A

a - Variable in class edu.utexas.clm.archipelago.data.Duplex

 

A(int[], int) - Static method in class fiji.threshold.Auto_Threshold

 

a - Variable in class fiji.util.Levenshtein

 

a - Variable in class ini.trakem2.display.Tree.Pair

Two nodes of a tree; there is a unique path that goes from a to b.

a - Variable in class math3d.Triangle

 

a - Variable in class mpicbg.models.InterpolatedCoordinateTransform

 

a - Variable in class mpicbg.models.InterpolatedModel

 

a - Variable in class mpicbg.models.PolynomialTransform2D

holds two coefficients for each polynomial coefficient, including 1 initialized at 0 order, i.e.

A - Variable in class mpicbg.spim.registration.bead.laplace.DoGMaximum

 

a - Variable in class mpicbg.trakem2.transform.ExportUnsignedShort.PatchIntensityRange

 

a - Variable in class mpicbg.trakem2.util.Downsampler.Pair

 

a - Variable in class mpicbg.trakem2.util.Pair

 

a - Variable in class mpicbg.trakem2.util.Triple

 

A - Variable in class net.imglib2.display.ARGBARGBColorConverter

 

A - Variable in class net.imglib2.display.ARGBtoRandomARGBColorConverter

 

a - Variable in class sc.fiji.timelapse.LinearRegression

 

a() - Method in class script.imglib.math.fn.BinaryOperation

 

a() - Method in class script.imglib.math.fn.UnaryOperation

Call a().eval() to obtain the result as a double of the computation encapsulated by the @field a.

a - Variable in class spim.fiji.datasetmanager.StackList.ViewSetupPrecursor

 

a00 - Variable in class vib.FastMatrix

 

a00 - Variable in class vib.FloatMatrix

 

a01 - Variable in class vib.FastMatrix

 

a01 - Variable in class vib.FloatMatrix

 

a02 - Variable in class vib.FastMatrix

 

a02 - Variable in class vib.FloatMatrix

 

a03 - Variable in class vib.FastMatrix

 

a03 - Variable in class vib.FloatMatrix

 

a10 - Variable in class vib.FastMatrix

 

a10 - Variable in class vib.FloatMatrix

 

a11 - Variable in class vib.FastMatrix

 

a11 - Variable in class vib.FloatMatrix

 

a12 - Variable in class vib.FastMatrix

 

a12 - Variable in class vib.FloatMatrix

 

a13 - Variable in class vib.FastMatrix

 

a13 - Variable in class vib.FloatMatrix

 

a20 - Variable in class vib.FastMatrix

 

a20 - Variable in class vib.FloatMatrix

 

a21 - Variable in class vib.FastMatrix

 

a21 - Variable in class vib.FloatMatrix

 

a22 - Variable in class vib.FastMatrix

 

a22 - Variable in class vib.FloatMatrix

 

a23 - Variable in class vib.FastMatrix

 

a23 - Variable in class vib.FloatMatrix

 

A_Image5D_test - Class in sc.fiji.i5d.plugin

 

A_Image5D_test() - Constructor for class sc.fiji.i5d.plugin.A_Image5D_test

 

abort() - Method in class bdv.tools.bookmarks.BookmarksEditor

 

abort() - Method in class bdv.tools.transformation.ManualTransformationEditor

 

abort() - Method in class ini.trakem2.display.FreeHandProfile

for abort (ESC pressed for instance)

About - Class in loci.plugins

Displays a small information dialog about the Bio-Formats Plugins package.

About() - Constructor for class loci.plugins.About

 

about() - Static method in class loci.plugins.About

 

About_RATS - Class in <Unnamed>

 

About_RATS() - Constructor for class About_RATS

 

AboutDialog - Class in org.imagearchive.lsm.toolbox.gui

 

AboutDialog(JFrame, MasterModel) - Constructor for class org.imagearchive.lsm.toolbox.gui.AboutDialog

 

AboutDialog() - Constructor for class org.imagearchive.lsm.toolbox.gui.AboutDialog

 

aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.ActionChooserDescriptor

 

aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.ConfigureViewsDescriptor

 

aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.DetectionDescriptor

 

aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.DetectorChoiceDescriptor

 

aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.DetectorConfigurationDescriptor

 

aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.GrapherDescriptor

 

aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.InitFilterDescriptor

 

aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.LogPanelDescriptor

 

aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.SomeDialogDescriptor

 

aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.SpotFilterDescriptor

 

aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.StartDialogDescriptor

 

aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.TrackerChoiceDescriptor

 

aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.TrackerConfigurationDescriptor

 

aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.TrackFilterDescriptor

 

aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.TrackingDescriptor

 

aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.ViewChoiceDescriptor

 

aboutToDisplayPanel() - Method in interface fiji.plugin.trackmate.gui.descriptors.WizardPanelDescriptor

This method is used to provide functionality that will be performed just before the panel is to be displayed.

aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.ActionChooserDescriptor

 

aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.ConfigureViewsDescriptor

 

aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.DetectionDescriptor

 

aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.DetectorChoiceDescriptor

 

aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.DetectorConfigurationDescriptor

 

aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.GrapherDescriptor

 

aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.InitFilterDescriptor

 

aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.LogPanelDescriptor

 

aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.SomeDialogDescriptor

 

aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.SpotFilterDescriptor

 

aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.StartDialogDescriptor

 

aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.TrackerChoiceDescriptor

 

aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.TrackerConfigurationDescriptor

 

aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.TrackFilterDescriptor

 

aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.TrackingDescriptor

 

aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.ViewChoiceDescriptor

 

aboutToHidePanel() - Method in interface fiji.plugin.trackmate.gui.descriptors.WizardPanelDescriptor

This method is used to perform functionality just before the panel is to be hidden.

aboveThresholdLengthAlong(PrincipalComponents, int, ImagePlus, Threshold) - Method in class vib.oldregistration.PCA_Registration

 

Abs(int[]) - Method in class GrayMorphology_

Calculates the absolute value of an array

Abs - Class in imglib.ops.operator.unary

TODO

Abs() - Constructor for class imglib.ops.operator.unary.Abs

 

abs() - Method in class loci.plugins.util.RecordedImageProcessor

 

Abs - Class in script.imglib.math

TODO

Abs(Image<? extends RealType<?>>) - Constructor for class script.imglib.math.Abs

 

Abs(IFunction) - Constructor for class script.imglib.math.Abs

 

Abs(Number) - Constructor for class script.imglib.math.Abs

 

ABS_PATH - Static variable in class ini.trakem2.persistence.FSLoader

 

absFreq - Variable in class mpicbg.spim.fusion.entropy.Entropy

 

absFreq - Variable in class mpicbg.spim.fusion.entropy.EntropyFloatArray3D

 

absolute(Tuple3d) - Method in class spim.vecmath.Tuple3d

Sets each component of the tuple parameter to its absolute value and places the modified values into this tuple.

absolute() - Method in class spim.vecmath.Tuple3d

Sets each component of this tuple to its absolute value.

absolute(Tuple3f) - Method in class spim.vecmath.Tuple3f

Sets each component of the tuple parameter to its absolute value and places the modified values into this tuple.

absolute() - Method in class spim.vecmath.Tuple3f

Sets each component of this tuple to its absolute value.

absolute(Tuple3i) - Method in class spim.vecmath.Tuple3i

Sets each component of the tuple parameter to its absolute value and places the modified values into this tuple.

absolute() - Method in class spim.vecmath.Tuple3i

Sets each component of this tuple to its absolute value.

absolute(Tuple4d) - Method in class spim.vecmath.Tuple4d

Sets each component of the tuple parameter to its absolute value and places the modified values into this tuple.

absolute() - Method in class spim.vecmath.Tuple4d

Sets each component of this tuple to its absolute value.

absolute(Tuple4f) - Method in class spim.vecmath.Tuple4f

Sets each component of the tuple parameter to its absolute value and places the modified values into this tuple.

absolute() - Method in class spim.vecmath.Tuple4f

Sets each component of this tuple to its absolute value.

AbsoluteFloatComparator() - Constructor for class fiji.features.Frangi_.AbsoluteFloatComparator

 

absoluteThreshold - Variable in class mpicbg.stitching.StitchingParameters

 

AbstractAffine3D<T extends NumericType<T>> - Class in script.imglib.algorithm.fn

TODO

AbstractAffine3D(Image<T>, float[], AbstractAffine3D.Mode, Number) - Constructor for class script.imglib.algorithm.fn.AbstractAffine3D

With a default OutOfBoundsStrategyValueFactory with @param outside.

AbstractAffine3D(Image<T>, float[], AbstractAffine3D.Mode, OutOfBoundsStrategyFactory<T>) - Constructor for class script.imglib.algorithm.fn.AbstractAffine3D

 

AbstractAffine3D(Image<T>, float, float, float, float, float, float, AbstractAffine3D.Mode, Number) - Constructor for class script.imglib.algorithm.fn.AbstractAffine3D

With a default OutOfBoundsStrategyValueFactory with @param outside.

AbstractAffine3D(Image<T>, float, float, float, float, float, float, AbstractAffine3D.Mode, OutOfBoundsStrategyFactory<T>) - Constructor for class script.imglib.algorithm.fn.AbstractAffine3D

 

AbstractAffine3D.Mode - Enum in script.imglib.algorithm.fn

 

AbstractAffineModel1D<M extends AbstractAffineModel1D<M>> - Class in mpicbg.models

 

AbstractAffineModel1D() - Constructor for class mpicbg.models.AbstractAffineModel1D

 

AbstractAffineModel2D<M extends AbstractAffineModel2D<M>> - Class in mpicbg.models

 

AbstractAffineModel2D() - Constructor for class mpicbg.models.AbstractAffineModel2D

 

AbstractAffineModel3D<M extends AbstractAffineModel3D<M>> - Class in mpicbg.models

 

AbstractAffineModel3D() - Constructor for class mpicbg.models.AbstractAffineModel3D

 

AbstractAffineModelChunk - Class in edu.utexas.clm.archipelago.ijsupport

 

AbstractAffineModelChunk(AbstractAffineModel2D<?>) - Constructor for class edu.utexas.clm.archipelago.ijsupport.AbstractAffineModelChunk

 

AbstractAffineTile2D<A extends Model<A> & Affine2D<A>> - Class in mpicbg.trakem2.align

 

AbstractAffineTile2D(A, Patch) - Constructor for class mpicbg.trakem2.align.AbstractAffineTile2D

 

AbstractAnimator - Class in bdv.viewer.animate

Mother abstract class for animators that can animate the current view in a ViewerFrame instance.

AbstractAnimator(long) - Constructor for class bdv.viewer.animate.AbstractAnimator

Create new animator with the given duration.

AbstractAnnotation - Class in fiji.util.gui

Abstract class dedicated to draw overlayed annotations on a OverlayedImageCanvas.

AbstractAnnotation() - Constructor for class fiji.util.gui.AbstractAnnotation

 

AbstractBlockFilter - Class in mpicbg.ij.plugin

Abstract base class for variance and STD filters.

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

 

AbstractBlockMatching - Class in mpicbg.ij.plugin

 

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

 

AbstractBlockStatistics - Class in mpicbg.ij.plugin

Abstract base class for variance and STD filters.

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

 

AbstractCachedViewerSetupImgLoader<T extends NativeType<T>,V extends Volatile<T> & NativeType<V>,A extends VolatileAccess> - Class in bdv

Abstract ViewerSetupImgLoader with a VolatileGlobalCellCache.

AbstractCachedViewerSetupImgLoader(int, long[][], int[][], double[][], T, V, CacheArrayLoader<A>, VolatileGlobalCellCache) - Constructor for class bdv.AbstractCachedViewerSetupImgLoader

 

AbstractCorrelationFit - Class in org.janelia.thickness.inference.fits

 

AbstractCorrelationFit() - Constructor for class org.janelia.thickness.inference.fits.AbstractCorrelationFit

 

AbstractDetection<T extends AbstractDetection<T>> - Class in mpicbg.spim.registration.detection

 

AbstractDetection(int, double[]) - Constructor for class mpicbg.spim.registration.detection.AbstractDetection

 

AbstractDetection(int, double[], double) - Constructor for class mpicbg.spim.registration.detection.AbstractDetection

 

AbstractFeatureGrapher - Class in fiji.plugin.trackmate.features

 

AbstractFeatureGrapher(String, Set<String>, Model) - Constructor for class fiji.plugin.trackmate.features.AbstractFeatureGrapher

 

AbstractImgFactoryImgLoader - Class in spim.fiji.spimdata.imgloaders

 

AbstractImgFactoryImgLoader() - Constructor for class spim.fiji.spimdata.imgloaders.AbstractImgFactoryImgLoader

 

AbstractImgLoader - Class in spim.fiji.spimdata.imgloaders

 

AbstractImgLoader() - Constructor for class spim.fiji.spimdata.imgloaders.AbstractImgLoader

 

AbstractInteractiveBlockFilter - Class in mpicbg.ij.integral

 

AbstractInteractiveBlockFilter() - Constructor for class mpicbg.ij.integral.AbstractInteractiveBlockFilter

 

AbstractInteractiveBlockFilter.PaintThread - Class in mpicbg.ij.integral

 

AbstractLayerAlignmentParam - Class in mpicbg.trakem2.align

 

AbstractLayerAlignmentParam() - Constructor for class mpicbg.trakem2.align.AbstractLayerAlignmentParam

 

AbstractLayerAlignmentParam(int, int, float, int, int, int, boolean, int, float, int, int, float, float, int, int, int, int, int, float, int, boolean, boolean, boolean, boolean) - Constructor for class mpicbg.trakem2.align.AbstractLayerAlignmentParam

 

AbstractLegacyViewerImgLoader<T,V extends Volatile<T>> - Class in bdv.spimdata.legacy

 

AbstractLegacyViewerImgLoader(T, V) - Constructor for class bdv.spimdata.legacy.AbstractLegacyViewerImgLoader

 

AbstractLUTGrid - Class in org.janelia.thickness.lut

 

AbstractLUTGrid(int, int, RandomAccessibleInterval<DoubleType>) - Constructor for class org.janelia.thickness.lut.AbstractLUTGrid

 

AbstractLUTGrid(int, int, RandomAccessibleInterval<DoubleType>, double[], double[]) - Constructor for class org.janelia.thickness.lut.AbstractLUTGrid

 

AbstractLUTRealTransform - Class in org.janelia.thickness.lut

Abstract base class for LUT based transforms.

AbstractLUTRealTransform(double[], int, int) - Constructor for class org.janelia.thickness.lut.AbstractLUTRealTransform

 

AbstractLUTRealTransformField - Class in org.janelia.thickness.lut

Abstract base class for LUT based transforms in 2D fields.

AbstractLUTRealTransformField(double[], int, int, long...) - Constructor for class org.janelia.thickness.lut.AbstractLUTRealTransformField

 

AbstractLUTRealTransformField(int, int, RandomAccessibleInterval<DoubleType>) - Constructor for class org.janelia.thickness.lut.AbstractLUTRealTransformField

 

AbstractMappingThread(ImagePlus, ImagePlus, ImageProcessor) - Constructor for class mpicbg.panorama.AbstractPanorama_View.AbstractMappingThread

 

AbstractModel<M extends AbstractModel<M>> - Class in mpicbg.models

Abstract class for arbitrary transformation models to be applied to Points in n-dimensional space.

AbstractModel() - Constructor for class mpicbg.models.AbstractModel

 

AbstractMovingLeastSquaresTransform - Class in mpicbg.models

Smooth coordinate transformation interpolating between a set of control points that are maped exactly on top of each other using landmark based deformation by means of Moving Least Squares as described by \citet{SchaeferAl06}.

AbstractMovingLeastSquaresTransform() - Constructor for class mpicbg.models.AbstractMovingLeastSquaresTransform

 

AbstractNormalize<T extends NumericType<T>> - Class in script.imglib.algorithm.fn

TODO

AbstractNormalize(Image<T>) - Constructor for class script.imglib.algorithm.fn.AbstractNormalize

 

AbstractOffscreenThread - Class in ini.trakem2.display

To be used in combination with the AbstractRepaintThread, as a thread to create graphics offscreen.

AbstractOffscreenThread.RepaintProperties - Interface in ini.trakem2.display

 

AbstractPanorama_View - Class in mpicbg.panorama

 

AbstractPanorama_View() - Constructor for class mpicbg.panorama.AbstractPanorama_View

 

AbstractPanorama_View.AbstractMappingThread - Class in mpicbg.panorama

 

AbstractPanorama_View.GUI - Class in mpicbg.panorama

 

AbstractPanorama_View.Mapper - Class in mpicbg.panorama

 

AbstractPerumtationTransform - Class in org.janelia.thickness.lut

Bijective integer transform mapping between integer coordinates in [0,n-1].

AbstractPerumtationTransform(int[]) - Constructor for class org.janelia.thickness.lut.AbstractPerumtationTransform

 

AbstractPointDescriptor<P extends Point,F extends AbstractPointDescriptor<P,F>> - Class in mpicbg.pointdescriptor

 

AbstractPointDescriptor(P, ArrayList<P>, SimilarityMeasure, Matcher) - Constructor for class mpicbg.pointdescriptor.AbstractPointDescriptor

 

AbstractPointEdit - Class in bigwarp.landmarks.actions

 

AbstractPointEdit(LandmarkTableModel) - Constructor for class bigwarp.landmarks.actions.AbstractPointEdit

 

AbstractProvider<K extends TrackMateModule> - Class in fiji.plugin.trackmate.providers

 

AbstractProvider(Class<K>) - Constructor for class fiji.plugin.trackmate.providers.AbstractProvider

 

AbstractRegionalExtremaFinder<T extends RealType<T>> - Class in mpicbg.imglib.algorithm.extremafinder

TODO

AbstractRegionalExtremaFinder() - Constructor for class mpicbg.imglib.algorithm.extremafinder.AbstractRegionalExtremaFinder

 

AbstractRepaintThread - Class in ini.trakem2.display

 

AbstractRepaintThread(Component, String, AbstractOffscreenThread) - Constructor for class ini.trakem2.display.AbstractRepaintThread

 

AbstractSemiAutoTracker<T extends RealType<T> & NativeType<T>> - Class in fiji.plugin.trackmate.detection.semiauto

A class made to perform semi-automated tracking of spots in TrackMate & friends

AbstractSemiAutoTracker(Model, SelectionModel, Logger) - Constructor for class fiji.plugin.trackmate.detection.semiauto.AbstractSemiAutoTracker

 

AbstractSemiAutoTracker.SearchRegion<R> - Class in fiji.plugin.trackmate.detection.semiauto

A utility class made to return the information on a neighborhood generated from a source around a Spot.

AbstractSequenceDescription<V extends BasicViewSetup,D extends BasicViewDescription<V>,L extends BasicImgLoader> - Class in mpicbg.spim.data.generic.sequence

A SPIM sequence consisting of a list of timepoints and a list of view setups.

AbstractSequenceDescription(TimePoints, Map<Integer, ? extends V>, L, MissingViews) - Constructor for class mpicbg.spim.data.generic.sequence.AbstractSequenceDescription

 

AbstractSequenceDescription() - Constructor for class mpicbg.spim.data.generic.sequence.AbstractSequenceDescription

 

AbstractSequenceDescriptionUtils - Class in mpicbg.spim.data.generic.sequence

 

AbstractSequenceDescriptionUtils() - Constructor for class mpicbg.spim.data.generic.sequence.AbstractSequenceDescriptionUtils

 

AbstractSortedGrayLevelIterator<T extends IntegerType<T>> - Class in mpicbg.imglib.cursor.special

Iterate over all pixels ordered by their gray level

AbstractSortedGrayLevelIterator(Image<T>) - Constructor for class mpicbg.imglib.cursor.special.AbstractSortedGrayLevelIterator

 

AbstractSource<T extends NumericType<T>> - Class in bdv.util

 

AbstractSource(T, String, VoxelDimensions) - Constructor for class bdv.util.AbstractSource

 

AbstractSource(T, String) - Constructor for class bdv.util.AbstractSource

 

AbstractSource(Supplier<T>, String) - Constructor for class bdv.util.AbstractSource

 

AbstractSpecialCursor<T extends Type<T>> - Class in mpicbg.imglib.cursor.special

This abstract cursor offer facilities for specialized cursor that are based on a LocalizableByDimCursor whose iteration domain is imposed.

AbstractSpecialCursor() - Constructor for class mpicbg.imglib.cursor.special.AbstractSpecialCursor

 

AbstractSpimData<S extends AbstractSequenceDescription<?,?,?>> - Class in mpicbg.spim.data.generic

 

AbstractSpimData(File, S, ViewRegistrations) - Constructor for class mpicbg.spim.data.generic.AbstractSpimData

 

AbstractSpimData() - Constructor for class mpicbg.spim.data.generic.AbstractSpimData

 

AbstractSpimSource<T extends NumericType<T>> - Class in bdv

 

AbstractSpimSource(AbstractSpimData<?>, int, String) - Constructor for class bdv.AbstractSpimSource

 

AbstractSpimSource.ImgKey - Class in bdv

 

AbstractStampFormat(String[], String, boolean, boolean, boolean) - Constructor for class Series_Labeler.AbstractStampFormat

 

AbstractTMAction - Class in fiji.plugin.trackmate.action

 

AbstractTMAction() - Constructor for class fiji.plugin.trackmate.action.AbstractTMAction

 

AbstractTool - Class in fiji.tool

 

AbstractTool() - Constructor for class fiji.tool.AbstractTool

 

AbstractTool.KeyProxy - Class in fiji.tool

 

AbstractTool.KeyProxyIfNotConsumed - Class in fiji.tool

 

AbstractTool.MouseMotionProxy - Class in fiji.tool

 

AbstractTool.MouseMotionProxyIfNotConsumed - Class in fiji.tool

 

AbstractTool.MouseProxy - Class in fiji.tool

 

AbstractTool.MouseWheelProxy - Class in fiji.tool

 

AbstractTool.MouseWheelProxyIfNotConsumed - Class in fiji.tool

 

AbstractTool.ToolbarMouseAdapter - Class in fiji.tool

This class is used to monitor tool toggles and double-clicks on the toolbar icon of this concrete tool.

AbstractTrackingTool - Class in fiji.tool

 

AbstractTrackingTool() - Constructor for class fiji.tool.AbstractTrackingTool

 

AbstractTrackMateModelView - Class in fiji.plugin.trackmate.visualization

An abstract class for spot displayers, that can overlay detected spots and tracks on top of the image data.

AbstractTrackMateModelView(Model, SelectionModel) - Constructor for class fiji.plugin.trackmate.visualization.AbstractTrackMateModelView

 

AbstractTransformAnimator - Class in bdv.viewer.animate

Mother abstract class for animators that animate the current view in a ViewerFrame instance by modifying the viewer transform.

AbstractTransformAnimator(long) - Constructor for class bdv.viewer.animate.AbstractTransformAnimator

Create new animator with the given duration.

AbstractTransformedBoxModel - Class in bdv.tools.boundingbox

A transformed box that can be modified and notifies listeners about changes.

AbstractTransformedBoxModel(AffineTransform3D) - Constructor for class bdv.tools.boundingbox.AbstractTransformedBoxModel

 

AbstractTransformedBoxModel.IntervalChangedListener - Interface in bdv.tools.boundingbox

 

AbstractTransformedBoxSelectionDialog<R> - Class in bdv.tools.boundingbox

 

AbstractTransformedBoxSelectionDialog(Window, String) - Constructor for class bdv.tools.boundingbox.AbstractTransformedBoxSelectionDialog

 

AbstractTransformedBoxSelectionDialog.OkCancelPanel - Class in bdv.tools.boundingbox

A panel containing OK and Cancel buttons, and callback lists for both.

AbstractTransformedBoxSelectionDialog.TimepointSelectionPanel - Class in bdv.tools.boundingbox

A panel that contains sliders to adjust timepoint, timepoint range, or nothing.

AbstractTransformMapping<T> - Class in mpicbg.ij.stack

Abstract base class Mapping from an source into an target.

AbstractTransformMapping(T) - Constructor for class mpicbg.ij.stack.AbstractTransformMapping

 

AbstractTransformMapping.ByteInterpolator - Class in mpicbg.ij.stack

 

AbstractTransformMapping.FloatInterpolator - Class in mpicbg.ij.stack

 

AbstractTransformMapping.Interpolator - Class in mpicbg.ij.stack

 

AbstractTransformMapping.RGBInterpolator - Class in mpicbg.ij.stack

 

AbstractTransformMapping.ShortInterpolator - Class in mpicbg.ij.stack

 

AbstractTreeTransferHandler - Class in ini.trakem2.tree

Adapted from freely available code by DeuDeu.

AbstractTreeTransferHandler(DNDTree, int, boolean) - Constructor for class ini.trakem2.tree.AbstractTreeTransferHandler

 

AbstractVector<V extends AbstractVector<V>> - Class in mpicbg.imglib.cursor.vector

TODO

AbstractVector(Dimensionality) - Constructor for class mpicbg.imglib.cursor.vector.AbstractVector

 

AbstractVector(int) - Constructor for class mpicbg.imglib.cursor.vector.AbstractVector

 

AbstractViewerSetupImgLoader<T,V extends Volatile<T>> - Class in bdv

 

AbstractViewerSetupImgLoader(T, V) - Constructor for class bdv.AbstractViewerSetupImgLoader

 

accept(File) - Method in class fiji.plugin.trackmate.util.DefaultFileFilter

Returns true if file is a directory or ends with the specified extension.

accept(File) - Method in class fiji.plugin.trackmate.util.DefaultFileFilter.EditorFileFilter

Returns true if the file is a directory or has a .xml or .xml.gz extension.

accept(File) - Method in class fiji.plugin.trackmate.util.DefaultFileFilter.ImageFileFilter

Returns true if the file is a directory or ends with a known image extension.

accept(File) - Method in class fsalign.FolderWatcher.FolderFilter

 

accept(Node<I>) - Method in class ini.trakem2.display.Node.BranchAndEndNodeIterator

 

accept(Node<I>) - Method in class ini.trakem2.display.Node.BranchNodeIterator

 

accept(Node<I>) - Method in class ini.trakem2.display.Node.EndNodeIterator

 

accept(Node<I>) - Method in class ini.trakem2.display.Node.FilteredIterator

 

accept(File, String) - Method in class ini.trakem2.io.ImageFileFilter

 

accept(File, String) - Method in class ini.trakem2.io.XMLFileFilter

 

accept(T) - Method in interface ini.trakem2.utils.Filter

 

accept(File) - Method in class org.imagearchive.lsm.toolbox.gui.AllKnownFilter

 

accept(File) - Method in class org.imagearchive.lsm.toolbox.gui.BatchFilter

 

accept(File) - Method in class org.imagearchive.lsm.toolbox.gui.ImageFilter

 

accept(BytePointer, int, int, int) - Method in class org.janelia.it.jacs.shared.ffmpeg.ByteGatherAcceptor

Accept one "page" of data, of width x height given, and with linesize bytes on each line of the page.

accept(byte[], int, int, int) - Method in class org.janelia.it.jacs.shared.ffmpeg.ByteGatherAcceptor

Accept one "page" of data, of width x height given, and with linesize bytes on each line of the page.

accept(BytePointer, int, int, int) - Method in interface org.janelia.it.jacs.shared.ffmpeg.FFMPGByteAcceptor

 

accept(byte[], int, int, int) - Method in interface org.janelia.it.jacs.shared.ffmpeg.FFMPGByteAcceptor

 

accept(byte[], int, int, int) - Method in interface org.janelia.it.jacs.shared.ffmpeg.H5JLoader.DataAcceptor

 

accept(BytePointer, int, int, int) - Method in class org.janelia.it.jacs.shared.ffmpeg.PPMFileAcceptor

 

accept(byte[], int, int, int) - Method in class org.janelia.it.jacs.shared.ffmpeg.PPMFileAcceptor

 

accept(File) - Method in class org.siox.example.ExtensionFileFilter

Whether the given file is regular file with recognized extension or a directory.

accept(T, T) - Method in class sc.fiji.coloc.algorithms.Accumulator

 

acceptingNodes() - Method in class edu.utexas.clm.archipelago.Cluster

 

accepts(Object) - Method in class edu.utexas.clm.archipelago.ijsupport.bottle.LayerBottler

 

accepts(Object) - Method in class edu.utexas.clm.archipelago.ijsupport.bottle.PatchBottler

 

accepts(Object) - Method in class edu.utexas.clm.archipelago.ijsupport.bottle.PointBottler

 

accepts(Object) - Method in class edu.utexas.clm.archipelago.ijsupport.bottle.SIFTParamBottler

 

accepts(Object) - Method in interface edu.utexas.clm.archipelago.network.translation.Bottler

Return true if this Bottler accepts the given Object.

accepts(Object) - Method in class edu.utexas.clm.archipelago.network.translation.FileBottler

 

Access() - Constructor for class bdv.tools.boundingbox.BoxRealRandomAccessible.Access

 

Access(BoxRealRandomAccessible<T>.Access) - Constructor for class bdv.tools.boundingbox.BoxRealRandomAccessible.Access

 

access - Variable in class mpicbg.imglib.labeling.LabelingType

 

access - Variable in class org.janelia.thickness.lut.AbstractLUTGrid

 

access - Variable in class org.janelia.thickness.lut.AbstractLUTRealTransformField

 

accessible - Variable in class bdv.util.RealRandomAccessibleSource

 

accessor - Variable in class mpicbg.imglib.cursor.dynamic.DynamicCursor

 

accumulate(Cursor<? extends A>[], B) - Method in class bdv.viewer.render.AccumulateProjector

 

accumulate(Cursor<? extends ARGBType>[], ARGBType) - Method in class bdv.viewer.render.AccumulateProjectorARGB

 

accumulate(RoiStatistics.Accessor) - Method in class fiji.statistics.RoiStatistics

 

AccumulateProjector<A,B> - Class in bdv.viewer.render

 

AccumulateProjector(ArrayList<VolatileProjector>, ArrayList<? extends RandomAccessible<? extends A>>, RandomAccessibleInterval<B>, int, ExecutorService) - Constructor for class bdv.viewer.render.AccumulateProjector

 

AccumulateProjectorARGB - Class in bdv.viewer.render

 

AccumulateProjectorARGB(ArrayList<VolatileProjector>, ArrayList<? extends RandomAccessible<? extends ARGBType>>, RandomAccessibleInterval<ARGBType>, int, ExecutorService) - Constructor for class bdv.viewer.render.AccumulateProjectorARGB

 

accumulateProjectorFactory(AccumulateProjectorFactory<ARGBType>) - Method in class bdv.util.BdvOptions

Set the factory for creating AccumulateProjector.

AccumulateProjectorFactory<A> - Interface in bdv.viewer.render

 

accumulateProjectorFactory - Variable in class bdv.viewer.render.MultiResolutionRenderer

TODO

accumulateProjectorFactory(AccumulateProjectorFactory<ARGBType>) - Method in class bdv.viewer.ViewerOptions

Set the factory for creating AccumulateProjector.

accumulator - Variable in class fiji.statistics.RoiStatistics

 

Accumulator<T extends RealType<T>> - Class in sc.fiji.coloc.algorithms

A class allowing an easy accumulation of values visited by a TwinCursor.

Accumulator(TwinCursor<T>) - Constructor for class sc.fiji.coloc.algorithms.Accumulator

The two values x and y from each cursor iteration to get summed up as single values and their combinations.

Accumulator(TwinCursor<T>, double, double) - Constructor for class sc.fiji.coloc.algorithms.Accumulator

The two values (x - xDiff) and (y - yDiff) from each cursor iteration to get summed up as single values and their combinations.

Accumulator(TwinCursor<T>, boolean, double, double) - Constructor for class sc.fiji.coloc.algorithms.Accumulator

 

accuracy - Variable in class ini.trakem2.imaging.filters.GaussianBlur

 

ACCURATE - Static variable in class Despeckle_

 

ACCURATE_MODE - Static variable in class bunwarpj.MainDialog

accurate mode constant

ACos - Class in script.imglib.math

TODO

ACos(Image<? extends RealType<?>>) - Constructor for class script.imglib.math.ACos

 

ACos(IFunction) - Constructor for class script.imglib.math.ACos

 

ACos(Number) - Constructor for class script.imglib.math.ACos

 

act(int, RandomAccessibleInterval<T>, RandomAccessibleInterval<T>, double[], int[], int[], double[], RandomAccessibleInterval<double[]>) - Method in class org.janelia.thickness.inference.visitor.CorrelationFitVisitor

 

act(int, RandomAccessibleInterval<T>, RandomAccessibleInterval<T>, double[], int[], int[], double[], RandomAccessibleInterval<double[]>) - Method in class org.janelia.thickness.inference.visitor.GlobalCorrelationFitVisitor

 

act(int, RandomAccessibleInterval<T>, RandomAccessibleInterval<T>, double[], int[], int[], double[], RandomAccessibleInterval<double[]>) - Method in class org.janelia.thickness.inference.visitor.LazyVisitor

 

act(int, RandomAccessibleInterval<T>, RandomAccessibleInterval<T>, double[], int[], int[], double[], RandomAccessibleInterval<double[]>) - Method in class org.janelia.thickness.inference.visitor.ListVisitor

 

act(int, RandomAccessibleInterval<T>, RandomAccessibleInterval<T>, double[], int[], int[], double[], RandomAccessibleInterval<double[]>) - Method in class org.janelia.thickness.inference.visitor.LUTVisitor

 

act(int, RandomAccessibleInterval<T>, RandomAccessibleInterval<T>, double[], int[], int[], double[], RandomAccessibleInterval<double[]>) - Method in class org.janelia.thickness.inference.visitor.MatrixVisitor

 

act(int, RandomAccessibleInterval<T>, RandomAccessibleInterval<T>, double[], int[], int[], double[], RandomAccessibleInterval<double[]>) - Method in class org.janelia.thickness.inference.visitor.PermutedLUTVisitor

 

act(int, RandomAccessibleInterval<T>, RandomAccessibleInterval<T>, double[], int[], int[], double[], RandomAccessibleInterval<double[]>) - Method in class org.janelia.thickness.inference.visitor.PermutedScalingFactorsVisitor

 

act(int, RandomAccessibleInterval<T>, RandomAccessibleInterval<T>, double[], int[], int[], double[], RandomAccessibleInterval<double[]>) - Method in class org.janelia.thickness.inference.visitor.ScalingFactorsVisitor

 

act(int, RandomAccessibleInterval<T>, RandomAccessibleInterval<T>, double[], int[], int[], double[], RandomAccessibleInterval<double[]>) - Method in interface org.janelia.thickness.inference.visitor.Visitor

 

ActElement() - Method in class view5d.My3DData

 

action(String) - Method in class fiji.help.Context_Help

 

Action(String, String) - Constructor for class fiji.util.gui.CommandFinderBase.Action

 

action(String) - Method in class fiji.util.MenuItemDiverter

 

ACTION_FINISHED - Variable in class fiji.plugin.trackmate.gui.panels.ActionChooserPanel

 

ACTION_STARTED - Variable in class fiji.plugin.trackmate.gui.panels.ActionChooserPanel

 

ActionChooserDescriptor - Class in fiji.plugin.trackmate.gui.descriptors

 

ActionChooserDescriptor(ActionProvider, TrackMate, TrackMateGUIController) - Constructor for class fiji.plugin.trackmate.gui.descriptors.ActionChooserDescriptor

 

actionChooserDescriptor - Variable in class fiji.plugin.trackmate.gui.TrackMateGUIController

 

ActionChooserPanel - Class in fiji.plugin.trackmate.gui.panels

 

ActionChooserPanel(ActionProvider, TrackMate, TrackMateGUIController) - Constructor for class fiji.plugin.trackmate.gui.panels.ActionChooserPanel

 

ActionListenablePanel - Class in fiji.plugin.trackmate.gui.panels

 

ActionListenablePanel() - Constructor for class fiji.plugin.trackmate.gui.panels.ActionListenablePanel

 

actionListeners - Variable in class fiji.plugin.trackmate.gui.panels.ActionListenablePanel

 

actionPerformed(ActionEvent) - Method in class bdv.ij.util.PluginHelper.ChooseXmlFileListener

 

actionPerformed(ActionEvent) - Method in class bdv.tools.ToggleDialogAction

 

actionPerformed(ActionEvent) - Method in class bdv.viewer.LandmarkPointMenu.ActivateSelectedHandler

 

actionPerformed(ActionEvent) - Method in class bdv.viewer.LandmarkPointMenu.ClearHandler

 

actionPerformed(ActionEvent) - Method in class bdv.viewer.LandmarkPointMenu.ClearSelectedHandler

 

actionPerformed(ActionEvent) - Method in class bdv.viewer.LandmarkPointMenu.DeactivateSelectedHandler

 

actionPerformed(ActionEvent) - Method in class bdv.viewer.LandmarkPointMenu.DeleteHandler

 

actionPerformed(ActionEvent) - Method in class bdv.viewer.LandmarkPointMenu.DeleteSelectedHandler

 

actionPerformed(ActionEvent) - Method in class bdv.viewer.WarpNavigationActions.AlignPlaneAction

 

actionPerformed(ActionEvent) - Method in class bdv.viewer.WarpNavigationActions.CardAction

 

actionPerformed(ActionEvent) - Method in class bdv.viewer.WarpNavigationActions.CollapseCardAction

 

actionPerformed(ActionEvent) - Method in class bdv.viewer.WarpNavigationActions.DisplayXfmAction

 

actionPerformed(ActionEvent) - Method in class bdv.viewer.WarpNavigationActions.ExpandCardAction

 

actionPerformed(ActionEvent) - Method in class bdv.viewer.WarpNavigationActions.RotatePlaneAction

 

actionPerformed(ActionEvent) - Method in class bdv.viewer.WarpNavigationActions.SetCurrentSourceOrGroupAction

 

actionPerformed(ActionEvent) - Method in class bdv.viewer.WarpNavigationActions.ToggleFusedModeAction

 

actionPerformed(ActionEvent) - Method in class bdv.viewer.WarpNavigationActions.ToggleGroupingAction

 

actionPerformed(ActionEvent) - Method in class bdv.viewer.WarpNavigationActions.ToggleInterPolationAction

 

actionPerformed(ActionEvent) - Method in class bdv.viewer.WarpNavigationActions.ToggleSourceOrGroupVisibilityAction

 

actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.AlignViewerPanelAction

 

actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.DebugAction

 

actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.EstimateWarpAction

 

actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.ExportAffineAction

 

actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.ExportImagePlusAction

 

actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.ExportWarpAction

 

actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.GarbageCollectionAction

 

actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.GoToBookmarkAction

 

actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.GoToBookmarkRotationAction

 

actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.LandmarkGridDialogAction

 

actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.LandmarkModeAction

 

actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.LoadLandmarksAction

 

actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.LoadSettingsAction

 

actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.PrintTransformAction

 

actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.ResetActiveViewerAction

 

actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.SaveLandmarksAction

 

actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.SaveSettingsAction

 

actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.SaveWarpedAction

Deprecated.

