Index

A B C D E F G I M O P S T V W
All Classes and Interfaces|All Packages

A

AddEdgeFilters - Class in org.anchoranalysis.plugin.imagej.bean.define

Adds edge filters and their gradients to a Define object.

AddEdgeFilters() - Constructor for class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters

addTo(Define) - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters

ApplyImageJMorphologicalOperation - Class in org.anchoranalysis.plugin.imagej.mask

Applies an ImageJ (2D) morphological operation to voxels.

applyOperation(BinaryVoxels<UnsignedByteBuffer>, String, int) - Static method in class org.anchoranalysis.plugin.imagej.mask.ApplyImageJMorphologicalOperation

Applies a specified morphological operation to the given binary voxels.

applyRankFilter(Channel, int, int) - Static method in class org.anchoranalysis.plugin.imagej.channel.provider.FilterHelper

Applies a 2D rank-filter to each slice independently of a Channel.

B

BackgroundSubtractor - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider

Subtracts background from a channel using ImageJ's BackgroundSubtracter.

BackgroundSubtractor() - Constructor for class org.anchoranalysis.plugin.imagej.bean.channel.provider.BackgroundSubtractor

C

createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.EdgeFilterIJ

createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.GaussianBlur2D

createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank.MedianFilter3D

createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.WithRadiusBase

createFromChannel(Channel, int) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.BackgroundSubtractor

createFromChannel(Channel, int) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.WithFilterBase

createFromChannel(Channel, int) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.WithRadiusBase

Creates a new channel from an existing channel and a radius.

createFromMask(Mask) - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.FillHoles

createFromMask(Mask) - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.MorphologicalOperation

createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.imagej.bean.object.provider.DrawLineAlongConvexHull

createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.imagej.bean.object.provider.FillHoles

createFromStack(Stack) - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices

D

DrawLineAlongConvexHull - Class in org.anchoranalysis.plugin.imagej.bean.object.provider

Draws a lines between successive points on the convex-hull of an object.

DrawLineAlongConvexHull() - Constructor for class org.anchoranalysis.plugin.imagej.bean.object.provider.DrawLineAlongConvexHull

E

EdgeFilterIJ - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter

Applies an edge detection filter to each slice of a Channel independently using ImageJ's FIND_EDGES filter.

EdgeFilterIJ() - Constructor for class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.EdgeFilterIJ

F

fill(BinaryVoxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.plugin.imagej.mask.ApplyImageJMorphologicalOperation

Applies the fill operation to the given binary voxels.

FillHoles - Class in org.anchoranalysis.plugin.imagej.bean.mask.provider

Fills holes in a mask, with options to skip holes touching the border or exceeding a maximum volume.

FillHoles - Class in org.anchoranalysis.plugin.imagej.bean.object.provider

Fills holes in an object.

FillHoles() - Constructor for class org.anchoranalysis.plugin.imagej.bean.mask.provider.FillHoles

FillHoles() - Constructor for class org.anchoranalysis.plugin.imagej.bean.object.provider.FillHoles

FilterHelper - Class in org.anchoranalysis.plugin.imagej.channel.provider

Helper class for applying filters to Channels and BinaryVoxels using ImageJ operations.

FloodFillEachIntensityLevel - Class in org.anchoranalysis.plugin.imagej.bean.object.segment

Creates an object for each separate intensity-value (beginning at startingColor) by flood-filling.

FloodFillEachIntensityLevel() - Constructor for class org.anchoranalysis.plugin.imagej.bean.object.segment.FloodFillEachIntensityLevel

G

GaussianBlur2D - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter

Applies a 2D Gaussian blur filter to each slice of a Channel independently.

GaussianBlur2D() - Constructor for class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.GaussianBlur2D

getBorderWidth() - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices

Adds a border around each part of the montage.

getChannelID() - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters

The ID of the channel that provides the input to the filter.

getColumns() - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices

How many columns to use in the montage, or 0 to guess an approximately square output.

getCommand() - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.MorphologicalOperation

One of: open, close, fill, erode, dilate, skel, outline

getGaussianSigmaMeters() - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters

The sigma value for the Gaussian filter in meters.

getIterations() - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.MorphologicalOperation

iterations for erode, dilate, open, close

getMask() - Method in class org.anchoranalysis.plugin.imagej.bean.object.provider.FillHoles

getMaxVolume() - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.FillHoles

The maximum volume of a hole to be filled.

