A B C D E F I K M N O P R S T U

A

AbstractBlockFilter - Class in mpicbg.ij.plugin

Abstract base class for variance and STD filters.

AbstractBlockFilter() - Constructor for class mpicbg.ij.plugin.AbstractBlockFilter

AbstractBlockStatistics - Class in mpicbg.ij.plugin

Abstract base class for variance and STD filters.

AbstractBlockStatistics() - Constructor for class mpicbg.ij.plugin.AbstractBlockStatistics

addHandle(int, int) - Method in class Transform_MovingLeastSquaresMesh

adjustmentValueChanged(AdjustmentEvent) - Method in class Stack_Rotate

AlignStacksWithLandmarks - Class in mpicbg.ij.plugin

AlignStacksWithLandmarks() - Constructor for class mpicbg.ij.plugin.AlignStacksWithLandmarks

apply() - Method in class Transform_SpringMesh

B

blockRadius - Static variable in class mpicbg.ij.plugin.MSEBlockFlow

blockRadius - Static variable in class mpicbg.ij.plugin.PMCCBlockFlow

blockRadiusX - Static variable in class mpicbg.ij.plugin.AbstractBlockFilter

blockRadiusX - Static variable in class mpicbg.ij.plugin.Mean

blockRadiusY - Static variable in class mpicbg.ij.plugin.AbstractBlockFilter

blockRadiusY - Static variable in class mpicbg.ij.plugin.Mean

brx - Variable in class mpicbg.ij.plugin.AbstractBlockFilter

bry - Variable in class mpicbg.ij.plugin.AbstractBlockFilter

bss - Variable in class mpicbg.ij.plugin.AbstractBlockStatistics

C

cent - Variable in class mpicbg.ij.plugin.NormalizeLocalContrast

center - Static variable in class mpicbg.ij.plugin.NormalizeLocalContrast

colorCircle(ColorProcessor) - Static method in class mpicbg.ij.plugin.MSEBlockFlow

colorCircle(ColorProcessor) - Static method in class mpicbg.ij.plugin.MSEGaussianFlow

colorCircle(ColorProcessor) - Static method in class mpicbg.ij.plugin.PMCCBlockFlow

copyParameters() - Method in class mpicbg.ij.plugin.AbstractBlockFilter

copyParameters() - Method in class mpicbg.ij.plugin.AbstractBlockStatistics

copyParameters() - Method in class mpicbg.ij.plugin.NormalizeLocalContrast

copyParameters() - Method in class mpicbg.ij.plugin.RemoveOutliers

createAlignedStack(ImagePlus, ImagePlus, Collection<PointMatch>, M) - Static method in class mpicbg.ij.plugin.AlignStacksWithLandmarks

createFeatureDescriptorImage(String, Feature) - Static method in class MOPS_ExtractPointRoi

createFeatureDescriptorShape(Feature) - Static method in class MOPS_ExtractPointRoi

Create a Shape that illustrates the descriptor patch.

createMapping() - Method in class Transform_MovingLeastSquaresMesh

createModel(int) - Static method in class mpicbg.ij.plugin.ElasticAlign

D

deserialize(String) - Static method in class mpicbg.ij.plugin.ElasticAlign

Attempts to find a file containing a serialized object.

deserialize(String) - Static method in class mpicbg.ij.plugin.ElasticMontage

Attempts to find a file containing a serialized object.