 

actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.SaveWarpedXmlAction

 

actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.SetBookmarkAction

 

actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.SetWarpMagBaseAction

 

actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.SetWarpVisGridTypeAction

 

actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.SetWarpVisTypeAction

 

actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.TableSelectionAction

 

actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.ToggleAlwaysEstimateTransformAction

 

actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.ToggleBoxAndTexOverlayVisibility

 

actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.ToggleLandmarkModeAction

 

actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.ToggleMovingImageDisplayAction

 

actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.TogglePointNameVisibleAction

 

actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.TogglePointsVisibleAction

 

actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.UndoRedoAction

 

actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.WarpToNearest

 

actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.WarpToNextAction

 

actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.WarpToSelectedAction

 

actionPerformed(ActionEvent) - Method in class bunwarpj.ClearAll

Actions to take place with the dialog for clearing everything

actionPerformed(ActionEvent) - Method in class bunwarpj.IODialog

Actions to be taking during the dialog.

actionPerformed(ActionEvent) - Method in class bunwarpj.MainDialog

Actions to be taken during the dialog.

actionPerformed(ActionEvent) - Method in class edu.utexas.clm.archipelago.ui.ClusterNodeStatusUI

 

actionPerformed(ActionEvent) - Method in class edu.utexas.clm.archipelago.ui.NodeConfigurationUI

 

actionPerformed(ActionEvent) - Method in class edu.utexas.clm.archipelago.ui.RootNodeConfigDialog

 

actionPerformed(ActionEvent) - Method in class fiji.plugin.timelapsedisplay.FileOpenMenuEntry

 

actionPerformed(ActionEvent) - Method in class fiji.plugin.timelapsedisplay.GraphFrame

 

actionPerformed(ActionEvent) - Method in class fiji.plugin.trackmate.gui.TrackMateGUIController

 

actionPerformed(ActionEvent) - Method in class fiji.plugin.trackmate.gui.TrackMateWizard

Simply forwards the caught event to listeners of this main frame.

actionPerformed(ActionEvent) - Method in class fiji.plugin.trackmate.visualization.trackscheme.SaveAction

 

actionPerformed(ActionEvent) - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeActions.EditAction

 

actionPerformed(ActionEvent) - Method in class fiji.plugin.volumeviewer.Gui

 

actionPerformed(ActionEvent) - Method in class fiji.util.ArrowTool

Is called when the user change a property using the option panel.

actionPerformed(ActionEvent) - Method in class fiji.util.gui.CommandFinderBase

 

actionPerformed(ActionEvent) - Method in class fiji.util.Recent_Commands

 

actionPerformed(ActionEvent) - Method in class fiji.Wiki_Editor

 

actionPerformed(ActionEvent) - Method in class ij3d.contextmenu.ContextMenu

 

actionPerformed(ActionEvent) - Method in class ij3d.gui.LUTDialog

 

actionPerformed(ActionEvent) - Method in class ij3d.Image3DMenubar

 

actionPerformed(ActionEvent) - Method in class ij3d.pointlist.PointListPanel

Handling the events coming from the popup menu.

actionPerformed(ActionEvent) - Method in class ij3d.RegistrationMenubar

 

actionPerformed(ActionEvent) - Method in class ini.trakem2.display.Display

 

actionPerformed(ActionEvent) - Method in class ini.trakem2.display.DisplayableChooser

 

actionPerformed(ActionEvent) - Method in class ini.trakem2.display.YesNoDialog

 

actionPerformed(ActionEvent) - Method in class ini.trakem2.tree.LayerTree

 

actionPerformed(ActionEvent) - Method in class ini.trakem2.tree.ProjectTree

 

actionPerformed(ActionEvent) - Method in class ini.trakem2.tree.TemplateTree

 

actionPerformed(ActionEvent) - Method in class IntSlider

 

actionPerformed(ActionEvent) - Method in class landmarks.ProgressWindow

 

actionPerformed(ActionEvent) - Method in class loci.plugins.config.ConfigWindow

 

actionPerformed(ActionEvent) - Method in class loci.plugins.in.SeriesDialog

 

actionPerformed(ActionEvent) - Method in class loci.plugins.shortcut.ShortcutPanel

Handles button presses.

actionPerformed(ActionEvent) - Method in class loci.plugins.util.DataBrowser

 

actionPerformed(ActionEvent) - Method in class loci.plugins.util.SearchableWindow

 

actionPerformed(ActionEvent) - Method in class Manual_Tracking

 

actionPerformed(ActionEvent) - Method in class mpicbg.spim.segmentation.InteractiveDoG.ApplyButtonListener

 

actionPerformed(ActionEvent) - Method in class mpicbg.spim.segmentation.InteractiveDoG.FinishedButtonListener

 

actionPerformed(ActionEvent) - Method in class mpicbg.spim.segmentation.InteractiveIntegral.FinishButtonListener

 

actionPerformed(ActionEvent) - Method in class net.imagej.ui.swing.ops.OpFinder

 

actionPerformed(ActionEvent) - Method in class sc.fiji.balloonSegmentation.BalloonSegmentation_

 

actionPerformed(ActionEvent) - Method in class sc.fiji.cellCounter.CellCounter

 

actionPerformed(ActionEvent) - Method in class sc.fiji.coloc.results.SingleWindowDisplay

 

actionPerformed(ActionEvent) - Method in class sc.fiji.hdf5.HDF5_Reader_Vibez

 

actionPerformed(ActionEvent) - Method in class sc.fiji.hdf5.HDF5_Writer_Vibez

 

actionPerformed(ActionEvent) - Method in class sc.fiji.i5d.gui.ChannelControl

 

actionPerformed(ActionEvent) - Method in class sc.fiji.i5d.gui.ChannelControl.ChannelColorChooser

 

actionPerformed(ActionEvent) - Method in class sc.fiji.i5d.gui.ChannelControl.ChannelSelectorOverlay

 

actionPerformed(ActionEvent) - Method in class selection.DoneButtonListener

 

actionPerformed(ActionEvent) - Method in class selection.LoadListener

 

actionPerformed(ActionEvent) - Method in class selection.RemoveItemListener

 

actionPerformed(ActionEvent) - Method in class selection.SaveListener

 

actionPerformed(ActionEvent) - Method in class sholl.gui.EnhancedGenericDialog

Deprecated.

 

actionPerformed(ActionEvent) - Method in class siox.SegmentationGUI

 

actionPerformed(ActionEvent) - Method in class spim.fiji.plugin.apply.BigDataViewerTransformationWindow.ApplyButtonListener

 

actionPerformed(ActionEvent) - Method in class spim.fiji.plugin.apply.BigDataViewerTransformationWindow.CancelButtonListener

 

actionPerformed(ActionEvent) - Method in class spim.fiji.plugin.removedetections.InteractiveProjections.FinishedButtonListener

 

actionPerformed(ActionEvent) - Method in class spim.fiji.plugin.removedetections.InteractiveProjections.RemoveInsideROIButtonListener

 

actionPerformed(ActionEvent) - Method in class spim.fiji.plugin.resave.PluginHelper.ChooseXmlFileListener

 

actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.ApplyTransformationPopup.MyActionListener

 

actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.BDVPopup.MyActionListener

 

actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.BoundingBoxPopup.MyActionListener

 

actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.DetectInterestPointsPopup.MyActionListener

 

actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.DisplayViewPopup.MyActionListener

 

actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.FusionPopup.MyActionListener

 

actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.InterestPointsExplorerPopup.MyActionListener

 

actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.MaxProjectPopup.MyActionListener

 

actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.RegisterInterestPointsPopup.MyActionListener

 

actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.RegistrationExplorerPopup.MyActionListener

 

actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.RemoveDetectionsPopup.MyActionListener

 

actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.RemoveTransformationPopup.MyActionListener

 

actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.ReorientSamplePopup.MyActionListener

 

actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.ResavePopup.MyActionListener

 

actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.SpecifyCalibrationPopup.MyActionListener

 

actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.VisualizeDetectionsPopup.MyActionListener

 

actionPerformed(ActionEvent) - Method in class spim.process.interestpointregistration.registrationstatistics.GraphFrame

 

actionPerformed(ActionEvent) - Method in class spim.process.interestpointregistration.registrationstatistics.SelectTimepointEntry

 

actionPerformed(ActionEvent) - Method in class spimopener.OpenerGenericDialog

 

actionPerformed(ActionEvent) - Method in class Sync_Measure_3D

Implementation of ActionListener interface.

actionPerformed(ActionEvent) - Method in class Sync_Windows

Implementation of ActionListener interface.

actionPerformed(ActionEvent) - Method in class tools.RoiPicker

 

actionPerformed(ActionEvent) - Method in class tracing.FillWindow

 

actionPerformed(ActionEvent) - Method in class tracing.NeuriteTracerResultsDialog

 

actionPerformed(ActionEvent) - Method in class tracing.PathWindow

 

actionPerformed(ActionEvent) - Method in class tracing.ShollAnalysisDialog

 

actionPerformed(ActionEvent) - Method in class tracing.ShollAnalysisDialog.GraphFrame

 

actionPerformed(ActionEvent) - Method in class tracing.SWCImportOptionsDialog

 

actionPerformed(ActionEvent) - Method in class util.ModelessQuestions

 

actionPerformed(ActionEvent) - Method in class util.Quantile_Based_Normalization

 

actionPerformed(ActionEvent) - Method in class vib.app.gui.FileGroupDialog

 

actionPerformed(ActionEvent) - Method in class vib.EditAmiraParameters_

 

actionPerformed(ActionEvent) - Method in class vib.Points_Dialog

 

actionPerformed(ActionEvent) - Method in class vib.Relabel_

 

actionPerformed(ActionEvent) - Method in class vib.segment.CustomStackWindow

 

actionPerformed(ActionEvent) - Method in class vib.segment.MaterialList

 

actionPerformed(ActionEvent) - Method in class vib.ShowHistogram

 

actionPerformed(ActionEvent) - Method in class VIB_Protocol

 

actionPerformed(ActionEvent) - Method in class video.Edit_Video

 

actionPerformed(ActionEvent) - Method in class view4d.TimelineGUI

 

actionProvider - Variable in class fiji.plugin.trackmate.gui.TrackMateGUIController

 

ActionProvider - Class in fiji.plugin.trackmate.providers

 

ActionProvider() - Constructor for class fiji.plugin.trackmate.providers.ActionProvider

 

actions - Variable in class fiji.util.gui.CommandFinderBase

 

actions - Static variable in class fiji.util.MenuItemDiverter

 

ACTIVATE - Static variable in class bdv.viewer.LandmarkPointMenu

 

activate() - Method in class fiji.plugin.trackmate.visualization.DummySpotColorGenerator

 

activate() - Method in class fiji.plugin.trackmate.visualization.DummyTrackColorGenerator

 

activate() - Method in interface fiji.plugin.trackmate.visualization.FeatureColorGenerator

When this color generator is reused, calling this method ensures that it is registered again, and will follow whatever changes subsequently happening to the model.

activate() - Method in class fiji.plugin.trackmate.visualization.ManualEdgeColorGenerator

 

activate() - Method in class fiji.plugin.trackmate.visualization.ManualSpotColorGenerator

 

activate() - Method in class fiji.plugin.trackmate.visualization.PerEdgeFeatureColorGenerator

 

activate() - Method in class fiji.plugin.trackmate.visualization.PerTrackFeatureColorGenerator

 

activate() - Method in class fiji.plugin.trackmate.visualization.SpotColorGenerator

 

activate() - Method in class fiji.plugin.trackmate.visualization.SpotColorGeneratorPerTrackFeature

 

ACTIVATE_SELECTED - Static variable in class bdv.viewer.LandmarkPointMenu

 

activateAllHandler - Variable in class bdv.viewer.LandmarkPointMenu

 

activateAllItem - Variable in class bdv.viewer.LandmarkPointMenu

 

activated5d - Variable in class sc.fiji.i5d.Image5D

 

activateRow(int) - Method in class bigwarp.landmarks.LandmarkTableModel

 

ActivateSelectedHandler(String) - Constructor for class bdv.viewer.LandmarkPointMenu.ActivateSelectedHandler

 

active() - Method in class edu.utexas.clm.archipelago.network.server.ArchipelagoServer

 

ACTIVE_DISPL_COLOR - Static variable in class ini.trakem2.tree.ProjectTree

 

activeCluster() - Static method in class edu.utexas.clm.archipelago.Cluster

 

ACTIVECOLUMN - Static variable in class bigwarp.landmarks.LandmarkTableModel

 

ActiveContours - Class in levelsets.algorithm

Implementation of the Levelset algorithm as originally implemented by Arne-Michael Toersel.

ActiveContours(ImageContainer, ImageProgressContainer, StateContainer, double, double, double, double) - Constructor for class levelsets.algorithm.ActiveContours

 

activeCursorIndex - Variable in class mpicbg.imglib.cursor.special.HyperSphereIterator

 

ActiveElement - Variable in class view5d.My3DData

 

activeHandle - Variable in class fiji.tool.AbstractTrackingTool

 

activeList - Variable in class bigwarp.landmarks.LandmarkTableModel

 

activeSourcesDialog - Variable in class bdv.BigDataViewer

 

activeSourcesDialogP - Variable in class bigwarp.BigWarp

 

activeSourcesDialogQ - Variable in class bigwarp.BigWarp

 

ActiveTime - Variable in class view5d.My3DData

 

actualSize - Variable in class fiji.util.ArrayBase

 

ADAPT_COEFFICIENTS - Static variable in class bunwarpj.IODialog

bUnwarpJ_ method name to adapt B-spline coefficients to a scale

adaptCanvasses(Image5DCanvas) - Method in class sc.fiji.i5d.gui.Image5DWindow

 

adaptChannelCanvasses() - Method in class sc.fiji.i5d.gui.Image5DCanvas

 

adaptChannelMouse() - Method in class sc.fiji.i5d.gui.Image5DCanvas

 

adaptChannelRois(boolean) - Method in class sc.fiji.i5d.gui.Image5DCanvas

 

adaptCoefficients(String, String, String) - Static method in class bunwarpj.bUnwarpJ_

Adapt the B-spline coefficients to a new image size.

adaptCoefficients(String, double, String) - Static method in class bunwarpj.MiscTools

Adapt B-spline coefficients based on a scale factor.

adaptCoefficients(double, double, int, double[][], double[][]) - Static method in class bunwarpj.MiscTools

Adapt B-spline coefficients to a scale factor

adaptCoefficientsMacro(String, String, String, String, String) - Static method in class bunwarpj.bUnwarpJ_

Method to adapt an elastic transformation given a new image size.

adaptedRandIndex3D(ImagePlus, ImagePlus) - Static method in class trainableSegmentation.metrics.RandError

Calculate the Rand index between to 3D clusters, as described by William M.

adaptedRandIndexFScore3D(ImagePlus, ImagePlus) - Static method in class trainableSegmentation.metrics.RandError

Calculate the F-score of the Rand index between to 3D clusters, as described by William M.

adaptedRandIndexStats3D(ImagePlus, ImagePlus) - Static method in class trainableSegmentation.metrics.RandError

Calculate the Rand index between to 3D clusters, as described by William M.

adaptedRandIndexStats3DN2(ImagePlus, ImagePlus) - Static method in class trainableSegmentation.metrics.RandError

Calculate the Rand index stats between to 3D clusters, as described by William M.

adapter - package adapter

 

adapter - Variable in class Manual_Tracking

 

AdaptiveNonMaximalSuppression<T extends RealType<T>> - Class in mpicbg.imglib.algorithm.scalespace

TODO

AdaptiveNonMaximalSuppression(List<DifferenceOfGaussianPeak<T>>, double) - Constructor for class mpicbg.imglib.algorithm.scalespace.AdaptiveNonMaximalSuppression

Performs adaptive non maximal suppression in the local neighborhood of each detection, seperately for minima and maxima.

adaptMouse(Image5DCanvas) - Method in class sc.fiji.i5d.gui.Image5DWindow

Hands on the cursor location and modifiers of i5dc to all channel canvasses of this window except i5dc.

adaptRois(Image5DCanvas) - Method in class sc.fiji.i5d.gui.Image5DWindow

Hands on the roi, cursor location and modifiers of i5dc to all channel canvasses of this window except i5dc.

add(BasicViewSetup, AbstractSequenceDescription<?, ?, ?>, ViewRegistrations, int[][], int[][]) - Method in class bdv.ij.export.SetupAggregator

Deprecated.

Add a new BasicViewSetup to the aggregator.

add(E) - Method in class bdv.util.WrappedList

 

add(int, E) - Method in class bdv.util.WrappedList

 

add(String) - Method in class bdv.viewer.animate.MessageOverlayAnimator

 

add(BigWarp.BigWarpData, Source<T>, int, int, boolean) - Static method in class bigwarp.BigWarpInit

 

add(double[], boolean) - Method in class bigwarp.landmarks.LandmarkTableModel

 

add(double[], boolean, RealTransform) - Method in class bigwarp.landmarks.LandmarkTableModel

 

add(CustomMesh) - Method in class customnode.CustomMultiMesh

 

add(Pnt) - Method in class delaunay.Pnt

Add.

add(float, float) - Method in class distance.Correlation

 

add(float, float) - Method in class distance.Euclidean

 

add(float, float) - Method in class distance.MutualInformation

 

add(float, float) - Method in interface distance.PixelPairs

 

add(float, float) - Method in class distance.Thresholded

 

add(float, float) - Method in class distance.TwoValues

 

add(Spot, Integer) - Method in class fiji.plugin.trackmate.SpotCollection

Adds the given spot to this collection, at the specified frame, and mark it as visible.

add(double) - Method in class fiji.plugin.trackmate.tracking.sparselap.costmatrix.ResizableDoubleArray

 

add(K, Point4d, Color4f) - Method in class fiji.plugin.trackmate.visualization.threedviewer.SpotGroupNode

 

add(double) - Method in class fiji.util.DoubleArray

Deprecated.

 

add(float) - Method in class fiji.util.FloatArray

Deprecated.

 

add(int) - Method in class fiji.util.IntArray

Deprecated.

 

ADD - Static variable in class ij3d.Executer

 

add(String, String, String, String, String, String, String, String, String) - Static method in class ij3d.ImageJ3DViewer

 

add(Content) - Method in class ij3d.ViewAdjuster

Add another Content which should be completely visible in the canvas.

add(Transform3D, Point3d) - Method in class ij3d.ViewAdjuster

Add another point which should be visible in the canvas; the point is expected to be in local coordinates, with the given local-to-vworld transformation.

add(Point3d) - Method in class ij3d.ViewAdjuster

Add another point which should be visible in the canvas; the point is expected to be in vworld coordinates.

add(DisplayChangeListener, DisplayChangeListener) - Static method in class IJEventMulticaster

Adds DisplayChange-listener-a with DisplayChange-listener-b and returns the resulting multicast listener.

Add - Class in imglib.ops.operator.binary

TODO

Add() - Constructor for class imglib.ops.operator.binary.Add

 

add(Project, TemplateTree, ProjectTree, LayerTree) - Static method in class ini.trakem2.ControlWindow

Beware that this method is asynchronous, as it delegates the launching to the SwingUtilities.invokeLater method to avoid havoc with Swing components.

add(long, ShapeRoi) - Method in class ini.trakem2.display.AreaList

Adds the given ROI, which is expected in world/LayerSet coordinates, to the area present at Layer with id layer_id, or set it if none present yet.

add(Area, Layer) - Method in class ini.trakem2.display.AreaWrapper

Add an area in world coordinates.

add(Area, AffineTransform) - Method in class ini.trakem2.display.AreaWrapper

Add an area that needs to be transformed by tmp first to bring it to world coordinates; will MODIFY the to_world AffineTransform object.

add(Layer, Displayable, boolean) - Static method in class ini.trakem2.display.Display

Find the displays that show the given Layer, and add the given Displayable to the GUI and sets it active only in the front Display and only if 'activate' is true.

add(Layer, Displayable) - Static method in class ini.trakem2.display.Display

 

add(LayerSet, ZDisplayable) - Static method in class ini.trakem2.display.Display

Add the ZDisplayable to all Displays that show a Layer belonging to the given LayerSet.

add(DoStep) - Method in class ini.trakem2.display.Displayable.DoEdit

 

add(String, Object) - Method in class ini.trakem2.display.Displayable.DoEdit

 

add(Displayable) - Method in class ini.trakem2.display.Layer

Add a displayable and update all Display instances showing this Layer.

add(Displayable, boolean) - Method in class ini.trakem2.display.Layer

 

add(Displayable, boolean, boolean) - Method in class ini.trakem2.display.Layer

 

add(Layer) - Method in class ini.trakem2.display.LayerSet

Add a new Layer, inserted according to its Z.

add(ZDisplayable) - Method in class ini.trakem2.display.LayerSet

Add a Displayable to be painted in all Layers, such as a Pipe.

add(Layer, double, double) - Method in class ini.trakem2.display.ManualAlignMode.Landmarks

Returns the index of the newly added point, or -1 if the layer doesn't match.

add(Node<T>, byte) - Method in class ini.trakem2.display.Node

Returns -1 when not added (e.g.

add(Shape, Color, Stroke) - Method in class ini.trakem2.display.Overlay

Add a new Shape to be painted above all other elements in the canvas.

add(Shape, Color, Stroke, boolean) - Method in class ini.trakem2.display.Overlay

 

add(Shape, Color, Stroke, boolean, boolean, float) - Method in class ini.trakem2.display.Overlay

 

add(Displayable) - Method in class ini.trakem2.display.Selection

 

add(Area, CoordinateTransform) - Method in class ini.trakem2.display.VectorDataTransform

Add a coordinate transform @param ct that applies to the @param roi Area only; ASSUMES all rois added do not overlap.

add(Patch) - Static method in class ini.trakem2.persistence.FilePathRepair

 

add(History.Step<?>) - Method in class ini.trakem2.utils.History

Append a new step.

add(String) - Method in class ini.trakem2.utils.Montage

 

add(String) - Method in class ini.trakem2.utils.ReconstructArea

To reconstruct from XML, takes a "M ....

add(Vector3, Vector3) - Method in class ini.trakem2.utils.Vector3

 

add(NamedPointWorld) - Method in class landmarks.NamedPointSet

 

add(double) - Method in class loci.plugins.util.RecordedImageProcessor

 

add(int) - Method in class loci.plugins.util.RecordedImageProcessor

 

add(Point3d) - Method in class math3d.NormalEstimator

 

add(LocalHistogram) - Method in class mmorpho.LocalHistogram

 

add(int) - Method in class mpicbg.imglib.cursor.vector.AbstractVector

 

add(V) - Method in class mpicbg.imglib.cursor.vector.AbstractVector

 

add(Vector) - Method in class mpicbg.imglib.cursor.vector.Vector

 

add(int) - Method in class mpicbg.imglib.cursor.vector.Vector

 

add(Vector1d) - Method in class mpicbg.imglib.cursor.vector.Vector1d

 

add(int) - Method in class mpicbg.imglib.cursor.vector.Vector1d

 

add(Vector2d) - Method in class mpicbg.imglib.cursor.vector.Vector2d

 

add(int) - Method in class mpicbg.imglib.cursor.vector.Vector2d

 

add(Vector3d) - Method in class mpicbg.imglib.cursor.vector.Vector3d

 

add(int) - Method in class mpicbg.imglib.cursor.vector.Vector3d

 

add(Vector4d) - Method in class mpicbg.imglib.cursor.vector.Vector4d

 

add(int) - Method in class mpicbg.imglib.cursor.vector.Vector4d

 

add(T) - Method in class mpicbg.imglib.image.Image

 

add(BitType) - Method in class mpicbg.imglib.type.logic.BitType

 

add(ComplexFloatType) - Method in class mpicbg.imglib.type.numeric.complex.ComplexFloatType

 

add(T) - Method in class mpicbg.imglib.type.numeric.complex.ComplexTypeImpl

 

add(T) - Method in class mpicbg.imglib.type.numeric.integer.GenericByteType

 

add(T) - Method in class mpicbg.imglib.type.numeric.integer.GenericIntType

 

add(T) - Method in class mpicbg.imglib.type.numeric.integer.GenericShortType

 

add(LongType) - Method in class mpicbg.imglib.type.numeric.integer.LongType

 

add(T) - Method in interface mpicbg.imglib.type.numeric.NumericType

 

add(FloatType) - Method in class mpicbg.imglib.type.numeric.real.FloatType

 

add(T) - Method in class mpicbg.imglib.type.numeric.real.RealTypeImpl

 

add(RGBALegacyType) - Method in class mpicbg.imglib.type.numeric.RGBALegacyType

 

add(E) - Method in class mpicbg.models.CoordinateTransformList

 

add(double) - Method in class mpicbg.models.ErrorStatistic

 

add(E) - Method in class mpicbg.models.InverseCoordinateTransformList

 

add(E) - Method in class mpicbg.models.InvertibleCoordinateTransformList

 

add(E) - Method in interface mpicbg.models.TransformList

 

add(Point, Point) - Static method in class mpicbg.pointdescriptor.test.TestPointDescriptor

 

add(LRFFT) - Method in class mpicbg.spim.postprocessing.deconvolution2.LRInput

 

add(double, double) - Method in class mpicbg.util.RealStreamPMCC

 

add(double) - Method in class mpicbg.util.RealSum

Add an element to the sum.

add(T) - Method in class mpicbg.util.RingBuffer

 

add(int, T) - Method in class mpicbg.util.RingBuffer

add(T) - Method in class mpicbg.util.RingBuffer.RingBufferListIterator

 

add(OpTreeTableNode) - Method in class net.imagej.ui.swing.ops.OpTreeTableNode

Add a child to this node.

add(Frame) - Method in class org.janelia.it.jacs.shared.ffmpeg.ImageStack

Add a Frame to the end of the stack

add(int, int, double, double) - Method in class org.janelia.thickness.inference.fits.AbstractCorrelationFit

 

add(int, int, double, double) - Method in class org.janelia.thickness.inference.fits.GlobalCorrelationFitAverage

 

add(int, int, double, double) - Method in class org.janelia.thickness.inference.fits.GlobalCorrelationFitAverageRegularized

 

add(int, int, double, double) - Method in class org.janelia.thickness.inference.fits.LocalCorrelationFitAverage

 

add(double, Color) - Method in class org.jfree.chart.renderer.InterpolatePaintScale

Add a color to the color list of this paint scale, at the position given by value.

add(int, int) - Method in class org.siox.util.IntArrayList

Inserts the specified element at the specified position in this list.

add(int) - Method in class org.siox.util.IntArrayList

Appends the specified element to the end of this list.

add(double[], double[]) - Method in class sc.fiji.balloonSegmentation.structure.Balloon

Math vector operators: addition of 2 vectors a+b (I made this before I start using JAMA library)

add(double, double) - Method in class sc.fiji.timelapse.LinearRegression

 

add(double) - Method in class sc.fiji.timelapse.StandardDeviation

 

Add - Class in script.imglib.math

TODO

Add(Image<? extends RealType<?>>, Image<? extends RealType<?>>) - Constructor for class script.imglib.math.Add

 

Add(IFunction, Image<? extends RealType<?>>) - Constructor for class script.imglib.math.Add

 

Add(Image<? extends RealType<?>>, IFunction) - Constructor for class script.imglib.math.Add

 

Add(IFunction, IFunction) - Constructor for class script.imglib.math.Add

 

Add(Image<? extends RealType<?>>, Number) - Constructor for class script.imglib.math.Add

 

Add(Number, Image<? extends RealType<?>>) - Constructor for class script.imglib.math.Add

 

Add(IFunction, Number) - Constructor for class script.imglib.math.Add

 

Add(Number, IFunction) - Constructor for class script.imglib.math.Add

 

Add(Number, Number) - Constructor for class script.imglib.math.Add

 

Add(Object...) - Constructor for class script.imglib.math.Add

 

add(ProfileEntry) - Method in class sholl.Profile

 

add(ViewDescription) - Method in class spim.fiji.plugin.apply.ModelLink

 

add(MVDeconFFT) - Method in class spim.process.fusion.deconvolution.MVDeconInput

 

add(double) - Method in class spim.vecmath.Matrix3d

Adds a scalar to each component of this matrix.

add(double, Matrix3d) - Method in class spim.vecmath.Matrix3d

Adds a scalar to each component of the matrix m1 and places the result into this.

add(Matrix3d, Matrix3d) - Method in class spim.vecmath.Matrix3d

Sets the value of this matrix to the matrix sum of matrices m1 and m2.

add(Matrix3d) - Method in class spim.vecmath.Matrix3d

Sets the value of this matrix to the sum of itself and matrix m1.

add(float) - Method in class spim.vecmath.Matrix3f

Adds a scalar to each component of this matrix.

add(float, Matrix3f) - Method in class spim.vecmath.Matrix3f

Adds a scalar to each component of the matrix m1 and places the result into this.

add(Matrix3f, Matrix3f) - Method in class spim.vecmath.Matrix3f

Sets the value of this matrix to the matrix sum of matrices m1 and m2.

add(Matrix3f) - Method in class spim.vecmath.Matrix3f

Sets the value of this matrix to the matrix sum of itself and matrix m1.

add(double) - Method in class spim.vecmath.Matrix4d

Adds a scalar to each component of this matrix.

add(double, Matrix4d) - Method in class spim.vecmath.Matrix4d

Adds a scalar to each component of the matrix m1 and places the result into this.

add(Matrix4d, Matrix4d) - Method in class spim.vecmath.Matrix4d

Sets the value of this matrix to the matrix sum of matrices m1 and m2.

add(Matrix4d) - Method in class spim.vecmath.Matrix4d

Sets the value of this matrix to sum of itself and matrix m1.

add(float) - Method in class spim.vecmath.Matrix4f

Adds a scalar to each component of this matrix.

add(float, Matrix4f) - Method in class spim.vecmath.Matrix4f

Adds a scalar to each component of the matrix m1 and places the result into this.

add(Matrix4f, Matrix4f) - Method in class spim.vecmath.Matrix4f

Sets the value of this matrix to the matrix sum of matrices m1 and m2.

add(Matrix4f) - Method in class spim.vecmath.Matrix4f

Sets the value of this matrix to the sum of itself and matrix m1.

add(Transform3D) - Method in class spim.vecmath.Transform3D

Adds this transform to transform t1 and places the result into this: this = this + t1.

add(Transform3D, Transform3D) - Method in class spim.vecmath.Transform3D

Adds transforms t1 and t2 and places the result into this transform.

add(Tuple3d, Tuple3d) - Method in class spim.vecmath.Tuple3d

Sets the value of this tuple to the sum of tuples t1 and t2.

add(Tuple3d) - Method in class spim.vecmath.Tuple3d

Sets the value of this tuple to the sum of itself and t1.

add(Tuple3f, Tuple3f) - Method in class spim.vecmath.Tuple3f

Sets the value of this tuple to the vector sum of tuples t1 and t2.

add(Tuple3f) - Method in class spim.vecmath.Tuple3f

Sets the value of this tuple to the vector sum of itself and tuple t1.

add(Tuple3i, Tuple3i) - Method in class spim.vecmath.Tuple3i

Sets the value of this tuple to the sum of tuples t1 and t2.

add(Tuple3i) - Method in class spim.vecmath.Tuple3i

Sets the value of this tuple to the sum of itself and t1.

add(Tuple4d, Tuple4d) - Method in class spim.vecmath.Tuple4d

Sets the value of this tuple to the tuple sum of tuples t1 and t2.

add(Tuple4d) - Method in class spim.vecmath.Tuple4d

Sets the value of this tuple to the sum of itself and tuple t1.

add(Tuple4f, Tuple4f) - Method in class spim.vecmath.Tuple4f

Sets the value of this tuple to the sum of tuples t1 and t2.

add(Tuple4f) - Method in class spim.vecmath.Tuple4f

Sets the value of this tuple to the sum of itself and t1.

add(ImageProcessor) - Method in class spimopener.GaussianStackFocuser

 

add(ImageProcessor) - Method in class spimopener.MaximumProjector

 

add(ImageProcessor) - Method in class spimopener.MinimumProjector

 

add(ImageProcessor) - Method in interface spimopener.Projector

 

add(double) - Method in class stitching.model.ErrorStatistic

 

add(int, int, int, double, int, boolean) - Method in class tracing.Fill

 

add(T, Object) - Method in class util.FibonacciHeap

 

add(double, Object) - Method in class util.FibonacciHeapDouble

 

add(int, Object) - Method in class util.FibonacciHeapInt

 

add(String) - Method in class vib.app.FileGroup

 

add(ImagePlus) - Method in class vib.Average_Images

 

add(int) - Method in class vib.NaiveResampler.Averager

 

add(int) - Method in class vib.NaiveResampler.IntAverager

 

add(int) - Method in class vib.NaiveResampler.MaxLikelihood

 

add(int) - Method in class vib.NaiveResampler.MinEntropy

 

add(BenesNamedPoint) - Method in class vib.PointList

 

add(String, double, double, double) - Method in class vib.PointList

 

add(double, double, double) - Method in class vib.PointList

 

add2Command(Container, String, String, String, String, ActionListener) - Static method in class gui.GuiBuilder

 

add3Command(Container, String, String, String, String, String, String, ActionListener) - Static method in class gui.GuiBuilder

 

add3DCube(int, int, int, int, int, int, Color) - Method in class jRenderer3D.JRenderer3D

Adds a cube (drawn with 12 lines) to the 3D scene.

add3DCube(int, int, int, int, int, int, int) - Method in class jRenderer3D.JRenderer3D

Adds a cube (drawn with 12 lines) to the 3D scene.

ADD_BOX - Static variable in class ij3d.Executer

 

ADD_CONE - Static variable in class ij3d.Executer

 

ADD_CROSS - Static variable in class bunwarpj.PointAction

constant to identify the add cross tool

ADD_EDGE - Static variable in class org.siox.SioxSegmentator

Add mode for the subpixel refinement.

