupath.opencv.ml.pixel
Helper methods for working with pixel classification.
PixelClassifierTools() - Constructor for class qupath.opencv.ml.pixel.PixelClassifierTools
 
PixelClassifierTools.CreateObjectOptions - Enum Class in qupath.opencv.ml.pixel
Options when creating objects from a pixel classifier.
PixelImageIJ - Class in qupath.imagej.tools
Very simple wrapper that allows some non-ImageJ-oriented QuPath commands to access ImageProcessor pixel values.
PixelImageIJ(ImageProcessor) - Constructor for class qupath.imagej.tools.PixelImageIJ
Constructor.
PixelProcessor<S,T,U> - Class in qupath.lib.experimental.pixels
A class for tiled image processing.
PixelProcessor.Builder<S,T,U> - Class in qupath.lib.experimental.pixels
Builder class for a PixelProcessor
PixelProcessorUtils - Class in qupath.lib.experimental.pixels
Utility functions to help with the PixelProcessor class.
PixelProcessorUtils() - Constructor for class qupath.lib.experimental.pixels.PixelProcessorUtils
 
pixelSize(double) - Method in class qupath.lib.experimental.pixels.PixelProcessor.Builder
Set the requested pixel size to use with requesting image regions.
pixelSize(PixelCalibration) - Method in class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapBuilder
Requested pixel size to determine the resolution of the density map, in calibrated units.
plus(Mat, Number) - Static method in class qupath.opencv.tools.GroovyCV
Add an array and a number.
plus(Mat, Mat) - Static method in class qupath.opencv.tools.GroovyCV
Add two arrays.
plus(Mat, Scalar) - Static method in class qupath.opencv.tools.GroovyCV
Add an array and a scalar.
PositiveCellDetection - Class in qupath.imagej.detect.cells
Alternative implementation of WatershedCellDetection that automatically applies 1 or 3 intensity thresholds to classify cells.
PositiveCellDetection() - Constructor for class qupath.imagej.detect.cells.PositiveCellDetection
Default constructor.
PositivePixelCounterIJ - Class in qupath.imagej.detect.tissue
Simple command to detect regions with positive staining.
PositivePixelCounterIJ() - Constructor for class qupath.imagej.detect.tissue.PositivePixelCounterIJ
 
postprocess(TaskRunner, ImageData<T>) - Method in class qupath.opencv.features.DelaunayClusteringPlugin
Deprecated.
 
postProcess(ObjectProcessor) - Method in class qupath.lib.experimental.pixels.PixelProcessor.Builder
Set an object post-processor to apply to any objects created when using a tiler.
postprocessing(Collection<? extends ImageOp>) - Method in class qupath.opencv.ml.PatchClassifierParams.Builder
Define the postprocessing steps from a collection.
postprocessing(ImageOp...) - Method in class qupath.opencv.ml.PatchClassifierParams.Builder
Define the postprocessing steps from an array.
power(double) - Static method in class qupath.opencv.ops.ImageOps.Core
Raise every pixel element to a power.
power(Mat, double) - Static method in class qupath.opencv.tools.GroovyCV
Raise elements of an array to a specified power.
predict(Map<String, Mat>) - Method in class qupath.opencv.dnn.AbstractDnnModel
Convenience method to convert input image patches to a blobs, apply a PredictionFunction (optionally with multiple inputs/outputs), and convert the output to a standard Mat.
predict(Map<String, Mat>) - Method in interface qupath.opencv.dnn.DnnModel
Prediction function that can take multiple inputs.
predict(Map<String, T>) - Method in interface qupath.opencv.dnn.PredictionFunction
Call a function that takes one or more inputs to produce zero or more outputs.
predict(Mat) - Method in class qupath.opencv.dnn.AbstractDnnModel
Convenience method to convert a single image patch to a blob, apply the PredictionFunction, and convert the output to a standard Mat.
predict(Mat) - Method in interface qupath.opencv.dnn.DnnModel
Prediction function that takes a single input and gives a single output.
predict(Mat, Mat, Mat) - Method in class qupath.opencv.ml.OpenCVClassifiers.BoostClassifier
Default implementation calling
predict(Mat, Mat, Mat) - Method in class qupath.opencv.ml.OpenCVClassifiers.DTreesClassifier
Default implementation calling
predict(Mat, Mat, Mat) - Method in class qupath.opencv.ml.OpenCVClassifiers.EMClusterer
Default implementation calling
predict(Mat, Mat, Mat) - Method in class qupath.opencv.ml.OpenCVClassifiers.LogisticRegressionClassifier
Default implementation calling
predict(Mat, Mat, Mat) - Method in class qupath.opencv.ml.OpenCVClassifiers.NormalBayesClassifierCV
Default implementation calling
predict(Mat, Mat, Mat) - Method in class qupath.opencv.ml.OpenCVClassifiers.RTreesClassifier
Default implementation calling
predict(Mat, Mat, Mat) - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMClassifierCV
Default implementation calling
predict(Mat, Mat, Mat) - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMSGDClassifierCV
Default implementation calling
predict(Mat, Mat, Mat) - Method in class qupath.opencv.ml.OpenCVClassifiers.OpenCVStatModel
Apply classification, optionally requesting probability estimates.
predict(T) - Method in interface qupath.opencv.dnn.PredictionFunction
Call a function that takes a single input and provides a single output.
prediction(DnnModel, Padding, String...) - Method in class qupath.opencv.ml.PatchClassifierParams.Builder
Define the DNN to be used for prediction, to be applied after preprocessing and before postprocessing.
prediction(ImageOp) - Method in class qupath.opencv.ml.PatchClassifierParams.Builder
Define the prediction image op, to be applied after preprocessing and before postprocessing.
PredictionFunction<T> - Interface in qupath.opencv.dnn
Prediction function, typically used with a deep learning framework.
predictWithLock(Mat, Mat, Mat) - Method in class qupath.opencv.ml.OpenCVClassifiers.BoostClassifier
Implement predictWithLock rather than predict to ensure predict is not called while training.
predictWithLock(Mat, Mat, Mat) - Method in class qupath.opencv.ml.OpenCVClassifiers.DTreesClassifier
Implement predictWithLock rather than predict to ensure predict is not called while training.
predictWithLock(Mat, Mat, Mat) - Method in class qupath.opencv.ml.OpenCVClassifiers.EMClusterer
Implement predictWithLock rather than predict to ensure predict is not called while training.
predictWithLock(Mat, Mat, Mat) - Method in class qupath.opencv.ml.OpenCVClassifiers.LogisticRegressionClassifier
Implement predictWithLock rather than predict to ensure predict is not called while training.
predictWithLock(Mat, Mat, Mat) - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMClassifierCV
Implement predictWithLock rather than predict to ensure predict is not called while training.
predictWithLock(Mat, Mat, Mat) - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMSGDClassifierCV
Implement predictWithLock rather than predict to ensure predict is not called while training.
predictWithLock(Mat, Mat, Mat) - Method in class qupath.opencv.ml.OpenCVClassifiers.NormalBayesClassifierCV
 
predictWithLock(Mat, Mat, Mat) - Method in class qupath.opencv.ml.OpenCVClassifiers.RTreesClassifier
 
preprocess(TaskRunner, ImageData<T>) - Method in class qupath.opencv.features.DelaunayClusteringPlugin
Deprecated.
 
preprocessing(Collection<? extends ImageOp>) - Method in class qupath.opencv.ml.PatchClassifierParams.Builder
Define the preprocessing steps from a collection.
preprocessing(ImageOp...) - Method in class qupath.opencv.ml.PatchClassifierParams.Builder
Define the preprocessing steps from an array.
Preprocessing - Class in qupath.opencv.ml.objects.features
Helper class for preprocessing input for machine learning algorithms using OpenCV Mats.
Preprocessing() - Constructor for class qupath.opencv.ml.objects.features.Preprocessing
 
Preprocessing.PCAProjector - Class in qupath.opencv.ml.objects.features
Helper class to apply PCA projection.
preprocessor(FeaturePreprocessor) - Static method in class qupath.opencv.ops.ImageOps.ML
Apply a FeaturePreprocessor to pixels, considering each channel as features.
process(Parameters<S, T>) - Method in interface qupath.lib.experimental.pixels.Processor
Processing method.
ProcessingCV - Class in qupath.opencv.tools
Static methods to enable existing code for watershed transforms and morphological reconstruction to be applied to OpenCV images.
ProcessingCV() - Constructor for class qupath.opencv.tools.ProcessingCV
 
processObjects(ImageData<BufferedImage>, Collection<? extends PathObject>) - Method in class qupath.lib.experimental.pixels.PixelProcessor
Process objects using the default TaskRunner.
processObjects(TaskRunner, ImageData<BufferedImage>, Collection<? extends PathObject>) - Method in class qupath.lib.experimental.pixels.PixelProcessor
Process objects using the specified TaskRunner.
processor(Processor<S, T, U>) - Method in class qupath.lib.experimental.pixels.PixelProcessor.Builder
Set the processor.
Processor<S,T,U> - Interface in qupath.lib.experimental.pixels
A generic processor designed to work with Parameters and provide an output.
project(Mat, Mat) - Method in class qupath.opencv.ml.objects.features.Preprocessing.PCAProjector
Apply the projection.
PROJECT_BASE_DIR - Static variable in class qupath.lib.scripting.QP
Placeholder for the path to the current project.
PROJECT_LOCATION - Static variable in class qupath.lib.analysis.heatmaps.DensityMaps
Default location to use when storing density maps in a project.
put0(int, int) - Method in class qupath.lib.analysis.features.CoocurranceMatrices
Record coocurrence for a (binned) value pair without rotation
put135(int, int) - Method in class qupath.lib.analysis.features.CoocurranceMatrices
Record coocurrence for a (binned) value pair with 135 degree rotation
put45(int, int) - Method in class qupath.lib.analysis.features.CoocurranceMatrices
Record coocurrence for a (binned) value pair with 45 degree rotation
put90(int, int) - Method in class qupath.lib.analysis.features.CoocurranceMatrices
Record coocurrence for a (binned) value pair with 90 degree rotation
putMeasurement(Roi, String, double) - Static method in class qupath.imagej.tools.IJProperties
Set a property storing a QuPath object measurement within a specified Roi.
putPixelsFloat(Mat, float[]) - Static method in class qupath.opencv.tools.OpenCVTools
Set pixels from a float array.
putPixelsUnsigned(Mat, byte[]) - Static method in class qupath.opencv.tools.OpenCVTools
Set pixels from a byte array.

