Uses of Class
org.anchoranalysis.bean.initializable.InitializableBean
Packages that use InitializableBean
Package
Description
Defining, loading, initializing Anchor Beans.
Setting, referencing and initializing key-value parameters.
Defines a root path directory on the filesystem whre files are read / written.
Beans pertaining to feature-calculation.
A feature-list (custom list type for features) and associated providers.
Features that are sufficiently generic to work on any input-type.
Provider of a single feature.
Defines base class
FeatureResults together with
some implementations.Core (bean) classes for image processing.
Base classes for performing operations on
Channels.Classes that aren't AnchorBeans that pertain to the initialization of image-related beans.
Beans pertaining to
ObjectMask and their
collections.Base classes for providers of different core data entities related to images.
A provider of
Stacks.Base classes to perform image segmentation, transforming an image into another meaningful entity
or entities.
Base classes to perform binary-segmentation.
Base classes to segment a channel into objects.
Beans to define entities or operate that consider Euclidian space.
Base classes for thresholding and calculating levels for thresholding.
Beans pertaining to feature definition and calculation.
Beans that define context (which feature, which energy-stack) for evaluating feature-inputs.
Features that operate on a
Histogram.Features that operate on a
ObjectCollection.Features that operate on a pair of
ObjectMasks.Features that operate on a single
ObjectMask.Features that convert to/from physical spatial units (e.g. meters) as opposed to pixels/voxels.
Instance-segmentation of a
Stack.Beans to specify the outputting of features into CSV from a
ObjectCollection.Beans to combine multiple stacks into a single stack before outputting.
Methods to provide a
Dictionary.Methods to provide a single file-path.
Beans pertaining to marked-point-processes.
Beans related to creating
Marks.Operations based on sets of points.
Fitting structures to sets of points.
Proposing
Marks or other data-structures with particular
attributes.Implementations and helper classes for calculating energy during an energy-minimization
optimization scheme.
Creating
EnergySchemes.Features calculated on a
Mark.Implementations of
ChannelProvider that use FIJI.Euclidean Distance Transform
implementations via FIJI.
Implementations of
MaskProvider that use FIJI.Implementations of
Thresholder that use FIJI.Implementations of
ConvertChannelTo and ConvertChannelToWithHistogram.Implementations of
ChannelProvider that are
generic base-classes or otherwise abstract or general.Implementations of
ChannelProvider that perform
arithmetic on voxels in one or more Channels.Implementations of
ChannelProvider that sets the
values of the voxels in a Channel.Implementations of
ChannelProvider that converts a
Channel from one voxel-type to another.Implementations of
ChannelProvider that calculate
the gradient of a Channel's voxels in one or more
dimensions.Implementations of
ChannelProvider that manipulate
the intensity-values of the voxels of a Channel's
voxels.Implementations of
ChannelProvider that involve
conversion from or application of Masks.Implementations of
ChannelProvider that involve
conversion from or application of ObjectMasks.Implementations of
ChannelProvider that assign a
score to particular subregions of a channel.Implementations of
ChannelProvider that process 3D
channels slice-by-slice.Implementations of
ColorProvider.Beans pertaining to
Dictionary.Implementations of
DimensionsProvider.Implementations of
HistogramProvider.Thresholding of intensity values represented in at
Histogram.Implementations of
MaskProvider.Implementations of
MaskProvider that combine
existing providers.Implementations of
MaskProvider that convert
providers of other types to ObjectMasks.Implementations of
MaskProvider that implement
morphological operations.Provides if-else conditions to a
MaskProvider.Implementations of
MaskProvider that process 3D
masks slice-by-slice.Implementations of
ObjectFilter.Implementations of
ObjectFilter that assess each
element in a collection collectively.Implementations of
ObjectFilter that combine two or
more other ObjectFilters.Implementations of
ObjectFilter that
independently assess each element in a collection.Implementations of
ObjectMatcher.Implementations of
ObjectCollectionProvider.Implementations of
ObjectCollectionProvider
involving connected-components.Implementations of
ObjectCollectionProvider
involving feature calculation.Implementations of
ObjectCollectionProvider that
filter objects.Implementations of
ObjectCollectionProvider
involving a Mask.Implementations of
ObjectCollectionProvider
involving merging objects together.Implementations of
ObjectCollectionProvider
involving morphological operations.Implementations of
ObjectCollectionProvider
involving segmentation.Implementations of
ObjectCollectionProvider
involving z-slice processing.Implementations of
ObjectCollectionProvider
involving splitting objects into smaller objects.Implementations of
SegmentChannelIntoObjects.Implementation of a Watershed transformation
based on Yeong et al. 2009.
Implementations of
ScaleCalculator for calculating
a scaling-factor from dimensions.Implementations of
BinarySegmentation.Implementations of
StackProvider.Implementations of
StackProvider that color
portions of an image.Features that are calculated from
Dimensions.Implementations of
FeatureHistogram that calculate
statistics.Implementations of
FeatureHistogram that perform
thresholding.Implementations of
FeatureListProvider.Implementations of
FeatureListProvider with
input-type FeatureInputPairObjects.Implementations of
FeatureListProvider that derive
new features with permuted property-values.Implementations of
FeatureImageMetadata.Implementations of
FeatureObjectCollection.Features from pairs of
ObjectMasks.Features that calculate the degree of overlap between two
ObjectMasks.Features that calculate how many other objects an
ObjectMask directly neighbors.Implementations of
FeatureSingleObject.Implementations of
FeatureSingleObject that determine if an
object lies at the border of an image.Implementations of
FeatureSingleObject that consider an
object's bounding-box.Implementations of
FeatureSingleObject that reference a
particular Channel in the associated EnergyStack.Implementations of
FeatureSingleObject that measure an object's
intensity on a corresponding Channel.Implementations of
FeatureSingleObject that measure an object's
gradient from corresponding Channels storing the
gradient.Implementations of
FeatureSingleObject based on calculating image moments, with or without image
intensity.Implementations of
FeatureSingleObject that implement
morphological operations.Implementations of
FeatureSingleObject that measure the shape
of the ObjectMask.Implementations of
FeatureSingleObject that use SharedObjects for calculations.Implementations of
FeatureSingleObject that use SharedObjects for calculations, and measure
the degree of intersection between objects.Implementations of
FeatureSingleObject that processes an object
slice-by-slice in the z-dimension.Implementations of
FeatureSingleObject that measures aspects of
the surface of an ObjectMask.Beans involving physical units for measurement.
Implementations of
VoxelScore.Beans involving
SharedObjects.Beans involving
SharedObjects and
ObjectCollection.Implementations of
FeatureStack or other features
that involve processing a Stack.Implementations of
FeatureStack that process an
ObjectCollection.Implementations of
ChannelProvider that call ImageJ.Non-linear filters using ImageJ that use the statistical moments of the
intensity values in the kernel.
Non-linear filters using ImageJ that use the statistical rank of the intensity values in the
kernel.
Implementations of
MaskProvider that call ImageJ.Implementations of
ObjectCollectionProvider that
call ImageJ.Implementations of
StackProvider that call
ImageJ.Implementations of
Thresholder that call ImageJ.Implementations of
ObjectCollectionProvider.Implementation of
MarkCollectionProvider.Implementations of
StackProvider involving
Mark or related classes.Segmenting a
Stack using the ONNX Runtime to produce
an ObjectCollection.Operations involving color-spaces and OpenCV.
Extracting features using OpenCV.
Segmentation of a
Stack using OpenCV.Features that combine or convert other features in a generic way.
Arithmetic involving features.
Conditional operations involving features.
Operations that extract a single value from a list of features.
Features that compare against a range of values.
Replaces particular values if they are returned from a feature.
Converts feature values based upon a statistical measure of distribution.
Converting to/from physical units.
Beans that fit or otherwise manipulate sets of points.
Convex hull operations.
Features related to points and fitting points to conics.
Fitting geometric structures to points.
Testing utilities and fixtures with no greater downstream dependency than
anchor-experiment or anchor-mpp or anchor-mpp-io.
A mocked feature internally using a feature-calculation.
