Anchor - merged Javadoc across key repositories. This documentation is a work-in-progress. 0.0.1-SNAPSHOT API

Packages

Package	Description
org.anchoranalysis.annotation	Ground truth for an image in diverse forms.
org.anchoranalysis.annotation.image	Annotations that apply to an image as a whole.
org.anchoranalysis.annotation.io	Reading and writing annotations to the filesystem.
org.anchoranalysis.annotation.io.assignment	A pairing of objects from two collections (bipartite matching).
org.anchoranalysis.annotation.io.assignment.generator	Generates output images to illustrate a Assignment between annotations.
org.anchoranalysis.annotation.io.bean	Beans related to reading / writing / specifying annotations.
org.anchoranalysis.annotation.io.bean.comparer	What to compare an annotation (ground truth) against?
org.anchoranalysis.annotation.io.comparer	Non-bean classes involving comparing results and annotations.
org.anchoranalysis.annotation.io.image	Reading and writing whole-image label annotations.
org.anchoranalysis.annotation.io.image.findable	The outcome of searching for annotations or images on the file-system.
org.anchoranalysis.annotation.io.mark	Reading and writing Mark-related annotations from/to the file-system.
org.anchoranalysis.annotation.mark	Annotations that use one or more marks to describe entities in an image.
org.anchoranalysis.bean	Defining, loading, initializing Anchor Beans.
org.anchoranalysis.bean.annotation	Annotations that decorate fields in an Anchor Bean.
org.anchoranalysis.bean.define	Define and related-classes.
org.anchoranalysis.bean.define.adder	DefineAdder and related-classes.
org.anchoranalysis.bean.exception	Exceptions that can occur executing generic operations on Anchor Beans.
org.anchoranalysis.bean.initializable	Initializing beans with particular parameters, including recursively.
org.anchoranalysis.bean.initializable.parameters	Some parameterization used when initializing beans.
org.anchoranalysis.bean.initializable.property	Initializating a bean with parameters.
org.anchoranalysis.bean.permute	Applying permutations to a bean's fields.
org.anchoranalysis.bean.permute.assign	Imposes a permutation value on one or more properties of a bean.
org.anchoranalysis.bean.permute.property	Applying permutations to the properties of a bean.
org.anchoranalysis.bean.primitive	Beans that implement collections of primitive element types, as well as String.
org.anchoranalysis.bean.shared	Utility beans which have a generally broader use than a specific module.
org.anchoranalysis.bean.shared.color	Beans that specify colors.
org.anchoranalysis.bean.shared.color.scheme	Beans that create lists or indices of colors according to particular schemes.
org.anchoranalysis.bean.shared.dictionary	Setting, referencing and initializing key-value parameters.
org.anchoranalysis.bean.shared.path	Defines a root path directory on the filesystem whre files are read / written.
org.anchoranalysis.bean.shared.random	Specifies a particular type of random-number generator.
org.anchoranalysis.bean.shared.regex	Specifies regular-expressions.
org.anchoranalysis.bean.shared.relation	Specifies a binary relation of some kind between scalars.
org.anchoranalysis.bean.shared.relation.threshold	Specifies a unary relation to a threshold value.
org.anchoranalysis.bean.xml	Reading Beans from XML files.
org.anchoranalysis.bean.xml.creator	Creates beans from XML.
org.anchoranalysis.bean.xml.exception	Exceptions that can thrown when loading beans from XML.
org.anchoranalysis.bean.xml.factory	Custom factories for loading beans in custom ways from XML.
org.anchoranalysis.bean.xml.factory.primitive	Factories to create beans in org.anchoranalysis.bean.primitive.
org.anchoranalysis.core.cache	Caching (memozing) calls to a method so an operation does not need to be repeated.
org.anchoranalysis.core.collection	Collection-related classes with general applicability that don't belong elsewhere.
org.anchoranalysis.core.color	Specifying particular colors and groups of colors.
org.anchoranalysis.core.exception	Very general exceptions and base classes for exceptions with wide applicability.
org.anchoranalysis.core.exception.combinable	Nested exceptions of similar type that can be combined together in a summary.
org.anchoranalysis.core.exception.friendly	Particular types of exceptions that are guaranteed to have a text/form that gives user-friendly error descriptions.
org.anchoranalysis.core.format	File formats and associated extensions.
org.anchoranalysis.core.functional	Utilities and interfaces for applying functional-programming.
org.anchoranalysis.core.functional.checked	Versions of many functional-interfaces in java.util.function that throw checked-exceptions.
org.anchoranalysis.core.functional.unchecked	Adds additional functional-interfaces, that are unavailable in java.util.function, and do not throw checked exceptions.
org.anchoranalysis.core.graph	Data-structures for directed and undirected graphs, with or without an edge payload.
org.anchoranalysis.core.identifier.getter	Data structures for adding a unique name (a String or integer identifier) to other entities.
org.anchoranalysis.core.identifier.name	Data structures for name (String) and value associations.
org.anchoranalysis.core.identifier.provider	A collection of named-elements, a NamedProvider and related operations.
org.anchoranalysis.core.identifier.provider.store	Data structures like NamedProvider with supporting for adding new elements.
org.anchoranalysis.core.index	Classes to support getting / setting / specifying unique-integers (indices) for elements.
org.anchoranalysis.core.index.range	A range of indices from minimum to maximum.
org.anchoranalysis.core.log	Interfaces to log messages, both information and error messages.
org.anchoranalysis.core.log.error	Mechanism for reporting errors (exceptions/throwables) to the user.
org.anchoranalysis.core.random	Generating random numbers.
org.anchoranalysis.core.serialize	Utilities for serializing and deserializing objects.
org.anchoranalysis.core.system	Utilities for interacting with the operating system or computer system generally
org.anchoranalysis.core.system.path	Utilities for converting/manipulating file-paths.
org.anchoranalysis.core.time	Recording the execution-time of operations for profiling.
org.anchoranalysis.core.value	Encapsulating values or sets of named-values.
org.anchoranalysis.experiment	Classes related to executing an experiment by calling jobs on inputs.
org.anchoranalysis.experiment.arguments	Arguments that can further specify an experiment in addition to its bean specification.
org.anchoranalysis.experiment.bean	Beans related to executing an experiment by calling jobs on inputs.
org.anchoranalysis.experiment.bean.identifier	Assigning unique names to experiments.
org.anchoranalysis.experiment.bean.io	Generic experiments that handle input and output in structured ways.
org.anchoranalysis.experiment.bean.log	Different approaches to where messages on the progress/status of an experiment are logged to.
org.anchoranalysis.experiment.bean.processor	How a task is executed on multiple inputs.
org.anchoranalysis.experiment.bean.require	A test whether certain conditions on arguments to experiments are fulfilled.
org.anchoranalysis.experiment.bean.task	Defines a task, which is a set of operations run on an input, that may or may not generate an output.
org.anchoranalysis.experiment.io	Interfaces for replacing attributes of an experiment: input, output, task etc.
org.anchoranalysis.experiment.log	Helpful classes for logging.
org.anchoranalysis.experiment.task	Non-bean classes related to a Task.
org.anchoranalysis.experiment.task.processor	Non-bean classes related to JobProcessor.
org.anchoranalysis.experiment.time	How long particular operations take to execute.
org.anchoranalysis.feature.bean	Beans pertaining to feature-calculation.
org.anchoranalysis.feature.bean.list	A feature-list (custom list type for features) and associated providers.
org.anchoranalysis.feature.bean.operator	Features that are sufficiently generic to work on any input-type.
org.anchoranalysis.feature.bean.provider	Provider of a single feature.
org.anchoranalysis.feature.bean.results	Defines base class FeatureResults together with some implementations.
org.anchoranalysis.feature.calculate	Sub-feature units of calculation that can be cached.
org.anchoranalysis.feature.calculate.bound	Interfaces like FeatureCalculator but bound to particular features.
org.anchoranalysis.feature.calculate.cache	Classes to cache feature-results or parts of feature-results that occur repeatedly among features or across calculations of the same feature.
org.anchoranalysis.feature.calculate.cache.part	Equivalent classes to org.anchoranalysis.feature.calculate.part after having been resolved against a cache.
org.anchoranalysis.feature.calculate.part	A sub-part of the calculation of a feature, that can be cached, and reused by other features.
org.anchoranalysis.feature.energy	A particular stack used in feature-calculations called a EnergyStack together with related classes.
org.anchoranalysis.feature.initialization	Initialization parameters used for beans in org.anchoranalysis.feature.bean.
org.anchoranalysis.feature.input	Base classes providing inputs to feature calculations.
org.anchoranalysis.feature.io.csv	Metadata for writing feature calculation-results in CSV format.
org.anchoranalysis.feature.io.csv.metadata	Writing the results of feature calculations to the file-system.
org.anchoranalysis.feature.io.csv.results	Writing the results from feature-calculation to a CSV file.
org.anchoranalysis.feature.io.csv.table	A Generator for writing a table of feature values as a CSV.
