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A

a - Variable in class bijnum.BIJJacobi
The matrix of which you want to compute E.
a - Variable in class bijnum.BIJpca
The matrix of images.
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.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 net.imglib2.display.RealARGBColorConverter
 
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
 
a - Variable in class spim.fiji.ImgLib2Temp.ValuePair
 
a00 - Variable in class vib.FastMatrix
 
a00 - Variable in class vib.FloatMatrix
 
a01 - Variable in class vib.FastMatrix
 
a01 - Variable in class vib.FloatMatrix
 
a02 - Variable in class vib.FastMatrix
 
a02 - Variable in class vib.FloatMatrix
 
a03 - Variable in class vib.FastMatrix
 
a03 - Variable in class vib.FloatMatrix
 
a10 - Variable in class vib.FastMatrix
 
a10 - Variable in class vib.FloatMatrix
 
a11 - Variable in class vib.FastMatrix
 
a11 - Variable in class vib.FloatMatrix
 
a12 - Variable in class vib.FastMatrix
 
a12 - Variable in class vib.FloatMatrix
 
a13 - Variable in class vib.FastMatrix
 
a13 - Variable in class vib.FloatMatrix
 
a20 - Variable in class vib.FastMatrix
 
a20 - Variable in class vib.FloatMatrix
 
a21 - Variable in class vib.FastMatrix
 
a21 - Variable in class vib.FloatMatrix
 
a22 - Variable in class vib.FastMatrix
 
a22 - Variable in class vib.FloatMatrix
 
a23 - Variable in class vib.FastMatrix
 
a23 - Variable in class vib.FloatMatrix
 
A_Image5D_test - Class in sc.fiji.i5d.plugin
 
A_Image5D_test() - Constructor for class sc.fiji.i5d.plugin.A_Image5D_test
 
abort() - Method in class bdv.tools.bookmarks.BookmarksEditor
 
abort() - Method in class bdv.tools.transformation.ManualTransformationEditor
 
abort() - Method in class ini.trakem2.display.FreeHandProfile
for abort (ESC pressed for instance)
About - Class in loci.plugins
Displays a small information dialog about the Bio-Formats Plugins package.
About() - Constructor for class loci.plugins.About
 
about() - Static method in class loci.plugins.About
 
About_RATS - Class in <Unnamed>
 
About_RATS() - Constructor for class About_RATS
 
AboutDialog - Class in org.imagearchive.lsm.toolbox.gui
 
AboutDialog(JFrame, MasterModel) - Constructor for class org.imagearchive.lsm.toolbox.gui.AboutDialog
 
AboutDialog() - Constructor for class org.imagearchive.lsm.toolbox.gui.AboutDialog
 
aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.ActionChooserDescriptor
 
aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.ConfigureViewsDescriptor
 
aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.DetectionDescriptor
 
aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.DetectorChoiceDescriptor
 
aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.DetectorConfigurationDescriptor
 
aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.GrapherDescriptor
 
aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.InitFilterDescriptor
 
aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.LogPanelDescriptor
 
aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.SomeDialogDescriptor
 
aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.SpotFilterDescriptor
 
aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.StartDialogDescriptor
 
aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.TrackerChoiceDescriptor
 
aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.TrackerConfigurationDescriptor
 
aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.TrackFilterDescriptor
 
aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.TrackingDescriptor
 
aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.ViewChoiceDescriptor
 
aboutToDisplayPanel() - Method in interface fiji.plugin.trackmate.gui.descriptors.WizardPanelDescriptor
This method is used to provide functionality that will be performed just before the panel is to be displayed.
aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.ActionChooserDescriptor
 
aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.ConfigureViewsDescriptor
 
aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.DetectionDescriptor
 
aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.DetectorChoiceDescriptor
 
aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.DetectorConfigurationDescriptor
 
aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.GrapherDescriptor
 
aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.InitFilterDescriptor
 
aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.LogPanelDescriptor
 
aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.SomeDialogDescriptor
 
aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.SpotFilterDescriptor
 
aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.StartDialogDescriptor
 
aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.TrackerChoiceDescriptor
 
aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.TrackerConfigurationDescriptor
 
aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.TrackFilterDescriptor
 
aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.TrackingDescriptor
 
aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.ViewChoiceDescriptor
 
aboutToHidePanel() - Method in interface fiji.plugin.trackmate.gui.descriptors.WizardPanelDescriptor
This method is used to perform functionality just before the panel is to be hidden.
aboveThresholdLengthAlong(PrincipalComponents, int, ImagePlus, Threshold) - Method in class vib.oldregistration.PCA_Registration
 
abs(float[]) - Static method in class bijnum.BIJmatrix
Return a vector with the absolutes of all elements in vector v.
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
 
AbstractAffineModelChunk - Class in edu.utexas.clm.archipelago.ijsupport
 
AbstractAffineModelChunk(AbstractAffineModel2D<?>) - Constructor for class edu.utexas.clm.archipelago.ijsupport.AbstractAffineModelChunk
 
AbstractAffineTile2D<A extends mpicbg.models.Model<A> & mpicbg.models.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
 
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
 
AbstractNormalize<T extends NumericType<T>> - Class in script.imglib.algorithm.fn
TODO
AbstractNormalize(Image<T>) - Constructor for class script.imglib.algorithm.fn.AbstractNormalize
 
AbstractOffscreenThread - Class in ini.trakem2.display
To be used in combination with the AbstractRepaintThread, as a thread to create graphics offscreen.
AbstractOffscreenThread.RepaintProperties - Interface in ini.trakem2.display
 
AbstractPanorama_View - Class in mpicbg.panorama
 
AbstractPanorama_View() - Constructor for class mpicbg.panorama.AbstractPanorama_View
 
AbstractPanorama_View.AbstractMappingThread - Class in mpicbg.panorama
 
AbstractPanorama_View.GUI - Class in mpicbg.panorama
 
AbstractPanorama_View.Mapper - Class in mpicbg.panorama
 
AbstractPerumtationTransform - Class in org.janelia.thickness.lut
Bijective integer transform mapping between integer coordinates in [0,n-1].
AbstractPerumtationTransform(int[]) - Constructor for class org.janelia.thickness.lut.AbstractPerumtationTransform
 
AbstractPointDescriptor<P extends mpicbg.models.Point,F extends AbstractPointDescriptor<P,F>> - Class in mpicbg.pointdescriptor
 
AbstractPointDescriptor(P, ArrayList<P>, SimilarityMeasure, Matcher) - Constructor for class mpicbg.pointdescriptor.AbstractPointDescriptor
 
AbstractPointEdit - Class in bigwarp.landmarks.actions
 
AbstractPointEdit(LandmarkTableModel) - Constructor for class bigwarp.landmarks.actions.AbstractPointEdit
 
AbstractProvider<K extends TrackMateModule> - Class in fiji.plugin.trackmate.providers
 
AbstractProvider(Class<K>) - Constructor for class fiji.plugin.trackmate.providers.AbstractProvider
 
AbstractRegionalExtremaFinder<T extends RealType<T>> - Class in mpicbg.imglib.algorithm.extremafinder
TODO
AbstractRegionalExtremaFinder() - Constructor for class mpicbg.imglib.algorithm.extremafinder.AbstractRegionalExtremaFinder
 
AbstractRepaintThread - Class in ini.trakem2.display
 
AbstractRepaintThread(Component, String, AbstractOffscreenThread) - Constructor for class ini.trakem2.display.AbstractRepaintThread
 
AbstractSemiAutoTracker<T extends RealType<T> & NativeType<T>> - Class in fiji.plugin.trackmate.detection.semiauto
A class made to perform semi-automated tracking of spots in TrackMate & friends
AbstractSemiAutoTracker(Model, SelectionModel, Logger) - Constructor for class fiji.plugin.trackmate.detection.semiauto.AbstractSemiAutoTracker
 
AbstractSemiAutoTracker.SearchRegion<R> - Class in fiji.plugin.trackmate.detection.semiauto
A utility class made to return the information on a neighborhood generated from a source around a Spot.
AbstractSequenceDescription<V extends BasicViewSetup,D extends BasicViewDescription<V>,L extends BasicImgLoader> - Class in mpicbg.spim.data.generic.sequence
A SPIM sequence consisting of a list of timepoints and a list of view setups.
AbstractSequenceDescription(TimePoints, Map<Integer, ? extends V>, L, MissingViews) - Constructor for class mpicbg.spim.data.generic.sequence.AbstractSequenceDescription
 
AbstractSequenceDescription() - Constructor for class mpicbg.spim.data.generic.sequence.AbstractSequenceDescription
 
AbstractSequenceDescriptionUtils - Class in mpicbg.spim.data.generic.sequence
 
AbstractSequenceDescriptionUtils() - Constructor for class mpicbg.spim.data.generic.sequence.AbstractSequenceDescriptionUtils
 
AbstractSortedGrayLevelIterator<T extends IntegerType<T>> - Class in mpicbg.imglib.cursor.special
Iterate over all pixels ordered by their gray level
AbstractSortedGrayLevelIterator(Image<T>) - Constructor for class mpicbg.imglib.cursor.special.AbstractSortedGrayLevelIterator
 
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.
AbstractTreeTransferHandler - Class in ini.trakem2.tree
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
 
AbstractVolatileNativeNumericType<N extends NumericType<N> & NativeType<N>,T extends AbstractVolatileNativeNumericType<N,T>> - Class in net.imglib2.type.volatiles
Abstract base class for VolatileNumericTypes that wrap native NumericTypes.
AbstractVolatileNativeNumericType(N, boolean) - Constructor for class net.imglib2.type.volatiles.AbstractVolatileNativeNumericType
 
AbstractVolatileNativeRealType<R extends RealType<R> & NativeType<R>,T extends AbstractVolatileNativeRealType<R,T>> - Class in net.imglib2.type.volatiles
Abstract base class for VolatileRealTypes that wrap native RealTypes.
AbstractVolatileNativeRealType(R, boolean) - Constructor for class net.imglib2.type.volatiles.AbstractVolatileNativeRealType
 
acc - Variable in class net.imglib2.interpolation.randomaccess.ClampingNLinearInterpolatorRealType
 
acc - Variable in class net.imglib2.interpolation.randomaccess.ClampingNLinearInterpolatorVolatileRealType
 
accA - Variable in class net.imglib2.interpolation.randomaccess.ClampingNLinearInterpolatorVolatileARGB
 
accB - Variable in class net.imglib2.interpolation.randomaccess.ClampingNLinearInterpolatorVolatileARGB
 
accept(File) - Method in class fiji.plugin.trackmate.util.DefaultFileFilter
Returns true if file is a directory or ends with the specified extension.
accept(File) - Method in class fiji.plugin.trackmate.util.DefaultFileFilter.EditorFileFilter
Returns true if the file is a directory or has a .xml or .xml.gz extension.
accept(File) - Method in class fiji.plugin.trackmate.util.DefaultFileFilter.ImageFileFilter
Returns true if the file is a directory or ends with a known image extension.
accept(File) - Method in class fsalign.FolderWatcher.FolderFilter
 
accept(Node<I>) - Method in class ini.trakem2.display.Node.BranchAndEndNodeIterator
 
accept(Node<I>) - Method in class ini.trakem2.display.Node.BranchNodeIterator
 
accept(Node<I>) - Method in class ini.trakem2.display.Node.EndNodeIterator
 
accept(Node<I>) - Method in class ini.trakem2.display.Node.FilteredIterator
 
accept(File, String) - Method in class ini.trakem2.io.ImageFileFilter
 
accept(File, String) - Method in class ini.trakem2.io.XMLFileFilter
 
accept(T) - Method in interface ini.trakem2.utils.Filter
 
accept(File) - Method in class org.imagearchive.lsm.toolbox.gui.AllKnownFilter
 
accept(File) - Method in class org.imagearchive.lsm.toolbox.gui.BatchFilter
 
accept(File) - Method in class org.imagearchive.lsm.toolbox.gui.ImageFilter
 
accept(BytePointer, int, int, int) - Method in class org.janelia.it.jacs.shared.ffmpeg.ByteGatherAcceptor
Accept one "page" of data, of width x height given, and with linesize bytes on each line of the page.
accept(byte[], int, int, int) - Method in class org.janelia.it.jacs.shared.ffmpeg.ByteGatherAcceptor
Accept one "page" of data, of width x height given, and with linesize bytes on each line of the page.
accept(BytePointer, int, int, int) - Method in interface org.janelia.it.jacs.shared.ffmpeg.FFMPGByteAcceptor
 
accept(byte[], int, int, int) - Method in interface org.janelia.it.jacs.shared.ffmpeg.FFMPGByteAcceptor
 
accept(byte[], int, int, int) - Method in interface org.janelia.it.jacs.shared.ffmpeg.H5JLoader.DataAcceptor
 
accept(BytePointer, int, int, int) - Method in class org.janelia.it.jacs.shared.ffmpeg.PPMFileAcceptor
 
accept(byte[], int, int, int) - Method in class org.janelia.it.jacs.shared.ffmpeg.PPMFileAcceptor
 
accept(File) - Method in class org.siox.example.ExtensionFileFilter
Whether the given file is regular file with recognized extension or a directory.
accept(T, T) - Method in class sc.fiji.coloc.algorithms.Accumulator
 
acceptingNodes() - Method in class edu.utexas.clm.archipelago.Cluster
 
accepts(Object) - Method in class edu.utexas.clm.archipelago.ijsupport.bottle.LayerBottler
 
accepts(Object) - Method in class edu.utexas.clm.archipelago.ijsupport.bottle.PatchBottler
 
accepts(Object) - Method in class edu.utexas.clm.archipelago.ijsupport.bottle.PointBottler
 
accepts(Object) - Method in class edu.utexas.clm.archipelago.ijsupport.bottle.SIFTParamBottler
 
accepts(Object) - Method in interface edu.utexas.clm.archipelago.network.translation.Bottler
Return true if this Bottler accepts the given Object.
accepts(Object) - Method in class edu.utexas.clm.archipelago.network.translation.FileBottler
 
Access() - Constructor for class bdv.tools.boundingbox.BoxRealRandomAccessible.Access
 
Access(BoxRealRandomAccessible<T>.Access) - Constructor for class bdv.tools.boundingbox.BoxRealRandomAccessible.Access
 
access - Variable in class mpicbg.imglib.labeling.LabelingType
 
access - Variable in class org.janelia.thickness.lut.AbstractLUTGrid
 
access - Variable in class org.janelia.thickness.lut.AbstractLUTRealTransformField
 
accessible - Variable in class bdv.util.RealRandomAccessibleSource
 
accessor - Variable in class mpicbg.imglib.cursor.dynamic.DynamicCursor
 
accG - Variable in class net.imglib2.interpolation.randomaccess.ClampingNLinearInterpolatorVolatileARGB
 
accR - Variable in class net.imglib2.interpolation.randomaccess.ClampingNLinearInterpolatorVolatileARGB
 
accumulate(Cursor<? extends A>[], B) - Method in class bdv.viewer.render.AccumulateProjector
 
accumulate(Cursor<? extends ARGBType>[], ARGBType) - Method in class bdv.viewer.render.AccumulateProjectorARGB
 
accumulate(RoiStatistics.Accessor) - Method in class fiji.statistics.RoiStatistics
 
AccumulateProjector<A,B> - Class in bdv.viewer.render
 
AccumulateProjector(ArrayList<VolatileProjector>, ArrayList<? extends RandomAccessible<? extends A>>, RandomAccessibleInterval<B>, int, ExecutorService) - Constructor for class bdv.viewer.render.AccumulateProjector
 
AccumulateProjectorARGB - Class in bdv.viewer.render
 
AccumulateProjectorARGB(ArrayList<VolatileProjector>, ArrayList<? extends RandomAccessible<? extends ARGBType>>, RandomAccessibleInterval<ARGBType>, int, ExecutorService) - Constructor for class bdv.viewer.render.AccumulateProjectorARGB
 
accumulateProjectorFactory(AccumulateProjectorFactory<ARGBType>) - Method in class bdv.util.BdvOptions
Set the factory for creating AccumulateProjector.
AccumulateProjectorFactory<A> - Interface in bdv.viewer.render
 
accumulateProjectorFactory - Variable in class bdv.viewer.render.MultiResolutionRenderer
TODO
accumulateProjectorFactory(AccumulateProjectorFactory<ARGBType>) - Method in class bdv.viewer.ViewerOptions
Set the factory for creating AccumulateProjector.
accumulator - Variable in class fiji.statistics.RoiStatistics
 
