All Classes and Interfaces
Class
Description
Abstract plugin aimed towards cases where new objects will be detected inside existing objects (normally TMA cores or annotations).
Abstract implementation of ImageServer providing some common functionality.
Abstract class to help with implementing an interactive plugin.
Abstract class to help with the creation of object classifiers.
General abstract plugin implementation, which defines some methods to facilitate
creating plugins that do parallel processing.
Abstract PluginRunner to help with the creation of plugin runners for specific circumstances,
e.g.
Abstract plugin used for detection tasks that support breaking large regions into smaller ones,
and analyzing these in parallel - optionally with overlaps.
Abstract
ImageServer for BufferedImages that internally breaks up requests into constituent tiles.ImageServer that dynamically applies an AffineTransform to an existing ImageServer.
Helper class for working with affine transforms.
Deprecated.
since v0.6.0 (but really not used in recent versions)
Simple wrappers for primitive arrays that returns values as doubles.
Simple wrapper for an array or list, enabling values to be returned as doubles.
A collection of static methods useful when working with AWT shapes and
ImageRegions.Parameter that can take on true of false value - or null.
Interface for normalizing a BufferedImage.
Static methods for working with BufferedImages and QuPath objects.
Helper class for working with PathObjects that represent cells.
A
TransformingImageServer that applies color transforms to generate channels.Parameter that supports a list of choices.
Simple class for representing - and inverting a 3x3 matrix.
Static methods to assist with color deconvolution.
Normalizes an image by applying color deconvolution to RGB input, rescaling intensities, and using color
'reconvolution' to generate a new RGB image.
Helper class for storing stain vectors and maximum channel values to be used for color deconvolution.
Enum for common stain defaults.
Helper class to manage colormaps, which are rather like lookup tables but easily support interpolation.
colormap, which acts as an interpolating lookup table with an arbitrary range.
Factory methods to help create ColorModels for use with BufferedImages.
Helper class for creating a JSON-serializable way to generate a
ColorModel.Simple builder to create a
ColorModel.Helper class to the display of a single channel (band) in a
ColorModel.Static functions to help work with RGB(A) colors using packed ints.
Helper class for converting between packed RGB colors and Java's AWT representation, as well as creating some ColorModels for BufferedImages.
Static methods for computing a range of color transforms for packed RGB values.
Enum consisting of color transforms that may be applied to RGB images.
Color transforms that may be used to extract single-channel images from BufferedImages.
Interface defining a color transform that can extract a float value from a BufferedImage.
TypeAdapter to support serializing a ColorTransforms.ColorTransform.A PluginRunner that simply logs progress and output.
A
SimpleProgressMonitor that sends progress to a log.Class to convert labelled images to Geometry objects, ROIs and PathObjects.
Helper class defining global thresholds to apply to a single image channel.
Helper method for calculating the convex hull from a list of points.
ImageServer that treats a particular sub-region of another ImageServer as a full image,
i.e.
Default comparator to enable objects to be sorted in a more predictable manner.
Deprecated.
v0.6.0, to be replaced by
DelaunayTools.SubdivisionDefault comparator to enable ROIs to be sorted in a more predictable manner.
A scriptable workflow step where the script is provided directly as an argument.
Default implementation of a TMAGrid.
Tools for creating and querying Delaunay triangulations and Voronoi diagrams.
Builder class to create a
DelaunayTools.Subdivision based on Delaunay triangulation.Helper class for extracting information from a Delaunay triangulation computed from PathObjects.
Helper methods to convert ObjectDetectors into runnable tasks, which take care of resolving
overlaps when using ParallelTileObjects after the detection is complete and firing notification
events in a PathObjectHierarchy.
Static methods for calculating distances between objects.
Parameter to represent a floating point numeric value.
Interface for classes that can calculate a downsample value to use when requesting pixels from an image.
Helper class to create downsample calculators, which can figure out how much to downsample a specified image region.
ROI implementing a circle, or (unrotated) ellipse.
Parameter that doesn't actually store any value, but might contain some
useful text (or a title) that may need to be displayed.
Compute a faster union of large numbers of polygons.
Class to wrap a collection of objects to indicate they should be export as a GeoJSON "FeatureCollection".
Helper class that, given a path, determines some basic file format information without enlisting
the help of an external library or performing extensive parsing of the data.
Interface defining some basic image metadata that may be extracted from an image file
to help ascertain whether an
ImageServerBuilder can handle it.Collection of generally useful static methods.
Marker interface to indicate that this ImageServer generates tiles on request.
ROI based on Java Topology Suite Geometry objects.
Convert between QuPath
ROI objects and Java Topology Suite Geometry objects.Builder to help define how ROIs and Geometry objects should be converted.
Helper class providing Gson instances with type adapters registered to serialize
several key classes.
A
TypeAdapterFactory that is suitable for handling class hierarchies.Class for storing histogram data & basic statistics.
The name and display color for a single image channel.
