Uses of Class
org.anchoranalysis.image.bean.ImageBean

Packages that use ImageBean

Package	Description
org.anchoranalysis.image.bean.channel	Base classes for performing operations on Channels.
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.feature.bean	Beans pertaining to feature definition and calculation.
org.anchoranalysis.image.inference.bean.segment.instance	Instance-segmentation of a Stack.
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.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.mask.provider	Implementations of MaskProvider that use FIJI.
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.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.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.yeong	Implementation of a Watershed transformation based on Yeong et al. 2009.
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.feature.bean.score	Implementations of VoxelScore.
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.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.mpp.bean.object.provider	Implementations of ObjectCollectionProvider.
org.anchoranalysis.plugin.mpp.bean.stack.provider	Implementations of StackProvider involving Mark or related classes.
org.anchoranalysis.plugin.onnx.bean.object.segment.stack	Segmenting a Stack using the ONNX Runtime to produce an ObjectCollection.
org.anchoranalysis.plugin.opencv.bean.color	Operations involving color-spaces and OpenCV.
org.anchoranalysis.plugin.opencv.bean.object.segment.stack	Segmentation of a Stack using OpenCV.
org.anchoranalysis.plugin.points.bean	Beans that fit or otherwise manipulate sets of points.
org.anchoranalysis.plugin.points.bean.convexhull	Convex hull operations.

Uses of ImageBean in org.anchoranalysis.image.bean.channel

Subclasses of ImageBean in org.anchoranalysis.image.bean.channel

Modifier and Type	Class	Description
class	ConvertChannelTo<T>	Creates a ChannelConverter for converting a channel to a particular type.

Uses of ImageBean in org.anchoranalysis.image.bean.object

Subclasses of ImageBean in org.anchoranalysis.image.bean.object

Modifier and Type	Class	Description
class	ObjectFilter	Base class for filtering an ObjectCollection to remove objects according to a criteria.
class	ObjectMatcher	Matches an object with other objects.

Uses of ImageBean in org.anchoranalysis.image.bean.provider

Subclasses of ImageBean in org.anchoranalysis.image.bean.provider

Modifier and Type	Class	Description
class	BeanProviderAsStackBase<T,S>	A provider base-class that as well as providing type S, also provides a Stack.
class	ChannelProvider	Base class for beans that implement Provider to provide a Channel and associated Stack.
class	ChannelProviderBinary	Implementation of ChannelProvider that calls two ChannelProviders that must provide Channels of the same dimensions.
class	ChannelProviderTernary	Implementation of ChannelProvider that calls three ChannelProviders that must provide Channels of the same dimensions.
class	ChannelProviderUnary	Implementation of ChannelProvider that calls a single delegate ChannelProvider.
class	DimensionsProvider	Base class for beans that implement Provider to provide Dimensions.
class	HistogramProvider	Base class for beans that implement Provider to provide a Histogram.
class	HistogramProviderUnary	Implementation of HistogramProvider that calls a single delegate HistogramProvider.
class	MaskProvider	Base class for beans that implement Provider to provide a Mask and associated Stack.
class	MaskProviderUnary	Implementation of MaskProvider that calls a single delegate MaskProvider.
class	ObjectCollectionProvider	Base class for beans that implement Provider to provide an ObjectCollection.
class	ObjectCollectionProviderUnary	Implementation of ObjectCollectionProvider that calls a single delegate Provider<ObjectCollection>.

Uses of ImageBean in org.anchoranalysis.image.bean.provider.stack

Subclasses of ImageBean in org.anchoranalysis.image.bean.provider.stack

Modifier and Type	Class	Description
class	Arrange	Creates a stack that combines other stacks.
class	StackProvider	Base class for beans that implement Provider to provide a Stack.
class	StackProviderUnary	Implementation of StackProvider that calls a single delegate Provider<Stack>.

Uses of ImageBean in org.anchoranalysis.image.bean.segment

Subclasses of ImageBean in org.anchoranalysis.image.bean.segment

Modifier and Type	Class	Description
class	SegmentationBean<T>	Performs some kind of segmentation on an image.

Uses of ImageBean in org.anchoranalysis.image.bean.segment.binary

Subclasses of ImageBean in org.anchoranalysis.image.bean.segment.binary

Modifier and Type	Class	Description
class	BinarySegmentation	Performs a segmentation on voxels so that each voxel has an on or off state after the operation.
class	BinarySegmentationReference	Uses an existing BinarySegmentation that is located by a unique identifier.
class	BinarySegmentationThreshold	Implementation of BinarySegmentation that performs global thresholding.
class	BinarySegmentationUnary	An implementation of BinarySegmentation that delegates to one other BinarySegmentation.

Uses of ImageBean in org.anchoranalysis.image.bean.segment.object

Subclasses of ImageBean in org.anchoranalysis.image.bean.segment.object

Modifier and Type	Class	Description
class	SegmentChannelIntoObjects	A base class for algorithms to segment a channel into one or more objects.
class	SegmentChannelIntoObjectsUnary	Implementation of SegmentChannelIntoObjects that calls a single delegate SegmentChannelIntoObjects.

Uses of ImageBean in org.anchoranalysis.image.bean.spatial

Subclasses of ImageBean in org.anchoranalysis.image.bean.spatial

Modifier and Type	Class	Description
class	ScaleCalculator	Calculating a scaling-factor from dimensions.