dialogItemChanged(GenericDialog, AWTEvent) - Method in class mpicbg.ij.plugin.AbstractBlockFilter

dialogItemChanged(GenericDialog, AWTEvent) - Method in class mpicbg.ij.plugin.Mean

dialogItemChanged(GenericDialog, AWTEvent) - Method in class mpicbg.ij.plugin.NormalizeLocalContrast

dialogItemChanged(GenericDialog, AWTEvent) - Method in class mpicbg.ij.plugin.RemoveOutliers

dialogTitle() - Method in class mpicbg.ij.plugin.AbstractBlockFilter

dialogTitle() - Method in class mpicbg.ij.plugin.NormalizeLocalContrast

dialogTitle() - Method in class mpicbg.ij.plugin.RemoveOutliers

dialogTitle() - Method in class mpicbg.ij.plugin.SampleVariance

dialogTitle() - Method in class mpicbg.ij.plugin.StandardDeviation

DiffusionMask - Class in mpicbg.ij.plugin

Diffuse

DiffusionMask() - Constructor for class mpicbg.ij.plugin.DiffusionMask

drawFeatureDescriptor(FloatProcessor, Feature) - Static method in class MOPS_ExtractPointRoi

E

ElasticAlign - Class in mpicbg.ij.plugin

ElasticAlign() - Constructor for class mpicbg.ij.plugin.ElasticAlign

ElasticMontage - Class in mpicbg.ij.plugin

ElasticMontage() - Constructor for class mpicbg.ij.plugin.ElasticMontage

exec(ImagePlus, ImagePlus, float, int, int, int, int, int, float, float, float, int) - Method in class SIFT_ExtractPointRoi

If unsure, just use default parameters by using exec(ImagePlus, ImagePlus, int) method, where only the model is specified.

exec(ImagePlus, ImagePlus, int) - Method in class SIFT_ExtractPointRoi

Execute with default parameters, except the model.

exec(ImagePlus, ImagePlus) - Method in class SIFT_ExtractPointRoi

Execute with default parameters (model is Rigid)