Add_Empty_Channel - Class in sc.fiji.i5d.plugin

 

Add_Empty_Channel() - Constructor for class sc.fiji.i5d.plugin.Add_Empty_Channel

 

Add_Empty_Frame - Class in video2

 

Add_Empty_Frame() - Constructor for class video2.Add_Empty_Frame

 

Add_Empty_Slice - Class in sc.fiji.i5d.plugin

 

Add_Empty_Slice() - Constructor for class sc.fiji.i5d.plugin.Add_Empty_Slice

 

ADD_SPHERE - Static variable in class ij3d.Executer

 

ADD_TRACE - Static variable in class trainableSegmentation.Weka_Segmentation

name of the macro method to add the current trace to a class

ADD_TUBE_POINT - Static variable in class ij3d.Executer

 

addAccelerator(Component, JComponent, ActionListener, int, int) - Static method in class Bug_Submitter.Bug_Submitter

Add a keyboard accelerator to a container.

addActionListender(JRadioButton) - Method in class bdv.gui.TransformTypeSelectDialog

 

addActionListener(ActionListener) - Method in class fiji.plugin.trackmate.gui.descriptors.SpotFilterDescriptor

Adds an ActionListener to this panel.

addActionListener(ActionListener) - Method in class fiji.plugin.trackmate.gui.descriptors.StartDialogDescriptor

Adds an ActionListener to this panel.

addActionListener(ActionListener) - Method in class fiji.plugin.trackmate.gui.descriptors.TrackFilterDescriptor

Adds an ActionListener to this panel.

addActionListener(ActionListener) - Method in class fiji.plugin.trackmate.gui.panels.ActionListenablePanel

Adds an ActionListener to this panel.

addActionListener(ActionListener) - Method in class fiji.plugin.trackmate.gui.panels.components.ImagePlusChooser

 

addActionListener(ActionListener) - Method in class fiji.plugin.trackmate.gui.TrackMateWizard

Adds an ActionListener to the list of listeners of this GUI, that will be notified when one the of push buttons is pressed.

addActionListener(ActionListener) - Method in class fiji.util.ArrowOptionPanel

 

addActionListener(ActionListener) - Method in class IntSlider

 

addActionListener(ActionListener) - Method in class vib.segment.CustomStackWindow

 

addActionListener(ActionListener) - Method in class vib.segment.ImageButton

 

addAddtionalParameters(GenericDialog) - Method in class spim.fiji.plugin.interestpointdetection.DifferenceOf

 

addAddtionalParameters(GenericDialog) - Method in class spim.fiji.plugin.interestpointdetection.DifferenceOfGaussian

 

addAddtionalParameters(GenericDialog) - Method in class spim.fiji.plugin.interestpointdetection.DifferenceOfMean

 

addAdjustmentListener(AdjustmentListener) - Method in class sc.fiji.i5d.gui.ScrollbarWithLabel

 

addAdvancedPoints(ArrayList<Point>, ArrayList<Point>) - Method in class mpicbg.pointdescriptor.test.TestPointDescriptor

 

addAlignmentFields(GenericDialog) - Method in class mpicbg.trakem2.align.Align.Param

 

addAlignmentFields(GenericDialog) - Method in class mpicbg.trakem2.align.Align.ParamOptimize

 

addAll(Collection<? extends E>) - Method in class bdv.util.WrappedList

 

addAll(int, Collection<? extends E>) - Method in class bdv.util.WrappedList

 

addAll(Layer, Collection<? extends Displayable>) - Static method in class ini.trakem2.display.Display

 

addAll(LayerSet, Collection<? extends ZDisplayable>) - Static method in class ini.trakem2.display.Display

 

addAll(Collection<? extends ZDisplayable>) - Method in class ini.trakem2.display.LayerSet

 

addAll(String[]) - Method in class ini.trakem2.utils.Montage

 

addAll(Collection<? extends T>) - Method in class mpicbg.imglib.image.Image

 

addAll(int[]) - Method in class org.siox.util.IntArrayList

Appends all of the elements in the specified array, in the order that they appear in the array.

addAll(Collection) - Method in class org.siox.util.IntArrayList

Appends all of the elements in the specified collection, in the order that they appear in the array.

addAll(int, Collection) - Method in class org.siox.util.IntArrayList

Inserts all of the elements in the specified array into this list, starting at the specified position.

addAll(int, int[]) - Method in class org.siox.util.IntArrayList

Inserts all of the elements in the specified array into this list, starting at the specified position.

addAllClasses(ClassifiedRegion) - Method in class mpicbg.stitching.fusion.ClassifiedRegion

Merges the classes attached to another region with the classes of this region.

addAllEdges(Collection<DefaultWeightedEdge>) - Method in class fiji.plugin.trackmate.ModelChangeEvent

 

addAllSpots(Collection<Spot>) - Method in class fiji.plugin.trackmate.ModelChangeEvent

 

addAlphaMask(Roi, int) - Method in class ini.trakem2.display.Patch

Add the given roi, in world coords, to the alpha mask, using the given fill value.

addAlphaMask(Area, int) - Method in class ini.trakem2.display.Patch

Add the given area, in world coords, to the alpha mask, using the given fill value.

addAlphaMaskLocal(Area, int) - Method in class ini.trakem2.display.Patch

Add the given area, in local coordinates, to the alpha mask, using the given fill value.

addAmiraLabelsList(GenericDialog, String) - Static method in class amira.AmiraParameters

 

addAmiraMeshList(GenericDialog, String) - Static method in class amira.AmiraParameters

 

addAmiraTableList(GenericDialog, String) - Static method in class amira.AmiraParameters

 

addAndFixTiles(List<ViewId>, HashMap<ViewId, Tile<M>>, GlobalOptimizationType, GlobalOptimizationSubset, boolean) - Static method in class spim.process.interestpointregistration.GlobalOpt

 

addAnisotropicDiffusion(ImagePlus, int, int, int, float, float, float) - Method in class trainableSegmentation.FeatureStack

Add anisotropic diffusion filtering images to current stack

addAppleA() - Method in class spim.fiji.spimdata.explorer.ViewSetupExplorerPanel

 

addArea(long, Area) - Method in class ini.trakem2.display.AreaList

Add a copy of an Area object to the existing, if any, area object at Layer with layer_id as given, or if not existing, just set the copy as it.

addAreaList(AreaList) - Method in class edu.utexas.clm.crop.AreaListCrop

 

AddARGBComposite - Class in ini.trakem2.display.graphics

 

addAsLinesTo3DViewer(Image3DUniverse, Color, ImagePlus) - Method in class tracing.Path

 

addAsLinesTo3DViewer(Image3DUniverse, Color3f, ImagePlus) - Method in class tracing.Path

 

addBall(double, double, double, long) - Method in class ini.trakem2.display.Ball

Used to add individual ball objects when parsing.

addBilateralFilter(ImagePlus, double, double) - Method in class trainableSegmentation.FeatureStack

Add bilateral filter image to current stack

addBinaryData(ImagePlus, FeatureStack, String) - Method in class trainableSegmentation.WekaSegmentation

Add instances to a specific class from a label (binary) image.

addBinaryData(ImagePlus, FeatureStack, String, String) - Method in class trainableSegmentation.WekaSegmentation

Add instances to two classes from a label (binary) image.

addBinaryData(List<Point3f>[], FeatureStackArray, String, String) - Method in class trainableSegmentation.WekaSegmentation

Add instances to two classes from lists of coordinates.

addBinaryData(ImagePlus, int, String, String) - Method in class trainableSegmentation.WekaSegmentation

Add label image as binary data

addBinaryData(ImagePlus, ImagePlus, String, String) - Method in class trainableSegmentation.WekaSegmentation

Add binary training data from input and label images.

addBinaryData(ImagePlus, ImagePlus, ImagePlus, String, String) - Method in class trainableSegmentation.WekaSegmentation

Add binary training data from input and label images.

addBottler(Bottler) - Method in class edu.utexas.clm.archipelago.Cluster

 

addBottler(Bottler) - Method in class edu.utexas.clm.archipelago.network.MessageXC

 

addBottler(Bottler) - Method in class edu.utexas.clm.archipelago.network.node.ClusterNode

 

addBottler(Bottler) - Method in class edu.utexas.clm.archipelago.network.node.NodeCoordinator

 

addBoundingBox(BoundingBox) - Method in class spim.fiji.spimdata.boundingbox.BoundingBoxes

 

addBox() - Method in class ij3d.Executer

 

addBox(Image3DUniverse) - Static method in class ij3d.gui.PrimitiveDialogs

 

addBox(String, String, String) - Static method in class ij3d.ImageJ3DViewer

Add a box into the current 3D universe

addBrowseToCellVoyagerFolder(GenericDialogPlus, String, String, int) - Static method in class bdv.ij.ExportCellVoyagerPlugIn

 

addButton(String, ActionListener) - Method in class fiji.util.gui.GenericDialogPlus

Add button to the dialog

addButton(String, ActionListener) - Method in class spim.fiji.plugin.queryXML.GenericLoadParseQueryXML

 

addCacheControl(CacheControl, int) - Method in class bdv.cache.CacheControl.CacheControls

 

addCacheControl(CacheControl) - Method in class bdv.cache.CacheControl.CacheControls

 

addCanvasListener(CustomCanvas.CanvasListener) - Method in class vib.segment.CustomCanvas

 

addCard(String, JComponent, boolean, Insets) - Method in class bdv.ui.CardPanel

Add a new JComponent to the card panel.

addCard(Object, String, JComponent, boolean, Insets) - Method in class bdv.ui.CardPanel

Add a new JComponent to the card panel.

addCard(String, JComponent, boolean) - Method in class bdv.ui.CardPanel

 

addCard(Object, String, JComponent, boolean) - Method in class bdv.ui.CardPanel

 

addCenter() - Method in class sholl.gui.ShollOverlay

 

addCenterLinesBinaryData(ImagePlus, int, String, String) - Method in class trainableSegmentation.WekaSegmentation

Add center lines of label image as binary data

addCenterOf(Iterable<Content>) - Method in class ij3d.ViewAdjuster

Make sure that the average center of all contents is visible in the canvas.

addChangeListener(ChangeListener) - Method in class fiji.plugin.trackmate.gui.descriptors.SpotFilterDescriptor

Add an ChangeListener to this panel.

addChangeListener(ChangeListener) - Method in class fiji.plugin.trackmate.gui.descriptors.TrackFilterDescriptor

Add an ChangeListener to this panel.

addChangeListener(ChangeListener) - Method in class fiji.plugin.trackmate.gui.panels.components.FilterGuiPanel

Add an ChangeListener to this panel.

addChangeListener(ChangeListener) - Method in class fiji.plugin.trackmate.gui.panels.FilterPanel

Add an ChangeListener to this panel.

addChangeTreesStep() - Method in class ini.trakem2.display.LayerSet

Add a step to undo the addition or deletion of one or more objects in this project and LayerSet.

addChangeTreesStep(Set<DoStep>) - Method in class ini.trakem2.display.LayerSet

Add a step to undo the addition or deletion of one or more objects in this project and LayerSet, along with an arbitrary set of steps that may alter, for example the data.

addCheckBox(Container, String) - Static method in class gui.GuiBuilder

 

addCheckbox(String, boolean) - Method in class ini.trakem2.utils.OptionPanel

 

addCheckbox(String, boolean, OptionPanel.Setter) - Method in class ini.trakem2.utils.OptionPanel

 

addCheckbox(GenericDialog, String) - Method in class loci.plugins.prefs.OptionsDialog

Adds a checkbox to the given dialog object corresponding to the boolean option identified by the specified key.

addCheckbox(String) - Method in class util.ModelessQuestions

 

addChild(Thing, DefaultMutableTreeNode) - Method in class ini.trakem2.tree.DNDTree

Appends at the end of the parent_node child list, and waits until the tree's UI is updated.

addChild(Thing) - Method in class ini.trakem2.tree.LayerThing

 

addChild(Thing) - Method in class ini.trakem2.tree.ProjectThing

 

addChild(ProjectThing, int) - Method in class ini.trakem2.tree.ProjectThing

In addition, if the child contains an object of class ini.trakem2.display.Profile, reorders all children of the parent Thing by the Z of the layers of the profiles.

addChild(ProjectThing, String, Displayable) - Method in class ini.trakem2.tree.ProjectTree

Attempt to add the d as a ProjectThing child of type childType to the parent ProjectThing parent.

addChild(Thing) - Method in class ini.trakem2.tree.TemplateThing

 

addChild(Thing) - Method in interface ini.trakem2.tree.Thing

 

addChoice(GenericDialog, String, Vector) - Static method in class amira.AmiraParameters

 

addChoice(GenericDialog, String, Vector, String) - Static method in class amira.AmiraParameters

 

addChoice(String, String[], int) - Method in class ini.trakem2.utils.OptionPanel

 

addChoice(String, String[], int, OptionPanel.Setter) - Method in class ini.trakem2.utils.OptionPanel

 

addChoice(GenericDialog, String) - Method in class loci.plugins.prefs.OptionsDialog

Adds a choice to the given dialog object corresponding to the string option identified by the specified key.

addChoice(String, String[]) - Method in class spimopener.OpenerGenericDialog

 

addCircle(ImagePlus, int, int, double) - Method in class selection.Select_Points

 

addCitationMessage() - Method in class sholl.gui.EnhancedGenericDialog

Deprecated.

Allows users to visit the manuscript from a dialog prompt

addClass(int) - Method in class mpicbg.stitching.fusion.ClassifiedRegion

Add a class, in the form an int value, to this region.

addClass(List<IFT_.Cls>, int, int, int, byte) - Static method in class process3d.IFT_

 

addClass() - Method in class trainableSegmentation.WekaSegmentation

Add new segmentation class.

addClickableURLtoLabel(Component, String, Color) - Static method in class sholl.gui.EnhancedGenericDialog

Deprecated.

 

addColorMode() - Method in class spim.fiji.spimdata.explorer.ViewSetupExplorerPanel

 

addColorMouseListener(ImageCanvas, double, double) - Static method in class fiji.analyze.directionality.Directionality_

 

addCommand(Container, String, String, ActionListener) - Static method in class gui.GuiBuilder

 

addCompletingButton(String, String) - Method in class util.ModelessQuestions

 

addComponent(Component) - Method in class fiji.util.gui.GenericDialogPlus

 

addComponent(Component, int, double) - Method in class fiji.util.gui.GenericDialogPlus

 

addComponentToGrid(Component, Container, int, int, int, int, int, int, double, double) - Static method in class org.imagearchive.lsm.toolbox.gui.GUIMaker

 

addCone() - Method in class ij3d.Executer

 

addCone(Image3DUniverse) - Static method in class ij3d.gui.PrimitiveDialogs

 

addCone(String, String, String, String) - Static method in class ij3d.ImageJ3DViewer

Add a cone into the current 3D universe

addConnectedTile(Tile<?>) - Method in class mpicbg.models.Tile

Add a Tile to the set of connected tiles.

addConnectedTile(Tile) - Method in class stitching.model.Tile

Add a Tile to the set of connected tiles.

AddConstant - Class in imglib.ops.operator.unary

TODO

AddConstant(double) - Constructor for class imglib.ops.operator.unary.AddConstant

 

addContent(ImagePlus, File) - Method in class ij3d.Executer

 

addContent(ImagePlus, Color3f, String, int, boolean[], int, int) - Method in class ij3d.Image3DUniverse

Add the specified image as a new Content to the universe.

addContent(ImagePlus, int, int) - Method in class ij3d.Image3DUniverse

Add the specified image as a new Content to the universe.

addContent(ImagePlus, int) - Method in class ij3d.Image3DUniverse

Add the specified image as a new Content to the universe.

addContent(Content) - Method in class ij3d.Image3DUniverse

Add the specified Content to the universe.

addContent(Collection<Content>) - Method in class ini.trakem2.display.Display3D

 

addContent(Content) - Method in class ini.trakem2.display.Display3D

 

addContentFromFile() - Method in class ij3d.Executer

 

addContentFromImage(ImagePlus) - Method in class ij3d.Executer

 

addContentLater(Content) - Method in class ij3d.Image3DUniverse

Add the specified Content to the universe.

addContentLater(String) - Method in class ij3d.Image3DUniverse

 

addContentLater(Collection<Content>) - Method in class ij3d.Image3DUniverse

Add the specified collection of Content to the universe.

addContour(Element, ReconstructSection) - Method in interface edu.utexas.clm.reconstructreader.reconstruct.ContourSet

 

addContour(Element, ReconstructSection) - Method in class edu.utexas.clm.reconstructreader.reconstruct.ReconstructAreaList

 

addContour(Element, ReconstructSection) - Method in class edu.utexas.clm.reconstructreader.reconstruct.ReconstructProfileList

 

addContour(Element, ReconstructSection) - Method in class edu.utexas.clm.reconstructreader.reconstruct.ReconstructZTrace

 

addCorrespondence(ExtendedPointMatch) - Method in class selection.Select_Points

 

addCorrespondences(List<PairwiseMatch>) - Method in class spim.process.interestpointregistration.optimizationtypes.GlobalOptimizationType

Add all correspondences the list for those that are compared here This method can be overwritten if saving, adding & clearing of correspondences is different for a certain type of registration

addCross(ImagePlus, int, int) - Method in class selection.Select_Points

 

addCrossLink(long, long, long) - Method in class ini.trakem2.persistence.DBLoader

 

addCrossLink(long, long, long) - Method in class ini.trakem2.persistence.Loader

 

addCtrlHint() - Method in class ij3d.gui.LUTDialog

 

addCursor(Cursor<T>) - Method in class mpicbg.imglib.image.Image

Adds a Cursor to the ArrayList of instantiated Cursors.

addCustomMesh(CustomMesh, String) - Method in class ij3d.Image3DUniverse

Add a custom mesh to the universe.

addCustomMesh(CustomMultiMesh, String) - Method in class ij3d.Image3DUniverse

Add a CustomMultiMesh to the universe.

addData(byte) - Method in class adt.PixelStats

 

addDataEditStep(Set<? extends Displayable>) - Method in class ini.trakem2.display.LayerSet

A new undo step for the "data" field of all Displayable in the set.

addDefaultFeatures() - Method in class trainableSegmentation.FeatureStack

Add the default features to the feature stack

addDefaultFiles() - Method in class fiji.packaging.Packager

 

addDefaultTableMouseListener() - Method in class bigwarp.BigWarp

 

addDependent(double[]) - Method in class ini.trakem2.vector.VectorString3D

Add an array that will get resampled along; must be of the same length as the value returned by length()

addDependents(Collection<DoStep>) - Method in class ini.trakem2.display.Displayable.DoEdits

 

addDependents(Set<DoStep>) - Method in class ini.trakem2.display.LayerSet.DoChangeTrees

 

addDerivatives(double, int, int) - Method in class trainableSegmentation.FeatureStack

Add derivatives features to current stack

addDetection(T) - Method in class mpicbg.spim.registration.detection.DetectionStructure

 

addDirectoryField(String, String) - Method in class fiji.util.gui.GenericDialogPlus

 

addDirectoryField(String, String, int) - Method in class fiji.util.gui.GenericDialogPlus

 

addDirectoryField(Container, String) - Static method in class gui.GuiBuilder

 

addDirectoryOrFileField(String, String) - Method in class fiji.util.gui.GenericDialogPlus

 

addDirectoryOrFileField(String, String, int) - Method in class fiji.util.gui.GenericDialogPlus

 

addDiscsTo3DViewer(Image3DUniverse, Color, ImagePlus) - Method in class tracing.Path

 

addDiscsTo3DViewer(Image3DUniverse, Color3f, ImagePlus) - Method in class tracing.Path

 

addDisplayChangeListener(ImageWindow, DisplayChangeListener) - Static method in class OpenImage5DAdapter

 

addDisplayChangeListener(DisplayChangeListener) - Method in class OpenImage5DWindow

 

addDisplayChangeListener(ImageWindow, DisplayChangeListener) - Static method in class OpenStackAdapter

 

addDisplayChangeListener(DisplayChangeListener) - Method in class OpenStackWindow

 

addDisplaySettingsChangeListener(DisplaySettingsListener) - Method in class fiji.plugin.trackmate.gui.panels.ConfigureViewsPanel

Adds the specified DisplaySettingsListener to the collection of listeners that will be notified when a display settings change is made on this GUI.

addDoG(float, float) - Method in class trainableSegmentation.FeatureStack

Add difference of Gaussians to feature stack (single thread version)

addDoubleSlider(String, int, int) - Method in class spimopener.OpenerGenericDialog

 

addDoubleSlider(String, int, int, int, int) - Method in class spimopener.OpenerGenericDialog

 

addDragOverlay(BigWarpDragOverlay) - Method in class bdv.viewer.BigWarpViewerPanel

 

added(BenesNamedPoint) - Method in class ij3d.pointlist.PointListPanel

 

added(BenesNamedPoint) - Method in class ij3d.pointlist.PointListShape

 

added(BenesNamedPoint) - Method in interface vib.PointList.PointListListener

 

added(BenesNamedPoint) - Method in class vib.Points_Dialog

 

addEdge(Spot, Spot, double) - Method in class fiji.plugin.trackmate.Model

Creates a new edge between two spots, with the specified weight.

addEdge(DefaultWeightedEdge) - Method in class fiji.plugin.trackmate.ModelChangeEvent

 

addEdge(double, double, double, double) - Method in class fiji.plugin.trackmate.util.XYEdgeSeries

 

addEdge(Edge) - Method in class sc.fiji.analyzeSkeleton.Graph

Add edge to the graph.

addEdgeAnalyzer(EdgeAnalyzer) - Method in class fiji.plugin.trackmate.Settings

Adds a EdgeAnalyzer to the List of edge analyzers configured.

addEdgeAnalyzer(int, EdgeAnalyzer) - Method in class fiji.plugin.trackmate.Settings

Adds a EdgeAnalyzer to the List of edge analyzers configured, at the specified index.

addEdgeManually(mxCell) - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackScheme

This method is called when the user has created manually an edge in the graph, by dragging a link between two spot cells.

addEdgeToSelection(DefaultWeightedEdge) - Method in class fiji.plugin.trackmate.SelectionModel

 

addEdgeToSelection(Collection<DefaultWeightedEdge>) - Method in class fiji.plugin.trackmate.SelectionModel

 

addEditor() - Method in class fiji.Wiki_Editor

 

addedPatchFrom(String, Patch) - Method in class ini.trakem2.persistence.FSLoader

All backslashes are converted to slashes to avoid havoc in MSWindows.

addedPatchFrom(String, Patch) - Method in class ini.trakem2.persistence.Loader

Subclasses can override this method to register the URL of the imported image.

AddElement(byte[], int, int, int, int, int) - Method in class view5d.View5D

 

AddElement(short[], int, int, int, int, int) - Method in class view5d.View5D

 

AddElement(char[], int, int, int, int, int) - Method in class view5d.View5D

 

AddElement(float[], int, int, int, int, int) - Method in class view5d.View5D

 

AddElement(double[], int, int, int, int, int) - Method in class view5d.View5D

 

AddElementC(float[], int, int, int, int, int) - Method in class view5d.View5D

 

addEmptyPoint() - Method in class vib.Points_Dialog

 

addEnablerListener(Checkbox, Component[], Component[]) - Static method in class ini.trakem2.utils.Utils

A helper for GenericDialog checkboxes to control other the enabled state of other GUI elements in the same dialog.

addEnablerListener(Checkbox, Component[], Component[]) - Static method in class Stitching_3D

 

addEntropy(int, int) - Method in class trainableSegmentation.FeatureStack

Add entropy filter to current stack

addEntry(Comparable<Object>, DefaultListModel) - Static method in class loci.plugins.config.ConfigWindow

 

addEqualLabels(int, int) - Method in class mpicbg.spim.registration.threshold.ConnectedComponent

 

addErodedBinaryData(ImagePlus, int, String, String) - Method in class trainableSegmentation.WekaSegmentation

Add eroded version of label image as binary data

addExample(int, Roi, int) - Method in class trainableSegmentation.WekaSegmentation

Adds a ROI to the list of examples for a certain class and slice.

addExternalTransformation(ViewStructure) - Method in class mpicbg.spim.Reconstruction

 

addFace(int, int, int) - Method in class customnode.FullInfoMesh

 

addFatPoint(String, LayerSet, double, double, double, double, Color) - Static method in class ini.trakem2.display.Display3D

Expects uncalibrated wx,wy,wz, (i.e.

addFeaturePenaltyToSettings(Map<?, ?>, Object, Object, Object, StringBuilder) - Static method in class fiji.plugin.trackmate.tracking.LAPUtils

Utility method to put a value in a map, contained in a mother map.

addFeaturesMT(ImagePlus) - Method in class trainableSegmentation.FeatureStack

Add features based on a list of filters in a multi-thread fashion

addFields(GenericDialog) - Method in class lenscorrection.Distortion_Correction.BasicParam

 

addFields(GenericDialog) - Method in class lenscorrection.Distortion_Correction.PluginParam

 

addFields(GenericDialog, FloatArray2DMOPS.Param) - Static method in class mpicbg.ij.MOPS

 

addFields(GenericDialog) - Method in class mpicbg.ij.plugin.AbstractBlockMatching

 

addFields(GenericDialog, FloatArray2DSIFT.Param) - Static method in class mpicbg.ij.SIFT

 

addFields(GenericDialog) - Method in class mpicbg.trakem2.align.Align.Param

 

addFields(GenericDialog) - Method in class mpicbg.trakem2.align.Align.ParamOptimize

 

addFile(String, boolean) - Method in class fiji.packaging.Packager

 

addFile(File) - Method in class org.imagearchive.lsm.toolbox.gui.LsmImageTableModel

 

addFileField(String, String) - Method in class fiji.util.gui.GenericDialogPlus

 

addFileField(String, String, int) - Method in class fiji.util.gui.GenericDialogPlus

 

addFileField(Container, String) - Static method in class gui.GuiBuilder

 

addFileField(String, String) - Method in class org.janelia.thickness.plugin.NonBlockingGenericDialogWithFileField

 

addFileField(String, String, int) - Method in class org.janelia.thickness.plugin.NonBlockingGenericDialogWithFileField

 

addFileSaveField(Container, String) - Static method in class gui.GuiBuilder

 

addFill(Fill) - Method in class tracing.PathAndFillManager

 

addFilterPanel() - Method in class fiji.plugin.trackmate.gui.panels.components.FilterGuiPanel

 

addFilterPanel(FeatureFilter) - Method in class fiji.plugin.trackmate.gui.panels.components.FilterGuiPanel

 

addFilterPanel(String) - Method in class fiji.plugin.trackmate.gui.panels.components.FilterGuiPanel

 

addFirst(Transform) - Method in class vib.transforms.OrderedTransformations

 

addFirst(OrderedTransformations) - Method in class vib.transforms.OrderedTransformations

 

addFittedMinimum(int) - Method in class sc.fiji.timelapse.Extrema

Fit a parabola to the interval [left;right].

addFixedPoint(RealPoint, boolean) - Method in class bigwarp.BigWarp.MouseLandmarkListener

Adds a point in the moving and fixed images at the same point.

addFrame() - Method in class video.Edit_Video

 

addFrames(ImagePlus, int, int) - Static method in class video2.Add_Empty_Frame

 

addGabor(ImagePlus, double, double, double, double, int) - Method in class trainableSegmentation.FeatureStack

Add Gabor features to current stack

addGaussianBlur(float) - Method in class trainableSegmentation.FeatureStack

Add Gaussian blur slice to current stack

addGaussianNoise(Image<FloatType>, Random, float, boolean) - Static method in class mpicbg.spim.postprocessing.deconvolution2.AdjustInput

Adds additive gaussian noise: i = i + gauss(x, sigma)

addGaussianNoiseAddMul(Image<FloatType>, Random, float, boolean) - Static method in class mpicbg.spim.postprocessing.deconvolution2.AdjustInput

Adds additive and multiplicative gaussian noise: i = i*gauss(x,sigma) + gauss(x, sigma)

addGeometricConsensusFilterFields(GenericDialog) - Method in class mpicbg.trakem2.align.Align.Param

 

addGradient(float) - Method in class trainableSegmentation.FeatureStack

Add Sobel filter version of the original image

addGroup(SourceGroup) - Method in class bdv.viewer.BasicViewerState

Add group to the state.

addGroup(SourceGroup) - Method in class bdv.viewer.state.ViewerState

Deprecated.

 

addGroup(SourceGroup) - Method in class bdv.viewer.SynchronizedViewerState

Add group to the state.

addGroup(SourceGroup) - Method in class bdv.viewer.ViewerPanel

Deprecated.

Modify ViewerPanel.state() directly

addGroup(SourceGroup) - Method in interface bdv.viewer.ViewerState

Add group to the state (optional operation).

addGroups(Collection<? extends SourceGroup>) - Method in class bdv.viewer.BasicViewerState

Add all groups in collection to the state.

addGroups(Collection<? extends SourceGroup>) - Method in class bdv.viewer.SynchronizedViewerState

Add all groups in collection to the state.

addGroups(Collection<? extends SourceGroup>) - Method in interface bdv.viewer.ViewerState

Add all groups in collection to the state (optional operation).

addHandle(int, int) - Method in class mpicbg.ij.InteractiveMapping

 

addHandle(int, int) - Method in class sc.fiji.timelapse.PolygonRoiPublic

 

addHandle(int, int) - Method in class Transform_MovingLeastSquaresMesh

 

addHandle(int, int) - Method in class Transform_ThinPlateSpline

 

addHessian(float) - Method in class trainableSegmentation.FeatureStack

Add Hessian features from original image (single thread version).

addHSB() - Method in class trainableSegmentation.FeatureStack

Add HSB features

addHyperlink(String) - Method in class sholl.gui.EnhancedWaitForUserDialog

Deprecated.

Adds a functional URL to the dialog's MultiLineLabel.

addHyperLink(GenericDialog, String, String) - Static method in class spim.fiji.plugin.util.GUIHelper

 

addHyperLinkListener(MultiLineLabel, String) - Static method in class fiji.plugin.Bead_Registration

 

addHyperLinkListener(MultiLineLabel, String) - Static method in class spim.fiji.plugin.util.GUIHelper

 

addHyperLinkListener(MultiLineLabel, String) - Static method in class stitching.CommonFunctions

 

addHyperlinkMessage(String, Font, Color, String) - Method in class sholl.gui.EnhancedGenericDialog

Deprecated.

Appends a message to the specified dialog consisting of one or more lines of text, and assigns a functional URL to it.

addIcospheres(List<Point3f>, Color3f, int, float, String) - Method in class ij3d.Image3DUniverse

At every Point3f in @param points, place an icosphere created with @param subdivisions and @param radius.

addICPCorrespondence(T) - Method in class mpicbg.spim.registration.detection.DetectionView

 

addICPCorrespondence(T, double) - Method in class mpicbg.spim.registration.detection.DetectionView

 

addIfValid(Algorithm<T>, List<Algorithm<T>>) - Method in class sc.fiji.coloc.Coloc_2

Adds the provided Algorithm to the list if it is not null.

addImage(String) - Method in class fiji.util.gui.GenericDialogPlus

Adds an image to the generic dialog

addImage(URL) - Method in class fiji.util.gui.GenericDialogPlus

Adds an image to the generic dialog

addImage(ImageIcon) - Method in class fiji.util.gui.GenericDialogPlus

Adds an image to the generic dialog

addImage(Image, String, String) - Method in class sc.fiji.coloc.results.PDFWriter

Prints an image into the opened PDF.

addImage(Image, String) - Method in class sc.fiji.io.PDF_Writer

 

addImageChoice(String, String) - Method in class fiji.util.gui.GenericDialogPlus

 

addImageList(GenericDialog, String, String, AmiraParameters.IsA) - Static method in class amira.AmiraParameters

 

addImagePlusPair(ImagePlus, ImagePlus) - Method in class util.Histogram_2D

 

addImagePlusPair(ImagePlus, ImagePlus, int) - Method in class util.Histogram_2D

 

addImagePlusPair(ImagePlus, ImagePlus, double, double, double, double, int, int) - Method in class util.Histogram_2D

 

addImageToList(ImagePlus, String) - Method in class sc.fiji.coloc.results.PDFWriter

 

addImageWindowListener(WindowListener) - Method in class org.siox.example.ControlJPanel

Add a WindowListener to any image display window (except internal frames), wether it is now open or opened in the future.

addImageWindowListener(InternalFrameListener) - Method in class org.siox.example.ControlJPanel

Add an InternalFrameListener to any internal frame for displaying an image.

addImgLibAlgorithms() - Method in class fiji.expressionparser.ImgLibParser

Add ImgLib algorithms to the parser, such as gaussian convolution.

addingNode(SearchNode) - Method in class tracing.AutoSearchThread

 

addingNode(SearchNode) - Method in class tracing.SearchThread

Override this method if you want to find out when a point was first discovered:

addInstant(ContentInstant) - Method in class ij3d.Content

 

addInteractiveBehavior(InteractiveBehavior) - Method in class ij3d.DefaultUniverse

 

addInterestPointList(String, InterestPointList) - Method in class spim.fiji.spimdata.interestpoints.ViewInterestPointLists

 

addInterpolationModeListener(InterpolationModeListener) - Method in class bdv.viewer.ViewerPanel

Add a InterpolationModeListener to notify when the interpolation mode is changed.

addInverseEnablerListener(Checkbox, Component[], Component[]) - Static method in class Stitching_3D

 

addIOButtons(GenericDialogPlus) - Method in class fiji.tool.AbstractTrackingTool

 

addItem(int, int, String) - Method in class ini.trakem2.display.Dissector

For reconstruction purposes from XML.

additionalSigmaX - Variable in class spim.fiji.plugin.interestpointdetection.DifferenceOf

 

additionalSigmaY - Variable in class spim.fiji.plugin.interestpointdetection.DifferenceOf

 

additionalSigmaZ - Variable in class spim.fiji.plugin.interestpointdetection.DifferenceOf

 

addJGraphTEdge(DefaultWeightedEdge) - Method in class fiji.plugin.trackmate.visualization.trackscheme.JGraphXAdapter

 

addJGraphTVertex(Spot) - Method in class fiji.plugin.trackmate.visualization.trackscheme.JGraphXAdapter

 

addJob(Bureaucrat) - Method in class ini.trakem2.persistence.Loader

Adds a new job to monitor.

addKey(String, File) - Method in class edu.utexas.clm.archipelago.network.shell.NodeShellParameters

 

addKey(String, String) - Method in class edu.utexas.clm.archipelago.network.shell.NodeShellParameters

 

addKey(String, int) - Method in class edu.utexas.clm.archipelago.network.shell.NodeShellParameters

 

addKey(String, float) - Method in class edu.utexas.clm.archipelago.network.shell.NodeShellParameters

 

addKeyAndContainerListenerRecursively(Component) - Method in class tracing.ClarifyingKeyListener

 

addKeyEventPostProcessor(KeyEventPostProcessor) - Method in class bigwarp.BigWarp

 

addKeyListener(Component) - Method in class fiji.tool.AbstractTool

 

addKeyListener(KeyListener) - Method in class sc.fiji.i5d.gui.ScrollbarWithLabel

 

addKuwaharaFeatures(ImagePlus, int, int, int) - Method in class trainableSegmentation.FeatureStack

Add Kuwahara filter features to the current stack

addLabel(int) - Method in class mpicbg.spim.registration.threshold.ConnectedComponent

 

addLabel(String) - Method in class util.ModelessQuestions

 

addLabeledData(ImagePlus, FeatureStack) - Method in class trainableSegmentation.WekaSegmentation

Add instances from a labeled image.

addLabeledData(ImageProcessor, FeatureStack, String[], int) - Method in class trainableSegmentation.WekaSegmentation

Add instances reading the pixel classes from a label image.

addLabeledData(ImageProcessor, FeatureStack, int[], int) - Method in class trainableSegmentation.WekaSegmentation

Add instances reading the pixel classes from a label image.

addLabeledData(ImagePlus, ImagePlus) - Method in class trainableSegmentation.WekaSegmentation

Add labeled training data from input and label images.

addLabeledData(ImagePlus, ImagePlus, String[], int) - Method in class trainableSegmentation.WekaSegmentation

Add training data from input and labeled images.

addLabeledData(ImagePlus, ImagePlus, int[], int) - Method in class trainableSegmentation.WekaSegmentation

Add training data from input and labeled images.

addLabeledNumericSpinner(Container, String, int, int, int, ChangeListener) - Static method in class gui.GuiBuilder

 

addLabeledSpinner(Container, String, SpinnerModel) - Static method in class gui.GuiBuilder

 

addLabelList(Container) - Static method in class oldsegmenters.Segmentator_

 

addLabelList(Container) - Static method in class oldsegmenters.Segmenter_

 

addLaplacian(double) - Method in class trainableSegmentation.FeatureStack

Add Laplacian features to current stack

addLast(Transform) - Method in class vib.transforms.OrderedTransformations

 

addLast(OrderedTransformations) - Method in class vib.transforms.OrderedTransformations

 

addLayer(LayerSet, Layer) - Method in class ini.trakem2.tree.LayerTree

Used by the Loader.importStack and the "many new layers" command.

addLayerChoice(String, Layer, GenericDialog) - Static method in class ini.trakem2.utils.Utils

 

addLayerContentStep(Layer) - Method in class ini.trakem2.display.LayerSet

For the Displayable contained in a Layer: their number, and their stack order.

addLayerEditedStep(Layer) - Method in class ini.trakem2.display.LayerSet

For the Z and thickness of a layer.

addLayerEditedStep(List<Layer>) - Method in class ini.trakem2.display.LayerSet

For the Z and thickness of a list of layers.

addLayerRangeChoices(Layer, GenericDialog) - Static method in class ini.trakem2.utils.Utils

 

addLayerRangeChoices(Layer, Layer, GenericDialog) - Static method in class ini.trakem2.utils.Utils

 

addLayoutComponent(Component, Object) - Method in class sc.fiji.i5d.gui.Image5DLayout

 

addLayoutComponent(String, Component) - Method in class sc.fiji.i5d.gui.Image5DLayout

 

addLeafs(List<? extends Thing>, Runnable) - Method in class ini.trakem2.tree.DNDTree

Will add only those for which a node doesn't exist already.

addLine3D(Line3D) - Method in class jRenderer3D.JRenderer3D

Adds a single 3D line to the 3D scene.

addLine3D(int, int, int, int, int, int, Color) - Method in class jRenderer3D.JRenderer3D

Adds a single 3D line to the 3D scene.

addLineMesh(List<Point3f>, Color3f, String, boolean) - Method in class ij3d.Image3DUniverse

Add a custom mesh, in particular a line mesh (a set of lines in 3D) to the universe.

addLines(Point3f[]) - Method in class customnode.CustomLineMesh

 

addLines3D(Line3D[]) - Method in class jRenderer3D.JRenderer3D

Adds an array of lines to the 3D scene.

addLipschitzFilter(ImagePlus, boolean, boolean, double) - Method in class trainableSegmentation.FeatureStack

Add Lipschitz filter image to current stack

addListener(NodeStateListener) - Method in class edu.utexas.clm.archipelago.network.node.ClusterNode

Adds a NodeStateListener to the list of listeners that are notified when the state of this ClusterNode changes.

addListener(FileListener) - Method in class fsalign.FolderWatcher

 

addListener(LUTDialog.Listener) - Method in class ij3d.gui.LUTDialog

 

addListener(SelectedViewDescriptionListener<AS>) - Method in class spim.fiji.spimdata.explorer.ViewSetupExplorer

 

addListener(SelectedViewDescriptionListener<AS>) - Method in class spim.fiji.spimdata.explorer.ViewSetupExplorerPanel

 

addListener(SNTListener) - Method in class tracing.SimpleNeuriteTracer

 

addListeners() - Method in class bigwarp.WarpVisFrame

 

addListeners(GenericDialog, Choice, MyMultiLineLabel, ArrayList<MultiViewDatasetDefinition>) - Method in class spim.fiji.plugin.Define_Multi_View_Dataset

 

addListeners(GenericDialog, TextField, TextField, TextField, Checkbox, Label) - Method in class spim.fiji.plugin.Merge_Cluster_Jobs

 

addListeners(GenericDialog, TextField, Label, Label) - Method in class spim.fiji.plugin.queryXML.GenericLoadParseQueryXML

 

addListeners(GenericDialog, Vector<?>, Label, long[]) - Method in class spim.process.fusion.boundingbox.AutomaticBoundingBox

 

addListeners(ImgExport) - Method in class spim.process.fusion.boundingbox.BoundingBoxGUI.ManageListeners

 

addListeners(GenericDialog, Choice, Label, Label) - Method in class spim.process.fusion.boundingbox.PreDefinedBoundingBox

 

AddLookUpTable(int, byte[], byte[], byte[]) - Static method in class view5d.Bundle

 

AddLookUpTable(int, byte[], byte[], byte[]) - Method in class view5d.My3DData

 

addLowerRightPoint(Point) - Method in class adt.Connectivity2D

the contract of calling this method is that the new point must be gauranteed to be the most far right lowest point (i.e.

addLThresh(double) - Method in class view5d.My3DData

 

AddMarkedElement() - Method in class view5d.My3DData

 

addMarker(CellCntrMarker) - Method in class sc.fiji.cellCounter.CellCntrMarkerVector

 

addMaskPoint(int, int) - Method in class bunwarpj.PointHandler

Add a point to the mask.

addMatch(PointMatch) - Method in class mpicbg.models.Tile

Add one PointMatch.

addMatch(PointMatch) - Method in class stitching.model.Tile

Add one match.

addMatches(Collection<PointMatch>) - Method in class mpicbg.models.Tile

Add more PointMatches.

addMatches(Collection<PointMatch>) - Method in class stitching.model.Tile

Add more PointMatches.

addMatchWeightedByDistance(PointMatch, double) - Method in class mpicbg.models.MovingLeastSquaresMesh

Add a PointMatch to all Tiles weighted by its distance to the corresponding vertex.

addMaterial(String, double, double, double) - Method in class amira.AmiraParameters

 

addMaterial(String, int, int, int) - Static method in class Segmentation_Editor

 

addMaterial() - Method in class vib.segment.MaterialList

 

addMax(float) - Method in class trainableSegmentation.FeatureStack

Add maximum filter to current feature stack.

addMean(float) - Method in class trainableSegmentation.FeatureStack

Add mean filter to current stack

addMedian(float) - Method in class trainableSegmentation.FeatureStack

Add median filter to the current feature stack.

addMembraneFeatures(int, int) - Method in class trainableSegmentation.FeatureStack

Add membrane features to the stack (single thread version)

addMesh(ImagePlus) - Method in class ij3d.Image3DUniverse

Add a new image as a content, displaying it as an isosurface.

addMesh(ImagePlus, int) - Method in class ij3d.Image3DUniverse

Add a new image as a content, displaying it as an isosurface.

addMesh(ImagePlus, Color3f, String, int, boolean[], int) - Method in class ij3d.Image3DUniverse

Add a new image as a content, displaying it as an iso-surface.

addMesh(List, Color3f, String, float, int) - Method in class ij3d.Image3DUniverse

Deprecated.

This method will not be supported in the future. The specified 'scale' will be ignored, and the applied scale will be calculated automatically from the minimum and maximum coordinates of the specified mesh. Use addTriangleMesh instead.

addMesh(List<Point3f>, Color3f, String, int) - Method in class ij3d.Image3DUniverse

Deprecated.