Q

QP - Class in qupath.lib.scripting
Collection of static methods that are useful for scripting.
QP() - Constructor for class qupath.lib.scripting.QP
 
quickShowImage(String, Roi, ImageProcessor...) - Static method in class qupath.imagej.tools.IJTools
Show an ImageProcessor (or array of similar ImageProcessors as a stack).
quickShowImage(String, ImageProcessor...) - Static method in class qupath.imagej.tools.IJTools
Show an ImageProcessor (or array of similar ImageProcessors as a stack).
qupath.imagej.detect.cells - package qupath.imagej.detect.cells
Classes to enable cell detection, implemented with the help of ImageJ as an image processing library.
qupath.imagej.detect.dearray - package qupath.imagej.detect.dearray
Classes to help with Tissue Microarray dearraying.
qupath.imagej.detect.tissue - package qupath.imagej.detect.tissue
Classes to enable tissue detection by thresholding.
qupath.imagej.images.servers - package qupath.imagej.images.servers
ImageServer implementation using ImageJ as the image reading library.
qupath.imagej.images.writers - package qupath.imagej.images.writers
Image writers, using ImageJ as the writing library.
qupath.imagej.processing - package qupath.imagej.processing
Static methods that add further processing methods when working with ImageJ images.
qupath.imagej.superpixels - package qupath.imagej.superpixels
Classes to generate superpixels.
qupath.imagej.tools - package qupath.imagej.tools
Helper classes and static methods for working with ImageJ images.
qupath.lib.algorithms - package qupath.lib.algorithms
Feature calculation plugins.
qupath.lib.analysis.algorithms - package qupath.lib.analysis.algorithms
Classes and static methods adding reusable processing and analysis functionality.
qupath.lib.analysis.features - package qupath.lib.analysis.features
Classes to help with calculating features.
qupath.lib.analysis.heatmaps - package qupath.lib.analysis.heatmaps
Classes and static methods associated with generating and querying heatmaps.
qupath.lib.experimental.pixels - package qupath.lib.experimental.pixels
Experimental package to simplify pixel operations for large images.
qupath.lib.lazy.interfaces - package qupath.lib.lazy.interfaces
Package containing interfaces for lazy values.
qupath.lib.lazy.objects - package qupath.lib.lazy.objects
Package containing LazyValue implementations for PathObject inputs.
qupath.lib.plugins.objects - package qupath.lib.plugins.objects
Plugins for manipulating objects and ROIs.
qupath.lib.scripting - package qupath.lib.scripting
Defines helper class for running scripts.
qupath.lib.scripting.languages - package qupath.lib.scripting.languages
Base classes for defining scripting languages that QuPath can support.
qupath.opencv - package qupath.opencv
Detection plugins using OpenCV.
qupath.opencv.dnn - package qupath.opencv.dnn
QuPath classes to use OpenCV's DNN module.
qupath.opencv.features - package qupath.opencv.features
Classes for feature calculation using OpenCV.
qupath.opencv.io - package qupath.opencv.io
Support for serializing and deserializing OpenCV objects.
qupath.opencv.ml - package qupath.opencv.ml
QuPath classes to apply machine learning to pixels and objects using OpenCV.
qupath.opencv.ml.objects - package qupath.opencv.ml.objects
QuPath object classifiers using OpenCV.
qupath.opencv.ml.objects.features - package qupath.opencv.ml.objects.features
Extract object features using OpenCV.
qupath.opencv.ml.pixel - package qupath.opencv.ml.pixel
QuPath pixel classifiers using OpenCV.
qupath.opencv.ops - package qupath.opencv.ops
Image operations, implemented with OpenCV.
qupath.opencv.tools - package qupath.opencv.tools
Additional processing methods for use with OpenCV Mats.

R

radius(double) - Method in class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapBuilder
The radius of the filter used to calculate densities.
read(JsonReader) - Method in class qupath.opencv.io.OpenCVTypeAdapters.OpenCVTypeAdapter
 
readAllMats(String) - Static method in class qupath.opencv.tools.NumpyTools
Read a all Mats from an .npy or .npz file.
readAllMats(String, boolean) - Static method in class qupath.opencv.tools.NumpyTools
Read a all Mats from an .npy or .npz file, optionally squeezing singleton dimensions.
readAllMats(Path) - Static method in class qupath.opencv.tools.NumpyTools
Read a all Mats from an .npy or .npz path.
readAllMats(Path, boolean) - Static method in class qupath.opencv.tools.NumpyTools
Read a all Mats from an .npy or .npz path, optionally squeezing singleton dimensions This will be a single Mat for .npy but may be multiple for .npz.
readClassifier(Path) - Static method in class qupath.opencv.ml.pixel.PixelClassifiers
Read a standard pixel classifier from a file.
readImageJRois(File) - Static method in class qupath.imagej.tools.IJTools
Read ImageJ Rois from a .roi or a RoiSet.zip file.
readMat(InputStream, boolean) - Static method in class qupath.opencv.tools.NumpyTools
Read a single Mat from an input stream, which should follow the .npy file format specification.
readMat(String) - Static method in class qupath.opencv.tools.NumpyTools
Read a single Mat from an .npy or .npz file.
readMat(String, boolean) - Static method in class qupath.opencv.tools.NumpyTools
Read a single Mat from an .npy or .npz file, optionally squeezing singleton dimensions.
readMat(Path) - Static method in class qupath.opencv.tools.NumpyTools
Read an OpenCV Mat from a Numpy .npy file.
readMat(Path, boolean) - Static method in class qupath.opencv.tools.NumpyTools
Read an OpenCV Mat from a Numpy .npy file, optionally squeezing singleton dimensions.
readPatch(ImageServer<BufferedImage>, ROI, double, int, int) - Static method in class qupath.opencv.dnn.DnnTools
Read an image patch, optionally with a fixed size and using zero-padding if required.
readPatch(ImageServer<BufferedImage>, ROI, double, int, int, int) - Static method in class qupath.opencv.dnn.DnnTools
Read an image patch, optionally with a fixed size.
readPathObjects() - Method in class qupath.imagej.images.servers.ImageJServer
 
readTile(TileRequest) - Method in class qupath.imagej.images.servers.ImageJServer
 
RefineAnnotationsPlugin<T> - Class in qupath.lib.plugins.objects
Plugin to create new annotations by expanding the size of existing annotations.
RefineAnnotationsPlugin() - Constructor for class qupath.lib.plugins.objects.RefineAnnotationsPlugin
 