-
Uses of InitializableBean in org.anchoranalysis.bean
Subclasses of InitializableBean in org.anchoranalysis.beanModifier and TypeClassDescriptionclassNamedBean<T extends AnchorBean<?>>A bean with an associated textual name.classA base class for beans that require initialization but the initializations needs no parameters. -
Uses of InitializableBean in org.anchoranalysis.feature.bean
Subclasses of InitializableBean in org.anchoranalysis.feature.beanModifier and TypeClassDescriptionclassFeature<T extends FeatureInput>Base class for a measurement that calculates a result (double) given input parameters.classBeans-related toFeatures, and which require initialization withFeatureRelatedInitialization. -
Uses of InitializableBean in org.anchoranalysis.feature.bean.list
Subclasses of InitializableBean in org.anchoranalysis.feature.bean.listModifier and TypeClassDescriptionclassDefine<T extends FeatureInput>Specifies a list of features directly without assigning any custom-naming.classDefinedNamed<T extends FeatureInput>Specifies features via a list of names and associated with features.classDefineSingle<T extends FeatureInput>Specifies a single feature directly without assigning any custom-naming.classFeatureListProvider<T extends FeatureInput>Provides a list ofFeatures with identical input-type.classPrepends a string to the custom-name of each feature in a list.classReferencingFeatureListProvider<T extends FeatureInput>A base class for implementations ofFeatureListProviderthat may reference features created elsewhere. -
Uses of InitializableBean in org.anchoranalysis.feature.bean.operator
Subclasses of InitializableBean in org.anchoranalysis.feature.bean.operatorModifier and TypeClassDescriptionclassConstant<T extends FeatureInput>A constant value that is entirely invariant to the feature-input.classFeatureBinary<T extends FeatureInput>A base class for aFeaturethat is a binary-function of the results from two other features.classFeatureFromList<T extends FeatureInput>A base class for aFeaturethat is a function of the results from a list of other features.classFeatureGeneric<T extends FeatureInput>Base class for features that broadly accept any type of feature-input.classFeatureUnary<T extends FeatureInput,S extends FeatureInput> A feature that contains another feature as a bean-parameter.classFeatureUnaryGeneric<T extends FeatureInput>AFeatureUnarythat accepts anyFeatureInputirrespective of type.classReference<T extends FeatureInput>Uses another feature to calculate the value.classSum<T extends FeatureInput>Sums the results after calculating a list ofFeatures. -
Uses of InitializableBean in org.anchoranalysis.feature.bean.provider
Subclasses of InitializableBean in org.anchoranalysis.feature.bean.providerModifier and TypeClassDescriptionclassFeatureProvider<T extends FeatureInput>Provides a singleFeature.classFeatureProviderBean<B,P> classFeatureProviderDefine<T extends FeatureInput>Defines a singleFeatureto provide via a bean property.classProvides an existingFeatureidentified by its name and optionally a feature-list in which is resides. -
Uses of InitializableBean in org.anchoranalysis.feature.bean.results
Subclasses of InitializableBean in org.anchoranalysis.feature.bean.resultsModifier and TypeClassDescriptionclassThe sum of the results from a particular feature.classFeatures that processResultsVectorList.classBase class for an instance ofFeatureResultsthat calculating a statistic across all results in theResultsVectorListfor a particular feature-value.classThe maximum of the results from a particular feature.classThe mean of the results from a particular feature.classThe minimum of the results from a particular feature.classA quantile of the results from a particular feature.classThe standard-deviation of the results from a particular feature.classThe sum of the results from a particular feature. -
Uses of InitializableBean in org.anchoranalysis.image.bean
Subclasses of InitializableBean in org.anchoranalysis.image.beanModifier and TypeClassDescriptionclassImageBean<T>A bean that must be initialized withImageInitializationbefore usage. -
Uses of InitializableBean in org.anchoranalysis.image.bean.channel
Subclasses of InitializableBean in org.anchoranalysis.image.bean.channelModifier and TypeClassDescriptionclassCreates aChannelConverterfor converting a channel to a particular type. -
Uses of InitializableBean in org.anchoranalysis.image.bean.nonbean.init
Methods in org.anchoranalysis.image.bean.nonbean.init with type parameters of type InitializableBeanModifier and TypeMethodDescription<S extends InitializableBean<S,V>>
voidPopulateStoreFromDefine.copyInitialize(Class<?> defineClass, NamedProviderStore<S> destination) Copies objects of a particular class from the define and initializes.<S extends InitializableBean<?,V> & Provider<T>, T>
voidPopulateStoreFromDefine.copyProviderInitialize(Class<?> defineClass, NamedProviderStore<T> destination) Copies objects of a particular class (which must be aProvider) fromdefineand initializes each. -
Uses of InitializableBean in org.anchoranalysis.image.bean.object
Subclasses of InitializableBean in org.anchoranalysis.image.bean.objectModifier and TypeClassDescriptionclassBase class for filtering anObjectCollectionto remove objects according to a criteria.classMatches an object with other objects. -
Uses of InitializableBean in org.anchoranalysis.image.bean.provider
Subclasses of InitializableBean in org.anchoranalysis.image.bean.providerModifier and TypeClassDescriptionclassA provider base-class that as well as providing typeS, also provides aStack.classclassImplementation ofChannelProviderthat calls twoChannelProviders that must provideChannels of the same dimensions.classImplementation ofChannelProviderthat calls threeChannelProviders that must provideChannels of the same dimensions.classImplementation ofChannelProviderthat calls a single delegateChannelProvider.classclassBase class for beans that implementProviderto provideDimensions.classclassImplementation ofHistogramProviderthat calls a single delegateHistogramProvider.classclassImplementation ofMaskProviderthat calls a single delegateMaskProvider.classBase class for beans that implementProviderto provide anObjectCollection.classImplementation ofObjectCollectionProviderthat calls a single delegateProvider<ObjectCollection>. -
Uses of InitializableBean in org.anchoranalysis.image.bean.provider.stack
Subclasses of InitializableBean in org.anchoranalysis.image.bean.provider.stackModifier and TypeClassDescriptionclassCreates a stack that combines other stacks.classclassImplementation ofStackProviderthat calls a single delegateProvider<Stack>. -
Uses of InitializableBean in org.anchoranalysis.image.bean.segment
Subclasses of InitializableBean in org.anchoranalysis.image.bean.segmentModifier and TypeClassDescriptionclassPerforms some kind of segmentation on an image. -
Uses of InitializableBean in org.anchoranalysis.image.bean.segment.binary
Subclasses of InitializableBean in org.anchoranalysis.image.bean.segment.binaryModifier and TypeClassDescriptionclassPerforms a segmentation on voxels so that each voxel has an on or off state after the operation.classUses an existingBinarySegmentationthat is located by a unique identifier.classImplementation ofBinarySegmentationthat performs global thresholding.classAn implementation ofBinarySegmentationthat delegates to one otherBinarySegmentation. -
Uses of InitializableBean in org.anchoranalysis.image.bean.segment.object
Subclasses of InitializableBean in org.anchoranalysis.image.bean.segment.objectModifier and TypeClassDescriptionclassA base class for algorithms to segment a channel into one or more objects.classImplementation ofSegmentChannelIntoObjectsthat calls a single delegateSegmentChannelIntoObjects. -
Uses of InitializableBean in org.anchoranalysis.image.bean.spatial
Subclasses of InitializableBean in org.anchoranalysis.image.bean.spatialModifier and TypeClassDescriptionclassCalculating a scaling-factor from dimensions. -
Uses of InitializableBean in org.anchoranalysis.image.bean.threshold
Subclasses of InitializableBean in org.anchoranalysis.image.bean.thresholdModifier and TypeClassDescriptionclassCalculates a threshold-level from a histogram.classImplementation ofCalculateLevelthat calls a single delegateCalculateLevel.classThresholds voxels to create a binary-voxels using global thresholding.classPerforms global thresholding. -
Uses of InitializableBean in org.anchoranalysis.image.feature.bean
Subclasses of InitializableBean in org.anchoranalysis.image.feature.beanModifier and TypeClassDescriptionclassFeatureEnergy<T extends FeatureInputEnergy>A base class for features that only require an input that extends fromFeatureInputEnergyclassA base class for features that accept a histogram as input.classA base class for a feature that accepts aFeatureInputImageMetadataas input.classAn abstract base class for features that operate on image stacks.classCalculates a per-voxel score. -
Uses of InitializableBean in org.anchoranalysis.image.feature.bean.evaluator
Subclasses of InitializableBean in org.anchoranalysis.image.feature.bean.evaluatorModifier and TypeClassDescriptionclassFeatureEvaluator<T extends FeatureInput>Defines a feature and provides a means to calculate inputs for it, a session.classFeatureListEvaluator<T extends FeatureInput>Defines a list of features and provides a means to calculate inputs for it, a session. -
Uses of InitializableBean in org.anchoranalysis.image.feature.bean.histogram
Subclasses of InitializableBean in org.anchoranalysis.image.feature.bean.histogramModifier and TypeClassDescriptionclassBase class forFeatureHistogramimplementations that calculate a statistic from theHistogram.classCalculates the mean value of a histogram. -
Uses of InitializableBean in org.anchoranalysis.image.feature.bean.object.collection
