All Classes and Interfaces
Class
Description
Adds a constant value to each voxel in a channel.
A condition to be checked after merging two
ObjectMasks.Creates a new mask of particular dimensionality where all values are off.
Creates a new mask of particular dimensionality where all values are on.
Specifies a single object that will always be the "match" for whatever source object.
Outputs the logical operation and voxelwise on both masks, modifying {mask} with the
result.
Applies multiples filter with logical AND i.e.
Combines two UpdatableBeforeConditions as LOGICAL ANDs
Reduce the size of individual objects (if neccessary, and minimally) to fit within a binary-mask.
Base-class for operations that perform a binary arithmetic operation with each voxel-value and a
constant.
Base class for arithmetic operations that conditionally overwrite voxel values with a constant.
Copies the pixels from
channelAssignFrom to channel (possibly masking).Assigns a value from a dictionary to all voxels in a channel.
Matches source-objects to target objects, based upon intersection, and assigns the value in the
respective source object to the target object
Abstract class for assigning priorities to potential object merges.
Allows merges if there is an increase in the payload i.e.
Calculates pair-feature on each potential merge, and this value determines priority..
Assigns a constant (scalar) value to the portion of the image covered by a mask
Extract a single
ObjectMask into a new collection.Perform a segmentation at a different scale, and then fit the results back to the original scale.
A condition to be checked before merging two
ObjectMasks.Performs a binary-segmentation using the upstream objects as masks.
Blurs an image using a particular strategy (defaults to a gaussian blur in each slice)
Performs a Gaussian Blur in 3D
Performs a Gaussian-blur in 2D on each slice independently
A method for applying blurring to an image.
Creates a
Mask where all pixels are on within a box region.Matches to another object, and then uses that object to bridge to another
Base class for
CalculateLevel implementations that operate on a list of other CalculateLevel objects.A
CalculateLevelUnary that calculates a level relative to a threshold, with an
alternative calculation method.Maps directions to chain codes and vice versa.
Clamps the input-histogram to a certain maximum value, and then delegates the calculate-level.
Base class for providers that draw entities (an outline or filled) on a background.
Like
ColoredBase but uses a generator to determine the colors for the objects.Draws a colored representation (outline or filled) of a
ObjectMask on a backgroundAn
ObjectMask with an associated color.Associates a
ColorList with a ObjectCollectionDraws a colored representation (outline or filled) of an
ObjectCollection on a backgroundBase class for combining two masks.
Combines one or more
ColorProviders into a unitary ColorProvider.An
ObjectCollectionProvider that concatenates multiple ObjectCollections from a
list of providers.Combines all the channels from one or more sources (stacks, channels etc.)
Performs a binary-segmentation of the channel and converts its connected-components into objects
Converts a binary-mask into its connected components
A constant value for thresholding.
Scale X and Y dimension by a constant floating-point number.
Converts a channel by applying a converter (no histogram is involved in the conversion).
Base class for channel providers that perform conversions on a single input channel.
Converts a channel to a different voxel data-type by applying a converter with an associated
histogram.
Creates a new channel with all values initialized to a constant (by default zero)
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
Ensures each object in a collection is a connected-component, decomposing it if necessary into
multiple objects.
Builds string-descriptions of a
NeighborGraph.Checks if a value in a
Dictionary is equal to an expected value.Performs a dilation morphological operation on
BinaryVoxels.Dilates each object in the collection, growing bounding-boxes as necessary in relevant
dimensions.
Utility class for checking and ensuring consistency of dimensions across channels and masks.
Calculates features values for all objects, and discards any object less than
quantile - (minRatio * stdDev)A
BeforeCondition that checks if two ObjectMasks are within a specified maximum
distance.Creates a duplicate of the input channel.
A provider that creates a duplicate of a given
Mask.Duplicates (deep copy) an object-collection.
Creates an empty object-collection.
Specifies a constant if a histogram is empty, otherwise delegates to another {#link
org.anchoranalysis.image.bean.threshold.CalculateLevel}
A wrapper around
UnsignedIntBuffer that provides methods for encoding and decoding
watershed-related information.An interface for encoding a 3D direction into an integer representation.
Represents voxels encoded with watershed-related information.
Performs an erosion morphological operation on
BinaryVoxels.Erodes each object in the collection, growing bounding-boxes as necessary in relevant dimensions.
Creates a 3D version of an object by replicating each input-object across the z-dimension to meet
(3D) dimensions.