refreshDuplicateIDs() - Static method in class qupath.lib.scripting.QP
Refresh all object IDs for the current hierarchy to ensure there are no duplicates, retaining the original IDs where possible.
refreshDuplicateIDs(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP
Refresh all object IDs for the current hierarchy to ensure there are no duplicates, retaining the original IDs where possible.
refreshIDs() - Static method in class qupath.lib.scripting.QP
Refresh all object IDs for the current hierarchy.
refreshIDs(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP
Refresh all object IDs for the current hierarchy.
region(RegionRequest) - Method in class qupath.lib.experimental.pixels.Parameters.Builder
Specify the region to use for processing.
regionalMaxima(ImageProcessor) - Static method in class qupath.imagej.processing.IJFilters
Find regional maxima in an image.
regionalMinima(ImageProcessor) - Static method in class qupath.imagej.processing.IJFilters
Find regional minima in an image.
registerBuilder(DnnModelBuilder) - Static method in class qupath.opencv.dnn.DnnModels
Register a new DnnModelBuilder.
registerDataOp(Class<? extends ImageDataOp>, String) - Static method in class qupath.opencv.ops.ImageOps
Register an ImageDataOp class for JSON serialization/deserialization.
registerDnnModel(Class<T>, String) - Static method in class qupath.opencv.dnn.DnnModels
Register a new DnnModel class for JSON serialization/deserialization.
registerDnnModel(Class<T>, String) - Static method in class qupath.opencv.dnn.DnnTools
Deprecated.
registerOp(Class<? extends ImageOp>, String) - Static method in class qupath.opencv.ops.ImageOps
Register an ImageOp class for JSON serialization/deserialization.
relabelTMAGrid(String, String, boolean) - Static method in class qupath.lib.scripting.QP
Relabel the current TMA grid.
relabelTMAGrid(PathObjectHierarchy, String, String, boolean) - Static method in class qupath.lib.scripting.QP
Relabel a TMA grid.
removeAllObjects() - Static method in class qupath.lib.scripting.QP
Remove all the objects in the current PathObjectHierarchy, and reset the selection.
removeAllObjects(Class<? extends PathObject>) - Static method in class qupath.lib.scripting.QP
Remove all the objects of a specified Java class.
removeAnnotationMeasurements() - Static method in class qupath.lib.scripting.QP
Remove the measurements from all annotations in the current hierarchy.
removeAnnotationMeasurements(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP
Remove the measurements from all annotations in a hierarchy.
removeAnnotations() - Static method in class qupath.lib.scripting.QP
Remove all the annotation objects from the current PathObjectHierarchy.
removeByAreas(ByteProcessor, double, double, boolean) - Static method in class qupath.imagej.processing.RoiLabeling
Remove objects containing < minPixels or > maxPixels.
removeCellMeasurements() - Static method in class qupath.lib.scripting.QP
Remove the measurements from all cells in the current hierarchy.
removeCellMeasurements(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP
Remove the measurements from all cells in a hierarchy.
removeChildObjectsTouchingSelectedBounds() - Static method in class qupath.lib.scripting.QP
Remove all objects that touch or overlap the bounds of the selected objects in the current image, and are direct children of the selected objects.
removeChildObjectsTouchingSelectedBounds(Predicate<PathObject>) - Static method in class qupath.lib.scripting.QP
Remove objects that touch or overlap the bounds of the selected objects in the current image, and are direct children of the selected objects.
removeChildObjectsTouchingSelectedBounds(PathObjectHierarchy, Predicate<PathObject>) - Static method in class qupath.lib.scripting.QP
Remove objects that touch or overlap the bounds of the selected objects in the specified image, and are direct children of the selected objects.
removeDetectionMeasurements() - Static method in class qupath.lib.scripting.QP
Remove the measurements from all detections in the current hierarchy.
removeDetectionMeasurements(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP
Remove the measurements from all detections in a hierarchy (including sub-classes of detections).
removeDetections() - Static method in class qupath.lib.scripting.QP
Remove all the detection objects from the current PathObjectHierarchy.
removeMeasurements() - Static method in class qupath.lib.scripting.QP
Remove the measurements from all detections in the current hierarchy.
removeMeasurements(Class<? extends PathObject>) - Static method in class qupath.lib.scripting.QP
Remove the measurements from objects of a specific class in the current hierarchy (subclasses are not included!).
removeMeasurements(Class<? extends PathObject>, String...) - Static method in class qupath.lib.scripting.QP
Remove measurements from objects of a specific class for the current image data.
removeMeasurements(PathObjectHierarchy, Class<? extends PathObject>) - Static method in class qupath.lib.scripting.QP
Remove the measurements from objects of a specific class in a hierarchy (subclasses are not included!).
removeMeasurements(PathObjectHierarchy, Class<? extends PathObject>, String...) - Static method in class qupath.lib.scripting.QP
Remove measurements from objects of a specific class for the specified hierarchy.
removeMeasurements(PathObjectHierarchy, Collection<? extends PathObject>) - Static method in class qupath.lib.scripting.QP
Remove the measurements from specified objects within a hierarchy.
removeMeasurements(PathObjectHierarchy, PathObject...) - Static method in class qupath.lib.scripting.QP
Remove the measurements from specified objects within a hierarchy.
removeObject(PathObject) - Static method in class qupath.lib.scripting.QP
Remove the specified object from the current PathObjectHierarchy, keeping any descendant objects.
removeObject(PathObject, boolean) - Static method in class qupath.lib.scripting.QP
Deprecated. 
removeObjectAndDescendants(PathObject) - Static method in class qupath.lib.scripting.QP
Remove the specified object and any descendant objects from the current PathObjectHierarchy.
removeObjects(Collection<? extends PathObject>) - Static method in class qupath.lib.scripting.QP
Remove the specified collection of objects from the current PathObjectHierarchy.
removeObjects(Collection<? extends PathObject>, boolean) - Static method in class qupath.lib.scripting.QP
removeObjects(PathObject...) - Static method in class qupath.lib.scripting.QP
Remove the specified array of objects from the current PathObjectHierarchy.
removeObjects(PathObject[], boolean) - Static method in class qupath.lib.scripting.QP
removeObjectsAndDescendants(Collection<? extends PathObject>) - Static method in class qupath.lib.scripting.QP
Remove the specified collection of objects from the current PathObjectHierarchy, and all their descendants.
removeObjectsAndDescendants(PathObject...) - Static method in class qupath.lib.scripting.QP
Remove the specified array of objects from the current PathObjectHierarchy, and all their descendants.
removeObjectsOutsideImage() - Static method in class qupath.lib.scripting.QP
Remove objects that are entirely outside the current image.
removeObjectsOutsideImage(boolean) - Static method in class qupath.lib.scripting.QP
Remove objects that are entirely or partially outside the current image.
removeObjectsOutsideImage(ImageData<?>) - Static method in class qupath.lib.scripting.QP
Remove objects that are entirely or outside the specified image.
removeObjectsOutsideImage(ImageData<?>, boolean) - Static method in class qupath.lib.scripting.QP
Remove objects that are entirely or partially outside the specified image.
removeObjectsTouchingImageBounds() - Static method in class qupath.lib.scripting.QP
Remove all objects that touch the boundary of the current image.
removeObjectsTouchingImageBounds(Predicate<PathObject>) - Static method in class qupath.lib.scripting.QP
Remove all objects that touch the boundary of the current image.
removeObjectsTouchingImageBounds(ImageData<?>, Predicate<PathObject>) - Static method in class qupath.lib.scripting.QP
Remove objects that touch the boundary of the specified image.
removeObjectsTouchingSelectedBounds() - Static method in class qupath.lib.scripting.QP
Remove all objects that touch or overlap the bounds of the selected objects in the current image.
removeObjectsTouchingSelectedBounds(Predicate<PathObject>) - Static method in class qupath.lib.scripting.QP
Remove objects that touch or overlap the bounds of the selected objects in the current image.
removeObjectsTouchingSelectedBounds(PathObjectHierarchy, Predicate<PathObject>) - Static method in class qupath.lib.scripting.QP
Remove objects that touch or overlap the bounds of the selected objects in the specified object hierarchy.
removeOrClipObjectsOutsideImage() - Static method in class qupath.lib.scripting.QP
Remove objects occurring outside the current image bounds, clipping annotations where possible to retain the part that is inside the image.
removeOrClipObjectsOutsideImage(ImageData<?>) - Static method in class qupath.lib.scripting.QP
Remove objects occurring outside the specified image bounds, clipping annotations where possible to retain the part that is inside the image.
removeRootMeasurements() - Static method in class qupath.lib.scripting.QP
Remove measurements from the root object of the current hierarchy.
removeRootMeasurements(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP
Remove the measurements from the root object.
removeSelectedObjects() - Static method in class qupath.lib.scripting.QP
Remove selected objects, but keep child (descendant) objects.
removeSelectedObjectsAndDescendants() - Static method in class qupath.lib.scripting.QP
Delete the selected objects from the current hierarchy, including all the child and descendant objects.
removeSmallAreas(ByteProcessor, double, boolean) - Static method in class qupath.imagej.processing.RoiLabeling
Remove objects having small areas, defined in terms of pixels
removeTileMeasurements() - Static method in class qupath.lib.scripting.QP
Remove the measurements from all tiles in the current hierarchy.
removeTileMeasurements(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP
Remove the measurements from all tiles in a hierarchy.
removeTMACoreMeasurements() - Static method in class qupath.lib.scripting.QP
Remove the measurements from all TMA core objects in the current hierarchy.
removeTMACoreMeasurements(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP
Remove the measurements from all TMA core objects in a hierarchy.
removeTMAGrid() - Static method in class qupath.lib.scripting.QP
Remove the TMA grid from the current PathObjectHierarchy.
repeat(int) - Static method in class qupath.opencv.ops.ImageOps.Channels
Repeat the channels a specified number of times.
replace(double, double) - Static method in class qupath.opencv.ops.ImageOps.Core
Create an op that replaces one pixel value in an image with another.
replaceClassification(String, String) - Static method in class qupath.lib.scripting.QP
Apply a new classification to all objects in the current hierarchy with a specified classification.
replaceClassification(Collection<PathObject>, PathClass, PathClass) - Static method in class qupath.lib.scripting.QP
Apply a new classification to all objects with a specified original classification in an object collection.
replaceClassification(PathClass, PathClass) - Static method in class qupath.lib.scripting.QP
Apply a new classification to all objects in the current hierarchy with a specified original classification.
replaceClassification(PathObjectHierarchy, PathClass, PathClass) - Static method in class qupath.lib.scripting.QP
Apply a new classification to all objects with a specified original classification in the provided hierarchy.
replaceNaNs(double) - Static method in class qupath.opencv.ops.ImageOps.Core
Create an op that replaces NaNs with a specified value.
replaceNaNs(Mat, double) - Static method in class qupath.opencv.tools.OpenCVTools
Replace NaNs in a floating point array.
replaceValues(Mat, double, double) - Static method in class qupath.opencv.tools.OpenCVTools
Replace a specific value in an array.
requestLazyInitialize() - Method in class qupath.opencv.dnn.DnnModelParams
Request that any model is loaded lazily on demand.
resetBatchProjectAndImage() - Static method in class qupath.lib.scripting.QP
Reset the Project and ImageData used for batch processing for the current thread.
resetClassifications(Class<? extends PathObject>) - Static method in class qupath.lib.scripting.QP
Reset the PathClass for all objects of the specified type in the current hierarchy.
resetClassifications(PathObjectHierarchy, Class<? extends PathObject>) - Static method in class qupath.lib.scripting.QP
Reset the PathClass for all objects of the specified type in the specified hierarchy.
resetDetectionClassifications() - Static method in class qupath.lib.scripting.QP
Reset the PathClass for all detection objects in the current hierarchy.
resetIntensityClassifications() - Static method in class qupath.lib.scripting.QP
Reset the intensity classifications for all detections in the current hierarchy.
resetIntensityClassifications(Collection<PathObject>) - Static method in class qupath.lib.scripting.QP
Reset the intensity classifications for all specified objects.
resetIntensityClassifications(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP
Reset the intensity classifications for all detections in the specified hierarchy.
resetSelection() - Static method in class qupath.lib.scripting.QP
Unselect the selected objects for the current PathObjectHierarchy.
resetTMAMetadata(boolean) - Static method in class qupath.lib.scripting.QP
Remove all TMA metadata from the current TMA grid.
resetTMAMetadata(PathObjectHierarchy, boolean) - Static method in class qupath.lib.scripting.QP
Remove all TMA metadata from the TMA grid of the specified hierarchy.
resolveHierarchy() - Static method in class qupath.lib.scripting.QP
Resolve the location of annotations in the current hierarchy by setting parent/child relationships.
resolveHierarchy(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP
Resolve the location of annotations in the specified hierarchy by setting parent/child relationships.
resolvePath(String) - Static method in class qupath.lib.scripting.QP
Resolve a path, replacing any placeholders.
retainHessian(boolean) - Method in class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder
Optionally retain the Hessian matrix per pixel.
ROI_NUM_POINTS - Static variable in class qupath.lib.lazy.objects.PathObjectLazyValues
 
ROI_TIMEPOINT - Static variable in class qupath.lib.lazy.objects.PathObjectLazyValues
 
ROI_TYPE - Static variable in class qupath.lib.lazy.objects.PathObjectLazyValues
Measurement to extract the name of a ROI type (e.g.
ROI_Z_SLICE - Static variable in class qupath.lib.lazy.objects.PathObjectLazyValues
 
RoiLabeling - Class in qupath.imagej.processing
Collection of static methods to help work with ROIs, binary & labelled images in ImageJ.
RoiLabeling() - Constructor for class qupath.imagej.processing.RoiLabeling
 
round() - Static method in class qupath.opencv.ops.ImageOps.Core
Create an op that rounds floating point values.
round(Mat) - Static method in class qupath.opencv.tools.OpenCVTools
Round values in a floating point Mat.
ROUND - Enum constant in enum class qupath.lib.plugins.objects.DilateAnnotationPlugin.LineCap
Round cap
runObjectClassifier(String...) - Static method in class qupath.lib.scripting.QP
Apply an object classifier to the current ImageData.
runObjectClassifier(ImageData, String...) - Static method in class qupath.lib.scripting.QP
Apply an object classifier to the specified ImageData.
runPlugin(String, String) - Static method in class qupath.lib.scripting.QP
Run the specified plugin on the current ImageData.
runPlugin(String, Map<String, ?>) - Static method in class qupath.lib.scripting.QP
Run the specified plugin on the current ImageData, using a map for arguments.
runPlugin(String, ImageData<?>, String) - Static method in class qupath.lib.scripting.QP
Run the specified plugin on the specified ImageData.
runPlugin(String, ImageData<?>, Map<String, ?>) - Static method in class qupath.lib.scripting.QP
Run the specified plugin on the specified ImageData, using a map for arguments.
runPlugin(Map<String, ?>, String) - Static method in class qupath.lib.scripting.QP
Run the specified plugin on the current ImageData, with Groovy keyword argument support.
runPlugin(Map<String, ?>, String, ImageData<?>) - Static method in class qupath.lib.scripting.QP
Run the specified plugin on the specified ImageData, with Groovy keyword argument support.
runPlugin(TaskRunner, ImageData<BufferedImage>, String) - Method in class qupath.imagej.detect.cells.SubcellularDetection
 
runPlugin(TaskRunner, ImageData<BufferedImage>, String) - Method in class qupath.lib.algorithms.IntensityFeaturesPlugin
 
runPlugin(TaskRunner, ImageData<T>, String) - Method in class qupath.lib.plugins.objects.FindConvexHullDetectionsPlugin
 

S

scalarMat(double, int) - Static method in class qupath.opencv.tools.OpenCVTools
Create a 1x1 single-channel Mat with a specific value.
scalarMatWithType(double, int) - Static method in class qupath.opencv.tools.OpenCVTools
Create a 1x1 Mat with a specific value, with 1 or more channels.
scale - Variable in class qupath.opencv.tools.LocalNormalization.LocalNormalizationType
Smoothing scale for Gaussian subtraction.
scale(double) - Method in class qupath.opencv.dnn.OpenCVDnn.Builder
Scale values, by which channels should be multiplied (after mean subtraction) before input to the Net.
scaleAllObjects(double) - Static method in class qupath.lib.scripting.QP
Resize the ROIs of all objects in the current object hierarchy.
scaleAllObjects(PathObjectHierarchy, double) - Static method in class qupath.lib.scripting.QP
Resize the ROIs of all objects in the specified object hierarchy.
scaleVariance - Variable in class qupath.opencv.tools.LocalNormalization.LocalNormalizationType
Smoothing scale for Gaussian-weighted standard deviation estimate.
ScriptAttributes - Class in qupath.lib.scripting
Default attributes that can be set when running scripts.
ScriptAttributes() - Constructor for class qupath.lib.scripting.ScriptAttributes
 