Subclasses of InitializableBean in org.anchoranalysis.image.feature.bean.object.collectionModifier and TypeClassDescriptionclassA base class for a feature that accepts aObjectCollectionas input. -
Uses of InitializableBean in org.anchoranalysis.image.feature.bean.object.pair
Subclasses of InitializableBean in org.anchoranalysis.image.feature.bean.object.pairModifier and TypeClassDescriptionclassBase class for evaluatingFeaturePairObjectsin terms of another feature that operates on elements (first, second, merged etc.).classAn abstract base class for features that operate on pairs of objects.classEvaluates a feature on the first object in a pair of objects.classEvaluates a feature on the merged object created from a pair of objects.classCalculates the minimum value of a feature applied to both objects in a pair.classRatio of first-object to second-object in a pair.classEvaluates a feature on the second object in a pair of objects.classSubtract second-object from first-object in a pair. -
Uses of InitializableBean in org.anchoranalysis.image.feature.bean.object.single
Subclasses of InitializableBean in org.anchoranalysis.image.feature.bean.object.singleModifier and TypeClassDescriptionclassCalculates the center of gravity of a single object along a specified axis.classAn abstract base class for features that operate on a single object.classCalculates the number of voxels in a single object. -
Uses of InitializableBean in org.anchoranalysis.image.feature.bean.physical
Subclasses of InitializableBean in org.anchoranalysis.image.feature.bean.physicalModifier and TypeClassDescriptionclassConverts a feature from physical volume units to voxel units.classConverts a feature value representing area in pixel units to physical area units in an isometric XY plane.classConverts a distance feature to physical units along a specified direction.classConverts a feature value representing volume in voxel units to physical volume units.classFeatureConvertUnits<T extends FeatureInputWithResolution>An abstract base class for features that convert units between physical and voxel space.classWithResolutionBase<T extends FeatureInputWithResolution>Base class for a feature that requires input resolution to be calculated. -
Uses of InitializableBean in org.anchoranalysis.image.inference.bean.segment.instance
Modifier and TypeClassDescriptionclassSegmentStackIntoObjectsPooled<T extends InferenceModel>A base class for algorithms to segment a stack into one or more objects - using a pool of modelsclassSegmentStackIntoObjectsScaleDecode<T,S extends ImageInferenceModel<T>> ASegmentStackIntoObjectsScaleDecodethat scales the input image, before performing inference, and then decodes the output.classSuppressNonMaximum<T extends InferenceModel>Applies a segmentation procedure followed by non-maximum suppression. -
Uses of InitializableBean in org.anchoranalysis.image.io.bean.object.feature
Subclasses of InitializableBean in org.anchoranalysis.image.io.bean.object.featureModifier and TypeClassDescriptionclassSpecifies a table of feature-calculations on objects. -
Uses of InitializableBean in org.anchoranalysis.image.io.bean.stack.combine
Subclasses of InitializableBean in org.anchoranalysis.image.io.bean.stack.combineModifier and TypeClassDescriptionclassCombines aProvider<Stack>with a label.classTiles a number ofStackProviderWithLabels as a singleStackProvider.classCreates an image that contains text only. -
Uses of InitializableBean in org.anchoranalysis.io.input.bean.dictionary
Subclasses of InitializableBean in org.anchoranalysis.io.input.bean.dictionary -
Uses of InitializableBean in org.anchoranalysis.io.input.bean.path.provider
Subclasses of InitializableBean in org.anchoranalysis.io.input.bean.path.providerModifier and TypeClassDescriptionclassclassCalls an existingFilePathProviderindirectly to provide an identical result.classExtracts a path from aFilesProvider. -
Uses of InitializableBean in org.anchoranalysis.mpp.bean
Subclasses of InitializableBean in org.anchoranalysis.mpp.beanModifier and TypeClassDescriptionclassMarksBean<T>An abstract base class for beans related to marks in MPP (Marked Point Process). -
Uses of InitializableBean in org.anchoranalysis.mpp.bean.mark.factory
Subclasses of InitializableBean in org.anchoranalysis.mpp.bean.mark.factoryModifier and TypeClassDescriptionclassA factory for creating marks with unique identifiers. -
Uses of InitializableBean in org.anchoranalysis.mpp.bean.points
Subclasses of InitializableBean in org.anchoranalysis.mpp.bean.pointsModifier and TypeClassDescriptionclassPointsBean<T>An abstract base class for beans that work with points and require initialization. -
Uses of InitializableBean in org.anchoranalysis.mpp.bean.points.fitter
Subclasses of InitializableBean in org.anchoranalysis.mpp.bean.points.fitterModifier and TypeClassDescriptionclassAbstract base class for fitting a mark (e.g., an ellipsoid) to a set of points. -
Uses of InitializableBean in org.anchoranalysis.mpp.bean.proposer
Subclasses of InitializableBean in org.anchoranalysis.mpp.bean.proposerModifier and TypeClassDescriptionclassAn abstract base class for proposing an entire collection (configuration) of marks.classAn abstract base class for proposing a selection of a single mark from a collection of marks.classAn abstract base class for proposing merges between marks.classAn abstract base class for proposing changes to a mark.classAn abstract base class for proposing splits of a mark into two new marks.classAn abstract base class for proposing orientations for marks.classAn abstract base class for proposing a list of points based on a given point and mark.classAn abstract base class for proposing positions.classProposerBean<T>An abstract base class for proposer beans in the MPP (Marked Point Process) framework.classAn abstract base class for proposing radii in a 3D space.classAn abstract base class for proposing scalar values. -
Uses of InitializableBean in org.anchoranalysis.mpp.bean.provider
Subclasses of InitializableBean in org.anchoranalysis.mpp.bean.providerModifier and TypeClassDescriptionclassAn abstract provider forMarkBounds.classProvides a collection of marksclassMarksBaseProvider<T,S> classProvides (maybe) a single mark -
Uses of InitializableBean in org.anchoranalysis.mpp.feature.bean.energy.element
Subclasses of InitializableBean in org.anchoranalysis.mpp.feature.bean.energy.elementModifier and TypeClassDescriptionclassExtracts one of the memos from the pair, and processes as aFeatureSingleMemoclassAn abstract base class for features that operate onFeatureInputAllMemo.classAn abstract base class for features that operate on pairs of memoized objects.classAn abstract base class for features that operate on a single memoized object. -
Uses of InitializableBean in org.anchoranalysis.mpp.feature.bean.energy.scheme
Subclasses of InitializableBean in org.anchoranalysis.mpp.feature.bean.energy.schemeModifier and TypeClassDescriptionclassAn abstract class for creatingEnergySchemeinstances.classCreates anEnergySchemeby combining individual elements and their interactions. -
Uses of InitializableBean in org.anchoranalysis.mpp.feature.bean.mark
Subclasses of InitializableBean in org.anchoranalysis.mpp.feature.bean.markModifier and TypeClassDescriptionclassA bean for evaluating marks using features and energy schemes. -
Uses of InitializableBean in org.anchoranalysis.plugin.fiji.bean.channel.provider
Subclasses of InitializableBean in org.anchoranalysis.plugin.fiji.bean.channel.providerModifier and TypeClassDescriptionclassPerforms Perona-Malik Anisotropic Diffusion.classApplies a minimum filter to a channel using ImageJ's MinMaxMedian plugin. -
Uses of InitializableBean in org.anchoranalysis.plugin.fiji.bean.channel.provider.distance
Modifier and TypeClassDescriptionclassEuclidian Distance Transform from ImageJ that works on 2D as well as 3D z-stacks.classLikeDistanceTransform3Dbut applies the distance transform separately for each object in a collection. -
Uses of InitializableBean in org.anchoranalysis.plugin.fiji.bean.mask.provider
Subclasses of InitializableBean in org.anchoranalysis.plugin.fiji.bean.mask.providerModifier and TypeClassDescriptionclassApplies local thresholding algorithm using Fiji's {link Auto_Local_Threshold} plugin -
Uses of InitializableBean in org.anchoranalysis.plugin.fiji.bean.threshold
Subclasses of InitializableBean in org.anchoranalysis.plugin.fiji.bean.thresholdModifier and TypeClassDescriptionclassApplies automatic thresholding using ImageJ's Auto_Threshold plugin. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.channel.convert
Subclasses of InitializableBean in org.anchoranalysis.plugin.image.bean.channel.convertModifier and TypeClassDescriptionclassScales by compressing a certain range of values into the 8-bit signal.classScales by compressing a certain range of values into the 8-bit signalclassConverts a channel to unsigned byte format, scaling the values based on the original voxel type.classConverts a channel to unsigned byte format without any scaling. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.channel.provider
Subclasses of InitializableBean in org.anchoranalysis.plugin.image.bean.channel.providerModifier and TypeClassDescriptionclassCreates a new channel with all values initialized to a constant (by default zero)classCreates a duplicate of the input channel.classAn abstract base class for creating a channel from specified dimensions.classFinds the input-stack using a conventional name ofinput_image- and extracts the first channelclassExtracts a channel from a provider of a stack.classProvides a channel based on a condition from a dictionary.classProvides a channel by referencing it from a a set of named-channels.classTakes the two channels and creates a NEW third channel whose pixels are a function of the two channelsclassAn abstract base class for creating a channel from an existing channel and a collection of objects.classAChannelProviderUnarywhich has a scalar value field. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