F

filter - Static variable in class mpicbg.ij.plugin.MSEGaussianFlow

Find_PointRoi - Class in <Unnamed>

Find_PointRoi() - Constructor for class Find_PointRoi

flags - Static variable in class mpicbg.ij.plugin.AbstractBlockFilter

flags - Static variable in class mpicbg.ij.plugin.Mean

fps - Variable in class mpicbg.ij.plugin.AbstractBlockFilter

I

imageClosed(ImagePlus) - Method in class MOPS_ExtractPointRoi

imageOpened(ImagePlus) - Method in class MOPS_ExtractPointRoi

imageUpdated(ImagePlus) - Method in class MOPS_ExtractPointRoi

init(ImagePlus) - Method in class mpicbg.ij.plugin.AbstractBlockFilter

init(ImagePlus) - Method in class mpicbg.ij.plugin.AbstractBlockStatistics

init(ImagePlus) - Method in class mpicbg.ij.plugin.NormalizeLocalContrast

init(ImagePlus) - Method in class mpicbg.ij.plugin.RemoveOutliers

init() - Method in class Transform_MovingLeastSquaresMesh

interpolate - Variable in class Stack_Rotate.MappingThread

K

keyPressed(KeyEvent) - Method in class MOPS_ExtractPointRoi

keyPressed(KeyEvent) - Method in class mpicbg.ij.plugin.ElasticAlign

keyPressed(KeyEvent) - Method in class mpicbg.ij.plugin.MSEGaussianFlow

keyPressed(KeyEvent) - Method in class SIFT_Align

keyPressed(KeyEvent) - Method in class SIFT_MultiChannel_Align

keyPressed(KeyEvent) - Method in class Stack_Rotate

keyPressed(KeyEvent) - Method in class Transform_SpringMesh

keyReleased(KeyEvent) - Method in class MOPS_ExtractPointRoi

keyReleased(KeyEvent) - Method in class mpicbg.ij.plugin.ElasticAlign

keyReleased(KeyEvent) - Method in class mpicbg.ij.plugin.MSEGaussianFlow

keyReleased(KeyEvent) - Method in class SIFT_Align

keyReleased(KeyEvent) - Method in class SIFT_MultiChannel_Align

keyReleased(KeyEvent) - Method in class Stack_Rotate

keyReleased(KeyEvent) - Method in class Transform_SpringMesh

keyTyped(KeyEvent) - Method in class MOPS_ExtractPointRoi

keyTyped(KeyEvent) - Method in class mpicbg.ij.plugin.ElasticAlign

keyTyped(KeyEvent) - Method in class mpicbg.ij.plugin.MSEGaussianFlow

keyTyped(KeyEvent) - Method in class SIFT_Align

keyTyped(KeyEvent) - Method in class SIFT_MultiChannel_Align

keyTyped(KeyEvent) - Method in class Stack_Rotate

keyTyped(KeyEvent) - Method in class Transform_SpringMesh

M

man - Static variable in class Transform_MovingLeastSquaresMesh

mapping - Variable in class Transform_SpringMesh

MappingThread(ImageStack, ImageProcessor, boolean) - Constructor for class Stack_Rotate.MappingThread

maxDistance - Static variable in class mpicbg.ij.plugin.MSEBlockFlow

maxDistance - Static variable in class mpicbg.ij.plugin.MSEGaussianFlow

maxDistance - Static variable in class mpicbg.ij.plugin.PMCCBlockFlow

Mean - Class in mpicbg.ij.plugin

Apply a mean filter.

Mean() - Constructor for class mpicbg.ij.plugin.Mean

mean - Variable in class mpicbg.ij.plugin.Mean

mesh - Variable in class Transform_MovingLeastSquaresMesh

mesh - Variable in class Transform_SpringMesh

model - Variable in class Transform_Affine

model - Variable in class Transform_Perspective

model - Variable in class Transform_RegularizedAffine

model - Variable in class Transform_Rigid

model - Variable in class Transform_Similarity

modifiers(int) - Static method in class MOPS_ExtractPointRoi

modifiers(int) - Static method in class Stack_Rotate

modifiers(int) - Static method in class Transform_SpringMesh

MOPS_ExtractPointRoi - Class in <Unnamed>

Extract landmark correspondences in two images as PointRoi.

MOPS_ExtractPointRoi() - Constructor for class MOPS_ExtractPointRoi

mouseClicked(MouseEvent) - Method in class MOPS_ExtractPointRoi

mouseClicked(MouseEvent) - Method in class Stack_Rotate

mouseClicked(MouseEvent) - Method in class Transform_SpringMesh

mouseDragged(MouseEvent) - Method in class Stack_Rotate

mouseDragged(MouseEvent) - Method in class Transform_SpringMesh

mouseEntered(MouseEvent) - Method in class MOPS_ExtractPointRoi

mouseEntered(MouseEvent) - Method in class Stack_Rotate

mouseEntered(MouseEvent) - Method in class Transform_SpringMesh

mouseExited(MouseEvent) - Method in class MOPS_ExtractPointRoi

mouseExited(MouseEvent) - Method in class Stack_Rotate

mouseExited(MouseEvent) - Method in class Transform_SpringMesh

mouseMoved(MouseEvent) - Method in class Stack_Rotate

mouseMoved(MouseEvent) - Method in class Transform_SpringMesh

mousePressed(MouseEvent) - Method in class MOPS_ExtractPointRoi

mousePressed(MouseEvent) - Method in class Stack_Rotate

mousePressed(MouseEvent) - Method in class Transform_SpringMesh

mouseReleased(MouseEvent) - Method in class MOPS_ExtractPointRoi

mouseReleased(MouseEvent) - Method in class Stack_Rotate

mouseReleased(MouseEvent) - Method in class Transform_SpringMesh

mouseWheelMoved(MouseWheelEvent) - Method in class Stack_Rotate

mpicbg.ij.clahe - package mpicbg.ij.clahe

mpicbg.ij.plugin - package mpicbg.ij.plugin

MSEBlockFlow - Class in mpicbg.ij.plugin

Transfer an image sequence into an optic flow field.