ScriptAutoCompletor - Interface in qupath.lib.scripting.languages
Interface for classes that implement auto-completion (e.g.
ScriptLanguage - Class in qupath.lib.scripting.languages
Abstract class to represent languages supported by the script editor.
ScriptLanguage(String, String) - Constructor for class qupath.lib.scripting.languages.ScriptLanguage
Default constructor for a ScriptLanguage.
ScriptLanguage(String, Collection<String>) - Constructor for class qupath.lib.scripting.languages.ScriptLanguage
Default constructor for a ScriptLanguage.
ScriptParameters - Class in qupath.lib.scripting
Class that stores key information that is useful for running scripts.
ScriptParameters.Builder - Class in qupath.lib.scripting
Builder class for ScriptParameters.
segment(SegmentationModel, Mat, Mat) - Static method in class qupath.opencv.dnn.DnnTools
Apply a segmentation model to an image region.
segment(SegmentationModel, ImageServer<BufferedImage>, RegionRequest) - Static method in class qupath.opencv.dnn.DnnTools
Apply a segmentation model to an image region.
segmentation() - Method in class qupath.opencv.dnn.OpenCVDnn.Builder
Set the model type to be OpenCVDnn.ModelType.SEGMENTATION.
SEGMENTATION - Enum constant in enum class qupath.opencv.dnn.OpenCVDnn.ModelType
SELECT_NEW - Enum constant in enum class qupath.opencv.ml.pixel.PixelClassifierTools.CreateObjectOptions
Set the new objects to be selected
selectAllObjects() - Static method in class qupath.lib.scripting.QP
Select all objects in the current hierarchy, excluding the root object.
selectAllObjects(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP
Select all objects in the specified hierarchy, excluding the root object.
selectAllObjects(PathObjectHierarchy, boolean) - Static method in class qupath.lib.scripting.QP
Set selected objects to contain all objects.
selectAnnotations() - Static method in class qupath.lib.scripting.QP
Select all annotation objects in the current hierarchy.
selectAnnotations(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP
Select all annotation objects in the specified hierarchy.
selectCells() - Static method in class qupath.lib.scripting.QP
Select all cell objects in the current hierarchy.
selectCells(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP
Select all cell objects in the specified hierarchy.
selectDetections() - Static method in class qupath.lib.scripting.QP
Select all detection objects in the current hierarchy.
selectDetections(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP
Select all detection objects in the specified hierarchy.
selectObjects(Collection<? extends PathObject>) - Static method in class qupath.lib.scripting.QP
Set all objects in a collection to be selected, without any being chosen as the main object.
selectObjects(Collection<? extends PathObject>, PathObject) - Static method in class qupath.lib.scripting.QP
Set all objects in a collection to be selected, including a specified main selected object.
selectObjects(Predicate<PathObject>) - Static method in class qupath.lib.scripting.QP
Set selected objects to contain (only) all objects in the current hierarchy according to a specified predicate.
selectObjects(PathObjectHierarchy, Predicate<PathObject>) - Static method in class qupath.lib.scripting.QP
Set selected objects to contain (only) all objects in the specified hierarchy according to a specified predicate.
selectObjects(PathObjectHierarchy, PathObject...) - Static method in class qupath.lib.scripting.QP
Set one or more objects to be selected within the specified hierarchy.
selectObjects(PathObject...) - Static method in class qupath.lib.scripting.QP
Set one or more objects to be selected within the current hierarchy.
selectObjectsByClass(Class<? extends PathObject>) - Static method in class qupath.lib.scripting.QP
Set objects that are a subclass of a specified class.
selectObjectsByClass(PathObjectHierarchy, Class<? extends PathObject>) - Static method in class qupath.lib.scripting.QP
Set objects that are a subclass of a specified class.
selectObjectsByClassification(String...) - Static method in class qupath.lib.scripting.QP
Select objects for the current hierarchy that have one of the specified classifications.
selectObjectsByClassification(PathObjectHierarchy, String...) - Static method in class qupath.lib.scripting.QP
Select objects for the specified hierarchy that have one of the specified classifications.
selectObjectsByMeasurement(ImageData<?>, String) - Static method in class qupath.lib.scripting.QP
Deprecated.
selectObjectsByPathClass(PathClass...) - Static method in class qupath.lib.scripting.QP
Select objects for the current hierarchy that have one of the specified PathClass classifications assigned.
selectObjectsByPathClass(PathObjectHierarchy, PathClass...) - Static method in class qupath.lib.scripting.QP
Select objects for the specified hierarchy that have one of the specified PathClass classifications assigned.
selectObjectsByPlane(int, int) - Static method in class qupath.lib.scripting.QP
Selected objects in the current hierarchy occurring on the specified z-slice and timepoint.
selectObjectsByPlane(PathObjectHierarchy, ImagePlane) - Static method in class qupath.lib.scripting.QP
Selected objects in the specified hierarchy occurring on the specified plane (z-slice and timepoint).
selectObjectsByPlane(ImagePlane) - Static method in class qupath.lib.scripting.QP
Selected objects in the current hierarchy occurring on the specified plane (z-slice and timepoint).
selectTiles() - Static method in class qupath.lib.scripting.QP
Select all tile objects in the current hierarchy.
selectTiles(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP
Select all tile objects in the specified hierarchy.
selectTMACores() - Static method in class qupath.lib.scripting.QP
Select all TMA core objects in the current hierarchy, excluding missing cores.
selectTMACores(boolean) - Static method in class qupath.lib.scripting.QP
Select all TMA core objects in the current hierarchy, optionally including missing cores.
selectTMACores(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP
Select all TMA core objects in the specified hierarchy, excluding missing cores.
selectTMACores(PathObjectHierarchy, boolean) - Static method in class qupath.lib.scripting.QP
Select all TMA core objects in the specified hierarchy, optionally including missing cores.
sepFilter2D(Mat, Mat, Mat) - Static method in class qupath.opencv.tools.OpenCVTools
Apply a separable filter to an image, with symmetric boundary padding.
sepFilter2D(Mat, Mat, Mat, int) - Static method in class qupath.opencv.tools.OpenCVTools
Apply a separable filter to an image.
sequential(Collection<? extends ImageOp>) - Static method in class qupath.opencv.ops.ImageOps.Core
Apply a collection of ops sequentially, chaining the output of one op as the input for the next.
sequential(ImageOp...) - Static method in class qupath.opencv.ops.ImageOps.Core
Apply an array of ops sequentially, chaining the output of one op as the input for the next.
server(ImageServer<BufferedImage>) - Method in class qupath.lib.experimental.pixels.Parameters.Builder
Set the server.
setArgs(String[]) - Method in class qupath.lib.scripting.ScriptParameters.Builder
Set optional string args to pass to the script.
setBatchIndex(int) - Method in class qupath.lib.scripting.ScriptParameters.Builder
Set the current image index for batch processing (default is 0).
setBatchProjectAndImage(Project<BufferedImage>, ImageData<BufferedImage>) - Static method in class qupath.lib.scripting.QP
Set the Project and ImageData to use for batch processing for the current thread.
setBatchSaveResult(boolean) - Method in class qupath.lib.scripting.ScriptParameters.Builder
Specify whether the script that is running should save results or not.
setBatchSize(int) - Method in class qupath.lib.scripting.ScriptParameters.Builder
Set the batch size for batch processing (default is 1).
setCellIntensityClassifications(String, double...) - Static method in class qupath.lib.scripting.QP
Set the intensity classifications for cells in the current hierarchy.
setCellIntensityClassifications(PathObjectHierarchy, String, double...) - Static method in class qupath.lib.scripting.QP
Set the intensity classifications for cells in the specified hierarchy.
setChannelColors(Integer...) - Static method in class qupath.lib.scripting.QP
Set the channel colors for the current ImageData.
setChannelColors(ImageData<?>, Integer...) - Static method in class qupath.lib.scripting.QP
Set the channel colors for the specified ImageData.
setChannelNames(String...) - Static method in class qupath.lib.scripting.QP
Set the channel names for the current ImageData.
setChannelNames(ImageData<?>, String...) - Static method in class qupath.lib.scripting.QP
Set the channel names for the specified ImageData.
setChannels(ImageData<?>, ImageChannel...) - Static method in class qupath.lib.scripting.QP
Set the channels for the specified ImageData.
setChannels(ImageChannel...) - Static method in class qupath.lib.scripting.QP
Set the channels for the current ImageData.
setClassification(Roi, String) - Static method in class qupath.imagej.tools.IJProperties
Set a property storing a QuPath object classification within a specified Roi.
setClassification(Roi, PathObject) - Static method in class qupath.imagej.tools.IJProperties
Set a property storing a QuPath object classification within a specified Roi.
setColorDeconvolutionStains(String) - Static method in class qupath.lib.scripting.QP
Set the color deconvolution stains for hte current image data using a (JSON) String representation
setColorDeconvolutionStains(Map<String, List<Number>>, String) - Static method in class qupath.lib.scripting.QP
Set the color deconvolution stains for the current image data.
setDebugMode(boolean) - Static method in class qupath.imagej.detect.cells.WatershedCellDetection
Set whether to use debug mode.
setDefaultImageData(ImageData<BufferedImage>) - Static method in class qupath.lib.scripting.QP
Set the default image data, which will be returned by QP.getCurrentImageData() if it would otherwise return null (i.e.
setDefaultImports(Collection<Class<?>>) - Method in class qupath.lib.scripting.ScriptParameters.Builder
 
setDefaultProject(Project<BufferedImage>) - Static method in class qupath.lib.scripting.QP
Set the default project, which will be returned by QP.getProject() if it would otherwise return null (i.e.
setDefaultStaticImports(Collection<Class<?>>) - Method in class qupath.lib.scripting.ScriptParameters.Builder
 
setDetectionIntensityClassifications(String, double...) - Static method in class qupath.lib.scripting.QP
Set the intensity classifications for detections in the current hierarchy.
setDetectionIntensityClassifications(PathObjectHierarchy, String, double...) - Static method in class qupath.lib.scripting.QP
Set the intensity classifications for detections in the specified hierarchy.
setErrorWriter(Writer) - Method in class qupath.lib.scripting.ScriptParameters.Builder
Set the main error writer.
setFile(File) - Method in class qupath.lib.scripting.ScriptParameters.Builder
 
setImageBackground(ImagePlus, ImageData.ImageType) - Static method in class qupath.imagej.tools.IJProperties
Set the IMAGE_BACKGROUND property as "dark" for fluorescence images or "light" for brightield images; otherwise, do nothing.
setImageData(ImageData<?>) - Method in class qupath.lib.scripting.ScriptParameters.Builder
Set the current image data for the script.
setImageRegion(ImagePlus, ImageRegion) - Static method in class qupath.imagej.tools.IJProperties
Set the IMAGE_REGION property as a string representation of the region's bounding box.
setImageType(ImagePlus, ImageData.ImageType) - Static method in class qupath.imagej.tools.IJProperties
Set the IMAGE_TYPE property based on the name of QuPath's image type, if available.
setImageType(String) - Static method in class qupath.lib.scripting.QP
Set the image type for the current image data, using a String to represent the enum ImageData.ImageType
setImageType(ImageData.ImageType) - Static method in class qupath.lib.scripting.QP
Set the image type for the current image data
setIntensityClassifications(Class<? extends PathObject>, String, double...) - Static method in class qupath.lib.scripting.QP
Set the intensity classifications for objects of the specified class in the current hierarchy.
setIntensityClassifications(Collection<? extends PathObject>, String, double...) - Static method in class qupath.lib.scripting.QP
Set the intensity classifications for the specified objects.
setIntensityClassifications(PathObjectHierarchy, Class<? extends PathObject>, String, double...) - Static method in class qupath.lib.scripting.QP
Set the intensity classifications for objects of the specified class in the specified hierarchy.
setIntensityClassificationsForSelected(PathObjectHierarchy, String, double...) - Static method in class qupath.lib.scripting.QP
Set intensity classifications for all selected (detection) objects in the specified hierarchy.
setMemoryThreshold(double) - Static method in class qupath.imagej.tools.IJTools
 