Modifier and TypeClassDescriptionfinal classAdds a constant value to each voxel in a channel.classBase-class for operations that perform a binary arithmetic operation with each voxel-value and a constant.classBase class for arithmetic operations that conditionally overwrite voxel values with a constant.classInverts the intensity values of aChannelby subtracting each voxel from the maximum value for the channel's data type.classCreates a new channel by taking the maximum value of corresponding voxels from two input channels.classReplaces voxel values with a constant value if the constant is greater than the original voxel value.classCreates a new channel that is the mean of three input channels.classCreates a new channel by taking the minimum value of corresponding voxels from two input channels.classReplaces voxel values with a constant value if the constant is less than the original voxel value.classMultiplies each voxel value in a channel by a constant value.classCreates a new channel by multiplying corresponding voxels from two input channels.classSubtracts each voxel value in a channel from a constant value.classSubtracts the mean intensity (of the entire channel or a masked portion thereof) from every voxel.classCreates a new channel by subtracting corresponding voxels of the second channel from the first channel. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.channel.provider.assign
Modifier and TypeClassDescriptionclassCopies the pixels fromchannelAssignFromtochannel(possibly masking).classAssigns a value from a dictionary to all voxels in a channel.classMatches source-objects to target objects, based upon intersection, and assigns the value in the respective source object to the target objectclassAssigns a constant (scalar) value to the portion of the image covered by a mask -
Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.channel.provider.convert
Modifier and TypeClassDescriptionclassConvert<T>Converts a channel by applying a converter (no histogram is involved in the conversion).classBase class for channel providers that perform conversions on a single input channel.classConverts a channel to a different voxel data-type by applying a converter with an associated histogram. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.channel.provider.gradient
Modifier and TypeClassDescriptionclassBase class to calculate the gradient of the voxels in aChannel.classLikeGradientBasebut allows an arbitrary constant to be added to voxels storing the gradient.classExtracts the gradient in the direction of a particular axis (identified by an index)classCalculates aChannel's gradient along the x and y axes.class3x3 Sobel Filter -
Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.channel.provider.intensity
Modifier and TypeClassDescriptionclassBlurs an image using a particular strategy (defaults to a gaussian blur in each slice)classCreates a new channel which is a merged version of two input channels according to rules.classApplies a median-filter with square kernelclassCorrects a channel in the following wayclassRewrites the intensity for each object-mask (assume no overlap) so that its mean is 128classChanges the voxel values to map the range of 0th quantile to xth quantile across the entire voxel data rangeclassScales the channel in the X and Y dimensions. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.channel.provider.mask
Modifier and TypeClassDescriptionclassclassA base class for aChannelProviderwhich also uses a binary-mask, but which doesn't use any otherChannelProvideras an input.classA base class for aChannelProviderUnarywhich also uses a binary mask.classSet pixels NOT IN the mask to 0, but keep pixels IN the mask identical. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.channel.provider.object
Modifier and TypeClassDescriptionclassCreates a channel with a level calculated for each object using various methods.classCreates a channel with different threshold-levels for each object, calculating the level only from the histogram of the particular object.classCalculates a threshold-level for each object collectively based on other objects -
Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.channel.provider.score
Modifier and TypeClassDescriptionclassAssigns a unique id number to each object.classCreates a channel by scoring objects based on a feature calculation.classAssigns a score (a value indicating how probable something is) to each voxel -
Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.channel.provider.slice
Modifier and TypeClassDescriptionclassExtracts the slice at the center (rounding down) of the range of z-stacks.classExtracts slices fromsliceStart(inclusive) tosliceEnd(inclusive).classCreates a maximum intensity projection of a 3DChannel.classCreates a mean intensity projection of a 3DChannel.classCreates a new channel with specific dimensions that repeatedly duplicates a slice from an existing channel -
Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.color.provider
Subclasses of InitializableBean in org.anchoranalysis.plugin.image.bean.color.providerModifier and TypeClassDescriptionclassCombines one or moreColorProviders into a unitaryColorProvider.classGenerates colors to match the size of an object-collection. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.dictionary
Subclasses of InitializableBean in org.anchoranalysis.plugin.image.bean.dictionaryModifier and TypeClassDescriptionclassChecks if a value in aDictionaryis equal to an expected value. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.dimensions.provider
Modifier and TypeClassDescriptionclassCreates image-dimensions by referencing them from aChannelProvider.classGuesses dimensions from an input-image if it exists.classSpecifies dimensions explicitly via bean properties. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.histogram.provider
Subclasses of InitializableBean in org.anchoranalysis.plugin.image.bean.histogram.providerModifier and TypeClassDescriptionclassThis cuts a Histogram below a threshold BUT TRANSFERS ALL THE COUNT greater than equal to the threshold into the bin just below the threshold valueclassclassThresholds a histogram using a CalculateLevel keeping only the values greater equal than the thresholdclassA provider that references an existingHistogramby its identifier. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.histogram.threshold
Modifier and TypeClassDescriptionclassBase class forCalculateLevelimplementations that operate on a list of otherCalculateLevelobjects.classACalculateLevelUnarythat calculates a level relative to a threshold, with an alternative calculation method.classClamps the input-histogram to a certain maximum value, and then delegates the calculate-level.classA constant value for thresholding.classSpecifies a constant if a histogram is empty, otherwise delegates to another {#link org.anchoranalysis.image.bean.threshold.CalculateLevel}classCalculates a level from the first delegate and if greater than a threshold, recalculates from a second delegate.classCalculates a level from the first delegate and if less than a threshold, recalculates from a second delegate.classThe maximum value of one or more {#link org.anchoranalysis.image.bean.threshold.CalculateLevel}classThe minimum value of one or more {#link org.anchoranalysis.image.bean.threshold.CalculateLevel}classPerforms auto-thresholding using Otsu's method.classSimilar to Otsu, but weighs the variances differently of background and foreground.classCalculates the threshold value from a quantile of a histogram. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.mask.provider
Subclasses of InitializableBean in org.anchoranalysis.plugin.image.bean.mask.providerModifier and TypeClassDescriptionclassCreates a new mask of particular dimensionality where all values are off.classCreates a new mask of particular dimensionality where all values are on.classA provider that creates a duplicate of a givenMask.classBase-class forMaskProviders that accept aChannelas input.classBase class forMaskProviders that create a mask based on given dimensions.classSwitches on voxels to off and vice-versa.classA provider that references an existingMaskby its identifier.classScales the mask in XY dimensions, but not in Z dimension. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.mask.provider.combine
Modifier and TypeClassDescriptionclassOutputs the logical operation and voxelwise on both masks, modifying {mask} with the result.classBase class for combining two masks.classOutputs the logical operationiff first==HIGH and second==LOW then LOWvoxelwise on both masks, modifying {mask} with the result.classOutputs the logical operation or voxelwise on both masks, modifying {mask} with the result.classOutputs the logical operation xor (exclusive or) voxelwise on both masks, modifying {mask} with the result. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.mask.provider.convert
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Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.mask.provider.morphological
Modifier and TypeClassDescriptionclassCreates aMaskwhere all pixels are on within a box region.classPerforms a dilation morphological operation onBinaryVoxels.classPerforms an erosion morphological operation onBinaryVoxels.classFinds the exterior outer contour for aMaskthat forms its outline.classFits a box around the on voxels.classBase class for performing morphological operations onBinaryVoxels. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.mask.provider.predicate