Accumulator<T extends RealType<T>> - Class in sc.fiji.coloc.algorithms
A class allowing an easy accumulation of values visited by a TwinCursor.
Accumulator(TwinCursor<T>) - Constructor for class sc.fiji.coloc.algorithms.Accumulator
The two values x and y from each cursor iteration to get summed up as single values and their combinations.
Accumulator(TwinCursor<T>, double, double) - Constructor for class sc.fiji.coloc.algorithms.Accumulator
The two values (x - xDiff) and (y - yDiff) from each cursor iteration to get summed up as single values and their combinations.
Accumulator(TwinCursor<T>, boolean, double, double) - Constructor for class sc.fiji.coloc.algorithms.Accumulator
 
accuracy(float[]) - Static method in class bijnum.BIJstats
Compute accuracy or observed proportion of overall agreement of a test for which the result is in exp and the ground truth in truth accuracy = true pos + true neg / (true neg + false pos + true pos + false neg) accuracy = (a+d) / (a+b+c+d)
accuracy - Variable in class ini.trakem2.imaging.filters.GaussianBlur
 
accuracyMultipleClasses(float[], float[], int) - Static method in class bijnum.BIJstats
Compute the accuracy of a test of which the result is in exp and the ground truth in truth, where test results in multiple classifications.
accuracyMultipleClasses(int[][]) - Static method in class bijnum.BIJstats
Compute the accuracy of a test of which the confusion matrix is in tablenxn.
ACCURATE - Static variable in class Despeckle_
 
ACCURATE_MODE - Static variable in class bunwarpj.MainDialog
accurate mode constant
ACos - Class in script.imglib.math
TODO
ACos(Image<? extends RealType<?>>) - Constructor for class script.imglib.math.ACos
 
ACos(IFunction) - Constructor for class script.imglib.math.ACos
 
ACos(Number) - Constructor for class script.imglib.math.ACos
 
act(int, RandomAccessibleInterval<T>, RandomAccessibleInterval<T>, double[], int[], int[], double[], RandomAccessibleInterval<double[]>) - Method in class org.janelia.thickness.inference.visitor.CorrelationFitVisitor
 
act(int, RandomAccessibleInterval<T>, RandomAccessibleInterval<T>, double[], int[], int[], double[], RandomAccessibleInterval<double[]>) - Method in class org.janelia.thickness.inference.visitor.GlobalCorrelationFitVisitor
 
act(int, RandomAccessibleInterval<T>, RandomAccessibleInterval<T>, double[], int[], int[], double[], RandomAccessibleInterval<double[]>) - Method in class org.janelia.thickness.inference.visitor.LazyVisitor
 
act(int, RandomAccessibleInterval<T>, RandomAccessibleInterval<T>, double[], int[], int[], double[], RandomAccessibleInterval<double[]>) - Method in class org.janelia.thickness.inference.visitor.ListVisitor
 
act(int, RandomAccessibleInterval<T>, RandomAccessibleInterval<T>, double[], int[], int[], double[], RandomAccessibleInterval<double[]>) - Method in class org.janelia.thickness.inference.visitor.LUTVisitor
 
act(int, RandomAccessibleInterval<T>, RandomAccessibleInterval<T>, double[], int[], int[], double[], RandomAccessibleInterval<double[]>) - Method in class org.janelia.thickness.inference.visitor.MatrixVisitor
 
act(int, RandomAccessibleInterval<T>, RandomAccessibleInterval<T>, double[], int[], int[], double[], RandomAccessibleInterval<double[]>) - Method in class org.janelia.thickness.inference.visitor.PermutedLUTVisitor
 
act(int, RandomAccessibleInterval<T>, RandomAccessibleInterval<T>, double[], int[], int[], double[], RandomAccessibleInterval<double[]>) - Method in class org.janelia.thickness.inference.visitor.PermutedScalingFactorsVisitor
 
act(int, RandomAccessibleInterval<T>, RandomAccessibleInterval<T>, double[], int[], int[], double[], RandomAccessibleInterval<double[]>) - Method in class org.janelia.thickness.inference.visitor.ScalingFactorsVisitor
 
act(int, RandomAccessibleInterval<T>, RandomAccessibleInterval<T>, double[], int[], int[], double[], RandomAccessibleInterval<double[]>) - Method in interface org.janelia.thickness.inference.visitor.Visitor
 
ActElement() - Method in class view5d.My3DData
 
action(String) - Method in class fiji.help.Context_Help
 
Action(String, String) - Constructor for class fiji.util.gui.CommandFinderBase.Action
 
action(String) - Method in class fiji.util.MenuItemDiverter
 
ACTION_FINISHED - Variable in class fiji.plugin.trackmate.gui.panels.ActionChooserPanel
 
ACTION_STARTED - Variable in class fiji.plugin.trackmate.gui.panels.ActionChooserPanel
 
ActionChooserDescriptor - Class in fiji.plugin.trackmate.gui.descriptors
 
ActionChooserDescriptor(ActionProvider, TrackMate, TrackMateGUIController) - Constructor for class fiji.plugin.trackmate.gui.descriptors.ActionChooserDescriptor
 
actionChooserDescriptor - Variable in class fiji.plugin.trackmate.gui.TrackMateGUIController
 
ActionChooserPanel - Class in fiji.plugin.trackmate.gui.panels
 
ActionChooserPanel(ActionProvider, TrackMate, TrackMateGUIController) - Constructor for class fiji.plugin.trackmate.gui.panels.ActionChooserPanel
 
ActionListenablePanel - Class in fiji.plugin.trackmate.gui.panels
 
ActionListenablePanel() - Constructor for class fiji.plugin.trackmate.gui.panels.ActionListenablePanel
 
actionListeners - Variable in class fiji.plugin.trackmate.gui.panels.ActionListenablePanel
 
actionPerformed(ActionEvent) - Method in class bdv.ij.util.PluginHelper.ChooseXmlFileListener
 
actionPerformed(ActionEvent) - Method in class bdv.tools.ToggleDialogAction
 
actionPerformed(ActionEvent) - Method in class bdv.viewer.WarpNavigationActions.AlignPlaneAction
 
actionPerformed(ActionEvent) - Method in class bdv.viewer.WarpNavigationActions.DisplayXfmAction
 
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.ExportImagePlusAction
 
actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.ExportVirtualImagePlusAction
 
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.LandmarkModeAction
 
actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.LoadLandmarksAction
 
actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.LoadSettingsAction
 
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
 
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.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 CellCounter
 
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 FlowJ.FlowJUserInterface
 
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.coloc.results.SingleWindowDisplay
 
actionPerformed(ActionEvent) - Method in class sc.fiji.i5d.gui.ChannelControl
 
actionPerformed(ActionEvent) - Method in class sc.fiji.i5d.gui.ChannelControl.ChannelColorChooser
 
actionPerformed(ActionEvent) - Method in class sc.fiji.i5d.gui.ChannelControl.ChannelSelectorOverlay
 
actionPerformed(ActionEvent) - Method in class selection.DoneButtonListener
 
actionPerformed(ActionEvent) - Method in class selection.LoadListener
 
actionPerformed(ActionEvent) - Method in class selection.RemoveItemListener
 
actionPerformed(ActionEvent) - Method in class selection.SaveListener
 
actionPerformed(ActionEvent) - Method in class sholl.gui.EnhancedGenericDialog
 
actionPerformed(ActionEvent) - Method in class siox.SegmentationGUI
 
actionPerformed(ActionEvent) - Method in class spim.fiji.plugin.apply.BigDataViewerTransformationWindow.ApplyButtonListener
 
actionPerformed(ActionEvent) - Method in class spim.fiji.plugin.apply.BigDataViewerTransformationWindow.CancelButtonListener
 
actionPerformed(ActionEvent) - Method in class spim.fiji.plugin.removedetections.InteractiveProjections.FinishedButtonListener
 
actionPerformed(ActionEvent) - Method in class spim.fiji.plugin.removedetections.InteractiveProjections.RemoveInsideROIButtonListener
 
actionPerformed(ActionEvent) - Method in class spim.fiji.plugin.resave.PluginHelper.ChooseXmlFileListener
 
actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.ApplyTransformationPopup.MyActionListener
 
actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.BDVPopup.MyActionListener
 
actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.BoundingBoxPopup.MyActionListener
 
actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.DetectInterestPointsPopup.MyActionListener
 
actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.DisplayViewPopup.MyActionListener
 
actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.FusionPopup.MyActionListener
 
actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.InterestPointsExplorerPopup.MyActionListener
 
actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.MaxProjectPopup.MyActionListener
 
actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.RegisterInterestPointsPopup.MyActionListener
 
actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.RegistrationExplorerPopup.MyActionListener
 
actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.RemoveDetectionsPopup.MyActionListener
 
actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.RemoveTransformationPopup.MyActionListener
 
actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.ReorientSamplePopup.MyActionListener
 
actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.ResavePopup.MyActionListener
 
actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.SpecifyCalibrationPopup.MyActionListener
 
actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.VisualizeDetectionsPopup.MyActionListener
 
actionPerformed(ActionEvent) - Method in class spim.process.interestpointregistration.registrationstatistics.GraphFrame
 
actionPerformed(ActionEvent) - Method in class spim.process.interestpointregistration.registrationstatistics.SelectTimepointEntry
 
actionPerformed(ActionEvent) - Method in class spimopener.OpenerGenericDialog
 
actionPerformed(ActionEvent) - Method in class Sync_Measure_3D
Implementation of ActionListener interface.
actionPerformed(ActionEvent) - Method in class Sync_Windows
Implementation of ActionListener interface.
actionPerformed(ActionEvent) - Method in class tools.RoiPicker
 
actionPerformed(ActionEvent) - Method in class tracing.FillWindow
 
actionPerformed(ActionEvent) - Method in class tracing.NeuriteTracerResultsDialog
 
actionPerformed(ActionEvent) - Method in class tracing.PathWindow
 
actionPerformed(ActionEvent) - Method in class tracing.ShollAnalysisDialog
 
actionPerformed(ActionEvent) - Method in class tracing.ShollAnalysisDialog.GraphFrame
 
actionPerformed(ActionEvent) - Method in class tracing.SWCImportOptionsDialog
 
actionPerformed(ActionEvent) - Method in class util.ModelessQuestions
 
actionPerformed(ActionEvent) - Method in class util.Quantile_Based_Normalization
 
actionPerformed(ActionEvent) - Method in class vib.app.gui.FileGroupDialog
 
actionPerformed(ActionEvent) - Method in class vib.EditAmiraParameters_
 
actionPerformed(ActionEvent) - Method in class vib.Points_Dialog
 
actionPerformed(ActionEvent) - Method in class vib.Relabel_
 
actionPerformed(ActionEvent) - Method in class vib.segment.CustomStackWindow
 
actionPerformed(ActionEvent) - Method in class vib.segment.MaterialList
 
actionPerformed(ActionEvent) - Method in class vib.ShowHistogram
 
actionPerformed(ActionEvent) - Method in class VIB_Protocol
 
actionPerformed(ActionEvent) - Method in class video.Edit_Video
 
actionPerformed(ActionEvent) - Method in class view4d.TimelineGUI
 
actionPerformed(ActionEvent) - Method in class VolumeJ.VJUserInterface
React to action e.
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() - 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
 
activateButtons(int) - Method in class VolumeJ.VJSurfaceJ
Activate the rendering and surface plot buttons, depending on whether or not there is a stack, an image, or nothing available.
activateButtons(int) - Method in class VolumeJ.VJUserInterface
Activate the rendering buttons, depending on whether or not there is a stack, an image, or nothing available.
activated5d - Variable in class sc.fiji.i5d.Image5D
 
activateRow(int) - Method in class bigwarp.landmarks.LandmarkTableModel
 
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
 
actuallyInitialize() - Method in class fiji.DefaultFijiService
 
actualSize - Variable in class fiji.util.ArrayBase
 
ADAPT_COEFFICIENTS - Static variable in class bunwarpj.IODialog
bUnwarpJ_ method name to adapt B-spline coefficients to a scale
adaptCanvasses(Image5DCanvas) - Method in class sc.fiji.i5d.gui.Image5DWindow
 
adaptChannelCanvasses() - Method in class sc.fiji.i5d.gui.Image5DCanvas
 
adaptChannelMouse() - Method in class sc.fiji.i5d.gui.Image5DCanvas
 
adaptChannelRois(boolean) - Method in class sc.fiji.i5d.gui.Image5DCanvas
 
adaptCoefficients(String, String, String) - Static method in class bunwarpj.bUnwarpJ_
Adapt the B-spline coefficients to a new image size.
adaptCoefficients(String, double, String) - Static method in class bunwarpj.MiscTools
Adapt B-spline coefficients based on a scale factor.
adaptCoefficients(double, double, int, double[][], double[][]) - Static method in class bunwarpj.MiscTools
Adapt B-spline coefficients to a scale factor
adaptCoefficientsMacro(String, String, String, String, String) - Static method in class bunwarpj.bUnwarpJ_
Method to adapt an elastic transformation given a new image size.
adaptedRandIndex3D(ImagePlus, ImagePlus) - Static method in class trainableSegmentation.metrics.RandError
Calculate the Rand index between to 3D clusters, as described by William M.
adaptedRandIndexFScore3D(ImagePlus, ImagePlus) - Static method in class trainableSegmentation.metrics.RandError
Calculate the F-score of the Rand index between to 3D clusters, as described by William M.
adaptedRandIndexStats3D(ImagePlus, ImagePlus) - Static method in class trainableSegmentation.metrics.RandError
Calculate the Rand index between to 3D clusters, as described by William M.
adaptedRandIndexStats3DN2(ImagePlus, ImagePlus) - Static method in class trainableSegmentation.metrics.RandError
Calculate the Rand index stats between to 3D clusters, as described by William M.
adapter - package adapter
 
adapter - Variable in class Manual_Tracking
 
AdaptiveNonMaximalSuppression<T extends RealType<T>> - Class in mpicbg.imglib.algorithm.scalespace
TODO
AdaptiveNonMaximalSuppression(List<DifferenceOfGaussianPeak<T>>, double) - Constructor for class mpicbg.imglib.algorithm.scalespace.AdaptiveNonMaximalSuppression
Performs adaptive non maximal suppression in the local neighborhood of each detection, seperately for minima and maxima.
adaptMouse(Image5DCanvas) - Method in class sc.fiji.i5d.gui.Image5DWindow
Hands on the cursor location and modifiers of i5dc to all channel canvasses of this window except i5dc.
adaptRois(Image5DCanvas) - Method in class sc.fiji.i5d.gui.Image5DWindow
Hands on the roi, cursor location and modifiers of i5dc to all channel canvasses of this window except i5dc.
add(BasicViewSetup, AbstractSequenceDescription<?, ?, ?>, ViewRegistrations, int[][], int[][]) - Method in class bdv.ij.export.SetupAggregator
Add a new BasicViewSetup to the aggregator.
add(String) - Method in class bdv.viewer.animate.MessageOverlayAnimator
 
add(double[], boolean) - Method in class bigwarp.landmarks.LandmarkTableModel
 
add(float[][], float[]) - Method in class bijnum.BIJknn
Add extra data and classification to this knn.
add(float[], float, float[]) - Static method in class bijnum.BIJmatrix
 
add(float[][], float[][], float[][]) - Static method in class bijnum.BIJmatrix
Add the elements of two matrices a and b and save the results in a matrix r.
add(float[][], double) - Static method in class bijnum.BIJmatrix
Add a scalar to all entries in a matrix m in place.
add(float[][], float[][]) - Static method in class bijnum.BIJmatrix
Add (elements in) a matrix b to a matrix a.
add(short[], float) - Static method in class bijnum.BIJShortMatrix
Add a scalar to all entries in a matrix.
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(CtClass) - Method in class fiji.JavassistHelper
Deprecated.
 
