Modifier and Type | Class and Description |
---|---|
class |
ConvertChannelTo<T>
Creates a
ChannelConverter for converting a channel to a particular type. |
Modifier and Type | Class and Description |
---|---|
class |
ObjectFilter
Base class for filtering an
ObjectCollection to remove objects according to a criteria. |
class |
ObjectMatcher
Matches an object with other objects.
|
Modifier and Type | Class and Description |
---|---|
class |
BeanProviderAsStackBase<T,S>
A provider base-class that as well as providing type
S , also provides a Stack . |
class |
ChannelProvider
|
class |
ChannelProviderBinary
Implementation of
ChannelProvider that calls two ChannelProvider s that
must provide Channel s of the same dimensions. |
class |
ChannelProviderTernary
Implementation of
ChannelProvider that calls three ChannelProvider s that
must provide Channel s 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
|
class |
HistogramProviderUnary
Implementation of
HistogramProvider that calls a single delegate HistogramProvider . |
class |
MaskProvider
|
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> . |
Modifier and Type | Class and Description |
---|---|
class |
Arrange
Creates a stack that combines other stacks.
|
class |
StackProvider
|
class |
StackProviderUnary
Implementation of
StackProvider that calls a single delegate Provider<Stack> . |
Modifier and Type | Class and Description |
---|---|
class |
SegmentationBean<T>
Performs some kind of segmentation on an image.
|
Modifier and Type | Class and 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 . |
Modifier and Type | Class and 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 . |
Modifier and Type | Class and Description |
---|---|
class |
ScaleCalculator
Calculating a scaling-factor from dimensions.
|
Modifier and Type | Class and Description |
---|---|
class |
VoxelScore
Calculates a per-voxel score.
|
Modifier and Type | Class and 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.
|
Modifier and Type | Class and Description |
---|---|
class |
OutputFeatureTable
Specifies a table of feature-calculations on objects.
|
Modifier and Type | Class and Description |
---|---|
class |
TileWithLabels
Tiles a number of
StackProviderWithLabel s as a single StackProvider . |
class |
WriteText
Creates an image that contains text only.
|
Modifier and Type | Class and Description |
---|---|
class |
AnisotropicDiffusion
Performs Perona-Malik Anisotropic
Diffusion.
|
class |
MinimumFilter |
Modifier and Type | Class and 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. |
Modifier and Type | Class and Description |
---|---|
class |
AutoLocalThreshold
Applies local thresholding algorithm using Fiji's {link Auto_Local_Threshold} plugin
|
Modifier and Type | Class and 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 |
class |
ToByte |
Modifier and Type | Class and Description |
---|---|
class |
CreateNew
Creates a new channel with all values initialized to a constant (by default zero)
|
class |
Duplicate |
class |
FromDimensionsBase |
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 |
class |
Reference |
class |
TwoVoxelMappingBase
Takes the two channels and creates a NEW third channel whose pixels are a function of the two
channels
|
class |
UnaryWithObjectsBase |
class |
UnaryWithValueBase
A
ChannelProviderUnary which has a scalar value field |
Modifier and Type | Class and Description |
---|---|
class |
AddConstant |
class |
ArithmeticWithConstantBase
Base-class for operations that perform a binary arithmetic operation with each voxel-value and a
constant.
|
class |
ArithmeticWithConstantConditionallyWriteBase |
class |
Invert
Subtracts each voxel from the maximum value for the channel's data type (e.g.
|
class |
MaxTwoChannels |
class |
MaxWithConstant |
class |
MeanThreeChannels
Creates a new channel that is the mean of three input channels
|
class |
MinTwoChannels |
class |
MinWithConstant |
class |
MultiplyConstant |
class |
MultiplyTwoChannels |
class |
SubtractFromConstant |
class |
SubtractMean
Subtract the mean (of the entire channel or a masked portion thereof) from every voxel
|
class |
SubtractTwoChannels |
Modifier and Type | Class and Description |
---|---|
class |
AssignFromChannel
Copies the pixels from
channelAssignFrom to channel (possibly masking) |
class |
AssignFromDictionary |
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
|
Modifier and Type | Class and Description |
---|---|
class |
Convert<T>
Converts a channel by applying a converter (no histogram is involved in the conversion).