Uses of ImageBean in org.anchoranalysis.image.feature.bean

Subclasses of ImageBean in org.anchoranalysis.image.feature.bean

Modifier and Type	Class	Description
class	VoxelScore	Calculates a per-voxel score.

Uses of ImageBean in org.anchoranalysis.image.inference.bean.segment.instance

Subclasses of ImageBean in org.anchoranalysis.image.inference.bean.segment.instance

Modifier and Type	Class	Description
class	SegmentStackIntoObjectsPooled<T extends InferenceModel>	A base class for algorithms to segment a stack into one or more objects - using a pool of models
class	SegmentStackIntoObjectsScaleDecode<T,S extends ImageInferenceModel<T>>	A SegmentStackIntoObjectsScaleDecode that scales the input image, before performing inference, and then decodes the output.
class	SuppressNonMaximum<T extends InferenceModel>	Applies a segmentation procedure followed by non-maximum suppression.

Uses of ImageBean in org.anchoranalysis.image.io.bean.object.feature

Subclasses of ImageBean in org.anchoranalysis.image.io.bean.object.feature

Modifier and Type	Class	Description
class	OutputFeatureTable	Specifies a table of feature-calculations on objects.

Uses of ImageBean in org.anchoranalysis.image.io.bean.stack.combine

Subclasses of ImageBean in org.anchoranalysis.image.io.bean.stack.combine

Modifier and Type	Class	Description
class	TileWithLabels	Tiles a number of StackProviderWithLabels as a single StackProvider.
class	WriteText	Creates an image that contains text only.

Uses of ImageBean in org.anchoranalysis.plugin.fiji.bean.channel.provider

Subclasses of ImageBean in org.anchoranalysis.plugin.fiji.bean.channel.provider

Modifier and Type	Class	Description
class	AnisotropicDiffusion	Performs Perona-Malik Anisotropic Diffusion.
class	MinimumFilter	Applies a minimum filter to a channel using ImageJ's MinMaxMedian plugin.

Uses of ImageBean in org.anchoranalysis.plugin.fiji.bean.channel.provider.distance

Subclasses of ImageBean in org.anchoranalysis.plugin.fiji.bean.channel.provider.distance

Modifier and Type	Class	Description
class	DistanceTransform3D	Euclidian Distance Transform from ImageJ that works on 2D as well as 3D z-stacks.
class	DistanceTransformForEachObject3D	Like DistanceTransform3D but applies the distance transform separately for each object in a collection.

Uses of ImageBean in org.anchoranalysis.plugin.fiji.bean.mask.provider

Subclasses of ImageBean in org.anchoranalysis.plugin.fiji.bean.mask.provider

Modifier and Type	Class	Description
class	AutoLocalThreshold	Applies local thresholding algorithm using Fiji's {link Auto_Local_Threshold} plugin

Uses of ImageBean in org.anchoranalysis.plugin.image.bean.channel.convert

Subclasses of ImageBean in org.anchoranalysis.plugin.image.bean.channel.convert

Modifier and Type	Class	Description
class	ScaleByDictionary	Scales by compressing a certain range of values into the 8-bit signal.
class	ScaleByMinMaxValue	Scales by compressing a certain range of values into the 8-bit signal
class	ScaleByTypeToByte	Converts a channel to unsigned byte format, scaling the values based on the original voxel type.
class	ToByte	Converts a channel to unsigned byte format without any scaling.

Uses of ImageBean in org.anchoranalysis.plugin.image.bean.channel.provider

Subclasses of ImageBean in org.anchoranalysis.plugin.image.bean.channel.provider

Modifier and Type	Class	Description
class	CreateNew	Creates a new channel with all values initialized to a constant (by default zero)
class	Duplicate	Creates a duplicate of the input channel.
class	FromDimensionsBase	An abstract base class for creating a channel from specified dimensions.
class	FromInput	Finds the input-stack using a conventional name of input_image - and extracts the first channel
class	FromStack	Extracts a channel from a provider of a stack.
class	IfParamEquals	Provides a channel based on a condition from a dictionary.
class	Reference	Provides a channel by referencing it from a a set of named-channels.
class	TwoVoxelMappingBase	Takes the two channels and creates a NEW third channel whose pixels are a function of the two channels
class	UnaryWithObjectsBase	An abstract base class for creating a channel from an existing channel and a collection of objects.
class	UnaryWithValueBase	A ChannelProviderUnary which has a scalar value field.

Uses of ImageBean in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic

Subclasses of ImageBean in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic

Modifier and Type	Class	Description
final class	AddConstant	Adds a constant value to each voxel in a channel.
class	ArithmeticWithConstantBase	Base-class for operations that perform a binary arithmetic operation with each voxel-value and a constant.
class	ArithmeticWithConstantConditionallyWriteBase	Base class for arithmetic operations that conditionally overwrite voxel values with a constant.
class	Invert	Inverts the intensity values of a Channel by subtracting each voxel from the maximum value for the channel's data type.
class	MaxTwoChannels	Creates a new channel by taking the maximum value of corresponding voxels from two input channels.
class	MaxWithConstant	Replaces voxel values with a constant value if the constant is greater than the original voxel value.
class	MeanThreeChannels	Creates a new channel that is the mean of three input channels.
class	MinTwoChannels	Creates a new channel by taking the minimum value of corresponding voxels from two input channels.
class	MinWithConstant	Replaces voxel values with a constant value if the constant is less than the original voxel value.
class	MultiplyConstant	Multiplies each voxel value in a channel by a constant value.
class	MultiplyTwoChannels	Creates a new channel by multiplying corresponding voxels from two input channels.
class	SubtractFromConstant	Subtracts each voxel value in a channel from a constant value.
class	SubtractMean	Subtracts the mean intensity (of the entire channel or a masked portion thereof) from every voxel.
class	SubtractTwoChannels	Creates a new channel by subtracting corresponding voxels of the second channel from the first channel.