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(SSD, SSD) - Method in class FlowJ.SSD
 
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(Point, Point) - Static method in class mpicbg.pointdescriptor.test.TestPointDescriptor
 
add(LRFFT) - Method in class mpicbg.spim.postprocessing.deconvolution2.LRInput
 
add(OpTreeTableNode) - Method in class net.imagej.ui.swing.ops.OpTreeTableNode
Add a child to this node.
add(Frame) - Method in class org.janelia.it.jacs.shared.ffmpeg.ImageStack
Add a Frame to the end of the stack
add(int, int, double, double) - Method in class org.janelia.thickness.inference.fits.AbstractCorrelationFit
 
add(int, int, double, double) - Method in class org.janelia.thickness.inference.fits.GlobalCorrelationFitAverage
 
add(int, int, double, double) - Method in class org.janelia.thickness.inference.fits.GlobalCorrelationFitAverageRegularized
 
add(int, int, double, double) - Method in class org.janelia.thickness.inference.fits.LocalCorrelationFitAverage
 
add(double, Color) - Method in class org.jfree.chart.renderer.InterpolatePaintScale
Add a color to the color list of this paint scale, at the position given by value.
add(int, int) - Method in class org.siox.util.IntArrayList
Inserts the specified element at the specified position in this list.
add(int) - Method in class org.siox.util.IntArrayList
Appends the specified element to the end of this list.
add(double[], double[]) - Method in class sc.fiji.balloonSegmentation.structure.Balloon
Math vector operators: addition of 2 vectors a+b (I made this before I start using JAMA library)
add(double, double) - Method in class sc.fiji.timelapse.LinearRegression
 
add(double) - Method in class sc.fiji.timelapse.StandardDeviation
 
Add - Class in script.imglib.math
TODO
Add(Image<? extends RealType<?>>, Image<? extends RealType<?>>) - Constructor for class script.imglib.math.Add
 
Add(IFunction, Image<? extends RealType<?>>) - Constructor for class script.imglib.math.Add
 
Add(Image<? extends RealType<?>>, IFunction) - Constructor for class script.imglib.math.Add
 
Add(IFunction, IFunction) - Constructor for class script.imglib.math.Add
 
Add(Image<? extends RealType<?>>, Number) - Constructor for class script.imglib.math.Add
 
Add(Number, Image<? extends RealType<?>>) - Constructor for class script.imglib.math.Add
 
Add(IFunction, Number) - Constructor for class script.imglib.math.Add
 
Add(Number, IFunction) - Constructor for class script.imglib.math.Add
 
Add(Number, Number) - Constructor for class script.imglib.math.Add
 
Add(Object...) - Constructor for class script.imglib.math.Add
 
add(ViewDescription) - Method in class spim.fiji.plugin.apply.ModelLink
 
add(MVDeconFFT) - Method in class spim.process.fusion.deconvolution.MVDeconInput
 
add(double) - Method in class spim.vecmath.Matrix3d
Adds a scalar to each component of this matrix.
add(double, Matrix3d) - Method in class spim.vecmath.Matrix3d
Adds a scalar to each component of the matrix m1 and places the result into this.
add(Matrix3d, Matrix3d) - Method in class spim.vecmath.Matrix3d
Sets the value of this matrix to the matrix sum of matrices m1 and m2.
add(Matrix3d) - Method in class spim.vecmath.Matrix3d
Sets the value of this matrix to the sum of itself and matrix m1.
add(float) - Method in class spim.vecmath.Matrix3f
Adds a scalar to each component of this matrix.
add(float, Matrix3f) - Method in class spim.vecmath.Matrix3f
Adds a scalar to each component of the matrix m1 and places the result into this.
add(Matrix3f, Matrix3f) - Method in class spim.vecmath.Matrix3f
Sets the value of this matrix to the matrix sum of matrices m1 and m2.
add(Matrix3f) - Method in class spim.vecmath.Matrix3f
Sets the value of this matrix to the matrix sum of itself and matrix m1.
add(double) - Method in class spim.vecmath.Matrix4d
Adds a scalar to each component of this matrix.
add(double, Matrix4d) - Method in class spim.vecmath.Matrix4d
Adds a scalar to each component of the matrix m1 and places the result into this.
add(Matrix4d, Matrix4d) - Method in class spim.vecmath.Matrix4d
Sets the value of this matrix to the matrix sum of matrices m1 and m2.
add(Matrix4d) - Method in class spim.vecmath.Matrix4d
Sets the value of this matrix to sum of itself and matrix m1.
add(float) - Method in class spim.vecmath.Matrix4f
Adds a scalar to each component of this matrix.
add(float, Matrix4f) - Method in class spim.vecmath.Matrix4f
Adds a scalar to each component of the matrix m1 and places the result into this.
add(Matrix4f, Matrix4f) - Method in class spim.vecmath.Matrix4f
Sets the value of this matrix to the matrix sum of matrices m1 and m2.
add(Matrix4f) - Method in class spim.vecmath.Matrix4f
Sets the value of this matrix to the sum of itself and matrix m1.
add(Transform3D) - Method in class spim.vecmath.Transform3D
Adds this transform to transform t1 and places the result into this: this = this + t1.
add(Transform3D, Transform3D) - Method in class spim.vecmath.Transform3D
Adds transforms t1 and t2 and places the result into this transform.
add(Tuple3d, Tuple3d) - Method in class spim.vecmath.Tuple3d
Sets the value of this tuple to the sum of tuples t1 and t2.
add(Tuple3d) - Method in class spim.vecmath.Tuple3d
Sets the value of this tuple to the sum of itself and t1.
add(Tuple3f, Tuple3f) - Method in class spim.vecmath.Tuple3f
Sets the value of this tuple to the vector sum of tuples t1 and t2.
add(Tuple3f) - Method in class spim.vecmath.Tuple3f
Sets the value of this tuple to the vector sum of itself and tuple t1.
add(Tuple3i, Tuple3i) - Method in class spim.vecmath.Tuple3i
Sets the value of this tuple to the sum of tuples t1 and t2.
add(Tuple3i) - Method in class spim.vecmath.Tuple3i
Sets the value of this tuple to the sum of itself and t1.
add(Tuple4d, Tuple4d) - Method in class spim.vecmath.Tuple4d
Sets the value of this tuple to the tuple sum of tuples t1 and t2.
add(Tuple4d) - Method in class spim.vecmath.Tuple4d
Sets the value of this tuple to the sum of itself and tuple t1.
add(Tuple4f, Tuple4f) - Method in class spim.vecmath.Tuple4f
Sets the value of this tuple to the sum of tuples t1 and t2.
add(Tuple4f) - Method in class spim.vecmath.Tuple4f
Sets the value of this tuple to the sum of itself and t1.
add(ImageProcessor) - Method in class spimopener.GaussianStackFocuser
 
add(ImageProcessor) - Method in class spimopener.MaximumProjector
 
add(ImageProcessor) - Method in class spimopener.MinimumProjector
 
add(ImageProcessor) - Method in interface spimopener.Projector
 
add(double) - Method in class stitching.model.ErrorStatistic
 
add(int, int, int, double, int, boolean) - Method in class tracing.Fill
 
add(T, Object) - Method in class util.FibonacciHeap
 
add(double, Object) - Method in class util.FibonacciHeapDouble
 
add(int, Object) - Method in class util.FibonacciHeapInt
 
add(String) - Method in class vib.app.FileGroup
 
add(ImagePlus) - Method in class vib.Average_Images
 
add(int) - Method in class vib.NaiveResampler.Averager
 
add(int) - Method in class vib.NaiveResampler.IntAverager
 
add(int) - Method in class vib.NaiveResampler.MaxLikelihood
 
add(int) - Method in class vib.NaiveResampler.MinEntropy
 
add(BenesNamedPoint) - Method in class vib.PointList
 
add(String, double, double, double) - Method in class vib.PointList
 
add(double, double, double) - Method in class vib.PointList
 
add(VolumeFloat) - Method in class volume.VolumeFloat
 
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.
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(Layer, Collection<? extends Displayable>) - Static method in class ini.trakem2.display.Display
 
addAll(LayerSet, Collection<? extends ZDisplayable>) - Static method in class ini.trakem2.display.Display
 
addAll(Collection<? extends ZDisplayable>) - Method in class ini.trakem2.display.LayerSet
 
addAll(String[]) - Method in class ini.trakem2.utils.Montage
 
addAll(Collection<? extends T>) - Method in class mpicbg.imglib.image.Image
 
addAll(int[]) - Method in class org.siox.util.IntArrayList
Appends all of the elements in the specified array, in the order that they appear in the array.
addAll(Collection) - Method in class org.siox.util.IntArrayList
Appends all of the elements in the specified collection, in the order that they appear in the array.
addAll(int, Collection) - Method in class org.siox.util.IntArrayList
Inserts all of the elements in the specified array into this list, starting at the specified position.
addAll(int, int[]) - Method in class org.siox.util.IntArrayList
Inserts all of the elements in the specified array into this list, starting at the specified position.
addAllClasses(ClassifiedRegion) - Method in class mpicbg.stitching.fusion.ClassifiedRegion
Merges the classes attached to another region with the classes of this region.
addAllEdges(Collection<DefaultWeightedEdge>) - Method in class fiji.plugin.trackmate.ModelChangeEvent
 
addAllSpots(Collection<Spot>) - Method in class fiji.plugin.trackmate.ModelChangeEvent
 
addAlphaMask(Roi, int) - Method in class ini.trakem2.display.Patch
Add the given roi, in world coords, to the alpha mask, using the given fill value.
addAlphaMask(Area, int) - Method in class ini.trakem2.display.Patch
Add the given area, in world coords, to the alpha mask, using the given fill value.
addAlphaMaskLocal(Area, int) - Method in class ini.trakem2.display.Patch
Add the given area, in local coordinates, to the alpha mask, using the given fill value.
addAmiraLabelsList(GenericDialog, String) - Static method in class amira.AmiraParameters
 
addAmiraMeshList(GenericDialog, String) - Static method in class amira.AmiraParameters
 
addAmiraTableList(GenericDialog, String) - Static method in class amira.AmiraParameters
 
addAndFixTiles(List<ViewId>, HashMap<ViewId, Tile<M>>, GlobalOptimizationType, GlobalOptimizationSubset, boolean) - Static method in class spim.process.interestpointregistration.GlobalOpt
 
addAnisotropicDiffusion(ImagePlus, int, int, int, float, float, float) - Method in class trainableSegmentation.FeatureStack
Add anisotropic diffusion filtering images to current stack
addAppleA() - Method in class spim.fiji.spimdata.explorer.ViewSetupExplorerPanel
 
addArea(long, Area) - Method in class ini.trakem2.display.AreaList
Add a copy of an Area object to the existing, if any, area object at Layer with layer_id as given, or if not existing, just set the copy as it.
addAreaList(AreaList) - Method in class edu.utexas.clm.crop.AreaListCrop
 
AddARGBComposite - Class in ini.trakem2.display.graphics
 
addAsLinesTo3DViewer(Image3DUniverse, Color, ImagePlus) - Method in class tracing.Path
 
addAsLinesTo3DViewer(Image3DUniverse, Color3f, ImagePlus) - Method in class tracing.Path
 
addBall(double, double, double, long) - Method in class ini.trakem2.display.Ball
Used to add individual ball objects when parsing.
addBilateralFilter(ImagePlus, double, double) - Method in class trainableSegmentation.FeatureStack
Add bilateral filter image to current stack
addBinaryData(ImagePlus, FeatureStack, String) - Method in class trainableSegmentation.WekaSegmentation
Add instances to a specific class from a label (binary) image.
addBinaryData(ImagePlus, FeatureStack, String, String) - Method in class trainableSegmentation.WekaSegmentation
Add instances to two classes from a label (binary) image.
addBinaryData(List<Point3f>[], FeatureStackArray, String, String) - Method in class trainableSegmentation.WekaSegmentation
Add instances to two classes from lists of coordinates.
addBinaryData(ImagePlus, int, String, String) - Method in class trainableSegmentation.WekaSegmentation
Add label image as binary data
addBinaryData(ImagePlus, ImagePlus, String, String) - Method in class trainableSegmentation.WekaSegmentation
Add binary training data from input and label images.
addBinaryData(ImagePlus, ImagePlus, ImagePlus, String, String) - Method in class trainableSegmentation.WekaSegmentation
Add binary training data from input and label images.
addBottler(Bottler) - Method in class edu.utexas.clm.archipelago.Cluster
 
addBottler(Bottler) - Method in class edu.utexas.clm.archipelago.network.MessageXC
 
addBottler(Bottler) - Method in class edu.utexas.clm.archipelago.network.node.ClusterNode
 
addBottler(Bottler) - Method in class edu.utexas.clm.archipelago.network.node.NodeCoordinator
 
addBoundingBox(BoundingBox) - Method in class spim.fiji.spimdata.boundingbox.BoundingBoxes
 
addBox() - Method in class ij3d.Executer
 
addBox(Image3DUniverse) - Static method in class ij3d.gui.PrimitiveDialogs
 
addBox(String, String, String) - Static method in class ij3d.ImageJ3DViewer
Add a box into the current 3D universe
addBrowseToCellVoyagerFolder(GenericDialogPlus, String, String, int) - Static method in class bdv.ij.ExportCellVoyagerPlugIn
 
addButton(String, ActionListener) - Method in class fiji.util.gui.GenericDialogPlus
Add button to the dialog
addButton(String, ActionListener) - Method in class spim.fiji.plugin.queryXML.GenericLoadParseQueryXML
 
addCacheControl(CacheControl, int) - Method in class bdv.cache.CacheControl.CacheControls
 
addCacheControl(CacheControl) - Method in class bdv.cache.CacheControl.CacheControls
 
addCanvasListener(CustomCanvas.CanvasListener) - Method in class vib.segment.CustomCanvas
 
addCenterLinesBinaryData(ImagePlus, int, String, String) - Method in class trainableSegmentation.WekaSegmentation
Add center lines of label image as binary data
addCenterOf(Iterable<Content>) - Method in class ij3d.ViewAdjuster
Make sure that the average center of all contents is visible in the canvas.
addChangeListener(ChangeListener) - Method in class fiji.plugin.trackmate.gui.descriptors.SpotFilterDescriptor
Add an ChangeListener to this panel.
addChangeListener(ChangeListener) - Method in class fiji.plugin.trackmate.gui.descriptors.TrackFilterDescriptor
Add an ChangeListener to this panel.
addChangeListener(ChangeListener) - Method in class fiji.plugin.trackmate.gui.panels.components.FilterGuiPanel
Add an ChangeListener to this panel.
addChangeListener(ChangeListener) - Method in class fiji.plugin.trackmate.gui.panels.FilterPanel
Add an ChangeListener to this panel.
addChangeTreesStep() - Method in class ini.trakem2.display.LayerSet
Add a step to undo the addition or deletion of one or more objects in this project and LayerSet.
addChangeTreesStep(Set<DoStep>) - Method in class ini.trakem2.display.LayerSet
Add a step to undo the addition or deletion of one or more objects in this project and LayerSet, along with an arbitrary set of steps that may alter, for example the data.
addCheckBox(Container, String) - Static method in class gui.GuiBuilder
 
addCheckbox(String, boolean) - Method in class ini.trakem2.utils.OptionPanel
 
addCheckbox(String, boolean, OptionPanel.Setter) - Method in class ini.trakem2.utils.OptionPanel
 
addCheckbox(GenericDialog, String) - Method in class loci.plugins.prefs.OptionsDialog
Adds a checkbox to the given dialog object corresponding to the boolean option identified by the specified key.
addCheckbox(String) - Method in class util.ModelessQuestions
 
addChild(Thing, DefaultMutableTreeNode) - Method in class ini.trakem2.tree.DNDTree
Appends at the end of the parent_node child list, and waits until the tree's UI is updated.
addChild(Thing) - Method in class ini.trakem2.tree.LayerThing
 
addChild(Thing) - Method in class ini.trakem2.tree.ProjectThing
 
addChild(ProjectThing, int) - Method in class ini.trakem2.tree.ProjectThing
In addition, if the child contains an object of class ini.trakem2.display.Profile, reorders all children of the parent Thing by the Z of the layers of the profiles.
addChild(ProjectThing, String, Displayable) - Method in class ini.trakem2.tree.ProjectTree
Attempt to add the d as a ProjectThing child of type childType to the parent ProjectThing parent.
addChild(Thing) - Method in class ini.trakem2.tree.TemplateThing
 
addChild(Thing) - Method in interface ini.trakem2.tree.Thing
 
addChoice(GenericDialog, String, Vector) - Static method in class amira.AmiraParameters
 
addChoice(GenericDialog, String, Vector, String) - Static method in class amira.AmiraParameters
 
addChoice(String, String[], int) - Method in class ini.trakem2.utils.OptionPanel
 
addChoice(String, String[], int, OptionPanel.Setter) - Method in class ini.trakem2.utils.OptionPanel
 
addChoice(GenericDialog, String) - Method in class loci.plugins.prefs.OptionsDialog
Adds a choice to the given dialog object corresponding to the string option identified by the specified key.
addChoice(String, String[]) - Method in class spimopener.OpenerGenericDialog
 
addCircle(ImagePlus, int, int, double) - Method in class selection.Select_Points
 
addCitationMessage() - Method in class sholl.gui.EnhancedGenericDialog
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.
addClassMap(String) - Method in class fiji.FijiClassLoader
Deprecated.
 
