A C E G H L M O P R S T V

A

actionPerformed(ActionEvent) - Method in class com.grocottlab.atlas_toolkit.ProjectToLabel_
 
actionPerformed(ActionEvent) - Method in class com.grocottlab.atlas_toolkit.Tree2Volume_.ColorEditor
 
adjustmentValueChanged(AdjustmentEvent) - Method in class com.grocottlab.atlas_toolkit.ProjectToLabel_
 
ApplyLabelRegistration_ - Class in com.grocottlab.atlas_toolkit
A class for applying an Orthogonal Transform Sequence to an image stack.
ApplyLabelRegistration_() - Constructor for class com.grocottlab.atlas_toolkit.ApplyLabelRegistration_
 

C

clearProgress() - Method in class com.grocottlab.atlas_toolkit.ProgressWindow
 
com.grocottlab.atlas_toolkit - package com.grocottlab.atlas_toolkit
 
computeAverageTransform(OrthogonalTransform[]) - Static method in class com.grocottlab.atlas_toolkit.OrthogonalTransform
Calculates the mean average X and Y coefficients from a set of OrthogonalTransform objects.

E

EDIT - Static variable in class com.grocottlab.atlas_toolkit.Tree2Volume_.ColorEditor
 
ExtractNuclearSignal_ - Class in com.grocottlab.atlas_toolkit
A class for extracting a normalized nuclear fluorescence signal.
ExtractNuclearSignal_() - Constructor for class com.grocottlab.atlas_toolkit.ExtractNuclearSignal_
 

G

getCellEditorValue() - Method in class com.grocottlab.atlas_toolkit.Tree2Volume_.ColorEditor
 
getCoefficientsX() - Method in class com.grocottlab.atlas_toolkit.OrthogonalTransform
Gets the X coefficients generated by bUnwarpJ.
getCoefficientsX(OrthogonalTransformSequence.OrthogonalPlane, int) - Method in class com.grocottlab.atlas_toolkit.OrthogonalTransformSequence
Gets the X coefficients of the 2D (XY) transform for the specified orthogonal plane and iteration.
getCoefficientsY() - Method in class com.grocottlab.atlas_toolkit.OrthogonalTransform
Gets the Y coefficients generated by bUnwarpJ.
getCoefficientsY(OrthogonalTransformSequence.OrthogonalPlane, int) - Method in class com.grocottlab.atlas_toolkit.OrthogonalTransformSequence
Gets the Y coefficients of the 2D (XY) transform for the specified orthogonal plane and iteration.
getDimensions() - Method in class com.grocottlab.atlas_toolkit.OrthogonalTransformSequence
 
getIntersection(ImagePlus[]) - Static method in class com.grocottlab.atlas_toolkit.LabelRegistration3D_
 
getIntervals() - Method in class com.grocottlab.atlas_toolkit.OrthogonalTransform
 
getIntervals(OrthogonalTransformSequence.OrthogonalPlane, int) - Method in class com.grocottlab.atlas_toolkit.OrthogonalTransformSequence
 
getIterations() - Method in class com.grocottlab.atlas_toolkit.OrthogonalTransformSequence
Gets the number of iterations in this OrthogonalTransformSequence.
getOrthogonalTransform(OrthogonalTransformSequence.OrthogonalPlane, int) - Method in class com.grocottlab.atlas_toolkit.OrthogonalTransformSequence
Gets the transformation coefficients (as an OrthogonalTransform object) for the given orthogonal plane and iteration.
getOrthogonalTransforms() - Method in class com.grocottlab.atlas_toolkit.StackRegister
 
getTableCellEditorComponent(JTable, Object, boolean, int, int) - Method in class com.grocottlab.atlas_toolkit.Tree2Volume_.ColorEditor
 
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class com.grocottlab.atlas_toolkit.Tree2Volume_.ColorRenderer
 
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class com.grocottlab.atlas_toolkit.Tree2Volume_.ProgressRenderer
 
getTransformedImage(OrthogonalTransform) - Method in class com.grocottlab.atlas_toolkit.StackRegister
 
getTransformedImages(OrthogonalTransform[]) - Method in class com.grocottlab.atlas_toolkit.StackRegister
 
getTransformedImages() - Method in class com.grocottlab.atlas_toolkit.StackRegister
 

H

hideProgress(int) - Method in class com.grocottlab.atlas_toolkit.ProgressWindow
 

L

LabelRegistration3D_ - Class in com.grocottlab.atlas_toolkit
A class for registering multiple 3D image stacks in group-wise fashion.
LabelRegistration3D_() - Constructor for class com.grocottlab.atlas_toolkit.LabelRegistration3D_
 

M

MergeRegisteredVolumes_ - Class in com.grocottlab.atlas_toolkit
A class for combining image stacks following registration by ApplyLabelRegistration.
MergeRegisteredVolumes_() - Constructor for class com.grocottlab.atlas_toolkit.MergeRegisteredVolumes_
 

O

openOTS(String) - Static method in class com.grocottlab.atlas_toolkit.OrthogonalTransformSequence
Generates an OrthogonalTransformSequence object from a previously saved ".ots" file.
OrthogonalTransform - Class in com.grocottlab.atlas_toolkit
A class for holding 2D (XY) transformation coefficients as generated by bUnwarpJ.
OrthogonalTransform(double[][], double[][], int) - Constructor for class com.grocottlab.atlas_toolkit.OrthogonalTransform
 