Class that brings together the main data in connection with the analysis of a single image.
Enum representing possible image types.
Helper class to store z-slice and time point indices, optionally along with a channel index as well.
Class for defining an image region.
Generic ImageServer, able to return pixels and metadata.
Helper class for creating ImageServers from a given URI and optional argument list.
Abstract ServerBuilder implementation that handles metadata.
Default
ImageServerBuilder.ServerBuilder that requires a URI and (optional) array of String arguments to create an ImageServer
with the help of a ImageServerBuilder.Interface that defines a class encapsulating all that is required to build an ImageServer.
Helper class to summarize which ImageServers can be build by a particular
ImageServerBuilder
for a given URI, and a level of confidence.Class for storing primary ImageServer metadata fields.
Builder to create a new
ImageServerMetadata object.Enum representing possible channel (band) types for an image.
Width and height of each resolution in a multi-level image pyramid.
Builder to create a list of
ImageServerMetadata.ImageResolutionLevel to represent pyramidal resolutions.Service provider for creating ImageServers from a given path - which may be a file path or URL.
Helper class for working with
ImageServer objects.Interface for defining class that can write images.
Static methods to access
ImageWriter objects and write images.An immutable alternative to Java's AWT Dimension.
Parameter to represent an integer numeric value.
ImageWriter implementation to write JPEG images using ImageIO.
ImageServerBuilder that constructs an ImageServer from a JSON representation.
Structure used to store data related to generating Kaplan-Meier survival curves.
Simple class to store event time and censored flag.
A special ImageServer implementation that doesn't have a backing image, but rather
constructs tiles from a
PathObjectHierarchy where pixel values are integer labels corresponding
stored and classified annotations.Helper class for building a
LabeledImageServer.ROI representing a straight line, defined by its end points.
Helper class to apply a log-rank test.
Simple structure used to manage the result of a log rank test.
Helper class for logging.
Basic interface to define a measurement.
Interface defining a feature measurement list, consisting of key value pairs.
Enum representing different types of measurement list, with different priorities regarding
flexibility and efficiency.
Factory for creating new measurement lists.
A strategy for handling measurements between objects being merged.
Deprecated.
v0.6.0.
Minimal interface to indicate that an object can provide a map of metadata key/value pairs.
Methods for normalizing features.
An ImageServer implementation used for stain normalization.
Abstract parameter to represent a numeric value.
Interface defining object classifiers, which assign PathClasses to PathObjects.
Helper class for creating ObjectClassifiers.
Builder to create a simple
ObjectClassifier that assigns a classification based upon whether the
measurement of an object is above, equal to or below a specified threshold.TypeAdapterFactory to help with serializing ObjectClassifiers to and from JSON.Minimal interface that may be used to plugins that perform detection within a specified ROI
and using a specified ImageData with set parameters.
Helper class for merging objects using different criteria.
Minimal interface for processing one or more objects.
Builder for the OverlapFixer.
Requested padding for a 2D image.
A temporary object, used during parallel processing to represent a tile currently being used for object
detection.
Current processing status for the tile.
Interface defining algorithm parameters, which need to be displayed to users somehow.
Interface for objects that need to be notified when parameters have their values changed.
Interface for indicating that the implementing class takes adjustable parameters.
A collection of Parameters, which can be used for analysis & queried to construct appropriate GUIs.
An annotation PathObject.
A subclass of a PathDetectionObject, which also supports storing an (optional) extra ROI to represent
the cell nucleus.
Representation of an object's classification - which can be defined using any unique string
identifier (e.g.
Enum representing standard classifications.
Deprecated.
since v0.4.0 in favor of methods added to
PathClass directly.Enum representing standard classifications.
Static methods for use with
PathClass objects.A detection PathObject.
Interface used when needing to associate pixel data with information regarding the image from which it was obtained.
Interface to define a PathPlugin that requires a list of (user-adjustable) parameters.
Primary class for loading/saving
ImageData objects.Options to customize the export of PathObjects as GeoJSON.
Fundamental object of interest in QuPath.
Deprecated.
v0.6.0, to be replaced by
DelaunayTools.SubdivisionData structure for storing multiple PathObjectConnectionGroups.
Enumeration of filters (predicates) that can be used to select objects based on their type.
A basic hierarchy in which to store PathObjects.
An event class for passing on information about modifications to a PathObjectHierarchy.
Enum representing different ways in which the hierarchy may have been updated.
A listener for modifications to a
PathObjectHierarchy (i.e.Classes to define JSON-serializable
Predicates for PathObjects.A JSON-serializable
Predicate for use with PathObjects.Interface for classes capable of reading PathObjects from some source.
Helper class to create
PathObject.A listener to selection changes within a PathObjectSelectionModel.
Model for handling selection of single and multiple PathObjects.
A collection of static methods to help work with PathObjects.
Primary interface for defining a 'plugin' command.
Abstract class used for PathObjects that have ROIs associated with them.
The root object used at the base of a PathObjectHierarchy.