addClassPath() - Method in class fiji.InspectJar
 
addColorMode() - Method in class spim.fiji.spimdata.explorer.ViewSetupExplorerPanel
 
addColorMouseListener(ImageCanvas) - 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 stitching.model.Tile
Add a Tile to the set of connected tiles.
AddConstant - Class in imglib.ops.operator.unary
TODO
AddConstant(double) - Constructor for class imglib.ops.operator.unary.AddConstant
 
addContent(ImagePlus, File) - Method in class ij3d.Executer
 
addContent(ImagePlus, Color3f, String, int, boolean[], int, int) - Method in class ij3d.Image3DUniverse
Add the specified image as a new Content to the universe.
addContent(ImagePlus, int, int) - Method in class ij3d.Image3DUniverse
Add the specified image as a new Content to the universe.
addContent(ImagePlus, int) - Method in class ij3d.Image3DUniverse
Add the specified image as a new Content to the universe.
addContent(Content) - Method in class ij3d.Image3DUniverse
Add the specified Content to the universe.
addContent(Collection<Content>) - Method in class ini.trakem2.display.Display3D
 
addContent(Content) - Method in class ini.trakem2.display.Display3D
 
addContentFromFile() - Method in class ij3d.Executer
 
addContentFromImage(ImagePlus) - Method in class ij3d.Executer
 
addContentLater(Content) - Method in class ij3d.Image3DUniverse
Add the specified Content to the universe.
addContentLater(String) - Method in class ij3d.Image3DUniverse
 
addContentLater(Collection<Content>) - Method in class ij3d.Image3DUniverse
Add the specified collection of Content to the universe.
addContour(Element, ReconstructSection) - Method in interface edu.utexas.clm.reconstructreader.reconstruct.ContourSet
 
addContour(Element, ReconstructSection) - Method in class edu.utexas.clm.reconstructreader.reconstruct.ReconstructAreaList
 
addContour(Element, ReconstructSection) - Method in class edu.utexas.clm.reconstructreader.reconstruct.ReconstructProfileList
 
addContour(Element, ReconstructSection) - Method in class edu.utexas.clm.reconstructreader.reconstruct.ReconstructZTrace
 
addCorrespondence(ExtendedPointMatch) - Method in class selection.Select_Points
 
addCorrespondences(List<PairwiseMatch>) - Method in class spim.process.interestpointregistration.optimizationtypes.GlobalOptimizationType
Add all correspondences the list for those that are compared here This method can be overwritten if saving, adding & clearing of correspondences is different for a certain type of registration
addCross(ImagePlus, int, int) - Method in class selection.Select_Points
 
addCrossLink(long, long, long) - Method in class ini.trakem2.persistence.DBLoader
 
addCrossLink(long, long, long) - Method in class ini.trakem2.persistence.Loader
 
addCtrlHint() - Method in class ij3d.gui.LUTDialog
 
addCursor(Cursor<T>) - Method in class mpicbg.imglib.image.Image
Adds a Cursor to the ArrayList of instantiated Cursors.
addCustomMesh(CustomMesh, String) - Method in class ij3d.Image3DUniverse
Add a custom mesh to the universe.
addCustomMesh(CustomMultiMesh, String) - Method in class ij3d.Image3DUniverse
Add a CustomMultiMesh to the universe.
addData(byte) - Method in class adt.PixelStats
 
addDataEditStep(Set<? extends Displayable>) - Method in class ini.trakem2.display.LayerSet
A new undo step for the "data" field of all Displayable in the set.
addDefaultFeatures() - Method in class trainableSegmentation.FeatureStack
Add the default features to the feature stack
addDefaultFiles() - Method in class fiji.packaging.Packager
 
addDefaultTableMouseListener() - Method in class bigwarp.BigWarp
 
addDependent(double[]) - Method in class ini.trakem2.vector.VectorString3D
Add an array that will get resampled along; must be of the same length as the value returned by length()
addDependents(Collection<DoStep>) - Method in class ini.trakem2.display.Displayable.DoEdits
 
addDependents(Set<DoStep>) - Method in class ini.trakem2.display.LayerSet.DoChangeTrees
 
addDerivatives(double, int, int) - Method in class trainableSegmentation.FeatureStack
Add derivatives features to current stack
addDetection(T) - Method in class mpicbg.spim.registration.detection.DetectionStructure
 
addDirectoryField(String, String) - Method in class fiji.util.gui.GenericDialogPlus
 
addDirectoryField(String, String, int) - Method in class fiji.util.gui.GenericDialogPlus
 
addDirectoryField(Container, String) - Static method in class gui.GuiBuilder
 
addDirectoryOrFileField(String, String) - Method in class fiji.util.gui.GenericDialogPlus
 
addDirectoryOrFileField(String, String, int) - Method in class fiji.util.gui.GenericDialogPlus
 
addDiscsTo3DViewer(Image3DUniverse, Color, ImagePlus) - Method in class tracing.Path
 
addDiscsTo3DViewer(Image3DUniverse, Color3f, ImagePlus) - Method in class tracing.Path
 
addDisplayChangeListener(ImageWindow, DisplayChangeListener) - Static method in class OpenImage5DAdapter
 
addDisplayChangeListener(DisplayChangeListener) - Method in class OpenImage5DWindow
 
addDisplayChangeListener(ImageWindow, DisplayChangeListener) - Static method in class OpenStackAdapter
 
addDisplayChangeListener(DisplayChangeListener) - Method in class OpenStackWindow
 
addDisplaySettingsChangeListener(DisplaySettingsListener) - Method in class fiji.plugin.trackmate.gui.panels.ConfigureViewsPanel
Adds the specified DisplaySettingsListener to the collection of listeners that will be notified when a display settings change is made on this GUI.
addDoG(float, float) - Method in class trainableSegmentation.FeatureStack
Add difference of Gaussians to feature stack (single thread version)
addDoubleSlider(String, int, int) - Method in class spimopener.OpenerGenericDialog
 
addDoubleSlider(String, int, int, int, int) - Method in class spimopener.OpenerGenericDialog
 
addDragOverlay(BigWarpDragOverlay) - Method in class bdv.viewer.BigWarpViewerPanel
 
added(BenesNamedPoint) - Method in class ij3d.pointlist.PointListPanel
 
added(BenesNamedPoint) - Method in class ij3d.pointlist.PointListShape
 
added(BenesNamedPoint) - Method in interface vib.PointList.PointListListener
 
added(BenesNamedPoint) - Method in class vib.Points_Dialog
 
addEdge(Spot, Spot, double) - Method in class fiji.plugin.trackmate.Model
Creates a new edge between two spots, with the specified weight.
addEdge(DefaultWeightedEdge) - Method in class fiji.plugin.trackmate.ModelChangeEvent
 
addEdge(double, double, double, double) - Method in class fiji.plugin.trackmate.util.XYEdgeSeries
 
addEdge(Edge) - Method in class sc.fiji.analyzeSkeleton.Graph
Add edge to the graph.
addEdgeAnalyzer(EdgeAnalyzer) - Method in class fiji.plugin.trackmate.Settings
Adds a EdgeAnalyzer to the List of edge analyzers configured.
addEdgeAnalyzer(int, EdgeAnalyzer) - Method in class fiji.plugin.trackmate.Settings
Adds a EdgeAnalyzer to the List of edge analyzers configured, at the specified index.
addEdgeManually(mxCell) - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackScheme
This method is called when the user has created manually an edge in the graph, by dragging a link between two spot cells.
addEdgeToSelection(DefaultWeightedEdge) - Method in class fiji.plugin.trackmate.SelectionModel
 
addEdgeToSelection(Collection<DefaultWeightedEdge>) - Method in class fiji.plugin.trackmate.SelectionModel
 
addEditor() - Method in class fiji.Wiki_Editor
 
addedPatchFrom(String, Patch) - Method in class ini.trakem2.persistence.FSLoader
All backslashes are converted to slashes to avoid havoc in MSWindows.
addedPatchFrom(String, Patch) - Method in class ini.trakem2.persistence.Loader
Subclasses can override this method to register the URL of the imported image.
AddElement(byte[], int, int, int, int, int) - Method in class view5d.View5D
 
AddElement(short[], int, int, int, int, int) - Method in class view5d.View5D
 
AddElement(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
 
addElements(double[], double[], double[]) - Static method in class bijnum.BIJmatrix
 
addElements(float[], float[], float[]) - Static method in class bijnum.BIJmatrix
 
addElements(float[], float[]) - Static method in class bijnum.BIJmatrix
 
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
 
addFallBack(ClassLoader) - Method in class fiji.FijiClassLoader
Deprecated.
 
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) - Method in class mpicbg.ij.plugin.AbstractBlockMatching
 
addFields(GenericDialog) - Method in class mpicbg.trakem2.align.Align.Param
 
addFields(GenericDialog) - Method in class mpicbg.trakem2.align.Align.ParamOptimize
 
addFile(File) - Method in class fiji.FijiClassLoader
Deprecated.
 
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
 
addFileSaveField(Container, String) - Static method in class gui.GuiBuilder
 
addFill(Fill) - Method in class tracing.PathAndFillManager
 
addFilterPanel() - Method in class fiji.plugin.trackmate.gui.panels.components.FilterGuiPanel
 
addFilterPanel(FeatureFilter) - Method in class fiji.plugin.trackmate.gui.panels.components.FilterGuiPanel
 
addFilterPanel(String) - Method in class fiji.plugin.trackmate.gui.panels.components.FilterGuiPanel
 
addFirst(Transform) - Method in class vib.transforms.OrderedTransformations
 
addFirst(OrderedTransformations) - Method in class vib.transforms.OrderedTransformations
 
addFittedMinimum(int) - Method in class sc.fiji.timelapse.Extrema
Fit a parabola to the interval [left;right].
addFixedPoint(RealPoint, boolean) - Method in class bigwarp.BigWarp.MouseLandmarkListener
Adds a point in the moving and fixed images at the same point.
addFrame() - Method in class video.Edit_Video
 
addFrames(ImagePlus, int, int) - Static method in class video2.Add_Empty_Frame
 
addGabor(ImagePlus, double, double, double, double, int) - Method in class trainableSegmentation.FeatureStack
Add Gabor features to current stack
addGaussianBlur(float) - Method in class trainableSegmentation.FeatureStack
Add Gaussian blur slice to current stack
addGaussianNoise(Image<FloatType>, Random, float, boolean) - Static method in class mpicbg.spim.postprocessing.deconvolution2.AdjustInput
Adds additive gaussian noise: i = i + gauss(x, sigma)
addGaussianNoiseAddMul(Image<FloatType>, Random, float, boolean) - Static method in class mpicbg.spim.postprocessing.deconvolution2.AdjustInput
Adds additive and multiplicative gaussian noise: i = i*gauss(x,sigma) + gauss(x, sigma)
addGeometricConsensusFilterFields(GenericDialog) - Method in class mpicbg.trakem2.align.Align.Param
 
addGradient(float) - Method in class trainableSegmentation.FeatureStack
Add Sobel filter version of the original image
addHandle(int, int) - Method in class sc.fiji.timelapse.PolygonRoiPublic
 
addHandle(int, int) - Method in class Transform_MovingLeastSquaresMesh
 
addHandle(int, int) - Method in class Transform_ThinPlateSpline
 
addHessian(float) - Method in class trainableSegmentation.FeatureStack
Add Hessian features from original image (single thread version).
addHSB() - Method in class trainableSegmentation.FeatureStack
Add HSB features
addHyperlink(String) - Method in class sholl.gui.EnhancedWaitForUserDialog
Adds a functional URL to the dialog's MultiLineLabel.
addHyperLink(GenericDialog, String, String) - Static method in class spim.fiji.plugin.util.GUIHelper
 
addHyperLinkListener(MultiLineLabel, String) - Static method in class fiji.plugin.Bead_Registration
 
addHyperLinkListener(MultiLineLabel, String) - Static method in class spim.fiji.plugin.util.GUIHelper
 
addHyperLinkListener(MultiLineLabel, String) - Static method in class stitching.CommonFunctions
 
addHyperlinkMessage(String, Font, Color, String) - Method in class sholl.gui.EnhancedGenericDialog
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) - Method in class sc.fiji.coloc.results.PDFWriter
Prints an image into the opened PDF.
addImage(Image, String) - Method in class sc.fiji.io.PDF_Writer
 
addImageChoice(String, String) - Method in class fiji.util.gui.GenericDialogPlus
 
addImageList(GenericDialog, String, String, AmiraParameters.IsA) - Static method in class amira.AmiraParameters
 
addImagePlusPair(ImagePlus, ImagePlus) - Method in class util.Histogram_2D
 
addImagePlusPair(ImagePlus, ImagePlus, int) - Method in class util.Histogram_2D
 
addImagePlusPair(ImagePlus, ImagePlus, double, double, double, double, int, int) - Method in class util.Histogram_2D
 
addImageToList(ImagePlus, String) - Method in class sc.fiji.coloc.results.PDFWriter
 
addImageWindowListener(WindowListener) - Method in class org.siox.example.ControlJPanel
Add a WindowListener to any image display window (except internal frames), wether it is now open or opened in the future.
addImageWindowListener(InternalFrameListener) - Method in class org.siox.example.ControlJPanel
Add an InternalFrameListener to any internal frame for displaying an image.
addImgLibAlgorithms() - Method in class fiji.expressionparser.ImgLibParser
Add ImgLib algorithms to the parser, such as gaussian convolution.
addingNode(SearchNode) - Method in class tracing.AutoSearchThread
 
addingNode(SearchNode) - Method in class tracing.SearchThread
Override this method if you want to find out when a point was first discovered:
addInstant(ContentInstant) - Method in class ij3d.Content
 
addInteractiveBehavior(InteractiveBehavior) - Method in class ij3d.DefaultUniverse
 
addInterestPointList(String, InterestPointList) - Method in class spim.fiji.spimdata.interestpoints.ViewInterestPointLists
 
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
 
addJar(JarFile) - Method in class fiji.InspectJar
 
addJar(URL) - Method in class fiji.InspectJar
 
addJar(String) - Method in class fiji.InspectJar
 
addJGraphTEdge(DefaultWeightedEdge) - Method in class fiji.plugin.trackmate.visualization.trackscheme.JGraphXAdapter
 
addJGraphTVertex(Spot) - Method in class fiji.plugin.trackmate.visualization.trackscheme.JGraphXAdapter
 
addJob(Bureaucrat) - Method in class ini.trakem2.persistence.Loader
Adds a new job to monitor.
addKey(String, File) - Method in class edu.utexas.clm.archipelago.network.shell.NodeShellParameters
 
addKey(String, String) - Method in class edu.utexas.clm.archipelago.network.shell.NodeShellParameters
 
addKey(String, int) - Method in class edu.utexas.clm.archipelago.network.shell.NodeShellParameters
 
addKey(String, float) - Method in class edu.utexas.clm.archipelago.network.shell.NodeShellParameters
 
addKeyAndContainerListenerRecursively(Component) - Method in class tracing.ClarifyingKeyListener
 
addKeyEventPostProcessor(KeyEventPostProcessor) - Method in class bigwarp.BigWarp
 
addKeyListener(Component) - Method in class fiji.tool.AbstractTool
 
addKeyListener(KeyListener) - Method in class sc.fiji.i5d.gui.ScrollbarWithLabel
 
addKuwaharaFeatures(ImagePlus, int, int, int) - Method in class trainableSegmentation.FeatureStack
Add Kuwahara filter features to the current stack
addLabel(int) - Method in class mpicbg.spim.registration.threshold.ConnectedComponent
 
addLabel(String) - Method in class util.ModelessQuestions
 
addLabeledData(ImagePlus, FeatureStack) - Method in class trainableSegmentation.WekaSegmentation
Add instances from a labeled image.
addLabeledData(ImagePlus, ImagePlus) - Method in class trainableSegmentation.WekaSegmentation
Add labeled training data from input and label images.
addLabeledNumericSpinner(Container, String, int, int, int, ChangeListener) - Static method in class gui.GuiBuilder
 
addLabeledSpinner(Container, String, SpinnerModel) - Static method in class gui.GuiBuilder
 
addLabelList(Container) - Static method in class oldsegmenters.Segmentator_
 
addLabelList(Container) - Static method in class oldsegmenters.Segmenter_
 
addLaplacian(double) - Method in class trainableSegmentation.FeatureStack
Add Laplacian features to current stack
addLast(Transform) - Method in class vib.transforms.OrderedTransformations
 
addLast(OrderedTransformations) - Method in class vib.transforms.OrderedTransformations
 
addLayer(LayerSet, Layer) - Method in class ini.trakem2.tree.LayerTree
Used by the Loader.importStack and the "many new layers" command.
addLayerChoice(String, Layer, GenericDialog) - Static method in class ini.trakem2.utils.Utils
 
addLayerContentStep(Layer) - Method in class ini.trakem2.display.LayerSet
For the Displayable contained in a Layer: their number, and their stack order.
addLayerEditedStep(Layer) - Method in class ini.trakem2.display.LayerSet
For the Z and thickness of a layer.
addLayerEditedStep(List<Layer>) - Method in class ini.trakem2.display.LayerSet
For the Z and thickness of a list of layers.
addLayerRangeChoices(Layer, GenericDialog) - Static method in class ini.trakem2.utils.Utils
 
addLayerRangeChoices(Layer, Layer, GenericDialog) - Static method in class ini.trakem2.utils.Utils
 
addLayoutComponent(Component, Object) - Method in class sc.fiji.i5d.gui.Image5DLayout
 
addLayoutComponent(String, Component) - Method in class sc.fiji.i5d.gui.Image5DLayout
 
addLeafs(List<? extends Thing>, Runnable) - Method in class ini.trakem2.tree.DNDTree
Will add only those for which a node doesn't exist already.
addLine3D(Line3D) - Method in class jRenderer3D.JRenderer3D
Adds a single 3D line to the 3D scene.
addLine3D(int, int, int, int, int, int, Color) - Method in class jRenderer3D.JRenderer3D
Adds a single 3D line to the 3D scene.
addLineMesh(List<Point3f>, Color3f, String, boolean) - Method in class ij3d.Image3DUniverse
Add a custom mesh, in particular a line mesh (a set of lines in 3D) to the universe.
addLines(Point3f[]) - Method in class customnode.CustomLineMesh
 
addLines3D(Line3D[]) - Method in class jRenderer3D.JRenderer3D
Adds an array of lines to the 3D scene.
addLipschitzFilter(ImagePlus, boolean, boolean, double) - Method in class trainableSegmentation.FeatureStack
Add Lipschitz filter image to current stack
addListener(NodeStateListener) - Method in class edu.utexas.clm.archipelago.network.node.ClusterNode
Adds a NodeStateListener to the list of listeners that are notified when the state of this ClusterNode changes.
addListener(FileListener) - Method in class fsalign.FolderWatcher
 
addListener(LUTDialog.Listener) - Method in class ij3d.gui.LUTDialog
 
addListener(SelectedViewDescriptionListener<AS>) - Method in class spim.fiji.spimdata.explorer.ViewSetupExplorer
 
addListener(SelectedViewDescriptionListener<AS>) - Method in class spim.fiji.spimdata.explorer.ViewSetupExplorerPanel
 
addListener(SNTListener) - Method in class tracing.SimpleNeuriteTracer
 
addListeners() - Method in class bigwarp.WarpVisFrame
 
addListeners(GenericDialog, Choice, MyMultiLineLabel, ArrayList<MultiViewDatasetDefinition>) - Method in class spim.fiji.plugin.Define_Multi_View_Dataset
 
addListeners(GenericDialog, TextField, TextField, TextField, Checkbox, Label) - Method in class spim.fiji.plugin.Merge_Cluster_Jobs
 
addListeners(GenericDialog, TextField, Label, Label) - Method in class spim.fiji.plugin.queryXML.GenericLoadParseQueryXML
 
addListeners(GenericDialog, Vector<?>, Label, long[]) - Method in class spim.process.fusion.boundingbox.AutomaticBoundingBox
 
addListeners(ImgExport) - Method in class spim.process.fusion.boundingbox.BoundingBoxGUI.ManageListeners
 
addListeners(GenericDialog, Choice, Label, Label) - Method in class spim.process.fusion.boundingbox.PreDefinedBoundingBox
 