Modifier and TypeClassDescriptionclassThe currentmaskis returned if a condition on key-values is satisfied otherwisemaskElseis returned.classThe currentmaskis returned if it's non-empty (at least one on voxel) otherwisemaskElseis returned.classThe currentmaskis returned if the mask (treated as an object) passed an object-filter, otherwisemaskElseis returned.classBase class which multiplexes between the current mask and an alternative depending if a condition is met.classThe currentmaskis a particular stack exists (at least one on voxel) otherwisemaskElseis returned. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.mask.provider.segment
Modifier and TypeClassDescriptionclassApplies aBinarySegmentationalgorithm to derive a mask from a channelclassThresholds a channel to produce a mask, reusing (and modifying) the input-buffers of the channel if possible. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.mask.provider.slice
Modifier and TypeClassDescriptionclassFlattens a mask in the z-dimension, so it is 2D instead of 3D (like a maximum intensity projection).classCreates a new mask with specific dimensions that repeatedly duplicates a slice from an existing mask -
Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.object.filter
Subclasses of InitializableBean in org.anchoranalysis.plugin.image.bean.object.filterModifier and TypeClassDescriptionclassUses a predicate to make a decision whether to keep objects or not.classAn independent object-filter that uses a relation in its predicate. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.object.filter.collective
Modifier and TypeClassDescriptionclassCalculates features values for all objects, and discards any object less thanquantile - (minRatio * stdDev)classMatches each object with others, and keeps only those where a relation holds true for all matches (in terms of features) -
Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.object.filter.combine
Modifier and TypeClassDescriptionclassApplies multiples filter with logical AND i.e. an object must pass all objects in the list to remain.classA filter that combines other filters (in a list)classApplies multiples filter with logical OR i.e. an object must pass any one of the filter steps to remain. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.object.filter.independent
Modifier and TypeClassDescriptionclassOnly accepts an object if it has greater (or EQUAL) intersection withobjectsGreaterthanobjectsLesserclassOnly keep objects where at least one voxel (on a particular channel) has intensity greater or equal to a threshold.classKeeps objects which intersects with ANY ONE of a collection of other objects.classKeeps only objects that are not adjacent to the scene-border (i.e. have a bounding-box on the very edge of the image)classOnly keeps objects whose feature-value satisfies a condition relative to a threshold.classOnly keeps objects whose feature-value satisfies a condition relative to a threshold. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.object.match
Subclasses of InitializableBean in org.anchoranalysis.plugin.image.bean.object.matchModifier and TypeClassDescriptionclassSpecifies a single object that will always be the "match" for whatever source object.classMatches to another object, and then uses that object to bridge to anotherclassAnObjectMatcherthat matches objects based on their intersection with a provided set of objects. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.object.provider
Subclasses of InitializableBean in org.anchoranalysis.plugin.image.bean.object.providerModifier and TypeClassDescriptionclassExtract a singleObjectMaskinto a new collection.classAnObjectCollectionProviderthat concatenates multipleObjectCollections from a list of providers.classDuplicates (deep copy) an object-collection.classCreates an empty object-collection.classMultiplexes between two object-collection-providers depending on whether a parameter value equals a particular stringclassPermutes some changes over anObjectCollectionProviderand collects all the results in anObjectCollectionclassAnObjectCollectionProviderthat references an existingObjectCollectionby its identifier.classReturns a object-collection by name if it exists, or else callsobjectsElseif it doesn't exist.classScales all the objects in the collection by a particular scale-factor.classBase class forObjectCollectionProviderUnarythat also requires aChannel.classBase class forObjectCollectionProviders that create objects from aChannel.classBase class forObjectCollectionProviderUnarythat take an optionalobjectsContainerbean-field.classBase class forObjectCollectionProviderUnaryclasses that require dimensions to be specified.classBase class forObjectCollectionProviderUnaryclasses that offer an optional means to specify dimensions. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.object.provider.connected
Modifier and TypeClassDescriptionclassConverts a binary-mask into its connected componentsclassEnsures each object in a collection is a connected-component, decomposing it if necessary into multiple objects.classRejects a set of objects, if any object is not fully connected (pixels form two or more separate connected components) -
Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.object.provider.feature
Modifier and TypeClassDescriptionclassAn abstract base class for object collection providers that use a feature evaluator.classFinds the object with the maximum feature-value from a collection.classFinds the object with the maximum feature among a group of matches for each object.classCreates a new object-collection with objects sorted by a derived feature-value (in ascending order) -
Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.object.provider.filter
Modifier and TypeClassDescriptionclassFilters anObjectCollectionusing the specifiedObjectFilter.classFilters anObjectCollectionby grouping objects and then applying a filter to each group.classReturns only the objects that intersect with at least one object in the containerclassProvides anObjectCollectionby matching objects using a specifiedObjectMatcher.classFilters objects to keep only those which are NOT in the container.classBase class for object collection providers that apply a filter to the objects.classConsiders all possible pairs of objects in a provider, and removes those that touch the border. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.object.provider.mask
Modifier and TypeClassDescriptionclassReduce the size of individual objects (if neccessary, and minimally) to fit within a binary-mask.classConverts a binary-mask to an object-collection (containing a single object) -
Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.object.provider.merge
Modifier and TypeClassDescriptionclassA base class for algorithms that merge object-masks.classNaive greedy merge strategy when any two neighboring objects are merged if it increases a feature.classMerges objects if a pair feature value satisfies a condition.classMerges neighboring objects if it results in an increase in the average feature-value calculated on each single object.classMerges itemwise objects from two collections.classBase class for object-merging strategies that involve calculating a feature.classExpandsMergeBaseby optionally imposing a maximum-distance requirement between objects that are possibly merged. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.object.provider.morphological
Subclasses of InitializableBean in org.anchoranalysis.plugin.image.bean.object.provider.morphologicalModifier and TypeClassDescriptionclassDilates each object in the collection, growing bounding-boxes as necessary in relevant dimensions.classErodes each object in the collection, growing bounding-boxes as necessary in relevant dimensions.classBase class for providers that apply morphological operations to anObjectCollection. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.object.provider.segment
Modifier and TypeClassDescriptionclassPerforms a binary-segmentation using the upstream objects as masks.classSegments a channel into objects using a specified segmentation algorithm.classPerforms segmentation of a channel using each object in the upstream collection as a mask.classSegmentStack<T extends InferenceModel>Segments a stack into objects.classTakes each object one-by-one fromobjectsSource, and finds matching seeds fromobjectsSeeds -
Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.object.provider.slice
Modifier and TypeClassDescriptionclassCreates a 3D version of an object by replicating each input-object across the z-dimension to meet (3D) dimensions.classExtends an object (2D/3D) as much as it can within the z-slices of a containing objectclassFlattens all object-masks in the z-dimension, so it is 2D instead of 3D (like a maximum intensity projection).classExtracts a specific slice from a collection of 3D objects. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.object.provider.split
Modifier and TypeClassDescriptionclassConsiders all possible pairs of objects in a provider, and removes any intersecting pixelsclassSplits objects in a collection based on intersections with another set of objects.classSplits objects into sub-objects by cutting by an orthogonal square lattice (like a chessboard). -
Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.object.segment.channel
Modifier and TypeClassDescriptionclassPerform a segmentation at a different scale, and then fit the results back to the original scale.classPerforms a binary-segmentation of the channel and converts its connected-components into objectsclassApplies an object-filter to the results of an upstream segmentation.classImposes minima in seed locations on the input-channel before performing the segmentationclassApplies the MSER algorithm from imglib2classPerform a segmentation in a MIP instead of z-stacks, and fits the result back into a 3D segmentation. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong
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Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.scale
Subclasses of InitializableBean in org.anchoranalysis.plugin.image.bean.scaleModifier and TypeClassDescriptionclassScale X and Y dimension by a constant floating-point number.classScales an image to approximately similar in size to aSizeXY.classInvert theScaleFactorcalculated by thescaleCalculatordelegate.classCalculates a scale factor to ensure a minimum XY resolution is achieved.classCalculates a scaling-factor to make the source image have identical dimensions asdimensionsTarget.classScales to the suggested-size if one is provided, otherwise callsfallback. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.segment.binary
Subclasses of InitializableBean in org.anchoranalysis.plugin.image.bean.segment.binaryModifier and TypeClassDescriptionclassPerforms a segmentation and inverts and on and off bytesclassRepeats a binary segmentation operation for a specified number of iterations.classPerforms a sequence of succesive segmentationsclassThresholds each voxels by comparing against another channel that has per-voxel thresholds -
Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.stack.provider
Subclasses of InitializableBean in org.anchoranalysis.plugin.image.bean.stack.providerModifier and TypeClassDescriptionclassCombines all the channels from one or more sources (stacks, channels etc.)classclassFinds the input-stack using a conventional name ofinput_imageclassRetrieves an existing stack. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.bean.stack.provider.color
Modifier and TypeClassDescriptionclassBase class for providers that draw entities (an outline or filled) on a background.classLikeColoredBasebut uses a generator to determine the colors for the objects.classDraws a colored representation (outline or filled) of aObjectMaskon a backgroundclassDraws a colored representation (outline or filled) of anObjectCollectionon a backgroundclassProvides aStackby combining up to three channels (red, green, blue) into an RGB image.classColors three collections of objects in RED, GREEN, BLUE channels on top of a background. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.feature.bean.dimensions
Subclasses of InitializableBean in org.anchoranalysis.plugin.image.feature.bean.dimensionsModifier and TypeClassDescriptionclassArea<T extends FeatureInputEnergy>Area of the stack (XY dimensions only, Z dimension is not considered).classExtent<T extends FeatureInputEnergy>Width/height/depth of energy-stack in pixels depending on axis.classForSpecificAxis<T extends FeatureInputEnergy>Dimensions-calculation for one specific axis only.classFromDimensionsBase<T extends FeatureInputDimensions>Base class for features that are calculated fromDimensions.classVolume<T extends FeatureInputEnergy>Calculates the volume (x, y and z dimensions) of the scene from the dimensionsclassVoxelPhysicalSize<T extends FeatureInputEnergy>The physical size of a pixel in a specific dimension. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
Modifier and TypeClassDescriptionclassCalculates the coefficient of variation of all the values in the histogram.classCounts the number of items in a histogram (posssibly in relation to a threshold: above, below etc.)classCalculates the kurtosis of all the values in the histogram.classCalculates the maximum value in a histogram.classCalculates the mean value in aHistogram, and raises it to a power.classCalculates the median value in aHistogram.classCalculates the minimum value in aHistogram.classCalculates the skewness of all the values in the histogram.classNumber of unique values in histogram.classCalculates a specified quantile value from aHistogram.classThe range (difference in values) between two quantilesclassCalculates the ratio of non-mode pixels to total pixels in aHistogram.classCalculates the skewness of all the values in the histogram.classCalculates the standard deviation of values in aHistogram.classCalculates the sum of all values in aHistogram.classCalculates the total count of all entries in aHistogram.classCalculates the variance of all the values in the histogram. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.feature.bean.histogram.threshold
Modifier and TypeClassDescriptionclassCalculates a level (a threshold-value) from a histogram.classCalculates the ratio of values in aHistogramthat satisfy a specified threshold condition.classThresholds the histogram (using a weightedOtsu) and then applies a feature to the thresholded version. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.feature.bean.list
Subclasses of InitializableBean in org.anchoranalysis.plugin.image.feature.bean.listModifier and TypeClassDescriptionclassCalculate various moment-related statistics about the intensity of each channel of an image. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.feature.bean.list.pair
Subclasses of InitializableBean in org.anchoranalysis.plugin.image.feature.bean.list.pairModifier and TypeClassDescriptionclassEmbeds each feature in aFeatureDeriveFromPairfeature (first, second or merge) and prepends with a string.classCalculates features on each part of a pair (first, second, merged etc.) and then reduces the calculation to a single number.classCalculates the aggregate of a feature applied to both the first and second objects in aFeatureInputPairObjects.classCalculates the aggregate of the ratio offirst:secondandsecond:firstfor aFeatureInputPairObjectsclassCalculatesmerged - reduce(first,second)for aFeatureInputPairObjects -
Uses of InitializableBean in org.anchoranalysis.plugin.image.feature.bean.list.permute
Modifier and TypeClassDescriptionclassPermuteDivideByParam<T extends FeatureInputDictionary>Similar to FeatureListProviderPermute but embeds the feature in a GaussianScoreclassPermuteFeature<S,T extends FeatureInput> Permutes one or more properties of a Feature, so as to create a set of FeaturesclassPermuteFeatureBase<T extends FeatureInput>Creates permutations of a feature by modifying a particular property of it in different ways.classPermutes a property on a feature with a sequence of integers.classPermuteFirstSecondOrder<T extends FeatureInputDictionary>Permutes a feature by applying first and second order statistical operations.classPermuteGaussianScore<T extends FeatureInputDictionary>Permutes a feature by embedding it in aGaussianCumulativescore.classPermuteZScore<T extends FeatureInputDictionary>Permutes a feature by embedding it in aZScore. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.feature.bean.metadata
Subclasses of InitializableBean in org.anchoranalysis.plugin.image.feature.bean.metadataModifier and TypeClassDescriptionclassThe bit-depth of the image per channel.classThe number of channels in an image.classThe number of frames in an image.classThe number of resolution-levels in an image in a file.classThe number of series in an image-file. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.feature.bean.object.collection
Modifier and TypeClassDescriptionclassCalculates the number of objects in aFeatureInputObjectCollection. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.feature.bean.object.pair
Modifier and TypeClassDescriptionclassFinds the intersection of two objects and calculates a feature on it -
Uses of InitializableBean in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
Modifier and TypeClassDescriptionclassTODO the center-of-gravity calculation can be turned into a FeatureCalculation which is cacheableclassExpresses the number of intersecting pixels between two objects as a ratio to a denominator.classCalculates the overlap ratio between two objects relative to the size of the first object.classOverlap ratio to the maximum number of pixelsclassCalculates the overlap ratio between two objects relative to the size of the merged object.classCalculates the overlap ratio between two objects relative to the size of the second object. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.feature.bean.object.pair.touching
Subclasses of InitializableBean in org.anchoranalysis.plugin.image.feature.bean.object.pair.touchingModifier and TypeClassDescriptionclassA simple scheme for counting the touching voxels.classA scheme for counting the touching voxels by intersection of object-masksclassA scheme for counting touching voxels.classBase class for features that calculate touching with a dilated bounding box intersection. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.feature.bean.object.single
Modifier and TypeClassDescriptionclassCalculates deterministically a point that is definitely inside the object-mask and outputs a selected axis value.classBase class for features that apply a kernel to the outline of an object. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.feature.bean.object.single.border
Subclasses of InitializableBean in org.anchoranalysis.plugin.image.feature.bean.object.single.borderModifier and TypeClassDescriptionclassBase class for features that check if an object is at the border of an image.classChecks if an object's bounding box is at the border of the image in the XY plane.classChecks if an object's bounding box is at the border of the image in the Z dimension.classCalculates the number of voxels at the border of an object. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox
Subclasses of InitializableBean in org.anchoranalysis.plugin.image.feature.bean.object.single.boundingboxModifier and TypeClassDescriptionclassBase class for features that calculate a value along a specific axis of an object's bounding box.classCalculates the extent of an object's bounding box along a specified axis.classCalculates the maximum coordinate of an object's bounding box along a specified axis.classCalculates the minimum coordinate of an object's bounding box along a specified axis.classCalculates the number of voxels in the bounding box of an object. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.feature.bean.object.single.energy