Extends an object (2D/3D) as much as it can within the z-slices of a containing object
Finds the exterior outer contour for a
Mask that forms its outline.Extracts the slice at the center (rounding down) of the range of z-stacks.
Extracts slices from
sliceStart (inclusive) to sliceEnd (inclusive).Filters an
ObjectCollection using the specified ObjectFilter.Applies an object-filter to the results of an upstream segmentation.
Filters an
ObjectCollection by grouping objects and then applying a filter to each group.Fits a box around the on voxels.
Scales an image to approximately similar in size to a
SizeXY.Flattens a mask in the z-dimension, so it is 2D instead of 3D (like a maximum intensity
projection).
Flattens all object-masks in the z-dimension, so it is 2D instead of 3D (like a maximum intensity
projection).
Creates image-dimensions by referencing them from a
ChannelProvider.Creates a
Histogram from a Channel, optionally using a mask.Creates a mask from an existing channel, reusing the channel's buffer and considering all 0
values as off, and 255 values as on.
Base-class for
MaskProviders that accept a Channel as input.Creates a
Stack from a Channel or Mask (reusing the voxel buffers).An abstract base class for creating a channel from specified dimensions.
Base class for
MaskProviders that create a mask based on given dimensions.Finds the input-stack using a conventional name of
input_image - and extracts the first
channelFinds the input-stack using a conventional name of
input_imageCreates a
Channel directly from a Mask without any modification.Converts a binary-mask to an object-collection (containing a single object)
A base class for a
ChannelProvider which also uses a binary-mask, but which doesn't use
any other ChannelProvider as an input.Creates a
Mask from a collection of object-masks.Extracts a channel from a provider of a stack.
Creates a
Mask from a specific channel in a stack.Generates colors to match the size of an object-collection.
Base class to calculate the gradient of the voxels in a
Channel.Like
GradientBase but allows an arbitrary constant to be added to voxels storing the
gradient.Extracts the gradient in the direction of a particular axis (identified by an index)
Calculates a
Channel's gradient along the x and y axes.A logger for graph operations, using a
DescribeGraph to generate descriptions.Abstract base class for performing grayscale reconstruction by erosion.
Implements grayscale reconstruction using Robinson's algorithm.
Only accepts an object if it has greater (or EQUAL) intersection with
objectsGreater than
objectsLesserThresholds a histogram using a CalculateLevel keeping only the values greater equal than the
threshold
Guesses dimensions from an input-image if it exists.
Utility class for thresholding histograms.
Assigns a unique id number to each object.
Calculates a level from the first delegate and if greater than a threshold, recalculates from a
second delegate.
Outputs the logical operation
iff first==HIGH and second==LOW then LOW voxelwise on both
masks, modifying {mask} with the result.The current
mask is returned if a condition on key-values is satisfied otherwise
maskElse is returned.Calculates a level from the first delegate and if less than a threshold, recalculates from a
second delegate.
The current
mask is returned if it's non-empty (at least one on voxel) otherwise
maskElse is returned.The current
mask is returned if the mask (treated as an object) passed an object-filter,
otherwise maskElse is returned.Multiplexes between two object-collection-providers depending on whether a parameter value equals
a particular string
Provides a channel based on a condition from a dictionary.
Base class which multiplexes between the current mask and an alternative depending if a condition
is met.
The current
mask is a particular stack exists (at least one on voxel) otherwise
maskElse is returned.Creates a new channel which is a merged version of two input channels according to rules.
Imposes minima in seed locations on the input-channel before performing the segmentation
An
AfterCondition that checks if merging two ObjectMasks increases a specific
feature value.Only keep objects where at least one voxel (on a particular channel) has intensity greater or
equal to a threshold.
Utility class for calculating mean intensity of objects in a channel.
An
ObjectMatcher that matches objects based on their intersection with a provided set of
objects.Keeps objects which intersects with ANY ONE of a collection of other objects.
Returns only the objects that intersect with at least one object in the container
Inverts the intensity values of a
Channel by subtracting each voxel from the maximum
value for the channel's data type.Switches on voxels to off and vice-versa.
Invert the
ScaleFactor calculated by the scaleCalculator delegate.Performs a segmentation and inverts and on and off bytes
Creates a channel with a level calculated for each object using various methods.
Creates a channel with different threshold-levels for each object, calculating the level only
from the histogram of the particular object.