AddLookUpTable(int, byte[], byte[], byte[]) - Static method in class view5d.Bundle
 
AddLookUpTable(int, byte[], byte[], byte[]) - Method in class view5d.My3DData
 
addLowerRightPoint(Point) - Method in class adt.Connectivity2D
the contract of calling this method is that the new point must be gauranteed to be the most far right lowest point (i.e.
addLThresh(double) - Method in class view5d.My3DData
 
AddMarkedElement() - Method in class view5d.My3DData
 
addMarker(CellCntrMarker) - Method in class CellCntrMarkerVector
 
addMaskPoint(int, int) - Method in class bunwarpj.PointHandler
Add a point to the mask.
addMatch(PointMatch) - Method in class stitching.model.Tile
Add one match.
addMatches(Collection<PointMatch>) - Method in class stitching.model.Tile
Add more PointMatches.
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
 
addMean(float) - Method in class trainableSegmentation.FeatureStack
Add mean filter to current stack
addMedian(float) - Method in class trainableSegmentation.FeatureStack
 
addMembraneFeatures(int, int) - Method in class trainableSegmentation.FeatureStack
Add membrane features to the stack (single thread version)
addMesh(ImagePlus) - Method in class ij3d.Image3DUniverse
Add a new image as a content, displaying it as an isosurface.
addMesh(ImagePlus, int) - Method in class ij3d.Image3DUniverse
Add a new image as a content, displaying it as an isosurface.
addMesh(ImagePlus, Color3f, String, int, boolean[], int) - Method in class ij3d.Image3DUniverse
Add a new image as a content, displaying it as an iso-surface.
addMesh(List, Color3f, String, float, int) - Method in class ij3d.Image3DUniverse
Deprecated.
This method will not be supported in the future. The specified 'scale' will be ignored, and the applied scale will be calculated automatically from the minimum and maximum coordinates of the specified mesh. Use addTriangleMesh instead.
addMesh(List<Point3f>, Color3f, String, int) - Method in class ij3d.Image3DUniverse
Deprecated.
This method will not be supported in the future. Use addTriangleMesh instead.
addMesh(LayerSet, VectorString3D, String, Color) - Static method in class ini.trakem2.display.Display3D
Creates a mesh from the given VectorString3D, which is unbound to any existing Pipe.
addMesh(LayerSet, VectorString3D, String, Color, double[], float) - Static method in class ini.trakem2.display.Display3D
Creates a mesh from the given VectorString3D, which is unbound to any existing Pipe.
addMeshes(Image3DUniverse, String) - Static method in class isosurface.AmiraSurface
 
addMessage(String) - Method in class ini.trakem2.utils.OptionPanel
 
addMessage(GenericDialog, String[], Font, Color) - Static method in class spim.fiji.plugin.util.MyMultiLineLabel
Adds a message consisting of one or more lines of text, which will be displayed using the specified font and color.
addMin(float) - Method in class trainableSegmentation.FeatureStack
 
addMinimum(int) - Method in class sc.fiji.timelapse.Extrema
 
addModelChangeListener(ModelChangeListener) - Method in class fiji.plugin.trackmate.Model
 
addModuleListener(ModuleListener) - Static method in class vib.app.module.Module
 
addMouseMotionListener(ImageCanvas) - Method in class fiji.tool.AbstractTool
 
addMouseWheelListener(ImageWindow) - Method in class fiji.tool.AbstractTool
 
addNatMethBeadsPaper(GenericDialog) - Static method in class spim.fiji.plugin.util.GUIHelper
 
addNatMethBeadsPaper(GenericDialog, String) - Static method in class spim.fiji.plugin.util.GUIHelper
 
addNeighborPair(int, byte[], int, int) - Method in class SRM_
 
addNeighborPair(int, byte[], byte[], int) - Method in class SRM_
 
addNeighbors(int, int) - Method in class trainableSegmentation.FeatureStack
Add 8 neighbors of the original image as features
AddNewBalloon(int[], int[]) - Method in class sc.fiji.balloonSegmentation.structure.BalloonPopulation
Add a balloon with custom shape defined by arrays X and Y
AddNewBalloon(int, int) - Method in class sc.fiji.balloonSegmentation.structure.BalloonPopulation
Add a circular balloon centrerd on x,y with id ID
addNewChildType(ProjectThing, String) - Method in class ini.trakem2.tree.TemplateTree
Add a new template thing to an existing ProjectThing, so that new instances of template new_child_type can be added to the ProjectThing pt.
addNewChildType(TemplateThing, String) - Method in class ini.trakem2.tree.TemplateTree
tt_parent is the parent TemplateThing tet_child is the child to add to tt parent, and to insert as child to all nodes that host the tt parent.
addNewImage(ImagePlus) - Method in class ini.trakem2.persistence.Loader
 
addNewImage(ImagePlus, double, double) - Method in class ini.trakem2.persistence.Loader
Mipmaps for this image are generated asynchronously.
addNewPoint() - Method in class landmarks.NamedPointSet
 
addNextPoint(SWCPoint) - Method in class tracing.SWCPoint
 
addNode(Node<T>, Node<T>, byte) - Method in class ini.trakem2.display.Tree
Will call calculateBoundingBox and repaint.
addNode(MutableTreeNode, Path, DefaultTreeModel) - Method in class tracing.PathWindow
 
addNode(SearchNode, boolean) - Method in class tracing.SearchThread
 
AddNoise - Class in imglib.ops.operator.unary
TODO
AddNoise(double, double, double) - Constructor for class imglib.ops.operator.unary.AddNoise
 
addNotify() - Method in class spim.fiji.plugin.util.MyMultiLineLabel
 
addNumericField(String, double, int) - Method in class ini.trakem2.utils.OptionPanel
 
addNumericField(String, double, int, OptionPanel.Setter) - Method in class ini.trakem2.utils.OptionPanel
 
addNumericField(String, int) - Method in class ini.trakem2.utils.OptionPanel
 
addNumericField(String, int, OptionPanel.Setter) - Method in class ini.trakem2.utils.OptionPanel
 
addObject(Object3D) - Method in class Utilities.Counter3D
Add the provided Object3D to the list
addObserver(Observer) - Method in class imglib.ops.operation.AssignOperation
 
addOctree(String, String) - Method in class ij3d.Image3DUniverse
Deprecated.
The octree methods will be outsourced into a different plugin.
addOrthoslice(ImagePlus) - Method in class ij3d.Image3DUniverse
Add a new image as a content, displaying it as orthoslices.
addOrthoslice(ImagePlus, int) - Method in class ij3d.Image3DUniverse
Add a new image as a content, displaying it as orthoslices.
addOrthoslice(ImagePlus, Color3f, String, int, boolean[], int) - Method in class ij3d.Image3DUniverse
Add a new image as a content, displaying it as orthoslices.
addOrthoslice(String, String, String, String, String, String, String) - Static method in class ij3d.ImageJ3DViewer
 
addOtherKeyListeners(KeyListener[]) - Method in class tracing.QueueJumpingKeyListener
This method should add the other key listeners in 'laterKeyListeners' that will be called for 'source' if this key listener isn't interested in the key press.
addOverlay(BigWarpOverlay) - Method in class bdv.viewer.BigWarpViewerPanel
 
addOverlay(Roi) - Method in class fiji.plugin.trackmate.visualization.hyperstack.HyperStackDisplayer
 
addOverlay(OverlayedImageCanvas.Overlay) - Method in class fiji.util.gui.OverlayedImageCanvas
 
addOverlay(Collection<OverlayedImageCanvas.Overlay>) - Method in class fiji.util.gui.OverlayedImageCanvas
Add the collection of overlays to the display list of this canvas
addOverlayAnimator(OverlayAnimator) - Method in class bdv.viewer.ViewerPanel
Add a new OverlayAnimator to the list of animators.
addp(int, int, double) - Method in class parObject
 
addp(double, double, double) - Method in class parObject
 
addPanel(Panel) - Method in class ij3d.pointlist.PointListDialog
Displays an optional panel at the bottom of the window.
addPanelIntoDialog(Panel) - Method in class Series_Labeler
The container Panel is added to the generic dialog.
addPanelsToDialog(Panel, Panel[]) - Method in class Series_Labeler
Adds different Panels to a container Panel.
addPath(String) - Method in class fiji.FijiClassLoader
Deprecated.
 
addPath(String, boolean) - Method in class fiji.FijiClassLoader
Deprecated.
 
addPath(Path) - Method in class tracing.PathAndFillManager
 
addPath(Path, boolean) - Method in class tracing.PathAndFillManager
 
addPathAndFillListener(PathAndFillListener) - Method in class tracing.PathAndFillManager
 
addPathPointsToShollList(Path, double, double, double, List<ShollAnalysisDialog.ShollPoint>) - Static method in class tracing.ShollAnalysisDialog
 
addPathsToOverlay(Overlay, int, boolean) - Method in class tracing.SimpleNeuriteTracer
 
addPeak(int) - Method in class sc.fiji.timelapse.Peak_Counter_Tool
 
addPlugIns(JPopupMenu, String, Project, Callable<Displayable>) - Static method in class ini.trakem2.utils.Utils
Returns false if none to add.
addPlugIns(String, Project, Callable<Displayable>) - Static method in class ini.trakem2.utils.Utils
Returns null if none to add.
addPoint(int, int) - Method in class adt.Connectivity2D
 
addPoint(Point) - Method in class adt.Connectivity2D
 
addPoint(int, int) - Method in class adt.Points
 
addPoint(Point) - Method in class adt.Points
 
addPoint(double[], boolean, BigWarpViewerPanel) - Method in class bigwarp.BigWarp
Updates the global variable ptBack
addPoint(double[], boolean) - Method in class bigwarp.BigWarp
Updates the global variable ptBack
addPoint(int, int) - Method in class bunwarpj.PointHandler
Add a point to the list of points.
addPoint(Point3f) - Method in class customnode.CustomPointMesh
 
addPoint(Content, int, int) - Method in class ij3d.behaviors.Picker
Adds a landmark point specfied by the canvas position
addPoint(Content, MouseEvent) - Method in class ij3d.behaviors.Picker
Adds a landmark point specfied by the position of the MouseEvent.
addPoint(double, double, long, double) - Method in class ini.trakem2.display.Ball
Add a point either at the end or between two existing points, with accuracy depending on magnification.
addPoint(int, int, double, double, long) - Method in class ini.trakem2.display.Pipe
Add a point either at the end or between two existing points, with accuracy depending on magnification.
addPoint(int, int, long, double) - Method in class ini.trakem2.display.Polyline
Add a point either at the end or between two existing points, with accuracy depending on magnification.
addPoint(double, double, double, double) - Method in class ini.trakem2.display.Profile
Add a point either at the end or between two existing points, with accuracy depending on magnification.
addPoint(Point) - Method in class sc.fiji.analyzeSkeleton.Vertex
Add point to the vertex.
addPoint(AutoPoint, AutoPoint) - Method in class tracing.SinglePathsGraph
 
addPoint3D(Point3D) - Method in class jRenderer3D.JRenderer3D
Adds a single Point3D to the 3D scene.
addPoint3D(int, int, int, int, Color, int) - Method in class jRenderer3D.JRenderer3D
Adds a point to the 3D scene.
addPoint3D(int, int, int, int, int, int) - Method in class jRenderer3D.JRenderer3D
Adds a point to the 3D scene.
addPointDescriptorCorrespondence(T) - Method in class mpicbg.spim.registration.detection.DetectionView
 
addPointDescriptorCorrespondence(T, double) - Method in class mpicbg.spim.registration.detection.DetectionView
 
AddPointEdit - Class in bigwarp.landmarks.actions
 
AddPointEdit(LandmarkTableModel, int, double[], boolean) - Constructor for class bigwarp.landmarks.actions.AddPointEdit
 
addPointList(String, PointListPanel) - Method in class ij3d.pointlist.PointListDialog
Adds the specified PointListPanel.
addPointListListener(PointList.PointListListener) - Method in class vib.PointList
 
addPointListPoint(Point3d) - Method in class ij3d.Content
Deprecated. 
addPointListPoint(Point3d) - Method in class ij3d.ContentInstant
Deprecated. 
addPointMatches(ArrayList<PointMatchGeneric<T>>, Tile<?>, Tile<?>) - Static method in class mpicbg.spim.registration.detection.DetectionRegistration
 
addPointMatches(ArrayList<PointMatch>, Tile<?>, Tile<?>) - Static method in class process.Matching
 
addPointMatches(ArrayList<PointMatchGeneric<Detection>>, Tile<?>, Tile<?>) - Static method in class spim.process.interestpointregistration.GlobalOpt
 
addPointMesh(List<Point3f>, Color3f, String) - Method in class ij3d.Image3DUniverse
Add a custom mesh, in particular a point mesh, to the universe.
addPointMesh(List<Point3f>, Color3f, float, String) - Method in class ij3d.Image3DUniverse
Add a custom mesh, in particular a point mesh, to the universe.
addPoints(Points) - Method in class adt.Points
 
addPoints(Point3f[]) - Method in class customnode.CustomPointMesh
 
addPoints3D(Point3D[]) - Method in class jRenderer3D.JRenderer3D
Adds an array with Point3D to the 3D scene.
addPointsAtBegin(double[][], double[][], double[][]) - Method in class ini.trakem2.display.Profile
 
addPointsAtEnd(double[][], double[][], double[][]) - Method in class ini.trakem2.display.Profile
 
addPopupMenu(JTable) - Method in class spim.fiji.spimdata.explorer.interestpoint.InterestPointExplorerPanel
 
addPopupMenu(JTable) - Method in class spim.fiji.spimdata.explorer.registration.RegistrationExplorerPanel
 
addPopupMenu(JTable) - Method in class spim.fiji.spimdata.explorer.ViewSetupExplorerPanel
 
addPossible(String) - Method in class loci.plugins.prefs.StringOption
Adds a possible value to the list.
addPostTask(Runnable) - Method in class ini.trakem2.utils.Bureaucrat
Add a task to run after the Worker has finished or quit.
addPreibischLabWebsite(GenericDialog) - Static method in class spim.fiji.plugin.util.GUIHelper
 
addProfile(ReconstructProfile) - Method in class edu.utexas.clm.reconstructreader.reconstruct.ReconstructSection
 
addProgressListener(SearchProgressCallback) - Method in class tracing.SearchThread
 
addProgressListener(SearchProgressCallback) - Method in class tracing.TubularGeodesicsTracer
 
addQuad(Point3f, Point3f, Point3f, Point3f) - Method in class customnode.CustomQuadMesh
 
addQuadMesh(List<Point3f>, Color3f, String) - Method in class ij3d.Image3DUniverse
Add a custom mesh, in particular a mesh consisting of quads, to the universe.
addQuads(Point3f[]) - Method in class customnode.CustomQuadMesh
 
addQuery(GenericDialog) - Method in class spim.fiji.plugin.interestpointdetection.DifferenceOfGaussian
 
addQuery(GenericDialog, Interest_Point_Registration.RegistrationType) - Method in class spim.fiji.plugin.interestpointregistration.InterestPointRegistration
adds the questions this registration wants to ask
addQuery(GenericDialog) - Method in interface spim.fiji.plugin.util.GenericDialogAppender
adds the questions this registration wants to ask
addQuery(GenericDialog, Interest_Point_Registration.RegistrationType) - Method in class spim.process.interestpointregistration.centerofmass.CenterOfMass
 
addQuery(GenericDialog, Interest_Point_Registration.RegistrationType) - Method in class spim.process.interestpointregistration.geometricdescriptor.RGLDM
 
addQuery(GenericDialog, Interest_Point_Registration.RegistrationType) - Method in class spim.process.interestpointregistration.geometrichashing.GeometricHashing
 
addQuery(GenericDialog, Interest_Point_Registration.RegistrationType) - Method in class spim.process.interestpointregistration.icp.IterativeClosestPoint
 