This method will not be supported in the future. Use addTriangleMesh instead.

addMesh(LayerSet, VectorString3D, String, Color) - Static method in class ini.trakem2.display.Display3D

Creates a mesh from the given VectorString3D, which is unbound to any existing Pipe.

addMesh(LayerSet, VectorString3D, String, Color, double[], float) - Static method in class ini.trakem2.display.Display3D

Creates a mesh from the given VectorString3D, which is unbound to any existing Pipe.

addMeshes(Image3DUniverse, String) - Static method in class isosurface.AmiraSurface

 

addMessage(String) - Method in class ini.trakem2.utils.OptionPanel

 

addMessage(GenericDialog, String[], Font, Color) - Static method in class spim.fiji.plugin.util.MyMultiLineLabel

Adds a message consisting of one or more lines of text, which will be displayed using the specified font and color.

addMin(float) - Method in class trainableSegmentation.FeatureStack

Add minimum filter to current feature stack.

addMinimum(int) - Method in class sc.fiji.timelapse.Extrema

 

addModelChangeListener(ModelChangeListener) - Method in class fiji.plugin.trackmate.Model

 

addModuleListener(ModuleListener) - Static method in class vib.app.module.Module

 

addMouseMotionListener(ImageCanvas) - Method in class fiji.tool.AbstractTool

 

addMouseWheelListener(ImageWindow) - Method in class fiji.tool.AbstractTool

 

addNatMethBeadsPaper(GenericDialog) - Static method in class spim.fiji.plugin.util.GUIHelper

 

addNatMethBeadsPaper(GenericDialog, String) - Static method in class spim.fiji.plugin.util.GUIHelper

 

addNeighborPair(int, byte[], int, int) - Method in class SRM_

 

addNeighborPair(int, byte[], byte[], int) - Method in class SRM_

 

addNeighbors(int, int) - Method in class trainableSegmentation.FeatureStack

Add 8 neighbors of the original image as features

AddNewBalloon(int[], int[]) - Method in class sc.fiji.balloonSegmentation.structure.BalloonPopulation

Add a balloon with custom shape defined by arrays X and Y

AddNewBalloon(int, int) - Method in class sc.fiji.balloonSegmentation.structure.BalloonPopulation

Add a circular balloon centrerd on x,y with id ID

addNewChildType(ProjectThing, String) - Method in class ini.trakem2.tree.TemplateTree

Add a new template thing to an existing ProjectThing, so that new instances of template new_child_type can be added to the ProjectThing pt.

addNewChildType(TemplateThing, String) - Method in class ini.trakem2.tree.TemplateTree

tt_parent is the parent TemplateThing tet_child is the child to add to tt parent, and to insert as child to all nodes that host the tt parent.

addNewImage(ImagePlus) - Method in class ini.trakem2.persistence.Loader

 

addNewImage(ImagePlus, double, double) - Method in class ini.trakem2.persistence.Loader

Mipmaps for this image are generated asynchronously.

addNewPoint() - Method in class landmarks.NamedPointSet

 

addNextPoint(SWCPoint) - Method in class tracing.SWCPoint

 

addNode(Node<T>, Node<T>, byte) - Method in class ini.trakem2.display.Tree

Will call calculateBoundingBox and repaint.

addNode(MutableTreeNode, Path, DefaultTreeModel) - Method in class tracing.PathWindow

 

addNode(SearchNode, boolean) - Method in class tracing.SearchThread

 

AddNoise - Class in imglib.ops.operator.unary

TODO

AddNoise(double, double, double) - Constructor for class imglib.ops.operator.unary.AddNoise

 

addNotify() - Method in class spim.fiji.plugin.util.MyMultiLineLabel

 

addNumericField(String, double, int) - Method in class ini.trakem2.utils.OptionPanel

 

addNumericField(String, double, int, OptionPanel.Setter) - Method in class ini.trakem2.utils.OptionPanel

 

addNumericField(String, int) - Method in class ini.trakem2.utils.OptionPanel

 

addNumericField(String, int, OptionPanel.Setter) - Method in class ini.trakem2.utils.OptionPanel

 

addObject(Object3D) - Method in class Utilities.Counter3D

Add the provided Object3D to the list

addObserver(Observer) - Method in class imglib.ops.operation.AssignOperation

 

addOctree(String, String) - Method in class ij3d.Image3DUniverse

Deprecated.

The octree methods will be outsourced into a different plugin.

addOrthoslice(ImagePlus) - Method in class ij3d.Image3DUniverse

Add a new image as a content, displaying it as orthoslices.

addOrthoslice(ImagePlus, int) - Method in class ij3d.Image3DUniverse

Add a new image as a content, displaying it as orthoslices.

addOrthoslice(ImagePlus, Color3f, String, int, boolean[], int) - Method in class ij3d.Image3DUniverse

Add a new image as a content, displaying it as orthoslices.

addOrthoslice(String, String, String, String, String, String, String) - Static method in class ij3d.ImageJ3DViewer

 

addOtherKeyListeners(KeyListener[]) - Method in class tracing.QueueJumpingKeyListener

This method should add the other key listeners in 'laterKeyListeners' that will be called for 'source' if this key listener isn't interested in the key press.

addOverlay(BigWarpOverlay) - Method in class bdv.viewer.BigWarpViewerPanel

 

addOverlay(Roi) - Method in class fiji.plugin.trackmate.visualization.hyperstack.HyperStackDisplayer

 

addOverlay(OverlayedImageCanvas.Overlay) - Method in class fiji.util.gui.OverlayedImageCanvas

 

addOverlay(Collection<OverlayedImageCanvas.Overlay>) - Method in class fiji.util.gui.OverlayedImageCanvas

Add the collection of overlays to the display list of this canvas

addOverlayAnimator(OverlayAnimator) - Method in class bdv.viewer.ViewerPanel

Add a new OverlayAnimator to the list of animators.

addp(int, int, double) - Method in class parObject

 

addp(double, double, double) - Method in class parObject

 

addPanel(Panel) - Method in class ij3d.pointlist.PointListDialog

Displays an optional panel at the bottom of the window.

addPanelIntoDialog(Panel) - Method in class Series_Labeler

The container Panel is added to the generic dialog.

addPanelsToDialog(Panel, Panel[]) - Method in class Series_Labeler

Adds different Panels to a container Panel.

addPassiveVertex(Vertex) - Method in class mpicbg.models.SpringMesh

Add a passive vertex.

addPath(Path) - Method in class tracing.PathAndFillManager

 

addPath(Path, boolean) - Method in class tracing.PathAndFillManager

 

addPathAndFillListener(PathAndFillListener) - Method in class tracing.PathAndFillManager

 

addPathPointsToShollList(Path, double, double, double, List<ShollAnalysisDialog.ShollPoint>) - Static method in class tracing.ShollAnalysisDialog

 

addPathsToOverlay(Overlay, int, boolean) - Method in class tracing.SimpleNeuriteTracer

 

addPeak(int) - Method in class sc.fiji.timelapse.Peak_Counter_Tool

 

addPlugIns(JPopupMenu, String, Project, Callable<Displayable>) - Static method in class ini.trakem2.utils.Utils

Returns false if none to add.

addPlugIns(String, Project, Callable<Displayable>) - Static method in class ini.trakem2.utils.Utils

Returns null if none to add.

addPoint(int, int) - Method in class adt.Connectivity2D

 

addPoint(Point) - Method in class adt.Connectivity2D

 

addPoint(int, int) - Method in class adt.Points

 

addPoint(Point) - Method in class adt.Points

 

addPoint(double[], boolean, BigWarpViewerPanel) - Method in class bigwarp.BigWarp

Updates the global variable ptBack

addPoint(double[], boolean) - Method in class bigwarp.BigWarp

Updates the global variable ptBack

addPoint(int, int) - Method in class bunwarpj.PointHandler

Add a point to the list of points.

addPoint(Point3f) - Method in class customnode.CustomPointMesh

 

addPoint(Content, int, int) - Method in class ij3d.behaviors.Picker

Adds a landmark point specfied by the canvas position

addPoint(Content, MouseEvent) - Method in class ij3d.behaviors.Picker

Adds a landmark point specfied by the position of the MouseEvent.

addPoint(double, double, long, double) - Method in class ini.trakem2.display.Ball

Add a point either at the end or between two existing points, with accuracy depending on magnification.

addPoint(int, int, double, double, long) - Method in class ini.trakem2.display.Pipe

Add a point either at the end or between two existing points, with accuracy depending on magnification.

addPoint(int, int, long, double) - Method in class ini.trakem2.display.Polyline

Add a point either at the end or between two existing points, with accuracy depending on magnification.

addPoint(double, double, double, double) - Method in class ini.trakem2.display.Profile

Add a point either at the end or between two existing points, with accuracy depending on magnification.

addPoint(Point) - Method in class sc.fiji.analyzeSkeleton.Vertex

Add point to the vertex.

addPoint(UPoint) - Method in class sholl.ProfileEntry

 

addPoint(AutoPoint, AutoPoint) - Method in class tracing.SinglePathsGraph

 

addPoint3D(Point3D) - Method in class jRenderer3D.JRenderer3D

Adds a single Point3D to the 3D scene.

addPoint3D(int, int, int, int, Color, int) - Method in class jRenderer3D.JRenderer3D

Adds a point to the 3D scene.

addPoint3D(int, int, int, int, int, int) - Method in class jRenderer3D.JRenderer3D

Adds a point to the 3D scene.

addPointDescriptorCorrespondence(T) - Method in class mpicbg.spim.registration.detection.DetectionView

 

addPointDescriptorCorrespondence(T, double) - Method in class mpicbg.spim.registration.detection.DetectionView

 

AddPointEdit - Class in bigwarp.landmarks.actions

 

AddPointEdit(LandmarkTableModel, int, double[], boolean) - Constructor for class bigwarp.landmarks.actions.AddPointEdit

 

addPointList(String, PointListPanel) - Method in class ij3d.pointlist.PointListDialog

Adds the specified PointListPanel.

addPointListListener(PointList.PointListListener) - Method in class vib.PointList

 

addPointListPoint(Point3d) - Method in class ij3d.Content

Deprecated. 

addPointListPoint(Point3d) - Method in class ij3d.ContentInstant

Deprecated. 

addPointMatches(ArrayList<PointMatchGeneric<T>>, Tile<?>, Tile<?>) - Static method in class mpicbg.spim.registration.detection.DetectionRegistration

 

addPointMatches(ArrayList<PointMatch>, Tile<?>, Tile<?>) - Static method in class process.Matching

 

addPointMatches(ArrayList<PointMatchGeneric<Detection>>, Tile<?>, Tile<?>) - Static method in class spim.process.interestpointregistration.GlobalOpt

 

addPointMesh(List<Point3f>, Color3f, String) - Method in class ij3d.Image3DUniverse

Add a custom mesh, in particular a point mesh, to the universe.

addPointMesh(List<Point3f>, Color3f, float, String) - Method in class ij3d.Image3DUniverse

Add a custom mesh, in particular a point mesh, to the universe.

addPoints(Points) - Method in class adt.Points

 

addPoints(Point3f[]) - Method in class customnode.CustomPointMesh

 

addPoints(double[], double[], int) - Method in class sholl.gui.ShollPlot

 

addPoints3D(Point3D[]) - Method in class jRenderer3D.JRenderer3D

Adds an array with Point3D to the 3D scene.

addPointsAtBegin(double[][], double[][], double[][]) - Method in class ini.trakem2.display.Profile

 

addPointsAtEnd(double[][], double[][], double[][]) - Method in class ini.trakem2.display.Profile

 

addPopupMenu(JTable) - Method in class spim.fiji.spimdata.explorer.interestpoint.InterestPointExplorerPanel

 

addPopupMenu(JTable) - Method in class spim.fiji.spimdata.explorer.registration.RegistrationExplorerPanel

 

addPopupMenu(JTable) - Method in class spim.fiji.spimdata.explorer.ViewSetupExplorerPanel

 

addPossible(String) - Method in class loci.plugins.prefs.StringOption

Adds a possible value to the list.

addPostTask(Runnable) - Method in class ini.trakem2.utils.Bureaucrat

Add a task to run after the Worker has finished or quit.

addPreibischLabWebsite(GenericDialog) - Static method in class spim.fiji.plugin.util.GUIHelper

 

addProfile(ReconstructProfile) - Method in class edu.utexas.clm.reconstructreader.reconstruct.ReconstructSection

 

addProgressListener(SearchProgressCallback) - Method in class tracing.SearchThread

 

addProgressListener(SearchProgressCallback) - Method in class tracing.TubularGeodesicsTracer

 

addQuad(Point3f, Point3f, Point3f, Point3f) - Method in class customnode.CustomQuadMesh

 

addQuadMesh(List<Point3f>, Color3f, String) - Method in class ij3d.Image3DUniverse

Add a custom mesh, in particular a mesh consisting of quads, to the universe.

addQuads(Point3f[]) - Method in class customnode.CustomQuadMesh

 

addQuery(GenericDialog) - Method in class spim.fiji.plugin.interestpointdetection.DifferenceOfGaussian

 

addQuery(GenericDialog, Interest_Point_Registration.RegistrationType) - Method in class spim.fiji.plugin.interestpointregistration.InterestPointRegistration

adds the questions this registration wants to ask

addQuery(GenericDialog) - Method in interface spim.fiji.plugin.util.GenericDialogAppender

adds the questions this registration wants to ask

addQuery(GenericDialog, Interest_Point_Registration.RegistrationType) - Method in class spim.process.interestpointregistration.centerofmass.CenterOfMass

 

addQuery(GenericDialog, Interest_Point_Registration.RegistrationType) - Method in class spim.process.interestpointregistration.geometricdescriptor.RGLDM

 

addQuery(GenericDialog, Interest_Point_Registration.RegistrationType) - Method in class spim.process.interestpointregistration.geometrichashing.GeometricHashing

 

addQuery(GenericDialog, Interest_Point_Registration.RegistrationType) - Method in class spim.process.interestpointregistration.icp.IterativeClosestPoint

 

addRadio(String, String) - Method in class util.ModelessQuestions

 

addRandomBalancedBinaryData(ImageProcessor, FeatureStack, String, String, int) - Method in class trainableSegmentation.WekaSegmentation

Add instances to two classes from a label (binary) image in a random and balanced way.

addRandomBalancedBinaryData(ImageProcessor, ImageProcessor, FeatureStack, String, String, int) - Method in class trainableSegmentation.WekaSegmentation

Add instances to two classes from a label (binary) image in a random and balanced way (with repetition).

addRandomBalancedBinaryData(List<Point3f>[], FeatureStackArray, String, String, int) - Method in class trainableSegmentation.WekaSegmentation

Add instances to two classes from lists of coordinates in a random and balanced way.

addRandomBalancedBinaryData(List<Point3f>[], FeatureStackArray, ImagePlus, String, String, int) - Method in class trainableSegmentation.WekaSegmentation

Add instances to two classes from lists of coordinates in a random and balanced way.

addRandomBalancedBinaryData(ImageProcessor, ImageProcessor, ImageProcessor, FeatureStack, String, String, int) - Method in class trainableSegmentation.WekaSegmentation

Add instances to two classes from a label (binary) image in a random and balanced way (with repetition).

addRandomBalancedBinaryData(ImagePlus, ImagePlus, String, String, int) - Method in class trainableSegmentation.WekaSegmentation

Add binary training data from input and label images in a random and balanced way (same number of samples per class).

addRandomBalancedBinaryData(ImagePlus, ImagePlus, String, String, int, ImagePlus) - Method in class trainableSegmentation.WekaSegmentation

Add binary training data from input and label images in a random and balanced way (same number of samples per class).

addRandomBalancedBinaryData(ImagePlus, ImagePlus, String, String, int, ImagePlus, ImagePlus) - Method in class trainableSegmentation.WekaSegmentation

Add binary training data from input and label images in a random and balanced way (same number of samples per class).

addRandomBalancedBinaryData(ImagePlus, ImagePlus, ImagePlus, String, String, int) - Method in class trainableSegmentation.WekaSegmentation

Add binary training data from input and label images in a random and balanced way (same number of samples per class).

addRandomBalancedLabeledData(ImageProcessor, FeatureStack, int) - Method in class trainableSegmentation.WekaSegmentation

Add instances from a labeled image in a random and balanced way.

addRandomBalancedLabeledData(ImageProcessor, int[], FeatureStack, int) - Method in class trainableSegmentation.WekaSegmentation

Add instances from a labeled image in a random and balanced way.

addRandomBalancedLabeledData(ImageProcessor, FeatureStack, String[], int) - Method in class trainableSegmentation.WekaSegmentation

Add instances reading the pixel classes from a label image in a random and balanced way.

addRandomBalancedLabeledData(ImagePlus, ImagePlus, int) - Method in class trainableSegmentation.WekaSegmentation

Add training data from input and labeled images in a random and balanced way (same number of samples per class).

addRandomBalancedLabeledData(ImagePlus, ImagePlus, int[], int) - Method in class trainableSegmentation.WekaSegmentation

Add training data from input and labeled images in a random and balanced way (same number of samples per class).

addRandomBalancedLabeledData(ImagePlus, ImagePlus, String[], int) - Method in class trainableSegmentation.WekaSegmentation

Add training data from input and labeled images in a random and balanced way (same number of samples per class).

addRandomData(ImagePlus, FeatureStack, String, int) - Method in class trainableSegmentation.WekaSegmentation

Add instances defined by a label (binary) image in a random way.

addRandomData(ImagePlus, ImagePlus, String, int) - Method in class trainableSegmentation.WekaSegmentation

Add training data from input and a binary label image in a random way.

addRANSACCorrespondence(T) - Method in class mpicbg.spim.registration.detection.DetectionView

 

addRANSACCorrespondence(T, double) - Method in class mpicbg.spim.registration.detection.DetectionView

 

addRegularizationFields(GenericDialog) - Method in class mpicbg.trakem2.align.Align.Param

 

addRenderTransformListener(TransformListener<AffineTransform3D>) - Method in class bdv.viewer.ViewerPanel

Add a TransformListener to notify about viewer transformation changes.

addRenderTransformListener(TransformListener<AffineTransform3D>, int) - Method in class bdv.viewer.ViewerPanel

Add a TransformListener to notify about viewer transformation changes.

addRGBColorSliders(GenericDialog, Color) - Static method in class ini.trakem2.utils.Utils

 

addRoi - Variable in class siox.SegmentationGUI

 

addRoiListener(RoiListener) - Method in class events.RoiWatcher

 

addRow(ResultsTable) - Method in class util.FindConnectedRegions.Region

 

addSaveAsFileField(GenericDialogPlus, String, String, int) - Static method in class bdv.ij.util.PluginHelper

 

addSaveAsFileField(GenericDialogPlus, String, String, int) - Static method in class spim.fiji.plugin.resave.PluginHelper

 

addScrollBars(Container) - Static method in class loci.plugins.util.WindowTools

Adds AWT scroll bars to the given container.

addScrollBars(Container) - Static method in class spim.fiji.plugin.util.GUIHelper

A copy of Curtis's method https://github.com/openmicroscopy/bioformats/blob/v4.4.8/components/loci-plugins/src/loci/plugins/util/WindowTools.java#L72

addScrollListener(ImagePlus, AdjustmentListener, MouseWheelListener) - Static method in class sc.fiji.i5d.Main

 

addSection(List<Document>, DocumentBuilder, File) - Static method in class edu.utexas.clm.reconstructreader.reconstruct.ReconstructTranslator

 

addSelectionChangeListener(SelectionChangeListener) - Method in class fiji.plugin.trackmate.SelectionModel

 

addSeries(XYEdgeSeries) - Method in class fiji.plugin.trackmate.util.XYEdgeSeriesCollection

 

addSetup(SpimRegistrationSequence, int, String, String) - Method in class bdv.ij.export.SetupAggregator

Deprecated.

addSetup(SpimRegistrationSequence, int, int[][], int[][]) - Method in class bdv.ij.export.SetupAggregator

Deprecated.

addSetup(ConverterSetup) - Method in class bdv.tools.brightness.MinMaxGroup

Add a ConverterSetup which will have its display range updated to the interval (BoundedIntervalDouble.getMinBoundedValue(), BoundedIntervalDouble.getMaxBoundedValue()).

addSetup(ConverterSetup) - Method in class bdv.tools.brightness.SetupAssignments

Deprecated.

Add the setup in a new group.

addSetups(SpimRegistrationSequence, String, String) - Method in class bdv.ij.export.SetupAggregator

Deprecated.

addSetups(SpimRegistrationSequence, int[][], int[][]) - Method in class bdv.ij.export.SetupAggregator

Deprecated.

addSetups(FusionResult, String, String) - Method in class bdv.ij.export.SetupAggregator

Deprecated.

addSetups(FusionResult, int[][], int[][]) - Method in class bdv.ij.export.SetupAggregator

Deprecated.

addShape(Shape, T, int[]) - Method in class mpicbg.imglib.container.shapelist.ShapeList

 

addSibling(Displayable, Displayable) - Method in class ini.trakem2.tree.ProjectTree

Finds the node for the elder and adds the sibling next to it, under the same parent.

addSIFTFields(GenericDialog) - Method in class mpicbg.trakem2.align.Align.Param

 

addSilently(DBObject) - Method in class ini.trakem2.display.Layer

Used for reconstruction purposes.

addSilently(Layer) - Method in class ini.trakem2.display.LayerSet

Add a new Layer silently, ordering by z as well.

addSilently(ZDisplayable) - Method in class ini.trakem2.display.LayerSet

Used for reconstruction purposes, avoids repainting or updating.

addSimplePoints(ArrayList<Point>, ArrayList<Point>) - Method in class mpicbg.pointdescriptor.test.TestPointDescriptor

 

addSlice(String, Object) - Method in class ini.trakem2.imaging.LayerStack

Does nothing.

addSlice(String, ImageProcessor) - Method in class ini.trakem2.imaging.LayerStack

Does nothing.

addSlice(String, ImageProcessor, int) - Method in class ini.trakem2.imaging.LayerStack

Does nothing.

addSlice(String) - Method in class ini.trakem2.imaging.LazyVirtualStack

 

addSlice(Callable<ImageProcessor>) - Method in class ini.trakem2.imaging.LazyVirtualStack

 

addSlice(String, ImageProcessor) - Method in class mpicbg.imglib.image.display.imagej.ImageJVirtualDisplay

Adds the image in 'ip' to the end of the stack.

addSlice(String, ImageProcessor, int) - Method in class mpicbg.imglib.image.display.imagej.ImageJVirtualDisplay

Adds the image in 'ip' to the stack following slice 'n'.

addSlice(String, ImageProcessor) - Method in class mpicbg.imglib.image.display.imagej.ImageJVirtualStack

Adds the image in 'ip' to the end of the stack.

addSlice(String, ImageProcessor, int) - Method in class mpicbg.imglib.image.display.imagej.ImageJVirtualStack

Adds the image in 'ip' to the stack following slice 'n'.

addSlice(String) - Method in class sc.fiji.i5d.I5DVirtualStack

Adds an image to the end of the stack.

addSlice(String, Object) - Method in class sc.fiji.i5d.I5DVirtualStack

Does nothing.

addSlice(String, ImageProcessor) - Method in class sc.fiji.i5d.I5DVirtualStack

Does nothing..

addSlice(String, ImageProcessor, int) - Method in class sc.fiji.i5d.I5DVirtualStack

Does noting.

addSlice(String) - Method in class spimopener.SPIMRegularStack

 

addSlice(ImageProcessor) - Method in class spimopener.SPIMRegularStack

 

addSlice(String) - Method in class spimopener.SPIMStack

 

addSlice(ImageProcessor) - Method in class spimopener.SPIMStack

 

addSlice(String) - Method in class spimopener.SPIMVirtualStack

Adds an image to the end of the stack.

addSlice(ImageProcessor) - Method in class spimopener.SPIMVirtualStack

 

addSlice(String, Object) - Method in class spimopener.SPIMVirtualStack

Does nothing.

addSlice(String, ImageProcessor) - Method in class spimopener.SPIMVirtualStack

Does nothing..

addSlice(String, ImageProcessor, int) - Method in class spimopener.SPIMVirtualStack

Does noting.

addSlice(int, ImageProcessor) - Method in class video.VideoStack

 

addSlice(String) - Method in class video2.WritableVirtualStack

Adds a slice to the end of the stack.

addSlice(String, Object) - Method in class video2.WritableVirtualStack

Adds a slice with the given pixels to the end of the stack.

addSlice(String, ImageProcessor) - Method in class video2.WritableVirtualStack

Adds the given ImageProcessor as a slice to the end of the stack.

addSlice(String, ImageProcessor, int) - Method in class video2.WritableVirtualStack

Adds the given ImageProcessor as a slice at the specified position in the stack.

addSliceListener(SliceListener) - Method in class events.SliceWatcher

 

addSource(SourceAndConverter<?>) - Method in class bdv.viewer.BasicViewerState

Add source to the state.

addSource(int) - Method in class bdv.viewer.state.SourceGroup

Deprecated.

 

addSource(SourceAndConverter<?>) - Method in class bdv.viewer.state.ViewerState

Deprecated.

 

addSource(SourceAndConverter<?>) - Method in class bdv.viewer.SynchronizedViewerState

Add source to the state.

addSource(SourceAndConverter<?>) - Method in class bdv.viewer.ViewerPanel

Deprecated.

Modify ViewerPanel.state() directly

addSource(SourceAndConverter<?>) - Method in interface bdv.viewer.ViewerState

Add source to the state (optional operation).

addSources(Collection<? extends SourceAndConverter<?>>) - Method in class bdv.viewer.BasicViewerState

Add all sources in collection to the state.

addSources(Collection<? extends SourceAndConverter<?>>) - Method in class bdv.viewer.SynchronizedViewerState

Add all sources in collection to the state.

addSources(Collection<SourceAndConverter<?>>) - Method in class bdv.viewer.ViewerPanel

Deprecated.

Modify ViewerPanel.state() directly

addSources(Collection<? extends SourceAndConverter<?>>) - Method in interface bdv.viewer.ViewerState

Add all sources in collection to the state (optional operation).

addSourcesToGroup(Collection<? extends SourceAndConverter<?>>, SourceGroup) - Method in class bdv.viewer.BasicViewerState

Add all sources in collection to group.

addSourcesToGroup(Collection<? extends SourceAndConverter<?>>, SourceGroup) - Method in class bdv.viewer.SynchronizedViewerState

Add all sources in collection to group.

addSourcesToGroup(Collection<? extends SourceAndConverter<?>>, SourceGroup) - Method in interface bdv.viewer.ViewerState

Add all sources in collection to group (optional operation).

addSourceToGroup(SourceAndConverter<?>, SourceGroup) - Method in class bdv.viewer.BasicViewerState

Add source to group.

addSourceToGroup(SourceAndConverter<?>, SourceGroup) - Method in class bdv.viewer.SynchronizedViewerState

Add source to group.

addSourceToGroup(SourceAndConverter<?>, SourceGroup) - Method in interface bdv.viewer.ViewerState

Add source to group (optional operation).

addSourceToGroup(int, int) - Method in class bdv.viewer.VisibilityAndGrouping

Deprecated.

addSphere() - Method in class ij3d.Executer

 

addSphere(Image3DUniverse) - Static method in class ij3d.gui.PrimitiveDialogs

 

addSphere(String, String, String) - Static method in class ij3d.ImageJ3DViewer

Add a sphere into the current 3D universe

addSphere(String, double, double, double, Color, double) - Method in class tracing.SimpleNeuriteTracer

 

addSpot(Spot) - Method in class fiji.plugin.trackmate.ModelChangeEvent

 

addSpotAnalyzerFactory(SpotAnalyzerFactory<?>) - Method in class fiji.plugin.trackmate.Settings

Adds a SpotAnalyzerFactory to the List of spot analyzers configured.

addSpotAnalyzerFactory(int, SpotAnalyzerFactory<?>) - Method in class fiji.plugin.trackmate.Settings

Adds a SpotAnalyzerFactory to the List of spot analyzers configured, at the specified index.

addSpotFilter(FeatureFilter) - Method in class fiji.plugin.trackmate.Settings

Add a filter to the list of spot filters.

addSpotTo(Spot, Integer) - Method in class fiji.plugin.trackmate.Model

Adds a single spot to the collections managed by this model, mark it as visible, then update its features.

addSpotToSelection(Spot) - Method in class fiji.plugin.trackmate.SelectionModel

 

addSpotToSelection(Collection<Spot>) - Method in class fiji.plugin.trackmate.SelectionModel

 

addSpring(Vertex, Spring) - Method in class mpicbg.models.Vertex

Add a Spring connecting this Vertex with another Vertex.

addSpring(Vertex, double[]) - Method in class mpicbg.models.Vertex

Add a Spring connecting this Vertex with another Vertex.

addSpring(Vertex, double[], double) - Method in class mpicbg.models.Vertex

Add a Spring connecting this Vertex with another Vertex.

addSpring(Vertex, double) - Method in class mpicbg.models.Vertex

Add a Spring connecting this Vertex with another Vertex.

addSpring(Vertex, double, double) - Method in class mpicbg.models.Vertex

Add a Spring connecting this Vertex with another Vertex.

addStandardFunctions() - Method in class fiji.expressionparser.ImgLibParser

 

addStateListener(ClusterStateListener) - Method in class edu.utexas.clm.archipelago.Cluster

 

addStatusListener(StatusListener) - Method in class loci.plugins.in.ImagePlusReader

 

addStatusListener(StatusListener) - Method in class loci.plugins.in.ImportProcess

 

addStatusListener(StatusListener) - Method in class mpicbg.imglib.io.ImageOpener

Adds a listener to those informed when progress occurs.

addStringField(String, String, int) - Method in class fiji.util.gui.GenericDialogPlus

 

addStructure(double, double) - Method in class trainableSegmentation.FeatureStack

Add structure tensor features to current stack It computes, for all pixels in the input image, the eigenvalues of the so-called structure tensor.

addSurfacePlot(ImagePlus) - Method in class ij3d.Image3DUniverse

Add a new image as a content, displaying it as a 2D surface plot.

addSurfacePlot(ImagePlus, int) - Method in class ij3d.Image3DUniverse

Add a new image as a content, displaying it as a 2D surface plot.

addSurfacePlot(ImagePlus, Color3f, String, int, boolean[], int) - Method in class ij3d.Image3DUniverse

Add a new image as a content, displaying it as a 2D surface plot.

AddSymbol(long, long) - Method in class customnode.u3d.ContextManager

 

addTab(String, Component) - Method in class ini.trakem2.display.Display

Returns the tab index in this Display's JTabbedPane.

addTag(Tag) - Method in class ini.trakem2.display.Node

 

addTag(Tag) - Method in interface ini.trakem2.display.Taggable

 

addTarget(float, float, long, float) - Method in class ini.trakem2.display.Connector

 

addTarget(double, double, long, double) - Method in class ini.trakem2.display.Connector

 

addText(String, Transform3D, Appearance) - Method in class ij3d.shapes.CoordinateSystem

 

addText3D(Text3D[]) - Method in class jRenderer3D.JRenderer3D

Adds an array of text to the 3D scene.

addText3D(String, int, int, int, Color, int) - Method in class jRenderer3D.JRenderer3D

Adds a text to the 3D scene.

addText3D(String, int, int, int, int, int) - Method in class jRenderer3D.JRenderer3D

Adds a text to the 3D scene.

addText3D(Text3D) - Method in class jRenderer3D.JRenderer3D

Adds a single 3D text to the 3D scene.

addTextField(String, int, String) - Method in class util.ModelessQuestions

 

addTextPair3D(Text3D, Text3D) - Method in class jRenderer3D.JRenderer3D

 

addTile(Tile<?>) - Method in class mpicbg.models.TileConfiguration

Add a single Tile.

addTile(TileSPIM) - Method in class mpicbg.spim.mpicbg.TileConfigurationSPIM

Add a single Tile.

addTile(Tile) - Method in class stitching.model.TileConfiguration

Add a single tile.

addTiles(Collection<? extends Tile<?>>) - Method in class mpicbg.models.TileConfiguration

Add a Collection of Tiles.

addTiles(TileConfiguration) - Method in class mpicbg.models.TileConfiguration

Add all Tiles of another TileConfiguration.

addTiles(Collection<? extends TileSPIM>) - Method in class mpicbg.spim.mpicbg.TileConfigurationSPIM

Add a Collection of Tiles.

addTiles(TileConfigurationSPIM) - Method in class mpicbg.spim.mpicbg.TileConfigurationSPIM

Add all Tiles of another TileConfiguration.

addTiles(Collection<Tile>) - Method in class stitching.model.TileConfiguration

Add a collection of tiles.

addTilesAsRois - Variable in class mpicbg.stitching.StitchingParameters

 

AddTime(byte[], int, int, int, int, int) - Method in class view5d.View5D

 

AddTime(short[], int, int, int, int, int) - Method in class view5d.View5D

 

AddTime(char[], int, int, int, int, int) - Method in class view5d.View5D

 

AddTime(float[], int, int, int, int, int) - Method in class view5d.View5D

 

AddTime(double[], int, int, int, int, int) - Method in class view5d.View5D

 

AddTimeC(float[], int, int, int, int, int) - Method in class view5d.View5D

 

addTimelapseFromFile() - Method in class ij3d.Executer

 

addTimelapseFromFolder() - Method in class ij3d.Executer

 

addTimelapseFromHyperstack(ImagePlus) - Method in class ij3d.Executer

 

addTimelapseListener(TimelapseListener) - Method in class ij3d.Image3DUniverse

 

addTimePointListener(TimePointListener) - Method in class bdv.viewer.ViewerPanel

Add a TimePointListener to notify about time-point changes.

addTimePointListener(TimePointListener, int) - Method in class bdv.viewer.ViewerPanel

Add a TimePointListener to notify about time-point changes.

addTo(Bdv) - Method in class bdv.util.BdvOptions

When showing content using one of the BdvFunctions methods, this option can be given to specify that the content should be added to an existing window.

addTo() - Method in class bdv.util.BdvOptions.Values

 

addTo3DViewer(Image3DUniverse, Color, ImagePlus) - Method in class tracing.Path

 

addTo3DViewer(Image3DUniverse, Color3f, ImagePlus) - Method in class tracing.Path

 

addTo3DViewer(Path) - Method in class tracing.PathAndFillManager

 

addToActionMap(ActionMap, BigWarpViewerFrame, int) - Static method in class bdv.viewer.WarpNavigationActions

 

addToDatabase(DBObject) - Method in class ini.trakem2.persistence.DBLoader

 

addToDatabase() - Method in class ini.trakem2.persistence.DBObject

 

addToDatabase(DBObject) - Method in class ini.trakem2.persistence.FSLoader

 

addToDatabase(DBObject) - Method in class ini.trakem2.persistence.Loader

 

addToDatabase(Project) - Method in class ini.trakem2.tree.TemplateThing

Recursive into children! Will add the attributes as well and grab an id for this instance.

addToLinkLater(Node<T>) - Method in class ini.trakem2.display.Tree

 

addToResultsTable() - Method in class tracing.ShollAnalysisDialog.ShollResults

 

addToRoiManager(int, Roi) - Method in class sc.fiji.timelapse.LOI_Interpolator

 

addToViewer() - Method in class bdv.tools.boundingbox.TransformedBoxOverlaySource

 

addTrace(String, String) - Static method in class trainableSegmentation.Weka_Segmentation

Add the current ROI to a specific class and slice.

addTrackAnalyzer(TrackAnalyzer) - Method in class fiji.plugin.trackmate.Settings

Adds a TrackAnalyzer to the List of track analyzers configured.

addTrackAnalyzer(int, TrackAnalyzer) - Method in class fiji.plugin.trackmate.Settings

Adds a TrackAnalyzer to the List of track analyzers configured, at the specified index.

addTrackFilter(FeatureFilter) - Method in class fiji.plugin.trackmate.Settings

Add a filter to the list of track filters.

addTransformListener(TransformListener<AffineTransform3D>) - Method in class bdv.viewer.render.TransformAwareBufferedImageOverlayRenderer

Add a TransformListener to notify about viewer transformation changes.

addTransformListener(TransformListener<AffineTransform3D>, int) - Method in class bdv.viewer.render.TransformAwareBufferedImageOverlayRenderer

Add a TransformListener to notify about viewer transformation changes.

addTransformListener(TransformListener<AffineTransform3D>) - Method in interface bdv.viewer.render.TransformAwareRenderTarget

 

addTransformListener(TransformListener<AffineTransform3D>, int) - Method in interface bdv.viewer.render.TransformAwareRenderTarget

 

addTransformListener(TransformListener<AffineTransform3D>) - Method in class bdv.viewer.ViewerPanel

Add a TransformListener to notify about viewer transformation changes.

addTransformListener(TransformListener<AffineTransform3D>, int) - Method in class bdv.viewer.ViewerPanel

Add a TransformListener to notify about viewer transformation changes.

addTransformListener(TransformListener<InvertibleRealTransform>) - Method in class bigwarp.BigWarp

 

addTransformStep(Layer) - Method in class ini.trakem2.display.LayerSet

Add an undo step for the transformations of all Displayable in the layer.

addTransformStep(List<Layer>) - Method in class ini.trakem2.display.LayerSet

 

addTransformStep(Collection<? extends Displayable>) - Method in class ini.trakem2.display.LayerSet

Add an undo step for the transformations of all Displayable in hs.

addTransformStep() - Method in class ini.trakem2.display.LayerSet

Add an undo step for the transformations of all Displayable in all layers.

addTransformStepWithData(Collection<? extends Displayable>) - Method in class ini.trakem2.display.LayerSet

Add an undo step for the transformations of all Displayable in col, with data as well (for Patch, data includes the CoordinateTransform).

addTransformStepWithDataForAll(Collection<Layer>) - Method in class ini.trakem2.display.LayerSet

Includes all ZDisplayable that paint at any of the given layers.

addTreeModelListener(TreeModelListener) - Method in class bdv.ui.sourcegrouptree.SourceGroupTreeModel

Adds a listener for the TreeModelEvent posted after the tree changes.

addTriangle(Point3f, Point3f, Point3f) - Method in class customnode.CustomTriangleMesh

 

addTriangle(ArrayList<PointMatch>) - Method in class mpicbg.models.TransformMesh

Add a triangle defined by 3 PointMatches that defines an AffineTransform2D.

addTriangleMesh(List<Point3f>, Color3f, String) - Method in class ij3d.Image3DUniverse

Add a custom mesh, in particular a triangle mesh, to the universe.

addTriangleMesh(List<Point3f>, List<Color3f>, String) - Method in class ij3d.Image3DUniverse

Add a custom mesh, in particular a triangle mesh, to the universe.

addTriangles(Point3f[]) - Method in class customnode.CustomTriangleMesh

 

addTube() - Method in class ij3d.Executer

 

addTube(Image3DUniverse) - Static method in class ij3d.gui.PrimitiveDialogs

 

addTubePoint(String) - Static method in class ij3d.ImageJ3DViewer

Add a point to the list that will conform a tube into the current 3D universe

addUndoMoveStep(Displayable) - Method in class ini.trakem2.display.LayerSet

To undo moving up/down/top/bottom.

addUndoStep(DoStep) - Method in class ini.trakem2.display.LayerSet

 

addUniqueType(TemplateThing) - Method in class ini.trakem2.Project

Returns false if the type exists already.

addUniverseListener(UniverseListener) - Method in class ij3d.DefaultUniverse

Register the specified UniverseListener

addUnseenChildrenOf(V) - Method in class fiji.plugin.trackmate.graph.SortedDepthFirstIterator

This is where we add the multiple children in proper sorted order.

addUnseenChildrenOf(Spot) - Method in class fiji.plugin.trackmate.graph.TimeDirectedDepthFirstIterator

 

addUnseenChildrenOf(Spot) - Method in class fiji.plugin.trackmate.graph.TimeDirectedSortedDepthFirstIterator

 

addUnsignedShortSlice(String, Object) - Method in class mpicbg.imglib.image.display.imagej.ImageJVirtualDisplay

Obsolete.

addUnsignedShortSlice(String, Object) - Method in class mpicbg.imglib.image.display.imagej.ImageJVirtualStack

Obsolete.

addUpdateListener(VisibilityAndGrouping.UpdateListener) - Method in class bdv.viewer.VisibilityAndGrouping

Deprecated.

addUThresh(double) - Method in class view5d.My3DData

 

addValue(double, int, double[]) - Method in class mpicbg.stitching.fusion.AveragePixelFusion

 

addValue(double, int, double[]) - Method in class mpicbg.stitching.fusion.AveragePixelFusionIgnoreZero

 

addValue(double, int, double[]) - Method in class mpicbg.stitching.fusion.BlendingPixelFusion

 

addValue(double, int, double[]) - Method in class mpicbg.stitching.fusion.BlendingPixelFusionIgnoreZero

 

addValue(double, int, double[]) - Method in class mpicbg.stitching.fusion.MaxPixelFusion

 

addValue(double, int, double[]) - Method in class mpicbg.stitching.fusion.MaxPixelFusionIgnoreZero

 

addValue(double, int, double[]) - Method in class mpicbg.stitching.fusion.MedianPixelFusion

 

addValue(double, int, double[]) - Method in class mpicbg.stitching.fusion.MedianPixelFusionIgnoreZero

 

addValue(double, int, double[]) - Method in class mpicbg.stitching.fusion.MinPixelFusion

 

addValue(double, int, double[]) - Method in class mpicbg.stitching.fusion.MinPixelFusionIgnoreZero

 

addValue(double, int, double[]) - Method in class mpicbg.stitching.fusion.OverlapFusion

 

addValue(double, int, double[]) - Method in interface mpicbg.stitching.fusion.PixelFusion

add a new value for the current output pixel

addVariance(float) - Method in class trainableSegmentation.FeatureStack

Add variance-filtered image to the stack (single thread version)

addVertex(Point3f) - Method in class customnode.FullInfoMesh

 

addVertex(Image3DUniverse, Color3f, float, float, float) - Method in class MC_Test

 

addVertex(Vertex, double) - Method in class mpicbg.models.SpringMesh

Add a Vertex to the mesh.

addVertex(Vertex) - Method in class sc.fiji.analyzeSkeleton.Graph

Add vertex to the graph.

addVertex(Extract_Surface.SurfaceVoxel) - Method in class vib.Extract_Surface

 

addVertexWeightedByDistance(Vertex, double, double) - Method in class mpicbg.models.SpringMesh

Add a Vertex to the mesh.

addVertices(Point3f[]) - Method in class customnode.CustomIndexedTriangleMesh

 

addVertices(Point3f[]) - Method in class customnode.CustomMesh

 

addVerticesToGeometryArray(Point3f[]) - Method in class customnode.CustomIndexedTriangleMesh

 

addVerticesToGeometryArray(Point3f[]) - Method in class customnode.CustomMesh

 

addVerticesToGeometryStripArray(Point3f[]) - Method in class customnode.CustomIndexedTriangleMesh

 

addVerticesToGeometryStripArray(Point3f[]) - Method in class customnode.CustomMesh

 

addView(TrackMateModelView) - Method in class fiji.plugin.trackmate.gui.TrackMateGUIModel

Adds the specified TrackMateModelView to the collection of views managed by this GUI.

addVirtualMatch(PointMatch) - Method in class mpicbg.trakem2.align.AbstractAffineTile2D

 

addVisibilityChangeListener(PlaceHolderOverlayInfo.VisibilityChangeListener) - Method in class bdv.util.PlaceHolderOverlayInfo

Deprecated.