org.anchoranalysis.feature.io.name	Naming items in a weay that breaks down into multiple elements.
org.anchoranalysis.feature.io.results	Writes feature-calculation results in different formats, also grouped results.
org.anchoranalysis.feature.io.results.group	Various different outputs that can be written for the a grouped version of the results in LabelledResultsCollector.
org.anchoranalysis.feature.name	Data objects for the names of features.
org.anchoranalysis.feature.results	Results from one or more feature calculations.
org.anchoranalysis.feature.session	A defined context in which one or more features are provided inputs and produce results.
org.anchoranalysis.feature.session.cache	Creates a FeatureCalculationCache to use during feature-calculations.
org.anchoranalysis.feature.session.cache.finder	Strategies to determine which child-cache (among hierarchy) to employ for a particular feature calculation.
org.anchoranalysis.feature.session.calculator	Base classes for methods to calculate results from features.
org.anchoranalysis.feature.session.replace	Strategies on whether to reuse or invalidate a feature-input's cache.
org.anchoranalysis.feature.shared	Features shared for referencing among calculations.
org.anchoranalysis.feature.store	A collection of named-Features.
org.anchoranalysis.image.bean	Core (bean) classes for image processing.
org.anchoranalysis.image.bean.channel	Base classes for performing operations on Channels.
org.anchoranalysis.image.bean.displayer
org.anchoranalysis.image.bean.interpolator	Beans for specifying image interpolators.
org.anchoranalysis.image.bean.nonbean	Classes that are used elsewhere in this package but which aren't themselves AnchorBeans.
org.anchoranalysis.image.bean.nonbean.init	Classes that aren't AnchorBeans that pertain to the initialization of image-related beans.
org.anchoranalysis.image.bean.nonbean.segment	Non-bean classes relating to image-segmentation.
org.anchoranalysis.image.bean.nonbean.spatial.align	Non-bean classes to help specify the position of one entity relative to the others.
org.anchoranalysis.image.bean.nonbean.spatial.arrange	Non-beans to specify how to form a single-image by spatially combining other images.
org.anchoranalysis.image.bean.object	Beans pertaining to ObjectMask and their collections.
org.anchoranalysis.image.bean.provider	Base classes for providers of different core data entities related to images.
org.anchoranalysis.image.bean.provider.stack	A provider of Stacks.
org.anchoranalysis.image.bean.segment	Base classes to perform image segmentation, transforming an image into another meaningful entity or entities.
org.anchoranalysis.image.bean.segment.binary	Base classes to perform binary-segmentation.
org.anchoranalysis.image.bean.segment.object	Base classes to segment a channel into objects.
org.anchoranalysis.image.bean.spatial	Beans to define entities or operate that consider Euclidian space.
org.anchoranalysis.image.bean.spatial.arrange	Beans to specify how to form a single-image by spatially combining other images.
org.anchoranalysis.image.bean.spatial.arrange.align	Aligning a BoundingBox to fit inside another BoundingBox.
org.anchoranalysis.image.bean.spatial.arrange.fill	Montages images together to completely fill the available space, while preserving aspect ratio.
org.anchoranalysis.image.bean.spatial.arrange.overlay	Combining other images through overlaying.
org.anchoranalysis.image.bean.spatial.arrange.tile	Combining other images through tiling.
org.anchoranalysis.image.bean.spatial.direction	Beans to specify a direction.
org.anchoranalysis.image.bean.threshold	Base classes for thresholding and calculating levels for thresholding.
org.anchoranalysis.image.bean.threshold.relation	Reusable relations to a threshold.
org.anchoranalysis.image.bean.unitvalue.distance	Converting quantities of distance between units.
org.anchoranalysis.image.bean.unitvalue.extent	Converting quantities of extent (area or volume) between units.
org.anchoranalysis.image.bean.unitvalue.extent.area	Converting quantities of area between units.
org.anchoranalysis.image.bean.unitvalue.extent.volume	Converting quantities of volume between units.
org.anchoranalysis.image.core.bufferedimage	Conversions and operations involving Java AWT's BufferedImage.
org.anchoranalysis.image.core.channel	The Channel core data-class and related operations and converters.
org.anchoranalysis.image.core.channel.convert	Converts a channel to other data-types.
org.anchoranalysis.image.core.channel.convert.attached	Converts a channel to another data-type based upon another object to which it is attached.
org.anchoranalysis.image.core.channel.convert.attached.channel	Converts a channel to another data-type based upon a Channel to which it is attached.
org.anchoranalysis.image.core.channel.convert.attached.histogram	Converts a channel to another data-type based upon a Histogram to which it is attached.
org.anchoranalysis.image.core.channel.factory	Factory classes for creating Channel for various voxel data-types.
org.anchoranalysis.image.core.contour	Finds outline voxels, the pixels on the contour/edge of the object.
org.anchoranalysis.image.core.dimensions	Classes to describe the size of images or components of images both in voxels and physically.
org.anchoranalysis.image.core.dimensions.size.suggestion	Suggestions on a size for an image.
org.anchoranalysis.image.core.mask	An image with only two permissible states.
org.anchoranalysis.image.core.mask.combine	Binary operations involving voxelwise combination of Mask.
org.anchoranalysis.image.core.merge	Merges two or more entities.
org.anchoranalysis.image.core.object	The key data entity org.anchoranalysis.image.voxel.object and related-classes and operations.
org.anchoranalysis.image.core.object.label	Labelling elements (object-masks or similar) with unique successive integers in a channel.
org.anchoranalysis.image.core.object.properties	An ObjectCollection with associated key-value pairs.
org.anchoranalysis.image.core.object.scale	Scaling object-collections, or lists of elements with object-representations.
org.anchoranalysis.image.core.object.scale.method	Scaling elements with an associated ObjectMask either collectively or independently.
org.anchoranalysis.image.core.points	Operations that extract points from image data entities or vice versa.
org.anchoranalysis.image.core.stack	Defines the key data object, Stack, and related classes.
org.anchoranalysis.image.core.stack.named	A collection of Stacks, each with a unique identifier as a name.
org.anchoranalysis.image.feature.bean	Beans pertaining to feature definition and calculation.
org.anchoranalysis.image.feature.bean.evaluator	Beans that define context (which feature, which energy-stack) for evaluating feature-inputs.
org.anchoranalysis.image.feature.bean.histogram	Features that operate on a Histogram.
org.anchoranalysis.image.feature.bean.object.collection	Features that operate on a ObjectCollection.
org.anchoranalysis.image.feature.bean.object.pair	Features that operate on a pair of ObjectMasks.
org.anchoranalysis.image.feature.bean.object.single	Features that operate on a single ObjectMask.
org.anchoranalysis.image.feature.bean.physical	Features that convert to/from physical spatial units (e.g.
org.anchoranalysis.image.feature.calculation	Reusable implementations of CalculationPart related to images.
org.anchoranalysis.image.feature.calculator	Implementations of FeatureCalculatorMulti related to images, especially to create tables of feature-calculations.
org.anchoranalysis.image.feature.calculator.merged	A particular implementation of FeatureCalculatorMulti for feature-calculations based upon pairs of image-objects.
org.anchoranalysis.image.feature.input	Image-related implementations of FeatureInput.
org.anchoranalysis.image.inference	Inference of machine learning models on images.
org.anchoranalysis.image.inference.bean.reduce	Beans to reduce the number of results that are returned from inference, by removing overlaping entities etc.
org.anchoranalysis.image.inference.bean.segment.instance	Instance-segmentation of a Stack.
org.anchoranalysis.image.inference.bean.segment.reduce	Non-bean classes to reduce the number of results that are returned from inference, by removing overlapping entities etc.
org.anchoranalysis.image.inference.segment	Non-beans pertaining to segmentation of images via model inference.
org.anchoranalysis.image.io	Reading and writing of image-related data objects to and from the filesystem.
org.anchoranalysis.image.io.bean.channel	Beans pertaining to reading Channels as input.
org.anchoranalysis.image.io.bean.object.draw	How to represent an object-mask in a raster that is being drawn.
org.anchoranalysis.image.io.bean.object.feature	Beans to specify the outputting of features into CSV from a ObjectCollection.
org.anchoranalysis.image.io.bean.stack.combine	Beans to combine multiple stacks into a single stack before outputting.
org.anchoranalysis.image.io.bean.stack.metadata.reader	Bean classes for reading ImageMetadata from the file-system.
org.anchoranalysis.image.io.bean.stack.reader	Bean classes for reading raster-files from the filesystem.
org.anchoranalysis.image.io.bean.stack.writer	Bean classes for writing raster-files to the filesystem.
org.anchoranalysis.image.io.channel.input	Non-bean classes for reading a Channel from the filesystem.
org.anchoranalysis.image.io.channel.map	Non-bean classes for a mapping of names to Channels.
org.anchoranalysis.image.io.channel.output	Non-bean classes for writing a Channel to the filesystem.