addRadio(String, String) - Method in class util.ModelessQuestions
 
addRandomBalancedBinaryData(ImageProcessor, FeatureStack, String, String, int) - Method in class trainableSegmentation.WekaSegmentation
Add instances to two classes from a label (binary) image in a random and balanced way.
addRandomBalancedBinaryData(ImageProcessor, ImageProcessor, FeatureStack, String, String, int) - Method in class trainableSegmentation.WekaSegmentation
Add instances to two classes from a label (binary) image in a random and balanced way (with repetition).
addRandomBalancedBinaryData(List<Point3f>[], FeatureStackArray, String, String, int) - Method in class trainableSegmentation.WekaSegmentation
Add instances to two classes from lists of coordinates in a random and balanced way.
addRandomBalancedBinaryData(List<Point3f>[], FeatureStackArray, ImagePlus, String, String, int) - Method in class trainableSegmentation.WekaSegmentation
Add instances to two classes from lists of coordinates in a random and balanced way.
addRandomBalancedBinaryData(ImageProcessor, ImageProcessor, ImageProcessor, FeatureStack, String, String, int) - Method in class trainableSegmentation.WekaSegmentation
Add instances to two classes from a label (binary) image in a random and balanced way (with repetition).
addRandomBalancedBinaryData(ImagePlus, ImagePlus, String, String, int) - Method in class trainableSegmentation.WekaSegmentation
Add binary training data from input and label images in a random and balanced way (same number of samples per class).
addRandomBalancedBinaryData(ImagePlus, ImagePlus, String, String, int, ImagePlus) - Method in class trainableSegmentation.WekaSegmentation
Add binary training data from input and label images in a random and balanced way (same number of samples per class).
addRandomBalancedBinaryData(ImagePlus, ImagePlus, String, String, int, ImagePlus, ImagePlus) - Method in class trainableSegmentation.WekaSegmentation
Add binary training data from input and label images in a random and balanced way (same number of samples per class).
addRandomBalancedBinaryData(ImagePlus, ImagePlus, ImagePlus, String, String, int) - Method in class trainableSegmentation.WekaSegmentation
Add binary training data from input and label images in a random and balanced way (same number of samples per class).
addRandomBalancedLabeledData(ImageProcessor, FeatureStack, int) - Method in class trainableSegmentation.WekaSegmentation
Add instances from a labeled image in a random and balanced way.
addRandomBalancedLabeledData(ImageProcessor, 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, 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
 
addSelectionUpdateListener(BoxSelectionPanel.SelectionUpdateListener) - Method in class bdv.tools.boundingbox.BoxSelectionPanel
 
addSeries(XYEdgeSeries) - Method in class fiji.plugin.trackmate.util.XYEdgeSeriesCollection
 
addSetup(SpimRegistrationSequence, int, String, String) - Method in class bdv.ij.export.SetupAggregator
Add the setup (angle) of the given SpimRegistrationSequence to this collection.
addSetup(SpimRegistrationSequence, int, int[][], int[][]) - Method in class bdv.ij.export.SetupAggregator
Add the setup (angle) of the given SpimRegistrationSequence to this collection.
addSetup(ConverterSetup) - Method in class bdv.tools.brightness.MinMaxGroup
addSetup(ConverterSetup) - Method in class bdv.tools.brightness.SetupAssignments
Add the setup in a new group.
addSetupChangeListener(PlaceHolderConverterSetup.SetupChangeListener) - Method in class bdv.util.PlaceHolderConverterSetup
Registers a SetupChangeListener, that will be notified when the display range or the color of this ConverterSetup changes.
addSetups(SpimRegistrationSequence, String, String) - Method in class bdv.ij.export.SetupAggregator
Add all setups (angles) of the given SpimRegistrationSequence to this collection.
addSetups(SpimRegistrationSequence, int[][], int[][]) - Method in class bdv.ij.export.SetupAggregator
Add all setups (angles) of the given SpimRegistrationSequence to this collection.
addSetups(FusionResult, String, String) - Method in class bdv.ij.export.SetupAggregator
Add result of SPIM fusion or deconvolution as a setup to this collection.
addSetups(FusionResult, int[][], int[][]) - Method in class bdv.ij.export.SetupAggregator
Add result of SPIM fusion or deconvolution as a setup to this collection.
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(int) - Method in class bdv.viewer.state.SourceGroup
 
addSource(SourceAndConverter<?>) - Method in class bdv.viewer.state.ViewerState
 
addSource(SourceAndConverter<?>) - Method in class bdv.viewer.ViewerPanel
 
addSourceToGroup(int, int) - Method in class bdv.viewer.VisibilityAndGrouping
 
addSphere() - Method in class ij3d.Executer
 
addSphere(Image3DUniverse) - Static method in class ij3d.gui.PrimitiveDialogs
 
addSphere(String, String, String) - Static method in class ij3d.ImageJ3DViewer
Add a sphere into the current 3D universe
addSphere(String, double, double, double, Color, double) - Method in class tracing.SimpleNeuriteTracer
 
addSpot(Spot) - Method in class fiji.plugin.trackmate.ModelChangeEvent
 
addSpotAnalyzerFactory(SpotAnalyzerFactory<?>) - Method in class fiji.plugin.trackmate.Settings
Adds a SpotAnalyzerFactory to the List of spot analyzers configured.
addSpotAnalyzerFactory(int, SpotAnalyzerFactory<?>) - Method in class fiji.plugin.trackmate.Settings
Adds a SpotAnalyzerFactory to the List of spot analyzers configured, at the specified index.
addSpotFilter(FeatureFilter) - Method in class fiji.plugin.trackmate.Settings
Add a filter to the list of spot filters.
addSpotTo(Spot, Integer) - Method in class fiji.plugin.trackmate.Model
Adds a single spot to the collections managed by this model, mark it as visible, then update its features.
addSpotToSelection(Spot) - Method in class fiji.plugin.trackmate.SelectionModel
 
addSpotToSelection(Collection<Spot>) - Method in class fiji.plugin.trackmate.SelectionModel
 
addStandardFunctions() - Method in class fiji.expressionparser.ImgLibParser
 
addStateListener(ClusterStateListener) - Method in class edu.utexas.clm.archipelago.Cluster
 
addStatusListener(StatusListener) - Method in class loci.plugins.in.ImagePlusReader
 
addStatusListener(StatusListener) - Method in class loci.plugins.in.ImportProcess
 
addStatusListener(StatusListener) - Method in class mpicbg.imglib.io.ImageOpener
Adds a listener to those informed when progress occurs.
addStringField(String, String, int) - Method in class fiji.util.gui.GenericDialogPlus
 
addStructure(double, double) - Method in class trainableSegmentation.FeatureStack
Add structure tensor features to current stack It computes, for all pixels in the input image, the eigenvalues of the so-called structure tensor.
addSurfacePlot(ImagePlus) - Method in class ij3d.Image3DUniverse
Add a new image as a content, displaying it as a 2D surface plot.
addSurfacePlot(ImagePlus, int) - Method in class ij3d.Image3DUniverse
Add a new image as a content, displaying it as a 2D surface plot.
addSurfacePlot(ImagePlus, Color3f, String, int, boolean[], int) - Method in class ij3d.Image3DUniverse
Add a new image as a content, displaying it as a 2D surface plot.
AddSymbol(long, long) - Method in class customnode.u3d.ContextManager
 
addTab(String, Component) - Method in class ini.trakem2.display.Display
Returns the tab index in this Display's JTabbedPane.
addTag(Tag) - Method in class ini.trakem2.display.Node
 
addTag(Tag) - Method in interface ini.trakem2.display.Taggable
 
addTarget(float, float, long, float) - Method in class ini.trakem2.display.Connector
 
addTarget(double, double, long, double) - Method in class ini.trakem2.display.Connector
 
addText(String, Transform3D, Appearance) - Method in class ij3d.shapes.CoordinateSystem
 
addText3D(Text3D[]) - Method in class jRenderer3D.JRenderer3D
Adds an array of text to the 3D scene.
addText3D(String, int, int, int, Color, int) - Method in class jRenderer3D.JRenderer3D
Adds a text to the 3D scene.
addText3D(String, int, int, int, int, int) - Method in class jRenderer3D.JRenderer3D
Adds a text to the 3D scene.
addText3D(Text3D) - Method in class jRenderer3D.JRenderer3D
Adds a single 3D text to the 3D scene.
addTextField(String, int, String) - Method in class util.ModelessQuestions
 
addTextPair3D(Text3D, Text3D) - Method in class jRenderer3D.JRenderer3D
 
addTile(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 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
 
addTimelapseFromFile() - Method in class ij3d.Executer
 
addTimelapseFromFolder() - Method in class ij3d.Executer
 
addTimelapseFromHyperstack(ImagePlus) - Method in class ij3d.Executer
 
addTimelapseListener(TimelapseListener) - Method in class ij3d.Image3DUniverse
 
addTimePointListener(TimePointListener) - Method in class bdv.viewer.ViewerPanel
Add a TimePointListener to notify about time-point changes.
addTimePointListener(TimePointListener, int) - Method in class bdv.viewer.ViewerPanel
Add a TimePointListener to notify about time-point changes.
addTo(Bdv) - Method in class bdv.util.BdvOptions
When showing content using one of the BdvFunctions methods, this option can be given to specify that the content should be added to an existing window.
addTo() - Method in class bdv.util.BdvOptions.Values
 
addTo3DViewer(Image3DUniverse, Color, ImagePlus) - Method in class tracing.Path
 
addTo3DViewer(Image3DUniverse, Color3f, ImagePlus) - Method in class tracing.Path
 
addTo3DViewer(Path) - Method in class tracing.PathAndFillManager
 
addToActionMap(ActionMap, BigWarpViewerPanel, int) - Static method in class bdv.viewer.WarpNavigationActions
 
addToDatabase(DBObject) - Method in class ini.trakem2.persistence.DBLoader
 
addToDatabase() - Method in class ini.trakem2.persistence.DBObject
 
addToDatabase(DBObject) - Method in class ini.trakem2.persistence.FSLoader
 
addToDatabase(DBObject) - Method in class ini.trakem2.persistence.Loader
 
addToDatabase(Project) - Method in class ini.trakem2.tree.TemplateThing
Recursive into children! Will add the attributes as well and grab an id for this instance.
addToLinkLater(Node<T>) - Method in class ini.trakem2.display.Tree
 
addToResultsTable() - Method in class tracing.ShollAnalysisDialog.ShollResults
 
addToRoiManager(int, Roi) - Method in class sc.fiji.timelapse.LOI_Interpolator
 
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.
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.
addTriangle(Point3f, Point3f, Point3f) - Method in class customnode.CustomTriangleMesh
 
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
 
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) - Method in class sc.fiji.analyzeSkeleton.Graph
Add vertex to the graph.
addVertex(Extract_Surface.SurfaceVoxel) - Method in class vib.Extract_Surface
 
addVertices(Point3f[]) - Method in class customnode.CustomIndexedTriangleMesh
 
addVertices(Point3f[]) - Method in class customnode.CustomMesh
 
addVerticesToGeometryArray(Point3f[]) - Method in class customnode.CustomIndexedTriangleMesh
 
addVerticesToGeometryArray(Point3f[]) - Method in class customnode.CustomMesh
 
addVerticesToGeometryStripArray(Point3f[]) - Method in class customnode.CustomIndexedTriangleMesh
 
addVerticesToGeometryStripArray(Point3f[]) - Method in class customnode.CustomMesh
 
addView(TrackMateModelView) - Method in class fiji.plugin.trackmate.gui.TrackMateGUIModel
Adds the specified TrackMateModelView to the collection of views managed by this GUI.
addVirtualMatch(PointMatch) - Method in class mpicbg.trakem2.align.AbstractAffineTile2D
 
addVisibilityChangeListener(PlaceHolderOverlayInfo.VisibilityChangeListener) - Method in class bdv.util.PlaceHolderOverlayInfo
Registers a VisibilityChangeListener, that will be notified when the visibility of the source represented by this PlaceHolderOverlayInfo changes.
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
 
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
 
adjustConfidence(int) - Method in class ini.trakem2.display.Node
Adjust the confidence value of this node with its parent.
adjustDimensions() - Method in class ini.trakem2.display.DisplayCanvas
Adjust srcRect and internal variables to the canvas' bounds.
adjustDisplayedImage(RandomAccessibleInterval<? extends RealType<?>>) - Method in class sc.fiji.coloc.results.SingleWindowDisplay
 
adjustEdgeConfidence(int, float, float, Layer, DisplayCanvas) - Method in class ini.trakem2.display.Tree
Expects world coordinates.
AdjustedRandError - Class in trainableSegmentation.metrics
This class implements the adjusted Rand error, defined as the 1 - adjusted Rand index.
AdjustedRandError(ImagePlus, ImagePlus) - Constructor for class trainableSegmentation.metrics.AdjustedRandError
Initialize adjusted Rand error metric.
adjustedRandError(ImageProcessor, ImageProcessor, double) - Static method in class trainableSegmentation.metrics.AdjustedRandError
Calculate the adjusted Rand error between some 2D original labels and the corresponding proposed labels.
adjustedRandIndex(ShortProcessor, ShortProcessor) - Static method in class trainableSegmentation.metrics.AdjustedRandError
Calculate the adjusted Rand index between to clusters, as described by Lawrence Hubert and Phipps Arabie \cite{Rand71}.
adjustGroupProperties(Collection<Displayable>) - Method in class ini.trakem2.display.Display
Pops up a dialog to adjust the alpha, visible, color, locked and compositeMode of all Displayables in col.
adjustImage(Image<FloatType>, float, float) - Static method in class mpicbg.spim.postprocessing.deconvolution2.AdjustInput
Adjusts an image so that the minimal intensity is minValue and the average is average
AdjustInput - Class in mpicbg.spim.postprocessing.deconvolution2
 
AdjustInput() - Constructor for class mpicbg.spim.postprocessing.deconvolution2.AdjustInput
 
AdjustInput - Class in spim.process.fusion.deconvolution
 
AdjustInput() - Constructor for class spim.process.fusion.deconvolution.AdjustInput
 
adjustLight() - Method in class ij3d.Executer
 
adjustLUTs(Content) - Method in class ij3d.Executer
 
adjustMeasurementOptions() - Method in class ini.trakem2.display.Display
 
adjustmentValueChanged(AdjustmentEvent) - Method in class _3D_objects_counter
 
adjustmentValueChanged(AdjustmentEvent) - Method in class fiji.tool.SliceObserver
 
adjustmentValueChanged(AdjustmentEvent) - Method in class fiji.util.CurrentSlice
 
adjustmentValueChanged(AdjustmentEvent) - Method in class ini.trakem2.display.Displayable.SliderListener
 
adjustmentValueChanged(AdjustmentEvent) - Method in class ini.trakem2.display.RollingPanel
Adjust the sublist of displayed DisplayablePanel.
adjustmentValueChanged(AdjustmentEvent) - Method in class IntSlider
 
adjustmentValueChanged(AdjustmentEvent) - Method in class loci.plugins.util.DataBrowser
 
adjustmentValueChanged(AdjustmentEvent) - Method in class mpicbg.spim.segmentation.InteractiveDoG.Sigma2Listener
 
adjustmentValueChanged(AdjustmentEvent) - Method in class mpicbg.spim.segmentation.InteractiveDoG.SigmaListener
 
adjustmentValueChanged(AdjustmentEvent) - Method in class mpicbg.spim.segmentation.InteractiveDoG.ThresholdListener
 
adjustmentValueChanged(AdjustmentEvent) - Method in class mpicbg.spim.segmentation.InteractiveIntegral.Radius1Listener
 
adjustmentValueChanged(AdjustmentEvent) - Method in class mpicbg.spim.segmentation.InteractiveIntegral.Radius2Listener
 
adjustmentValueChanged(AdjustmentEvent) - Method in class mpicbg.spim.segmentation.InteractiveIntegral.ThresholdListener
 
adjustmentValueChanged(AdjustmentEvent) - Method in class OpenImage5DWindow
Handles changes in the scrollbars for z and t.
adjustmentValueChanged(AdjustmentEvent) - Method in class OpenStackWindow
Calls super.updateSliceSelector() and issues a DisplayChangeEvent to registered listeners.
adjustmentValueChanged(AdjustmentEvent) - Method in class sc.fiji.balloonSegmentation.BalloonSegmentation_
 
adjustmentValueChanged(AdjustmentEvent) - Method in class sc.fiji.i5d.gui.ChannelControl
Executed if scrollbar has been moved.
adjustmentValueChanged(AdjustmentEvent) - Method in class sc.fiji.i5d.gui.Image5DWindow
Handles changes in the scrollbars for z and t.
adjustmentValueChanged(AdjustmentEvent) - Method in class sc.fiji.i5d.gui.ScrollbarWithLabel
 
adjustmentValueChanged(AdjustmentEvent) - Method in class sc.fiji.timelapse.LOI_Interpolator.SliderListener
 
adjustmentValueChanged(AdjustmentEvent) - Method in class Stack_Rotate
 
adjustmentValueChanged(AdjustmentEvent) - Method in class surfaceplot.SurfacePlotGroup
Implements AdjustmentListener interface to automatically update the surface plot when the slice slider in the stack window is dragged.
adjustmentValueChanged(AdjustmentEvent) - Method in class vib.segment.CustomStackWindow
 
adjustmentValueChanged(AdjustmentEvent) - Method in class view5d.ImageCanvas
 
adjustMinAndMaxGUI() - Method in class ini.trakem2.display.Display
 
adjustNodeColors(Node<T>) - Method in class ini.trakem2.display.Tree
 
adjustNodeRadius(float, float, float, Layer, DisplayCanvas) - Method in class ini.trakem2.display.Treeline
 
