Index (Fiji Javadocs 2.0.0-SNAPSHOT API)

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _

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)
abortCurrentOperation() - Method in class sc.fiji.snt.SNTUI
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> - Class in mpicbg.pointdescriptor
AbstractPointDescriptor(P, ArrayList, 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) - Method in class ini.trakem2.display.Node.BranchAndEndNodeIterator
accept(Node) - Method in class ini.trakem2.display.Node.BranchNodeIterator
accept(Node) - Method in class ini.trakem2.display.Node.EndNodeIterator
accept(Node) - 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
accessToValidImageData() - Method in class sc.fiji.snt.SNT
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, 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
acronym() - Method in class sc.fiji.snt.annotation.AllenCompartment
acronym() - Method in interface sc.fiji.snt.annotation.BrainAnnotation
acronym() - Method in class sc.fiji.snt.annotation.InsectBrainCompartment
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 sc.fiji.snt.FillManagerUI
actionPerformed(ActionEvent) - Method in class sc.fiji.snt.gui.EnhancedGenericDialog: Deprecated.
actionPerformed(ActionEvent) - Method in class sc.fiji.snt.gui.ShollAnalysisDialog: Deprecated.
actionPerformed(ActionEvent) - Method in class sc.fiji.snt.gui.SWCImportOptionsDialog
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 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 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
activateFinishedPath - Variable in class sc.fiji.snt.SNT
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
adapter - Variable in class sc.fiji.snt.viewer.geditor.SNTGraphComponent
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(ProfileEntry) - Method in class sc.fiji.snt.analysis.sholl.Profile
add(int, int, int, double, int, boolean) - Method in class sc.fiji.snt.Fill
add(Path) - Method in class sc.fiji.snt.Path
add(Path) - Method in class sc.fiji.snt.Tree: Adds a new Path to this Tree.
add(Tree) - Method in class sc.fiji.snt.viewer.Viewer2D: Appends a tree to the viewer using default options.
add(List<Tree>, String) - Method in class sc.fiji.snt.viewer.Viewer2D: Adds a list of trees while assigning each tree to a LUT index.
add(Tree, ColorRGB) - Method in class sc.fiji.snt.viewer.Viewer2D: Appends a tree to the viewer.
add(Tree, String) - Method in class sc.fiji.snt.viewer.Viewer2D: Appends a tree to the viewer.
add(Tree, String, ColorTable, double, double) - Method in class sc.fiji.snt.viewer.Viewer2D: Appends a tree to the viewer rendered after the specified measurement.
add(Tree, String, String) - Method in class sc.fiji.snt.viewer.Viewer2D: Appends a tree to the viewer rendered after the specified measurement.
add(Tree, String, String, double, double) - Method in class sc.fiji.snt.viewer.Viewer2D: Appends a tree to the viewer rendered after the specified measurement.
add(File[], String) - Method in class sc.fiji.snt.viewer.Viewer3D: Adds a collection of trees or meshes from input files.
add(Object) - Method in class sc.fiji.snt.viewer.Viewer3D: Script friendly method to add a supported object (Tree, OBJMesh, AbstractDrawable, etc.) to this viewer.
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(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(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.
addAllAnalyzers() - Method in class fiji.plugin.trackmate.Settings: All the spot analyzers, edge analyzers and track analyzers discovered at runtime.
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 sc.fiji.snt.Path: Deprecated.
addAsLinesTo3DViewer(Image3DUniverse, Color3f, ImagePlus) - Method in class sc.fiji.snt.Path: Deprecated.