org.anchoranalysis.image.io.histogram.input	Non-bean classes for reading a Histogram from the filesystem.
org.anchoranalysis.image.io.histogram.output	Non-bean classes for writing a Histogram to the filesystem.
org.anchoranalysis.image.io.object	Non-bean classes for reading / writing an ObjectCollection from and to the filesystem.
org.anchoranalysis.image.io.object.input	Non-bean classes for reading an ObjectCollection from the filesystem.
org.anchoranalysis.image.io.object.output.grayscale	Writing an ObjectCollection to the filesystem as a single-channeled stack.
org.anchoranalysis.image.io.object.output.hdf5	Writing an ObjectCollection to the filesystem in HDF5 format.
org.anchoranalysis.image.io.object.output.mask	Writing an ObjectCollection to the filesystem as multiple binary singled-channeled images.
org.anchoranalysis.image.io.object.output.rgb	Writing an ObjectCollection to the filesystem as RGB raster-images.
org.anchoranalysis.image.io.stack	Non-bean classes for reading / writing a Stack from and to the filesystem.
org.anchoranalysis.image.io.stack.input	Non-bean classes for reading a Stack from the filesystem.
org.anchoranalysis.image.io.stack.output	Non-bean classes for writing a Stack to the filesystem.
org.anchoranalysis.image.io.stack.output.box	Base classes for generators that ultimately write only a bounding-box portion of a Stack to the filesystem.
org.anchoranalysis.image.io.stack.output.generator	Base classes for generators that ultimately write a Stack to the filesystem.
org.anchoranalysis.image.io.stack.time	A time-sequence of Stacks.
org.anchoranalysis.image.voxel	Data-structures to store and manipulate image raster-data or voxels.
org.anchoranalysis.image.voxel.arithmetic	Arithmetic operations for Voxels.
org.anchoranalysis.image.voxel.assigner	Assigns values to some or all voxels.
org.anchoranalysis.image.voxel.binary	The BinaryVoxels class and related operations.
org.anchoranalysis.image.voxel.binary.connected	Creating an ObjectCollection that is a connected component labelling of a BinaryVoxels.
org.anchoranalysis.image.voxel.binary.values	Defining on and off intensity-values to interpret an image in a binary way.
org.anchoranalysis.image.voxel.buffer	A buffer of voxel-values, usually corresponding to a single z-slice in Voxels.
org.anchoranalysis.image.voxel.buffer.primitive	Conversion of both primitive data types and image structures between Anchor's data-structures and other representations.
org.anchoranalysis.image.voxel.buffer.slice	A container with voxel-buffers for each z-slice.
org.anchoranalysis.image.voxel.convert	Converting Voxels to different data-types.
org.anchoranalysis.image.voxel.convert.bufferedimage	Converts anchor data-structures to the BufferedImage used by Java's AWT.
org.anchoranalysis.image.voxel.convert.imglib2	Converts anchor data-structures to those used by ImgLib2.
org.anchoranalysis.image.voxel.datatype	The different data-types that can be used to represent voxels.
org.anchoranalysis.image.voxel.extracter	Methods to read/copy/duplicate portions of voxels.
org.anchoranalysis.image.voxel.extracter.predicate	Methods to find or count voxels that satisfy a predicate.
org.anchoranalysis.image.voxel.factory	Creates new instances of Voxels and VoxelsUntyped with specific data-types.
org.anchoranalysis.image.voxel.iterator	Utilities to iterate over voxel-locations in images and sub-regions of images.
org.anchoranalysis.image.voxel.iterator.intersecting	Like org.anchoranalysis.image.voxel.iterator but refers to iterators that operation over the intersecting regions of two entities.
org.anchoranalysis.image.voxel.iterator.neighbor	Iterating over a point's neighboring voxels.
org.anchoranalysis.image.voxel.iterator.neighbor.kernel	Routines for moving a KernelPointCursor around the neighboring voxels of the point.
org.anchoranalysis.image.voxel.iterator.predicate	Functional-interfaces for processing different combinations of points and buffers that return a boolean.
org.anchoranalysis.image.voxel.iterator.process	Functional-interfaces for processing different combinations of points and buffers that do not return a value.
org.anchoranalysis.image.voxel.iterator.process.buffer	Functional-interfaces for processing different combinations of points and raw buffers, but not VoxelBuffer.
org.anchoranalysis.image.voxel.iterator.process.voxelbuffer	Functional-interfaces for processing different combinations of points and VoxelBuffer but not raw buffers.
org.anchoranalysis.image.voxel.kernel	Applying a kernel via convolution to voxels.
org.anchoranalysis.image.voxel.kernel.count	Kernels to count the number of voxels that are equal to a particular value.
org.anchoranalysis.image.voxel.kernel.morphological	Kernels that apply morphological operations.
org.anchoranalysis.image.voxel.kernel.outline	Kernel to find outline voxels on an object.
org.anchoranalysis.image.voxel.neighborhood	A region in proximity to a voxel, encompassing this voxel as well as others.
org.anchoranalysis.image.voxel.object	The fundamental data class that is an ObjectMask and related structures.
org.anchoranalysis.image.voxel.object.morphological	Morphological operations applied to ObjectMasks.
org.anchoranalysis.image.voxel.object.morphological.predicate	Predicates to match certain voxels as used in org.anchoranalysis.image.voxel.object.morphological.
org.anchoranalysis.image.voxel.projection	Classes for calculating differnet kind of projections of voxel values across multiple buffers.
org.anchoranalysis.image.voxel.projection.extrema	Classes for performing both a Maximum Intensity Projection and a minimum projection.
org.anchoranalysis.image.voxel.resizer	Different interpolator methods to use when scaling voxels.
org.anchoranalysis.image.voxel.statistics	Statistics about aggregated voxel intensities.
org.anchoranalysis.image.voxel.thresholder	Thresholding operations on voxels.
org.anchoranalysis.inference	High-level classes for performing machine learning model inference.
org.anchoranalysis.inference.concurrency	Specifying how many CPUs and GPUs can be allocated for some purpose.
org.anchoranalysis.io.bioformats	Non-bean classes for filesystem I/O using Bioformats.
org.anchoranalysis.io.bioformats.bean	Beans for filesystem I/O using Bioformats.
org.anchoranalysis.io.bioformats.bean.options	User-specified options that can modify metadata or other attributes of a loaded Bioformats image.
org.anchoranalysis.io.bioformats.bean.writer	Writing stacks to the file system using the Bioformats library.
org.anchoranalysis.io.bioformats.copyconvert	Converts the byte stream opened by Bioformats into channels of particular data-type.
org.anchoranalysis.io.bioformats.copyconvert.tobyte	Converts the byte stream opened by Bioformats into channels of ByteBuffer.
org.anchoranalysis.io.bioformats.copyconvert.tofloat	Converts the byte stream opened by Bioformats into channels of FloatBuffer.
org.anchoranalysis.io.bioformats.copyconvert.toint	Converts the byte stream opened by Bioformats into channels of IntBuffer.
org.anchoranalysis.io.bioformats.copyconvert.toshort	Converts the byte stream opened by Bioformats into channels of ShortBuffer.
org.anchoranalysis.io.bioformats.metadata	Reading metadata information from files using EXIF and/or other metadata headers.
org.anchoranalysis.io.generator	Base-classes and utilities for generators, which write different types of objects to the file system.
org.anchoranalysis.io.generator.collection	Outputting more than one element collectively using a generator.
org.anchoranalysis.io.generator.combined	Combining multiple generators into one.
org.anchoranalysis.io.generator.sequence	Writing a sequence of elements using a generator.
org.anchoranalysis.io.generator.sequence.pattern	A particular naming pattern files follow when outputted.
org.anchoranalysis.io.generator.serialized	Generators for writing serialized objects.
org.anchoranalysis.io.generator.tabular	Generators for writing tabular data, including CSV.
org.anchoranalysis.io.generator.text	Generators for writing textual data, including strings.
org.anchoranalysis.io.generator.xml	Generators for writing XML data.
org.anchoranalysis.io.imagej.bean.interpolator	Performing interpolation with ImageJ.
org.anchoranalysis.io.imagej.bean.stack.writer	Raster-writers that use ImageJ to write images to the filesystem.
org.anchoranalysis.io.imagej.convert	Converts to and from ImageJ data-structures for images.
org.anchoranalysis.io.imagej.resizer	Image interpolation when scaling using ImageJ.
org.anchoranalysis.io.input	Classes relating to creating inputs for an experiment / task.
org.anchoranalysis.io.input.bean	Beans related to collecting inputs from the file-system for an experiment.
org.anchoranalysis.io.input.bean.dictionary	Methods to provide a Dictionary.
org.anchoranalysis.io.input.bean.files	Methods to provide a collection of Files.
org.anchoranalysis.io.input.bean.grouper	Determines how inputs are aggregated into groups, if at all.
org.anchoranalysis.io.input.bean.namer	Beans to derive names (compact unique identifiers) from files.