Uses of ImageBean in org.anchoranalysis.plugin.image.bean.channel.provider.assign

Subclasses of ImageBean in org.anchoranalysis.plugin.image.bean.channel.provider.assign

Modifier and Type	Class	Description
class	AssignFromChannel	Copies the pixels from channelAssignFrom to channel (possibly masking).
class	AssignFromDictionary	Assigns a value from a dictionary to all voxels in a channel.
class	AssignFromIntersectingObjects	Matches source-objects to target objects, based upon intersection, and assigns the value in the respective source object to the target object
class	AssignValue	Assigns a constant (scalar) value to the portion of the image covered by a mask

Uses of ImageBean in org.anchoranalysis.plugin.image.bean.channel.provider.convert

Subclasses of ImageBean in org.anchoranalysis.plugin.image.bean.channel.provider.convert

Modifier and Type	Class	Description
class	Convert<T>	Converts a channel by applying a converter (no histogram is involved in the conversion).
class	ConvertBase	Base class for channel providers that perform conversions on a single input channel.
class	ConvertWithHistogram<T>	Converts a channel to a different voxel data-type by applying a converter with an associated histogram.

Uses of ImageBean in org.anchoranalysis.plugin.image.bean.channel.provider.gradient

Subclasses of ImageBean in org.anchoranalysis.plugin.image.bean.channel.provider.gradient

Modifier and Type	Class	Description
class	GradientBase	Base class to calculate the gradient of the voxels in a Channel.
class	GradientBaseAddSum	Like GradientBase but allows an arbitrary constant to be added to voxels storing the gradient.
class	GradientForAxis	Extracts the gradient in the direction of a particular axis (identified by an index)
class	GradientXY	Calculates a Channel's gradient along the x and y axes.
class	Sobel	3x3 Sobel Filter

Uses of ImageBean in org.anchoranalysis.plugin.image.bean.channel.provider.intensity

Subclasses of ImageBean in org.anchoranalysis.plugin.image.bean.channel.provider.intensity

Modifier and Type	Class	Description
class	Blur	Blurs an image using a particular strategy (defaults to a gaussian blur in each slice)
class	IfVoxelZero	Creates a new channel which is a merged version of two input channels according to rules.
class	Median	Applies a median-filter with square kernel
class	NormalizeDifferenceToMedian	Corrects a channel in the following way
class	NormalizeObjectIntensity	Rewrites the intensity for each object-mask (assume no overlap) so that its mean is 128
class	QuantileStretch	Changes the voxel values to map the range of 0th quantile to xth quantile across the entire voxel data range
class	ScaleXY	Scales the channel in the X and Y dimensions.

Uses of ImageBean in org.anchoranalysis.plugin.image.bean.channel.provider.mask

Subclasses of ImageBean in org.anchoranalysis.plugin.image.bean.channel.provider.mask

Modifier and Type	Class	Description
class	FromMask	Creates a Channel directly from a Mask without any modification.
class	FromMaskBase	A base class for a ChannelProvider which also uses a binary-mask, but which doesn't use any other ChannelProvider as an input.
class	UnaryWithMaskBase	A base class for a ChannelProviderUnary which also uses a binary mask.
class	ZeroOutsideMask	Set pixels NOT IN the mask to 0, but keep pixels IN the mask identical.

Uses of ImageBean in org.anchoranalysis.plugin.image.bean.channel.provider.object

Subclasses of ImageBean in org.anchoranalysis.plugin.image.bean.channel.provider.object

Modifier and Type	Class	Description
class	LevelPerObjectBase	Creates a channel with a level calculated for each object using various methods.
class	LevelPerObjectIndependently	Creates a channel with different threshold-levels for each object, calculating the level only from the histogram of the particular object.
class	LevelPerObjectNeighbors	Calculates a threshold-level for each object collectively based on other objects

Uses of ImageBean in org.anchoranalysis.plugin.image.bean.channel.provider.score

Subclasses of ImageBean in org.anchoranalysis.plugin.image.bean.channel.provider.score

Modifier and Type	Class	Description
class	IdentifyObjects	Assigns a unique id number to each object.
class	ScoreObjects	Creates a channel by scoring objects based on a feature calculation.
class	ScoreVoxels	Assigns a score (a value indicating how probable something is) to each voxel

Uses of ImageBean in org.anchoranalysis.plugin.image.bean.channel.provider.slice

Subclasses of ImageBean in org.anchoranalysis.plugin.image.bean.channel.provider.slice

Modifier and Type	Class	Description
class	ExtractCenterSlice	Extracts the slice at the center (rounding down) of the range of z-stacks.
class	ExtractSliceRange	Extracts slices from sliceStart (inclusive) to sliceEnd (inclusive).
class	MaximumIntensityProjection	Creates a maximum intensity projection of a 3D Channel.
class	MeanIntensityProjection	Creates a mean intensity projection of a 3D Channel.
class	RepeatSlice	Creates a new channel with specific dimensions that repeatedly duplicates a slice from an existing channel

Uses of ImageBean in org.anchoranalysis.plugin.image.bean.dictionary

Subclasses of ImageBean in org.anchoranalysis.plugin.image.bean.dictionary

Modifier and Type	Class	Description
class	DictionaryCondition	Checks if a value in a Dictionary is equal to an expected value.