Subclasses of InitializableBean in org.anchoranalysis.plugin.image.feature.bean.object.single.energyModifier and TypeClassDescriptionclassCounts the number of voxels in an object that have a specific intensity value in a channel.classCalculates the number of voxels on the object that have a neighbor.classA base class for features that operate on a specific channel from the energy stack. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity
Subclasses of InitializableBean in org.anchoranalysis.plugin.image.feature.bean.object.single.intensityModifier and TypeClassDescriptionclassA feature that uses a channel from the energy-stack as identified by an index.classCalculates a statistic from the intensity values covered by a single object-mask in a channel.classCalculates the maximum mean intensity across all slices of an object in a channel.classConstructs a 'shell' around an object by a number of dilation/erosion operations (not including the original object-mask) and measures the mean intensity of this shellclassConstructs a shell around an object-mask using a standard dilation and erosion process.classConstructs a 'shell' around an object by a number of dilation/erosion operations (not including the original object-mask) and measures the mean intensity of this shellclassFrom Page 727 from Lin et al (A Multi-Model Approach to Simultaneous Segmentation and Classification of Heterogeneous Populations of Cell Nuclei -
Uses of InitializableBean in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient
Subclasses of InitializableBean in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradientModifier and TypeClassDescriptionclassCalculates the mean of the intensity-gradient defined by multiple Energy channels in a particular directionclassCalculates the mean of the intensity-gradient defined by multiple Energy channels in a particular directionclassBase class for features that calculate intensity gradients from multiple channels. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.feature.bean.object.single.moments
Subclasses of InitializableBean in org.anchoranalysis.plugin.image.feature.bean.object.single.momentsModifier and TypeClassDescriptionclassA base class for features that are calculated using image-moments.classCalculates the eccentricity of the Principal Axes (as defined by Image Moments).classThe length of a principal-axis (as defined by Image Moments).classAn element from orientation of a principal-axis (as defined by Image Moments).classCalculates the ratio of prinicpal-axis length using Image Moments.classA feature based on one specific principal-axis as identified by image moments. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.feature.bean.object.single.morphological
Subclasses of InitializableBean in org.anchoranalysis.plugin.image.feature.bean.object.single.morphologicalModifier and TypeClassDescriptionclassA base class for features that operate on a derived object mask and calculate a feature on it.classA feature that erodes an object mask and then calculates another feature on the eroded object.classHow many pixels are removed after a morphological closing operation on the object-mask.classCreates a shell around anObjectMaskby applying morphological operations. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.feature.bean.object.single.shape
Modifier and TypeClassDescriptionclassCalculates the standard deviation of distances from surface voxels to the centroid of anObjectMask.classCalculates the shape regularity of the center slice of anObjectMask.classCalculates the shape regularity of the maximum intensity projection of anObjectMask. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.feature.bean.object.single.slice
Modifier and TypeClassDescriptionclassMaximum number of voxels on any slice's contour (edge voxels) across all slices.classMaximum number of voxels in the object-mask across all slices. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.feature.bean.object.single.surface
Subclasses of InitializableBean in org.anchoranalysis.plugin.image.feature.bean.object.single.surfaceModifier and TypeClassDescriptionclassThe number of voxel-faces along the surface (the faces of each voxel that touch outside)classThe number of voxels on the surface (all voxels on the exterior of the object)classA base class for features that calculate the number of voxels on the surface of an object. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.feature.bean.physical
Subclasses of InitializableBean in org.anchoranalysis.plugin.image.feature.bean.physicalModifier and TypeClassDescriptionclassUnitsWithinRange<T extends FeatureInputWithResolution>Checks if a value lies within a range defined by units (a minimum and maximum boundary) -
Uses of InitializableBean in org.anchoranalysis.plugin.image.feature.bean.score
Subclasses of InitializableBean in org.anchoranalysis.plugin.image.feature.bean.scoreModifier and TypeClassDescriptionclassCalculates a level score based on voxel intensity and a given threshold.classBase class for calculating a score based on a threshold level derived from a histogram.classclassSimilar toDifferencebut calculates the width as the standard-deviation of the histogramclassAn abstract base class for features that require aDictionaryfor initialization.classA voxel score that can optionally normalize and adjust the intensity values.classA voxel score that imposes a value relation to a histogram.classNormalizes the voxel intensity by dividing it by a constant value.classThis assumes the histograms correspond to the energy channels exactly (in terms of indexing)classCalculates a voxel score based on whether the voxel intensity is outside a specified range.classRejects voxels with intensity less than a specified minimum, otherwise calculates a score using anotherVoxelScore.classA score that is calculated on a single channel only. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.feature.bean.stack.intensity
Modifier and TypeClassDescriptionclassDataTypeMaxIntensity<T extends FeatureInputEnergy>The maximum-intensity allowed by the data-type of the stack.classThe intensity of a particular channel of the stack, by default the mean-intensity.classThe number of channels in an image-stack. -
Uses of InitializableBean in org.anchoranalysis.plugin.image.feature.bean.stack.object
Modifier and TypeClassDescriptionclassTreats a channel as an object-mask, assuming binary values of 0 and 255 and calls an object-mask featureclassCalculates the median of a feature applied to each connected component -
Uses of InitializableBean in org.anchoranalysis.plugin.imagej.bean.channel.provider
Subclasses of InitializableBean in org.anchoranalysis.plugin.imagej.bean.channel.providerModifier and TypeClassDescriptionclassSubtracts background from a channel using ImageJ'sBackgroundSubtracter.classA base class for applying ImageJ rank filters to channels.classAChannelProviderUnarywith a 'radius' parameter. -
Uses of InitializableBean in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter
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Uses of InitializableBean in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments
Subclasses of InitializableBean in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.momentsModifier and TypeClassDescriptionclassApplies a 2D mean filter to a channel using ImageJ'sRankFilters.classApplies a 2D variance filter to a channel using ImageJ'sRankFilters. -
Uses of InitializableBean in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank
Subclasses of InitializableBean in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rankModifier and TypeClassDescriptionclassApplies a 2D median filter to a channel using ImageJ'sRankFilters.classApplies a 3D median filter to a channel using a hybrid 3D median filter ImageJ plugin. -
Uses of InitializableBean in org.anchoranalysis.plugin.imagej.bean.mask.provider
Subclasses of InitializableBean in org.anchoranalysis.plugin.imagej.bean.mask.providerModifier and TypeClassDescriptionclassFills holes in a mask, with options to skip holes touching the border or exceeding a maximum volume.classApplies an ImageJ (2D) morphological operation to each slice -
Uses of InitializableBean in org.anchoranalysis.plugin.imagej.bean.object.provider
Subclasses of InitializableBean in org.anchoranalysis.plugin.imagej.bean.object.providerModifier and TypeClassDescriptionclassDraws a lines between successive points on the convex-hull of an object.classFills holes in an object. -
Uses of InitializableBean in org.anchoranalysis.plugin.imagej.bean.object.segment
Subclasses of InitializableBean in org.anchoranalysis.plugin.imagej.bean.object.segmentModifier and TypeClassDescriptionclassCreates an object for each separate intensity-value (beginning atstartingColor) by flood-filling. -
Uses of InitializableBean in org.anchoranalysis.plugin.imagej.bean.stack.provider
Subclasses of InitializableBean in org.anchoranalysis.plugin.imagej.bean.stack.provider -
Uses of InitializableBean in org.anchoranalysis.plugin.imagej.bean.threshold
Subclasses of InitializableBean in org.anchoranalysis.plugin.imagej.bean.thresholdModifier and TypeClassDescriptionclassA thresholder that applies a simple intensity threshold and then fills holes in 2D. -
Uses of InitializableBean in org.anchoranalysis.plugin.mpp.bean.object.provider
Subclasses of InitializableBean in org.anchoranalysis.plugin.mpp.bean.object.providerModifier and TypeClassDescriptionclassCreates object-masks from aMarkCollectionwhere (a particular region of) each mark creates an object. -
Uses of InitializableBean in org.anchoranalysis.plugin.mpp.bean.provider.collection