|
class |
ConvertBase |
class |
ConvertWithHistogram<T>
Converts a channel to a different voxel data-type by applying a converter with an associated
histogram.
|
Modifier and Type | Class and 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
|
Modifier and Type | Class and 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.
|
Modifier and Type | Class and Description |
---|---|
class |
FromMask |
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 |
class |
ZeroOutsideMask
Set pixels NOT IN the mask to 0, but keep pixels IN the mask identical.
|
Modifier and Type | Class and Description |
---|---|
class |
LevelPerObjectBase
Creates a channel with a level calculated for each object variously
|
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
|
Modifier and Type | Class and Description |
---|---|
class |
IdentifyObjects
Assigns a unique id number to each object.
|
class |
ScoreObjects |
class |
ScoreVoxels
Assigns a score (a value indicating how probable something is) to each voxel
|
Modifier and Type | Class and 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 |
class |
MeanIntensityProjection |
class |
RepeatSlice
Creates a new channel with specific dimensions that repeatedly duplicates a slice from an
existing channel
|
Modifier and Type | Class and Description |
---|---|
class |
DictionaryCondition
Checks if a value in a
Dictionary is equal to an expected-value. |
Modifier and Type | Class and Description |
---|---|
class |
GuessDimensions
Guesses dimensions from an input-image if it exists.
|
class |
SpecifyDimensions
Specifies dimensions explicitly via bean properties.
|
Modifier and Type | Class and 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 |
GreaterThanThreshold
Thresholds a histogram using a CalculateLevel keeping only the values greater equal than the
threshold
|
Modifier and Type | Class and 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 |
FromChannelBase
Base-class for
MaskProvider s that accept a Channel as input. |
Modifier and Type | Class and Description |
---|---|
class |
And
Outputs the logical operation and voxelwise on both masks, modifying {mask} with the
result.
|
class |
CombineBase |
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.
|
Modifier and Type | Class and 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 |
Modifier and Type | Class and 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 . |
Modifier and Type | Class and 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. |
Modifier and Type | Class and 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.
|
Modifier and Type | Class and Description |
---|---|
class |
FlattenZ
Flattens a mask in the z-dimension, so it is 2D instead of 3D (like a maximum intensity
projection).
|
Modifier and Type | Class and 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.
|
Modifier and Type | Class and 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)
|
Modifier and Type | Class and Description |
---|---|
class |
ObjectFilterCombine
A filter that combines other filters (in a list)
|
Modifier and Type | Class and 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.
|
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.
|
Modifier and Type | Class and 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 |
Modifier and Type | Class and Description |
---|---|
class |
AtIndex
Extract a single
ObjectMask into a new 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 |
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 |
class |
WithChannelBase |
class |
WithContainerBase
Base class for
ObjectCollectionProvider 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. |
Modifier and Type | Class and 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)
|
Modifier and Type | Class and Description |
---|---|
class |
ObjectCollectionProviderWithFeature |
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)
|
Modifier and Type | Class and Description |
---|---|
class |
Filter |
class |
FilterByGroup |
class |
IntersectsWithContainer
Returns only the objects that intersect with at least one object in the container
|
class |
Match |
class |
NotInContainer
Filters objects to keep only those which are NOT in the container.
|
class |
ObjectCollectionProviderFilterBase |
class |
RemoveTouchingBorder
Considers all possible pairs of objects in a provider, and removes those that touch the border.
|
Modifier and Type | Class and Description |
---|---|
class |
AndObjectsWithMasks
Reduce the size of individual objects (if neccessary, and minimally) to fit within a binary-mask.
|
Modifier and Type | Class and 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. |
Modifier and Type | Class and Description |
---|---|
class |
ObjectCollectionProviderMorphological |
Modifier and Type | Class and Description |
---|---|
class |
BinarySegmentByObject
Performs a binary-segmentation using the upstream objects as masks.
|
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 |
Modifier and Type | Class and 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 |
SliceAt |
Modifier and Type | Class and Description |
---|---|
class |
RemoveIntersectingVoxels
Considers all possible pairs of objects in a provider, and removes any intersecting pixels
|
class |
SplitByObjects |
class |
SplitIntoSquares
Splits objects into sub-objects by cutting by an orthogonal square lattice (like a chessboard).