Use visibilityChangeListeners().add(listener) instead.

addVisitor(Visitor) - Method in class org.janelia.thickness.inference.visitor.ListVisitor

 

addVisitor(String, Visitor) - Static method in class org.janelia.thickness.plugin.ZPositionCorrection

 

addVisitor(String, ZPositionCorrection.VisitorFactory) - Static method in class org.janelia.thickness.plugin.ZPositionCorrection

 

addVoltex(ImagePlus) - Method in class ij3d.Image3DUniverse

Add a new image as a content, displaying it as a volume rendering.

addVoltex(ImagePlus, int) - Method in class ij3d.Image3DUniverse

Add a new image as a content, displaying it as a volume rendering.

addVoltex(ImagePlus, Color3f, String, int, boolean[], int) - Method in class ij3d.Image3DUniverse

Add a new image as a content, displaying it as a volume rendering.

addVolume(String, String, String, String, String, String, String) - Static method in class ij3d.ImageJ3DViewer

 

addVolumeColor(Color) - Method in class volumeCalculator.Volumes

The user has created another Volume Color.

addVoxel(int, int, int, int, boolean, float) - Method in class Utilities.Object3D

Adds a new voxel to the specified Object3D, at the next available slot in the object.

addWarning(String, String) - Method in class sc.fiji.coloc.algorithms.Algorithm

Adds a warning to the list of warnings.

addWebsite(GenericDialog) - Static method in class spim.fiji.plugin.util.GUIHelper

 

addWebsite(GenericDialog, String) - Static method in class spim.fiji.plugin.util.GUIHelper

 

addWeight(double) - Method in class mpicbg.models.Spring

 

addWindowList(GenericDialog, String, boolean) - Static method in class amira.AmiraParameters

 

addWorkload(int) - Static method in class bunwarpj.ProgressBar

Extend the amount of work to perform by batch.

addWorldAreaTo(Node<?>, Area) - Method in class ini.trakem2.display.AreaTree

Assumes nd is an AreaNode.

addZDisplayable(ZDisplayable) - Method in class ini.trakem2.display.LayerSet

Useful for typeless scripts so that a ZDisplayable can be added; the overloaded method add(Layer) and add(ZDisplayable) is not distinguishable otherwise.

ADJUST_BOTH - Static variable in class ij3d.ViewAdjuster

Fit the points both horizontally and vertically

ADJUST_HORIZONTAL - Static variable in class ij3d.ViewAdjuster

Fit the points horizontally

ADJUST_VERTICAL - Static variable in class ij3d.ViewAdjuster

Fit the points vertically

adjustChannels(ImagePlus, boolean[]) - Static method in class ij3d.ColorTable

 

adjustChannels(Image) - Method in class ini.trakem2.display.Patch

Takes an image and scales its channels according to the values packed in this.channels.

adjustChannels(Patch, int) - Method in class ini.trakem2.persistence.Loader

 

adjustColorMapLThresh(double) - Method in class view5d.My3DData

 

adjustColorMapUThresh(double) - Method in class view5d.My3DData

 

adjustColumn(int) - Method in class sc.fiji.hdf5.TableColumnAdjuster

 

adjustColumns() - Method in class sc.fiji.hdf5.TableColumnAdjuster

 

adjustConfidence(int) - Method in class ini.trakem2.display.Node

Adjust the confidence value of this node with its parent.

adjustDimensions() - Method in class ini.trakem2.display.DisplayCanvas

Adjust srcRect and internal variables to the canvas' bounds.

adjustDisplayedImage(RandomAccessibleInterval<? extends RealType<?>>) - Method in class sc.fiji.coloc.results.SingleWindowDisplay

 

adjustEdgeConfidence(int, float, float, Layer, DisplayCanvas) - Method in class ini.trakem2.display.Tree

Expects world coordinates.

AdjustedRandError - Class in trainableSegmentation.metrics

This class implements the adjusted Rand error, defined as the 1 - adjusted Rand index.

AdjustedRandError(ImagePlus, ImagePlus) - Constructor for class trainableSegmentation.metrics.AdjustedRandError

Initialize adjusted Rand error metric.

adjustedRandError(ImageProcessor, ImageProcessor, double) - Static method in class trainableSegmentation.metrics.AdjustedRandError

Calculate the adjusted Rand error between some 2D original labels and the corresponding proposed labels.

adjustedRandIndex(ShortProcessor, ShortProcessor) - Static method in class trainableSegmentation.metrics.AdjustedRandError

Calculate the adjusted Rand index between to clusters, as described by Lawrence Hubert and Phipps Arabie \cite{Rand71}.

adjustGroupProperties(Collection<Displayable>) - Method in class ini.trakem2.display.Display

Pops up a dialog to adjust the alpha, visible, color, locked and compositeMode of all Displayables in col.

adjustImage(Image<FloatType>, float, float) - Static method in class mpicbg.spim.postprocessing.deconvolution2.AdjustInput

Adjusts an image so that the minimal intensity is minValue and the average is average

AdjustInput - Class in mpicbg.spim.postprocessing.deconvolution2

 

AdjustInput() - Constructor for class mpicbg.spim.postprocessing.deconvolution2.AdjustInput

 

AdjustInput - Class in spim.process.fusion.deconvolution

 

AdjustInput() - Constructor for class spim.process.fusion.deconvolution.AdjustInput

 

adjustLight() - Method in class ij3d.Executer

 

adjustLUTs(Content) - Method in class ij3d.Executer

 

adjustMeasurementOptions() - Method in class ini.trakem2.display.Display

 

adjustmentValueChanged(AdjustmentEvent) - Method in class _3D_objects_counter

 

adjustmentValueChanged(AdjustmentEvent) - Method in class fiji.tool.SliceObserver

 

adjustmentValueChanged(AdjustmentEvent) - Method in class fiji.util.CurrentSlice

 

adjustmentValueChanged(AdjustmentEvent) - Method in class ini.trakem2.display.Displayable.SliderListener

 

adjustmentValueChanged(AdjustmentEvent) - Method in class ini.trakem2.display.RollingPanel

Adjust the sublist of displayed DisplayablePanel.

adjustmentValueChanged(AdjustmentEvent) - Method in class IntSlider

 

adjustmentValueChanged(AdjustmentEvent) - Method in class loci.plugins.util.DataBrowser

 

adjustmentValueChanged(AdjustmentEvent) - Method in class mpicbg.spim.segmentation.InteractiveDoG.Sigma2Listener

 

adjustmentValueChanged(AdjustmentEvent) - Method in class mpicbg.spim.segmentation.InteractiveDoG.SigmaListener

 

adjustmentValueChanged(AdjustmentEvent) - Method in class mpicbg.spim.segmentation.InteractiveDoG.ThresholdListener

 

adjustmentValueChanged(AdjustmentEvent) - Method in class mpicbg.spim.segmentation.InteractiveIntegral.Radius1Listener

 

adjustmentValueChanged(AdjustmentEvent) - Method in class mpicbg.spim.segmentation.InteractiveIntegral.Radius2Listener

 

adjustmentValueChanged(AdjustmentEvent) - Method in class mpicbg.spim.segmentation.InteractiveIntegral.ThresholdListener

 

adjustmentValueChanged(AdjustmentEvent) - Method in class OpenImage5DWindow

Handles changes in the scrollbars for z and t.

adjustmentValueChanged(AdjustmentEvent) - Method in class OpenStackWindow

Calls super.updateSliceSelector() and issues a DisplayChangeEvent to registered listeners.

adjustmentValueChanged(AdjustmentEvent) - Method in class sc.fiji.balloonSegmentation.BalloonSegmentation_

 

adjustmentValueChanged(AdjustmentEvent) - Method in class sc.fiji.i5d.gui.ChannelControl

Executed if scrollbar has been moved.

adjustmentValueChanged(AdjustmentEvent) - Method in class sc.fiji.i5d.gui.Image5DWindow

Handles changes in the scrollbars for z and t.

adjustmentValueChanged(AdjustmentEvent) - Method in class sc.fiji.i5d.gui.ScrollbarWithLabel

 

adjustmentValueChanged(AdjustmentEvent) - Method in class sc.fiji.timelapse.LOI_Interpolator.SliderListener

 

adjustmentValueChanged(AdjustmentEvent) - Method in class Stack_Rotate

 

adjustmentValueChanged(AdjustmentEvent) - Method in class surfaceplot.SurfacePlotGroup

Implements AdjustmentListener interface to automatically update the surface plot when the slice slider in the stack window is dragged.

adjustmentValueChanged(AdjustmentEvent) - Method in class vib.segment.CustomStackWindow

 

adjustmentValueChanged(AdjustmentEvent) - Method in class view5d.ImageCanvas

 

adjustMinAndMaxGUI() - Method in class ini.trakem2.display.Display

 

adjustNodeColors(Node<T>) - Method in class ini.trakem2.display.Tree

 

adjustNodeRadius(float, float, float, Layer, DisplayCanvas) - Method in class ini.trakem2.display.Treeline

 

AdjustOffset() - Method in class view5d.ImgPanel

 

AdjustOffsetToROIMean() - Method in class view5d.My3DData

 

adjustProperties() - Method in class ini.trakem2.display.AreaList

 

adjustProperties() - Method in class ini.trakem2.display.Ball

 

adjustProperties() - Method in class ini.trakem2.display.Display

 

adjustProperties() - Method in class ini.trakem2.display.Displayable

Shows a dialog to adjust properties of this object.

adjustProperties() - Method in class ini.trakem2.display.DLabel

 

adjustProperties() - Method in class ini.trakem2.Project

 

adjustRoiOffset(long[], long[], long[]) - Method in class sc.fiji.coloc.gadgets.DataContainer

Make sure that the ROI offset has the same dimensionality as the image.

adjustRoiSize(long[], long[], long[], long[]) - Method in class sc.fiji.coloc.gadgets.DataContainer

Transforms a ROI size array to a dimensionality.

adjustSegmentationStateToData(Instances) - Method in class trainableSegmentation.WekaSegmentation

Adjust current segmentation state (attributes and classes) to loaded data

adjustSourceRect(double, int, int) - Method in class fiji.util.gui.JImagePanel

 

adjustSourceRectI5d(double, int, int) - Method in class sc.fiji.i5d.gui.Image5DCanvas

 

adjustSrcRect(int, int) - Method in class ini.trakem2.display.DisplayCanvas

Adjust srcRect to new dimensions.

AdjustThresh(int) - Method in class view5d.My3DData

 

AdjustThresh(boolean) - Method in class view5d.My3DData

 

AdjustThresh() - Method in class view5d.My3DData

 

AdjustThreshGlobal() - Method in class view5d.My3DData

 

adjustView() - Method in class ij3d.Image3DUniverse

Fit all contents optimally into the canvas.

adjustView(int) - Method in class ij3d.Image3DUniverse

Fit all contents optimally into the canvas.

adjustView(Iterable<Content>) - Method in class ij3d.Image3DUniverse

Fit the specified contents optimally into the canvas.

adjustView(Iterable<Content>, int) - Method in class ij3d.Image3DUniverse

Fit the specified contents optimally into the canvas.

adjustView(Content, int) - Method in class ij3d.Image3DUniverse

Fit the specified content optimally into the canvas.

adjustView(Content) - Method in class ij3d.Image3DUniverse

Fit the specified content optimally into the canvas.

adt - package adt

 

advance() - Method in class mpicbg.imglib.labeling.LocalizableLabelingCursor

 

advanced - Variable in class mpicbg.imglib.labeling.LocalizableLabelingCursor

 

ADVANCED - Variable in class org.imagearchive.lsm.toolbox.info.LUTInfo

 

advanced - Static variable in class register_virtual_stack.Register_Virtual_Stack_MT

advance options flag

advanceElement(int) - Method in class view5d.My3DData

 

AdvancePos() - Method in class view5d.ImgPanel

 

advanceTime(int) - Method in class view5d.My3DData

 

ADVECTION_FORCE - Variable in class levelsets.algorithm.ActiveContours

 

affine - Variable in class bdv.BehaviourTransformEventHandler3D

Current source to screen transform.

AFFINE - Static variable in class bdv.gui.TransformTypeSelectDialog

 

affine - Variable in class bdv.util.BehaviourTransformEventHandlerPlanar

Current source to screen transform.

affine() - Method in class bigwarp.BigWarp

Returns an AffineGet that represents the the transform if the transform is linear, or is the affine part of the transform if it is non-linear.

affine - Variable in class lenscorrection.Distortion_Correction.PointMatchCollectionAndAffine

 

AFFINE - Static variable in class Moving_Least_Squares

 

affine - Variable in class mpicbg.models.InterpolatedAffineModel1D

 

affine - Variable in class mpicbg.models.InterpolatedAffineModel2D

 

affine - Variable in class mpicbg.models.InterpolatedAffineModel3D

 

affine - Variable in class mpicbg.spim.data.registration.ViewTransformAffine

 

affine - Variable in class net.imglib2.ui.TransformEventHandler2Dto3D

Current source to screen transform.

AFFINE - Static variable in class register_virtual_stack.Register_Virtual_Stack_MT

affine registration model id

AFFINE - Static variable in class spim.vecmath.Transform3D

An affine matrix can translate, rotate, reflect, scale anisotropically, and shear.

Affine1D<T extends Affine1D<T>> - Interface in mpicbg.models

 

affine2d() - Method in class bigwarp.BigWarp

Returns an AffineTransform2D that represents the the transform if the transform is linear, or is the affine part of the transform if it is non-linear.

Affine2D<T extends Affine2D<T>> - Interface in mpicbg.models

 

Affine2D<N extends NumericType<N>> - Class in script.imglib.algorithm

TODO

Affine2D(Object, Number, Number, Number, Number, Number, Number) - Constructor for class script.imglib.algorithm.Affine2D

Affine transform the image with the best interpolation mode available.

Affine2D(Object, Number, Number, Number, Number, Number, Number, AbstractAffine3D.Mode, Number) - Constructor for class script.imglib.algorithm.Affine2D

Affine transform the image with the best interpolation mode available.

Affine2D(Object, AffineTransform) - Constructor for class script.imglib.algorithm.Affine2D

 

Affine2D(Object, AffineTransform, AbstractAffine3D.Mode) - Constructor for class script.imglib.algorithm.Affine2D

 

Affine2D(Object, AffineTransform, Number) - Constructor for class script.imglib.algorithm.Affine2D

 

Affine2D(Object, AffineTransform, AbstractAffine3D.Mode, Number) - Constructor for class script.imglib.algorithm.Affine2D

 

Affine2D(Object, float, float, float, float, float, float, AbstractAffine3D.Mode, OutOfBoundsStrategyFactory<N>) - Constructor for class script.imglib.algorithm.Affine2D

 

affine3d() - Method in class bigwarp.BigWarp

Returns an AffineTransform3D that represents the the transform if the transform is linear, or is the affine part of the transform if it is non-linear.

affine3d - Variable in class bigwarp.TransformHandler3DWrapping2D

 

Affine3D<T extends Affine3D<T>> - Interface in mpicbg.models

 

Affine3D<T extends NumericType<T>> - Class in script.imglib.algorithm

Performs a mathematically correct transformation of an image.

Affine3D(Image<T>, float[], AbstractAffine3D.Mode) - Constructor for class script.imglib.algorithm.Affine3D

 

Affine3D(Object, float[], AbstractAffine3D.Mode, Number) - Constructor for class script.imglib.algorithm.Affine3D

 

Affine3D(Object, float[], AbstractAffine3D.Mode, OutOfBoundsStrategyFactory<T>) - Constructor for class script.imglib.algorithm.Affine3D

 

Affine3D(Object, float, float, float, float, float, float, AbstractAffine3D.Mode, Number) - Constructor for class script.imglib.algorithm.Affine3D

 

Affine3D(Object, float, float, float, float, float, float, AbstractAffine3D.Mode, OutOfBoundsStrategyFactory<T>) - Constructor for class script.imglib.algorithm.Affine3D

 

Affine3DHelpers - Class in bdv.util

Helpers to extract parts (rotation, scale, etc) from AffineTransform3D.

Affine3DHelpers() - Constructor for class bdv.util.Affine3DHelpers

 

Affine_From_Landmarks - Class in landmarks

 

Affine_From_Landmarks() - Constructor for class landmarks.Affine_From_Landmarks

 

affineDragStart - Variable in class bdv.BehaviourTransformEventHandler3D

Copy of current transform when mouse dragging started.

affineDragStart - Variable in class bdv.util.BehaviourTransformEventHandlerPlanar

Copy of current transform when mouse dragging started.

affineDragStart - Variable in class net.imglib2.ui.TransformEventHandler2Dto3D

Copy of current transform when mouse dragging started.

AffineFromLandmarks - Class in landmarks

 

AffineFromLandmarks() - Constructor for class landmarks.AffineFromLandmarks

 

AffineFromLandmarks.CandidateAffine - Class in landmarks

 

AffineModel1D - Class in mpicbg.models

 

AffineModel1D() - Constructor for class mpicbg.models.AffineModel1D

 

AffineModel2D - Class in mpicbg.models

2d-affine transformation models to be applied to points in 2d-space.

AffineModel2D() - Constructor for class mpicbg.models.AffineModel2D

 

AffineModel2D - Class in mpicbg.trakem2.transform

 

AffineModel2D() - Constructor for class mpicbg.trakem2.transform.AffineModel2D

 

AffineModel3D - Class in mpicbg.models

3d-affine transformation models to be applied to points in 3d-space.

AffineModel3D() - Constructor for class mpicbg.models.AffineModel3D

 

AffineModel3D - Class in mpicbg.trakem2.transform

 

AffineModel3D() - Constructor for class mpicbg.trakem2.transform.AffineModel3D

 

affinePartOfTpsHC() - Method in class bigwarp.BigWarp

Returns the affine part of the thin plate spline model, as a matrix in homogeneous coordinates.

AffineTile2D - Class in mpicbg.trakem2.align

 

AffineTile2D(AffineModel2D, Patch) - Constructor for class mpicbg.trakem2.align.AffineTile2D

 

AffineTile2D(Patch) - Constructor for class mpicbg.trakem2.align.AffineTile2D

 

affineToString() - Method in class bigwarp.BigWarp

 

affineTransform3DElement(String, AffineGet) - Static method in class mpicbg.spim.data.XmlHelpers

 

AffineTransform3DJsonSerializer - Class in bdv.img.remote

 

AffineTransform3DJsonSerializer() - Constructor for class bdv.img.remote.AffineTransform3DJsonSerializer

 

AffineTransformMode - Class in ini.trakem2.display

 

AffineTransformMode(Display) - Constructor for class ini.trakem2.display.AffineTransformMode

 

afs - Variable in class mpicbg.models.InterpolatedAffineModel1D

 

afs - Variable in class mpicbg.models.InterpolatedAffineModel2D

 

afs - Variable in class mpicbg.models.InterpolatedAffineModel3D

 

afterEachPlane(boolean) - Method in interface bdv.export.ExportScalePyramid.AfterEachPlane

Called after a "plane of blocks" is written.

age - Variable in class mpicbg.imglib.algorithm.labeling.Watershed.PixelIntensity

 

ai - package ai

 

ai - Variable in class lenscorrection.DistortionCorrectionTask.AppendCoordinateTransformThread

 

ai - Variable in class lenscorrection.DistortionCorrectionTask.SetCoordinateTransformThread

 

ai - Variable in class mpicbg.trakem2.align.Align.ExtractFeaturesThread

 

ai - Variable in class mpicbg.trakem2.align.Align.MatchFeaturesAndFindModelThread

 

AI1 - Variable in class sc.fiji.io.FIBSEM_Reader.FIBSEMData

 

AI2 - Variable in class sc.fiji.io.FIBSEM_Reader.FIBSEMData

 

AI3 - Variable in class sc.fiji.io.FIBSEM_Reader.FIBSEMData

 

AI4 - Variable in class sc.fiji.io.FIBSEM_Reader.FIBSEMData

 

AIdelay - Variable in class sc.fiji.io.FIBSEM_Reader.FIBSEMData

 

Albert_Test - Class in tracing

 

Albert_Test() - Constructor for class tracing.Albert_Test

 

Algorithm - Interface in mpicbg.imglib.algorithm

TODO

Algorithm<T extends RealType<T>> - Class in sc.fiji.coloc.algorithms

An algorithm is an abstraction of techniques like the calculation of the Persons coefficient or Li'S ICQ.

Algorithm(String) - Constructor for class sc.fiji.coloc.algorithms.Algorithm

 

AlgorithmUtil - Class in script.imglib.algorithm.fn

TODO

AlgorithmUtil() - Constructor for class script.imglib.algorithm.fn.AlgorithmUtil

 

align(ImageProcessor, Line, ImageProcessor, Line) - Static method in class Align_Image

Align an image to another image given line selections in each.

align(ImageProcessor, Line, ImageProcessor, Line, boolean, boolean) - Static method in class Align_Image

Align an image to another image given line selections in each.

align(ViewerPanel.AlignPlane) - Method in class bdv.viewer.BigWarpViewerPanel

 

align(ViewerPanel.AlignPlane) - Method in class bdv.viewer.ViewerPanel

Align the XY, ZY, or XZ plane of the local coordinate system of the currently active source with the viewer coordinate system.

Align - Class in mpicbg.trakem2.align

A collection of methods regarding SIFT-based alignment TODO Bring the methods and tasks into a class for each method and clean up this mess.

Align() - Constructor for class mpicbg.trakem2.align.Align

 

Align.ExtractFeaturesThread - Class in mpicbg.trakem2.align

Extracts SIFT-features from a List of Tiles and saves them to disk.

Align.MatchFeaturesAndFindModelThread - Class in mpicbg.trakem2.align

 

Align.Param - Class in mpicbg.trakem2.align

 

Align.ParamOptimize - Class in mpicbg.trakem2.align

 

Align_Image - Class in <Unnamed>

Select two images with a Line ROI in each, and rotate/translate/scale one to the other.

Align_Image() - Constructor for class Align_Image

 

Align_Image.BilinearInterpolator - Class in <Unnamed>

 

Align_Image.Interpolator - Class in <Unnamed>

 

ALIGN_PLANE - Static variable in class bdv.viewer.NavigationActions

 

ALIGN_PLANE - Static variable in class bdv.viewer.WarpNavigationActions

 

ALIGN_VIEW_TRANSFORMS - Static variable in class bigwarp.BigWarpActions

 

AlignDisplayTo(AnElement) - Method in class view5d.AnElement

 

AlignImage(ImagePlus, ImageProcessor) - Method in class MultipleImageProcessor

 

alignImagesBatch(ImagePlus, ImagePlus, ImageProcessor, ImageProcessor, int, int, int, int, double, double, double, double, double, double) - Static method in class bunwarpj.bUnwarpJ_

Method for images alignment with no graphical interface.

alignImagesBatch(ImagePlus, ImagePlus, ImageProcessor, ImageProcessor, Param) - Static method in class bunwarpj.bUnwarpJ_

Method for images alignment with no graphical interface.

alignImagesBatch(ImagePlus, ImagePlus, ImageProcessor, ImageProcessor, int, int, int, int, double, double, double, double, double, double, double, double) - Static method in class bunwarpj.bUnwarpJ_

Method for images alignment with no graphical interface.

alignLayer(Layer, int) - Static method in class mpicbg.trakem2.align.Align

Align all patches in a Layer.

alignLayers(Layer) - Static method in class mpicbg.trakem2.align.AlignLayersTask

 

alignLayers(Layer, Rectangle) - Static method in class mpicbg.trakem2.align.AlignLayersTask

 

alignLayersLinearly(List<Layer>, int) - Static method in class mpicbg.trakem2.align.Align

Align a range of layers by accumulating pairwise alignments of contiguous layers.

alignLayersLinearly(List<Layer>, int, Filter<Patch>) - Static method in class mpicbg.trakem2.align.Align

Align a range of layers by accumulating pairwise alignments of contiguous layers.

alignLayersLinearlyJob(LayerSet, int, int, boolean, Rectangle, Filter<Patch>) - Static method in class mpicbg.trakem2.align.AlignLayersTask

 

alignLayersNonLinearlyJob(LayerSet, int, int, boolean, Rectangle, Filter<Patch>) - Static method in class mpicbg.trakem2.align.AlignLayersTask

 

AlignLayersTask - Class in mpicbg.trakem2.align

Register a range of layers using linear or non-linear transformations.

alignLayersTask(Layer) - Static method in class mpicbg.trakem2.align.AlignLayersTask

 

alignLayersTask(Layer, Rectangle) - Static method in class mpicbg.trakem2.align.AlignLayersTask

 

AlignmentUtils - Class in mpicbg.trakem2.align

 

AlignmentUtils.ParamPointMatch - Class in mpicbg.trakem2.align

 

alignMultiLayerMosaic(Layer, Patch) - Static method in class mpicbg.trakem2.align.AlignTask

Align a multi-layer mosaic.

alignMultiLayerMosaicTask(Layer) - Static method in class mpicbg.trakem2.align.AlignTask

 

alignMultiLayerMosaicTask(Layer, Patch) - Static method in class mpicbg.trakem2.align.AlignTask

 

alignMultiLayerMosaicTask(List<Layer>, Patch, Align.Param, Align.ParamOptimize, Align.ParamOptimize, boolean, boolean, boolean, boolean, boolean) - Static method in class mpicbg.trakem2.align.AlignTask

 

alignPatches(List<Patch>, Set<Patch>, int) - Static method in class mpicbg.trakem2.align.AlignTask

 

alignPatches(Align.ParamOptimize, List<Patch>, Collection<Patch>, boolean, boolean, boolean, boolean, boolean) - Static method in class mpicbg.trakem2.align.AlignTask

 

alignPatches(Align.ParamOptimize, List<Patch>, Collection<Patch>, boolean, boolean, boolean, boolean) - Static method in class mpicbg.trakem2.align.AlignTask

 

alignPatchesTask(List<Patch>, Set<Patch>) - Static method in class mpicbg.trakem2.align.AlignTask

 

alignPlaneAction(ViewerPanel, ViewerPanel.AlignPlane, String...) - Method in class bdv.viewer.NavigationActions

 

AlignPlaneAction(ViewerPanel, ViewerPanel.AlignPlane) - Constructor for class bdv.viewer.WarpNavigationActions.AlignPlaneAction

 

alignPlanes(ViewerPanel) - Method in class bdv.viewer.NavigationActions

 

alignSelectedPatches(Selection, int) - Static method in class mpicbg.trakem2.align.Align

Align a selection of patches in a Layer.

alignSelection(Selection, int) - Static method in class mpicbg.trakem2.align.AlignTask

 

alignSelectionTask(Selection) - Static method in class mpicbg.trakem2.align.AlignTask

 

AlignStacksWithLandmarks - Class in mpicbg.ij.plugin

 

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

 

AlignTask - Class in mpicbg.trakem2.align

Methods collection to be called from the GUI for alignment tasks.

AlignTask() - Constructor for class mpicbg.trakem2.align.AlignTask

 

AlignTask.ReferenceData - Class in mpicbg.trakem2.align

 

alignTileCollections(Align.Param, Collection<AbstractAffineTile2D<?>>, Collection<AbstractAffineTile2D<?>>) - Static method in class mpicbg.trakem2.align.Align

Align two collections of tiles

alignTiles(Align.ParamOptimize, List<AbstractAffineTile2D<?>>, List<AbstractAffineTile2D<?>>, boolean, int) - Static method in class mpicbg.trakem2.align.Align

Align a set of tiles using the following procedure: Extract SIFT-features from all tiles. Establish point-correspondences from consistent sets of feature matches among tile pairs, optionally inspect only those that are already overlapping. Globally align the tile configuration. Both feature extraction and matching are executed in multiple Threads, with the number of Threads being a parameter of the method.

alignTiles(Align.ParamOptimize, List<AbstractAffineTile2D<?>>, List<AbstractAffineTile2D<?>>, int) - Static method in class mpicbg.trakem2.align.Align

Align a set of overlapping tiles using the following procedure: Extract SIFT-features from all tiles. Establish point-correspondences from consistent sets of feature matches among overlapping tiles. Globally align the tile configuration. Both feature extraction and matching are executed in multiple Threads, with the number of Threads being a parameter of the method.

alignTiles(Align.ParamOptimize, List<AbstractAffineTile2D<?>>, List<AbstractAffineTile2D<?>>, boolean, boolean, boolean, boolean, boolean) - Static method in class mpicbg.trakem2.align.AlignTask

 

alignTiles(Align.ParamOptimize, List<AbstractAffineTile2D<?>>, List<AbstractAffineTile2D<?>>, boolean, boolean, boolean, boolean) - Static method in class mpicbg.trakem2.align.AlignTask

 

AlignTo4Byte() - Method in class customnode.u3d.BitStreamWrite

 

AlignToByte() - Method in class customnode.u3d.BitStreamWrite

 

AlignViewerPanelAction(BigWarp, BigWarpActions.AlignViewerPanelAction.TYPE) - Constructor for class bigwarp.BigWarpActions.AlignViewerPanelAction

 

ALIVE - Static variable in class levelsets.algorithm.FastMarching

Constant for ALIVE elements

ALL_PLOTS - Static variable in class sholl.Options

Deprecated.

 

allAttributeInstances - Variable in class spim.fiji.plugin.queryXML.GenericLoadParseQueryXML

 

allChannels - Static variable in class bdv.ij.ExportSpimFusionPlugIn

Deprecated.

 

allChannels - Static variable in class bdv.ij.ExportSpimSequencePlugIn

Deprecated.

 

allChoices - Static variable in class plugin.GridType

 

AllConnectedComponents - Class in mpicbg.imglib.algorithm.labeling

Label all 8-connected components of a binary image

AllConnectedComponents() - Constructor for class mpicbg.imglib.algorithm.labeling.AllConnectedComponents

 

AllConnectedComponents.PositionStack - Class in mpicbg.imglib.algorithm.labeling

 

allContentsString() - Method in class ij3d.Image3DUniverse

 

allIdentical(List<T>) - Method in class fiji.util.KDTree

 

allIdentical(List<T>) - Method in class mpicbg.imglib.algorithm.kdtree.KDTree

 

allImageSizesEqual() - Method in class spim.fiji.datasetmanager.LightSheetZ1MetaData

 

AllKnownFilter - Class in org.imagearchive.lsm.toolbox.gui

 

AllKnownFilter() - Constructor for class org.imagearchive.lsm.toolbox.gui.AllKnownFilter

 

allocated - Variable in class fiji.util.ArrayBase

 

allowCZIAutostitch() - Static method in class loci.plugins.util.LociPrefs

 

allowed - Variable in class fiji.plugin.trackmate.tracking.oldlap.costfunction.GapClosingCostFunction

If false, gap closing will be prohibited.

allowedBitDepth(int) - Method in class util.Histogram_2D

 

allowEdgeExtrema(boolean) - Method in class mpicbg.imglib.algorithm.extremafinder.AbstractRegionalExtremaFinder

 

allowEdgeExtrema(boolean) - Method in interface mpicbg.imglib.algorithm.extremafinder.RegionalExtremaFinder

If set to true before the Algorithm.process() method is called, then extrema found at the edges of the image bounds (including time edges) will not be pruned, and will be included in the result array.

allowEdgeMax - Variable in class mpicbg.imglib.algorithm.extremafinder.AbstractRegionalExtremaFinder

 

allowShow - Variable in class loci.plugins.util.DataBrowser

 

allPeaks - Variable in class sc.fiji.timelapse.Peak_Counter_Tool

 

allPeaksMap - Variable in class sc.fiji.timelapse.Peak_Counter_Tool

 

allPointsIterator() - Method in class tracing.PathAndFillManager

 

AllPointsIterator() - Constructor for class tracing.PathAndFillManager.AllPointsIterator

 

allRegions - Variable in class util.FindConnectedRegions.Results

 

allSame - Variable in class ai.SplitFunction

 

allSelectedUsingFittedVersion() - Method in class tracing.PathWindow

 

AllToAllRegistration - Class in spim.process.interestpointregistration.optimizationtypes

 

AllToAllRegistration(SpimData2, List<ViewId>, List<ChannelProcess>, boolean) - Constructor for class spim.process.interestpointregistration.optimizationtypes.AllToAllRegistration

 

AllToAllRegistrationWithRange - Class in spim.process.interestpointregistration.optimizationtypes

 

AllToAllRegistrationWithRange(SpimData2, List<ViewId>, List<ChannelProcess>, int, boolean) - Constructor for class spim.process.interestpointregistration.optimizationtypes.AllToAllRegistrationWithRange

 

allUsingFittedVersion(Set<Path>) - Method in class tracing.PathWindow

 

alpha - Variable in class fiji.features.Frangi_.VesselnessCalculator

 

alpha - Variable in class ini.trakem2.display.Displayable

 

alpha(int) - Static method in class mpicbg.imglib.type.numeric.RGBALegacyType

 

alpha - Variable in class mpicbg.models.AbstractMovingLeastSquaresTransform

 

alpha - Variable in class mpicbg.models.ElasticMovingLeastSquaresMesh

 

alpha - Variable in class mpicbg.spim.io.SPIMConfiguration

 

Alpha - Class in script.imglib.color

TODO

Alpha(Image<? extends RGBALegacyType>) - Constructor for class script.imglib.color.Alpha

Extract the alpha channel of each pixel, in the range [0, 255].

alpha - Variable in class Stitch_Image_Collection

 

alpha - Variable in class Stitch_Multiple_Series_File

 

alpha - Variable in class stitching.GridLayout

 

alpha - Variable in class Stitching_2D

 

alpha - Variable in class Stitching_3D

 

ALPHA_ADVECTION - Variable in class levelsets.algorithm.GeodesicActiveContour

 

AlphaMaskPath() - Constructor for class ini.trakem2.persistence.StaleFiles.AlphaMaskPath

 

AlphanumComparator - Class in fiji.plugin.trackmate.util

The Alphanum Algorithm is an improved sorting algorithm for strings containing numbers.

alphaStatic - Static variable in class Stitch_Image_Collection

 

alphaStatic - Static variable in class Stitch_Image_Directory

 

alphaStatic - Static variable in class Stitch_Image_Grid

 

alphaStatic - Static variable in class Stitch_Image_Grid_Sequence

 

alphaStatic - Static variable in class Stitch_Many_Images

 

alphaStatic - Static variable in class Stitch_Multiple_Series_File

 

alphaStatic - Static variable in class Stitching_2D

 

alphaStatic - Static variable in class Stitching_3D

 

AlternateViewer - Class in view5d

 

AlternateViewer(Container) - Constructor for class view5d.AlternateViewer

 

AlternateViewer(Container, int, int) - Constructor for class view5d.AlternateViewer

 

alternatingPath(int) - Method in class fiji.plugin.trackmate.tracking.oldlap.hungarian.MunkresKuhnAlgorithm

 

aLUT - Variable in class ij3d.ContentInstant

 

always_interpolate_areas_with_distance_map - Static variable in class ini.trakem2.utils.AreaUtils

Project property key.

alwaysCopy - Static variable in class mpicbg.stitching.StitchingParameters

If you want to force that the ContainerFactory above is always used set this to true

alwaysShowWindow - Static variable in class vib.VIB

 

aMatrix - Variable in class jitk.spline.ThinPlateR2LogRSplineKernelTransform

 

ambigous - Static variable in class ini.trakem2.utils.MCCube

 

ambigous - Static variable in class marchingcubes.MCCube

 

amira - package amira

 

AmiraImporter - Class in ini.trakem2.io

Parses an amira labelfield and imports the labels as AreaList instances into the project tree.