Subclasses of InitializableBean in org.anchoranalysis.plugin.mpp.bean.provider.collectionModifier and TypeClassDescriptionclassCreates a new empty collection of marksclassCreates aMarkCollectionfrom a single mark provided by aSingleMarkProvider.classCreates aMarkCollectionof point marks from anObjectCollection.classProvides aMarkCollectionby referencing it from the initialization context using an ID.classReturns an existing marks-collection or an empty set if it doesn't existclassScales the X and Y coordinates of marks in aMarkCollectionusing aScaleCalculator. -
Uses of InitializableBean in org.anchoranalysis.plugin.mpp.bean.stack.provider
Subclasses of InitializableBean in org.anchoranalysis.plugin.mpp.bean.stack.providerModifier and TypeClassDescriptionclassDraws a colored representation (outline or filled) of anMarkCollectionon a background -
Uses of InitializableBean in org.anchoranalysis.plugin.onnx.bean.object.segment.stack
Modifier and TypeClassDescriptionclassPerforms instance-segmentation using the ONNX Runtime and an.onnxmodel file. -
Uses of InitializableBean in org.anchoranalysis.plugin.opencv.bean.color
Subclasses of InitializableBean in org.anchoranalysis.plugin.opencv.bean.colorModifier and TypeClassDescriptionclassConverts a RGB stack into another color space using OpenCV.classConverts a RGB image to the HSV color space.classConverts a RGB image to the Lab color space. -
Uses of InitializableBean in org.anchoranalysis.plugin.opencv.bean.feature
Subclasses of InitializableBean in org.anchoranalysis.plugin.opencv.bean.featureModifier and TypeClassDescriptionclassCreates the entire HOG descriptor for an image.classOne part of a Histogram of Oriented Gradients descriptor, as applied to an image stack. -
Uses of InitializableBean in org.anchoranalysis.plugin.opencv.bean.object.segment.stack
Modifier and TypeClassDescriptionclassPerforms instance-segmentation using OpenCV's DNN module and a TensorFlow.pbSavedModel file. -
Uses of InitializableBean in org.anchoranalysis.plugin.operator.feature.bean
Subclasses of InitializableBean in org.anchoranalysis.plugin.operator.feature.beanModifier and TypeClassDescriptionclassFromDictionary<T extends FeatureInputDictionary>Extracts a key-value from aDictionaryas a double.classWithValueBase<T extends FeatureInput>A base class for operations that use a specified constant value in combination with a feature. -
Uses of InitializableBean in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
Modifier and TypeClassDescriptionclassAbsoluteValue<T extends FeatureInput>A feature that calculates the absolute value of another feature's result.classAddConstantTo<T extends FeatureInput>A feature that adds a constant value to the result of another feature.classConstantToThePowerOf<T extends FeatureInput>A feature that raises a constant value to the power of another feature's result.classDivide<T extends FeatureInput>A feature that divides the results of multiple features sequentially.classDivideByConstant<T extends FeatureInput>A feature that divides the result of another feature by a constant value.classInvertedMax<T extends FeatureInput>Finds the repciprocal (multiplicate inverse), but imposes a maximum ceiling via a constant.classMultiply<T extends FeatureInput>A feature that multiplies the results of multiple features together.classMultiplyByConstant<T extends FeatureInput>A feature that multiplies the result of another feature by a constant value.classSubtractFrom<T extends FeatureInput>A feature that subtracts the result of another feature from a constant value.classToThePowerOfConstant<T extends FeatureInput>A feature that raises the result of another feature to the power of a constant value. -
Uses of InitializableBean in org.anchoranalysis.plugin.operator.feature.bean.conditional
Modifier and TypeClassDescriptionclassIfCondition<T extends FeatureInput>The result of featureCondition is compared to a threshold, and then either the underlying feature is calculated (positive case), or featureElse is (negative case) -
Uses of InitializableBean in org.anchoranalysis.plugin.operator.feature.bean.list
Subclasses of InitializableBean in org.anchoranalysis.plugin.operator.feature.bean.listModifier and TypeClassDescriptionclassMaximum<T extends FeatureInput>A feature that calculates the maximum value from a list of features.classMean<T extends FeatureInput>Arithmetic mean of a list of featuresclassMeanGeometric<T extends FeatureInput>A feature that calculates the geometric mean of a list of features.classMinimum<T extends FeatureInput>A feature that calculates the minimum value from a list of features. -
Uses of InitializableBean in org.anchoranalysis.plugin.operator.feature.bean.range
Subclasses of InitializableBean in org.anchoranalysis.plugin.operator.feature.bean.rangeModifier and TypeClassDescriptionclassCompareWithRange<T extends FeatureInput>Compares a value with a range, returning specified constants if its inside the range, below it or above itclassCompareWithRangeFeature<T extends FeatureInput>LikeCompareWithRangebut uses features to calculate boundary valuesclassIfConditionWithinRange<T extends FeatureInput>Calculates a value if a condition lies within a certain range, otherwise returns constantsclassIfOutsideRange<T extends FeatureInput>Clamps a feature value if it lies outside a specified range.classNormalizedRange<T extends FeatureInput>The range of two feature values (i.e. max - min), divided by their mean.classRange<T extends FeatureInput>Calculates the statistical range between two feature values, with optional weighting.classRangeCompareBase<T extends FeatureInput>A base class for features that compare a value against a range and return different results based on the comparison.classRangeCompareFromScalars<T extends FeatureInput>A base class for setting the boundaries of a range using constant scalar values. -
Uses of InitializableBean in org.anchoranalysis.plugin.operator.feature.bean.replace
Subclasses of InitializableBean in org.anchoranalysis.plugin.operator.feature.bean.replaceModifier and TypeClassDescriptionclassReplaceInfinity<T extends FeatureInput>Replaces infinite values in a feature's result with a specified replacement value.classReplaceNaN<T extends FeatureInput>Replaces NaN (Not a Number) values in a feature's result with a specified replacement value.classReplaceUnusualValue<T extends FeatureInput>Calculates the underlying feature, but replaces the result with a constant if it is an "unusual" value. -
Uses of InitializableBean in org.anchoranalysis.plugin.operator.feature.bean.statistics
Modifier and TypeClassDescriptionclassGaussianCumulative<T extends FeatureInput>Calculates a score between 0 and 1 based on the Cumulative Distribution Function (CDF) of a Gaussian distribution.classStatisticalBase<T extends FeatureInput>Calculates a score based upon the statistical mean and standard deviation.classZScore<T extends FeatureInput>Calculates the Z-score of a value based on the mean and standard deviation. -
Uses of InitializableBean in org.anchoranalysis.plugin.operator.feature.physical
Subclasses of InitializableBean in org.anchoranalysis.plugin.operator.feature.physicalModifier and TypeClassDescriptionclassConvertUnits<T extends FeatureInput>Converts a feature value from one unit type to another. -
Uses of InitializableBean in org.anchoranalysis.plugin.points.bean
Subclasses of InitializableBean in org.anchoranalysis.plugin.points.beanModifier and TypeClassDescriptionclassclassAMarkCollectionProviderthat fits points from objects to create marks.classSplits a 2D contour represented by an object-mask into several contours, splitting at "turn" points. -
Uses of InitializableBean in org.anchoranalysis.plugin.points.bean.convexhull
Subclasses of InitializableBean in org.anchoranalysis.plugin.points.bean.convexhullModifier and TypeClassDescriptionclassSets particular voxels to high only if they exist on the convex-hull of the outline of a mask.classCalculates a 3D convex hull from a binary mask.classBase class for convex hull implementations. -
Uses of InitializableBean in org.anchoranalysis.plugin.points.bean.feature
Subclasses of InitializableBean in org.anchoranalysis.plugin.points.bean.featureModifier and TypeClassDescriptionclassCalculates the axis ratio of anEllipsoid.classBase class for features that calculate properties of anEllipsoidfitted to an object.classCalculates the ellipsoidicity of an object by fitting anEllipsoidto it.classCalculates the ellipticity of anObjectMask(on the center of gravity slice if it's a z-stack). -
Uses of InitializableBean in org.anchoranalysis.plugin.points.bean.fitter
Subclasses of InitializableBean in org.anchoranalysis.plugin.points.bean.fitterModifier and TypeClassDescriptionclassBase class for conic fitters, providing common properties and methods.classFits a set of points to an ellipse using a linear least squares method.classFits an ellipsoid to points using a linear least squares approachclassBase class for linear least squares fitting using the normal equation method.classA bean for fitting points to a mark using a specified points fitter.classAPointsFitterthat references anotherPointsFitterby its ID.classReflects points in each axes if all points are within a certain distance from it -
Uses of InitializableBean in org.anchoranalysis.test.experiment
Methods in org.anchoranalysis.test.experiment with type parameters of type InitializableBeanModifier and TypeMethodDescriptionstatic <T extends InitializableBean<?,P>, P extends BeanInitialization>
TBeanTestChecker.checkAndInit(T bean, P initialization, Logger logger) Checks if a bean has all necessary items as withBeanTestChecker.check(T)and also initializes the bean. -
Uses of InitializableBean in org.anchoranalysis.test.feature.plugins.mockfeature
Subclasses of InitializableBean in org.anchoranalysis.test.feature.plugins.mockfeatureModifier and TypeClassDescriptionclassA feature that returns the number-of-voxels in an object by using am internal mock-calculation.