org.anchoranalysis.io.input.bean.path	Beans pertaining to manipulating and matching against file-paths.
org.anchoranalysis.io.input.bean.path.matcher	Beans to find a subset of files that match a particular conditions on their paths.
org.anchoranalysis.io.input.bean.path.provider	Methods to provide a single file-path.
org.anchoranalysis.io.input.csv	Classes for reading comma-separated-values (CSV) files.
org.anchoranalysis.io.input.file	Non-bean classes that relate to using files during inputting.
org.anchoranalysis.io.input.grouper	Non-bean classes pertaining grouping inputs.
org.anchoranalysis.io.input.path	Non-bean classes pertaining to getting/extracting/manipulating paths as used in inputting.
org.anchoranalysis.io.input.path.matcher	Non-bean classes to help with org.anchoranalysis.io.input.bean.path.matcher.
org.anchoranalysis.io.output.bean	Beans for the framework around writing files to the file-system.
org.anchoranalysis.io.output.bean.enabled	Beans indicating whether a particular output is enabled or not.
org.anchoranalysis.io.output.bean.path.prefixer	Beans for generating paths for outputting files by adding a prefix, suffix etc.
org.anchoranalysis.io.output.bean.rules	Rules for determining if a particular output is enabled or not in a context of a hierarchy.
org.anchoranalysis.io.output.enabled	Non-beans pertaining to whether a particular output is enabled or not.
org.anchoranalysis.io.output.enabled.multi	Non-beans that pertain to whether multiple-levels have outputs that are enabled or not.
org.anchoranalysis.io.output.enabled.single	Non-beans that pertain to whether a single level has outputs that are enabled or not.
org.anchoranalysis.io.output.error	Exceptions that may be thrown when writing files to the file-system.
org.anchoranalysis.io.output.namestyle	Methods of naming a file with an index in the file-name.
org.anchoranalysis.io.output.outputter	Classes for outputting to particular directories.
org.anchoranalysis.io.output.outputter.directory	BoundDirectory and related classes.
org.anchoranalysis.io.output.path.prefixer	Non-beans for generating paths for outputting files by adding a prefix, suffix etc.
org.anchoranalysis.io.output.recorded	Classes for recording the output-names used as they are written / queried.
org.anchoranalysis.io.output.writer	Allows a generators to write element(s) to the filesystem.
org.anchoranalysis.io.output.xml	Outputting XML to the file-system.
org.anchoranalysis.launcher	Parent package and entry-point classes for the Anchor command-line launcher application.
org.anchoranalysis.launcher.config	Specifies a configuration of the launcher for a particular application.
org.anchoranalysis.launcher.executor	Runs a particular experiment after identifying necessary paths and input files.
org.anchoranalysis.launcher.executor.selectparam	Different methods of selecting a object T that is used as a parameter for an experiment.
org.anchoranalysis.launcher.executor.selectparam.experiment	SelectParams for loading a Experiment.
org.anchoranalysis.launcher.executor.selectparam.path	SelectParams for loading a Optional<Path> for inputs, outputs or tasks.
org.anchoranalysis.launcher.executor.selectparam.path.convert	Converting paths to/from different formats as needed by org.anchoranalysis.launcher.executor.selectparam.path.
org.anchoranalysis.launcher.options	A centralized location for all command-line options used by the launcher.
org.anchoranalysis.launcher.options.process	Adding/removing/changing the arguments (input and output) from the experiment via command-line-options.
org.anchoranalysis.launcher.resources	Reading and integrating resources for the launcher.
org.anchoranalysis.launcher.run	Parses command-line arguments and runs an experiment.
org.anchoranalysis.launcher.run.tasks	Loading and displaying pre-defined tasks.
org.anchoranalysis.math.arithmetic	Performing primitive type conversion, counting and summing.
org.anchoranalysis.math.equation	Solving or manipulating equations.
org.anchoranalysis.math.histogram	The Histogram data class and related operations.
org.anchoranalysis.math.optimization	Mathemathical optimization algorithms.
org.anchoranalysis.math.relation	Different kinds of binary-relations.
org.anchoranalysis.math.statistics	Data structures and algorithms to calculate statistics.
org.anchoranalysis.math.statistics.moment	Calculates first and second image moments from a covariance matrix of points.
org.anchoranalysis.mpp.bean	Beans pertaining to marked-point-processes.
org.anchoranalysis.mpp.bean.bound	Lower and upper limits set around variables.
org.anchoranalysis.mpp.bean.bound.rotation	Bounds on how to rotate an entity in Euclidean space.
org.anchoranalysis.mpp.bean.mark	Beans generally related to Marks.
org.anchoranalysis.mpp.bean.mark.factory	Beans related to creating Marks.
org.anchoranalysis.mpp.bean.points	Operations based on sets of points.
org.anchoranalysis.mpp.bean.points.fitter	Fitting structures to sets of points.
org.anchoranalysis.mpp.bean.proposer	Proposing Marks or other data-structures with particular attributes.
org.anchoranalysis.mpp.bean.provider	Implementations of Provider involving Marks.
org.anchoranalysis.mpp.bean.regionmap	Voxel subregions of Marks.
org.anchoranalysis.mpp.feature.addcriteria	Criteria for adding edges during optimization of marked-point-processes.
org.anchoranalysis.mpp.feature.bean.energy.element	Implementations and helper classes for calculating energy during an energy-minimization optimization scheme.
org.anchoranalysis.mpp.feature.bean.energy.scheme	Creating EnergySchemes.
org.anchoranalysis.mpp.feature.bean.mark	Features calculated on a Mark.
org.anchoranalysis.mpp.feature.bean.mark.collection	Features calculated on a org.anchoranalysis.mpp.feature.bean.mark.collection.
org.anchoranalysis.mpp.feature.energy	Non-bean classes pertaining to calculating energy during an energy-minimization optimization scheme.
org.anchoranalysis.mpp.feature.energy.marks	Non-bean classes pertaining to calculating energy of {org.anchoranalysis.mpp.mark.Mark}s.
org.anchoranalysis.mpp.feature.energy.saved	Saved snapshots of energy-calculations.
org.anchoranalysis.mpp.feature.energy.scheme	Factorized form of storing the energy during an energy-minimization optimization scheme.
org.anchoranalysis.mpp.feature.error	Exceptions relating to Features involving classes from anchor-mpp.
org.anchoranalysis.mpp.feature.input	Inputs to mark-point-processes related Features.
org.anchoranalysis.mpp.feature.mark	Non-bean classes for calculating feature-values related to Marks.
org.anchoranalysis.mpp.index	Indexing voxel-values in different ways.
org.anchoranalysis.mpp.index.factory	Factories for classes in org.anchoranalysis.mpp.index.
org.anchoranalysis.mpp.init	Parameters used to initialize certain types of beans.
org.anchoranalysis.mpp.io.bean.input	Beans for reading data structures related to marked point processes from the file system.
org.anchoranalysis.mpp.io.bean.report.feature	Beans for communicating feature-values from data-structures in human-readable manner.
org.anchoranalysis.mpp.io.input	Non-beans for reading data structures related to marked point processes from the file system.
org.anchoranalysis.mpp.io.marks	Non-beans to help write visualization of Marks to the filesystem.
org.anchoranalysis.mpp.io.marks.generator	Generator base classes to help write visualization of Marks to the filesystem.
org.anchoranalysis.mpp.io.output	Non-beans for writing data structures related to marked point processes from the file system.
org.anchoranalysis.mpp.mark	Non-bean classes related to Marks.
org.anchoranalysis.mpp.mark.conic	Marks implementing conic sections.
org.anchoranalysis.mpp.mark.points	Marks implementing structures based on points.
org.anchoranalysis.mpp.mark.voxelized	A mark after a voxel-representation has been inferred.
org.anchoranalysis.mpp.mark.voxelized.memo	Memoization of VoxelizedMarks.
org.anchoranalysis.mpp.overlap	Calculating overlaps between two Marks.
org.anchoranalysis.mpp.overlay	Any Overlay related to a Mark.
org.anchoranalysis.mpp.pair	Pairs of Marks.
org.anchoranalysis.mpp.proposer	Non-bean classes for proposing Marks or other data-structures with particular attributes.
org.anchoranalysis.mpp.proposer.error	Recording errors related to proposing Marks or other data-structures with particular attributes.
org.anchoranalysis.mpp.segment.bean	Beans for segmentation algorithms related to marked-point-processes.
org.anchoranalysis.mpp.segment.bean.define	DefineOutputter and its sub-classes.
org.anchoranalysis.mpp.segment.bean.optimization	Schemes for finding optima (minima or maxima) via optimization.
org.anchoranalysis.mpp.segment.bean.optimization.feedback	Providing feedback on the progress of a OptimizationScheme.
org.anchoranalysis.mpp.segment.bean.optimization.kernel	Base classes for kernels that transition a configuration of marks (a MarkCollection) into an altered version.
org.anchoranalysis.mpp.segment.bean.optimization.termination	In which circumstances to terminate an OptimizationScheme that is underway.