AdjustOffset() - Method in class view5d.ImgPanel
 
AdjustOffsetToROIMean() - Method in class view5d.My3DData
 
adjustProperties() - Method in class ini.trakem2.display.AreaList
 
adjustProperties() - Method in class ini.trakem2.display.Ball
 
adjustProperties() - Method in class ini.trakem2.display.Display
 
adjustProperties() - Method in class ini.trakem2.display.Displayable
Shows a dialog to adjust properties of this object.
adjustProperties() - Method in class ini.trakem2.display.DLabel
 
adjustProperties() - Method in class ini.trakem2.Project
 
adjustRoiOffset(long[], long[], long[]) - Method in class sc.fiji.coloc.gadgets.DataContainer
Make sure that the ROI offset has the same dimensionality as the image.
adjustRoiSize(long[], long[], long[], long[]) - Method in class sc.fiji.coloc.gadgets.DataContainer
Transforms a ROI size array to a dimensionality.
adjustSegmentationStateToData(Instances) - Method in class trainableSegmentation.WekaSegmentation
Adjust current segmentation state (attributes and classes) to loaded data
adjustSourceRect(double, int, int) - Method in class fiji.util.gui.JImagePanel
 
adjustSourceRectI5d(double, int, int) - Method in class sc.fiji.i5d.gui.Image5DCanvas
 
adjustSrcRect(int, int) - Method in class ini.trakem2.display.DisplayCanvas
Adjust srcRect to new dimensions.
AdjustThresh(boolean) - 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
 
advanceInit(VJCell, double, double, double) - Method in class VolumeJ.VJBinaryShell
Initialization of depth search routine.
AdvancePos() - Method in class view5d.ImgPanel
 
advancePrepare(double, double, double) - Method in class VolumeJ.VJBinaryShell
Prepare surface search for a ray with a specific direction vector.
advanceTime(int) - Method in class view5d.My3DData
 
advanceToSurface(VJCell) - Method in class VolumeJ.VJBinaryShell
Advance a cell to a surface along the ray.
advanceToSurfaceTracing(VJCell) - Method in class VolumeJ.VJBinaryShell
Advance a cell to a surface along the ray.
ADVECTION_FORCE - Variable in class levelsets.algorithm.ActiveContours
 
affine - Variable in class lenscorrection.Distortion_Correction.PointMatchCollectionAndAffine
 
AFFINE - Static variable in class Moving_Least_Squares
 
affine - Variable in class mpicbg.spim.data.registration.ViewTransformAffine
 
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.
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 - Variable in class bigwarp.TransformHandler3DWrapping2D
 
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
 
AffineFromLandmarks - Class in landmarks
 
AffineFromLandmarks() - Constructor for class landmarks.AffineFromLandmarks
 
AffineFromLandmarks.CandidateAffine - Class in landmarks
 
AffineModel2D - Class in mpicbg.trakem2.transform
 
AffineModel2D() - Constructor for class mpicbg.trakem2.transform.AffineModel2D
 
AffineModel3D - Class in mpicbg.trakem2.transform
 
AffineModel3D() - Constructor for class mpicbg.trakem2.transform.AffineModel3D
 
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
 
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
 
afterEachPlane(boolean) - Method in interface bdv.export.WriteSequenceToHdf5.AfterEachPlane
 
age - Variable in class mpicbg.imglib.algorithm.labeling.Watershed.PixelIntensity
 
ai - package ai
 
ai - Variable in class lenscorrection.DistortionCorrectionTask.AppendCoordinateTransformThread
 
ai - Variable in class lenscorrection.DistortionCorrectionTask.SetCoordinateTransformThread
 
ai - Variable in class mpicbg.trakem2.align.Align.ExtractFeaturesThread
 
ai - Variable in class mpicbg.trakem2.align.Align.MatchFeaturesAndFindModelThread
 
AI1 - Variable in class sc.fiji.io.FIBSEM_Reader.FIBSEMData
 
AI2 - Variable in class sc.fiji.io.FIBSEM_Reader.FIBSEMData
 
AI3 - Variable in class sc.fiji.io.FIBSEM_Reader.FIBSEMData
 
AI4 - Variable in class sc.fiji.io.FIBSEM_Reader.FIBSEMData
 
AIdelay - Variable in class sc.fiji.io.FIBSEM_Reader.FIBSEMData
 
Albert_Test - Class in tracing
 
Albert_Test() - Constructor for class tracing.Albert_Test
 
Algorithm - Interface in mpicbg.imglib.algorithm
TODO
Algorithm<T extends RealType<T>> - Class in sc.fiji.coloc.algorithms
An algorithm is an abstraction of techniques like the calculation of the Persons coefficient or Li'S ICQ.
Algorithm(String) - Constructor for class sc.fiji.coloc.algorithms.Algorithm
 
AlgorithmUtil - Class in script.imglib.algorithm.fn
TODO
AlgorithmUtil() - Constructor for class script.imglib.algorithm.fn.AlgorithmUtil
 
align(ImageProcessor, Line, ImageProcessor, Line) - Static method in class Align_Image
Align an image to another image given line selections in each.
align(ImageProcessor, Line, ImageProcessor, Line, boolean, boolean) - Static method in class Align_Image
Align an image to another image given line selections in each.
align(ViewerPanel.AlignPlane) - Method in class bdv.viewer.BigWarpViewerPanel
 
align(ViewerPanel.AlignPlane) - Method in class bdv.viewer.ViewerPanel
Align the XY, ZY, or XZ plane of the local coordinate system of the currently active source with the viewer coordinate system.
Align - Class in mpicbg.trakem2.align
A collection of methods regarding SIFT-based alignment TODO Bring the methods and tasks into a class for each method and clean up this mess.
Align() - Constructor for class mpicbg.trakem2.align.Align
 
Align.ExtractFeaturesThread - Class in mpicbg.trakem2.align
Extracts SIFT-features from a List of Tiles and saves them to disk.
Align.MatchFeaturesAndFindModelThread - Class in mpicbg.trakem2.align
 
Align.Param - Class in mpicbg.trakem2.align
 
Align.ParamOptimize - Class in mpicbg.trakem2.align
 
Align_Image - Class in <Unnamed>
Select two images with a Line ROI in each, and rotate/translate/scale one to the other.
Align_Image() - Constructor for class Align_Image
 
Align_Image.BilinearInterpolator - Class in <Unnamed>
 
Align_Image.Interpolator - Class in <Unnamed>
 
ALIGN_PLANE - Static variable in class bdv.viewer.NavigationActions
 
ALIGN_PLANE - Static variable in class bdv.viewer.WarpNavigationActions
 
ALIGN_VIEW_TRANSFORMS - Static variable in class bigwarp.BigWarpActions
 
AlignDisplayTo(AnElement) - Method in class view5d.AnElement
 
AlignImage(ImagePlus, ImageProcessor) - Method in class MultipleImageProcessor
 
alignImagesBatch(ImagePlus, ImagePlus, ImageProcessor, ImageProcessor, int, int, int, int, double, double, double, double, double, double) - Static method in class bunwarpj.bUnwarpJ_
Method for images alignment with no graphical interface.
alignImagesBatch(ImagePlus, ImagePlus, ImageProcessor, ImageProcessor, Param) - Static method in class bunwarpj.bUnwarpJ_
Method for images alignment with no graphical interface.
alignImagesBatch(ImagePlus, ImagePlus, ImageProcessor, ImageProcessor, int, int, int, int, double, double, double, double, double, double, double, double) - Static method in class bunwarpj.bUnwarpJ_
Method for images alignment with no graphical interface.
alignLayer(Layer, int) - Static method in class mpicbg.trakem2.align.Align
Align all patches in a Layer.
alignLayers(Layer) - Static method in class mpicbg.trakem2.align.AlignLayersTask
 
alignLayers(Layer, Rectangle) - Static method in class mpicbg.trakem2.align.AlignLayersTask
 
alignLayersLinearly(List<Layer>, int) - Static method in class mpicbg.trakem2.align.Align
Align a range of layers by accumulating pairwise alignments of contiguous layers.
alignLayersLinearly(List<Layer>, int, Filter<Patch>) - Static method in class mpicbg.trakem2.align.Align
Align a range of layers by accumulating pairwise alignments of contiguous layers.
alignLayersLinearlyJob(LayerSet, int, int, boolean, Rectangle, Filter<Patch>) - Static method in class mpicbg.trakem2.align.AlignLayersTask
 
alignLayersNonLinearlyJob(LayerSet, int, int, boolean, Rectangle, Filter<Patch>) - Static method in class mpicbg.trakem2.align.AlignLayersTask
 
AlignLayersTask - Class in mpicbg.trakem2.align
Register a range of layers using linear or non-linear transformations.
alignLayersTask(Layer) - Static method in class mpicbg.trakem2.align.AlignLayersTask
 
alignLayersTask(Layer, Rectangle) - Static method in class mpicbg.trakem2.align.AlignLayersTask
 
AlignmentUtils - Class in mpicbg.trakem2.align
 
AlignmentUtils.ParamPointMatch - Class in mpicbg.trakem2.align
 
alignMultiLayerMosaic(Layer, Patch) - Static method in class mpicbg.trakem2.align.AlignTask
Align a multi-layer mosaic.
alignMultiLayerMosaicTask(Layer) - Static method in class mpicbg.trakem2.align.AlignTask
 
alignMultiLayerMosaicTask(Layer, Patch) - Static method in class mpicbg.trakem2.align.AlignTask
 
alignMultiLayerMosaicTask(List<Layer>, Patch, Align.Param, Align.ParamOptimize, Align.ParamOptimize, boolean, boolean, boolean, boolean, boolean) - Static method in class mpicbg.trakem2.align.AlignTask
 
alignPatches(List<Patch>, Set<Patch>, int) - Static method in class mpicbg.trakem2.align.AlignTask
 
alignPatches(Align.ParamOptimize, List<Patch>, Collection<Patch>, boolean, boolean, boolean, boolean, boolean) - Static method in class mpicbg.trakem2.align.AlignTask
 
alignPatches(Align.ParamOptimize, List<Patch>, Collection<Patch>, boolean, boolean, boolean, boolean) - Static method in class mpicbg.trakem2.align.AlignTask
 
alignPatchesTask(List<Patch>, Set<Patch>) - Static method in class mpicbg.trakem2.align.AlignTask
 
alignPlaneAction(ViewerPanel, ViewerPanel.AlignPlane, String...) - Method in class bdv.viewer.NavigationActions
 
AlignPlaneAction(ViewerPanel, ViewerPanel.AlignPlane) - Constructor for class bdv.viewer.WarpNavigationActions.AlignPlaneAction
 
alignPlanes(ViewerPanel) - Method in class bdv.viewer.NavigationActions
 
alignSelectedPatches(Selection, int) - Static method in class mpicbg.trakem2.align.Align
Align a selection of patches in a Layer.
alignSelection(Selection, int) - Static method in class mpicbg.trakem2.align.AlignTask
 
alignSelectionTask(Selection) - Static method in class mpicbg.trakem2.align.AlignTask
 
AlignStacksWithLandmarks - Class in mpicbg.ij.plugin
 
AlignStacksWithLandmarks() - Constructor for class mpicbg.ij.plugin.AlignStacksWithLandmarks
 
AlignTask - Class in mpicbg.trakem2.align
Methods collection to be called from the GUI for alignment tasks.
AlignTask() - Constructor for class mpicbg.trakem2.align.AlignTask
 
AlignTask.ReferenceData - Class in mpicbg.trakem2.align
 
alignTileCollections(Align.Param, Collection<AbstractAffineTile2D<?>>, Collection<AbstractAffineTile2D<?>>) - Static method in class mpicbg.trakem2.align.Align
Align two collections of tiles
alignTiles(Align.ParamOptimize, List<AbstractAffineTile2D<?>>, List<AbstractAffineTile2D<?>>, boolean, int) - Static method in class mpicbg.trakem2.align.Align
Align a set of tiles using the following procedure: Extract SIFT-features from all tiles. Establish point-correspondences from consistent sets of feature matches among tile pairs, optionally inspect only those that are already overlapping. Globally align the tile configuration. Both feature extraction and matching are executed in multiple Threads, with the number of Threads being a parameter of the method.
alignTiles(Align.ParamOptimize, List<AbstractAffineTile2D<?>>, List<AbstractAffineTile2D<?>>, int) - Static method in class mpicbg.trakem2.align.Align
Align a set of overlapping tiles using the following procedure: Extract SIFT-features from all tiles. Establish point-correspondences from consistent sets of feature matches among overlapping tiles. Globally align the tile configuration. Both feature extraction and matching are executed in multiple Threads, with the number of Threads being a parameter of the method.
alignTiles(Align.ParamOptimize, List<AbstractAffineTile2D<?>>, List<AbstractAffineTile2D<?>>, boolean, boolean, boolean, boolean, boolean) - Static method in class mpicbg.trakem2.align.AlignTask
 
alignTiles(Align.ParamOptimize, List<AbstractAffineTile2D<?>>, List<AbstractAffineTile2D<?>>, boolean, boolean, boolean, boolean) - Static method in class mpicbg.trakem2.align.AlignTask
 
AlignTo4Byte() - Method in class customnode.u3d.BitStreamWrite
 
AlignToByte() - Method in class customnode.u3d.BitStreamWrite
 
AlignViewerPanelAction(BigWarp, BigWarpActions.AlignViewerPanelAction.TYPE) - Constructor for class bigwarp.BigWarpActions.AlignViewerPanelAction
 
ALIVE - Static variable in class levelsets.algorithm.FastMarching
Constant for ALIVE elements
allAttributeInstances - Variable in class spim.fiji.plugin.queryXML.GenericLoadParseQueryXML
 
allChannels - Static variable in class bdv.ij.ExportSpimFusionPlugIn
 
allChannels - Static variable in class bdv.ij.ExportSpimSequencePlugIn
 
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
 
allHandler - Variable in class bdv.viewer.LandmarkPointMenu
 
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
 
allJFileChoosers - Static variable in class fiji.gui.JFileChooserDecorator
 
AllKnownFilter - Class in org.imagearchive.lsm.toolbox.gui
 
AllKnownFilter() - Constructor for class org.imagearchive.lsm.toolbox.gui.AllKnownFilter
 
allocated - Variable in class fiji.util.ArrayBase
 
allowCZIAutostitch() - Static method in class loci.plugins.util.LociPrefs
 
allowed - Variable in class fiji.plugin.trackmate.tracking.oldlap.costfunction.GapClosingCostFunction
If false, gap closing will be prohibited.
allowedBitDepth(int) - Method in class util.Histogram_2D
 
allowEdgeExtrema(boolean) - Method in class mpicbg.imglib.algorithm.extremafinder.AbstractRegionalExtremaFinder
 
allowEdgeExtrema(boolean) - Method in interface mpicbg.imglib.algorithm.extremafinder.RegionalExtremaFinder
If set to true before the Algorithm.process() method is called, then extrema found at the edges of the image bounds (including time edges) will not be pruned, and will be included in the result array.
allowEdgeMax - Variable in class mpicbg.imglib.algorithm.extremafinder.AbstractRegionalExtremaFinder
 
allowShow - Variable in class loci.plugins.util.DataBrowser
 
allPeaks - Variable in class sc.fiji.timelapse.Peak_Counter_Tool
 
allPeaksMap - Variable in class sc.fiji.timelapse.Peak_Counter_Tool
 
allPointsIterator() - Method in class tracing.PathAndFillManager
 
AllPointsIterator() - Constructor for class tracing.PathAndFillManager.AllPointsIterator
 
allRegions - Variable in class util.FindConnectedRegions.Results
 
allSame - Variable in class ai.SplitFunction
 
allSelectedUsingFittedVersion() - Method in class tracing.PathWindow
 
AllToAllRegistration - Class in spim.process.interestpointregistration.optimizationtypes
 
AllToAllRegistration(SpimData2, List<ViewId>, List<ChannelProcess>, boolean) - Constructor for class spim.process.interestpointregistration.optimizationtypes.AllToAllRegistration
 
AllToAllRegistrationWithRange - Class in spim.process.interestpointregistration.optimizationtypes
 
AllToAllRegistrationWithRange(SpimData2, List<ViewId>, List<ChannelProcess>, int, boolean) - Constructor for class spim.process.interestpointregistration.optimizationtypes.AllToAllRegistrationWithRange
 
allUsingFittedVersion(Set<Path>) - Method in class tracing.PathWindow
 
almostOpaque() - Method in class VolumeJ.VJAlphaColor
Return whether this alphacolor is almost opaque.
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.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 - Variable in class VolumeJ.VJAlphaColor
 