AmiraImporter() - Constructor for class ini.trakem2.io.AmiraImporter

 

AmiraMeshDecoder - Class in amira

 

AmiraMeshDecoder() - Constructor for class amira.AmiraMeshDecoder

 

AmiraMeshDecoder() - Method in class amira.AmiraMeshDecoder

 

AmiraMeshEncoder - Class in amira

 

AmiraMeshEncoder(String) - Constructor for class amira.AmiraMeshEncoder

 

AmiraMeshReader_ - Class in <Unnamed>

 

AmiraMeshReader_() - Constructor for class AmiraMeshReader_

 

AmiraMeshWriter_ - Class in <Unnamed>

 

AmiraMeshWriter_() - Constructor for class AmiraMeshWriter_

 

AmiraParameters - Class in amira

 

AmiraParameters(ImagePlus) - Constructor for class amira.AmiraParameters

 

AmiraParameters(Properties) - Constructor for class amira.AmiraParameters

 

AmiraParameters(String) - Constructor for class amira.AmiraParameters

 

AmiraParameters.IsA - Interface in amira

 

AmiraParameters.Material - Class in amira

 

AmiraSurface - Class in isosurface

 

AmiraSurface() - Constructor for class isosurface.AmiraSurface

 

AmiraTable - Class in amira

 

AmiraTable(String, String, String) - Constructor for class amira.AmiraTable

 

AmiraTable(String, String, String, boolean) - Constructor for class amira.AmiraTable

 

AmiraTableEncoder - Class in amira

 

AmiraTableEncoder(TextWindow) - Constructor for class amira.AmiraTableEncoder

 

AmiraTableWriter_ - Class in <Unnamed>

 

AmiraTableWriter_() - Constructor for class AmiraTableWriter_

 

AMPLITUDE_DIR_TAG - Static variable in class spim.fiji.spimdata.imgloaders.XmlIoDHMImgLoader

 

AMPLITUDE_ID_TAG - Static variable in class spim.fiji.spimdata.imgloaders.XmlIoDHMImgLoader

 

Analyse_Particles - Class in QuickPALM

This plugin detectes sub-diffraction particles in a sequence of images, it is the main plugin for the QuickPALM package.

Analyse_Particles() - Constructor for class QuickPALM.Analyse_Particles

 

ANALYSER_ELEMENT_KEY - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys

 

ANALYSER_KEY_ATTRIBUTE - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys

 

analysisMenu - Variable in class tracing.NeuriteTracerResultsDialog

 

AnalysisResults<T extends RealType<T>> - Class in sc.fiji.coloc.results

Data structure housing all colocalisation results.

AnalysisResults() - Constructor for class sc.fiji.coloc.results.AnalysisResults

 

analyze2D(int, int, double[], double, int, int, ImagePlus) - Method in class sholl.Sholl_Analysis

Deprecated.

analyze3D(int, int, int, double[], ImagePlus) - Method in class sholl.Sholl_Analysis

Deprecated.

Analyze_Reader - Class in sc.fiji.io

This plugin loads Analyze format files.

Analyze_Reader() - Constructor for class sc.fiji.io.Analyze_Reader

 

Analyze_Writer - Class in sc.fiji.io

This plugin saves Analyze format files.

Analyze_Writer() - Constructor for class sc.fiji.io.Analyze_Writer

 

analyzeButton - Variable in class tracing.ShollAnalysisDialog

 

analyzeMaximum(LocalizableByDimCursor3D<FloatType>, float, int, int, int, float, float, float, RejectStatistics, ArrayList<DoGMaximum>) - Static method in class mpicbg.spim.registration.bead.laplace.LaPlaceFunctions

 

analyzePeak(DifferenceOfGaussianPeak<T>) - Method in class mpicbg.imglib.algorithm.scalespace.SubpixelLocalization

 

analyzeProfile(double[], double[], boolean) - Method in class sholl.Sholl_Analysis

Deprecated.

Analyzes a sampled profile.

ANALYZER_COLLECTION_ELEMENT_KEY - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys

 

AnalyzeSkeleton_ - Class in sc.fiji.analyzeSkeleton

Main class of the ImageJ/Fiji plugin for skeleton analysis.

AnalyzeSkeleton_() - Constructor for class sc.fiji.analyzeSkeleton.AnalyzeSkeleton_

 

analyzeTabularInput(ResultsTable, int, int, boolean) - Method in class sholl.Sholl_Analysis

Deprecated.

Instructs the plugin to parse the specified table expected to contain a sampled profile.

analyzeTabularInput(File, int, int, boolean) - Method in class sholl.Sholl_Analysis

Deprecated.

Instructs the plugin to parse the specified file expected to contain a sampled profile.

AnalyzeTracings_ - Class in tracing

 

AnalyzeTracings_() - Constructor for class tracing.AnalyzeTracings_

 

analyzeWithShollAnalysisPlugin(String, double) - Method in class tracing.ShollAnalysisDialog.ShollResults

Instructs the Sholl Analysis plugin to analyze the profile sampled by .

ANCHORS - Static variable in class ini.trakem2.display.LayerSet

 

And() - Constructor for class fiji.expressionparser.function.ImgLibLogical.And

 

And<T extends RealType<T>> - Class in imglib.ops.condition

TODO

And(Condition<T>, Condition<T>) - Constructor for class imglib.ops.condition.And

 

And - Class in imglib.ops.operator.binary

TODO

And() - Constructor for class imglib.ops.operator.binary.And

 

and(int) - Method in class loci.plugins.util.RecordedImageProcessor

 

and(T) - Method in interface mpicbg.imglib.type.BooleanType

 

and(BitType) - Method in class mpicbg.imglib.type.logic.BitType

 

And - Class in script.imglib.math

TODO

And(Image<? extends RealType<?>>, Image<? extends RealType<?>>) - Constructor for class script.imglib.math.And

 

And(IFunction, Image<? extends RealType<?>>) - Constructor for class script.imglib.math.And

 

And(Image<? extends RealType<?>>, IFunction) - Constructor for class script.imglib.math.And

 

And(IFunction, IFunction) - Constructor for class script.imglib.math.And

 

And(Image<? extends RealType<?>>, Number) - Constructor for class script.imglib.math.And

 

And(Number, Image<? extends RealType<?>>) - Constructor for class script.imglib.math.And

 

And(IFunction, Number) - Constructor for class script.imglib.math.And

 

And(Number, IFunction) - Constructor for class script.imglib.math.And

 

And(Number, Number) - Constructor for class script.imglib.math.And

 

And(Object...) - Constructor for class script.imglib.math.And

 

AndConstant - Class in imglib.ops.operator.unary

TODO

AndConstant(long) - Constructor for class imglib.ops.operator.unary.AndConstant

 

AnElement - Class in view5d

 

angle(Pnt) - Method in class delaunay.Pnt

Angle (in radians) between two Pnts (treated as vectors).

Angle - Class in mpicbg.spim.data.sequence

Defines an angle which is part of the ViewSetup.

Angle(int, String, double, double[]) - Constructor for class mpicbg.spim.data.sequence.Angle

 

Angle(int, String) - Constructor for class mpicbg.spim.data.sequence.Angle

 

Angle(int) - Constructor for class mpicbg.spim.data.sequence.Angle

 

Angle() - Constructor for class mpicbg.spim.data.sequence.Angle

 

angle - Variable in class mpicbg.spim.registration.ViewDataBeads

the acquisition angle

angle(double, double, double, double) - Method in class sc.fiji.balloonSegmentation.structure.Balloon

Math vector operators: determine angle between v2 (x2, y2) and v1 (x1,y1) (I made this before I start using JAMA library)

angle - Variable in class spim.vecmath.AxisAngle4d

The angle of rotation in radians.

angle - Variable in class spim.vecmath.AxisAngle4f

The angle of rotation in radians.

angle(Vector3d) - Method in class spim.vecmath.Vector3d

Returns the angle in radians between this vector and the vector parameter; the return value is constrained to the range [0,PI].

angle(Vector3f) - Method in class spim.vecmath.Vector3f

Returns the angle in radians between this vector and the vector parameter; the return value is constrained to the range [0,PI].

angle(Vector4d) - Method in class spim.vecmath.Vector4d

Returns the (4-space) angle in radians between this vector and the vector parameter; the return value is constrained to the range [0,PI].

angle(Vector4f) - Method in class spim.vecmath.Vector4f

Returns the (4-space) angle in radians between this vector and the vector parameter; the return value is constrained to the range [0,PI].

angle2d(AffineTransform3D, int) - Static method in class bigwarp.util.Rotation2DHelpers

 

ANGLE_PATTERN - Static variable in class spim.fiji.datasetmanager.StackList

 

ANGLE_ROTATIONAXIS_TAG - Static variable in class mpicbg.spim.data.XmlKeys

 

ANGLE_ROTATIONDEGREES_TAG - Static variable in class mpicbg.spim.data.XmlKeys

 

ANGLE_TAG - Static variable in class mpicbg.spim.data.XmlKeys

 

angleAttributeKey - Static variable in class mpicbg.spim.data.sequence.ViewSetup

 

angleBetween(double[], double[]) - Static method in class vib.FastMatrix

 

angleBetween(float[], float[]) - Static method in class vib.FloatMatrix

 

angleChoice - Static variable in class spim.fiji.plugin.Duplicate_Transformation

 

angleEnd - Variable in class spimopener.SPIMExperiment

 

angleIndicies - Variable in class mpicbg.spim.fusion.MappingFusionSequentialDifferentOutput

 

angleIndiciesStatic - Static variable in class mpicbg.spim.fusion.MappingFusionSequentialDifferentOutput

 

angleMult(double[], double[], double) - Static method in class bigwarp.util.Rotation2DHelpers

 

angleNameList - Variable in class spim.fiji.datasetmanager.StackList

 

angleNames - Variable in class spim.fiji.spimdata.imgloaders.MultipageTiffReader

 

anglePattern - Variable in class mpicbg.spim.io.SPIMConfiguration

 

angles - Static variable in class fiji.plugin.Bead_Registration

 

angles - Variable in class mpicbg.spim.io.SPIMConfiguration

 

angles() - Method in class spim.fiji.datasetmanager.LightSheetZ1MetaData

 

angles - Variable in class spim.fiji.datasetmanager.SlideBook6Image

 

angles(int) - Method in class spim.fiji.datasetmanager.SlideBook6MetaData

 

angles - Variable in class spim.fiji.datasetmanager.StackList

 

angles() - Method in class spim.fiji.plugin.apply.ModelLink

 

angles - Variable in class spimopener.SPIMExperiment

 

ANGLES_TAG - Static variable in class mpicbg.spim.data.XmlKeys

 

angleStart - Variable in class spimopener.SPIMExperiment

 

anim - Variable in class loci.plugins.util.DataBrowser

 

animate - Variable in class loci.plugins.util.DataBrowser

 

ANIMATE_TG - Static variable in class ij3d.DefaultUniverse

The index of the transform group in the viewing platform's MultiTransformGroup which is responsible for animation

animateBrowsing(int, int) - Method in class ini.trakem2.display.DisplayCanvas

Smoothly move the canvas from x0,y0,layer0 to x1,y1,layer1

animateBrowsing(Rectangle, Layer) - Method in class ini.trakem2.display.DisplayCanvas

Smoothly move the canvas from its current position until the given rectangle is included within the srcRect.

animateBrowsingTo(Coordinate<?>) - Method in class ini.trakem2.display.Display

 

Animated_Gif_Reader - Class in sc.fiji.io

 

Animated_Gif_Reader() - Constructor for class sc.fiji.io.Animated_Gif_Reader

 

animateTransformation(AffineTransform3D, int) - Method in class bdv.viewer.BigWarpViewerPanel

 

animateTransformation(AffineTransform3D) - Method in class bdv.viewer.BigWarpViewerPanel

 

anisotropic_diffusion - package anisotropic_diffusion

 

ANISOTROPIC_DIFFUSION - Static variable in class trainableSegmentation.FeatureStack

Anisotropic diffusion filter flag index

Anisotropic_Diffusion_2D - Class in anisotropic_diffusion

 

Anisotropic_Diffusion_2D() - Constructor for class anisotropic_diffusion.Anisotropic_Diffusion_2D

 

AnisotropicDiffusion<T extends RealType<T>> - Class in mpicbg.imglib.algorithm.pde

Perona & Malik Anisotropic diffusion

AnisotropicDiffusion(Image<T>, double, AnisotropicDiffusion.DiffusionFunction) - Constructor for class mpicbg.imglib.algorithm.pde.AnisotropicDiffusion

Instantiate the Perona & Malik anisotropic diffusion process, with a custom diffusion function.

AnisotropicDiffusion(Image<T>, double, double) - Constructor for class mpicbg.imglib.algorithm.pde.AnisotropicDiffusion

Instantiate the Perona & Malik anisotropic diffusion process, with the default strong-edge diffusion function.

AnisotropicDiffusion.DiffusionFunction - Interface in mpicbg.imglib.algorithm.pde

The interface that function suitable to be diffusion function must implement.

AnisotropicDiffusion.StrongEdgeEnhancer - Class in mpicbg.imglib.algorithm.pde

The first diffusion function proposed by Perona & Malik.

AnisotropicDiffusion.WideRegionEnhancer - Class in mpicbg.imglib.algorithm.pde

The second diffusion function proposed by Perona & Malik.

annotation - Variable in class ini.trakem2.display.Displayable

 

annotationsDescriptionChanged() - Method in class sholl.plugin.ShollAnalysisImg

 

ANNULUS - Static variable in interface sholl.math.ShollStats

Flag for annulus normalization (Semi-log/Log-log method)

antiAliasedText - Static variable in class Series_Labeler

 

antiSymmetricPadding(double[][], int) - Static method in class bunwarpj.MathTools

 

antiSymmetricPadding(double[], int, int) - Static method in class bunwarpj.MathTools

 

antiSymmetricPadding(float[], int, int) - Static method in class bunwarpj.MathTools

 

anyListeners() - Method in class tracing.SimpleNeuriteTracer

 

anySelected() - Method in class tracing.PathAndFillManager

 

ap - Variable in class mpicbg.trakem2.align.Align.ExtractFeaturesThread

 

ap - Variable in class mpicbg.trakem2.align.Align.MatchFeaturesAndFindModelThread

 

ap - Variable in class org.janelia.thickness.plugin.RealSumFloatNCC

 

ap - Variable in class org.janelia.thickness.trakem2.RealSumARGBNCC

 

appCreator - Variable in class voltex.VolumeRenderer

The AppearanceCreator, which creates the textures.

AppearanceCreator - Class in octree

 

AppearanceCreator - Class in voltex

This class is a helper class whose main task is to create Appearance objects for a specified axis and direction.

AppearanceCreator(VoltexVolume) - Constructor for class voltex.AppearanceCreator

Constructor.

AppearanceCreator(VoltexVolume, Color3f, float) - Constructor for class voltex.AppearanceCreator

Initializes this AppearanceCreator with the given image data, color and transparency values.

append(Line3D) - Method in class ini.trakem2.analysis.Compare.Chain

 

append(History.Step<?>) - Method in class ini.trakem2.utils.History

Appends a step at the end of the list, without modifying the current index.

append(ILoggingEvent) - Method in class loci.plugins.util.IJStatusEchoer

 

append(StringBuilder, HashSet<String>, String) - Static method in class mpicbg.trakem2.transform.DTD

 

append(String) - Method in class vib.app.gui.Console

 

appendBezierPathXML(StringBuilder, double[]) - Static method in class edu.utexas.clm.reconstructreader.Utils

 

appendCalibration(StringBuilder) - Method in class edu.utexas.clm.reconstructreader.reconstruct.ReconstructTranslator

 

appendClosedPathXML(StringBuilder, double[]) - Static method in class edu.utexas.clm.reconstructreader.Utils

 

appendCoordinateTransform(CoordinateTransform) - Method in class ini.trakem2.display.Patch

Append a CoordinateTransform to the current CoordinateTransformList.

appendCoordinateTransform(List<Patch>, CoordinateTransform, int) - Static method in class lenscorrection.DistortionCorrectionTask

 

AppendCoordinateTransformThread(List<Patch>, CoordinateTransform, AtomicInteger) - Constructor for class lenscorrection.DistortionCorrectionTask.AppendCoordinateTransformThread

 

appendDisplay(StringBuilder) - Method in class edu.utexas.clm.reconstructreader.reconstruct.ReconstructTranslator

 

appendDTD(StringBuilder) - Method in class edu.utexas.clm.reconstructreader.reconstruct.ReconstructTranslator

 

appendFilters(IFilter[]) - Method in class ini.trakem2.display.Patch

Append an array of IFilter to the array of existing IFilter.

appendGUIState(TrackMateGUIModel) - Method in class fiji.plugin.trackmate.io.TmXmlWriter

Appends the current GUI state as a state string to the document.

appendLayerSet(StringBuilder) - Method in class edu.utexas.clm.reconstructreader.reconstruct.ReconstructTranslator

 

appendLayerSetXML(StringBuilder, List<ReconstructSection>) - Method in class edu.utexas.clm.reconstructreader.reconstruct.ReconstructAreaList

 

appendLog(String) - Method in class fiji.plugin.trackmate.io.TmXmlWriter

Appends the log content to the document.

appendModel(Model) - Method in class fiji.plugin.trackmate.io.TmXmlWriter

Appends the content of a Model to the file generated by this writer.

appendOpenPathXML(StringBuilder, double[]) - Static method in class edu.utexas.clm.reconstructreader.Utils

 

appendPatch(StringBuilder, Element) - Method in class edu.utexas.clm.reconstructreader.reconstruct.ReconstructSection

 

appendPoint(int, int, long) - Method in class ini.trakem2.display.Polyline

Append a point at the end.

appendPoints(double[], double[], long[], int) - Method in class ini.trakem2.display.Polyline

 

appendProject(StringBuilder) - Method in class edu.utexas.clm.reconstructreader.reconstruct.ReconstructTranslator

 

appendProjectXML(StringBuilder) - Method in class edu.utexas.clm.reconstructreader.reconstruct.ReconstructAreaList

 

appendProjectXML(StringBuilder) - Method in class edu.utexas.clm.reconstructreader.reconstruct.ReconstructProfileList

 

appendProjectXML(StringBuilder) - Method in class edu.utexas.clm.reconstructreader.reconstruct.ReconstructZTrace

 

appendSettings(Settings) - Method in class fiji.plugin.trackmate.io.TmXmlWriter

Appends the content of a Settings object to the document.

appendShortest(float, float, StringBuilder) - Static method in class ini.trakem2.utils.M

Appends to @param sb the shortest possible String representation of a float number, according to the desired decimal @param precision.

AppendSpimData2 - Class in spim.process.fusion.export

 

AppendSpimData2() - Constructor for class spim.process.fusion.export.AppendSpimData2

 

appendSpimData2(SpimData2, List<TimePoint>, List<ViewSetup>) - Static method in class spim.process.fusion.export.AppendSpimData2

Assembles a new SpimData2 based on the timepoints and viewsetups.

AppendSpimData2HDF5 - Class in spim.process.fusion.export

 

AppendSpimData2HDF5() - Constructor for class spim.process.fusion.export.AppendSpimData2HDF5

 

appendText(String) - Static method in class vib.BatchLog_

 

AppendTo - Variable in class view5d.My3DData

 

AppendTo - Variable in class view5d.View5D_

 

appendToExistingFile(ExportSpimFusionPlugIn.Parameters) - Static method in class bdv.ij.ExportSpimFusionPlugIn

Deprecated.

 

appendToPath(String, String) - Static method in class fiji.scripting.Compiler

 

appendXML(StringBuilder) - Method in class edu.utexas.clm.reconstructreader.reconstruct.ReconstructProfile

 

appendXML(StringBuilder) - Method in class edu.utexas.clm.reconstructreader.reconstruct.ReconstructSection

 

appendXML(StringBuilder) - Method in class edu.utexas.clm.reconstructreader.reconstruct.ReconstructZTrace

 

applet - Variable in class view5d.My3DData

 

applied() - Method in interface ij3d.gui.LUTDialog.Listener

 

applies(Object) - Method in class edu.utexas.clm.archipelago.ijsupport.TrakEM2Archipelago

 

applies(Object) - Method in class edu.utexas.clm.crop.AreaList_Crop

 

applies(Object) - Method in class edu.utexas.clm.reconstructreader.trakem2.Reconstruct_Writer

 

applies(Object) - Method in interface ini.trakem2.plugin.TPlugIn

Returns true if this plugin can be applied to an Object like @param ob.

applies(Object) - Method in class lineage.Identify

 

applies(Object) - Method in class org.janelia.intensity.MatchIntensities

 

applies(Object) - Method in class org.janelia.thickness.trakem2.LayerZPosition

 

applies(Object) - Method in class treeline.TreelineGraphEditor

 

apply(ImagePlus, ImagePlus, LandmarkTableModel, String, String, String, double[], double[], double[], Interpolation, boolean, int) - Static method in class bdv.ij.ApplyBigwarpPlugin

 

apply(BigWarp.BigWarpData<T>, LandmarkTableModel, String, String, String, double[], double[], double[], Interpolation, boolean, int) - Static method in class bdv.ij.ApplyBigwarpPlugin

 

apply(Interpolation) - Method in class bdv.util.DefaultInterpolators

 

apply(double[]) - Method in class bdv.viewer.animate.SimilarityModel3D

 

apply(double[], double[]) - Method in class bigwarp.BigWarp.WrappedCoordinateTransform

 

apply(RealLocalizable, RealPositionable) - Method in class bigwarp.BigWarp.WrappedCoordinateTransform

 

apply(double[]) - Method in class bunwarpj.trakem2.transform.CubicBSplineTransform

 

apply(PathIterator) - Method in class fiji.geom.AreaCalculations.Calculation

 

apply(V) - Method in class fiji.plugin.trackmate.graph.RecursiveCumSum

 

apply(HashMap<String, String>, Image3DUniverse) - Method in class ij3d.SaveSession

 

apply(Image3DUniverse) - Static method in class ij3d.UniverseSettings

 

apply() - Method in class ij3d.ViewAdjuster

After all points/contents were added, apply() finally adjusts center and zoom transformations of the view.

apply() - Method in class ini.trakem2.display.AffineTransformMode

 

apply(Layer, Area, CoordinateTransform) - Method in class ini.trakem2.display.AreaList

 

apply(VectorDataTransform) - Method in class ini.trakem2.display.AreaList

 

apply(CoordinateTransform, Area) - Method in class ini.trakem2.display.AreaTree.AreaNode

 

apply(VectorDataTransform) - Method in class ini.trakem2.display.AreaTree.AreaNode

 

apply(Layer, Area, CoordinateTransform) - Method in class ini.trakem2.display.Ball

 

apply(VectorDataTransform) - Method in class ini.trakem2.display.Ball

 

apply() - Method in class ini.trakem2.display.ContrastAdjustmentMode

 

apply() - Method in class ini.trakem2.display.DefaultMode

 

apply(int) - Method in class ini.trakem2.display.Displayable.DoEdit

Set the stored data to the stored Displayable.

apply(int) - Method in class ini.trakem2.display.Displayable.DoEdits

 

apply(int) - Method in class ini.trakem2.display.Displayable.DoTransforms

 

apply(Layer, Area, CoordinateTransform) - Method in class ini.trakem2.display.Dissector

 

apply(VectorDataTransform) - Method in class ini.trakem2.display.Dissector

 

apply(Layer, Area, CoordinateTransform) - Method in class ini.trakem2.display.DLabel

 

apply(VectorDataTransform) - Method in class ini.trakem2.display.DLabel

 

apply(int) - Method in interface ini.trakem2.display.DoStep

Returns true on success.

apply() - Method in class ini.trakem2.display.inspect.InspectPatchTrianglesMode

 

apply(Class<?>, AffineTransform) - Method in class ini.trakem2.display.Layer

Preconcatenate the given AffineTransform to all Displayable objects of class c, without respecting their links.

apply(int) - Method in class ini.trakem2.display.Layer.DoMoveDisplayable

 

apply(int) - Method in class ini.trakem2.display.LayerSet.DoChangeTrees

 

apply(int) - Method in class ini.trakem2.display.LayerSet.DoMoveZDisplayable

 

apply() - Method in class ini.trakem2.display.ManualAlignMode

 

apply() - Method in interface ini.trakem2.display.Mode

 

apply(CoordinateTransform, Area) - Method in class ini.trakem2.display.Node

 

apply(VectorDataTransform) - Method in class ini.trakem2.display.Node

 

apply(Node.Operation<T>, Iterator<Node<T>>) - Method in class ini.trakem2.display.Node

 

apply(Node<I>) - Method in interface ini.trakem2.display.Node.Operation

 

apply() - Method in class ini.trakem2.display.NonLinearTransformMode

 

apply(Set<Layer>) - Method in class ini.trakem2.display.NonLinearTransformMode

 

apply(Layer, Area, CoordinateTransform) - Method in class ini.trakem2.display.Pipe

 

apply(VectorDataTransform) - Method in class ini.trakem2.display.Pipe

 

apply(Layer, Area, CoordinateTransform) - Method in class ini.trakem2.display.Polyline

 

apply(VectorDataTransform) - Method in class ini.trakem2.display.Polyline

 

apply(Layer, Area, CoordinateTransform) - Method in class ini.trakem2.display.Profile

 

apply(VectorDataTransform) - Method in class ini.trakem2.display.Profile

 

apply(int, double[]) - Method in class ini.trakem2.display.Selection

 

apply(Layer, Area, CoordinateTransform) - Method in class ini.trakem2.display.Tree

 

apply(VectorDataTransform) - Method in class ini.trakem2.display.Tree

 

apply(CoordinateTransform, Area) - Method in class ini.trakem2.display.Treeline.RadiusNode

 

apply(VectorDataTransform) - Method in class ini.trakem2.display.Treeline.RadiusNode

 

apply(Layer, Area, CoordinateTransform) - Method in interface ini.trakem2.display.VectorData

Applies the 2D transform @ict (which is expected to operate on the world coordinates version of the data contained here) only to the data that falls within the @param roi (in world coords), and then recomputes the bounding box and affine transform (to a translation or identity).

apply(VectorDataTransform) - Method in interface ini.trakem2.display.VectorData

 

apply(Collection<Displayable>) - Method in class ini.trakem2.imaging.ContrastEnhancerWrapper

 

apply(int) - Method in class ini.trakem2.tree.RenameThingStep

 

apply(CoordinateTransform, Area, Area) - Static method in class ini.trakem2.utils.M

Apply in place the @param ict to the Area @param a, but only for the part that intersects the roi.

apply(VectorDataTransform, Area) - Static method in class ini.trakem2.utils.M

 

apply(VectorDataTransform, Area, boolean) - Static method in class ini.trakem2.utils.M

Parts of @param a not intersected by any of @param vdt rois will be left untouched if @param remove_outside is false.

apply(CoordinateTransform, double[][], int, double[]) - Static method in class ini.trakem2.utils.M

Reuses the @param fp to apply in place.

apply(O) - Method in interface ini.trakem2.utils.Operation

 

apply(double[], double[]) - Method in class jitk.spline.ThinPlateR2LogRSplineKernelTransform

 

apply(double[], double[], boolean) - Method in class jitk.spline.ThinPlateR2LogRSplineKernelTransform

Transform a source vector pt into a target vector result.

apply(double[]) - Method in class jitk.spline.ThinPlateR2LogRSplineKernelTransform

Transforms the input point according to the thin plate spline stored by this object.

apply(double[]) - Method in class lenscorrection.PolynomialModel2D

 

apply(Point3d) - Method in class math3d.Bookstein

 

apply(double[][], double[]) - Static method in class math3d.FastMatrixN

Calculates b in Ax = b

apply(float[][], float[]) - Static method in class math3d.FloatMatrixN

Calculates b in Ax = b

apply(double[]) - Method in class mpicbg.models.AbstractMovingLeastSquaresTransform

 

apply(double[]) - Method in class mpicbg.models.AffineModel1D

 

apply(double[]) - Method in class mpicbg.models.AffineModel2D

 

apply(double[]) - Method in class mpicbg.models.AffineModel3D

 

apply(double[]) - Method in class mpicbg.models.ConstantModel

 

apply(double[]) - Method in interface mpicbg.models.CoordinateTransform

Apply the CoordinateTransform to a location.

apply(double[]) - Method in class mpicbg.models.CoordinateTransformList

 

apply(double[]) - Method in class mpicbg.models.CoordinateTransformMap2D

 

apply(double[]) - Method in class mpicbg.models.HomographyModel2D

 

apply(double[]) - Method in class mpicbg.models.IdentityModel

 

apply(double[]) - Method in class mpicbg.models.InterpolatedAffineModel1D

 

apply(double[]) - Method in class mpicbg.models.InterpolatedAffineModel2D

 

apply(double[]) - Method in class mpicbg.models.InterpolatedAffineModel3D

 

apply(double[]) - Method in class mpicbg.models.InterpolatedCoordinateTransform

 

apply(double[]) - Method in class mpicbg.models.InterpolatedModel

 

apply(double[]) - Method in class mpicbg.models.InvertibleCoordinateTransformList

 

apply(CoordinateTransform) - Method in class mpicbg.models.MovingLeastSquaresMesh

Apply an arbitrary coordinate transformation to each Tile's PointMatches.

apply(CoordinateTransform) - Method in class mpicbg.models.Point

Apply a CoordinateTransform to the Point.

apply(CoordinateTransform, double) - Method in class mpicbg.models.Point

Apply a CoordinateTransform to the Point by a given amount.

apply(CoordinateTransform, Iterable<P>) - Static method in class mpicbg.models.Point

Apply a CoordinateTransform to an Iterable collection of Points.

apply(CoordinateTransform) - Method in class mpicbg.models.PointMatch

Apply a CoordinateTransform to PointMatch.p1, update distance.

apply(CoordinateTransform, double) - Method in class mpicbg.models.PointMatch

Apply a CoordinateTransform to PointMatch.p1 with a given amount, update distance.

apply(Collection<? extends PointMatch>, CoordinateTransform) - Static method in class mpicbg.models.PointMatch

Apply a CoordinateTransform to PointMatch.p1 a Collection of PointMatches, update their distances.

apply(double[]) - Method in class mpicbg.models.PolynomialTransform2D

 

apply(double[]) - Method in class mpicbg.models.RigidModel2D

 

apply(double[]) - Method in class mpicbg.models.RigidModel3D

 

apply(double[]) - Method in class mpicbg.models.SimilarityModel2D

 

apply(double[]) - Method in class mpicbg.models.SimilarityModel3D

 

apply() - Method in class mpicbg.models.Tile

Apply the current AbstractModel to all local point coordinates.

apply(double) - Method in class mpicbg.models.Tile

Apply the current AbstractModel to all local point coordinates.

apply() - Method in class mpicbg.models.TileConfiguration

Apply the model of each Tile to all its PointMatches.

apply(double[]) - Method in class mpicbg.models.TransformMesh

 

apply(double[]) - Method in class mpicbg.models.TranslationModel1D

 

apply(double[]) - Method in class mpicbg.models.TranslationModel2D

 

apply(double[]) - Method in class mpicbg.models.TranslationModel3D

 

apply(double[]) - Method in class mpicbg.panorama.EquirectangularProjection

 

apply(double[]) - Method in class mpicbg.panorama.RectlinearCamera

 

apply(double[]) - Method in class mpicbg.pointdescriptor.model.FixedModel

 

apply(double[]) - Method in class mpicbg.pointdescriptor.model.TranslationInvariantAffineModel3D

 

apply(double[]) - Method in class mpicbg.pointdescriptor.model.TranslationInvariantFixedModel

 

apply(double[]) - Method in class mpicbg.pointdescriptor.model.TranslationInvariantRigidModel2D

 

apply(double[]) - Method in class mpicbg.pointdescriptor.model.TranslationInvariantRigidModel3D

 

apply(double[]) - Method in class mpicbg.pointdescriptor.model.TranslationInvariantSimilarityModel3D

 

apply(double[]) - Method in class mpicbg.trakem2.transform.NonLinearCoordinateTransform

 

apply(double[]) - Method in class mpicbg.trakem2.transform.ThinPlateSplineTransform

 

apply(double[], double[]) - Method in class net.imglib2.realtransform.Wrapped2DTransformAs3D

 

apply(RealLocalizable, RealPositionable) - Method in class net.imglib2.realtransform.Wrapped2DTransformAs3D

 

apply(double) - Method in class org.janelia.thickness.lut.AbstractLUTGrid

 

apply(double) - Method in class org.janelia.thickness.lut.AbstractLUTRealTransform

 

apply(double, int, int) - Method in class org.janelia.thickness.lut.AbstractLUTRealTransformField

 

apply(int) - Method in class org.janelia.thickness.lut.AbstractPerumtationTransform

 

apply(double[], double[]) - Method in class org.janelia.thickness.lut.LUTGrid

 

apply(float[], float[]) - Method in class org.janelia.thickness.lut.LUTGrid

 

apply(RealLocalizable, RealPositionable) - Method in class org.janelia.thickness.lut.LUTGrid

 

apply(double[], double[]) - Method in class org.janelia.thickness.lut.LUTRealTransform

 

apply(float[], float[]) - Method in class org.janelia.thickness.lut.LUTRealTransform

 

apply(RealLocalizable, RealPositionable) - Method in class org.janelia.thickness.lut.LUTRealTransform

 

apply(double[], double[]) - Method in class org.janelia.thickness.lut.LUTRealTransformField

 

apply(float[], float[]) - Method in class org.janelia.thickness.lut.LUTRealTransformField

 

apply(RealLocalizable, RealPositionable) - Method in class org.janelia.thickness.lut.LUTRealTransformField

 

apply(long[], long[]) - Method in class org.janelia.thickness.lut.PermutationTransform

 

apply(int[], int[]) - Method in class org.janelia.thickness.lut.PermutationTransform

 

apply(Localizable, Positionable) - Method in class org.janelia.thickness.lut.PermutationTransform

 

apply(double[], double[]) - Method in class org.janelia.thickness.lut.SingleDimensionLUTGrid

 

apply(float[], float[]) - Method in class org.janelia.thickness.lut.SingleDimensionLUTGrid

 

apply(RealLocalizable, RealPositionable) - Method in class org.janelia.thickness.lut.SingleDimensionLUTGrid

 

apply(double[], double[]) - Method in class org.janelia.thickness.lut.SingleDimensionLUTRealTransform

 

apply(float[], float[]) - Method in class org.janelia.thickness.lut.SingleDimensionLUTRealTransform

 

apply(RealLocalizable, RealPositionable) - Method in class org.janelia.thickness.lut.SingleDimensionLUTRealTransform

 

apply(double[], double[]) - Method in class org.janelia.thickness.lut.SingleDimensionLUTRealTransformField

 

apply(float[], float[]) - Method in class org.janelia.thickness.lut.SingleDimensionLUTRealTransformField

 

apply(RealLocalizable, RealPositionable) - Method in class org.janelia.thickness.lut.SingleDimensionLUTRealTransformField

 

apply(long[], long[]) - Method in class org.janelia.thickness.lut.SingleDimensionPermutationTransform

 

apply(int[], int[]) - Method in class org.janelia.thickness.lut.SingleDimensionPermutationTransform

 

apply(Localizable, Positionable) - Method in class org.janelia.thickness.lut.SingleDimensionPermutationTransform

 

apply(IFunction, R, int) - Static method in class script.imglib.math.Compute

Execute the given IFunction, which runs for each pixel, and store the results in an Image with the type defined by , which has to be a subclass of RealType.

apply(IFunction, RGBALegacyType, int) - Static method in class script.imglib.math.Compute

Execute the given IFunction, which runs for each pixel, and store the results in an Image of type RGBALegacyType.

apply(float[]) - Method in interface stitching.model.CoordinateTransform

Apply the CoordinateTransform to a location.

apply(Model) - Method in class stitching.model.Point

Apply a Model to the Point.

apply(Model, float) - Method in class stitching.model.Point

Apply a Model to the Point by a given amount.

apply(Model) - Method in class stitching.model.PointMatch

Apply a Model to PointMatch.p1, update distance.

apply(float[]) - Method in class stitching.model.TranslationModel2D

 

apply(float[]) - Method in class stitching.model.TranslationModel3D

 

apply() - Method in class trainableSegmentation.utils.WatershedTransform2D

Apply fast watersheds using flooding simulations, as described by Soille, Pierre, and Luc M.

apply() - Method in class Transform_SpringMesh

 

apply(double, double, double) - Method in class vib.FastMatrix

 

apply(Point3d) - Method in class vib.FastMatrix

 

apply(double[]) - Method in class vib.FastMatrix

 

apply(float, float, float) - Method in class vib.FloatMatrix

 

apply(Point3d) - Method in class vib.FloatMatrix

 

apply(float[]) - Method in class vib.FloatMatrix

 

apply() - Method in class vib.segment.Thresholder

 

apply(ImageProcessor, Roi, int, int, int, boolean) - Method in class vib.segment.Thresholder

 

apply(double, double, double, double[]) - Method in class vib.transforms.BooksteinTransform

 

apply(double, double, double) - Method in class vib.transforms.BooksteinTransform

 

apply(double, double, double, double[]) - Method in class vib.transforms.FastMatrixTransform

 

apply(double, double, double, double[]) - Method in class vib.transforms.OrderedTransformations

 

apply(double, double, double) - Method in class vib.transforms.OrderedTransformations

 

apply(Point3d) - Method in class vib.transforms.OrderedTransformations

 

apply(double, double, double, double[]) - Method in interface vib.transforms.Transform

 

apply_bandpass_filter - Variable in class ini.trakem2.imaging.Segmentation.FastMarchingParam

 

APPLY_CLASSIFIER - Static variable in class trainableSegmentation.Weka_Segmentation

name of the macro method to apply the current classifier to an image or stack

Apply_External_Transformation - Class in fiji.plugin

 

Apply_External_Transformation() - Constructor for class fiji.plugin.Apply_External_Transformation

 

apply_grey_value_erosion - Variable in class ini.trakem2.imaging.Segmentation.FastMarchingParam

 

APPLY_TRANSFORM - Static variable in class ij3d.Executer

 

Apply_Transformation - Class in spim.fiji.plugin

 

Apply_Transformation() - Constructor for class spim.fiji.plugin.Apply_Transformation

 

applyAndPropagate(Set<Layer>) - Method in class ini.trakem2.display.AffineTransformMode

Skips current layer, since its done already.

applyAngles(LoadParseQueryXML) - Method in class spim.fiji.plugin.Duplicate_Transformation

 

applyAxis() - Method in class spim.fiji.datasetmanager.LightSheetZ1MetaData

 

applyAxis(SpimData, double) - Static method in class spim.fiji.datasetmanager.SlideBook6

 

applyAxis(SpimData) - Static method in class spim.fiji.plugin.Apply_Transformation

 

applyAxis - Variable in class spim.fiji.spimdata.imgloaders.MultipageTiffReader

 

applyAxis() - Method in class spim.fiji.spimdata.imgloaders.MultipageTiffReader

 

applyBigWarpHelper(AbstractSpimData<?>[], AbstractSpimData<?>[], ImagePlus, LandmarkTableModel, Interpolation) - Static method in class bigwarp.BigWarpBatchTransformFOV

 

ApplyBigwarpPlugin - Class in bdv.ij

Apply a bigwarp transform to a 2d or 3d ImagePlus

ApplyBigwarpPlugin() - Constructor for class bdv.ij.ApplyBigwarpPlugin

 

ApplyButtonListener() - Constructor for class mpicbg.spim.segmentation.InteractiveDoG.ApplyButtonListener

 

ApplyButtonListener(Frame, BigDataViewer) - Constructor for class spim.fiji.plugin.apply.BigDataViewerTransformationWindow.ApplyButtonListener

 

applyByStrength(Model, float) - Method in class stitching.model.PointMatch

Apply a Model to PointMatch.p1 with a given amount, update distance.

applyCal(Specify_Calibration.Cal, SpimData, List<ViewId>) - Static method in class spim.fiji.plugin.Specify_Calibration

 

applyCalibration(ImagePlus) - Method in class loci.plugins.in.Calibrator

Applies spatial calibrations to an image stack.

applyChannels(LoadParseQueryXML) - Method in class spim.fiji.plugin.Duplicate_Transformation

 

applyChecked(double) - Method in class org.janelia.thickness.lut.AbstractLUTGrid

 

applyChecked(double) - Method in class org.janelia.thickness.lut.AbstractLUTRealTransform

 

applyChecked(double, int, int) - Method in class org.janelia.thickness.lut.AbstractLUTRealTransformField

 

applyChecked(int) - Method in class org.janelia.thickness.lut.AbstractPerumtationTransform

 

applyClassifier(Instances, int, int, int) - Method in class trainableSegmentation.Trainable_Segmentation

Deprecated.