Uses of ImageBean in org.anchoranalysis.plugin.image.bean.dimensions.provider

Subclasses of ImageBean in org.anchoranalysis.plugin.image.bean.dimensions.provider

Modifier and Type	Class	Description
class	FromChannel	Creates image-dimensions by referencing them from a ChannelProvider.
class	GuessDimensions	Guesses dimensions from an input-image if it exists.
class	SpecifyDimensions	Specifies dimensions explicitly via bean properties.

Uses of ImageBean in org.anchoranalysis.plugin.image.bean.histogram.provider

Subclasses of ImageBean in org.anchoranalysis.plugin.image.bean.histogram.provider

Modifier and Type	Class	Description
class	CutBelowThreshold	This cuts a Histogram below a threshold BUT TRANSFERS ALL THE COUNT greater than equal to the threshold into the bin just below the threshold value
class	FromChannel	Creates a Histogram from a Channel, optionally using a mask.
class	GreaterThanThreshold	Thresholds a histogram using a CalculateLevel keeping only the values greater equal than the threshold
class	Reference	A provider that references an existing Histogram by its identifier.

Uses of ImageBean in org.anchoranalysis.plugin.image.bean.mask.provider

Subclasses of ImageBean in org.anchoranalysis.plugin.image.bean.mask.provider

Modifier and Type	Class	Description
class	AllValuesOff	Creates a new mask of particular dimensionality where all values are off.
class	AllValuesOn	Creates a new mask of particular dimensionality where all values are on.
class	Duplicate	A provider that creates a duplicate of a given Mask.
class	FromChannelBase	Base-class for MaskProviders that accept a Channel as input.
class	FromDimensionsBase	Base class for MaskProviders that create a mask based on given dimensions.
class	Invert	Switches on voxels to off and vice-versa.
class	Reference	A provider that references an existing Mask by its identifier.
class	ScaleXY	Scales the mask in XY dimensions, but not in Z dimension.

Uses of ImageBean in org.anchoranalysis.plugin.image.bean.mask.provider.combine

Subclasses of ImageBean in org.anchoranalysis.plugin.image.bean.mask.provider.combine

Modifier and Type	Class	Description
class	And	Outputs the logical operation and voxelwise on both masks, modifying {mask} with the result.
class	CombineBase	Base class for combining two masks.
class	IfHighLow	Outputs the logical operation iff first==HIGH and second==LOW then LOW voxelwise on both masks, modifying {mask} with the result.
class	Or	Outputs the logical operation or voxelwise on both masks, modifying {mask} with the result.
class	Xor	Outputs the logical operation xor (exclusive or) voxelwise on both masks, modifying {mask} with the result.

Uses of ImageBean in org.anchoranalysis.plugin.image.bean.mask.provider.convert

Subclasses of ImageBean in org.anchoranalysis.plugin.image.bean.mask.provider.convert

Modifier and Type	Class	Description
class	FromChannel	Creates a mask from an existing channel, reusing the channel's buffer and considering all 0 values as off, and 255 values as on.
class	FromObjects	Creates a Mask from a collection of object-masks.
class	FromStackChannel	Creates a Mask from a specific channel in a stack.

Uses of ImageBean in org.anchoranalysis.plugin.image.bean.mask.provider.morphological

Subclasses of ImageBean in org.anchoranalysis.plugin.image.bean.mask.provider.morphological

Modifier and Type	Class	Description
class	Box	Creates a Mask where all pixels are on within a box region.
class	Dilate	Performs a dilation morphological operation on BinaryVoxels.
class	Erode	Performs an erosion morphological operation on BinaryVoxels.
class	ExteriorContour	Finds the exterior outer contour for a Mask that forms its outline.
class	FitBoxToOnVoxels	Fits a box around the on voxels.
class	MorphologicalOperatorBase	Base class for performing morphological operations on BinaryVoxels.

Uses of ImageBean in org.anchoranalysis.plugin.image.bean.mask.provider.predicate

Subclasses of ImageBean in org.anchoranalysis.plugin.image.bean.mask.provider.predicate

Modifier and Type	Class	Description
class	IfKeyValueCondition	The current mask is returned if a condition on key-values is satisfied otherwise maskElse is returned.
class	IfNotEmpty	The current mask is returned if it's non-empty (at least one on voxel) otherwise maskElse is returned.
class	IfObjectFilter	The current mask is returned if the mask (treated as an object) passed an object-filter, otherwise maskElse is returned.
class	IfPredicateBase	Base class which multiplexes between the current mask and an alternative depending if a condition is met.
class	IfStackExists	The current mask is a particular stack exists (at least one on voxel) otherwise maskElse is returned.