MSEBlockFlow() - Constructor for class mpicbg.ij.plugin.MSEBlockFlow

MSEGaussianFlow - Class in mpicbg.ij.plugin

Transfer an image sequence into an optic flow field.

MSEGaussianFlow() - Constructor for class mpicbg.ij.plugin.MSEGaussianFlow

myModel() - Method in class Transform_Affine

myModel() - Method in class Transform_Perspective

myModel() - Method in class Transform_RegularizedAffine

myModel() - Method in class Transform_Rigid

myModel() - Method in class Transform_Similarity

N

NL - Static variable in class Transform_MovingLeastSquaresMesh

nlcs - Variable in class mpicbg.ij.plugin.NormalizeLocalContrast

NormalizeLocalContrast - Class in mpicbg.ij.plugin

Normalize contrast based on per-pixel mean and STD.

NormalizeLocalContrast() - Constructor for class mpicbg.ij.plugin.NormalizeLocalContrast

O

onReturn() - Method in class Transform_Affine

onReturn() - Method in class Transform_RegularizedAffine

onReturn() - Method in class Transform_Rigid

onReturn() - Method in class Transform_Similarity

P

pingPong(int, int) - Static method in class mpicbg.ij.plugin.MSEBlockFlow

pingPong(int, int) - Static method in class mpicbg.ij.plugin.MSEGaussianFlow

pip - Variable in class mpicbg.ij.plugin.AbstractBlockFilter

pip - Variable in class mpicbg.ij.plugin.Mean

PlugIn - Class in mpicbg.ij.clahe

"Contrast Limited Adaptive Histogram Equalization" as described in BibTeX: @article{zuiderveld94, author = {Zuiderveld, Karel}, title = {Contrast limited adaptive histogram equalization}, book = {Graphics gems IV}, year = {1994}, isbn = {0-12-336155-9}, pages = {474--485}, publisher = {Academic Press Professional, Inc.}, address = {San Diego, CA, USA}, }

PlugIn() - Constructor for class mpicbg.ij.clahe.PlugIn

PMCCBlockFlow - Class in mpicbg.ij.plugin

Transfer an image sequence into an optic flow field.

PMCCBlockFlow() - Constructor for class mpicbg.ij.plugin.PMCCBlockFlow

process(int) - Method in class mpicbg.ij.plugin.AbstractBlockFilter

process(int) - Method in class mpicbg.ij.plugin.NormalizeLocalContrast

process(int) - Method in class mpicbg.ij.plugin.RemoveOutliers

process(int) - Method in class mpicbg.ij.plugin.SampleVariance

process(int) - Method in class mpicbg.ij.plugin.StandardDeviation

R

RemoveOutliers - Class in mpicbg.ij.plugin

Remove saturated pixels by diffusing the neighbors in.

RemoveOutliers() - Constructor for class mpicbg.ij.plugin.RemoveOutliers

RemoveSaturated - Class in mpicbg.ij.plugin

Remove saturated pixels by diffusing the neighbors in.

RemoveSaturated() - Constructor for class mpicbg.ij.plugin.RemoveSaturated

repaint() - Method in class Stack_Rotate.MappingThread

rmos - Variable in class mpicbg.ij.plugin.RemoveOutliers

run(String) - Method in class Find_PointRoi

run(String) - Method in class MOPS_ExtractPointRoi

run(String) - Method in class mpicbg.ij.clahe.PlugIn

PlugIn access

run(ImagePlus) - Static method in class mpicbg.ij.clahe.PlugIn

Process an ImagePlus with the static parameters.