Apply current classifier to set of instances

applyClassifier(String, String, String, String, String, String) - Static method in class trainableSegmentation.Weka_Segmentation

Apply current classifier to specific image (2D or stack)

applyClassifier(ImagePlus) - Method in class trainableSegmentation.WekaSegmentation

Apply current classifier to a given image.

applyClassifier(ImagePlus, int, boolean) - Method in class trainableSegmentation.WekaSegmentation

Apply current classifier to a given image.

applyClassifier(ImagePlus, ImagePlus, int, boolean) - Method in class trainableSegmentation.WekaSegmentation

Apply current classifier to a given image with precomputed features.

applyClassifier(ImagePlus, FeatureStackArray, int, boolean) - Method in class trainableSegmentation.WekaSegmentation

Apply current classifier to a given image with precomputed features.

applyClassifier(boolean) - Method in class trainableSegmentation.WekaSegmentation

Apply current classifier to current image.

applyClassifier(int, boolean) - Method in class trainableSegmentation.WekaSegmentation

Apply current classifier to current image.

applyClassifier(ImagePlus, int[], int, boolean) - Method in class trainableSegmentation.WekaSegmentation

Apply the current classifier to an image subdividing the image in tiles for memory saving.

applyClassifier(ImagePlus, int[], int[], int, boolean) - Method in class trainableSegmentation.WekaSegmentation

Apply current classifier to a user-defined ROI of a given image.

applyClassifier(Instances, int, int, int, boolean) - Method in class trainableSegmentation.WekaSegmentation

Apply current classifier to set of instances

applyClassifier(FeatureStackArray, int, boolean) - Method in class trainableSegmentation.WekaSegmentation

Apply current classifier to a set of feature vectors (given in a feature stack array).

applyClassifierMT(ImagePlus, int, boolean) - Method in class trainableSegmentation.WekaSegmentation

Apply current classifier to a given image in a complete concurrent way.

applyClassifierToTestData() - Method in class trainableSegmentation.Trainable_Segmentation

Deprecated.

Apply classifier to test data

applyClassifierToTestData() - Method in class trainableSegmentation.Weka_Segmentation

Apply classifier to test data.

applyClassifierToTestImage(ImagePlus, int) - Method in class trainableSegmentation.Trainable_Segmentation

Deprecated.

Apply current classifier to image

applyColors(List<ImagePlus>) - Method in class loci.plugins.in.Colorizer

 

applyColors(ImagePlus, int, Color[], int) - Static method in class org.imagearchive.lsm.toolbox.ReaderToolkit

 

applyCoordinateTransform(ImagePlus, CoordinateTransform, int, boolean, int[]) - Static method in class register_virtual_stack.Transform_Virtual_Stack_MT

Apply a coordinate transform to a given image

applyCorrection - Variable in class lenscorrection.Distortion_Correction.PluginParam

 

applyEntropy(ImageProcessor, int, int) - Method in class trainableSegmentation.filters.Entropy_Filter

Apply entropy filter to an image

applyFilter(Filter) - Method in class levelsets.ij.ImageContainer

Applies the passed Filter on every image in the container.

applyFilter(Filter, int, int) - Method in class levelsets.ij.ImageContainer

Applies the passed filter on the selected range of images

applyFilter(ImageProcessor, int, int, int) - Method in class trainableSegmentation.filters.Kuwahara

Apply filter to input image (in place)

applyFilters(Image) - Method in class ini.trakem2.display.Display

 

applyFilters(ImageProcessor) - Method in class ini.trakem2.display.Display

 

applyFilters(ImagePlus) - Method in class ini.trakem2.display.Display

 

ApplyHistSelection() - Method in class view5d.My3DData

 

applyIllums(LoadParseQueryXML) - Method in class spim.fiji.plugin.Duplicate_Transformation

 

applyInPlace(double[]) - Method in class bdv.viewer.animate.SimilarityModel3D

 

applyInPlace(double[]) - Method in class bunwarpj.trakem2.transform.CubicBSplineTransform

 

applyInPlace(double[]) - Method in class jitk.spline.ThinPlateR2LogRSplineKernelTransform

Transform pt in place.

applyInPlace(double[]) - Method in class lenscorrection.PolynomialModel2D

 

applyInPlace(double[]) - Method in class mpicbg.models.AffineModel1D

 

applyInPlace(double[]) - Method in class mpicbg.models.AffineModel2D

 

applyInPlace(double[]) - Method in class mpicbg.models.AffineModel3D

 

applyInPlace(double[]) - Method in class mpicbg.models.ConstantModel

 

applyInPlace(double[]) - Method in interface mpicbg.models.CoordinateTransform

Apply the CoordinateTransform to a location.

applyInPlace(double[]) - Method in class mpicbg.models.CoordinateTransformList

 

applyInPlace(double[]) - Method in class mpicbg.models.CoordinateTransformMap2D

 

applyInPlace(double[]) - Method in class mpicbg.models.HomographyModel2D

 

applyInPlace(double[]) - Method in class mpicbg.models.IdentityModel

 

applyInPlace(double[]) - Method in class mpicbg.models.InterpolatedAffineModel1D

 

applyInPlace(double[]) - Method in class mpicbg.models.InterpolatedAffineModel2D

 

applyInPlace(double[]) - Method in class mpicbg.models.InterpolatedAffineModel3D

 

applyInPlace(double[]) - Method in class mpicbg.models.InterpolatedCoordinateTransform

 

applyInPlace(double[]) - Method in class mpicbg.models.InterpolatedModel

 

applyInPlace(double[]) - Method in class mpicbg.models.InvertibleCoordinateTransformList

 

applyInPlace(double[]) - Method in class mpicbg.models.MovingLeastSquaresTransform

 

applyInPlace(double[]) - Method in class mpicbg.models.MovingLeastSquaresTransform2

 

applyInPlace(double[]) - Method in class mpicbg.models.PolynomialTransform2D

 

applyInPlace(double[]) - Method in class mpicbg.models.RigidModel2D

 

applyInPlace(double[]) - Method in class mpicbg.models.RigidModel3D

 

applyInPlace(double[]) - Method in class mpicbg.models.SimilarityModel2D

 

applyInPlace(double[]) - Method in class mpicbg.models.SimilarityModel3D

 

applyInPlace(double[]) - Method in class mpicbg.models.TransformMesh

 

applyInPlace(double[]) - Method in class mpicbg.models.TranslationModel1D

 

applyInPlace(double[]) - Method in class mpicbg.models.TranslationModel2D

 

applyInPlace(double[]) - Method in class mpicbg.models.TranslationModel3D

 

applyInPlace(double[]) - Method in class mpicbg.panorama.EquirectangularProjection

 

applyInPlace(double[]) - Method in class mpicbg.panorama.RectlinearCamera

 

applyInPlace(double[]) - Method in class mpicbg.pointdescriptor.model.FixedModel

 

applyInPlace(double[]) - Method in class mpicbg.pointdescriptor.model.TranslationInvariantAffineModel3D

 

applyInPlace(double[]) - Method in class mpicbg.pointdescriptor.model.TranslationInvariantFixedModel

 

applyInPlace(double[]) - Method in class mpicbg.pointdescriptor.model.TranslationInvariantRigidModel2D

 

applyInPlace(double[]) - Method in class mpicbg.pointdescriptor.model.TranslationInvariantRigidModel3D

 

applyInPlace(double[]) - Method in class mpicbg.pointdescriptor.model.TranslationInvariantSimilarityModel3D

 

applyInPlace(AbstractAffineModel3D<?>, Point3d) - Static method in class mpicbg.spim.mpicbg.Java3d

 

applyInPlace(AbstractAffineModel3D<?>, Point3d, double[]) - Static method in class mpicbg.spim.mpicbg.Java3d

 

applyInPlace(double[]) - Method in class mpicbg.trakem2.transform.MovingLeastSquaresTransform

 

applyInPlace(double[]) - Method in class mpicbg.trakem2.transform.MovingLeastSquaresTransform2

Multi-threading safe version of the original applyInPlace method.

applyInPlace(double[]) - Method in class mpicbg.trakem2.transform.NonLinearCoordinateTransform

 

applyInPlace(double[]) - Method in class mpicbg.trakem2.transform.ThinPlateSplineTransform

 

applyInPlace(float[]) - Method in interface stitching.model.CoordinateTransform

Apply the CoordinateTransform to a location.

applyInPlace(float[]) - Method in class stitching.model.TranslationModel2D

 

applyInPlace(float[]) - Method in class stitching.model.TranslationModel3D

 

applyInverse(double[]) - Method in class bdv.viewer.animate.SimilarityModel3D

 

applyInverse(double[], double[]) - Method in class bigwarp.BigWarp.WrappedCoordinateTransform

 

applyInverse(RealPositionable, RealLocalizable) - Method in class bigwarp.BigWarp.WrappedCoordinateTransform

 

applyInverse(double[]) - Method in class mpicbg.models.AffineModel1D

 

applyInverse(double[]) - Method in class mpicbg.models.AffineModel2D

 

applyInverse(double[]) - Method in class mpicbg.models.AffineModel3D

 

applyInverse(double[]) - Method in class mpicbg.models.HomographyModel2D

 

applyInverse(double[]) - Method in class mpicbg.models.IdentityModel

 

applyInverse(double[]) - Method in class mpicbg.models.InterpolatedAffineModel1D

 

applyInverse(double[]) - Method in class mpicbg.models.InterpolatedAffineModel2D

 

applyInverse(double[]) - Method in class mpicbg.models.InterpolatedAffineModel3D

 

applyInverse(double[]) - Method in interface mpicbg.models.InverseCoordinateTransform

Apply the inverse of the model to a point location

applyInverse(double[]) - Method in class mpicbg.models.InverseCoordinateTransformList

 

applyInverse(double[]) - Method in class mpicbg.models.InverseCoordinateTransformMap2D

 

applyInverse(double[]) - Method in class mpicbg.models.InvertibleConstantModel

 

applyInverse(double[]) - Method in class mpicbg.models.InvertibleCoordinateTransformList

 

applyInverse(double[]) - Method in class mpicbg.models.InvertibleInterpolatedModel

 

applyInverse(InverseCoordinateTransform) - Method in class mpicbg.models.Point

Apply the inverse of an InvertibleCoordinateTransform to the Point.

applyInverse(InverseCoordinateTransform, Iterable<Point>) - Static method in class mpicbg.models.Point

Apply an InverseCoordinateTransform to an Iterable collection of Points.

applyInverse(double[]) - Method in class mpicbg.models.RigidModel2D

 

applyInverse(double[]) - Method in class mpicbg.models.RigidModel3D

 

applyInverse(double[]) - Method in class mpicbg.models.SimilarityModel2D

 

applyInverse(double[]) - Method in class mpicbg.models.SimilarityModel3D

 

applyInverse(double[]) - Method in class mpicbg.models.TransformMesh

 

applyInverse(double[]) - Method in class mpicbg.models.TranslationModel1D

 

applyInverse(double[]) - Method in class mpicbg.models.TranslationModel2D

 

applyInverse(double[]) - Method in class mpicbg.models.TranslationModel3D

 

applyInverse(double[]) - Method in class mpicbg.panorama.EquirectangularProjection

 

applyInverse(double[]) - Method in class mpicbg.panorama.RectlinearCamera

 

applyInverse(double[], double[]) - Method in class net.imglib2.realtransform.Wrapped2DTransformAs3D

 

applyInverse(RealPositionable, RealLocalizable) - Method in class net.imglib2.realtransform.Wrapped2DTransformAs3D

 

applyInverse(double) - Method in class org.janelia.thickness.lut.AbstractLUTGrid

 

applyInverse(double) - Method in class org.janelia.thickness.lut.AbstractLUTRealTransform

 

applyInverse(double, int, int) - Method in class org.janelia.thickness.lut.AbstractLUTRealTransformField

 

applyInverse(int) - Method in class org.janelia.thickness.lut.AbstractPerumtationTransform

 

applyInverse(double[], double[]) - Method in class org.janelia.thickness.lut.LUTGrid

 

applyInverse(float[], float[]) - Method in class org.janelia.thickness.lut.LUTGrid

 

applyInverse(RealPositionable, RealLocalizable) - Method in class org.janelia.thickness.lut.LUTGrid

 

applyInverse(double[], double[]) - Method in class org.janelia.thickness.lut.LUTRealTransform

 

applyInverse(float[], float[]) - Method in class org.janelia.thickness.lut.LUTRealTransform

 

applyInverse(RealPositionable, RealLocalizable) - Method in class org.janelia.thickness.lut.LUTRealTransform

 

applyInverse(double[], double[]) - Method in class org.janelia.thickness.lut.LUTRealTransformField

 

applyInverse(float[], float[]) - Method in class org.janelia.thickness.lut.LUTRealTransformField

 

applyInverse(RealPositionable, RealLocalizable) - Method in class org.janelia.thickness.lut.LUTRealTransformField

 

applyInverse(long[], long[]) - Method in class org.janelia.thickness.lut.PermutationTransform

 

applyInverse(int[], int[]) - Method in class org.janelia.thickness.lut.PermutationTransform

 

applyInverse(Positionable, Localizable) - Method in class org.janelia.thickness.lut.PermutationTransform

 

applyInverse(double[], double[]) - Method in class org.janelia.thickness.lut.SingleDimensionLUTGrid

 

applyInverse(float[], float[]) - Method in class org.janelia.thickness.lut.SingleDimensionLUTGrid

 

applyInverse(RealPositionable, RealLocalizable) - Method in class org.janelia.thickness.lut.SingleDimensionLUTGrid

 

applyInverse(double[], double[]) - Method in class org.janelia.thickness.lut.SingleDimensionLUTRealTransform

 

applyInverse(float[], float[]) - Method in class org.janelia.thickness.lut.SingleDimensionLUTRealTransform

 

applyInverse(RealPositionable, RealLocalizable) - Method in class org.janelia.thickness.lut.SingleDimensionLUTRealTransform

 

applyInverse(double[], double[]) - Method in class org.janelia.thickness.lut.SingleDimensionLUTRealTransformField

 

applyInverse(float[], float[]) - Method in class org.janelia.thickness.lut.SingleDimensionLUTRealTransformField

 

applyInverse(RealPositionable, RealLocalizable) - Method in class org.janelia.thickness.lut.SingleDimensionLUTRealTransformField

 

applyInverse(long[], long[]) - Method in class org.janelia.thickness.lut.SingleDimensionPermutationTransform

 

applyInverse(int[], int[]) - Method in class org.janelia.thickness.lut.SingleDimensionPermutationTransform

 

applyInverse(Positionable, Localizable) - Method in class org.janelia.thickness.lut.SingleDimensionPermutationTransform

 

applyInverse(float[]) - Method in interface stitching.model.InvertibleCoordinateTransform

Apply the inverse of the model to a point location

applyInverse(InvertibleModel) - Method in class stitching.model.Point

Apply the inverse of a InvertibleModel to the Point.

applyInverse(float[]) - Method in class stitching.model.TranslationModel2D

 

applyInverse(float[]) - Method in class stitching.model.TranslationModel3D

 

applyInverseChecked(double) - Method in class org.janelia.thickness.lut.AbstractLUTGrid

 

applyInverseChecked(double) - Method in class org.janelia.thickness.lut.AbstractLUTRealTransform

 

applyInverseChecked(double, int, int) - Method in class org.janelia.thickness.lut.AbstractLUTRealTransformField

 

applyInverseChecked(int) - Method in class org.janelia.thickness.lut.AbstractPerumtationTransform

 

applyInverseInPlace(double[]) - Method in class bdv.viewer.animate.SimilarityModel3D

 

applyInverseInPlace(double[]) - Method in class mpicbg.models.AffineModel1D

 

applyInverseInPlace(double[]) - Method in class mpicbg.models.AffineModel2D

 

applyInverseInPlace(double[]) - Method in class mpicbg.models.AffineModel3D

 

applyInverseInPlace(double[]) - Method in class mpicbg.models.HomographyModel2D

 

applyInverseInPlace(double[]) - Method in class mpicbg.models.IdentityModel

 

applyInverseInPlace(double[]) - Method in class mpicbg.models.InterpolatedAffineModel1D

 

applyInverseInPlace(double[]) - Method in class mpicbg.models.InterpolatedAffineModel2D

 

applyInverseInPlace(double[]) - Method in class mpicbg.models.InterpolatedAffineModel3D

 

applyInverseInPlace(double[]) - Method in interface mpicbg.models.InverseCoordinateTransform

apply the inverse of the model to a point location

applyInverseInPlace(double[]) - Method in class mpicbg.models.InverseCoordinateTransformList

 

applyInverseInPlace(double[]) - Method in class mpicbg.models.InverseCoordinateTransformMap2D

 

applyInverseInPlace(double[]) - Method in class mpicbg.models.InvertibleConstantModel

 

applyInverseInPlace(double[]) - Method in class mpicbg.models.InvertibleCoordinateTransformList

 

applyInverseInPlace(double[]) - Method in class mpicbg.models.InvertibleInterpolatedModel

 

applyInverseInPlace(double[]) - Method in class mpicbg.models.RigidModel2D

 

applyInverseInPlace(double[]) - Method in class mpicbg.models.RigidModel3D

 

applyInverseInPlace(double[]) - Method in class mpicbg.models.SimilarityModel2D

 

applyInverseInPlace(double[]) - Method in class mpicbg.models.SimilarityModel3D

 

applyInverseInPlace(double[]) - Method in class mpicbg.models.TransformMesh

 

applyInverseInPlace(double[]) - Method in class mpicbg.models.TranslationModel1D

 

applyInverseInPlace(double[]) - Method in class mpicbg.models.TranslationModel2D

 

applyInverseInPlace(double[]) - Method in class mpicbg.models.TranslationModel3D

 

applyInverseInPlace(double[]) - Method in class mpicbg.panorama.EquirectangularProjection

 

applyInverseInPlace(double[]) - Method in class mpicbg.panorama.RectlinearCamera

 

applyInverseInPlace(AbstractAffineModel3D<?>, Point3d) - Static method in class mpicbg.spim.mpicbg.Java3d

 

applyInverseInPlace(AbstractAffineModel3D<?>, Point3d, double[]) - Static method in class mpicbg.spim.mpicbg.Java3d

 

applyInverseInPlace(double[]) - Method in class mpicbg.trakem2.transform.TransformMesh

Catch non-invertible locations outside of the meshes boundaries and transfer them with the affine defined by the `closest' affine (the affine whose summed up control points distances to location are smallest).

applyInverseInPlace(float[]) - Method in interface stitching.model.InvertibleCoordinateTransform

apply the inverse of the model to a point location

applyInverseInPlace(float[]) - Method in class stitching.model.TranslationModel2D

 

applyInverseInPlace(float[]) - Method in class stitching.model.TranslationModel3D

 

applyLayerTransformToPatch(Patch, CoordinateTransform) - Static method in class mpicbg.trakem2.align.Util

 

applyLayerWise(Collection<Layer>) - Method in class ini.trakem2.imaging.ContrastEnhancerWrapper

 

applyLocalizedPattern(String) - Method in class HybridDateFormat

This method sets the formatting pattern that should be used by this object.

ApplyLog(double) - Method in class view5d.PixelDisplay

 

applyLSTAMP(ImagePlus, LSMFileInfo) - Method in class org.imagearchive.lsm.toolbox.gui.ControlPanelFrame

 

applyMedianFilter(RandomAccessibleInterval<R>) - Static method in class fiji.plugin.trackmate.detection.DetectionUtils

Apply a simple 3x3 median filter to the target image.

applyMetaData(Image<?>, IFormatReader) - Static method in class mpicbg.imglib.io.LOCI

 

applyMethodStack(List<RecordedImageProcessor.MethodEntry>) - Method in class loci.plugins.util.RecordedImageProcessor

 

applyModels(SpimData, double, int, Map<ViewDescription, Pair<double[], String>>) - Method in class spim.fiji.plugin.Apply_Transformation

 

applyOffset(double, double, double) - Method in class sholl.UPoint

 

ApplyParameters - Class in spim.fiji.plugin.apply

 

ApplyParameters() - Constructor for class spim.fiji.plugin.apply.ApplyParameters

 

applyPatchTask(List<Patch>, String, Operation<Boolean, Patch>, Filter<Patch>) - Method in class ini.trakem2.display.Display

Meant for tasks that require setting an undo and regenerating mipmaps.

applyPattern(String) - Method in class HybridDateFormat

This method sets the formatting pattern that should be used by this object.

applyPrecomputedSignatures(int[], float[], int, double) - Method in class org.siox.SioxSegmentator

Segments the given image with the previously calculated color signatures.

applyRawTransformationToSource(double[][], double[][]) - Method in class bunwarpj.MainDialog

Apply a raw transformation to the source image.

applyRawTransformationToSource(ImagePlus, ImagePlus, BSplineModel, double[][], double[][]) - Static method in class bunwarpj.MiscTools

Apply a given raw transformation to the source image.

applyRawTransformToSource(String, ImagePlus, ImagePlus) - Static method in class bunwarpj.bUnwarpJ_

Apply a raw transform loaded from file to the source image.

applyRotation(int, double) - Method in class ij3d.Content

 

applyScaling - Static variable in class process.Matching

 

applySelection(float) - Method in class org.siox.example.ScrollDisplay

Applies the given value to the confidence matrix entries within the selected area.

applyShifts(double[], double[], double[], PermutationTransform, Options) - Method in class org.janelia.thickness.inference.InferFromMatrix

 

applySurfaceColors(ImagePlus) - Method in class ij3d.Content

 

applySurfaceColors(ImagePlus) - Method in class ij3d.ContentInstant

 

applySurfaceColors(Content) - Method in class ij3d.Executer

 

applyTable(int[]) - Method in class loci.plugins.util.RecordedImageProcessor

 

applyThreshold(ImageProcessor, Roi, int, int) - Static method in class vib.Local_Threshold

 

applyTimepoints(LoadParseQueryXML) - Method in class spim.fiji.plugin.Duplicate_Transformation

 

applyTo - Variable in class spim.fiji.plugin.apply.ApplyParameters

 

applyToChoice - Static variable in class spim.fiji.plugin.Apply_Transformation

 

applyToSlab(Node.Operation<T>) - Method in class ini.trakem2.display.Node

Apply @param op to this Node and all its subtree nodes until reaching a branch node or end node, inclusive.

applyToSubtree(Node.Operation<T>) - Method in class ini.trakem2.display.Node

Apply @param op to this Node and all its subtree nodes.

applyTransform(double[]) - Method in class ij3d.Content

 

applyTransform(Transform3D) - Method in class ij3d.Content

 

applyTransform(double[]) - Method in class ij3d.ContentInstant

 

applyTransform(Transform3D) - Method in class ij3d.ContentInstant

 

applyTransform(Content) - Method in class ij3d.Executer

 

applyTransform(String) - Static method in class ij3d.ImageJ3DViewer

 

applyTransform() - Method in class ini.trakem2.display.DisplayCanvas

 

applyTransform(ArrayList<Point>) - Method in class mpicbg.pointdescriptor.test.TestPointDescriptor

 

applyTransformationMT(ImagePlus, ImagePlus, BSplineModel, int, double[][], double[][]) - Static method in class bunwarpj.MiscTools

Apply a given B-spline transformation to the source (gray-scale) image.

ApplyTransformationPopup - Class in spim.fiji.spimdata.explorer.popup

 

ApplyTransformationPopup() - Constructor for class spim.fiji.spimdata.explorer.popup.ApplyTransformationPopup

 

ApplyTransformationPopup.MyActionListener - Class in spim.fiji.spimdata.explorer.popup

 

applyTransformationToSource(int, double[][], double[][]) - Method in class bunwarpj.MainDialog

Apply the transformation defined by the spline coefficients to the source image.

applyTransformationToSource(ImagePlus, ImagePlus, BSplineModel, int, double[][], double[][]) - Static method in class bunwarpj.MiscTools

Deprecated. 

applyTransformationToSource(ImagePlus, ImagePlus, BSplineModel, BSplineModel, BSplineModel, int, double[][], double[][]) - Static method in class bunwarpj.MiscTools

Deprecated. 

applyTransformationToSourceMT(ImagePlus, ImagePlus, int, double[][], double[][]) - Static method in class bunwarpj.MiscTools

Apply a given B-spline transformation to the source (gray-scale) image.

applyTransformationToSourceMT(ImagePlus, ImagePlus, BSplineModel, int, double[][], double[][]) - Static method in class bunwarpj.MiscTools

Apply a given B-spline transformation to the source (gray-scale) image.

applyTransformReverse(List<PointMatch>, CoordinateTransform) - Static method in class register_virtual_stack.Register_Virtual_Stack_MT

Apply a transformation to the second point (P2) of a list of Point matches

applyTransformRotationXYZ(double, double, double) - Method in class jRenderer3D.JRenderer3D

Changes the rotation of x-, y-, and z-axis by the values of changeX and changeY.

applyTransforms(Map<Displayable, AffineTransform>) - Static method in class ini.trakem2.display.LayerSet

 

applyTransformToLayer(Layer, CoordinateTransform, Filter<Patch>) - Static method in class mpicbg.trakem2.align.ElasticLayerAlignment

 

applyTransformToLayer(Layer, AffineTransform, Filter<Patch>) - Static method in class mpicbg.trakem2.align.RegularizedAffineLayerAlignment

 

applyTransformToSource(String, ImagePlus, ImagePlus) - Static method in class bunwarpj.bUnwarpJ_

Apply transform loaded from file to source image (in place).

applyTransformToStack(String, ImagePlus, ImagePlus) - Static method in class bunwarpj.MiscTools

Apply transform saved on a file to all slices of moving image

applyTranslation(float, float, float) - Method in class ij3d.Content

 

applyTSTAMP(ImagePlus, LSMFileInfo) - Method in class org.imagearchive.lsm.toolbox.gui.ControlPanelFrame

 

applyWithoutTranslation(double, double, double) - Method in class vib.FastMatrix

 

applyWithoutTranslation(Point3d) - Method in class vib.FastMatrix

 

applyWithoutTranslation(float, float, float) - Method in class vib.FloatMatrix

 

applyWithoutTranslation(Point3d) - Method in class vib.FloatMatrix

 

applyZSTAMP(ImagePlus, LSMFileInfo) - Method in class org.imagearchive.lsm.toolbox.gui.ControlPanelFrame

 

approximateEntropy(RandomAccessibleInterval<FloatType>, ImgFactory<ComplexFloatType>, double[], double[]) - Method in class spim.process.fusion.weights.ContentBased

 

approximateInverseCoords(double[], ImagePlus, double[][], double[][]) - Static method in class bunwarpj.MiscTools

Approximate the transformed coordinates of a point from the moving image into the fixed image.

approximateTransferPixel(int[]) - Method in class ini.trakem2.display.Patch

Transfer an 8-bit or RGB pixel to this image color space, interpolating; the pvalue is modified in place.

approxNumberOfPoints() - Method in class bigwarp.landmarks.LandmarkGridGenerator

 

apv - Variable in class mpicbg.models.SpringMesh

 

ArchipelagoClient - Class in edu.utexas.clm.archipelago.network.client

 

ArchipelagoClient(long, InputStream, OutputStream) - Constructor for class edu.utexas.clm.archipelago.network.client.ArchipelagoClient

 

ArchipelagoClient(long, InputStream, OutputStream, TransceiverExceptionListener) - Constructor for class edu.utexas.clm.archipelago.network.client.ArchipelagoClient

 

ArchipelagoFuture<T> - Class in edu.utexas.clm.archipelago.compute

 

ArchipelagoFuture(Scheduler) - Constructor for class edu.utexas.clm.archipelago.compute.ArchipelagoFuture

 

ArchipelagoFuture(Scheduler, T) - Constructor for class edu.utexas.clm.archipelago.compute.ArchipelagoFuture

 

ArchipelagoServer - Class in edu.utexas.clm.archipelago.network.server

 

ArchipelagoUI - Interface in edu.utexas.clm.archipelago.ui

 

ArchipelagoUtils - Class in edu.utexas.archipelago

 

ArchiveClient - Class in client

 

ArchiveClient(Applet) - Constructor for class client.ArchiveClient

 

ArchiveClient(Applet, String) - Constructor for class client.ArchiveClient

 

archiveClient - Variable in class tracing.SimpleNeuriteTracer

 

area(PathIterator) - Static method in class fiji.geom.AreaCalculations

Computes the surface area of the path or multiple specified paths.

Area() - Constructor for class fiji.geom.AreaCalculations.Area

 

area - Variable in class ini.trakem2.display.Patch.TransformProperties

 

area - Variable in class sc.fiji.balloonSegmentation.structure.Balloon

 

area - Variable in class sc.fiji.balloonSegmentation.structure.BalloonPopulation

 

AREA - Static variable in interface sholl.math.ShollStats

Flag for area normalization (Semi-log/Log-log method)

area_color_cues - Variable in class ini.trakem2.display.LayerSet

 

AREA_DOWNSAMPLING - Static variable in class ini.trakem2.persistence.Loader

 

AreaCalculations - Class in fiji.geom

 

AreaCalculations() - Constructor for class fiji.geom.AreaCalculations

 

AreaCalculations.Area - Class in fiji.geom

 

AreaCalculations.Calculation - Class in fiji.geom

 

AreaCalculations.Centroid - Class in fiji.geom

 

AreaCalculations.Circumference - Class in fiji.geom

 

AreaContainer - Interface in ini.trakem2.display

 

areaInInts(Area) - Static method in class ini.trakem2.utils.M

Converts all points in @param area to ints by casting.

areaInIntsByRounding(Area) - Static method in class ini.trakem2.utils.M

Converts all points in @param area to ints by rounding.

AreaList - Class in ini.trakem2.display

A list of brush painted areas similar to a set of labelfields in Amira.

AreaList(Project, String, double, double) - Constructor for class ini.trakem2.display.AreaList

 

AreaList(Project, long, HashMap<String, String>, HashMap<Displayable, String>) - Constructor for class ini.trakem2.display.AreaList

Reconstruct from XML.

AreaList(Project, long, String, float, float, float, boolean, Color, boolean, ArrayList<Long>, AffineTransform) - Constructor for class ini.trakem2.display.AreaList

Reconstruct from the database.

AreaList_Crop - Class in edu.utexas.clm.crop

 

AreaList_Crop() - Constructor for class edu.utexas.clm.crop.AreaList_Crop

 

AreaListCrop - Class in edu.utexas.clm.crop

 

AreaListCrop() - Constructor for class edu.utexas.clm.crop.AreaListCrop

 

AreaListVolume - Class in ij3d

Wraps a list of Areas to be triangulated.

AreaListVolume(List<List<Area>>, double, double, double, double) - Constructor for class ij3d.AreaListVolume

 

areAllRoisEmpty() - Method in class vib.segment.CustomStackWindow

 

AreaNode(float, float, Layer) - Constructor for class ini.trakem2.display.AreaTree.AreaNode

 

AreaNode(HashMap<String, String>) - Constructor for class ini.trakem2.display.AreaTree.AreaNode

To reconstruct from XML, without a layer.

AreaTree - Class in ini.trakem2.display

 

AreaTree(Project, String) - Constructor for class ini.trakem2.display.AreaTree

 

AreaTree(Project, long, HashMap<String, String>, HashMap<Displayable, String>) - Constructor for class ini.trakem2.display.AreaTree

Reconstruct from XML.

AreaTree(Project, long, String, float, float, float, boolean, Color, boolean, AffineTransform) - Constructor for class ini.trakem2.display.AreaTree

For cloning purposes, does not call addToDatabase()

AreaTree.AreaNode - Class in ini.trakem2.display

 

AreaUtils - Class in ini.trakem2.utils

 

AreaWrapper - Class in ini.trakem2.display

 

AreaWrapper(Displayable, Area) - Constructor for class ini.trakem2.display.AreaWrapper

 

AreaWrapper() - Constructor for class ini.trakem2.display.AreaWrapper

 

AreaWrapper(Area) - Constructor for class ini.trakem2.display.AreaWrapper

 

AreaWrapper.PaintParameters - Class in ini.trakem2.display

 

areLandmarksVisible() - Method in class bdv.viewer.BigWarpViewerSettings

 

areNamesVisible() - Method in class bdv.viewer.BigWarpViewerSettings

 

areThereLayerCrossLinks(Set<Layer>, boolean) - Static method in class ini.trakem2.display.Displayable

Returns true if any Displayable objects of different layers in sublist are linked to each other.

areTransformsTheSame(RealTransform, RealTransform, Interval, double) - Static method in class bdv.ij.BigWarpToDeformationFieldPlugIn

 

arg - Variable in class loci.plugins.LociExporter

Argument passed to setup method.

argb(int, int, int) - Static method in class mpicbg.util.ColorStream

 

ARGB(double, double) - Constructor for class net.imglib2.display.ScaledARGBConverter.ARGB

 

argb(int, int, int) - Static method in class spim.fiji.spimdata.explorer.util.ColorStream

 

ARGBARGBColorConverter<R> - Class in net.imglib2.display

 

ARGBARGBColorConverter(double, double) - Constructor for class net.imglib2.display.ARGBARGBColorConverter

 

ARGBARGBColorConverter.ToGray - Class in net.imglib2.display

A converter from a ARGB to ARGB that initially converts the input color to grayscale, then scales the resulting grayscale value with the set color.

ARGBARGBColorConverter.VolatileToGray - Class in net.imglib2.display

 

ARGBtoRandomARGBColorConverter<R> - Class in net.imglib2.display

 

ARGBtoRandomARGBColorConverter(double, double) - Constructor for class net.imglib2.display.ARGBtoRandomARGBColorConverter

 

ARGBtoRandomARGBColorConverter.ToGray - Class in net.imglib2.display

A converter from a ARGB to ARGB that initially converts the input color to grayscale, then scales the resulting grayscale value with the set color.

ARGBtoRandomARGBColorConverter.VolatileToGray - Class in net.imglib2.display

 

args - Static variable in class loci.plugins.shortcut.ShortcutPanel

Details for installed plugins.