org.anchoranalysis.mpp.segment.define	Non-bean classes used in org.anchoranalysis.mpp.segment.bean.define
org.anchoranalysis.mpp.segment.optimization	Non-bean classes used in org.anchoranalysis.mpp.segment.bean.optimization
org.anchoranalysis.mpp.segment.optimization.feedback	Non-bean classes used in org.anchoranalysis.mpp.segment.bean.optimization.feedback
org.anchoranalysis.mpp.segment.optimization.feedback.aggregate	Aggregating optimization feedback over time.
org.anchoranalysis.mpp.segment.optimization.feedback.period	Collecting optimization feedback periodically.
org.anchoranalysis.mpp.segment.optimization.kernel	Non-bean classes used in org.anchoranalysis.mpp.segment.bean.optimization.kernel
org.anchoranalysis.mpp.segment.optimization.step	Describes an individual step in the optimization.
org.anchoranalysis.mpp.segment.transformer	Mapping one type of optimization state to another.
org.anchoranalysis.overlay	Overlays and related classes involving drawing entities on top of an image.
org.anchoranalysis.overlay.bean	Beans relating to drawing an Overlay on an image.
org.anchoranalysis.overlay.collection	Collections of Overlays.
org.anchoranalysis.overlay.object	An implementation of an Overlay that draws an ObjectMask on an image.
org.anchoranalysis.overlay.writer	Drawing an overlay on an image.
org.anchoranalysis.plugin.annotation.bean.aggregate	Beans to combine two or more annotations.
org.anchoranalysis.plugin.annotation.bean.comparer	Comparing the similarity of annotations from two images to each other.
org.anchoranalysis.plugin.annotation.bean.comparison	Task to compare a set of annotations to a segmentation or another set of annotations.
org.anchoranalysis.plugin.annotation.bean.comparison.assigner	Pairs annotations from two different sets, creating an assignment of some type.
org.anchoranalysis.plugin.annotation.bean.file	FilesProviders for providing annotations.
org.anchoranalysis.plugin.annotation.bean.label	A label as used for annotating.
org.anchoranalysis.plugin.annotation.bean.strategy	Strategies for how to annotate an image, such label per image etc.
org.anchoranalysis.plugin.annotation.comparison	Non-bean classes for comparing two sets of annotations.
org.anchoranalysis.plugin.annotation.counter	Utility classes for counting images incrementally.
org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction	Morphological grayscale-reconstruction algorithm.
org.anchoranalysis.plugin.fiji.bean.channel.provider	Implementations of ChannelProvider that use FIJI.
org.anchoranalysis.plugin.fiji.bean.channel.provider.distance	Euclidean Distance Transform implementations via FIJI.
org.anchoranalysis.plugin.fiji.bean.define	Implementations of DefineAdderBean that use FIJI.
org.anchoranalysis.plugin.fiji.bean.mask.provider	Implementations of MaskProvider that use FIJI.
org.anchoranalysis.plugin.fiji.bean.threshold	Implementations of Thresholder that use FIJI.
org.anchoranalysis.plugin.image.bean.blur	Filters that perform blurring.
org.anchoranalysis.plugin.image.bean.channel.aggregator	Implementations of ConvertChannelTo and ConvertChannelToWithHistogram.
org.anchoranalysis.plugin.image.bean.channel.convert	Implementations of ConvertChannelTo and ConvertChannelToWithHistogram.
org.anchoranalysis.plugin.image.bean.channel.provider	Implementations of ChannelProvider that are generic base-classes or otherwise abstract or general.
org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic	Implementations of ChannelProvider that perform arithmetic on voxels in one or more Channels.
org.anchoranalysis.plugin.image.bean.channel.provider.assign	Implementations of ChannelProvider that sets the values of the voxels in a Channel.
org.anchoranalysis.plugin.image.bean.channel.provider.convert	Implementations of ChannelProvider that converts a Channel from one voxel-type to another.
org.anchoranalysis.plugin.image.bean.channel.provider.gradient	Implementations of ChannelProvider that calculate the gradient of a Channel's voxels in one or more dimensions.
org.anchoranalysis.plugin.image.bean.channel.provider.intensity	Implementations of ChannelProvider that manipulate the intensity-values of the voxels of a Channel's voxels.
org.anchoranalysis.plugin.image.bean.channel.provider.mask	Implementations of ChannelProvider that involve conversion from or application of Masks.
org.anchoranalysis.plugin.image.bean.channel.provider.object	Implementations of ChannelProvider that involve conversion from or application of ObjectMasks.
org.anchoranalysis.plugin.image.bean.channel.provider.score	Implementations of ChannelProvider that assign a score to particular subregions of a channel.
org.anchoranalysis.plugin.image.bean.channel.provider.slice	Implementations of ChannelProvider that process 3D channels slice-by-slice.
org.anchoranalysis.plugin.image.bean.color.provider	Implementations of ColorProvider.
org.anchoranalysis.plugin.image.bean.dictionary	Beans pertaining to Dictionary.
org.anchoranalysis.plugin.image.bean.dimensions.provider	Implementations of DimensionsProvider.
org.anchoranalysis.plugin.image.bean.histogram.provider	Implementations of HistogramProvider.
org.anchoranalysis.plugin.image.bean.histogram.threshold	Thresholding of intensity values represented in at Histogram.
org.anchoranalysis.plugin.image.bean.mask.provider	Implementations of MaskProvider.
org.anchoranalysis.plugin.image.bean.mask.provider.combine	Implementations of MaskProvider that combine existing providers.
org.anchoranalysis.plugin.image.bean.mask.provider.convert	Implementations of MaskProvider that convert providers of other types to ObjectMasks.
org.anchoranalysis.plugin.image.bean.mask.provider.morphological	Implementations of MaskProvider that implement morphological operations.
org.anchoranalysis.plugin.image.bean.mask.provider.predicate	Provides if-else conditions to a MaskProvider.
org.anchoranalysis.plugin.image.bean.mask.provider.segment	Implementations of MaskProvider where an ObjectCollection is created by segmenting a Channel.
org.anchoranalysis.plugin.image.bean.mask.provider.slice	Implementations of MaskProvider that process 3D masks slice-by-slice.
org.anchoranalysis.plugin.image.bean.object.filter	Implementations of ObjectFilter.
org.anchoranalysis.plugin.image.bean.object.filter.collective	Implementations of ObjectFilter that assess each element in a collection collectively.
org.anchoranalysis.plugin.image.bean.object.filter.combine	Implementations of ObjectFilter that combine two or more other ObjectFilters.
org.anchoranalysis.plugin.image.bean.object.filter.independent	Implementations of ObjectFilter that independently assess each element in a collection.
org.anchoranalysis.plugin.image.bean.object.match	Implementations of ObjectMatcher.
org.anchoranalysis.plugin.image.bean.object.provider	Implementations of ObjectCollectionProvider.
org.anchoranalysis.plugin.image.bean.object.provider.connected	Implementations of ObjectCollectionProvider involving connected-components.
org.anchoranalysis.plugin.image.bean.object.provider.feature	Implementations of ObjectCollectionProvider involving feature calculation.
org.anchoranalysis.plugin.image.bean.object.provider.filter	Implementations of ObjectCollectionProvider that filter objects.
org.anchoranalysis.plugin.image.bean.object.provider.mask	Implementations of ObjectCollectionProvider involving a Mask.
org.anchoranalysis.plugin.image.bean.object.provider.merge	Implementations of ObjectCollectionProvider involving merging objects together.
org.anchoranalysis.plugin.image.bean.object.provider.morphological	Implementations of ObjectCollectionProvider involving morphological operations.
org.anchoranalysis.plugin.image.bean.object.provider.segment	Implementations of ObjectCollectionProvider involving segmentation.
org.anchoranalysis.plugin.image.bean.object.provider.slice	Implementations of ObjectCollectionProvider involving z-slice processing.
org.anchoranalysis.plugin.image.bean.object.provider.split	Implementations of ObjectCollectionProvider involving splitting objects into smaller objects.
org.anchoranalysis.plugin.image.bean.object.segment.channel	Implementations of SegmentChannelIntoObjects.
org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima	Minima imposition for a Watershed transformation.
org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction	Grayscale reconstruction to support the Watershed transformation.
org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong	Implementation of a Watershed transformation based on Yeong et al.
org.anchoranalysis.plugin.image.bean.object.segment.reduce	Strategies for reducing the number of elements with a list by merging/removing lower-confidence elements that overlap.
org.anchoranalysis.plugin.image.bean.scale	Implementations of ScaleCalculator for calculating a scaling-factor from dimensions.
org.anchoranalysis.plugin.image.bean.segment.binary	Implementations of BinarySegmentation.
org.anchoranalysis.plugin.image.bean.stack.provider	Implementations of StackProvider.
org.anchoranalysis.plugin.image.bean.stack.provider.color	Implementations of StackProvider that color portions of an image.