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 sc.fiji.snt.analysis.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 sc.fiji.snt.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 sc.fiji.snt.gui.EnhancedGenericDialog: Deprecated.
addColorBarLegend(String, double, double) - Method in class sc.fiji.snt.viewer.Viewer2D
addColorBarLegend(ColorTable, double, double) - Method in class sc.fiji.snt.viewer.Viewer2D: Adds a color bar legend (LUT ramp).
addColorBarLegend(T) - Method in class sc.fiji.snt.viewer.Viewer2D: Adds a color bar legend (LUT ramp) from a ColorMapper.
addColorBarLegend() - Method in class sc.fiji.snt.viewer.Viewer2D: Adds a color bar legend (LUT ramp) to the viewer.
addColorBarLegend(T) - Method in class sc.fiji.snt.viewer.Viewer3D: Adds a color bar legend (LUT ramp) from a ColorMapper.
addColorBarLegend(ColorTable, double, double) - Method in class sc.fiji.snt.viewer.Viewer3D: Adds a color bar legend (LUT ramp) using default settings.
addColorBarLegend(ColorTable, double, double, Font, int, int) - Method in class sc.fiji.snt.viewer.Viewer3D: Adds a color bar legend (LUT ramp).
addColorChangedListener(ColorChangedListener) - Method in class sc.fiji.snt.gui.ColorChooserButton
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 sc.fiji.snt.Path: Deprecated.
addDiscsTo3DViewer(Image3DUniverse, Color3f, ImagePlus) - Method in class sc.fiji.snt.Path: Deprecated.
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 sc.fiji.snt.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).
addGroup(Collection<Tree>, String) - Method in class sc.fiji.snt.analysis.GroupedTreeStatistics: Adds a comparison group to the analysis queue.
addGroup(Collection<Tree>, String, String...) - Method in class sc.fiji.snt.analysis.GroupedTreeStatistics: Adds a comparison group to the analysis queue.
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 sc.fiji.snt.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 sc.fiji.snt.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 sc.fiji.snt.SearchThread: This method can be overridden if one needs 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
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 sc.fiji.snt.viewer.Viewer3D: Adds an annotation label to the scene.
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(SNTListener) - Method in class sc.fiji.snt.SNT
addListener(SelectedViewDescriptionListener<AS>) - Method in class spim.fiji.spimdata.explorer.ViewSetupExplorer
addListener(SelectedViewDescriptionListener<AS>) - Method in class spim.fiji.spimdata.explorer.ViewSetupExplorerPanel
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.
addMesh(OBJMesh) - Method in class sc.fiji.snt.viewer.Viewer3D: Loads a Wavefront .OBJ file.
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
addNode(Node<T>, Node<T>, byte) - Method in class ini.trakem2.display.Tree: Will call calculateBoundingBox and repaint.
addNode(PointInImage) - Method in class sc.fiji.snt.Path: Appends a node to this Path.
addNode(SearchNode, boolean) - Method in class sc.fiji.snt.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
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 sc.fiji.snt.PathAndFillManager: Adds a new path.
addPath(Path, boolean) - Method in class sc.fiji.snt.PathAndFillManager
addPath(Path, boolean, boolean) - Method in class sc.fiji.snt.PathAndFillManager
addPath(Path, boolean, boolean, boolean) - Method in class sc.fiji.snt.PathAndFillManager
addPath(Path, int, int) - Method in class sc.fiji.snt.PathAndFillManager
addPathAndFillListener(PathAndFillListener) - Method in class sc.fiji.snt.PathAndFillManager: Adds a PathAndFillListener.
addPathPointsToShollList(Path, double, double, double, List<ShollAnalysisDialog.ShollPoint>) - Static method in class sc.fiji.snt.gui.ShollAnalysisDialog: Deprecated.
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(ShollPoint) - Method in class sc.fiji.snt.analysis.sholl.ProfileEntry
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
addPointDouble(double, double, double) - Method in class sc.fiji.snt.Path
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 sc.fiji.snt.analysis.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 sc.fiji.snt.ManualTracerThread
addProgressListener(SearchProgressCallback) - Method in class sc.fiji.snt.SearchThread
addProgressListener(SearchProgressCallback) - Method in class sc.fiji.snt.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
addSeparator(JComponent, String, boolean, GridBagConstraints) - Static method in class sc.fiji.snt.gui.GuiUtils
addSeparator(JComponent, JLabel, boolean, GridBagConstraints) - Static method in class sc.fiji.snt.gui.GuiUtils
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 sc.fiji.snt.SNT
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.