setObjectId(Roi, UUID) - Static method in class qupath.imagej.tools.IJProperties
Set a property storing a QuPath object ID within a specified Roi.
setObjectId(Roi, PathObject) - Static method in class qupath.imagej.tools.IJProperties
Set a property storing a QuPath object ID within a specified Roi.
setObjectName(Roi, String) - Static method in class qupath.imagej.tools.IJProperties
Set a property storing a QuPath object name within a specified Roi.
setObjectName(Roi, PathObject) - Static method in class qupath.imagej.tools.IJProperties
Set a property storing a QuPath object name within a specified Roi.
setPixelSizeMicrons(Number, Number) - Static method in class qupath.lib.scripting.QP
Set the metadata for the current ImageData to have the required pixel sizes.
setPixelSizeMicrons(Number, Number, Number) - Static method in class qupath.lib.scripting.QP
Set the metadata for the current ImageData to have the required pixel sizes and z-spacing.
setPixelSizeMicrons(ImageData<?>, Number, Number, Number) - Static method in class qupath.lib.scripting.QP
Set the metadata for an ImageServer to have the required pixel sizes and z-spacing.
setProject(Project<?>) - Method in class qupath.lib.scripting.ScriptParameters.Builder
Set the current project for the script.
setRegionRequest(ImagePlus, RegionRequest) - Static method in class qupath.imagej.tools.IJProperties
Store a json representation of a RegionRequest as a property in an image.
setScript(String) - Method in class qupath.lib.scripting.ScriptParameters.Builder
 
setSelectedObject(PathObject) - Static method in class qupath.lib.scripting.QP
Set the selected object for the current PathObjectHierarchy.
setSystemWriters() - Method in class qupath.lib.scripting.ScriptParameters.Builder
Set the output and error writers to use System.out and System.err.
setTitleFromObject(PathImage<ImagePlus>, PathObject) - Static method in class qupath.imagej.tools.IJTools
Set the name of an image based on a PathObject.
setUseCuda(boolean) - Static method in class qupath.opencv.dnn.DnnTools
Request that CUDA is used.
setValue(int, int, float) - Method in class qupath.imagej.tools.PixelImageIJ
 
setWriter(Writer) - Method in class qupath.lib.scripting.ScriptParameters.Builder
Set the main output writer.
shape(Mat) - Static method in class qupath.opencv.tools.GroovyCV
Get the shape of a multidimensional Mat.
ShapeFeaturesPlugin<T> - Class in qupath.lib.plugins.objects
Add shape measurements
ShapeFeaturesPlugin() - Constructor for class qupath.lib.plugins.objects.ShapeFeaturesPlugin
Constructor.
shrinkLabels(Mat) - Static method in class qupath.opencv.tools.OpenCVTools
Shrink labels to a single point.
sigmaX(double) - Method in class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder
Set all Gaussian sigma values for the horizontal filter.
sigmaXY(double) - Method in class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder
Set all Gaussian sigma values (x, y) to the same value.
sigmaY(double) - Method in class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder
Set all Gaussian sigma values for the vertical filter.
sigmaZ(double) - Method in class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder
Set all Gaussian sigma values for the z-dimension filter.
sigmoid() - Static method in class qupath.opencv.ops.ImageOps.Normalize
Replace Mat values by 1.0/(1.0 + Math.exp(-value))
SimpleThresholding - Class in qupath.imagej.processing
Collection of static methods to threshold images, either with single global thresholds or using the pixel values of a second image.
SimpleThresholding() - Constructor for class qupath.imagej.processing.SimpleThresholding
 
SimpleTissueDetection2 - Class in qupath.imagej.detect.tissue
Very basic global thresholding command to identify tissue regions.
SimpleTissueDetection2() - Constructor for class qupath.imagej.detect.tissue.SimpleTissueDetection2
Constructor.
simplifyAllAnnotations(double) - Static method in class qupath.lib.scripting.QP
Simplify all annotations to a given threshold
simplifySelectedAnnotations(double) - Static method in class qupath.lib.scripting.QP
Simplify the currently selected annotations to a given threshold
simplifySpecifiedAnnotations(Collection<? extends PathObject>, double) - Static method in class qupath.lib.scripting.QP
Simplify a set of pathObjects to a given threshold.
singleChannel(String, ColorTransforms.ColorTransform, Function<double[], Double>) - Static method in class qupath.lib.experimental.pixels.MeasurementProcessor.Measurements
Create a new object measurement that requires one channel as input, using the main ROI of the object as a mask.
singleChannel(String, ColorTransforms.ColorTransform, Function<double[], Double>, Function<PathObject, ROI>) - Static method in class qupath.lib.experimental.pixels.MeasurementProcessor.Measurements
Create a new object measurement that requires one channel as input.
size() - Method in class qupath.opencv.dnn.DnnShape
Total number of elements in a blob with this shape This is the product of the lengths returned by DnnShape.getShape() or DnnShape.UNKNOWN_SHAPE.
size(int, int) - Method in class qupath.opencv.dnn.OpenCVDnn.Builder
Input width and height.
size(Size) - Method in class qupath.opencv.dnn.OpenCVDnn.Builder
Input width and height.
SLICSuperpixelsPlugin - Class in qupath.imagej.superpixels
An implementation of SLIC superpixels, as described at http://ivrl.epfl.ch/research/superpixels
SLICSuperpixelsPlugin() - Constructor for class qupath.imagej.superpixels.SLICSuperpixelsPlugin
 
SmoothFeaturesPlugin<T> - Class in qupath.lib.plugins.objects
Plugin to supplement the measurements for detection objects with the weighted sum of measurements from nearby objects, using weights derived from a 2D Gaussian function.
SmoothFeaturesPlugin() - Constructor for class qupath.lib.plugins.objects.SmoothFeaturesPlugin
Default constructor.
smoothImage(BufferedImage) - Static method in class qupath.lib.analysis.algorithms.EstimateStainVectors
Smooth out compression artefacts by running 3x3 filter twice (roughly approximates a small Gaussian filter).
smoothMeasurements(List<PathObject>, List<String>, double, String, boolean, boolean) - Static method in class qupath.lib.plugins.objects.SmoothFeaturesPlugin
Using the centroids of the ROIs within PathObjects, 'smooth' measurements by summing up the corresponding measurements of nearby objects, weighted by centroid distance.
SOLIDITY - Enum constant in enum class qupath.lib.analysis.features.ObjectMeasurements.ShapeFeatures
Ratio of the area to the convex area.
spearmansCorrelation() - Static method in class qupath.lib.experimental.pixels.MeasurementProcessor.Functions
Create a function to calculate Spearman's correlation coefficient.
SPLIT - Enum constant in enum class qupath.opencv.ml.pixel.PixelClassifierTools.CreateObjectOptions
Split connected components
splitAdd(ImageOp, ImageOp) - Static method in class qupath.opencv.ops.ImageOps.Core
Create an op that duplicates a Mat, applies different operations to each duplicate, and combines the result by adding corresponding values.
splitAllAnnotationAreasByLines() - Static method in class qupath.lib.scripting.QP
Split annotation objects with area ROIs using dividing lines extracted from annotations objects with line ROIs, then remove the lines from the object hierarchy.
splitAllAnnotationAreasByLines(double, boolean) - Static method in class qupath.lib.scripting.QP
Split annotation objects with area ROIs using dividing lines extracted from annotations objects with line ROIs, with an optional line thickness and optionally removing the dividing lines.
splitAllAnnotationAreasByLines(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP
Split annotation objects with area ROIs using dividing lines extracted from annotations objects with line ROIs, then remove the lines from the object hierarchy.
splitAllAnnotationAreasByLines(PathObjectHierarchy, double, boolean) - Static method in class qupath.lib.scripting.QP
Split annotation objects with area ROIs using dividing lines extracted from annotations objects with line ROIs, with an optional line thickness and optionally removing the dividing lines.
SplitAnnotationsPlugin<T> - Class in qupath.lib.plugins.objects
Plugin to create new annotations by expanding the size of existing annotations.
SplitAnnotationsPlugin() - Constructor for class qupath.lib.plugins.objects.SplitAnnotationsPlugin
 
splitChannels(Mat) - Static method in class qupath.opencv.tools.GroovyCV
Split channels of an array.
splitChannels(Mat) - Static method in class qupath.opencv.tools.OpenCVTools
Split channels from a Mat.
splitDivide(ImageOp, ImageOp) - Static method in class qupath.opencv.ops.ImageOps.Core
Create an op that duplicates a Mat, applies different operations to each duplicate, and combines the result by dividing corresponding values.
splitMerge(Collection<? extends ImageOp>) - Static method in class qupath.opencv.ops.ImageOps.Core
Create an op that applies all the specified ops to the input Mat, concatenating the results as channels of the output.
splitMerge(ImageOp...) - Static method in class qupath.opencv.ops.ImageOps.Core
Create an op that applies all the specified ops to the input Mat, concatenating the results as channels of the output.
splitMultiply(ImageOp, ImageOp) - Static method in class qupath.opencv.ops.ImageOps.Core
Create an op that duplicates a Mat, applies different operations to each duplicate, and combines the result by multiplying corresponding values.
splitSelectedAnnotationAreasByLines() - Static method in class qupath.lib.scripting.QP
Split selected annotation objects with area ROIs using dividing lines extracted from annotations objects with line ROIs, then remove the lines from the object hierarchy.
splitSelectedAnnotationAreasByLines(double, boolean) - Static method in class qupath.lib.scripting.QP
Split selected annotation objects with area ROIs using dividing lines extracted from annotations objects with line ROIs, with an optional line thickness and optionally removing the dividing lines.
splitSelectedAnnotationAreasByLines(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP
Split selected annotation objects with area ROIs using dividing lines extracted from annotations objects with line ROIs, then remove the lines from the object hierarchy.
splitSelectedAnnotationAreasByLines(PathObjectHierarchy, double, boolean) - Static method in class qupath.lib.scripting.QP
Split selected annotation objects with area ROIs using dividing lines extracted from annotations objects with line ROIs, with an optional line thickness and optionally removing the dividing lines.
splitSpecifiedAreasByLines(PathObjectHierarchy, Collection<? extends PathObject>, double, boolean) - Static method in class qupath.lib.scripting.QP
Split the specified objects with area ROIs using dividing lines extracted from specified objects with line ROIs, with an optional line thickness and optionally removing the dividing lines.
splitSubtract(ImageOp, ImageOp) - Static method in class qupath.opencv.ops.ImageOps.Core
Create an op that duplicates a Mat, applies different operations to each duplicate, and combines the result by subtracting corresponding values.
sqrt() - Static method in class qupath.opencv.ops.ImageOps.Core
Calculate the square root of all pixel values.
SQUARE - Enum constant in enum class qupath.lib.plugins.objects.DilateAnnotationPlugin.LineCap
Square cap
statModel(OpenCVClassifiers.OpenCVStatModel, boolean) - Static method in class qupath.opencv.ops.ImageOps.ML
Apply a StatModel to pixels to generate a prediction.
std(Mat) - Static method in class qupath.opencv.tools.GroovyCV
Calculate the standard deviation of all elements in a Mat, ignoring NaNs.
STD_DEV - Enum constant in enum class qupath.lib.analysis.features.ObjectMeasurements.Measurements
Standard deviation value
stdDev(int) - Static method in class qupath.opencv.ops.ImageOps.Filters
Apply a 2D circular standard deviation filter.
stdDev(Mat) - Static method in class qupath.opencv.tools.OpenCVTools
Get the standard deviation of an image, across all pixels (regardless of channels), ignoring NaNs.
stdDevFilter(Mat, int) - Static method in class qupath.opencv.tools.OpenCVTools
Apply a circular 2D local standard deviation filter to all channels of an image, with symmetric boundary padding.
stdDevFilter(Mat, int, int) - Static method in class qupath.opencv.tools.OpenCVTools
Apply a circular 2D local standard deviation filter to all channels of an image.
STRUCTURE_TENSOR_COHERENCE - Enum constant in enum class qupath.opencv.tools.MultiscaleFeatures.MultiscaleFeature
Coherence, defined as ((l1 - l2)/(l1 + l2))^2 where l1 and l2 are the largest and second largest eigenvalues of the structure tensor respectively.
STRUCTURE_TENSOR_EIGENVALUE_MAX - Enum constant in enum class qupath.opencv.tools.MultiscaleFeatures.MultiscaleFeature
Maximum eigenvalue of the 2x2 or 3x3 structure tensor, calculated per pixel (by value, not absolute value)
STRUCTURE_TENSOR_EIGENVALUE_MIDDLE - Enum constant in enum class qupath.opencv.tools.MultiscaleFeatures.MultiscaleFeature
Middle eigenvalue of the 3x3 structure tensor, calculated per pixel (by value, not absolute value)
STRUCTURE_TENSOR_EIGENVALUE_MIN - Enum constant in enum class qupath.opencv.tools.MultiscaleFeatures.MultiscaleFeature
Minimum eigenvalue of the 2x2 or 3x3 structure tensor, calculated per pixel (by value, not absolute value)
structureTensorEigenvalues(boolean) - Method in class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder
Calculate the eigenvalues of the structure tensor (not yet implemented!).
SubcellularDetection - Class in qupath.imagej.detect.cells
Experimental plugin to help with the quantification of subcellular structures.
SubcellularDetection() - Constructor for class qupath.imagej.detect.cells.SubcellularDetection
 
