Index
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
Matthat strictly requires a specific input size. - applyToChannels(Mat, Consumer<Mat>) - Static method in class qupath.opencv.tools.OpenCVTools
- 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
- asType(ImageProcessor, Class<T>) - Static method in class qupath.opencv.tools.GroovyCV
-
Helper method to convert an
ImageProcessorto aMatusing Groovy's 'as' syntax. - asType(BufferedImage, Class<T>) - Static method in class qupath.opencv.tools.GroovyCV
-
Helper method to convert a
BufferedImageto aMat,ImageProcessororImagePlususing Groovy's 'as' syntax. - asType(Number, Class<T>) - Static method in class qupath.opencv.tools.GroovyCV
- asType(Mat, Class<T>) - Static method in class qupath.opencv.tools.GroovyCV
-
Helper method to convert a
Matto aBufferedImage,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
PixelProcessorfrom the current state of the builder. - build() - Method in class qupath.lib.scripting.ScriptParameters.Builder
-
Build the
ScriptParameterswith 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
-
Build a
FeaturePreprocessor. - buildClassifier(ImageData<BufferedImage>) - Method in class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapBuilder
-
Build a
PixelClassifierfor a density map using the current parameters and the specifiedImageData. - buildDnnModel(Model) - Static method in class qupath.opencv.ml.BioimageIoTools
-
Attempt to build a
DnnModelthat 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
-
Create a
FeaturePreprocessor.Builderto build a customFeaturePreprocessor. - 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
PixelProcessorthat can make custom measurements for an image object. - builder(DensityMaps.DensityMapBuilder) - Static method in class qupath.lib.analysis.heatmaps.DensityMaps
-
Create a new
DensityMaps.DensityMapBuilderinitialized 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.Builderfor an ImageJImagePlus. - builder(Processor<Mat, Mat, Mat>) - Static method in class qupath.lib.experimental.pixels.OpenCVProcessor
-
Create a
PixelProcessor.Builderfor an OpenCVMat. - builder(PathObjectPredicates.PathObjectPredicate) - Static method in class qupath.lib.analysis.heatmaps.DensityMaps
-
Create a new
DensityMaps.DensityMapBuilderto 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
DnnModelif possible, or return null otherwise. - buildModel(DnnModelParams) - Static method in class qupath.opencv.dnn.DnnModels
-
Build a
DnnModelfrom 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.DensityMapParametersobject containing the main density map parameters. - buildPatchClassifierParams(Model, int, int, ImageOp...) - Static method in class qupath.opencv.ml.BioimageIoTools
-
Create an instance of
PatchClassifierParamsfrom a model spec. - buildPatchClassifierParams(Model, ImageOp...) - Static method in class qupath.opencv.ml.BioimageIoTools
-
Create an instance of
PatchClassifierParamsfrom 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.
- buildServer(String, String...) - Static method in class qupath.lib.scripting.QP
-
Build an
ImageServerwith the classBufferedImage. - buildServer(URI, String...) - Method in class qupath.imagej.images.servers.ImageJServerBuilder
- buildServer(URI, String...) - Static method in class qupath.lib.scripting.QP
-
Build an
ImageServerwith the classBufferedImage. - buildServer(ImageData<BufferedImage>) - Method in class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapBuilder
-
Build an
ImageServerrepresenting this density map. - buildServer(ImageData<BufferedImage>, ImageDataOp, PixelCalibration) - Static method in class qupath.opencv.ops.ImageOps
- buildServer(ImageData<BufferedImage>, ImageDataOp, PixelCalibration, int, int) - Static method in class qupath.opencv.ops.ImageOps
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
PathObjectbased 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
-
Refers to
ClassificationModel. - 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
-
Set a
ColorModels.ColorModelBuilderthat can be used in conjunction withDensityMaps.DensityMapBuilder.buildServer(ImageData). - 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
ImagePlusto 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
-
Deprecated.
- 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
ImagePlusto 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
-
Deprecated.
- convertToFloatProcessor(SimpleImage) - Static method in class qupath.imagej.tools.IJTools
-
Convert a
SimpleImageto anImageProcessor. - 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
BufferedImageinto aPathImage<ImagePlus>. - convertToImagePlus(ImageServer<BufferedImage>, RegionRequest) - Static method in class qupath.imagej.tools.IJTools
-
Read a region from an
ImageServer<BufferedImageas aPathImage<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
PathObjectfor a specific ImageJ Roi. - convertToPathObject(Roi, double, Function<ROI, PathObject>, ImagePlus) - Static method in class qupath.imagej.tools.IJTools
-
Create a
PathObjectfor a specific ImageJ Roi, using anImagePlusto help set properties. - convertToPathObject(ImagePlus, ImageServer<?>, Roi, double, Function<ROI, PathObject>, ImagePlane) - Static method in class qupath.imagej.tools.IJTools
-
Deprecated.