AddTextAnnotationCmd - Class in sc.fiji.snt.gui.cmds: Implements Reconstruction Viewer's 'Add Annotation Label...' commands.
AddTextAnnotationCmd() - Constructor for class sc.fiji.snt.gui.cmds.AddTextAnnotationCmd
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 sc.fiji.snt.Path: Deprecated.
addTo3DViewer(Image3DUniverse, Color3f, ImagePlus) - Method in class sc.fiji.snt.Path: Deprecated.
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
addTooltip(JComponent, String) - Method in class sc.fiji.snt.gui.GuiUtils
addToResultsTable() - Method in class sc.fiji.snt.gui.ShollAnalysisDialog.ShollResults: Deprecated.
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.
addTree(Tree) - Method in class sc.fiji.snt.PathAndFillManager: Adds a Tree.
addTree(Tree) - Method in class sc.fiji.snt.SciViewSNT: Adds a tree to the associated SciView instance.
addTree(Tree) - Method in class sc.fiji.snt.viewer.Viewer2D: Deprecated.
Use Viewer2D.add(Tree) instead
addTree(Tree) - Method in class sc.fiji.snt.viewer.Viewer3D: Adds a tree to this viewer.
addTreeModelListener(TreeModelListener) - Method in class bdv.ui.sourcegrouptree.SourceGroupTreeModel: Adds a listener for the TreeModelEvent posted after the tree changes.
addTrees(Collection<Tree>, String, String...) - Method in class sc.fiji.snt.viewer.Viewer3D: Adds a collection of trees.
addTrees(Collection<Tree>, String) - Method in class sc.fiji.snt.viewer.Viewer3D: Adds a collection of trees.
addTrees(Collection<Tree>, boolean) - Method in class sc.fiji.snt.viewer.Viewer3D: Deprecated.
use Viewer3D.addTrees(Collection, String) instead
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.
addViewer(Viewer3D) - Static method in class sc.fiji.snt.SNTUtils
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
adjustListPlaceholder() - Method in class sc.fiji.snt.FillManagerUI
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
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
aliases() - Method in class sc.fiji.snt.annotation.AllenCompartment
aliases() - Method in interface sc.fiji.snt.annotation.BrainAnnotation
aliases() - Method in class sc.fiji.snt.annotation.InsectBrainCompartment
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_FLAGS - Static variable in class sc.fiji.snt.analysis.MultiTreeStatistics
ALL_PLOTS - Static variable in class sc.fiji.snt.plugin.ij1.ShollOptions: 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
AllenCompartment - Class in sc.fiji.snt.annotation: Defines an Allen Reference Atlas (ARA) [Allen Mouse Common Coordinate Framework] annotation.
AllenCompartment(UUID) - Constructor for class sc.fiji.snt.annotation.AllenCompartment: Instantiates a new ARA annotation from an UUID (as used by MouseLight's database).
AllenCompartment(int) - Constructor for class sc.fiji.snt.annotation.AllenCompartment: Instantiates a new ARA annotation from its identifier.
AllenCompartment(JSONObject, UUID) - Constructor for class sc.fiji.snt.annotation.AllenCompartment
AllenUtils - Class in sc.fiji.snt.annotation: Utility methods for accessing/handling AllenCompartments
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
allPathsShareSameSpatialCalibration() - Method in class sc.fiji.snt.PathAndFillManager
allPeaks - Variable in class sc.fiji.timelapse.Peak_Counter_Tool
allPeaksMap - Variable in class sc.fiji.timelapse.Peak_Counter_Tool
allPointsIterator() - Method in class sc.fiji.snt.PathAndFillManager
AllPointsIterator() - Constructor for class sc.fiji.snt.PathAndFillManager.AllPointsIterator
allRegions - Variable in class util.FindConnectedRegions.Results
allSame - Variable in class ai.SplitFunction
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
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
alphaColor(Color, double) - Static method in class sc.fiji.snt.util.SNTColor: Adds an alpha component to a AWT color.
