Index

A C D G I M O R S T
All Classes and Interfaces|All Packages

A

AnisotropicDiffusion - Class in org.anchoranalysis.plugin.fiji.bean.channel.provider

Performs Perona-Malik Anisotropic Diffusion.

AnisotropicDiffusion() - Constructor for class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion

AutoLocalThreshold - Class in org.anchoranalysis.plugin.fiji.bean.mask.provider

Applies local thresholding algorithm using Fiji's {link Auto_Local_Threshold} plugin

AutoLocalThreshold() - Constructor for class org.anchoranalysis.plugin.fiji.bean.mask.provider.AutoLocalThreshold

C

createDistanceMapForVoxels(BinaryVoxels<UnsignedByteBuffer>, Optional<Resolution>, float) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D

Creates a distance map for binary voxels.

createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion

createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.MinimumFilter

createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransformForEachObject3D

createFromMask(Mask) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D

createFromSource(Channel) - Method in class org.anchoranalysis.plugin.fiji.bean.mask.provider.AutoLocalThreshold

D

DistanceTransform3D - Class in org.anchoranalysis.plugin.fiji.bean.channel.provider.distance

Euclidian Distance Transform from ImageJ that works on 2D as well as 3D z-stacks.

DistanceTransform3D() - Constructor for class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D

DistanceTransformForEachObject3D - Class in org.anchoranalysis.plugin.fiji.bean.channel.provider.distance

Like DistanceTransform3D but applies the distance transform separately for each object in a collection.

DistanceTransformForEachObject3D() - Constructor for class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransformForEachObject3D

G

getDeltat() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion

the integration constant for the numerical integration scheme.

getIterations() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion

How many iterations to perform diffusion.

getKappa() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion

A parameter kappa associated with the diffusion functions.

getMethod() - Method in class org.anchoranalysis.plugin.fiji.bean.mask.provider.AutoLocalThreshold

getMethod() - Method in class org.anchoranalysis.plugin.fiji.bean.threshold.ThresholderAutoIJ

The thresholding method to use.

getMultiplyBy() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D

A factor to multiply the distance values by.

getObjects() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransformForEachObject3D

getRadius() - Method in class org.anchoranalysis.plugin.fiji.bean.mask.provider.AutoLocalThreshold

GrayscaleReconstruction2DIJ - Class in org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction

Performs 2D grayscale reconstruction using ImageJ's implementation.

GrayscaleReconstruction2DIJ() - Constructor for class org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction.GrayscaleReconstruction2DIJ

I

isApplyResolution() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D

If true, multiplies the values by the x-resolution, if it exists.

isCreateShort() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D

If true, creates a short (16-bit) output instead of byte (8-bit).

isCreateShort() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransformForEachObject3D

isDo3D() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion

Whether to perform the diffusion in 3D direction, or rather only in the 2D plane.

isIgnoreZIfNaN() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D

If true and the z-resolution is undefined, the z dimension is ignored.

isNoBlack() - Method in class org.anchoranalysis.plugin.fiji.bean.threshold.ThresholderAutoIJ

If true, the thresholding algorithm will not consider black pixels (value 0) in its calculations.

isStrongEdgeEnhancer() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion

If true uses, the strong-edge-enhancer diffusion function, otherwise the wide-region-enhancer.

isSuppressZ() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D

If true, suppresses the z-dimension in distance calculations.

isSuppressZ() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransformForEachObject3D

M

MinimumFilter - Class in org.anchoranalysis.plugin.fiji.bean.channel.provider

Applies a minimum filter to a channel using ImageJ's MinMaxMedian plugin.

MinimumFilter() - Constructor for class org.anchoranalysis.plugin.fiji.bean.channel.provider.MinimumFilter

O

org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction - package org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction

Morphological grayscale-reconstruction algorithm.

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

Implementations of ChannelProvider that use FIJI.

org.anchoranalysis.plugin.fiji.bean.channel.provider.distance - package org.anchoranalysis.plugin.fiji.bean.channel.provider.distance

Euclidean Distance Transform implementations via FIJI.

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

Implementations of MaskProvider that use FIJI.

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

Implementations of Thresholder that use FIJI.

R

reconstruction(VoxelsUntyped, VoxelsUntyped, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction.GrayscaleReconstruction2DIJ

S

setApplyResolution(boolean) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D

If true, multiplies the values by the x-resolution, if it exists.

setCreateShort(boolean) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D

If true, creates a short (16-bit) output instead of byte (8-bit).

setCreateShort(boolean) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransformForEachObject3D

setDeltat(double) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion

the integration constant for the numerical integration scheme.

setDo3D(boolean) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion

Whether to perform the diffusion in 3D direction, or rather only in the 2D plane.

setIgnoreZIfNaN(boolean) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D

If true and the z-resolution is undefined, the z dimension is ignored.

setIterations(int) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion

How many iterations to perform diffusion.

setKappa(double) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion

A parameter kappa associated with the diffusion functions.

setMethod(String) - Method in class org.anchoranalysis.plugin.fiji.bean.mask.provider.AutoLocalThreshold

setMethod(String) - Method in class org.anchoranalysis.plugin.fiji.bean.threshold.ThresholderAutoIJ

The thresholding method to use.

setMultiplyBy(float) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D

A factor to multiply the distance values by.

setNoBlack(boolean) - Method in class org.anchoranalysis.plugin.fiji.bean.threshold.ThresholderAutoIJ

If true, the thresholding algorithm will not consider black pixels (value 0) in its calculations.

setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransformForEachObject3D

setRadius(int) - Method in class org.anchoranalysis.plugin.fiji.bean.mask.provider.AutoLocalThreshold

setStrongEdgeEnhancer(boolean) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion

If true uses, the strong-edge-enhancer diffusion function, otherwise the wide-region-enhancer.

setSuppressZ(boolean) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D

If true, suppresses the z-dimension in distance calculations.

setSuppressZ(boolean) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransformForEachObject3D

T

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

ThresholderAutoIJ - Class in org.anchoranalysis.plugin.fiji.bean.threshold

Applies automatic thresholding using ImageJ's Auto_Threshold plugin.

ThresholderAutoIJ() - Constructor for class org.anchoranalysis.plugin.fiji.bean.threshold.ThresholderAutoIJ

A C D G I M O R S T
All Classes and Interfaces|All Packages