org.anchoranalysis.plugin.image.bean.thumbnail.object	Implementations of ThumbnailFromObjects.
org.anchoranalysis.plugin.image.bean.thumbnail.stack	Implementations of ThumbnailFromStack.
org.anchoranalysis.plugin.image.channel	Non-beans for operations or calculations relating to Channels.
org.anchoranalysis.plugin.image.feature.bean.dimensions	Features that are calculated from Dimensions.
org.anchoranalysis.plugin.image.feature.bean.histogram.statistic	Implementations of FeatureHistogram that calculate statistics.
org.anchoranalysis.plugin.image.feature.bean.histogram.threshold	Implementations of FeatureHistogram that perform thresholding.
org.anchoranalysis.plugin.image.feature.bean.list	Implementations of FeatureListProvider.
org.anchoranalysis.plugin.image.feature.bean.list.pair	Implementations of FeatureListProvider with input-type FeatureInputPairObjects.
org.anchoranalysis.plugin.image.feature.bean.list.permute	Implementations of FeatureListProvider that derive new features with permuted property-values.
org.anchoranalysis.plugin.image.feature.bean.metadata	Implementations of FeatureImageMetadata.
org.anchoranalysis.plugin.image.feature.bean.morphological	Beans that affects how morphological operations occur.
org.anchoranalysis.plugin.image.feature.bean.object.collection	Implementations of FeatureObjectCollection.
org.anchoranalysis.plugin.image.feature.bean.object.combine	Features from combinations of ObjectMasks.
org.anchoranalysis.plugin.image.feature.bean.object.pair	Features from pairs of ObjectMasks.
org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap	Features that calculate the degree of overlap between two ObjectMasks.
org.anchoranalysis.plugin.image.feature.bean.object.pair.touching	Features that calculate how many other objects an ObjectMask directly neighbors.
org.anchoranalysis.plugin.image.feature.bean.object.single	Implementations of FeatureSingleObject.
org.anchoranalysis.plugin.image.feature.bean.object.single.border	Implementations of FeatureSingleObject that determine if an object lies at the border of an image.
org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox	Implementations of FeatureSingleObject that consider an object's bounding-box.
org.anchoranalysis.plugin.image.feature.bean.object.single.energy	Implementations of FeatureSingleObject that reference a particular Channel in the associated EnergyStack.
org.anchoranalysis.plugin.image.feature.bean.object.single.intensity	Implementations of FeatureSingleObject that measure an object's intensity on a corresponding Channel.
org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient	Implementations of FeatureSingleObject that measure an object's gradient from corresponding Channels storing the gradient.
org.anchoranalysis.plugin.image.feature.bean.object.single.moments	Implementations of FeatureSingleObject based on calculating image moments, with or without image intensity.
org.anchoranalysis.plugin.image.feature.bean.object.single.morphological	Implementations of FeatureSingleObject that implement morphological operations.
org.anchoranalysis.plugin.image.feature.bean.object.single.shape	Implementations of FeatureSingleObject that measure the shape of the ObjectMask.
org.anchoranalysis.plugin.image.feature.bean.object.single.shared	Implementations of FeatureSingleObject that use SharedObjects for calculations.
org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting	Implementations of FeatureSingleObject that use SharedObjects for calculations, and measure the degree of intersection between objects.
org.anchoranalysis.plugin.image.feature.bean.object.single.slice	Implementations of FeatureSingleObject that processes an object slice-by-slice in the z-dimension.
org.anchoranalysis.plugin.image.feature.bean.object.single.surface	Implementations of FeatureSingleObject that measures aspects of the surface of an ObjectMask.
org.anchoranalysis.plugin.image.feature.bean.physical	Beans involving physical units for measurement.
org.anchoranalysis.plugin.image.feature.bean.score	Implementations of VoxelScore.
org.anchoranalysis.plugin.image.feature.bean.shared	Beans involving SharedObjects.
org.anchoranalysis.plugin.image.feature.bean.shared.object	Beans involving SharedObjects and ObjectCollection.
org.anchoranalysis.plugin.image.feature.bean.stack.intensity	Implementations of FeatureStack or other features that involve processing a Stack.
org.anchoranalysis.plugin.image.feature.bean.stack.object	Implementations of FeatureStack that process an ObjectCollection.
org.anchoranalysis.plugin.image.feature.object	Non-bean classes that help calculate features from ObjectMasks.
org.anchoranalysis.plugin.image.feature.object.calculation.delegate	Implementations of CalculationPart as used by features elsewhere in this package.
org.anchoranalysis.plugin.image.feature.object.calculation.single	Implementations of CalculationPart that that process a single ObjectMask.
org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological	Implementations of CalculationPart that that process a single ObjectMask - with morphological operations.
org.anchoranalysis.plugin.image.feature.stack.calculation	Implementations of CalculationPart that process Stacks as used by features elsewhere in this package.
org.anchoranalysis.plugin.image.intensity	Non-bean for operations or calculations relating to intensity.
org.anchoranalysis.plugin.image.intensity.level	Non-beans for calculating a thresholding level from itensity values.
org.anchoranalysis.plugin.image.object	Non-beans pertaining to ObjectMasks.
org.anchoranalysis.plugin.image.object.merge	Merging ObjectMasks.
org.anchoranalysis.plugin.image.object.merge.condition	Conditions for merging ObjectMasks.
org.anchoranalysis.plugin.image.object.merge.priority	Assigning priority when merging ObjectMasks.
org.anchoranalysis.plugin.image.provider	Non-bean classes pertaining to Providers.
org.anchoranalysis.plugin.image.segment.thresholder.slice	Non-beans pertaining to segmenting a z-stack slice-by-slice.
org.anchoranalysis.plugin.image.segment.watershed.encoding	Encoding voxels in a watershed-transformation implementation.
org.anchoranalysis.plugin.image.task.bean	A parent package for many different kinds of tasks.
org.anchoranalysis.plugin.image.task.bean.combine	Combining multiple images together into a single image.
org.anchoranalysis.plugin.image.task.bean.feature	Tasks pertaining to Features.
org.anchoranalysis.plugin.image.task.bean.feature.source	Source of rows in feature-tables with FeatureSource and derived classes.
org.anchoranalysis.plugin.image.task.bean.format	Tasks for converting image-formats.
org.anchoranalysis.plugin.image.task.bean.format.convertstyle	Different approaches for converting sets of channels (RGB, independently etc.) to another image format.
org.anchoranalysis.plugin.image.task.bean.grouped	Tasks that involved stacks (usually each channel from an image) that are somehow grouped-together.
org.anchoranalysis.plugin.image.task.bean.grouped.histogram	Task(s) to export histograms of intensity values.
org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels	Selecting a subset of a set of channels.
org.anchoranalysis.plugin.image.task.bean.labeller	Associating labels with images.
org.anchoranalysis.plugin.image.task.bean.scale	Tasks to scale an image.
org.anchoranalysis.plugin.image.task.bean.segment	Tasks to segment an image.
org.anchoranalysis.plugin.image.task.bean.slice	Tasks that process on one or more slices from a z-stack.
org.anchoranalysis.plugin.image.task.channel.aggregator	Combines multiple Channels voxel-wise to form a single aggregated Channel.
org.anchoranalysis.plugin.image.task.feature	Non-bean classes pertaining to Features as used in tasks.
org.anchoranalysis.plugin.image.task.feature.calculator	Non-beans for calculating Features.
org.anchoranalysis.plugin.image.task.grouped	Non-bean classes about grouping channels or other inputs.
org.anchoranalysis.plugin.image.task.labeller	Non-bean classes about labelling images.
org.anchoranalysis.plugin.image.task.segment	Non-bean classes for image-segmentation.
org.anchoranalysis.plugin.image.task.size	Non-bean classes pertaining to determining the size of an image.
org.anchoranalysis.plugin.image.task.slice	Non-bean classes pertaining to combining stacks into a single stack.
org.anchoranalysis.plugin.image.task.stack	Non-bean classes pertaining to stacks and channels as used in tasks.
org.anchoranalysis.plugin.image.thumbnail	Non-bean classes for thumbnail creation.
org.anchoranalysis.plugin.imagej.bean.channel.provider	Implementations of ChannelProvider that call ImageJ.
org.anchoranalysis.plugin.imagej.bean.channel.provider.filter	Filters using ImageJ.
org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments	Non-linear filters using ImageJ that use the statistical moments of the intensity values in the kernel.
org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank	Non-linear filters using ImageJ that use the statistical rank of the intensity values in the kernel.
org.anchoranalysis.plugin.imagej.bean.define	Implementations of DefineAdderBean that call ImageJ.
org.anchoranalysis.plugin.imagej.bean.mask.provider	Implementations of MaskProvider that call ImageJ.
org.anchoranalysis.plugin.imagej.bean.object.provider	Implementations of ObjectCollectionProvider that call ImageJ.
org.anchoranalysis.plugin.imagej.bean.object.segment	Implementations of ObjectCollectionProvider that call ImageJ to perform segmentation.