Uses of ImageBean in org.anchoranalysis.plugin.image.bean.mask.provider.segment

Subclasses of ImageBean in org.anchoranalysis.plugin.image.bean.mask.provider.segment

Modifier and Type	Class	Description
class	SegmentChannel	Applies a BinarySegmentation algorithm to derive a mask from a channel
class	Threshold	Thresholds a channel to produce a mask, reusing (and modifying) the input-buffers of the channel if possible.

Uses of ImageBean in org.anchoranalysis.plugin.image.bean.mask.provider.slice

Subclasses of ImageBean in org.anchoranalysis.plugin.image.bean.mask.provider.slice

Modifier and Type	Class	Description
class	FlattenZ	Flattens a mask in the z-dimension, so it is 2D instead of 3D (like a maximum intensity projection).
class	RepeatSlice	Creates a new mask with specific dimensions that repeatedly duplicates a slice from an existing mask

Uses of ImageBean in org.anchoranalysis.plugin.image.bean.object.filter

Subclasses of ImageBean in org.anchoranalysis.plugin.image.bean.object.filter

Modifier and Type	Class	Description
class	ObjectFilterPredicate	Uses a predicate to make a decision whether to keep objects or not.
class	ObjectFilterRelation	An independent object-filter that uses a relation in its predicate.

Uses of ImageBean in org.anchoranalysis.plugin.image.bean.object.filter.collective

Subclasses of ImageBean in org.anchoranalysis.plugin.image.bean.object.filter.collective

Modifier and Type	Class	Description
class	DiscardOutliers	Calculates features values for all objects, and discards any object less than quantile - (minRatio * stdDev)
class	RelationWithMatches	Matches each object with others, and keeps only those where a relation holds true for all matches (in terms of features)

Uses of ImageBean in org.anchoranalysis.plugin.image.bean.object.filter.combine

Subclasses of ImageBean in org.anchoranalysis.plugin.image.bean.object.filter.combine

Modifier and Type	Class	Description
class	And	Applies multiples filter with logical AND i.e. an object must pass all objects in the list to remain.
class	ObjectFilterCombine	A filter that combines other filters (in a list)
class	Or	Applies multiples filter with logical OR i.e. an object must pass any one of the filter steps to remain.

Uses of ImageBean in org.anchoranalysis.plugin.image.bean.object.filter.independent

Subclasses of ImageBean in org.anchoranalysis.plugin.image.bean.object.filter.independent

Modifier and Type	Class	Description
class	GreaterIntersectionWith	Only accepts an object if it has greater (or EQUAL) intersection with objectsGreater than objectsLesser
class	IntensityGreaterEqualThan	Only keep objects where at least one voxel (on a particular channel) has intensity greater or equal to a threshold.
class	IntersectsWith	Keeps objects which intersects with ANY ONE of a collection of other objects.
class	NotTouchingSceneBorder	Keeps only objects that are not adjacent to the scene-border (i.e. have a bounding-box on the very edge of the image)
class	ThresholdedFeature	Only keeps objects whose feature-value satisfies a condition relative to a threshold.
class	ThresholdedVolume	Only keeps objects whose feature-value satisfies a condition relative to a threshold.

Uses of ImageBean in org.anchoranalysis.plugin.image.bean.object.match

Subclasses of ImageBean in org.anchoranalysis.plugin.image.bean.object.match

Modifier and Type	Class	Description
class	Always	Specifies a single object that will always be the "match" for whatever source object.
class	Bridge	Matches to another object, and then uses that object to bridge to another
class	Intersection	An ObjectMatcher that matches objects based on their intersection with a provided set of objects.

Uses of ImageBean in org.anchoranalysis.plugin.image.bean.object.provider

Subclasses of ImageBean in org.anchoranalysis.plugin.image.bean.object.provider

Modifier and Type	Class	Description
class	AtIndex	Extract a single ObjectMask into a new collection.
class	Concatenate	An ObjectCollectionProvider that concatenates multiple ObjectCollections from a list of providers.
class	Duplicate	Duplicates (deep copy) an object-collection.
class	Empty	Creates an empty object-collection.
class	IfParamEqual	Multiplexes between two object-collection-providers depending on whether a parameter value equals a particular string
class	Permute	Permutes some changes over an ObjectCollectionProvider and collects all the results in an ObjectCollection
class	Reference	An ObjectCollectionProvider that references an existing ObjectCollection by its identifier.
class	ReferenceOrElse	Returns a object-collection by name if it exists, or else calls objectsElse if it doesn't exist.
class	Scale	Scales all the objects in the collection by a particular scale-factor.
class	UnaryWithChannelBase	Base class for ObjectCollectionProviderUnary that also requires a Channel.
class	WithChannelBase	Base class for ObjectCollectionProviders that create objects from a Channel.
class	WithContainerBase	Base class for ObjectCollectionProviderUnary that take an optional objectsContainer bean-field.
class	WithDimensionsBase	Base class for ObjectCollectionProviderUnary classes that require dimensions to be specified.
class	WithOptionalDimensionsBase	Base class for ObjectCollectionProviderUnary classes that offer an optional means to specify dimensions.