run(ImageProcessor) - Method in class mpicbg.ij.plugin.AbstractBlockFilter

run(String) - Method in class mpicbg.ij.plugin.AlignStacksWithLandmarks

run(ImageProcessor, FloatProcessor, int) - Static method in class mpicbg.ij.plugin.DiffusionMask

run(String) - Method in class mpicbg.ij.plugin.DiffusionMask

run(String) - Method in class mpicbg.ij.plugin.ElasticAlign

run() - Method in class mpicbg.ij.plugin.ElasticAlign

run(String) - Method in class mpicbg.ij.plugin.ElasticMontage

run() - Method in class mpicbg.ij.plugin.ElasticMontage

run(ImageProcessor) - Method in class mpicbg.ij.plugin.Mean

run(String) - Method in class mpicbg.ij.plugin.MSEBlockFlow

run(String) - Method in class mpicbg.ij.plugin.MSEGaussianFlow

run(ImageProcessor, int, int, float, boolean, boolean) - Static method in class mpicbg.ij.plugin.NormalizeLocalContrast

Apply local contrast enhancement to and ImageProcessor.

run(String) - Method in class mpicbg.ij.plugin.PMCCBlockFlow

run(ImageProcessor, int, int, float) - Static method in class mpicbg.ij.plugin.RemoveOutliers

Remove outlier pixels from an ImageProcessor.

run(ImageProcessor, float) - Static method in class mpicbg.ij.plugin.RemoveSaturated

run(String) - Method in class mpicbg.ij.plugin.RemoveSaturated

run(String) - Method in class SIFT_Align

run(String) - Method in class SIFT_ExtractPointRoi

run(String) - Method in class SIFT_MultiChannel_Align

run(String) - Method in class SIFT_Test

run() - Method in class Stack_Rotate.MappingThread

run(String) - Method in class Stack_Rotate

run(String) - Method in class Transform_Roi

run(String) - Method in class Transform_SpringMesh

S

SampleVariance - Class in mpicbg.ij.plugin

Sample variance block filter.

SampleVariance() - Constructor for class mpicbg.ij.plugin.SampleVariance

serialize(Object, String) - Static method in class mpicbg.ij.plugin.ElasticAlign

Serializes the given object into the path.

serialize(Object, String) - Static method in class mpicbg.ij.plugin.ElasticMontage

Serializes the given object into the path.

setHandles() - Method in class Transform_Affine

setHandles() - Method in class Transform_Perspective

setHandles() - Method in class Transform_RegularizedAffine

setHandles() - Method in class Transform_Rigid

setHandles() - Method in class Transform_Similarity

setNPasses(int) - Method in class mpicbg.ij.plugin.AbstractBlockFilter

setNPasses(int) - Method in class mpicbg.ij.plugin.Mean

setup(String, ImagePlus) - Method in class mpicbg.ij.plugin.AbstractBlockFilter

setup(String, ImagePlus) - Method in class mpicbg.ij.plugin.Mean

setup() - Method in class Transform_Roi

showColors - Static variable in class mpicbg.ij.plugin.MSEBlockFlow

showColors - Static variable in class mpicbg.ij.plugin.MSEGaussianFlow

showColors - Static variable in class mpicbg.ij.plugin.PMCCBlockFlow

showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class mpicbg.ij.plugin.AbstractBlockFilter

showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class mpicbg.ij.plugin.Mean

showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class mpicbg.ij.plugin.NormalizeLocalContrast

showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class mpicbg.ij.plugin.RemoveOutliers

SIFT_Align - Class in <Unnamed>

Align a stack consecutively using automatically extracted robust landmark correspondences.

SIFT_Align() - Constructor for class SIFT_Align

SIFT_ExtractPointRoi - Class in <Unnamed>

Extract landmark correspondences in two images as PointRoi.

SIFT_ExtractPointRoi() - Constructor for class SIFT_ExtractPointRoi

SIFT_MultiChannel_Align - Class in <Unnamed>

MultiChannel version of SIFT_Align, please check it for documentation

SIFT_MultiChannel_Align() - Constructor for class SIFT_MultiChannel_Align

SIFT_Test - Class in <Unnamed>

Extract and display Scale Invariant Features after the method of David Lowe \cite{Lowe04} in an image.