Helper interface to define plugin tasks that require post-processing on a specific thread
(i.e.
A subclass of PathDetectionObject, generally used to represent an image region that doesn't
(in itself) correspond to any particularly interesting structure.
Class used to represent pixel sizes.
Builder class for
PixelCalibration objects.ImageServer that delivers pixels derived from applying a PixelClassifier to another ImageServer.
Interface defining a pixel classifier.
Metadata to control the behavior of a pixel classifier.
Builder to create
PixelClassifierMetadata objects.Image bit-depths and types.
ImageWriter implementation to write PNG images using ImageIO.
Simple interface defining a point.
A 2D point (x & y coordinates).
Helper class for reading/writing point objects in terms of their x,y coordinates.
ROI representing a collection of 2D points (distinct x,y coordinates).
ROI representing an arbitrary closed polygon.
ROI representing an arbitrary open polyline.
Core QuPath preferences.
Data structure to manage images and associated data in QuPath.
Class to represent an image entry within a project.
Read QuPath projects.
Static methods to help when working with Projects.
Simple image server to swap the red and blue channels of an RGB image.
Helper class when classifying PathObjects.
ROI representing a square or rectangle (unrotated).
Class for defining an image region that can also be used to request these region from an
ImageServer.Manage the storage and retrieval of resources with a
ResourceManager.Simple manager to handle saving and retrieving resources of different kinds, for example from projects
or a user directory.
Base interface for defining regions of interest (ROIs) within QuPath.
Enum representing the major different types of ROI.
Helper class for interactively modifying existing ROIs.
This class consists exclusively of static methods that operate on or return regions of interest (ROIs).
A collection of static methods for working with ROIs.
Methods of combining two ROIs.
ImageServer that wraps another ImageServer, but intercepts region requests to
effectively rotate the image by 90, 180 or 270 degrees.
Enum for rotations in increments of 90 degrees.
Helper class for computing basic statistics from values as they are added.
WorkflowStep for running a saved PathObjectClassifier.
A WorkflowStep that can also return some Javascript that, if run, would perform the step.
Static methods helpful when dealing with ImageServers.
Helper methods for simplifying shapes, such removing polygon points while retaining a similar overall
shape at a coarser level.
A minimal interface for accessing pixel values in a single-channel image.
Create
SimpleImage instances for basic pixel processing.A minimal interface to define a means to provide access to pixel values from a 2D, 1-channel image.
Updated version of DefaultPluginWorkflowStep, adapted to use Externalizable and to avoid storing the plugin class as a class object
(preferring a String instead).
Class for monitoring the process of a plugin and displaying feedback to the user.
ImageServer that treats a particular set of z-slices and timepoints of another ImageServer
as a full image.
An ImageServer that combines regions from multiple separate ImageServers,
repositioning these as necessary to generate one larger field of view.
Builder to create a new
SparseImageServer.Helper class for SparseImageServers, capable of returning the appropriate ImageServer for
different ImageRegions and different resolutions.
Representation of a color deconvolution stain vector, defined in terms of RGB optical densities.
Enum representing default stains.
Static methods for computing statistics from images, with or without a corresponding labeled image.
Parameter to represent a String value.
Normalizes the pixel values of a BufferedImage by subtracting and offset and multiplying by a scale factor.
A minimal interface for a class capable of running tasks in parallel, giving feedback to the user.
A utility class to help with the creation of
TaskRunner instances.Marker interface used to indicate that child objects shouldn't be added to any cache for display.
Create a thread factory that supports adding a prefix to the name and setting daemon status.
An ImageServer implementation used to apply transforms to another ImageServer.
Helper class for exporting image tiles, typically for further analysis elsewhere or for training up an AI algorithm.
Enum representing the possible alignments for tiles.
A wrapper for a
RegionRequest, useful to precisely specify image tiles at a particular resolution.Helper class to manage tile requests from an
ImageServer.Helper class to time code execution.
Class representing a named checkpoint with a timestamp in nanoseconds.
A special PathObject used exclusively to represent TMA cores.
Interface defining a (rectangular) TMA grid.
Helper class for importing data in connection with TMA slides.
Helper class for creating an
ImageServer that applies one or more transforms to another (wrapped) ImageServer.An ImageServer implementation used to apply transforms to another ImageServer.
An ImageServer implementation that converts the pixel type of an image.
Interface for objects that depend upon URIs.
Helper class for updating URIs, for example whenever files have moved or projects have been transferred between computers.
Wrapper for a URI, providing access to a
Path if available.Enum representing the status of a URI, i.e.
Helper class for working with semantic versioning.
A collection of steps that relate to how an image has been - or should be - processed.
Interface for listening to changes in Workflows, e.g.
Basic interface for a loggable workflow step.
Implementation of an
ImageServer that simply wraps an existing BufferedImage.An image server that combine similar images into a z-stack.
An image server that converts a z-stack into a 2D image with a projection.
A type of projection on the Z-axis.