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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.
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