subsample(int[], int) - Static method in class qupath.lib.analysis.algorithms.EstimateStainVectors
Subsample an array so that it contains no more than maxEntries.
SUBSTRING_TOKENIZER - Static variable in class qupath.lib.scripting.languages.AutoCompletions
A completion tokenizer that simply takes the first part of the text up to the caret position.
subtract(double...) - Static method in class qupath.opencv.ops.ImageOps.Core
Subtract a constant from all pixels.
subtract(T, ImageProcessor...) - Static method in class qupath.imagej.processing.IJProcessing
Pixelwise subtraction of one or more images from the first image passed as a parameter.
sum() - Static method in class qupath.opencv.ops.ImageOps.Channels
Add all channels together, to give a single-channel output.
sum(int) - Static method in class qupath.opencv.ops.ImageOps.Filters
Apply a 2D circular sum filter.
sum(Mat) - Static method in class qupath.opencv.tools.GroovyCV
Calculate the sum of all elements in a Mat, ignoring NaNs.
sum(Mat) - Static method in class qupath.opencv.tools.OpenCVTools
Get the sum of an image, across all pixels (regardless of channels), ignoring NaNs.
SUM - Enum constant in enum class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapType
No normalization; maps provide raw object counts in a defined radius.
sumFilter(Mat, int) - Static method in class qupath.opencv.tools.OpenCVTools
Apply a circular 2D sum filter to all channels of an image, with symmetric boundary padding.
sumFilter(Mat, int, int) - Static method in class qupath.opencv.tools.OpenCVTools
Apply a circular 2D sum filter to all channels of an image.
summarize(Net, int, int, int) - Static method in class qupath.opencv.dnn.DnnTools
Create a (multiline) summary String for a Net, given the specified image input dimensions.
supports2D() - Method in enum class qupath.opencv.tools.MultiscaleFeatures.MultiscaleFeature
Returns true if the feature can be computed for 2D images.
supports3D() - Method in enum class qupath.opencv.tools.MultiscaleFeatures.MultiscaleFeature
Returns true if the feature can be computed for 3D images (z-stacks).
supportsAutoUpdate() - Method in class qupath.opencv.ml.OpenCVClassifiers.BoostClassifier
Returns true (the default value).
supportsAutoUpdate() - Method in class qupath.opencv.ml.OpenCVClassifiers.DTreesClassifier
Returns true (the default value).
supportsAutoUpdate() - Method in class qupath.opencv.ml.OpenCVClassifiers.EMClusterer
Returns true (the default value).
supportsAutoUpdate() - Method in class qupath.opencv.ml.OpenCVClassifiers.LogisticRegressionClassifier
Returns true (the default value).
supportsAutoUpdate() - Method in class qupath.opencv.ml.OpenCVClassifiers.NormalBayesClassifierCV
Returns true (the default value).
supportsAutoUpdate() - Method in class qupath.opencv.ml.OpenCVClassifiers.RTreesClassifier
Returns true (the default value).
supportsAutoUpdate() - Method in class qupath.opencv.ml.OpenCVClassifiers.OpenCVStatModel
Classifier can be trained interactively (i.e.
supportsAutoUpdate() - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMClassifierCV
 
supportsAutoUpdate() - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMSGDClassifierCV
 
supportsImage(ImageData<BufferedImage>) - Method in interface qupath.opencv.ops.ImageDataOp
Query whether this transform can be applied to the specified image.
supportsImageType(ImageServer<BufferedImage>) - Method in class qupath.imagej.images.writers.TiffWriterIJ
 
supportsImageType(ImageServer<BufferedImage>) - Method in class qupath.imagej.images.writers.ZipWriterIJ
 
supportsMissingValues() - Method in class qupath.opencv.ml.OpenCVClassifiers.BoostClassifier
Tree classifiers in OpenCV support missing values, others do not.
supportsMissingValues() - Method in class qupath.opencv.ml.OpenCVClassifiers.DTreesClassifier
Tree classifiers in OpenCV support missing values, others do not.
supportsMissingValues() - Method in class qupath.opencv.ml.OpenCVClassifiers.EMClusterer
Tree classifiers in OpenCV support missing values, others do not.
supportsMissingValues() - Method in class qupath.opencv.ml.OpenCVClassifiers.LogisticRegressionClassifier
Tree classifiers in OpenCV support missing values, others do not.
supportsMissingValues() - Method in class qupath.opencv.ml.OpenCVClassifiers.NormalBayesClassifierCV
Tree classifiers in OpenCV support missing values, others do not.
supportsMissingValues() - Method in class qupath.opencv.ml.OpenCVClassifiers.RTreesClassifier
Tree classifiers in OpenCV support missing values, others do not.
supportsMissingValues() - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMClassifierCV
Tree classifiers in OpenCV support missing values, others do not.
supportsMissingValues() - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMSGDClassifierCV
Tree classifiers in OpenCV support missing values, others do not.
supportsMissingValues() - Method in class qupath.opencv.ml.OpenCVClassifiers.OpenCVStatModel
Classifier can handle missing (NaN) values
supportsMulticlass() - Method in class qupath.opencv.ml.OpenCVClassifiers.BoostClassifier
Returns false (the default value).
supportsMulticlass() - Method in class qupath.opencv.ml.OpenCVClassifiers.DTreesClassifier
Returns false (the default value).
supportsMulticlass() - Method in class qupath.opencv.ml.OpenCVClassifiers.EMClusterer
Returns false (the default value).
supportsMulticlass() - Method in class qupath.opencv.ml.OpenCVClassifiers.LogisticRegressionClassifier
Returns false (the default value).
supportsMulticlass() - Method in class qupath.opencv.ml.OpenCVClassifiers.NormalBayesClassifierCV
Returns false (the default value).
supportsMulticlass() - Method in class qupath.opencv.ml.OpenCVClassifiers.RTreesClassifier
Returns false (the default value).
supportsMulticlass() - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMClassifierCV
Returns false (the default value).
supportsMulticlass() - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMSGDClassifierCV
Returns false (the default value).
supportsMulticlass() - Method in class qupath.opencv.ml.OpenCVClassifiers.OpenCVStatModel
Classifier is able to handle more than one outputs for a single sample.
supportsPixelSize() - Method in class qupath.imagej.images.writers.TiffWriterIJ
 
supportsPixelSize() - Method in class qupath.imagej.images.writers.ZipWriterIJ
 
supportsProbabilities() - Method in class qupath.opencv.ml.OpenCVClassifiers.BoostClassifier
 
supportsProbabilities() - Method in class qupath.opencv.ml.OpenCVClassifiers.DTreesClassifier
 
supportsProbabilities() - Method in class qupath.opencv.ml.OpenCVClassifiers.EMClusterer
 
supportsProbabilities() - Method in class qupath.opencv.ml.OpenCVClassifiers.LogisticRegressionClassifier
 
supportsProbabilities() - Method in class qupath.opencv.ml.OpenCVClassifiers.NormalBayesClassifierCV
 
supportsProbabilities() - Method in class qupath.opencv.ml.OpenCVClassifiers.RTreesClassifier
 
supportsProbabilities() - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMClassifierCV
 
supportsProbabilities() - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMSGDClassifierCV
 
supportsProbabilities() - Method in class qupath.opencv.ml.OpenCVClassifiers.OpenCVStatModel
Classifier can output a prediction confidence (expressed between 0 and 1), so may be interpreted as a probability...
supportsPyramidal() - Method in class qupath.imagej.images.writers.TiffWriterIJ
 
supportsPyramidal() - Method in class qupath.imagej.images.writers.ZipWriterIJ
 
supportsRGB() - Method in class qupath.imagej.images.writers.TiffWriterIJ
 
supportsRGB() - Method in class qupath.imagej.images.writers.ZipWriterIJ
 
supportsT() - Method in class qupath.imagej.images.writers.TiffWriterIJ
 
supportsT() - Method in class qupath.imagej.images.writers.ZipWriterIJ
 
supportsZ() - Method in class qupath.imagej.images.writers.TiffWriterIJ
 
supportsZ() - Method in class qupath.imagej.images.writers.ZipWriterIJ
 

T

target(int) - Method in class qupath.opencv.dnn.OpenCVDnn.Builder
Specify the target, e.g.
TEXT_DETECTION_DB - Enum constant in enum class qupath.opencv.dnn.OpenCVDnn.ModelType
TEXT_DETECTION_EAST - Enum constant in enum class qupath.opencv.dnn.OpenCVDnn.ModelType
TEXT_RECOGNITION - Enum constant in enum class qupath.opencv.dnn.OpenCVDnn.ModelType
thin(Mat) - Static method in class qupath.opencv.tools.Thinning
Thin the binary image in Mat.
Thinning - Class in qupath.opencv.tools
Implementation of the 3D binary thinning algorithm of Lee et al.
Thinning() - Constructor for class qupath.opencv.tools.Thinning
 
threshold(double...) - Static method in class qupath.opencv.ops.ImageOps.Threshold
Apply a fixed threshold.
threshold(PathObjectHierarchy, ImageServer<BufferedImage>, int, double, PixelClassifierTools.CreateObjectOptions...) - Static method in class qupath.lib.analysis.heatmaps.DensityMaps
Threshold a single channel of a density map to generate new annotations.
threshold(PathObjectHierarchy, ImageServer<BufferedImage>, Map<Integer, ? extends Number>, String, PixelClassifierTools.CreateObjectOptions...) - Static method in class qupath.lib.analysis.heatmaps.DensityMaps
Threshold one or more channels of a density map to generate new annotations.
Threshold() - Constructor for class qupath.opencv.ops.ImageOps.Threshold
 