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
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 sc.fiji.snt.plugin.ij1.Sholl_Analysis: Deprecated.
analyze3D(int, int, int, double[], ImagePlus) - Method in class sc.fiji.snt.plugin.ij1.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
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 sc.fiji.snt.plugin.ij1.Sholl_Analysis: Deprecated.

Analyzes a sampled profile.
ANALYZER_COLLECTION_ELEMENT_KEY - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
AnalyzerCmd - Class in sc.fiji.snt.plugin: Command for measuring Tree(s).
AnalyzerCmd() - Constructor for class sc.fiji.snt.plugin.AnalyzerCmd
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 sc.fiji.snt.plugin.ij1.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 sc.fiji.snt.plugin.ij1.Sholl_Analysis: Deprecated.

Instructs the plugin to parse the specified file expected to contain a sampled profile.
analyzeWithShollAnalysisPlugin(String, double) - Method in class sc.fiji.snt.gui.ShollAnalysisDialog.ShollResults: Deprecated.
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
animateLayoutChange - Variable in class sc.fiji.snt.viewer.geditor.GraphEditor
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.
annotate(String) - Method in class sc.fiji.snt.analysis.SNTChart: Adds a subtitle to the chart.
annotateCategory(String, String) - Method in class sc.fiji.snt.analysis.SNTChart: Annotates the specified category (Category plots only)
annotateCategory(String, String, String) - Method in class sc.fiji.snt.analysis.SNTChart: Annotates the specified category (Category plots only).
annotateLine(Collection<? extends SNTPoint>, String) - Method in class sc.fiji.snt.viewer.Viewer3D: Adds a line annotation to this viewer.
annotatePoint(double, double, String) - Method in class sc.fiji.snt.analysis.SNTChart: Highlights a point in a histogram/XY plot by drawing a labeled arrow at the specified location.
annotatePoint(double, double, String, String) - Method in class sc.fiji.snt.analysis.SNTChart: Highlights a point in a histogram/XY plot by drawing a labeled arrow at the specified location.
annotatePoint(SNTPoint, String) - Method in class sc.fiji.snt.viewer.Viewer3D: Adds an highlighting point annotation to this viewer.
annotatePoints(Collection<? extends SNTPoint>, String) - Method in class sc.fiji.snt.viewer.Viewer3D: Adds a scatter (point cloud) annotation to this viewer.
annotateSurface(Collection<? extends SNTPoint>, String) - Method in class sc.fiji.snt.viewer.Viewer3D
annotateSurface(Collection<? extends SNTPoint>, String, boolean) - Method in class sc.fiji.snt.viewer.Viewer3D: Computes a convex hull from a collection of points and adds it to the scene as an annotation.
annotateXline(double, String) - Method in class sc.fiji.snt.analysis.SNTChart: Annotates the specified X-value (XY plots and histograms).
annotateXline(double, String, String) - Method in class sc.fiji.snt.analysis.SNTChart: Annotates the specified X-value (XY plots and histograms).
annotateYline(double, String) - Method in class sc.fiji.snt.analysis.SNTChart: Annotates the specified Y-value (XY plots and histograms).
annotateYline(double, String, String) - Method in class sc.fiji.snt.analysis.SNTChart: Annotates the specified Y-value (XY plots and histograms).
annotation - Variable in class ini.trakem2.display.Displayable
Annotation3D - Class in sc.fiji.snt.viewer: An Annotation3D is a triangulated surface or a cloud of points (scatter) rendered in Viewer3D that can be used to highlight nodes in a Tree or locations in a mesh.