OrthogonalTransform(Transformation) - Constructor for class com.grocottlab.atlas_toolkit.OrthogonalTransform
 
OrthogonalTransformSequence - Class in com.grocottlab.atlas_toolkit
A class for storing a sequence of orthogonal 2D transformation coefficients generated by bUnwarpJ.
OrthogonalTransformSequence(OrthogonalTransform[][], int[]) - Constructor for class com.grocottlab.atlas_toolkit.OrthogonalTransformSequence
Constructor.
OrthogonalTransformSequence.OrthogonalPlane - Enum in com.grocottlab.atlas_toolkit
 

P

ProgressWindow - Class in com.grocottlab.atlas_toolkit
Provides the user with progress information about the registration process.
ProgressWindow(int, int) - Constructor for class com.grocottlab.atlas_toolkit.ProgressWindow
 
ProjectToLabel_ - Class in com.grocottlab.atlas_toolkit
A class for projecting the extracted nuclear signal onto the surface morphology of a tissue.
ProjectToLabel_() - Constructor for class com.grocottlab.atlas_toolkit.ProjectToLabel_
 

R

reslice(ImagePlus) - Static method in class com.grocottlab.atlas_toolkit.LabelRegistration3D_
 
run(String) - Method in class com.grocottlab.atlas_toolkit.ApplyLabelRegistration_
 
run(String) - Method in class com.grocottlab.atlas_toolkit.ExtractNuclearSignal_
 
run(String) - Method in class com.grocottlab.atlas_toolkit.LabelRegistration3D_
 
run(String) - Method in class com.grocottlab.atlas_toolkit.MergeRegisteredVolumes_
 
run(String) - Method in class com.grocottlab.atlas_toolkit.ProjectToLabel_
 
run(String) - Method in class com.grocottlab.atlas_toolkit.SampleVolumes_
 
run(String) - Method in class com.grocottlab.atlas_toolkit.Tree2Volume_
 

S

SampleVolumes_ - Class in com.grocottlab.atlas_toolkit
This class is used to format registered datasets ready for hierarchical clustering by the software Cluster 3.0.
SampleVolumes_() - Constructor for class com.grocottlab.atlas_toolkit.SampleVolumes_
 
saveToFile(String) - Method in class com.grocottlab.atlas_toolkit.OrthogonalTransformSequence
Saves this OrthogonalTransformSequence object to an ".ots" file.
setOrthogonalTransform(OrthogonalTransform, OrthogonalTransformSequence.OrthogonalPlane, int) - Method in class com.grocottlab.atlas_toolkit.OrthogonalTransformSequence
Sets the transformation coefficients (as an OrthogonalTransform object) for the given orthogonal plane and iteration.
setProgress(int, int) - Method in class com.grocottlab.atlas_toolkit.ProgressWindow
 
showDialog() - Method in class com.grocottlab.atlas_toolkit.ProjectToLabel_
 
showProgress(int, int, int) - Method in class com.grocottlab.atlas_toolkit.ProgressWindow
 
showStatus(int, String) - Method in class com.grocottlab.atlas_toolkit.ProgressWindow
 
StackRegister - Class in com.grocottlab.atlas_toolkit
This class performs group-wise registration of a multiple 3D (XYZ) image stacks in a single 2D (e.g XY, YZ, ZX) plane.
StackRegister(ImagePlus[]) - Constructor for class com.grocottlab.atlas_toolkit.StackRegister
 
StackRegister(ImagePlus[], ProgressWindow) - Constructor for class com.grocottlab.atlas_toolkit.StackRegister
 
StackRegister(ImagePlus) - Constructor for class com.grocottlab.atlas_toolkit.StackRegister
 

T

Tree2Volume_ - Class in com.grocottlab.atlas_toolkit
A class for 3D reconstruction of hierarchical clustering results generated by the Cluster 3.0 software.
Tree2Volume_() - Constructor for class com.grocottlab.atlas_toolkit.Tree2Volume_
 
Tree2Volume_.ColorEditor - Class in com.grocottlab.atlas_toolkit
 
Tree2Volume_.ColorEditor() - Constructor for class com.grocottlab.atlas_toolkit.Tree2Volume_.ColorEditor
 
Tree2Volume_.ColorRenderer - Class in com.grocottlab.atlas_toolkit
 
Tree2Volume_.ColorRenderer(boolean) - Constructor for class com.grocottlab.atlas_toolkit.Tree2Volume_.ColorRenderer
 
Tree2Volume_.ProgressRenderer - Class in com.grocottlab.atlas_toolkit
 
Tree2Volume_.ProgressRenderer(boolean) - Constructor for class com.grocottlab.atlas_toolkit.Tree2Volume_.ProgressRenderer
 

V

valueOf(String) - Static method in enum com.grocottlab.atlas_toolkit.OrthogonalTransformSequence.OrthogonalPlane
Returns the enum constant of this type with the specified name.
values() - Static method in enum com.grocottlab.atlas_toolkit.OrthogonalTransformSequence.OrthogonalPlane
Returns an array containing the constants of this enum type, in the order they are declared.

A C E G H L M O P R S T V

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