thresholdAbove(ImageProcessor, double) - Static method in class qupath.imagej.processing.SimpleThresholding
Created a binary image by thresholding pixels to find where ip1 > threshold
thresholdAboveEquals(ImageProcessor, double) - Static method in class qupath.imagej.processing.SimpleThresholding
Created a binary image by thresholding pixels to find where ip1 >= threshold
thresholdBelow(ImageProcessor, double) - Static method in class qupath.imagej.processing.SimpleThresholding
Created a binary image by thresholding pixels to find where ip1 < threshold
thresholdBelowEquals(ImageProcessor, double) - Static method in class qupath.imagej.processing.SimpleThresholding
Created a binary image by thresholding pixels to find where ip1 ≤ threshold
thresholdBetween(ImageProcessor, double, double) - Static method in class qupath.imagej.processing.SimpleThresholding
Created a binary image by thresholding pixels to find where ip >= lowThreshold and ip <= highThreshold
thresholdMeanStd(double...) - Static method in class qupath.opencv.ops.ImageOps.Threshold
Threshold each channel based upon the channel mean and standard deviation.
thresholdMedianAbsDev(double...) - Static method in class qupath.opencv.ops.ImageOps.Threshold
Threshold each channel based upon the channel median and median absolute deviation.
thresholdToRoi(ImageProcessor) - Static method in class qupath.imagej.processing.IJProcessing
Create an ImageJ ROI from a thresholded image.
thresholdToROI(ImageProcessor, RegionRequest) - Static method in class qupath.imagej.processing.SimpleThresholding
Generate a QuPath ROI from an ImageProcessor.
thresholdToROI(BufferedImage, double, double, int, RegionRequest) - Static method in class qupath.imagej.processing.SimpleThresholding
Generate a QuPath ROI by thresholding an image channel image.
thresholdToROI(Raster, double, double, int, TileRequest) - Static method in class qupath.imagej.processing.SimpleThresholding
Generate a QuPath ROI by thresholding an image channel image, deriving coordinates from a TileRequest.
thresholdToSplitRois(ImageProcessor, int) - Static method in class qupath.imagej.processing.IJProcessing
Create a list of ImageJ ROIs by tracing connected components in a thresholded image.
TiffWriterIJ - Class in qupath.imagej.images.writers
ImageWriter implementation to write TIFF images using ImageJ.
TiffWriterIJ() - Constructor for class qupath.imagej.images.writers.TiffWriterIJ
 
tile(int, int) - Method in class qupath.lib.experimental.pixels.PixelProcessor.Builder
Set a default tiler to use, with a specified tile size.
tile(TileRequest) - Method in class qupath.lib.experimental.pixels.Parameters.Builder
Specify the tile relevant for processing.
TileClassificationsToAnnotationsPlugin<T> - Class in qupath.lib.plugins.objects
Plugin to merge classified tiles into annotation objects.
TileClassificationsToAnnotationsPlugin() - Constructor for class qupath.lib.plugins.objects.TileClassificationsToAnnotationsPlugin
 
tiler(Tiler) - Method in class qupath.lib.experimental.pixels.PixelProcessor.Builder
Set a tiler to use.
TilerPlugin<T> - Class in qupath.lib.algorithms
Simple plugin to create square tiles, which may later have measurements added.
TilerPlugin() - Constructor for class qupath.lib.algorithms.TilerPlugin
Default constructor.
TMA_CORE_MISSING - Static variable in class qupath.lib.lazy.objects.PathObjectLazyValues
 
TMA_CORE_NAME - Static variable in class qupath.lib.lazy.objects.PathObjectLazyValues
Measurement to extract the name of a TMA core, or of the TMA core that is an ancestor of the provided object.
TMADearrayer - Class in qupath.imagej.detect.dearray
Static methods used by the TMA dearrayer plugin.
TMADearrayer() - Constructor for class qupath.imagej.detect.dearray.TMADearrayer
 
TMADearrayerPluginIJ - Class in qupath.imagej.detect.dearray
Plugin for automatically dearraying tissue microarrays (TMAs).
TMADearrayerPluginIJ() - Constructor for class qupath.imagej.detect.dearray.TMADearrayerPluginIJ
Default constructor.
toBlob(Mat...) - Method in interface qupath.opencv.dnn.BlobFunction
Convert one or more mats to a blob.
toString() - Method in class qupath.lib.analysis.features.HaralickFeatures
 
toString() - Method in enum class qupath.lib.analysis.features.ObjectMeasurements.ShapeFeatures
 
toString() - Method in enum class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapType
 
toString() - Method in enum class qupath.lib.plugins.objects.DilateAnnotationPlugin.LineCap
 
toString() - Method in class qupath.lib.scripting.languages.ScriptLanguage
 
toString() - Method in class qupath.opencv.dnn.DnnShape
 
toString() - Method in class qupath.opencv.dnn.DnnTools.DNNLayer
 
toString() - Method in class qupath.opencv.ml.FeaturePreprocessor
 
toString() - Method in class qupath.opencv.ml.objects.OpenCVMLClassifier
 
toString() - Method in class qupath.opencv.ml.OpenCVClassifiers.BoostClassifier
 
toString() - Method in class qupath.opencv.ml.OpenCVClassifiers.DTreesClassifier
 
toString() - Method in class qupath.opencv.ml.OpenCVClassifiers.EMClusterer
 
toString() - Method in class qupath.opencv.ml.OpenCVClassifiers.LogisticRegressionClassifier
 
toString() - Method in class qupath.opencv.ml.OpenCVClassifiers.NormalBayesClassifierCV
 
toString() - Method in class qupath.opencv.ml.OpenCVClassifiers.RTreesClassifier
 
toString() - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMClassifierCV
 
toString() - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMSGDClassifierCV
 
toString() - Method in class qupath.opencv.ml.OpenCVClassifiers.OpenCVStatModel
 
toString() - Method in enum class qupath.opencv.ml.pixel.PixelClassifierTools.CreateObjectOptions
 
toString() - Method in class qupath.opencv.tools.LocalNormalization.SmoothingScale
 
toString() - Method in enum class qupath.opencv.tools.MultiscaleFeatures.MultiscaleFeature
 
trackedMemory() - Static method in class qupath.opencv.tools.OpenCVTools
Get a brief, one-line report on tracked memory use, based on JavaCPP's Pointer class.
train(TrainData) - Method in class qupath.opencv.ml.OpenCVClassifiers.BoostClassifier
 
train(TrainData) - Method in class qupath.opencv.ml.OpenCVClassifiers.DTreesClassifier
 
train(TrainData) - Method in class qupath.opencv.ml.OpenCVClassifiers.EMClusterer
 
train(TrainData) - Method in class qupath.opencv.ml.OpenCVClassifiers.LogisticRegressionClassifier
 
train(TrainData) - Method in class qupath.opencv.ml.OpenCVClassifiers.NormalBayesClassifierCV
 
train(TrainData) - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMClassifierCV
 
train(TrainData) - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMSGDClassifierCV
 
train(TrainData) - Method in class qupath.opencv.ml.OpenCVClassifiers.OpenCVStatModel
Train the classifier using data in an appropriate format.
train(TrainData) - Method in class qupath.opencv.ml.OpenCVClassifiers.RTreesClassifier
 
trainWithLock(TrainData) - Method in class qupath.opencv.ml.OpenCVClassifiers.BoostClassifier
Implement trainWithLock rather than train directly to ensure a lock is set when training, which can be used to prevent prediction occurring simultaneously.
trainWithLock(TrainData) - Method in class qupath.opencv.ml.OpenCVClassifiers.DTreesClassifier
Implement trainWithLock rather than train directly to ensure a lock is set when training, which can be used to prevent prediction occurring simultaneously.
trainWithLock(TrainData) - Method in class qupath.opencv.ml.OpenCVClassifiers.EMClusterer
Implement trainWithLock rather than train directly to ensure a lock is set when training, which can be used to prevent prediction occurring simultaneously.
trainWithLock(TrainData) - Method in class qupath.opencv.ml.OpenCVClassifiers.LogisticRegressionClassifier
Implement trainWithLock rather than train directly to ensure a lock is set when training, which can be used to prevent prediction occurring simultaneously.
trainWithLock(TrainData) - Method in class qupath.opencv.ml.OpenCVClassifiers.NormalBayesClassifierCV
Implement trainWithLock rather than train directly to ensure a lock is set when training, which can be used to prevent prediction occurring simultaneously.
trainWithLock(TrainData) - Method in class qupath.opencv.ml.OpenCVClassifiers.RTreesClassifier
Implement trainWithLock rather than train directly to ensure a lock is set when training, which can be used to prevent prediction occurring simultaneously.
trainWithLock(TrainData) - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMClassifierCV
Implement trainWithLock rather than train directly to ensure a lock is set when training, which can be used to prevent prediction occurring simultaneously.
trainWithLock(TrainData) - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMSGDClassifierCV
Implement trainWithLock rather than train directly to ensure a lock is set when training, which can be used to prevent prediction occurring simultaneously.
transformAllObjects(AffineTransform) - Static method in class qupath.lib.scripting.QP
Apply an affine transform to all selected objects in the current hierarchy.
transformAllObjects(PathObjectHierarchy, AffineTransform) - Static method in class qupath.lib.scripting.QP
Apply an affine transform to all selected objects in the specified hierarchy.
transformPadded(Mat) - Method in class qupath.opencv.ops.ImageOps.PaddedOp
Apply the op, but ignoring padding.
transformSelectedObjects(AffineTransform) - Static method in class qupath.lib.scripting.QP
Apply an affine transform to all objects in the current hierarchy, retaining parent-child relationships between objects.
transformSelectedObjects(PathObjectHierarchy, AffineTransform) - Static method in class qupath.lib.scripting.QP
Apply an affine transform to all objects in the specified hierarchy, retaining parent-child relationships between objects.
transformsToOp(Collection<? extends Processing>) - Static method in class qupath.opencv.ml.BioimageIoTools
Create an ImageOp that applies the specified transforms sequentially.
transformToOp(Processing) - Static method in class qupath.opencv.ml.BioimageIoTools
Create an ImageOp that applies the specified transforms, if possible.
translateAllObjects(double, double) - Static method in class qupath.lib.scripting.QP
Translate (move) the ROIs of all objects in the current object hierarchy.
translateAllObjects(PathObjectHierarchy, double, double) - Static method in class qupath.lib.scripting.QP
Translate (move) the ROIs of all objects in the specified object hierarchy.
tryToClassify(List<? extends PathObject>, ImageServer<BufferedImage>, double, IntFunction<PathClass>) - Method in class qupath.opencv.dnn.DnnObjectClassifier
Try to classify a batch of objects.
tryToClassify(ClassificationModel, PathObject, ImageServer<BufferedImage>, double, IntFunction<PathClass>) - Method in class qupath.opencv.dnn.OpenCVModelObjectClassifier
 
tryToClassify(PathObject, ImageServer<BufferedImage>, double, IntFunction<PathClass>) - Method in class qupath.opencv.dnn.DnnObjectClassifier
 
tryToParseMicrons(double, String) - Static method in class qupath.imagej.tools.IJTools
Based on a value and its units, try to get something suitable in microns.
type(DensityMaps.DensityMapType) - Method in class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapBuilder
The type of the density map, which determines any associated normalization.
typeToChannels(int) - Static method in class qupath.opencv.tools.OpenCVTools
Determine the number of channels from a specified Mat type (which also encodes depth).
typeToDepth(int) - Static method in class qupath.opencv.tools.OpenCVTools
Determine the depth from a specified Mat type (which may also encode the number of channels).