Annotation3D(Viewer3D, Collection<Annotation3D>) - Constructor for class sc.fiji.snt.viewer.Annotation3D
Annotation3D(Viewer3D, Collection<? extends SNTPoint>, int) - Constructor for class sc.fiji.snt.viewer.Annotation3D
Annotation3D(Viewer3D, SNTPoint) - Constructor for class sc.fiji.snt.viewer.Annotation3D
AnnotationGraph - Class in sc.fiji.snt.analysis.graph
AnnotationGraph() - Constructor for class sc.fiji.snt.analysis.graph.AnnotationGraph
AnnotationGraph(Collection<Tree>, String, double, int) - Constructor for class sc.fiji.snt.analysis.graph.AnnotationGraph
AnnotationGraphAdapter - Class in sc.fiji.snt.viewer.geditor
AnnotationGraphAdapter(AnnotationGraph) - Constructor for class sc.fiji.snt.viewer.geditor.AnnotationGraphAdapter
AnnotationGraphAdapter(AnnotationGraph, String) - Constructor for class sc.fiji.snt.viewer.geditor.AnnotationGraphAdapter
AnnotationGraphComponent - Class in sc.fiji.snt.viewer.geditor
AnnotationGraphComponent(AnnotationGraphAdapter, Context) - Constructor for class sc.fiji.snt.viewer.geditor.AnnotationGraphComponent
AnnotationGraphGeneratorCmd - Class in sc.fiji.snt.gui.cmds
AnnotationGraphGeneratorCmd() - Constructor for class sc.fiji.snt.gui.cmds.AnnotationGraphGeneratorCmd
AnnotationGraphRecViewerCmd - Class in sc.fiji.snt.gui.cmds
AnnotationGraphRecViewerCmd() - Constructor for class sc.fiji.snt.gui.cmds.AnnotationGraphRecViewerCmd
AnnotationGraphUtils - Class in sc.fiji.snt.analysis.graph: Utilities for AnnotationGraph handling and manipulation.
AnnotationGraphUtils() - Constructor for class sc.fiji.snt.analysis.graph.AnnotationGraphUtils
annotationsDescriptionChanged() - Method in class sc.fiji.snt.plugin.ShollAnalysisImgCmd
AnnotationWeightedEdge - Class in sc.fiji.snt.analysis.graph
AnnotationWeightedEdge() - Constructor for class sc.fiji.snt.analysis.graph.AnnotationWeightedEdge
ANNULUS - Static variable in interface sc.fiji.snt.analysis.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
ANY_HEMISPHERE - Static variable in interface sc.fiji.snt.annotation.BrainAnnotation
anyListeners() - Method in class sc.fiji.snt.SNT
anySelected() - Method in class sc.fiji.snt.PathAndFillManager: Checks whether at least one Path is currently selected in the UI.
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(Iterator<? extends SNTPoint>) - Method in class sc.fiji.snt.util.BoundingBox: Computes the bounding box of the specified point cloud and appends it to this bounding box, resizing it as needed.
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.
appendToLastRow(String, Object) - Method in class sc.fiji.snt.analysis.SNTTable
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) - 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) - 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.
applyCanvasOffset(double, double, double) - Method in class sc.fiji.snt.Tree: Specifies the offset to be used when rendering this Tree in a TracerCanvas.
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
applyIcon(AbstractButton, float, IconFactory.GLYPH) - Static method in class sc.fiji.snt.gui.IconFactory
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
applyLayout(mxIGraphLayout) - Method in class sc.fiji.snt.viewer.geditor.GraphEditor
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
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.
applySelectionFilter(String, Number, Number) - Method in class sc.fiji.snt.PathManagerUI: Selects paths matching a morphometric criteria.
applySelectionFilter(String) - Method in class sc.fiji.snt.PathManagerUI: Selects paths matching a text-based criteria.
applySelectionFilter(String, Number) - Method in class sc.fiji.snt.PathManagerUI: Selects paths matching a morphometric criteria.
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
applyTag(String) - Method in class sc.fiji.snt.PathManagerUI: Applies a tag/ color to selected Path(s).