Calculates a threshold-level for each object collectively based on other objects
Represents the result of a level operation, containing the level value, object mask, and
histogram.
A collection of
LevelResult objects that can be iterated over and searched.Factory for creating
LevelResultCollection objects.Provides an
ObjectCollection by matching objects using a specified ObjectMatcher.Helper class for matching objects based on intersection.
The maximum value of one or more {#link org.anchoranalysis.image.bean.threshold.CalculateLevel}
Creates a maximum intensity projection of a 3D
Channel.Maximum-intensity-projection
across
Channels.Creates a new channel by taking the maximum value of corresponding voxels from two input
channels.
Replaces voxel values with a constant value if the constant is greater than the original voxel
value.
Creates a mean intensity projection of a 3D
Channel.Mean-intensity-projection across
Channels.Creates a new channel that is the mean of three input channels.
Applies a median-filter with square kernel
A base class for algorithms that merge object-masks.
Functional interface for merging objects.
A graph that stores each object as a vertex, where edges represent a neighborhood relation.
Naive greedy merge strategy when any two neighboring objects are merged if it increases a
feature.
Merges objects if a pair feature value satisfies a condition.
Merges neighboring objects if it results in an increase in the average feature-value calculated
on each single object.
Merges itemwise objects from two collections.
Base class for object-merging strategies that involve calculating a feature.
Expands
MergeBase by optionally imposing a maximum-distance requirement between objects
that are possibly merged.Abstract base class for imposing minima on a channel for watershed segmentation.
Imposes minima on a channel using grayscale reconstruction by erosion.
The minimum value of one or more {#link org.anchoranalysis.image.bean.threshold.CalculateLevel}
Calculates a scale factor to ensure a minimum XY resolution is achieved.
Minimum-intensity-projection across
Channels.Creates a new channel by taking the minimum value of corresponding voxels from two input
channels.
Replaces voxel values with a constant value if the constant is less than the original voxel
value.
Base class for performing morphological operations on
BinaryVoxels.Applies the MSER algorithm from imglib2
Multiplies each voxel value in a channel by a constant value.
Creates a new channel by multiplying corresponding voxels from two input channels.
A condition to determine if two objects are potential neighbors and candidates for merging.
Corrects a channel in the following way
Rewrites the intensity for each object-mask (assume no overlap) so that its mean is 128
Filters objects to keep only those which are NOT in the container.
Keeps only objects that are not adjacent to the scene-border (i.e.
Base class for object collection providers that apply a filter to the objects.
Base class for providers that apply morphological operations to an
ObjectCollection.An abstract base class for object collection providers that use a feature evaluator.
A filter that combines other filters (in a list)
Uses a predicate to make a decision whether to keep objects or not.
An independent object-filter that uses a relation in its predicate.
Utility class for removing intersecting voxels between objects in a collection.
A vertex in a merge graph representing an object (and an associated payload).
Finds the object with the maximum feature-value from a collection.
Finds the object with the maximum feature among a group of matches for each object.
Outputs the logical operation or voxelwise on both masks, modifying {mask} with the
result.
Applies multiples filter with logical OR i.e.
Performs auto-thresholding using Otsu's method.
Similar to Otsu, but weighs the variances differently of background and foreground.
Create a thumbnail by drawing an outline of an object at a particular-scale, and placing it
centered in a window of a certain size.
Calculates a payload value for an
ObjectMask.Permutes some changes over an
ObjectCollectionProvider and collects all the results in an
ObjectCollectionA vertex with a priority attached, and a boolean flag as to whether it can be merged or not
Creates a priority between two vertices for object merging.
Implements a priority queue based upon a range of values from 0 to maxValue.
An aggregator that calculates the aggregation of every voxel across successive channels
via a
ProjectableBuffer.Calculates the threshold value from a quantile of a histogram.
Changes the voxel values to map the range of 0th quantile to xth quantile across the entire voxel
data range
Provides a channel by referencing it from a a set of named-channels.
A provider that references an existing
Histogram by its identifier.A provider that references an existing
Mask by its identifier.An
ObjectCollectionProvider that references an existing ObjectCollection by its
identifier.Retrieves an existing stack.
Creates reference (i.e.
Returns a object-collection by name if it exists, or else calls
objectsElse if it doesn't
exist.Rejects a set of objects, if any object is not fully connected (pixels form two or more separate
connected components)
Matches each object with others, and keeps only those where a relation holds true for all matches
(in terms of features)
Considers all possible pairs of objects in a provider, and removes any intersecting pixels
Considers all possible pairs of objects in a provider, and removes those that touch the border.