org.anchoranalysis.plugin.imagej.bean.stack.provider	Implementations of StackProvider that call ImageJ.
org.anchoranalysis.plugin.imagej.bean.threshold	Implementations of Thresholder that call ImageJ.
org.anchoranalysis.plugin.imagej.channel.provider	Implementations of ChannelProvider that call ImageJ.
org.anchoranalysis.plugin.imagej.mask	Non-bean classes involving ObjectMask that call ImageJ.
org.anchoranalysis.plugin.io.bean.channel.map	Implementations of ChannelMapCreator.
org.anchoranalysis.plugin.io.bean.file.copy.method	Methods for copying files on the file-system.
org.anchoranalysis.plugin.io.bean.file.copy.naming	Rules for preserving or changing the naming of files when copying on the file-system.
org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster	Implementations of CopyFilesNaming that perform clustering of files.
org.anchoranalysis.plugin.io.bean.file.group	Grouping files together so that they collectively represent a single entity.
org.anchoranalysis.plugin.io.bean.file.group.check	Tests that are applied when grouping files in org.anchoranalysis.plugin.io.bean.file.group
org.anchoranalysis.plugin.io.bean.file.group.parser	Parsing file-paths to determine file-grouping in org.anchoranalysis.plugin.io.bean.file.group
org.anchoranalysis.plugin.io.bean.file.namer	Implementations of FileNamer.
org.anchoranalysis.plugin.io.bean.file.namer.patternspan	Implementations of FileNamer that look for a pattern across many files.
org.anchoranalysis.plugin.io.bean.file.path	Beans to specify a file-path.
org.anchoranalysis.plugin.io.bean.file.path.prefixer	Implementations of PathPrefixer.
org.anchoranalysis.plugin.io.bean.file.pattern	Extracting a pattern from a file-path.
org.anchoranalysis.plugin.io.bean.file.provider	Implementations of FilesProvider.
org.anchoranalysis.plugin.io.bean.grouper	Implementations of Grouper.
org.anchoranalysis.plugin.io.bean.input	Implementations of InputManager.
org.anchoranalysis.plugin.io.bean.input.channel	InputManagers that accept a set of named-channels.
org.anchoranalysis.plugin.io.bean.input.files	InputManagers that accept a set of named-files.
org.anchoranalysis.plugin.io.bean.input.files.provider	Implementations of FilesProvider.
org.anchoranalysis.plugin.io.bean.input.filter	Implementations of InputManager that filter inputs.
org.anchoranalysis.plugin.io.bean.input.stack	Implementations of InputManager that process Stacks.
org.anchoranalysis.plugin.io.bean.metadata.header	Different types of image-file-formats whose headers can provide ImageMetadata.
org.anchoranalysis.plugin.io.bean.metadata.reader	Implementations of ImageMetadataReader.
org.anchoranalysis.plugin.io.bean.path.derive	Implementations of DerivePath.
org.anchoranalysis.plugin.io.bean.stack.reader	Implementations of StackReader.
org.anchoranalysis.plugin.io.bean.stack.writer	Implementations of StackWriter.
org.anchoranalysis.plugin.io.bean.summarizer	Summarizing a set of elements into a descriptive-string.
org.anchoranalysis.plugin.io.bean.summarizer.image	Implementations of Summarizer that summarize images.
org.anchoranalysis.plugin.io.bean.summarizer.input	Implementations of Summarizer that summarize generically InputFromManagers.
org.anchoranalysis.plugin.io.bean.summarizer.path	Implementations of Summarizer that summarize generically Paths.
org.anchoranalysis.plugin.io.bean.task	Implementations of Task related to file-system I/O.
org.anchoranalysis.plugin.io.file.copy	Non-bean classes to help tasks in org.anchoranalysis.plugin.io.bean.file.copy.
org.anchoranalysis.plugin.io.input.filter	Non-bean classes to help tasks in org.anchoranalysis.plugin.io.bean.input.filter.
org.anchoranalysis.plugin.io.input.path	Non-bean classes to help in processing paths.
org.anchoranalysis.plugin.io.multifile	Non-bean classes to help use multiple files to represent a single Stack.
org.anchoranalysis.plugin.io.multifile.buffer	Buffers used in org.anchoranalysis.plugin.io.multifile.
org.anchoranalysis.plugin.io.naming.interval	How to write parts of a time-interval in a file-name.
org.anchoranalysis.plugin.io.shared	Objects used in shared-state in Tasks in this plugin.
org.anchoranalysis.plugin.io.xml	Reading and writing metadata XML.
org.anchoranalysis.plugin.ml.bean.classifier	Beans that perform classification in some way.
org.anchoranalysis.plugin.ml.bean.cluster	Beans that perform clustering in some way.
org.anchoranalysis.plugin.mpp.bean.addcriteria	Implementations of AddCriteriaPair involving Mark or related classes.
org.anchoranalysis.plugin.mpp.bean.bound	Implementations of MarkBoundsProvider.
org.anchoranalysis.plugin.mpp.bean.check	Implementations of CheckMark.
org.anchoranalysis.plugin.mpp.bean.contour	Retrieving the contour outline pixels along the exterior outer contour of an ObjectMask.
org.anchoranalysis.plugin.mpp.bean.contour.visitscheduler	The VisitScheduler and related classes, as used in TraverseOuterContourOnImage.
org.anchoranalysis.plugin.mpp.bean.define	Beans related to Define involving Mark or related classes.
org.anchoranalysis.plugin.mpp.bean.object.provider	Implementations of ObjectCollectionProvider.
org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection	Implementations of MarkCollectionProposer.
org.anchoranalysis.plugin.mpp.bean.proposer.mark.single	Implementations of MarkProposer.
org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection	Implementations of MarkFromCollectionProposer.
org.anchoranalysis.plugin.mpp.bean.proposer.merge	Implementations of MarkMergeProposer.
org.anchoranalysis.plugin.mpp.bean.proposer.orientation	Implementations of OrientationProposer.
org.anchoranalysis.plugin.mpp.bean.proposer.points	Implementations of PointsProposer.
org.anchoranalysis.plugin.mpp.bean.proposer.points.contour	Finding a point on the external outer contour of an ObjectMask.
org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation	PointsFromOrientationProposer and implementations.
org.anchoranalysis.plugin.mpp.bean.proposer.position	Implementations of PositionProposer involving Mark or related classes.
org.anchoranalysis.plugin.mpp.bean.proposer.radii	Implementations of RadiiProposer involving Mark or related classes.
org.anchoranalysis.plugin.mpp.bean.proposer.scalar	Implementations of ScalarProposer involving Mark or related classes.
org.anchoranalysis.plugin.mpp.bean.proposer.split	Implementations of MarkSplitProposer.
org.anchoranalysis.plugin.mpp.bean.provider.collection	Implementation of MarkCollectionProvider.
org.anchoranalysis.plugin.mpp.bean.provider.single	Implementations of SingleMarkProvider.
org.anchoranalysis.plugin.mpp.bean.region	Implementations of MarkRegion.
org.anchoranalysis.plugin.mpp.bean.segment.binary	Implementations of BinarySegmentation involving Mark or related classes.
org.anchoranalysis.plugin.mpp.bean.stack.provider	Implementations of StackProvider involving Mark or related classes.
org.anchoranalysis.plugin.mpp.contour	Performs a walk on every voxel on the contour of an object-mask.
org.anchoranalysis.plugin.mpp.contour.distance	A list of visited pixels which forms one contiguous path where each voxel neighbors each other.
org.anchoranalysis.plugin.mpp.contour.path	A set of contiguously neighboring points along the outline of an object.
org.anchoranalysis.plugin.mpp.contour.path.merge	Merging multiple ContiguousVoxelPath together.
org.anchoranalysis.plugin.mpp.contour.path.merge.strategy	Strategies on which ContiguousVoxelPath should be prioritized for merging.
org.anchoranalysis.plugin.mpp.experiment.bean.convert	Converting from NamedChannelsInput to the input-type expected by a Task.
org.anchoranalysis.plugin.mpp.experiment.bean.define	Tasks that use a DefineOutputter or related classes.
org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task	Tasks that calculate and export ReportFeatures.
org.anchoranalysis.plugin.mpp.experiment.bean.feature.source	Implementations of FeatureSource.
org.anchoranalysis.plugin.mpp.experiment.bean.objects	Tasks involving ObjectMasks.
org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition	Defining columns used in ExportObjectsFromCSV.
org.anchoranalysis.plugin.mpp.experiment.bean.segment	Tasks that segment an image to produce a MarkCollection.
org.anchoranalysis.plugin.mpp.experiment.objects	Non-bean classes used in org.anchoranalysis.plugin.mpp.experiment.bean.objects.
org.anchoranalysis.plugin.mpp.experiment.objects.csv	Reading rows from a CSV file.
org.anchoranalysis.plugin.mpp.experiment.shared	Shared-state use across tasks in this JAR.