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
appTitle - Variable in class sc.fiji.snt.viewer.geditor.GraphEditor
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
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 sc.fiji.snt.analysis.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
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.
askUserConfirmation - Variable in class sc.fiji.snt.SNTUI
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 sc.fiji.snt.SearchNode
asPathReversed(double, double, double, String) - Method in class sc.fiji.snt.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.
assembleStats(TreeStatistics.StatisticsInstance, String) - Method in class sc.fiji.snt.analysis.MultiTreeStatistics
assembleStats(TreeStatistics.StatisticsInstance, String) - Method in class sc.fiji.snt.analysis.TreeStatistics
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
assessIfBranchesHaveBeenAssigned() - Method in class sc.fiji.snt.analysis.NodeStatistics
Assign3DData(Container, ImgPanel, My3DData) - Method in class view5d.AlternateViewer
assignBranches(Tree) - Method in class sc.fiji.snt.analysis.NodeStatistics: Associates the nodes being analyzed to the branches of the specified tree
ASSIGNED_VALUE - Static variable in class sc.fiji.snt.analysis.MultiTreeColorMapper: Mapping property: Assigned Tree value
ASSIGNED_VALUE - Static variable in class sc.fiji.snt.analysis.MultiTreeStatistics: Flag specifying Tree value statistics
assignEdgeWeightsEuclidean() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph: For all edges, sets the Euclidean distance between the source and target vertex as the weight.
assignEditor(GraphEditor) - Method in class sc.fiji.snt.viewer.geditor.SNTGraphComponent: Assigns an editor.
assignHemisphereTags(DirectedWeightedGraph) - Static method in class sc.fiji.snt.annotation.AllenUtils
assignHemisphereTags(Tree) - Static method in class sc.fiji.snt.annotation.AllenUtils
assignImage(ImagePlus) - Method in class sc.fiji.snt.analysis.sholl.Profile
assignImage(ImagePlus) - Method in class sc.fiji.snt.Tree: Assigns the spatial calibration of an image to this Tree.
assignListenerToHelpButton(String, ActionListener) - Method in class sc.fiji.snt.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, List) - Method in interface mpicbg.icp.PointMatchIdentification
assignPointMatches(List, List) - Method in class mpicbg.icp.SimplePointMatchIdentification
assignPoints(Set<ShollPoint>) - Method in class sc.fiji.snt.analysis.sholl.ProfileEntry
assignPopupToHelpButton(JPopupMenu) - Method in class sc.fiji.snt.gui.EnhancedGenericDialog: Deprecated.

Attaches the specified JPopupMenu to the GenericDialog "Help" button renamed "More »".
assignPopupToHelpButton(String, JPopupMenu) - Method in class sc.fiji.snt.gui.EnhancedGenericDialog: Deprecated.

Adds a "Help" button and attaches the specified JPopupMenu to it.
assignProperty(String) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay
assignSliceTo(int, Roi, int) - Method in class vib.segment.CustomStackWindow
assignSpatialSettings(ImagePlus) - Method in class sc.fiji.snt.PathAndFillManager
assignToLeftHemisphere(Tree) - Static method in class sc.fiji.snt.annotation.AllenUtils
assignToRightHemisphere(Tree) - Static method in class sc.fiji.snt.annotation.AllenUtils
assignUniqueColors(Collection<Tree>) - Static method in class sc.fiji.snt.Tree
assignUniqueColors(Collection<String>) - Method in class sc.fiji.snt.viewer.Viewer3D
assignValue(double) - Method in class sc.fiji.snt.Tree: Assigns a numeric property to this Tree.
assignValues() - Method in class sc.fiji.snt.analysis.PathProfiler: Calls PathProfiler.assignValues(Path) on the Paths of the profiled Tree
assignValues(int) - Method in class sc.fiji.snt.analysis.PathProfiler
assignValues(Path) - Method in class sc.fiji.snt.analysis.PathProfiler: Retrieves pixel intensities at each node of the Path storing them as Path values
assignValues(Path, int) - Method in class sc.fiji.snt.analysis.PathProfiler
assignValues(boolean) - Method in class sc.fiji.snt.SNTService: Assigns pixel intensities at each Path node, storing them as Path values.
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 sc.fiji.snt.SearchThread
atGoal(int, int, int, boolean) - Method in class sc.fiji.snt.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
autoCanvasActivation - Variable in class sc.fiji.snt.SNT
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