Uses of ImageBean in org.anchoranalysis.plugin.image.bean.object.provider.connected

Subclasses of ImageBean in org.anchoranalysis.plugin.image.bean.object.provider.connected

Modifier and Type	Class	Description
class	ConnectedComponentsFromMask	Converts a binary-mask into its connected components
class	DecomposeIntoConnectedComponents	Ensures each object in a collection is a connected-component, decomposing it if necessary into multiple objects.
class	RejectIfNotConnected	Rejects a set of objects, if any object is not fully connected (pixels form two or more separate connected components)

Uses of ImageBean in org.anchoranalysis.plugin.image.bean.object.provider.feature

Subclasses of ImageBean in org.anchoranalysis.plugin.image.bean.object.provider.feature

Modifier and Type	Class	Description
class	ObjectCollectionProviderWithFeature	An abstract base class for object collection providers that use a feature evaluator.
class	ObjectWithMaximumFeature	Finds the object with the maximum feature-value from a collection.
class	ObjectWithMaximumFeatureFromEachMatchedCollection	Finds the object with the maximum feature among a group of matches for each object.
class	SortByFeature	Creates a new object-collection with objects sorted by a derived feature-value (in ascending order)

Uses of ImageBean in org.anchoranalysis.plugin.image.bean.object.provider.filter

Subclasses of ImageBean in org.anchoranalysis.plugin.image.bean.object.provider.filter

Modifier and Type	Class	Description
class	Filter	Filters an ObjectCollection using the specified ObjectFilter.
class	FilterByGroup	Filters an ObjectCollection by grouping objects and then applying a filter to each group.
class	IntersectsWithContainer	Returns only the objects that intersect with at least one object in the container
class	Match	Provides an ObjectCollection by matching objects using a specified ObjectMatcher.
class	NotInContainer	Filters objects to keep only those which are NOT in the container.
class	ObjectCollectionProviderFilterBase	Base class for object collection providers that apply a filter to the objects.
class	RemoveTouchingBorder	Considers all possible pairs of objects in a provider, and removes those that touch the border.

Uses of ImageBean in org.anchoranalysis.plugin.image.bean.object.provider.mask

Subclasses of ImageBean in org.anchoranalysis.plugin.image.bean.object.provider.mask

Modifier and Type	Class	Description
class	AndObjectsWithMasks	Reduce the size of individual objects (if neccessary, and minimally) to fit within a binary-mask.
class	FromMask	Converts a binary-mask to an object-collection (containing a single object)

Uses of ImageBean in org.anchoranalysis.plugin.image.bean.object.provider.merge

Subclasses of ImageBean in org.anchoranalysis.plugin.image.bean.object.provider.merge

Modifier and Type	Class	Description
class	MergeBase	A base class for algorithms that merge object-masks.
class	MergeGreedyToIncreaseObjectFeature	Naive greedy merge strategy when any two neighboring objects are merged if it increases a feature.
class	MergePairs	Merges objects if a pair feature value satisfies a condition.
class	MergeToIncreaseObjectFeature	Merges neighboring objects if it results in an increase in the average feature-value calculated on each single object.
class	MergeTwoCollectionsItemwise	Merges itemwise objects from two collections.
class	MergeWithFeature	Base class for object-merging strategies that involve calculating a feature.
class	MergeWithOptionalDistanceConstraint	Expands MergeBase by optionally imposing a maximum-distance requirement between objects that are possibly merged.

Uses of ImageBean in org.anchoranalysis.plugin.image.bean.object.provider.morphological

Subclasses of ImageBean in org.anchoranalysis.plugin.image.bean.object.provider.morphological

Modifier and Type	Class	Description
class	Dilate	Dilates each object in the collection, growing bounding-boxes as necessary in relevant dimensions.
class	Erode	Erodes each object in the collection, growing bounding-boxes as necessary in relevant dimensions.
class	ObjectCollectionProviderMorphological	Base class for providers that apply morphological operations to an ObjectCollection.

Uses of ImageBean in org.anchoranalysis.plugin.image.bean.object.provider.segment

Subclasses of ImageBean in org.anchoranalysis.plugin.image.bean.object.provider.segment

Modifier and Type	Class	Description
class	BinarySegmentByObject	Performs a binary-segmentation using the upstream objects as masks.
class	SegmentChannel	Segments a channel into objects using a specified segmentation algorithm.
class	SegmentChannelByObject	Performs segmentation of a channel using each object in the upstream collection as a mask.
class	SegmentStack<T extends InferenceModel>	Segments a stack into objects.
class	SegmentWithSeeds	Takes each object one-by-one from objectsSource, and finds matching seeds from objectsSeeds

Uses of ImageBean in org.anchoranalysis.plugin.image.bean.object.provider.slice

Subclasses of ImageBean in org.anchoranalysis.plugin.image.bean.object.provider.slice

Modifier and Type	Class	Description
class	ExtendInZ	Creates a 3D version of an object by replicating each input-object across the z-dimension to meet (3D) dimensions.
class	ExtendInZWithinContainer	Extends an object (2D/3D) as much as it can within the z-slices of a containing object
class	FlattenZ	Flattens all object-masks in the z-dimension, so it is 2D instead of 3D (like a maximum intensity projection).
class	SliceAt	Extracts a specific slice from a collection of 3D objects.