org.anchoranalysis.plugin.mpp.feature.bean.mark.collection	Implementations of FeatureMarkCollection.
org.anchoranalysis.plugin.mpp.feature.bean.mark.direction	Implementations of FeatureMark to measure direction.
org.anchoranalysis.plugin.mpp.feature.bean.mark.radii	Implementations of FeatureMark to measure or calculate radii.
org.anchoranalysis.plugin.mpp.feature.bean.mark.region	Implementations of FeatureMark to measure regions of Marks.
org.anchoranalysis.plugin.mpp.feature.bean.memo.all	Implementations of FeatureAllMemo.
org.anchoranalysis.plugin.mpp.feature.bean.memo.ind	Implementations of FeatureSingleMemo.
org.anchoranalysis.plugin.mpp.feature.bean.memo.pair	Implementations of FeaturePairMemo.
org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance	Implementations of FeaturePairMemo to measure distance between Marks.
org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap	Implementations of FeaturePairMemo to measure overlap between Marks.
org.anchoranalysis.plugin.mpp.feature.bean.unit	Beans to convert between units.
org.anchoranalysis.plugin.mpp.feature.overlap	Implementations of CalculationPart to calculate overlap between two entities.
org.anchoranalysis.plugin.mpp.segment.bean.annealing	Implementations of AnnealScheme.
org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark	Implementations of KernelBirth that are dependent.
org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent	Implementations of KernelBirth that are independent.
org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.voxelized	Implementations of KernelBirth that are independent but use the voxelized state of a Mark.
org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer	Implementations of KernelProposerOption.
org.anchoranalysis.plugin.mpp.segment.bean.marks	Beans to perform segmentation involving Marks and related classes.
org.anchoranalysis.plugin.mpp.segment.bean.marks.dual	Implementations of StateTransformerBean involving DualVoxelizedMarks.
org.anchoranalysis.plugin.mpp.segment.bean.marks.partition	Implementations of StateTransformerBean involving MarksFromPartition.
org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized	Implementations of StateTransformerBean involving VoxelizedMarksWithEnergy.
org.anchoranalysis.plugin.mpp.segment.bean.marks.weight	Deriving a weight for a Mark.
org.anchoranalysis.plugin.mpp.segment.bean.optimization	Beans related to performing optimization with marked-point-processes.
org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract	Implementations of ExtractScoreSize.
org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge	KernelStateBridge and implementations.
org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode	AssignMode and implementations.
org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter	Implementations of FeedbackReceiverBean.
org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme	Implementations of OptimizationScheme.
org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter	Implementations of StateReporter.
org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination	Implementations of TerminationCondition.
org.anchoranalysis.plugin.mpp.segment.kernel.assigner	Implementations of KernelAssigner.
org.anchoranalysis.plugin.mpp.segment.kernel.updater	KernelUpdater and implementations.
org.anchoranalysis.plugin.mpp.segment.optimization	Non-bean classes to help with optimization in org.anchoranalysis.plugin.mpp.segment.bean.optimization and sub-packages.
org.anchoranalysis.plugin.mpp.segment.shared	Stared-state for segmentation tasks involving mark-point-processes.
org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.maskrcnn	Decodes the outputted tensors from a Mask R-CNN implementation.
org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.text	Decodes the outputted tensors from text-segmentation models.
org.anchoranalysis.plugin.onnx.bean.object.segment.stack	Segmenting a Stack using the ONNX Runtime to produce an ObjectCollection.
org.anchoranalysis.plugin.onnx.model	Non-bean classes for running an inference model with the ONNX Runtime.
org.anchoranalysis.plugin.opencv	Plugins that call OpenCV.
org.anchoranalysis.plugin.opencv.bean.color	Operations involving color-spaces and OpenCV.
org.anchoranalysis.plugin.opencv.bean.feature	Extracting features using OpenCV.
org.anchoranalysis.plugin.opencv.bean.interpolate	Interpolation beans that use OpenCV.
org.anchoranalysis.plugin.opencv.bean.object.segment.stack	Segmentation of a Stack using OpenCV.
org.anchoranalysis.plugin.opencv.bean.stack	Implementations of StackWriter and StackReader that involve OpenCV.
org.anchoranalysis.plugin.opencv.convert	Conversion to/from OpenCV data-structures.
org.anchoranalysis.plugin.opencv.resizer	Interpolation non-beans that use OpenCV.
org.anchoranalysis.plugin.opencv.segment	Non-bean classes pertaining to segmentation.
org.anchoranalysis.plugin.operator.feature.bean	Features that combine or convert other features in a generic way.
org.anchoranalysis.plugin.operator.feature.bean.arithmetic	Arithmetic involving features.
org.anchoranalysis.plugin.operator.feature.bean.conditional	Conditional operations involving features.
org.anchoranalysis.plugin.operator.feature.bean.list	Operations that extract a single value from a list of features.
org.anchoranalysis.plugin.operator.feature.bean.range	Features that compare against a range of values.
org.anchoranalysis.plugin.operator.feature.bean.replace	Replaces particular values if they are returned from a feature.
org.anchoranalysis.plugin.operator.feature.bean.statistics	Converts feature values based upon a statistical measure of distribution.
org.anchoranalysis.plugin.operator.feature.physical	Converting to/from physical units.
org.anchoranalysis.plugin.operator.feature.statistics	Non-bean statistical operations.
org.anchoranalysis.plugin.points.bean	Beans that fit or otherwise manipulate sets of points.
org.anchoranalysis.plugin.points.bean.convexhull	Convex hull operations.
org.anchoranalysis.plugin.points.bean.feature	Features related to points and fitting points to conics.
org.anchoranalysis.plugin.points.bean.fitter	Fitting geometric structures to points.
org.anchoranalysis.plugin.points.calculate.ellipse	CalculationPart related to fitting ellipses to points by least-squares.
org.anchoranalysis.plugin.points.calculate.ellipsoid	CalculationPart related to fitting ellipsoids to points by least-squares.
org.anchoranalysis.plugin.points.convexhull	Non-bean convex hull operations.
org.anchoranalysis.plugin.quick.bean.experiment	Quickly defining experiments via several assumptions, including particular file-paths.
org.anchoranalysis.plugin.quick.bean.input	Specifying inputs when quickly defining an experiment.
org.anchoranalysis.plugin.quick.bean.input.filepathappend	Appending other entities to inputs when quickly defining experiments.
org.anchoranalysis.plugin.quick.bean.structure	Specifying a structure of subdirectories and filenames when quickly defining an experiment.
org.anchoranalysis.spatial.axis	Identifying the three standard axes in 3D cartesian coordinates.
org.anchoranalysis.spatial.box	Axis-aligned bounding-boxes and related operations.
org.anchoranalysis.spatial.orientation	Various methods to specify the orientation (general direction) of an entity.
org.anchoranalysis.spatial.point	A cartesian-coordinate, across varying primitive types, in 2D and 3D space.
org.anchoranalysis.spatial.point.consumer	Functional interfaces that accept cartesian coordinate points specified in different ways.
org.anchoranalysis.spatial.rtree	R-Tree data structure and related operations.
org.anchoranalysis.spatial.scale	How to much to scale an entity in Cartesian space by.
org.anchoranalysis.test	Testing utilities and fixtures with no greater downstream dependency than anchor-core.
org.anchoranalysis.test.experiment	Testing utilities and fixtures with no greater downstream dependency than anchor-experiment or anchor-mpp or anchor-mpp-io.
org.anchoranalysis.test.experiment.launcher	Launches an anchor binary from a shell and runs an experiment.
org.anchoranalysis.test.experiment.task	Helper classes to execute Tasks in tests.
org.anchoranalysis.test.feature	Testing utilities and fixtures with no greater downstream dependency than anchor-feature.
org.anchoranalysis.test.feature.plugins	Testing utilities and fixtures with no greater downstream dependency than anchor-image-feature or anchor-mpp.
org.anchoranalysis.test.feature.plugins.mockfeature	A mocked feature internally using a feature-calculation.
org.anchoranalysis.test.feature.plugins.objects	Fixtures for creating object-masks and related feature-inputs.
org.anchoranalysis.test.image	Testing utilities and fixtures with no greater downstream dependency than anchor-image-io or anchor-io-bioformats or anchor-imagej.
org.anchoranalysis.test.image.csv	Comparing two CSV files for equality (by a certain definition).
org.anchoranalysis.test.image.io	Utilities for testing-related reading and writing to the filesystem.
org.anchoranalysis.test.image.load	Load test image data.
org.anchoranalysis.test.image.object	Fixtures for creating object-masks.
org.anchoranalysis.test.image.rasterwriter.comparison	Different ways for comparing images.
org.anchoranalysis.test.image.segment	Fixtures or other helper classes for testing image segmentation algorithms.
org.anchoranalysis.test.image.stackwriter	Fixtures for testing StackWriter and related classes.
org.anchoranalysis.test.io.output	Fixtures for an OutputManager and related-classes.