- 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
LazyValuewith 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
ObjectClassifierthat uses anOpenCVClassifiers.OpenCVStatModelfor 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.OutputToObjectConverterthat attempts to convert the output into annotation objects. - createAnnotationConverter() - Static method in class qupath.lib.experimental.pixels.OpenCVProcessor
-
Create an
OutputHandler.OutputToObjectConverterthat 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.OutputToObjectConverterthat attempts to convert the output into annotation objects. - createAnnotationOutputHandler() - Static method in class qupath.lib.experimental.pixels.ImageJProcessor
-
Create an
OutputHandlerthat attempts to convert the output into annotation objects. - createAnnotationOutputHandler() - Static method in class qupath.lib.experimental.pixels.OpenCVProcessor
-
Create an
OutputHandlerthat attempts to convert the output into annotation objects. - createAnnotationOutputHandler(Map<? extends Number, String>) - Static method in class qupath.lib.experimental.pixels.OpenCVProcessor
-
Create an
OutputHandlerthat 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
ImageServerthat 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.DisplayBandto 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.DisplayBandto 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
LazyBooleanValuewith 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
ImageDataOpinto a simple classifier. - createClassifier(ImageDataOp, PixelCalibration, Map<Integer, PathClass>) - Static method in class qupath.opencv.ml.pixel.PixelClassifiers
-
Convert an
ImageDataOpinto 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.ColorModelBuilderwith 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.OutputToObjectConverterthat attempts to convert the output into detection objects. - createDetectionConverter() - Static method in class qupath.lib.experimental.pixels.OpenCVProcessor
-
Create an
OutputHandler.OutputToObjectConverterthat 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.OutputToObjectConverterthat 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
OutputHandlerthat attempts to convert the output into detection objects. - createDetectionOutputHandler() - Static method in class qupath.lib.experimental.pixels.OpenCVProcessor
-
Create an
OutputHandlerthat attempts to convert the output into detection objects. - createDetectionOutputHandler(Map<? extends Number, String>) - Static method in class qupath.lib.experimental.pixels.OpenCVProcessor
-
Create an
OutputHandlerthat 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
ImageServerthat 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
ImageSupplierthat returns an ImageJImagePlus. - createImagePlusMaskSupplier() - Static method in class qupath.lib.experimental.pixels.ImageJProcessor
-
Create a
MaskSupplierthat returns an ImageJByteProcessor. - 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
Writerthat 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
ImageSupplierthat returns an OpenCVMat. - createMatMaskSupplier() - Static method in class qupath.lib.experimental.pixels.OpenCVProcessor
-
Create a
MaskSupplierthat returns an OpenCVMat. - createMeasurementListFeatureExtractor(List<String>) - Static method in class qupath.opencv.ml.objects.features.FeatureExtractors
- 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
PixelClassificationMeasurementManagerthat 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
PixelClassificationMeasurementManagerthat can be used to generate measurements from anImageServerwhere 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
Normalizerwith 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
FeatureExtractorto apply normalization prior to returning the values. - createNumeric(String, String, Function<S, Number>) - Static method in interface qupath.lib.lazy.interfaces.LazyValue
-
Create a
LazyNumericValuewith specified name and help text. - createObjectConverter(Class<U>, Function<ROI, PathObject>) - Static method in class qupath.lib.experimental.pixels.ImageJProcessor
-
Create an
OutputHandler.OutputToObjectConverterfor one specify type. - createObjectConverter(BiFunction<ROI, Number, PathObject>) - Static method in class qupath.lib.experimental.pixels.OpenCVProcessor
-
Create an
OutputHandler.OutputToObjectConverterto 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.OutputToObjectConverterthat 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.OutputToObjectConverterto 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.OutputToObjectConverterto 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
ImageServerthat 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
PathImagefrom an ImagePlus and region. - createPCAProjectFeatureExtractor(FeatureExtractor<T>, Preprocessing.PCAProjector) - Static method in class qupath.opencv.ml.objects.features.FeatureExtractors
-
Wrap an existing
FeatureExtractorto 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
ImageServerthat displays the results of applying aPixelClassifierto an image. - createPixelClassificationServer(ImageData<BufferedImage>, PixelClassifier, String, ColorModel, boolean) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools
-
Create an
ImageServerthat displays the results of applying aPixelClassifierto 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.v0.4.0 use
QP.createFullImageAnnotation(boolean)instead - createSelectAllObject(boolean, int, int) - Static method in class qupath.lib.scripting.QP
-
Deprecated.v0.4.0 use
QP.createFullImageAnnotation(boolean, int, int)instead - createServerBuilder() - Method in class qupath.imagej.images.servers.ImageJServer
- createStatModel(Class<? extends StatModel>) - Static method in class qupath.opencv.ml.OpenCVClassifiers
-
Create an
OpenCVClassifiers.OpenCVStatModelfor a specific class ofStatModel. - createString(String, String, Function<S, String>) - Static method in interface qupath.lib.lazy.interfaces.LazyValue
-
Create a
LazyStringValuewith specified name and help text. - createThresholdClassifier(PixelCalibration, int, double, PathClass, PathClass) - Static method in class qupath.opencv.ml.pixel.PixelClassifiers
-
Create a new
PixelClassifierthat 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
PixelClassifierthat 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
ImageServerby 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
ImageServerby 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
TMAGridand 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
TMAGridand 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
Modelclass. - 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
ImageServerrepresenting a density map or forDensityMaps.DensityMapParameters. - DensityMaps.DensityMapParameters - Class in qupath.lib.analysis.heatmaps
-
Class for storing parameters to build a
ImageServerrepresenting 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
DnnModelto 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
DnnModelfromDnnModelParams. - 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
ObjectClassifierusing 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
Matis continuous, creating a copy of the data if necessary. - ensureType(PixelType) - Static method in class qupath.opencv.ops.ImageOps.Core
-
Convert the
Matto 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
ScriptAutoCompletorobject 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() - 1is 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
-
Deprecated.Use instead
QP.makeRGB(int, int, int)orQP.makeARGB(int, int, int, int) - 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
PathObjectHierarchyof the currentImageData. - 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
ImageServerof the currentImageData. - getCurrentServerPath() - Static method in class qupath.lib.scripting.QP
-
Get the path to the
ImageServerof the currentImageData. - 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.Hessianassociated 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
ImageDatathat should be used with the script. - getImageData() - Method in interface qupath.opencv.ops.ImageDataServer
-
Get the
ImageDatawrapped by theImageDataServer. - getImagePlane(Roi, ImagePlus) - Static method in class qupath.imagej.tools.IJTools
-
Get the
ImagePlaneof 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
ROIfor the primary selected object within the currentPathObjectHierarchy. - 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
TypeAdapterFactorydefault used forFeatureExtractorobjects. - getTypeAdapterFactory() - Static method in class qupath.opencv.ml.pixel.PixelClassifiers
-
Get the
TypeAdapterFactorydefault used forPixelClassifierobjects. - 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
ImagePlusproperty storing either"light"or"darkdepending 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
ImagePlusproperties to store the bounding box of a QuPathImageRegion. - IMAGE_REQUEST - Static variable in class qupath.imagej.tools.IJProperties
-
Key for an
ImagePlusproperty to store a json representation of aRegionRequestused to request the image. - IMAGE_TYPE - Static variable in class qupath.imagej.tools.IJProperties
-
Key for an
ImagePlusproperty to store a string representing a QuPathImageData.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
ImageServerthat wraps anImageData. - 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
PixelProcessorwhen 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
ImageOpandImageDataOpobjects. - 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
ImageOpto 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
Indexerusing bilinear interpolation. - interp3D(Indexer, double, double, double) - Static method in class qupath.opencv.tools.Interpolation
-
Request a value from an
Indexerusing 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
trueif 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.Use
OpenCVTools.label(Mat, Mat, int)instead. - 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
-
Deprecated.since v0.6.0; use
IJProcessing.labelsToRoisArray(ImageProcessor)orIJProcessing.labelsToRois(ImageProcessor)instead. - 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
- lazyInitialize(boolean) - Method in class qupath.opencv.dnn.DnnModelParams.Builder
-
Optionally request lazy initialization.