Uses of ImageBean in org.anchoranalysis.plugin.image.bean.object.provider.split

Subclasses of ImageBean in org.anchoranalysis.plugin.image.bean.object.provider.split

Modifier and Type	Class	Description
class	RemoveIntersectingVoxels	Considers all possible pairs of objects in a provider, and removes any intersecting pixels
class	SplitByObjects	Splits objects in a collection based on intersections with another set of objects.
class	SplitIntoSquares	Splits objects into sub-objects by cutting by an orthogonal square lattice (like a chessboard).

Uses of ImageBean in org.anchoranalysis.plugin.image.bean.object.segment.channel

Subclasses of ImageBean in org.anchoranalysis.plugin.image.bean.object.segment.channel

Modifier and Type	Class	Description
class	AtScale	Perform a segmentation at a different scale, and then fit the results back to the original scale.
class	ConnectedComponentsFromBinarySegmentation	Performs a binary-segmentation of the channel and converts its connected-components into objects
class	Filter	Applies an object-filter to the results of an upstream segmentation.
class	ImposeMinima	Imposes minima in seed locations on the input-channel before performing the segmentation
class	Mser	Applies the MSER algorithm from imglib2
class	SegmentOnMaximumIntensityAndExpandInZ	Perform a segmentation in a MIP instead of z-stacks, and fits the result back into a 3D segmentation.

Uses of ImageBean in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong

Subclasses of ImageBean in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong

Modifier and Type	Class	Description
class	WatershedYeong	A 'rainfall' watershed algorithm

Uses of ImageBean in org.anchoranalysis.plugin.image.bean.scale

Subclasses of ImageBean in org.anchoranalysis.plugin.image.bean.scale

Modifier and Type	Class	Description
class	ConstantScaleFactor	Scale X and Y dimension by a constant floating-point number.
class	FitTo	Scales an image to approximately similar in size to a SizeXY.
class	Invert	Invert the ScaleFactor calculated by the scaleCalculator delegate.
class	MinimumXYResolution	Calculates a scale factor to ensure a minimum XY resolution is achieved.
class	ToDimensions	Calculates a scaling-factor to make the source image have identical dimensions as dimensionsTarget.
class	ToSuggested	Scales to the suggested-size if one is provided, otherwise calls fallback.

Uses of ImageBean in org.anchoranalysis.plugin.image.bean.segment.binary

Subclasses of ImageBean in org.anchoranalysis.plugin.image.bean.segment.binary

Modifier and Type	Class	Description
class	Invert	Performs a segmentation and inverts and on and off bytes
class	Repeat	Repeats a binary segmentation operation for a specified number of iterations.
class	Sequence	Performs a sequence of succesive segmentations
class	ThresholdAgainstChannel	Thresholds each voxels by comparing against another channel that has per-voxel thresholds

Uses of ImageBean in org.anchoranalysis.plugin.image.bean.stack.provider

Subclasses of ImageBean in org.anchoranalysis.plugin.image.bean.stack.provider

Modifier and Type	Class	Description
class	Concatenate	Combines all the channels from one or more sources (stacks, channels etc.)
class	FromChannelOrMask	Creates a Stack from a Channel or Mask (reusing the voxel buffers).
class	FromInput	Finds the input-stack using a conventional name of input_image
class	Reference	Retrieves an existing stack.

Uses of ImageBean in org.anchoranalysis.plugin.image.bean.stack.provider.color

Subclasses of ImageBean in org.anchoranalysis.plugin.image.bean.stack.provider.color

Modifier and Type	Class	Description
class	ColoredBase	Base class for providers that draw entities (an outline or filled) on a background.
class	ColoredBaseWithGenerator	Like ColoredBase but uses a generator to determine the colors for the objects.
class	ColoredMask	Draws a colored representation (outline or filled) of a ObjectMask on a background
class	ColoredObjects	Draws a colored representation (outline or filled) of an ObjectCollection on a background
class	ThreeChannels	Provides a Stack by combining up to three channels (red, green, blue) into an RGB image.
class	ThreeColoredObjects	Colors three collections of objects in RED, GREEN, BLUE channels on top of a background.

Uses of ImageBean in org.anchoranalysis.plugin.image.feature.bean.score

Subclasses of ImageBean in org.anchoranalysis.plugin.image.feature.bean.score

Modifier and Type	Class	Description
class	CalculateLevel	Calculates a level score based on voxel intensity and a given threshold.
class	CalculateLevelBase	Base class for calculating a score based on a threshold level derived from a histogram.
class	Difference
class	DifferenceCalculateLevelStandardDeviation	Similar to Difference but calculates the width as the standard-deviation of the histogram
class	FromDictionaryBase	An abstract base class for features that require a Dictionary for initialization.
class	Identity	A voxel score that can optionally normalize and adjust the intensity values.
class	IdentityImposeValueRelationToHistogram	A voxel score that imposes a value relation to a histogram.
class	NormalizeByConstant	Normalizes the voxel intensity by dividing it by a constant value.
class	NormalizeByMax	This assumes the histograms correspond to the energy channels exactly (in terms of indexing)
class	OutsideRange	Calculates a voxel score based on whether the voxel intensity is outside a specified range.
class	RejectIfIntensityLessThan	Rejects voxels with intensity less than a specified minimum, otherwise calculates a score using another VoxelScore.
class	SingleChannel	A score that is calculated on a single channel only.