U

UNKNOWN_LENGTH - Static variable in class qupath.opencv.dnn.DnnShape
Constant to represent an unknown dimension length.
UNKNOWN_SHAPE - Static variable in class qupath.opencv.dnn.DnnShape
Constant to represent an unknown shape.
UNKNOWN_SIZE - Static variable in class qupath.opencv.dnn.DnnShape
Constant to represent an unknown size (i.e.
updateCooccurrenceMatrices(CoocurranceMatrices, SimpleImage, SimpleImage, int, double, double, int) - Static method in class qupath.lib.analysis.features.HaralickFeatureComputer
Update existing CoocurranceMatrices with the values in a SimpleImage.
updateURIs(Map<URI, URI>) - Method in class qupath.opencv.dnn.DnnObjectClassifier
 
updateURIs(Map<URI, URI>) - Method in class qupath.opencv.dnn.OpenCVDnn
 
updateURIs(Map<URI, URI>) - Method in class qupath.opencv.dnn.OpenCVModelObjectClassifier
 
updateURIs(Map<URI, URI>) - Method in interface qupath.opencv.ops.ImageOp
Default implementation makes no changes; classes should override this if necessary.
URIs(URI...) - Method in class qupath.opencv.dnn.DnnModelParams.Builder
Specify the URIs.
URIs(Collection<URI>) - Method in class qupath.opencv.dnn.DnnModelParams.Builder
Specify the URIs as a collection.
useCompiled() - Method in class qupath.lib.scripting.ScriptParameters
Request that any script should be compiled before being evaluated, and previously compiled versions reused when possible.
useCompiled(boolean) - Method in class qupath.lib.scripting.ScriptParameters.Builder
Request that the script is compiled before being evaluated, or a previously compiled version is used where available.
useCuda() - Static method in class qupath.opencv.dnn.DnnTools
Returns true if CUDA is available and requested.
useLogWriters() - Method in class qupath.lib.scripting.ScriptParameters.Builder
Set the output and error writers to append to the default logger.
useLogWriters(Logger) - Method in class qupath.lib.scripting.ScriptParameters.Builder
Set the output and error writers to append to the specified logger.
USER_HOME - Static variable in class qupath.lib.scripting.QP
The user's home directory, as obtained from System.getProperty("user.home").

V

validateMarkerMask(ImageProcessor, ImageProcessor) - Static method in class qupath.imagej.processing.MorphologicalReconstruction
Check that marker and mask images have the same size, and ensure that marker pixels are <= mask pixels, making this if necessary.
valueOf(String) - Static method in enum class qupath.lib.analysis.features.ObjectMeasurements.Compartments
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.analysis.features.ObjectMeasurements.Measurements
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.analysis.features.ObjectMeasurements.ShapeFeatures
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.plugins.objects.DilateAnnotationPlugin.LineCap
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.opencv.dnn.OpenCVDnn.ModelType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.opencv.ml.pixel.PixelClassifierTools.CreateObjectOptions
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.opencv.tools.LocalNormalization.NormalizationType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.opencv.tools.MultiscaleFeatures.MultiscaleFeature
Returns the enum constant of this class with the specified name.
values() - Static method in enum class qupath.lib.analysis.features.ObjectMeasurements.Compartments
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.analysis.features.ObjectMeasurements.Measurements
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.analysis.features.ObjectMeasurements.ShapeFeatures
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.plugins.objects.DilateAnnotationPlugin.LineCap
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.opencv.dnn.OpenCVDnn.ModelType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.opencv.ml.pixel.PixelClassifierTools.CreateObjectOptions
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.opencv.tools.LocalNormalization.NormalizationType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.opencv.tools.MultiscaleFeatures.MultiscaleFeature
Returns an array containing the constants of this enum class, in the order they are declared.
variance(int) - Static method in class qupath.opencv.ops.ImageOps.Filters
Apply a 2D circular variance filter.
VARIANCE - Enum constant in enum class qupath.lib.analysis.features.ObjectMeasurements.Measurements
Variance value
varianceFilter(Mat, int) - Static method in class qupath.opencv.tools.OpenCVTools
Apply a circular 2D local variance filter to all channels of an image, with symmetric boundary padding.
varianceFilter(Mat, int, int) - Static method in class qupath.opencv.tools.OpenCVTools
Apply a circular 2D local variance filter to all channels of an image.
vConcat(Collection<? extends Mat>, Mat) - Static method in class qupath.opencv.tools.OpenCVTools
Vertical concatenation for a Mat.
VERSION - Static variable in class qupath.lib.scripting.QP
The current QuPath version, parsed according to semantic versioning.

W

wandToRoi(Wand) - Static method in class qupath.imagej.processing.IJProcessing
Convert a traced outline from the ImageJ Wand into a PolygonRoi.
wandToRoi(Wand) - Static method in class qupath.imagej.processing.RoiLabeling
Deprecated.
since v0.6.0; use IJProcessing.wandToRoi(Wand) instead.
Watershed - Class in qupath.imagej.processing
Implementation of 2D watershed transform for ImageJ.
Watershed - Class in qupath.lib.analysis.algorithms
Implementation of 2D watershed transform.
Watershed() - Constructor for class qupath.imagej.processing.Watershed
 
Watershed() - Constructor for class qupath.lib.analysis.algorithms.Watershed
 
WatershedCellDetection - Class in qupath.imagej.detect.cells
Default command for cell detection within QuPath, assuming either a nuclear or cytoplasmic staining.
WatershedCellDetection() - Constructor for class qupath.imagej.detect.cells.WatershedCellDetection
 
WatershedCellMembraneDetection - Class in qupath.imagej.detect.cells
Cell detection that takes into consideration membrane staining.
WatershedCellMembraneDetection() - Constructor for class qupath.imagej.detect.cells.WatershedCellMembraneDetection
Default constructor.
watershedExpandLabels(ImageProcessor, double, boolean) - Static method in class qupath.imagej.processing.Watershed
Expand non-zero regions in a labeled image up to a maximum distance, using a watershed transform to prevent region merging.
watershedIntensitySplit(Mat, Mat, double, int) - Static method in class qupath.opencv.tools.OpenCVTools
Apply a watershed transform to refine a binary image, guided either by a distance transform or a supplied intensity image.
WEIGHTED_STD_DEV - Enum constant in enum class qupath.opencv.tools.MultiscaleFeatures.MultiscaleFeature
Weighted standard deviation
weightedStdDev(boolean) - Method in class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder
Calculate a Gaussian-weighted standard deviation.
whiteTopHat(ImageProcessor, double) - Static method in class qupath.imagej.processing.IJFilters
Apply a white tophat filter; this is equivalent to subtracting the original image from the a 'closed' image.
wrapInPointerScope(Processor<S, T, U>) - Static method in class qupath.lib.experimental.pixels.OpenCVProcessor
Wrap a processor in a second processor that uses a PointerScope to ensure that pointers are released (except for any output).
wrapStatModel(StatModel) - Static method in class qupath.opencv.ml.OpenCVClassifiers
Create an OpenCVClassifiers.OpenCVStatModel by wrapping an existing StatModel.
write(JsonWriter, T) - Method in class qupath.opencv.io.OpenCVTypeAdapters.OpenCVTypeAdapter
 
writeClassifier(PixelClassifier, Path) - Static method in class qupath.opencv.ml.pixel.PixelClassifiers
Write a pixel classifier to a file.
writeDensityMapImage(String, String) - Static method in class qupath.lib.scripting.QP
Write the output of applying a density map to the current image image.
writeDensityMapImage(ImageData<BufferedImage>, DensityMaps.DensityMapBuilder, String) - Static method in class qupath.lib.scripting.QP
Write the output of applying a density map to an image.
writeImage(ImagePlus, OutputStream) - Method in class qupath.imagej.images.writers.TiffWriterIJ
 
writeImage(ImagePlus, OutputStream) - Method in class qupath.imagej.images.writers.ZipWriterIJ
 
writeImage(ImagePlus, String) - Method in class qupath.imagej.images.writers.TiffWriterIJ
 
writeImage(ImagePlus, String) - Method in class qupath.imagej.images.writers.ZipWriterIJ
 
writeImage(BufferedImage, OutputStream) - Method in class qupath.imagej.images.writers.TiffWriterIJ
 
writeImage(BufferedImage, OutputStream) - Method in class qupath.imagej.images.writers.ZipWriterIJ
 
writeImage(BufferedImage, String) - Method in class qupath.imagej.images.writers.TiffWriterIJ
 
writeImage(BufferedImage, String) - Method in class qupath.imagej.images.writers.ZipWriterIJ
 
writeImage(BufferedImage, String) - Static method in class qupath.lib.scripting.QP
Write an image to the specified path.
writeImage(ImageServer<BufferedImage>, OutputStream) - Method in class qupath.imagej.images.writers.TiffWriterIJ
 
writeImage(ImageServer<BufferedImage>, OutputStream) - Method in class qupath.imagej.images.writers.ZipWriterIJ
 
writeImage(ImageServer<BufferedImage>, String) - Method in class qupath.imagej.images.writers.TiffWriterIJ
 
writeImage(ImageServer<BufferedImage>, String) - Method in class qupath.imagej.images.writers.ZipWriterIJ
 
writeImage(ImageServer<BufferedImage>, String) - Static method in class qupath.lib.scripting.QP
Write a full image to the specified path.
writeImage(ImageServer<BufferedImage>, RegionRequest, OutputStream) - Method in class qupath.imagej.images.writers.TiffWriterIJ
 
writeImage(ImageServer<BufferedImage>, RegionRequest, OutputStream) - Method in class qupath.imagej.images.writers.ZipWriterIJ
 
writeImage(ImageServer<BufferedImage>, RegionRequest, String) - Method in class qupath.imagej.images.writers.TiffWriterIJ
 
writeImage(ImageServer<BufferedImage>, RegionRequest, String) - Method in class qupath.imagej.images.writers.ZipWriterIJ
 
writeImageRegion(ImageServer<BufferedImage>, RegionRequest, String) - Static method in class qupath.lib.scripting.QP
Write an image region image to the specified path.
writePredictionImage(String, String) - Static method in class qupath.lib.scripting.QP
Write the output of applying a pixel classifier to the current image image.
writePredictionImage(ImageData<BufferedImage>, PixelClassifier, String) - Static method in class qupath.lib.scripting.QP
Write the output of applying a pixel classifier to an image.

X

xor(Mat, Mat) - Static method in class qupath.opencv.tools.GroovyCV
Compute the bitwise XOR of two arrays.

Z

zeroMeanUnitVariance(boolean) - Static method in class qupath.opencv.ops.ImageOps.Normalize
Normalize a Mat by subtracting the mean value and dividing by the standard deviation.
zeroMeanUnitVariance(boolean, double) - Static method in class qupath.opencv.ops.ImageOps.Normalize
Normalize a Mat by subtracting the mean value and dividing by the standard deviation + eps.
ZipWriterIJ - Class in qupath.imagej.images.writers
ImageWriter implementation to write zipped TIFF images using ImageJ.
ZipWriterIJ() - Constructor for class qupath.imagej.images.writers.ZipWriterIJ
 
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