- LazyNumericValue<S> - Interface in qupath.lib.lazy.interfaces
- LazyStringValue<S> - Interface in qupath.lib.lazy.interfaces
- 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.DensityMapBuilderfrom 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
Fileobject. - makeInverseAnnotation() - Static method in class qupath.lib.scripting.QP
-
Make an inverse annotation using the current
ImageDataand its current selected objects. - makeInverseAnnotation(ImageData<?>) - Static method in class qupath.lib.scripting.QP
-
Make an inverse annotation using the specified
ImageDataand 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.v0.6.0, use
QP.createDirectoryInProject(String...)instead. - 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
MatVectorinto an ImageJImagePlus. - matToImagePlus(Mat, String) - Static method in class qupath.opencv.tools.OpenCVTools
-
Convert an OpenCV
Matinto an ImageJImagePlus. - matToImageProcessor(Mat) - Static method in class qupath.opencv.tools.OpenCVTools
-
Convert a single-channel OpenCV
Matinto an ImageJImageProcessor. - 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
PixelProcessorinstances 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
Pointerclass. - 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
PathClassandImagePlaneas 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
PathClassandImagePlanefor 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
-
Deprecated.v0.6.0, use
PixelProcessor.Builder.postProcess(ObjectProcessor)instead - 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.Hessianif 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
Normalizerto 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
DnnShapewith 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
Modelsupported by OpenCV. - OpenCVDnnModelBuilder - Class in qupath.opencv.dnn
-
A
DnnModelBuilderimplementation that uses OpenCV's DNN module to build aNet. - OpenCVDnnModelBuilder() - Constructor for class qupath.opencv.dnn.OpenCVDnnModelBuilder
- OpenCVMLClassifier<T> - Class in qupath.opencv.ml.objects
-
An
ObjectClassifierthat uses anOpenCVClassifiers.OpenCVStatModelfor classification. - OpenCVModelObjectClassifier - Class in qupath.opencv.dnn
-
Initial implementation of a patch-based
ObjectClassifierusing 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
PixelProcessorwhen 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, - Interface in qupath.lib.experimental.pixelsU> -
A functional interface for handling the output of a
Processor. - OutputHandler.ObjectOutputHandler<S,
T, - Class in qupath.lib.experimental.pixelsU> - OutputHandler.OutputToObjectConverter<S,
T, - Interface in qupath.lib.experimental.pixelsU> - 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
Matdimensions from aMatShapeVector. - 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
LazyValueinstances. - 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
Pointerclass. - 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, - Class in qupath.lib.experimental.pixelsU> -
A class for tiled image processing.
- PixelProcessor.Builder<S,
T, - Class in qupath.lib.experimental.pixelsU> -
Builder class for a
PixelProcessor - PixelProcessorUtils - Class in qupath.lib.experimental.pixels
-
Utility functions to help with the
PixelProcessorclass. - 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
WatershedCellDetectionthat 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 standardMat. - 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 standardMat. - 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
FeaturePreprocessorto 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, - Interface in qupath.lib.experimental.pixelsU> -
A generic processor designed to work with
Parametersand 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
-
ImageServerimplementation 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
LazyValueimplementations forPathObjectinputs. - 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
ImageDataOpclass for JSON serialization/deserialization. - registerDnnModel(Class<T>, String) - Static method in class qupath.opencv.dnn.DnnModels
-
Register a new
DnnModelclass for JSON serialization/deserialization. - registerDnnModel(Class<T>, String) - Static method in class qupath.opencv.dnn.DnnTools
-
Deprecated.since v0.4.0; use
DnnModels.registerDnnModel(Class, String)instead. - registerOp(Class<? extends ImageOp>, String) - Static method in class qupath.opencv.ops.ImageOps
-
Register an
ImageOpclass 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
-
Deprecated.
- 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
-
Deprecated.
- 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
ProjectandImageDataused 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
-
Refers to
SegmentationModel. - 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
PathClassclassifications assigned. - selectObjectsByPathClass(PathObjectHierarchy, PathClass...) - Static method in class qupath.lib.scripting.QP
-
Select objects for the specified hierarchy that have one of the specified
PathClassclassifications 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
ProjectandImageDatato 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_BACKGROUNDproperty 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_REGIONproperty 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_TYPEproperty 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.outandSystem.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()orDnnShape.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
StatModelto 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))^2wherel1andl2are 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
-
Refers to
TextDetectionModel_DB. - TEXT_DETECTION_EAST - Enum constant in enum class qupath.opencv.dnn.OpenCVDnn.ModelType
-
Refers to
TextDetectionModel_EAST. - TEXT_RECOGNITION - Enum constant in enum class qupath.opencv.dnn.OpenCVDnn.ModelType
-
Refers to
TextRecognitionModel. - 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
Pointerclass. - 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
ImageOpthat applies the specified transforms sequentially. - transformToOp(Processing) - Static method in class qupath.opencv.ml.BioimageIoTools
-
Create an
ImageOpthat 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
PointerScopeto ensure that pointers are released (except for any output). - wrapStatModel(StatModel) - Static method in class qupath.opencv.ml.OpenCVClassifiers
-
Create an
OpenCVClassifiers.OpenCVStatModelby wrapping an existingStatModel. - 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
All Classes and Interfaces|All Packages|Constant Field Values
BufferedImageis the class, useQP.buildServer(String, String...)instead because it handles default args.