Repeats a binary segmentation operation for a specified number of iterations.
Creates a new channel with specific dimensions that repeatedly duplicates a slice from an
existing channel
Creates a new mask with specific dimensions that repeatedly duplicates a slice from an existing
mask
Scales all the objects in the collection by a particular scale-factor.
Scales by compressing a certain range of values into the 8-bit signal.
Scales by compressing a certain range of values into the 8-bit signal
Converts a channel to unsigned byte format, scaling the values based on the original voxel type.
Create a thumbnail by scales an image to a particular size.
Scales the channel in the X and Y dimensions.
Scales the mask in XY dimensions, but not in Z dimension.
Creates a channel by scoring objects based on a feature calculation.
Assigns a score (a value indicating how probable something is) to each voxel
Applies a
BinarySegmentation algorithm to derive a mask from a channelSegments a channel into objects using a specified segmentation algorithm.
Performs segmentation of a channel using each object in the upstream collection as a mask.
Perform a segmentation in a MIP instead of z-stacks, and fits the result back into a 3D
segmentation.
Segments a stack into objects.
Takes each object one-by-one from
objectsSource, and finds matching seeds from
objectsSeedsPerforms a sequence of succesive segmentations
Extracts a specific slice from a collection of 3D objects.
Segmenting a z-
Stack slice-by-slice.A slice thresholder that applies thresholding within a mask region.
A slice thresholder that applies thresholding to the entire image without using a mask.
3x3 Sobel Filter
Creates a new object-collection with objects sorted by a derived feature-value (in ascending
order)
Specifies dimensions explicitly via bean properties.
Splits objects in a collection based on intersections with another set of objects.
Splits objects into sub-objects by cutting by an orthogonal square lattice (like a chessboard).
Projection of the standard-deviation of voxels values across all inputs.
Calculates the steepest descent direction for voxels in a watershed segmentation.
Subtracts each voxel value in a channel from a constant value.
Subtracts the mean intensity (of the entire channel or a masked portion thereof) from every
voxel.
Creates a new channel by subtracting corresponding voxels of the second channel from the first
channel.
Provides a
Stack by combining up to three channels (red, green, blue) into an RGB image.Colors three collections of objects in RED, GREEN, BLUE channels on top of a background.
Thresholds a channel to produce a mask, reusing (and modifying) the input-buffers of the channel
if possible.
Thresholds each voxels by comparing against another channel that has per-voxel thresholds
Combines object-masks by projecting the maximum confidence-level for each voxel and thresholding.
Only keeps objects whose feature-value satisfies a condition relative to a threshold.
Only keeps objects whose feature-value satisfies a condition relative to a threshold.
Creates thumbnails for a particular batch of objects that can be calibrated to have similar
properties (identical scale etc.)
Creates a thumbnail of one or more objects on a stack by drawing the outline of the objects.
Creates a thumbnail from a stack.
Converts a channel to unsigned byte format without any scaling.
Converts a channel to unsigned byte format using upper and lower quantile intensities from a
histogram.
Calculates a scaling-factor to make the source image have identical dimensions as
dimensionsTarget.Scales to the suggested-size if one is provided, otherwise calls
fallback.Takes the two channels and creates a NEW third channel whose pixels are a function of the two
channels
Base class for
ObjectCollectionProviderUnary that also requires a Channel.A base class for a
ChannelProviderUnary which also uses a binary mask.An abstract base class for creating a channel from an existing channel and a collection of
objects.
A
ChannelProviderUnary which has a scalar value field.A two-stage process for checking if two
ObjectMasks should be merged.Encodes watershed-related information in an integer range.
A 'rainfall' watershed algorithm
Base class for
ObjectCollectionProviders that create objects from a Channel.Base class for
ObjectCollectionProviderUnary that take an optional
objectsContainer bean-field.Base class for
ObjectCollectionProviderUnary classes that require dimensions to be
specified.Base class for
ObjectCollectionProviderUnary classes that offer an optional means to
specify dimensions.Wraps a BeforeCondition as an UpdatableBefoerCondition
Outputs the logical operation xor (exclusive or) voxelwise on both masks, modifying {mask}
with the result.
Set pixels NOT IN the mask to 0, but keep pixels IN the mask identical.