|
Modifier and Type | Class and 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 |
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.
|
Modifier and Type | Class and Description |
---|---|
class |
WatershedYeong
A 'rainfall' watershed algorithm
|
Modifier and Type | Class and 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 |
MinimumXYResolution |
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 . |
Modifier and Type | Class and Description |
---|---|
class |
Repeat |
class |
Sequence
Performs a sequence of succesive segmentations
|
class |
ThresholdAgainstChannel
Thresholds each voxels by comparing against another channel that has per-voxel thresholds
|
Modifier and Type | Class and 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)
|
Modifier and Type | Class and 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 |
class |
ThreeColoredObjects
Colors three collections of objects in RED, GREEN, BLUE channels on top of a background.
|
Modifier and Type | Class and Description |
---|---|
class |
CalculateLevel |
class |
CalculateLevelBase |
class |
Difference |
class |
DifferenceCalculateLevelStandardDeviation
Similar to
Difference but calculates the width as the standard-deviation of the histogram |
class |
FromDictionaryBase |
class |
Identity |
class |
IdentityImposeValueRelationToHistogram |
class |
NormalizeByConstant |
class |
NormalizeByMax
This assumes the histograms correspond to the energy channels exactly (in terms of indexing)
|
class |
OutsideRange |
class |
RejectIfIntensityLessThan |
class |
SingleChannel
A score that is calculated on a single channel only
|
Modifier and Type | Class and Description |
---|---|
class |
BackgroundSubtractor |
class |
WithFilterBase |
class |
WithRadiusBase
A
ChannelProviderUnary with a 'radius' parameter |
Modifier and Type | Class and Description |
---|---|
class |
EdgeFilterIJ |
class |
GaussianBlur2D |
Modifier and Type | Class and Description |
---|---|
class |
MeanFilter2D |
class |
VarianceFilter2D |
Modifier and Type | Class and Description |
---|---|
class |
MedianFilter2D |
class |
MedianFilter3D |
Modifier and Type | Class and Description |
---|---|
class |
FillHoles |
class |
MorphologicalOperation
Applies an ImageJ (2D) morphological operation to each slice
|
Modifier and Type | Class and Description |
---|---|
class |
DrawLineAlongConvexHull
Draws a lines between successive points on the convex-hull of an object.
|
Modifier and Type | Class and Description |
---|---|
class |
FloodFillEachIntensityLevel
Creates an object for each separate intensity-value (beginning at
startingColor ) by
flood-filling. |
Modifier and Type | Class and Description |
---|---|
class |
MontageSlices |
Modifier and Type | Class and Description |
---|---|
class |
MergeSpatialClusters
Merges spatially-adjacent objects using the DBScan clustering algorithm.
|
Modifier and Type | Class and Description |
---|---|
class |
FromMarks
Creates object-masks from a
MarkCollection where (a particular region of) each mark
creates an object. |
Modifier and Type | Class and Description |
---|---|
class |
SegmentThresholdAboveMinBound |
Modifier and Type | Class and Description |
---|---|
class |
ColoredMarks
Draws a colored representation (outline or filled) of an
MarkCollection on a background |
Modifier and Type | Class and Description |
---|---|
class |
SegmentObjectsFromONNXModel
Performs instance-segmentation using the ONNX Runtime and an
.onnx model file. |
Modifier and Type | Class and 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.
|
Modifier and Type | Class and Description |
---|---|
class |
SegmentObjectsFromTensorFlowModel
Performs instance-segmentation using OpenCV's DNN module and a TensorFlow
.pb SavedModel file. |
Modifier and Type | Class and Description |
---|---|
class |
SplitContourAtSaddlePoints
Splits a 2D contour represented by an object-mask into several contours, splitting at "turn"
points.
|
Modifier and Type | Class and Description |
---|---|
class |
ConvexHull2D
Sets particular voxels to high only if they exist on the convex-hull of the outline of a mask.
|
class |
ConvexHull3D |
class |
ConvexHullBase |
Copyright © 2010–2023 Owen Feehan, ETH Zurich, University of Zurich, Hoffmann-La Roche. All rights reserved.