ARMED - Static variable in class vib.segment.ImageButton

 

armijoCondition(double, double) - Method in class jitk.spline.TransformInverseGradientDescent

Returns true if the armijo condition is satisfied.

arrangement - Variable in class stitching.GridLayout

 

arrangeWindowsMenuItem - Variable in class tracing.NeuriteTracerResultsDialog

 

Array<T extends Type<T>,A extends DataAccess> - Class in mpicbg.imglib.container.array

TODO

Array(ArrayContainerFactory, A, int[], int) - Constructor for class mpicbg.imglib.container.array.Array

 

Array3D<T extends Type<T>,A extends DataAccess> - Class in mpicbg.imglib.container.array

TODO

Array3D(ArrayContainerFactory, A, int, int, int, int) - Constructor for class mpicbg.imglib.container.array.Array3D

 

Array3DLocalizableByDimCursor<T extends Type<T>> - Class in mpicbg.imglib.cursor.array

TODO

Array3DLocalizableByDimCursor(Array3D<T, ?>, Image<T>, T) - Constructor for class mpicbg.imglib.cursor.array.Array3DLocalizableByDimCursor

 

Array3DLocalizableByDimOutOfBoundsCursor<T extends Type<T>> - Class in mpicbg.imglib.cursor.array

TODO

Array3DLocalizableByDimOutOfBoundsCursor(Array3D<T, ?>, Image<T>, T, OutOfBoundsStrategyFactory<T>) - Constructor for class mpicbg.imglib.cursor.array.Array3DLocalizableByDimOutOfBoundsCursor

 

Array3DLocalizableCursor<T extends Type<T>> - Class in mpicbg.imglib.cursor.array

TODO

Array3DLocalizableCursor(Array3D<T, ?>, Image<T>, T) - Constructor for class mpicbg.imglib.cursor.array.Array3DLocalizableCursor

 

ArrayBase<ArrayType,BaseType> - Class in fiji.util

 

ArrayBase(int, int, Class) - Constructor for class fiji.util.ArrayBase

 

ArrayBase(int, Class) - Constructor for class fiji.util.ArrayBase

 

ArrayContainerFactory - Class in mpicbg.imglib.container.array

TODO

ArrayContainerFactory() - Constructor for class mpicbg.imglib.container.array.ArrayContainerFactory

 

ArrayConverter - Class in mpi.fruitfly.general

Title:

ArrayConverter() - Constructor for class mpi.fruitfly.general.ArrayConverter

 

ArrayCursor<T extends Type<T>> - Class in mpicbg.imglib.cursor.array

TODO

ArrayCursor(Array<T, ?>, Image<T>, T) - Constructor for class mpicbg.imglib.cursor.array.ArrayCursor

 

ArrayDataAccess<A> - Interface in mpicbg.imglib.container.basictypecontainer.array

TODO

ArrayImgLoader(T) - Constructor for class bdv.ij.export.imgloader.FusionImageLoader.ArrayImgLoader

Deprecated.

 

arrayIndex - Variable in class mpicbg.imglib.labeling.LocalizableLabelingCursor

 

ArrayIterable(Iterable<double[]>) - Constructor for class org.janelia.thickness.inference.visitor.CorrelationFitVisitor.ArrayIterable

 

ArrayLocalizableByDimCursor<T extends Type<T>> - Class in mpicbg.imglib.cursor.array

TODO

ArrayLocalizableByDimCursor(Array<T, ?>, Image<T>, T) - Constructor for class mpicbg.imglib.cursor.array.ArrayLocalizableByDimCursor

 

ArrayLocalizableByDimOutOfBoundsCursor<T extends Type<T>> - Class in mpicbg.imglib.cursor.array

TODO

ArrayLocalizableByDimOutOfBoundsCursor(Array<T, ?>, Image<T>, T, OutOfBoundsStrategyFactory<T>) - Constructor for class mpicbg.imglib.cursor.array.ArrayLocalizableByDimOutOfBoundsCursor

 

ArrayLocalizableCursor<T extends Type<T>> - Class in mpicbg.imglib.cursor.array

TODO

ArrayLocalizableCursor(Array<T, ?>, Image<T>, T) - Constructor for class mpicbg.imglib.cursor.array.ArrayLocalizableCursor

 

ArrayLocalizablePlaneCursor<T extends Type<T>> - Class in mpicbg.imglib.cursor.array

TODO

ArrayLocalizablePlaneCursor(Array<T, ?>, Image<T>, T) - Constructor for class mpicbg.imglib.cursor.array.ArrayLocalizablePlaneCursor

 

ArraySortedIndices - Class in org.janelia.utility.arrays

 

ArraySortedIndices() - Constructor for class org.janelia.utility.arrays.ArraySortedIndices

 

ArrayToByteProcessor(ImageProcessor, int[][]) - Static method in class mpi.fruitfly.general.ImageArrayConverter

 

ArrayToByteProcessor(ImageProcessor, float[][]) - Static method in class mpi.fruitfly.general.ImageArrayConverter

 

ArrayToFloatProcessor(ImageProcessor, double[], int, int) - Static method in class mpi.fruitfly.general.ImageArrayConverter

 

ArrayToFloatProcessor(ImageProcessor, float[], int, int) - Static method in class mpi.fruitfly.general.ImageArrayConverter

 

arrayType - Variable in class mpicbg.imglib.cursor.special.SortedGrayLevelIteratorArrayContainerOnly

 

ARROW - Static variable in class ini.trakem2.display.DLabel

 

Arrow - Class in util

 

Arrow(Color, double, double, double, double, double, double, int) - Constructor for class util.Arrow

 

ArrowDisplayer - Interface in util

 

ArrowOptionPanel - Class in fiji.util

 

ArrowOptionPanel(ArrowShape, BasicStroke) - Constructor for class fiji.util.ArrowOptionPanel

Instantiates the config panel with using settings from arguments.

ArrowOptionPanel() - Constructor for class fiji.util.ArrowOptionPanel

 

ArrowShape - Class in fiji.util

 

ArrowShape() - Constructor for class fiji.util.ArrowShape

 

ArrowShape(ArrowShape.ArrowStyle) - Constructor for class fiji.util.ArrowShape

 

ArrowShape(ArrowShape.ArrowStyle, double) - Constructor for class fiji.util.ArrowShape

 

ArrowShape.ArrowStyle - Enum in fiji.util

 

ArrowTool - Class in fiji.util

ArrowTool plugin

ArrowTool() - Constructor for class fiji.util.ArrowTool

 

asAffine3D() - Method in interface mpicbg.spim.data.registration.ViewTransform

A representation of this ViewTransform as a 3D AffineGet.

asAffine3D() - Method in class mpicbg.spim.data.registration.ViewTransformAffine

 

asArray(int, double) - Static method in class script.imglib.algorithm.fn.AlgorithmUtil

Copy the given double value into each index of a double[] array of length .

asBufferedImage(Image) - Static method in class ini.trakem2.io.ImageSaver

 

asChart() - Method in class script.imglib.analysis.Histogram

 

asChart(boolean) - Method in class script.imglib.analysis.Histogram

Return the JFreeChart with this histogram, and as a side effect, show it in a JFrame that provides the means to edit the dimensions and also the plot properties via a popup menu.

ASCII - Variable in class amira.AmiraMeshDecoder

 

ASCII - Static variable in class isosurface.MeshExporter

 

asContent(Display3D) - Method in class ini.trakem2.display.Display3D.VectorStringContent

 

asDoubleArray(Collection<Number>) - Static method in class script.imglib.algorithm.fn.AlgorithmUtil

 

asDoubleArray(float[]) - Static method in class script.imglib.algorithm.fn.AlgorithmUtil

 

asGrey(BufferedImage) - Static method in class ini.trakem2.io.ImageSaver

If the given BufferedImage is of type TYPE_BYTE_GRAY, it will simply return it.

asHexRGBColor(Color) - Static method in class ini.trakem2.utils.Utils

 

asHexRGBColor(StringBuilder, Color) - Static method in class ini.trakem2.utils.Utils

 

asImage() - Method in class script.imglib.analysis.BarChart

 

asImage(JFreeChart) - Static method in class script.imglib.analysis.ChartUtils

 

asImage(JFreeChart, int, int) - Static method in class script.imglib.analysis.ChartUtils

 

asImage() - Method in class script.imglib.analysis.Histogram

 

asImage() - Method in class script.imglib.color.fn.ColorFunction

 

asImage(int) - Method in class script.imglib.color.fn.ColorFunction

 

asImage() - Method in class script.imglib.math.fn.FloatImageOperation

Evaluate this operation as an Image<FloatType>.

asImage(int) - Method in class script.imglib.math.fn.FloatImageOperation

Evaluate this operation as an Image<FloatType> using the defined number of parallel threads.

asImage() - Method in interface script.imglib.math.fn.ImageComputation

 

asImage(int) - Method in interface script.imglib.math.fn.ImageComputation

 

ASin - Class in script.imglib.math

TODO

ASin(Image<? extends RealType<?>>) - Constructor for class script.imglib.math.ASin

 

ASin(IFunction) - Constructor for class script.imglib.math.ASin

 

ASin(Number) - Constructor for class script.imglib.math.ASin

 

ask_params - Variable in class levelsets.ij.LevelSet

 

askAdjustRadius(Node<Float>) - Method in class ini.trakem2.display.Treeline

 

askForFileForLoading(File, String, Frame, Logger) - Static method in class fiji.plugin.trackmate.io.IOUtils

Prompts the user for a xml file to load from.

askForFileForSaving(File, Frame, Logger) - Static method in class fiji.plugin.trackmate.io.IOUtils

Prompts the user for a xml file to save to.

askForFixedTiles(GlobalOptimizationSubset, GlobalOptimizationType, Set<ViewId>, String) - Method in class spim.fiji.plugin.Interest_Point_Registration

 

askForFolder(File, String, Frame, Logger) - Static method in class fiji.plugin.trackmate.io.IOUtils

Prompts the user for a target folder.

askForNewTag(int) - Method in class ini.trakem2.display.LayerSet

 

askForReferenceTile(GlobalOptimizationSubset, GlobalOptimizationType, String) - Method in class spim.fiji.plugin.Interest_Point_Registration

 

askForRegistrations(GenericDialog) - Method in class spim.fiji.plugin.Duplicate_Transformation

 

askForXMLTemplate(Project) - Method in class ini.trakem2.persistence.Loader

Ask for the user to provide a template XML file to extract a root TemplateThing.

askToFinish() - Method in class landmarks.FineTuneThread

 

askToRemoveTag(int) - Method in class ini.trakem2.display.LayerSet

Returns false if the dialog was canceled or there wasn't any tag to remove.

askWhenMoreThan - Static variable in class spim.fiji.spimdata.explorer.popup.DisplayViewPopup

 

askWhenMoreThan - Static variable in class spim.fiji.spimdata.explorer.popup.RemoveTransformationPopup

 

askWhenMoreThan - Static variable in class spim.fiji.spimdata.explorer.popup.ResavePopup

 

asList(long[]) - Static method in class ini.trakem2.utils.Utils

 

asList(long[], int, int) - Static method in class ini.trakem2.utils.Utils

 

asMask() - Method in class bdv.tools.boundingbox.TransformedRealBoxSelectionDialog.Result

Returns the transformed box as an imglib2 roi.

asOptionPanel() - Method in class ini.trakem2.display.AreaWrapper.PaintParameters

 

asOptionPanel() - Method in class ini.trakem2.imaging.Segmentation.FastMarchingParam

 

asPaintable(List<? extends Paintable>) - Method in class ini.trakem2.display.graphics.DefaultGraphicsSource

Returns the list given as argument without any modification.

asPaintable(List<? extends Paintable>) - Method in interface ini.trakem2.display.graphics.GraphicsSource

Takes as list of Paintable and returns the same or another list with perhaps a different number of Paintable objects, or some replaced by new Paintable instances.

asPaintable(List<? extends Paintable>) - Method in class ini.trakem2.display.graphics.TestGraphicsSource

Replaces all Patch instances by a smiley face.

asPaintable(List<? extends Paintable>) - Method in class ini.trakem2.display.GroupingMode.GroupedGraphicsSource

Returns the list given as argument without any modification.

asPath(double, double, double, String) - Method in class tracing.SearchNode

 

asPathReversed(double, double, double, String) - Method in class tracing.SearchNode

 

asPoint() - Method in class ini.trakem2.display.Node

 

asPoint(Node<T>, boolean) - Method in class ini.trakem2.display.Tree

Return the Node as a point in space.

asPoints(float[]) - Method in class script.imglib.analysis.DoGPeaks

Returns a list of peaks as Java3D points if possible: Point2f for 2D images Point3f for 3D images Point4f for 4D images

asPoints() - Method in class script.imglib.analysis.DoGPeaks

Returns a list of peaks as Java3D points: Point2f for 2D images, Point3f for 3D images, and Point4f for 4D images.

asPoints(Number) - Method in class script.imglib.analysis.DoGPeaks

Returns a list of peaks as Java3D points: Point2f for 2D images, Point3f for 3D images, and Point4f for 4D images.

asRGBABytes(int[], byte[], byte[]) - Static method in class ini.trakem2.imaging.P

 

asRGBBytes(int[]) - Static method in class ini.trakem2.imaging.P

 

asSafePath(String) - Static method in class ini.trakem2.persistence.FSLoader

Takes a String and returns a copy with the following conversions: / to -, space to _, and \ to -.

assembleAllMetaData(SequenceDescription, Collection<? extends ViewId>) - Static method in class spim.fiji.plugin.Apply_Transformation

Should be called before registration to make sure all metadata is right

assembleAllViewPairs() - Method in class spim.process.interestpointregistration.optimizationtypes.AllToAllRegistration

 

assembleAllViewPairs() - Method in class spim.process.interestpointregistration.optimizationtypes.AllToAllRegistrationWithRange

 

assembleAllViewPairs() - Method in class spim.process.interestpointregistration.optimizationtypes.GlobalOptimizationType

 

assembleAllViewPairs() - Method in class spim.process.interestpointregistration.optimizationtypes.IndividualTimepointRegistration

 

assembleAllViewPairs() - Method in class spim.process.interestpointregistration.optimizationtypes.ReferenceTimepointRegistration

 

assembleAngles(List<Angle>) - Method in class spim.fiji.plugin.Duplicate_Transformation

 

assembleAvailableCorrespondences(HashMap<Channel, ArrayList<EfficientBayesianBased.Correspondence>>, HashMap<Channel, Integer>, boolean) - Method in class spim.process.fusion.deconvolution.EfficientBayesianBased

 

assembleChannels(List<Channel>) - Method in class spim.fiji.plugin.Duplicate_Transformation

 

assembleChannels(List<Channel>) - Method in class spim.process.fusion.boundingbox.AutomaticBoundingBox

 

assembleDefaultPattern() - Method in class spim.fiji.datasetmanager.StackList

 

assembleFixedTiles(SpimData2, List<ViewId>, List<ChannelProcess>, TimePoint) - Static method in class spim.process.interestpointregistration.optimizationtypes.ReferenceTimepointRegistration

All tiles of the reference timepoint are fixed, nothing else

assembleIllums(List<Illumination>) - Method in class spim.fiji.plugin.Duplicate_Transformation

 

assembleInputData(SpimData2, TimePoint, Channel, List<ViewId>) - Static method in class spim.process.fusion.FusionHelper

 

assembleNewViewSetupsFusion(SpimData2, List<ViewId>, BoundingBoxGUI, String, String) - Static method in class spim.process.fusion.weightedavg.WeightedAverageFusion

Creates one new Angle and one new Illumination for the fused dataset.

assembleNewViewSetupsSequential(SpimData2, List<ViewId>, BoundingBoxGUI) - Static method in class spim.process.fusion.weightedavg.WeightedAverageFusion

Duplicates all Angles and Illuminations that are processed.

assemblePartialSpimData2(SpimData2, List<ViewId>, File, List<String>) - Static method in class spim.fiji.plugin.resave.Resave_TIFF

Assembles a new SpimData2 based on the subset of timepoints and viewsetups as selected by the user.

assembleRegistrationNames(SpimData, List<ViewId>) - Static method in class spim.fiji.plugin.util.GUIHelper

 

assembleResults() - Method in class sc.fiji.analyzeSkeleton.AnalyzeSkeleton_

Returns the analysis results in a SkeletonResult object.

assembleSpimData2(List<TimePoint>, List<ViewSetup>, File) - Static method in class spim.process.fusion.export.ExportSpimData2TIFF

Assembles a new SpimData2 based on the timepoints and viewsetups.

assembleTimepoints(List<TimePoint>) - Method in class spim.fiji.plugin.Duplicate_Transformation

 

assembleTimepoints(TimePoints) - Static method in class spim.fiji.plugin.Interest_Point_Registration

 

assembleTimepoints(List<TimePoint>) - Method in class spim.process.fusion.boundingbox.AutomaticBoundingBox

 

assertEquals(String, Object, String, Object) - Static method in class sc.fiji.timelapse.PolygonRoiPublic

 

assertEquals(String, Object, String, Object, int) - Static method in class sc.fiji.timelapse.PolygonRoiPublic

 

assertEquals(String, boolean, String, boolean) - Static method in class sc.fiji.timelapse.PolygonRoiPublic

 

assertEquals(String, byte, String, byte) - Static method in class sc.fiji.timelapse.PolygonRoiPublic

 

assertEquals(String, short, String, short) - Static method in class sc.fiji.timelapse.PolygonRoiPublic

 

assertEquals(String, int, String, int) - Static method in class sc.fiji.timelapse.PolygonRoiPublic

 

assertEquals(String, long, String, long) - Static method in class sc.fiji.timelapse.PolygonRoiPublic

 

assertEquals(String, float, String, float) - Static method in class sc.fiji.timelapse.PolygonRoiPublic

 

assertEquals(String, double, String, double) - Static method in class sc.fiji.timelapse.PolygonRoiPublic

 

assertEquals(String, String, String, String) - Static method in class sc.fiji.timelapse.PolygonRoiPublic

 

Assign3DData(Container, ImgPanel, My3DData) - Method in class view5d.AlternateViewer

 

assignImage(ImagePlus) - Method in class sholl.Profile

 

assignListenerToHelpButton(String, ActionListener) - Method in class sholl.gui.EnhancedGenericDialog

Deprecated.

Adds a "Help" button and attaches the specified listener to it.

Assignment(int, int, double) - Constructor for class fiji.plugin.trackmate.tracking.sparselap.costmatrix.DefaultCostMatrixCreator.Assignment

 

AssignmentAlgorithm - Interface in fiji.plugin.trackmate.tracking.oldlap.hungarian

Just in case I want to try more than one implementation of the assignment algorithm.

AssignmentProblem - Class in fiji.plugin.trackmate.tracking.oldlap.hungarian

An implementation of this: http://en.wikipedia.org/wiki/Hungarian_algorithm

AssignmentProblem(double[][]) - Constructor for class fiji.plugin.trackmate.tracking.oldlap.hungarian.AssignmentProblem

 

assignNewAttributeIds(AbstractSpimData<?>, Map<String, Set<Integer>>) - Static method in class bdv.spimdata.tools.ChangeAttributeId

For the specified spimData data set, re-assign attribute id's that are already in use.

assignNewViewSetupIds(AbstractSpimData<?>, Set<Integer>) - Static method in class bdv.spimdata.tools.ChangeViewSetupId

For the specified spimData data set, re-assign setup id's that are already in use.

AssignOperation<T extends RealType<T>> - Class in imglib.ops.operation

An AssignOperation computes values in an output image.

AssignOperation(Image<T>[], Image<T>, RealFunction<T>) - Constructor for class imglib.ops.operation.AssignOperation

 

assignOtherChannel(Channel, HashMap<Channel, ChannelPSF>) - Method in class spim.process.fusion.deconvolution.ProcessForDeconvolution

 

AssignPixelDisplay(PixelDisplay) - Method in class view5d.AlternateViewer

 

assignPointMatches(List<P>, List<P>) - Method in interface mpicbg.icp.PointMatchIdentification

 

assignPointMatches(List<P>, List<P>) - Method in class mpicbg.icp.SimplePointMatchIdentification

 

assignPoints(Set<UPoint>) - Method in class sholl.ProfileEntry

 

assignPopupToHelpButton(JPopupMenu) - Method in class sholl.gui.EnhancedGenericDialog

Deprecated.

Attaches the specified JPopupMenu to the GenericDialog "Help" button renamed "More »".

assignPopupToHelpButton(String, JPopupMenu) - Method in class sholl.gui.EnhancedGenericDialog

Deprecated.

Adds a "Help" button and attaches the specified JPopupMenu to it.

assignProperty(String) - Method in class sholl.gui.ShollOverlay

 

assignSliceTo(int, Roi, int) - Method in class vib.segment.CustomStackWindow

 

assignViewsToTiles(M, List<ViewId>, boolean) - Static method in class spim.process.interestpointregistration.GlobalOpt

 

assoc(BufferedImage) - Method in class ini.trakem2.display.DisplayCanvas.Screenshot

Associate @param img to this, with a new sid.

asVectorString2D(Polygon, double) - Static method in class ini.trakem2.utils.M

 

asVectorString3D() - Method in interface ini.trakem2.display.Line3D

 

asVectorString3D() - Method in class ini.trakem2.display.Pipe

Returns a non-calibrated VectorString3D.

asVectorString3D() - Method in class ini.trakem2.display.Polyline

Returns a non-calibrated VectorString3D.

asVertices() - Method in class ini.trakem2.display.Tree

Return a representation of this Tree with Vertex instead of Node.

asVolatile(V, SharedQueue) - Method in class bdv.util.RandomAccessibleIntervalMipmapSource

 

asVolatile(Supplier<V>, SharedQueue) - Method in class bdv.util.RandomAccessibleIntervalMipmapSource

 

asVolatile(SharedQueue) - Method in class bdv.util.RandomAccessibleIntervalMipmapSource

 

asVolatile() - Method in class bdv.viewer.SourceAndConverter

 

asVolatile() - Method in class bdv.viewer.state.SourceState

Deprecated.

 

asWorldPoints() - Method in class ini.trakem2.display.Ball

Returns a Point3f for every x,y,z ball, in calibrated world space.

at - Variable in class ini.trakem2.display.Displayable

 

at - Variable in class ini.trakem2.display.Displayable.DataPackage

 

at - Variable in class ini.trakem2.display.Patch.TransformProperties

 

ATan - Class in script.imglib.math

TODO

ATan(Image<? extends RealType<?>>) - Constructor for class script.imglib.math.ATan

 

ATan(IFunction) - Constructor for class script.imglib.math.ATan

 

ATan(Number) - Constructor for class script.imglib.math.ATan

 

ATan2 - Class in script.imglib.math

TODO

ATan2(Image<? extends RealType<?>>, Image<? extends RealType<?>>) - Constructor for class script.imglib.math.ATan2

 

ATan2(IFunction, Image<? extends RealType<?>>) - Constructor for class script.imglib.math.ATan2

 

ATan2(Image<? extends RealType<?>>, IFunction) - Constructor for class script.imglib.math.ATan2

 

ATan2(IFunction, IFunction) - Constructor for class script.imglib.math.ATan2

 

ATan2(Image<? extends RealType<?>>, Number) - Constructor for class script.imglib.math.ATan2

 

ATan2(Number, Image<? extends RealType<?>>) - Constructor for class script.imglib.math.ATan2

 

ATan2(IFunction, Number) - Constructor for class script.imglib.math.ATan2

 

ATan2(Number, IFunction) - Constructor for class script.imglib.math.ATan2

 

ATan2(Number, Number) - Constructor for class script.imglib.math.ATan2

 

atGoal(int, int, int, boolean) - Method in class tracing.SearchThread

 

atGoal(int, int, int, boolean) - Method in class tracing.TracerThread

 

attNumVals - Variable in class hr.irb.fastRandomForest.DataCache

Attribute description - holds a 0 for numeric attributes, and the number of available categories for nominal attributes.

ATTRIBUTE_COORD_SYSTEM - Static variable in class ij3d.DefaultUniverse

Constant used in showAttribute() specifying whether a global coordinate system should be displayed or not.

ATTRIBUTE_SCALEBAR - Static variable in class ij3d.DefaultUniverse

Constant used in showAttribute() specifying whether a scalebar should be displayed or not.

attributeChoice - Variable in class spim.fiji.plugin.queryXML.GenericLoadParseQueryXML

 

attributeChoiceList - Static variable in class spim.fiji.plugin.queryXML.GenericLoadParseQueryXML

 

AttributeClassPair - Class in ai

Inner class to order attributes while preserving class indices

attributeInstancesToProcess - Variable in class spim.fiji.plugin.queryXML.GenericLoadParseQueryXML

 

attributeMap - Variable in class mpicbg.spim.data.generic.sequence.XmlIoBasicViewSetup

Maps attribute tag name to map from id to entity.

attributes - Variable in class spim.fiji.plugin.queryXML.GenericLoadParseQueryXML

 

ATTRIBUTES_NAME_ATTRIBUTE_NAME - Static variable in class mpicbg.spim.data.XmlKeys

 

ATTRIBUTES_SPECIALIZED_ATTRIBUTE_NAME - Static variable in class mpicbg.spim.data.XmlKeys

 

ATTRIBUTES_TAG - Static variable in class mpicbg.spim.data.XmlKeys

 

attributesSwitch - Variable in class ij3d.DefaultUniverse

Switch which holds the optionally displayable scalebar and coordinate system.

attributeValue - Variable in class ai.AttributeClassPair

real value of the corresponding attribute

attrs - Static variable in class lineage.LineageClassifier

 

ATYPICAL_MONOCHROMACY - Static variable in class Daltonize_

 

AugmentedLandmarkWarp_ - Class in vib

 

AugmentedLandmarkWarp_() - Constructor for class vib.AugmentedLandmarkWarp_

 

augmentPath(int) - Method in class fiji.plugin.trackmate.tracking.oldlap.hungarian.MunkresKuhnAlgorithm

 

AuthenticationException - Exception in edu.utexas.clm.archipelago.exception

 

AuthenticationException() - Constructor for exception edu.utexas.clm.archipelago.exception.AuthenticationException

 

AuthenticationException(String) - Constructor for exception edu.utexas.clm.archipelago.exception.AuthenticationException

 

AuthenticationException(String, Throwable) - Constructor for exception edu.utexas.clm.archipelago.exception.AuthenticationException

 

AuthenticationException(Throwable) - Constructor for exception edu.utexas.clm.archipelago.exception.AuthenticationException

 

Auto_Threshold - Class in fiji.threshold

 

Auto_Threshold() - Constructor for class fiji.threshold.Auto_Threshold

 

Auto_Tracer - Class in tracing

 

Auto_Tracer() - Constructor for class tracing.Auto_Tracer

 

Auto_Tracer.TubenessComparator - Class in tracing

 

autoActivationMenuItem - Variable in class tracing.NeuriteTracerResultsDialog

 

autoCanvasActivation - Variable in class tracing.SimpleNeuriteTracer

 

AutoLabeller - Class in oldsegmenters

User: Tom Larkworthy Date: 12-Jul-2006 Time: 19:10:47

AutoLabeller(String) - Constructor for class oldsegmenters.AutoLabeller

 

AutoLabeller.LabelStats - Class in oldsegmenters

 

AutoLabellerNaive - Class in oldsegmenters

User: Tom Larkworthy Date: 12-Jul-2006 Time: 19:12:08

AutoLabellerNaive(String) - Constructor for class oldsegmenters.AutoLabellerNaive

 

AutomaticAngleSetup - Class in mpicbg.spim.preprocessing

 

AutomaticAngleSetup(ViewStructure) - Constructor for class mpicbg.spim.preprocessing.AutomaticAngleSetup

 

AutomaticBoundingBox - Class in spim.process.fusion.boundingbox

 

AutomaticBoundingBox(SpimData2, List<ViewId>) - Constructor for class spim.process.fusion.boundingbox.AutomaticBoundingBox

 

AutomaticReorientation - Class in spim.process.fusion.boundingbox

 

AutomaticReorientation(SpimData2, List<ViewId>) - Constructor for class spim.process.fusion.boundingbox.AutomaticReorientation

 

AutomaticReorientation.Reorientation - Enum in spim.process.fusion.boundingbox

 

autoMinMax() - Method in class fiji.plugin.trackmate.gui.panels.components.ColorByFeatureGUIPanel

 

autoMinMax() - Method in class fiji.plugin.trackmate.gui.panels.components.SetColorScaleDialog

 

autoMinMax() - Method in class fiji.plugin.trackmate.visualization.DummySpotColorGenerator

 

autoMinMax() - Method in class fiji.plugin.trackmate.visualization.DummyTrackColorGenerator

 

autoMinMax() - Method in class fiji.plugin.trackmate.visualization.ManualEdgeColorGenerator

 

autoMinMax() - Method in class fiji.plugin.trackmate.visualization.ManualSpotColorGenerator

 

autoMinMax() - Method in interface fiji.plugin.trackmate.visualization.MinMaxAdjustable

Automatically computes the min & max values from this object current content.

autoMinMax() - Method in class fiji.plugin.trackmate.visualization.PerEdgeFeatureColorGenerator

 

autoMinMax() - Method in class fiji.plugin.trackmate.visualization.PerTrackFeatureColorGenerator

 

autoMinMax() - Method in class fiji.plugin.trackmate.visualization.SpotColorGenerator

 

autoMinMax() - Method in class fiji.plugin.trackmate.visualization.SpotColorGeneratorPerTrackFeature

 

AutoPoint - Class in tracing

 

AutoPoint(int, int, int) - Constructor for class tracing.AutoPoint

 

autoSavePdf - Variable in class sc.fiji.coloc.Coloc_2

 

autosaver - Static variable in class ini.trakem2.persistence.FSLoader

 

autoscale_after_filtering - Variable in class ini.trakem2.imaging.Segmentation.FastMarchingParam

 

autoscaleBox - Variable in class loci.plugins.in.MainDialog

 

autoscroll(Point) - Method in class ini.trakem2.tree.DNDTree

 

AutoSearchThread - Class in tracing

 

AutoSearchThread(ImagePlus, float[][], AutoPoint, float, SinglePathsGraph) - Constructor for class tracing.AutoSearchThread

 

autoThreshold() - Method in class loci.plugins.util.RecordedImageProcessor

 

AutoThresholdRegression<T extends RealType<T>> - Class in sc.fiji.coloc.algorithms

A class implementing the automatic finding of a threshold used for Pearson colocalisation calculation.

AutoThresholdRegression(PearsonsCorrelation<T>) - Constructor for class sc.fiji.coloc.algorithms.AutoThresholdRegression

 

AutoThresholdRegression(PearsonsCorrelation<T>, AutoThresholdRegression.Implementation) - Constructor for class sc.fiji.coloc.algorithms.AutoThresholdRegression

 

AutoThresholdRegression.Implementation - Enum in sc.fiji.coloc.algorithms

 

autoTrace(ImagePlus) - Method in class tracing.Auto_Tracer

 

AutoTracerCanvas - Class in tracing

 

AutoTracerCanvas(ImagePlus, PaneOwner, int, PathAndFillManager) - Constructor for class tracing.AutoTracerCanvas

 

av - Variable in class mpicbg.models.TransformMesh

 

available - Static variable in class ini.trakem2.imaging.filters.FilterEditor

 

availableFeatures - Static variable in class trainableSegmentation.FeatureStack

names of available filters

availableFeatures - Static variable in class trainableSegmentation.FeatureStack3D

names of available filters

avef() - Method in class parObject

 

average - Variable in class ij3d.Volume

Flag indicating that the channels should be averaged

Average - Class in imglib.ops.operator.binary

TODO

Average() - Constructor for class imglib.ops.operator.binary.Average

 

average(Point3d[]) - Static method in class math3d.Point3d

 

average(int, int) - Static method in class org.siox.util.Utils

Averages two ARGB colors.

Average - Class in script.imglib.math

TODO

Average(Image<? extends RealType<?>>, Image<? extends RealType<?>>) - Constructor for class script.imglib.math.Average

 

Average(IFunction, Image<? extends RealType<?>>) - Constructor for class script.imglib.math.Average

 

Average(Image<? extends RealType<?>>, IFunction) - Constructor for class script.imglib.math.Average

 

Average(IFunction, IFunction) - Constructor for class script.imglib.math.Average

 

Average(Image<? extends RealType<?>>, Number) - Constructor for class script.imglib.math.Average

 

Average(Number, Image<? extends RealType<?>>) - Constructor for class script.imglib.math.Average

 

Average(IFunction, Number) - Constructor for class script.imglib.math.Average

 

Average(Number, IFunction) - Constructor for class script.imglib.math.Average

 

Average(Number, Number) - Constructor for class script.imglib.math.Average

 

Average(Object...) - Constructor for class script.imglib.math.Average

 

average(List<UPoint>) - Static method in class sholl.UPoint

 

average(FastMatrix[]) - Static method in class vib.FastMatrix

 

average(FloatMatrix[]) - Static method in class vib.FloatMatrix

 

Average_Color - Class in <Unnamed>

 

Average_Color() - Constructor for class Average_Color

 

Average_Images - Class in vib

 

Average_Images() - Constructor for class vib.Average_Images

 

Average_Torsten_Results - Class in util

 

Average_Torsten_Results() - Constructor for class util.Average_Torsten_Results

 

averageAllChannels(Image<T>, int[], ImagePlus, int) - Static method in class mpicbg.stitching.PairWiseStitchingImgLib

Averages all channels into the target image.

averageAllChannels(Image<T>, ArrayList<Image<S>>, int[]) - Static method in class mpicbg.stitching.PairWiseStitchingImgLib

Averages all channels into the target image.

AverageBrain - Class in vib.app.module

 

AverageBrain() - Constructor for class vib.app.module.AverageBrain

 

AverageBrain_ - Class in vib

 

AverageBrain_() - Constructor for class vib.AverageBrain_

 

AverageByteLoader(Volume.InputImage) - Constructor for class ij3d.Volume.AverageByteLoader

 

AverageContent - Class in mpicbg.spim.fusion

 

AverageContent(ViewDataBeads, ContainerFactory) - Constructor for class mpicbg.spim.fusion.AverageContent

 

AverageContentFactory - Class in mpicbg.spim.fusion

 

AverageContentFactory(ContainerFactory) - Constructor for class mpicbg.spim.fusion.AverageContentFactory

 

averageFromDirectoryList(ArrayList<File>) - Static method in class util.Average_Torsten_Results

 

AveragePixelFusion - Class in mpicbg.stitching.fusion

 

AveragePixelFusion() - Constructor for class mpicbg.stitching.fusion.AveragePixelFusion

 

AveragePixelFusionIgnoreZero - Class in mpicbg.stitching.fusion

 

AveragePixelFusionIgnoreZero() - Constructor for class mpicbg.stitching.fusion.AveragePixelFusionIgnoreZero

 

Averager() - Constructor for class vib.NaiveResampler.Averager

 

avex() - Method in class parObject

 

avey() - Method in class parObject

 

avg - Variable in class CPU_Meter.CPUMeter

 

avg(int) - Method in class mpicbg.imglib.image.display.imagej.RGBALegacyTypeDisplay

 

AVG - Static variable in class stitching.CommonFunctions

 

avg_grey - Variable in class levelsets.ij.StateContainer

 

AVG_PHYS_DIST - Static variable in class ini.trakem2.analysis.Compare

 

avgError - Variable in class mpicbg.spim.registration.bead.error.GlobalErrorStatisticsImpl

 

avgError - Variable in class mpicbg.spim.registration.bead.error.ViewErrorPairWise

 

AvgFunction<T extends RealType<T>> - Class in imglib.ops.function.pn

TODO

AvgFunction() - Constructor for class imglib.ops.function.pn.AvgFunction

 

avgLocalError - Variable in class mpicbg.spim.registration.bead.error.GlobalErrorStatisticsImpl

 

avgPixels - Variable in class spim.fiji.plugin.fusion.Fusion

 

awtEventMaskList - Static variable in class org.janelia.utility.ui.RepeatingReleasedEventsFixer

 

ax - Variable in class mpicbg.pointdescriptor.LocalCoordinateSystemPointDescriptor

 

axes - Variable in class plugin.Descriptor_based_registration

 

axes - Variable in class tracing.ShollAnalysisDialog.ShollResults

 

AXES_LOG_LOG - Static variable in class tracing.ShollAnalysisDialog

 

AXES_NORMAL - Static variable in class tracing.ShollAnalysisDialog

 

AXES_SEMI_LOG - Static variable in class tracing.ShollAnalysisDialog

 

axesChoice - Variable in class spim.fiji.plugin.Apply_Transformation

 

axesGroup - Variable in class tracing.ShollAnalysisDialog

 

axesParameters - Static variable in class tracing.ShollAnalysisDialog

 

axis - Variable in class bdv.BehaviourTransformEventHandler3D

Current rotation axis for rotating with keyboard, indexed x->0, y->1, z->2.

AxisAngle4d - Class in spim.vecmath

A four-element axis angle represented by double-precision floating point x,y,z,angle components.

AxisAngle4d(double, double, double, double) - Constructor for class spim.vecmath.AxisAngle4d

Constructs and initializes an AxisAngle4d from the specified x, y, z, and angle.

AxisAngle4d(double[]) - Constructor for class spim.vecmath.AxisAngle4d

Constructs and initializes an AxisAngle4d from the components contained in the array.

AxisAngle4d(AxisAngle4d) - Constructor for class spim.vecmath.AxisAngle4d

Constructs and initializes an AxisAngle4d from the specified AxisAngle4d.

AxisAngle4d(AxisAngle4f) - Constructor for class spim.vecmath.AxisAngle4d

Constructs and initializes an AxisAngle4d from the specified AxisAngle4f.

AxisAngle4d(Vector3d, double) - Constructor for class spim.vecmath.AxisAngle4d

Constructs and initializes an AxisAngle4d from the specified axis and angle.

AxisAngle4d() - Constructor for class spim.vecmath.AxisAngle4d

Constructs and initializes an AxisAngle4d to (0,0,1,0).

AxisAngle4f - Class in spim.vecmath

A four-element axis angle represented by single-precision floating point x,y,z,angle components.

AxisAngle4f(float, float, float, float) - Constructor for class spim.vecmath.AxisAngle4f

Constructs and initializes a AxisAngle4f from the specified xyzw coordinates.

AxisAngle4f(float[]) - Constructor for class spim.vecmath.AxisAngle4f

Constructs and initializes an AxisAngle4f from the array of length 4.

AxisAngle4f(AxisAngle4f) - Constructor for class spim.vecmath.AxisAngle4f

Constructs and initializes an AxisAngle4f from the specified AxisAngle4f.

AxisAngle4f(AxisAngle4d) - Constructor for class spim.vecmath.AxisAngle4f

Constructs and initializes an AxisAngle4f from the specified AxisAngle4d.

AxisAngle4f(Vector3f, float) - Constructor for class spim.vecmath.AxisAngle4f

Constructs and initializes an AxisAngle4f from the specified axis and angle.

AxisAngle4f() - Constructor for class spim.vecmath.AxisAngle4f

Constructs and initializes an AxisAngle4f to (0,0,1,0).

AxisConstants - Interface in ij3d

This interface stores some common constants.

axisIndex - Variable in class voltex.VolumeRenderer

The index in the switch, given the direction

AxisLessThan<T extends RealType<T>> - Class in imglib.ops.condition

TODO

AxisLessThan(int, int) - Constructor for class imglib.ops.condition.AxisLessThan

 

AxisOrder - Enum in bdv.util

 

axisOrder(AxisOrder) - Method in class bdv.util.BdvOptions

Specified when adding a stack.

axisOrder() - Method in class bdv.util.BdvOptions.Values

 

axisSwitch - Variable in class voltex.VolumeRenderer

A Switch, which holds 6 OrderedGroups, one for each direction