Uses of ImageBean in org.anchoranalysis.plugin.imagej.bean.channel.provider

Subclasses of ImageBean in org.anchoranalysis.plugin.imagej.bean.channel.provider

Modifier and Type	Class	Description
class	BackgroundSubtractor	Subtracts background from a channel using ImageJ's BackgroundSubtracter.
class	WithFilterBase	A base class for applying ImageJ rank filters to channels.
class	WithRadiusBase	A ChannelProviderUnary with a 'radius' parameter.

Uses of ImageBean in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter

Subclasses of ImageBean in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter

Modifier and Type	Class	Description
class	EdgeFilterIJ	Applies an edge detection filter to each slice of a Channel independently using ImageJ's FIND_EDGES filter.
class	GaussianBlur2D	Applies a 2D Gaussian blur filter to each slice of a Channel independently.

Uses of ImageBean in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments

Subclasses of ImageBean in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments

Modifier and Type	Class	Description
class	MeanFilter2D	Applies a 2D mean filter to a channel using ImageJ's RankFilters.
class	VarianceFilter2D	Applies a 2D variance filter to a channel using ImageJ's RankFilters.

Uses of ImageBean in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank

Subclasses of ImageBean in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank

Modifier and Type	Class	Description
class	MedianFilter2D	Applies a 2D median filter to a channel using ImageJ's RankFilters.
class	MedianFilter3D	Applies a 3D median filter to a channel using a hybrid 3D median filter ImageJ plugin.

Uses of ImageBean in org.anchoranalysis.plugin.imagej.bean.mask.provider

Subclasses of ImageBean in org.anchoranalysis.plugin.imagej.bean.mask.provider

Modifier and Type	Class	Description
class	FillHoles	Fills holes in a mask, with options to skip holes touching the border or exceeding a maximum volume.
class	MorphologicalOperation	Applies an ImageJ (2D) morphological operation to each slice

Uses of ImageBean in org.anchoranalysis.plugin.imagej.bean.object.provider

Subclasses of ImageBean in org.anchoranalysis.plugin.imagej.bean.object.provider

Modifier and Type	Class	Description
class	DrawLineAlongConvexHull	Draws a lines between successive points on the convex-hull of an object.
class	FillHoles	Fills holes in an object.

Uses of ImageBean in org.anchoranalysis.plugin.imagej.bean.object.segment

Subclasses of ImageBean in org.anchoranalysis.plugin.imagej.bean.object.segment

Modifier and Type	Class	Description
class	FloodFillEachIntensityLevel	Creates an object for each separate intensity-value (beginning at startingColor) by flood-filling.

Uses of ImageBean in org.anchoranalysis.plugin.imagej.bean.stack.provider

Subclasses of ImageBean in org.anchoranalysis.plugin.imagej.bean.stack.provider

Modifier and Type	Class	Description
class	MontageSlices	Creates a montage of slices from a stack.

Uses of ImageBean in org.anchoranalysis.plugin.mpp.bean.object.provider

Subclasses of ImageBean in org.anchoranalysis.plugin.mpp.bean.object.provider

Modifier and Type	Class	Description
class	FromMarks	Creates object-masks from a MarkCollection where (a particular region of) each mark creates an object.

Uses of ImageBean in org.anchoranalysis.plugin.mpp.bean.stack.provider

Subclasses of ImageBean in org.anchoranalysis.plugin.mpp.bean.stack.provider

Modifier and Type	Class	Description
class	ColoredMarks	Draws a colored representation (outline or filled) of an MarkCollection on a background

Uses of ImageBean in org.anchoranalysis.plugin.onnx.bean.object.segment.stack

Subclasses of ImageBean in org.anchoranalysis.plugin.onnx.bean.object.segment.stack

Modifier and Type	Class	Description
class	SegmentObjectsFromONNXModel	Performs instance-segmentation using the ONNX Runtime and an .onnx model file.

Uses of ImageBean in org.anchoranalysis.plugin.opencv.bean.color

Subclasses of ImageBean in org.anchoranalysis.plugin.opencv.bean.color

Modifier and Type	Class	Description
class	ColorConverterBase	Converts a RGB stack into another color space using OpenCV.
class	ConvertRGBToHSV	Converts a RGB image to the HSV color space.
class	ConvertRGBToLab	Converts a RGB image to the Lab color space.

Uses of ImageBean in org.anchoranalysis.plugin.opencv.bean.object.segment.stack

Subclasses of ImageBean in org.anchoranalysis.plugin.opencv.bean.object.segment.stack

Modifier and Type	Class	Description
class	SegmentObjectsFromTensorFlowModel	Performs instance-segmentation using OpenCV's DNN module and a TensorFlow .pb SavedModel file.

Uses of ImageBean in org.anchoranalysis.plugin.points.bean

Subclasses of ImageBean in org.anchoranalysis.plugin.points.bean

Modifier and Type	Class	Description
class	SplitContourAtSaddlePoints	Splits a 2D contour represented by an object-mask into several contours, splitting at "turn" points.

Uses of ImageBean in org.anchoranalysis.plugin.points.bean.convexhull

Subclasses of ImageBean in org.anchoranalysis.plugin.points.bean.convexhull

Modifier and Type	Class	Description
class	ConvexHull2D	Sets particular voxels to high only if they exist on the convex-hull of the outline of a mask.
class	ConvexHull3D	Calculates a 3D convex hull from a binary mask.
class	ConvexHullBase	Base class for convex hull implementations.