getMedianRadiusMeters() - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters

The radius of the median filter in meters.

getMinimumBoundingBoxVolume() - Method in class org.anchoranalysis.plugin.imagej.bean.object.segment.FloodFillEachIntensityLevel

Only objects whose bounding-box volume is greater or equal to this threshold are included.

getMinIntensity() - Method in class org.anchoranalysis.plugin.imagej.bean.threshold.ThresholderSimpleFillHoles2D

The minimum intensity value for thresholding.

getRadius() - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.WithRadiusBase

The radius of the operation.

getScale() - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices

Whether to increase or reduce the size of the images.

getSigma() - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.GaussianBlur2D

The standard deviation of the Gaussian distribution used for blurring.

getSliceFirst() - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices

First slice to include in the montage.

getSliceLast() - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices

Last slice to include in the montage.

getStartingIntensity() - Method in class org.anchoranalysis.plugin.imagej.bean.object.segment.FloodFillEachIntensityLevel

The first intensity-value to consider as a valid object (e.g.

I

isGaussian() - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters

If true, the Gaussian filter is included.

isLabel() - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices

If true, a label is added beside every image showing the slice index.

isMedian() - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters

If true, the median filter is included.

isRadiusInMeters() - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.WithRadiusBase

If true, treats the radius as being in meters.

isSkipAtBorder() - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.FillHoles

If true, holes that touch the border of the mask are not filled.

M

MeanFilter2D - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments

Applies a 2D mean filter to a channel using ImageJ's RankFilters.

MeanFilter2D() - Constructor for class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments.MeanFilter2D

Creates a new MeanFilter2D instance.

MedianFilter2D - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank

Applies a 2D median filter to a channel using ImageJ's RankFilters.

MedianFilter2D() - Constructor for class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank.MedianFilter2D

Creates a new MedianFilter2D instance.

MedianFilter3D - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank

Applies a 3D median filter to a channel using a hybrid 3D median filter ImageJ plugin.

MedianFilter3D() - Constructor for class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank.MedianFilter3D

MontageSlices - Class in org.anchoranalysis.plugin.imagej.bean.stack.provider

Creates a montage of slices from a stack.

MontageSlices() - Constructor for class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices

MorphologicalOperation - Class in org.anchoranalysis.plugin.imagej.bean.mask.provider

Applies an ImageJ (2D) morphological operation to each slice

MorphologicalOperation() - Constructor for class org.anchoranalysis.plugin.imagej.bean.mask.provider.MorphologicalOperation

O

org.anchoranalysis.plugin.imagej.bean.channel.provider - package org.anchoranalysis.plugin.imagej.bean.channel.provider

Implementations of ChannelProvider that call ImageJ.

org.anchoranalysis.plugin.imagej.bean.channel.provider.filter - package org.anchoranalysis.plugin.imagej.bean.channel.provider.filter

Filters using ImageJ.

org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments - package 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 - package org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank

Non-linear filters using ImageJ that use the statistical rank of the intensity values in the kernel.

org.anchoranalysis.plugin.imagej.bean.define - package org.anchoranalysis.plugin.imagej.bean.define

Implementations of DefineAdderBean that call ImageJ.

org.anchoranalysis.plugin.imagej.bean.mask.provider - package org.anchoranalysis.plugin.imagej.bean.mask.provider

Implementations of MaskProvider that call ImageJ.

org.anchoranalysis.plugin.imagej.bean.object.provider - package org.anchoranalysis.plugin.imagej.bean.object.provider

Implementations of ObjectCollectionProvider that call ImageJ.

org.anchoranalysis.plugin.imagej.bean.object.segment - package org.anchoranalysis.plugin.imagej.bean.object.segment

Implementations of ObjectCollectionProvider that call ImageJ to perform segmentation.

org.anchoranalysis.plugin.imagej.bean.stack.provider - package org.anchoranalysis.plugin.imagej.bean.stack.provider

Implementations of StackProvider that call ImageJ.

org.anchoranalysis.plugin.imagej.bean.threshold - package org.anchoranalysis.plugin.imagej.bean.threshold

Implementations of Thresholder that call ImageJ.

org.anchoranalysis.plugin.imagej.channel.provider - package org.anchoranalysis.plugin.imagej.channel.provider

Implementations of ChannelProvider that call ImageJ.

org.anchoranalysis.plugin.imagej.mask - package org.anchoranalysis.plugin.imagej.mask

Non-bean classes involving ObjectMask that call ImageJ.