SIFT_Test() - Constructor for class SIFT_Test

sigma - Static variable in class mpicbg.ij.plugin.MSEGaussianFlow

source - Variable in class Stack_Rotate.MappingThread

source - Variable in class Transform_Roi

Stack_Rotate - Class in <Unnamed>

Stack_Rotate() - Constructor for class Stack_Rotate

Stack_Rotate.MappingThread - Class in <Unnamed>

StandardDeviation - Class in mpicbg.ij.plugin

STD block filter.

StandardDeviation() - Constructor for class mpicbg.ij.plugin.StandardDeviation

standardDeviations - Static variable in class mpicbg.ij.plugin.NormalizeLocalContrast

standardDeviations - Static variable in class mpicbg.ij.plugin.RemoveOutliers

stds - Variable in class mpicbg.ij.plugin.NormalizeLocalContrast

stds - Variable in class mpicbg.ij.plugin.RemoveOutliers

stret - Variable in class mpicbg.ij.plugin.NormalizeLocalContrast

stretch - Static variable in class mpicbg.ij.plugin.NormalizeLocalContrast

T

target - Variable in class Stack_Rotate.MappingThread

temp - Variable in class Stack_Rotate.MappingThread

template - Variable in class Transform_Roi

toByte(byte[]) - Method in class mpicbg.ij.plugin.AbstractBlockFilter

toByte(byte[]) - Method in class mpicbg.ij.plugin.SampleVariance

toggleInterpolation() - Method in class Stack_Rotate.MappingThread

toRGB(int[]) - Method in class mpicbg.ij.plugin.AbstractBlockFilter

toRGB(int[]) - Method in class mpicbg.ij.plugin.SampleVariance

toShort(short[]) - Method in class mpicbg.ij.plugin.AbstractBlockFilter

toShort(short[]) - Method in class mpicbg.ij.plugin.SampleVariance

transform(CoordinateTransform, ImageProcessor, ImageProcessor) - Static method in class Transform_Roi

Transform_Affine - Class in <Unnamed>

Transform_Affine() - Constructor for class Transform_Affine

Transform_MovingLeastSquaresMesh - Class in <Unnamed>

Smooth image deformation using landmark based deformation by means of Moving Least Squares as described by \citet{SchaeferAl06} inspired by the implementation of Johannes Schindelin.

Transform_MovingLeastSquaresMesh() - Constructor for class Transform_MovingLeastSquaresMesh

Transform_Perspective - Class in <Unnamed>

Transform_Perspective() - Constructor for class Transform_Perspective

Transform_RegularizedAffine - Class in <Unnamed>

Transform_RegularizedAffine() - Constructor for class Transform_RegularizedAffine

Transform_Rigid - Class in <Unnamed>

Transform_Rigid() - Constructor for class Transform_Rigid

Transform_Roi - Class in <Unnamed>

Use two sets of landmarks selected in two images to map one image to the other.

Transform_Roi() - Constructor for class Transform_Roi

Transform_Similarity - Class in <Unnamed>

Transform_Similarity() - Constructor for class Transform_Similarity

Transform_SpringMesh - Class in <Unnamed>

Transform_SpringMesh() - Constructor for class Transform_SpringMesh

transformInterpolated(CoordinateTransform, ImageProcessor, ImageProcessor) - Static method in class Transform_Roi

U

updateHandles(int, int) - Method in class Transform_Affine

updateHandles(int, int) - Method in class Transform_MovingLeastSquaresMesh

updateHandles(int, int) - Method in class Transform_Perspective

updateHandles(int, int) - Method in class Transform_RegularizedAffine

updateHandles(int, int) - Method in class Transform_Rigid

updateHandles(int, int) - Method in class Transform_Similarity

updateIllustration() - Method in class Transform_MovingLeastSquaresMesh

updateMapping() - Method in class Transform_MovingLeastSquaresMesh

A B C D E F I K M N O P R S T U