P

processEachSlice(Channel, Consumer<ImageProcessor>) - Static method in class org.anchoranalysis.plugin.imagej.channel.provider.FilterHelper

Applies a Consumer to each slice independently of a Channel.

processEachSlice(BinaryVoxels<UnsignedByteBuffer>, Consumer<ImageProcessor>) - Static method in class org.anchoranalysis.plugin.imagej.channel.provider.FilterHelper

Applies a Consumer to each slice independently of a BinaryVoxels with UnsignedByteBuffer.

S

segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>) - Method in class org.anchoranalysis.plugin.imagej.bean.object.segment.FloodFillEachIntensityLevel

setBorderWidth(int) - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices

Adds a border around each part of the montage.

setChannelID(String) - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters

The ID of the channel that provides the input to the filter.

setColumns(int) - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices

How many columns to use in the montage, or 0 to guess an approximately square output.

setCommand(String) - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.MorphologicalOperation

One of: open, close, fill, erode, dilate, skel, outline

setGaussian(boolean) - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters

If true, the Gaussian filter is included.

setGaussianSigmaMeters(double) - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters

The sigma value for the Gaussian filter in meters.

setIterations(int) - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.MorphologicalOperation

iterations for erode, dilate, open, close

setLabel(boolean) - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices

If true, a label is added beside every image showing the slice index.

setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.imagej.bean.object.provider.FillHoles

setMaxVolume(UnitValueExtent) - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.FillHoles

The maximum volume of a hole to be filled.

setMedian(boolean) - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters

If true, the median filter is included.

setMedianRadiusMeters(double) - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters

The radius of the median filter in meters.

setMinimumBoundingBoxVolume(int) - Method in class org.anchoranalysis.plugin.imagej.bean.object.segment.FloodFillEachIntensityLevel

Only objects whose bounding-box volume is greater or equal to this threshold are included.

setMinIntensity(int) - Method in class org.anchoranalysis.plugin.imagej.bean.threshold.ThresholderSimpleFillHoles2D

The minimum intensity value for thresholding.

setRadius(double) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.WithRadiusBase

The radius of the operation.

setRadiusInMeters(boolean) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.WithRadiusBase

If true, treats the radius as being in meters.

setScale(double) - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices

Whether to increase or reduce the size of the images.

setSigma(double) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.GaussianBlur2D

The standard deviation of the Gaussian distribution used for blurring.

setSkipAtBorder(boolean) - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.FillHoles

If true, holes that touch the border of the mask are not filled.

setSliceFirst(int) - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices

First slice to include in the montage.

setSliceLast(int) - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices

Last slice to include in the montage.

setStartingIntensity(int) - Method in class org.anchoranalysis.plugin.imagej.bean.object.segment.FloodFillEachIntensityLevel

The first intensity-value to consider as a valid object (e.g.

T

threshold(VoxelsUntyped, BinaryValuesByte, Optional<Histogram>, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.imagej.bean.threshold.ThresholderSimpleFillHoles2D

ThresholderSimpleFillHoles2D - Class in org.anchoranalysis.plugin.imagej.bean.threshold

A thresholder that applies a simple intensity threshold and then fills holes in 2D.

ThresholderSimpleFillHoles2D() - Constructor for class org.anchoranalysis.plugin.imagej.bean.threshold.ThresholderSimpleFillHoles2D

ThresholderSimpleFillHoles2D(int) - Constructor for class org.anchoranalysis.plugin.imagej.bean.threshold.ThresholderSimpleFillHoles2D

Creates a new ThresholderSimpleFillHoles2D instance.

V

VarianceFilter2D - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments

Applies a 2D variance filter to a channel using ImageJ's RankFilters.

VarianceFilter2D() - Constructor for class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments.VarianceFilter2D

Creates a new VarianceFilter2D instance.

W

WithFilterBase - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider

A base class for applying ImageJ rank filters to channels.

WithFilterBase(int) - Constructor for class org.anchoranalysis.plugin.imagej.bean.channel.provider.WithFilterBase

Creates a new WithFilterBase instance.

WithRadiusBase - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider

A ChannelProviderUnary with a 'radius' parameter.

WithRadiusBase() - Constructor for class org.anchoranalysis.plugin.imagej.bean.channel.provider.WithRadiusBase

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