ALPHA_ADVECTION - Variable in class levelsets.algorithm.GeodesicActiveContour
 
alphacolor(VJValue, VJGradient) - Method in class VolumeJ.VJClassifier
The classification method, defining how a value/gradient combination will be classified as an VJAlphaColor (argb).
alphacolor(VJValue) - Method in class VolumeJ.VJClassifier
This method can be overloaded as necessary.
alphacolor(VJValue, VJGradient) - Method in class VolumeJ.VJClassifierGradientCT
Classify the (interpolated) voxel value and gradient magnitude into a alpha and rgb-value.
alphacolor(VJValue, VJGradient) - Method in class VolumeJ.VJClassifierInteger
 
alphacolor(VJValue, VJGradient) - Method in class VolumeJ.VJClassifierIsosurface
Classify the voxel value into RGB.
alphacolor(VJValue, VJGradient) - Method in class VolumeJ.VJClassifierLevoy
Classify the (interpolated) voxel value and gradient magnitude into a alpha and rgb-value.
alphacolor(VJValue) - Method in class VolumeJ.VJClassifierLevoy
Slice view classification.
alphacolor(VJValue, VJGradient) - Method in class VolumeJ.VJClassifierLevoyCueing
Classify the (interpolated) voxel value and gradient magnitude into a alpha and rgb-value.
alphacolor(VJValue, VJGradient) - Method in class VolumeJ.VJClassifierLNoIndex
 
alphacolor(VJrgbValue, VJGradient) - Method in class VolumeJ.VJClassifierRGB
 
alphacolor(VJValue, VJGradient) - Method in class VolumeJ.VJClassifierValue
Classify the interpolated voxel value into a VJAlphaColor.
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
 
an - Variable in class bijnum.BIJpca
 
Analyse_Particles - Class in QuickPALM
This plugin detectes sub-diffraction particles in a sequence of images, it is the main plugin for the QuickPALM package.
Analyse_Particles() - Constructor for class QuickPALM.Analyse_Particles
 
ANALYSER_ELEMENT_KEY - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
 
ANALYSER_KEY_ATTRIBUTE - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
 
analysisMenu - Variable in class tracing.NeuriteTracerResultsDialog
 
AnalysisResults<T extends RealType<T>> - Class in sc.fiji.coloc.results
Data structure housing all colocalisation results.
AnalysisResults() - Constructor for class sc.fiji.coloc.results.AnalysisResults
 
analyze2D(int, int, double[], double, int, int, ImageProcessor) - Method in class sholl.Sholl_Analysis
Does the actual 2D analysis.
analyze3D(int, int, int, double[], ImagePlus) - Method in class sholl.Sholl_Analysis
Measures intersections for each sphere surface (does the actual 3D analysis).
Analyze_Reader - Class in sc.fiji.io
This plugin loads Analyze format files.
Analyze_Reader() - Constructor for class sc.fiji.io.Analyze_Reader
 
Analyze_Writer - Class in sc.fiji.io
This plugin saves Analyze format files.
Analyze_Writer() - Constructor for class sc.fiji.io.Analyze_Writer
 
analyzeButton - Variable in class tracing.ShollAnalysisDialog
 
analyzeMaximum(LocalizableByDimCursor3D<FloatType>, float, int, int, int, float, float, float, RejectStatistics, ArrayList<DoGMaximum>) - Static method in class mpicbg.spim.registration.bead.laplace.LaPlaceFunctions
 
analyzePeak(DifferenceOfGaussianPeak<T>) - Method in class mpicbg.imglib.algorithm.scalespace.SubpixelLocalization
 
analyzeProfile(double[], double[], boolean) - Method in class sholl.Sholl_Analysis
Analyzes a sampled profile.
ANALYZER_COLLECTION_ELEMENT_KEY - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
 
AnalyzeSkeleton_ - Class in sc.fiji.analyzeSkeleton
Main class of the ImageJ/Fiji plugin for skeleton analysis.
AnalyzeSkeleton_() - Constructor for class sc.fiji.analyzeSkeleton.AnalyzeSkeleton_
 
analyzeTabularInput(ResultsTable, int, int, boolean) - Method in class sholl.Sholl_Analysis
Instructs the plugin to parse the specified table expected to contain a sampled profile.
analyzeTabularInput(File, int, int, boolean) - Method in class sholl.Sholl_Analysis
Instructs the plugin to parse the specified file expected to contain a sampled profile.
AnalyzeTracings_ - Class in tracing
 
AnalyzeTracings_() - Constructor for class tracing.AnalyzeTracings_
 
analyzeWithShollAnalysisPlugin(String, double) - Method in class tracing.ShollAnalysisDialog.ShollResults
Instructs the Sholl Analysis plugin to analyze the profile sampled by .
ANCHORS - Static variable in class ini.trakem2.display.LayerSet
 
And() - Constructor for class fiji.expressionparser.function.ImgLibLogical.And
 
And<T extends RealType<T>> - Class in imglib.ops.condition
TODO
And(Condition<T>, Condition<T>) - Constructor for class imglib.ops.condition.And
 
And - Class in imglib.ops.operator.binary
TODO
And() - Constructor for class imglib.ops.operator.binary.And
 
and(int) - Method in class loci.plugins.util.RecordedImageProcessor
 
and(T) - Method in interface mpicbg.imglib.type.BooleanType
 
and(BitType) - Method in class mpicbg.imglib.type.logic.BitType
 
And - Class in script.imglib.math
TODO
And(Image<? extends RealType<?>>, Image<? extends RealType<?>>) - Constructor for class script.imglib.math.And
 
And(IFunction, Image<? extends RealType<?>>) - Constructor for class script.imglib.math.And
 
And(Image<? extends RealType<?>>, IFunction) - Constructor for class script.imglib.math.And
 
And(IFunction, IFunction) - Constructor for class script.imglib.math.And
 
And(Image<? extends RealType<?>>, Number) - Constructor for class script.imglib.math.And
 
And(Number, Image<? extends RealType<?>>) - Constructor for class script.imglib.math.And
 
And(IFunction, Number) - Constructor for class script.imglib.math.And
 
And(Number, IFunction) - Constructor for class script.imglib.math.And
 
And(Number, Number) - Constructor for class script.imglib.math.And
 
And(Object...) - Constructor for class script.imglib.math.And
 
AndConstant - Class in imglib.ops.operator.unary
TODO
AndConstant(long) - Constructor for class imglib.ops.operator.unary.AndConstant
 
AnElement - Class in view5d
 
angle(Pnt) - Method in class delaunay.Pnt
Angle (in radians) between two Pnts (treated as vectors).
Angle - Class in mpicbg.spim.data.sequence
Defines an angle which is part of the ViewSetup.
Angle(int, String, double, double[]) - Constructor for class mpicbg.spim.data.sequence.Angle
 
Angle(int, String) - Constructor for class mpicbg.spim.data.sequence.Angle
 
Angle(int) - Constructor for class mpicbg.spim.data.sequence.Angle
 
Angle() - Constructor for class mpicbg.spim.data.sequence.Angle
 
angle - Variable in class mpicbg.spim.registration.ViewDataBeads
the acquisition angle
angle(double, double, double, double) - Method in class sc.fiji.balloonSegmentation.structure.Balloon
Math vector operators: determine angle between v2 (x2, y2) and v1 (x1,y1) (I made this before I start using JAMA library)
angle - Variable in class spim.vecmath.AxisAngle4d
The angle of rotation in radians.
angle - Variable in class spim.vecmath.AxisAngle4f
The angle of rotation in radians.
angle(Vector3d) - Method in class spim.vecmath.Vector3d
Returns the angle in radians between this vector and the vector parameter; the return value is constrained to the range [0,PI].
angle(Vector3f) - Method in class spim.vecmath.Vector3f
Returns the angle in radians between this vector and the vector parameter; the return value is constrained to the range [0,PI].
angle(Vector4d) - Method in class spim.vecmath.Vector4d
Returns the (4-space) angle in radians between this vector and the vector parameter; the return value is constrained to the range [0,PI].
angle(Vector4f) - Method in class spim.vecmath.Vector4f
Returns the (4-space) angle in radians between this vector and the vector parameter; the return value is constrained to the range [0,PI].
ANGLE_PATTERN - Static variable in class spim.fiji.datasetmanager.StackList
 
ANGLE_ROTATIONAXIS_TAG - Static variable in class mpicbg.spim.data.XmlKeys
 
ANGLE_ROTATIONDEGREES_TAG - Static variable in class mpicbg.spim.data.XmlKeys
 
ANGLE_TAG - Static variable in class mpicbg.spim.data.XmlKeys
 
angleAttributeKey - Static variable in class mpicbg.spim.data.sequence.ViewSetup
 
angleBetween(double[], double[]) - Static method in class vib.FastMatrix
 
angleBetween(float[], float[]) - Static method in class vib.FloatMatrix
 
angleChoice - Static variable in class spim.fiji.plugin.Duplicate_Transformation
 
angleEnd - Variable in class spimopener.SPIMExperiment
 
angleIndicies - Variable in class mpicbg.spim.fusion.MappingFusionSequentialDifferentOutput
 
angleIndiciesStatic - Static variable in class mpicbg.spim.fusion.MappingFusionSequentialDifferentOutput
 
angleMult(double[], double[], double) - Static method in class bigwarp.util.Rotation2DHelpers
 
angleNameList - Variable in class spim.fiji.datasetmanager.StackList
 
angleNames - Variable in class spim.fiji.spimdata.imgloaders.MultipageTiffReader
 
anglePattern - Variable in class mpicbg.spim.io.SPIMConfiguration
 
angles - Static variable in class fiji.plugin.Bead_Registration
 
angles - Variable in class mpicbg.spim.io.SPIMConfiguration
 
angles() - Method in class spim.fiji.datasetmanager.LightSheetZ1MetaData
 
angles - Variable in class spim.fiji.datasetmanager.SlideBook6Image
 
angles(int) - Method in class spim.fiji.datasetmanager.SlideBook6MetaData
 
angles - Variable in class spim.fiji.datasetmanager.StackList
 
angles() - Method in class spim.fiji.plugin.apply.ModelLink
 
angles - Variable in class spimopener.SPIMExperiment
 
ANGLES_TAG - Static variable in class mpicbg.spim.data.XmlKeys
 
angleStart - Variable in class spimopener.SPIMExperiment
 
anim - Variable in class loci.plugins.util.DataBrowser
 
animate - Variable in class loci.plugins.util.DataBrowser
 
ANIMATE_TG - Static variable in class ij3d.DefaultUniverse
The index of the transform group in the viewing platform's MultiTransformGroup which is responsible for animation
animateBrowsing(int, int) - Method in class ini.trakem2.display.DisplayCanvas
Smoothly move the canvas from x0,y0,layer0 to x1,y1,layer1
animateBrowsing(Rectangle, Layer) - Method in class ini.trakem2.display.DisplayCanvas
Smoothly move the canvas from its current position until the given rectangle is included within the srcRect.
animateBrowsingTo(Coordinate<?>) - Method in class ini.trakem2.display.Display
 
Animated_Gif_Reader - Class in sc.fiji.io
 
Animated_Gif_Reader() - Constructor for class sc.fiji.io.Animated_Gif_Reader
 
animateTransformation(AffineTransform3D, int) - Method in class bdv.viewer.BigWarpViewerPanel
 
animateTransformation(AffineTransform3D) - Method in class bdv.viewer.BigWarpViewerPanel
 
anisotropic_diffusion - package anisotropic_diffusion
 
ANISOTROPIC_DIFFUSION - Static variable in class trainableSegmentation.FeatureStack
Anisotropic diffusion filter flag index
Anisotropic_Diffusion_2D - Class in anisotropic_diffusion
 
Anisotropic_Diffusion_2D() - Constructor for class anisotropic_diffusion.Anisotropic_Diffusion_2D
 
AnisotropicDiffusion<T extends RealType<T>> - Class in mpicbg.imglib.algorithm.pde
Perona & Malik Anisotropic diffusion
AnisotropicDiffusion(Image<T>, double, AnisotropicDiffusion.DiffusionFunction) - Constructor for class mpicbg.imglib.algorithm.pde.AnisotropicDiffusion
Instantiate the Perona & Malik anisotropic diffusion process, with a custom diffusion function.
AnisotropicDiffusion(Image<T>, double, double) - Constructor for class mpicbg.imglib.algorithm.pde.AnisotropicDiffusion
Instantiate the Perona & Malik anisotropic diffusion process, with the default strong-edge diffusion function.
AnisotropicDiffusion.DiffusionFunction - Interface in mpicbg.imglib.algorithm.pde
The interface that function suitable to be diffusion function must implement.
AnisotropicDiffusion.StrongEdgeEnhancer - Class in mpicbg.imglib.algorithm.pde
The first diffusion function proposed by Perona & Malik.
AnisotropicDiffusion.WideRegionEnhancer - Class in mpicbg.imglib.algorithm.pde
The second diffusion function proposed by Perona & Malik.
annotation - Variable in class ini.trakem2.display.Displayable
 
antiAliasedText - Static variable in class Series_Labeler
 
antiSymmetricPadding(double[][], int) - Static method in class bunwarpj.MathTools
 
antiSymmetricPadding(double[], int, int) - Static method in class bunwarpj.MathTools
 
antiSymmetricPadding(float[], int, int) - Static method in class bunwarpj.MathTools
 
anyListeners() - Method in class tracing.SimpleNeuriteTracer
 
anySelected() - Method in class tracing.PathAndFillManager
 
ap - Variable in class mpicbg.trakem2.align.Align.ExtractFeaturesThread
 
ap - Variable in class mpicbg.trakem2.align.Align.MatchFeaturesAndFindModelThread
 
ap - Variable in class org.janelia.thickness.plugin.RealSumFloatNCC
 
ap - Variable in class org.janelia.thickness.trakem2.RealSumARGBNCC
 
appCreator - Variable in class voltex.VolumeRenderer
The AppearanceCreator, which creates the textures.
AppearanceCreator - Class in octree
 
AppearanceCreator - Class in voltex
This class is a helper class whose main task is to create Appearance objects for a specified axis and direction.
AppearanceCreator(VoltexVolume) - Constructor for class voltex.AppearanceCreator
Constructor.
AppearanceCreator(VoltexVolume, Color3f, float) - Constructor for class voltex.AppearanceCreator
Initializes this AppearanceCreator with the given image data, color and transparency values.
append(Line3D) - Method in class ini.trakem2.analysis.Compare.Chain
 
append(History.Step<?>) - Method in class ini.trakem2.utils.History
Appends a step at the end of the list, without modifying the current index.
append(ILoggingEvent) - Method in class loci.plugins.util.IJStatusEchoer
 
append(StringBuilder, HashSet<String>, String) - Static method in class mpicbg.trakem2.transform.DTD
 
append(String) - Method in class vib.app.gui.Console
 
appendBezierPathXML(StringBuilder, double[]) - Static method in class edu.utexas.clm.reconstructreader.Utils
 
appendCalibration(StringBuilder) - Method in class edu.utexas.clm.reconstructreader.reconstruct.ReconstructTranslator
 
appendClosedPathXML(StringBuilder, double[]) - Static method in class edu.utexas.clm.reconstructreader.Utils
 
appendCoordinateTransform(CoordinateTransform) - Method in class ini.trakem2.display.Patch
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
 
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(double[], double[]) - Method in class bdv.img.TpsTransformWrapper
 
apply(float[], float[]) - Method in class bdv.img.TpsTransformWrapper
 
apply(RealLocalizable, RealPositionable) - Method in class bdv.img.TpsTransformWrapper
 
apply(double[]) - Method in class bdv.viewer.animate.SimilarityModel3D
 
apply(double[]) - Method in class bunwarpj.trakem2.transform.CubicBSplineTransform
 
apply(PathIterator) - Method in class fiji.geom.AreaCalculations.Calculation
 
apply(V) - Method in class fiji.plugin.trackmate.graph.RecursiveCumSum
 
apply(HashMap<String, String>, Image3DUniverse) - Method in class ij3d.SaveSession
 
apply(Image3DUniverse) - Static method in class ij3d.UniverseSettings
 
apply() - Method in class ij3d.ViewAdjuster
After all points/contents were added, apply() finally adjusts center and zoom transformations of the view.
apply() - Method in class ini.trakem2.display.AffineTransformMode
 
apply(Layer, Area, CoordinateTransform) - Method in class ini.trakem2.display.AreaList
 
apply(VectorDataTransform) - Method in class ini.trakem2.display.AreaList
 
apply(CoordinateTransform, Area) - Method in class ini.trakem2.display.AreaTree.AreaNode
 
apply(VectorDataTransform) - Method in class ini.trakem2.display.AreaTree.AreaNode
 
apply(Layer, Area, CoordinateTransform) - Method in class ini.trakem2.display.Ball
 
apply(VectorDataTransform) - Method in class ini.trakem2.display.Ball
 
apply() - Method in class ini.trakem2.display.ContrastAdjustmentMode
 
apply() - Method in class ini.trakem2.display.DefaultMode
 
apply(int) - Method in class ini.trakem2.display.Displayable.DoEdit
Set the stored data to the stored Displayable.
apply(int) - Method in class ini.trakem2.display.Displayable.DoEdits
 
apply(int) - Method in class ini.trakem2.display.Displayable.DoTransforms
 
apply(Layer, Area, CoordinateTransform) - Method in class ini.trakem2.display.Dissector
 
apply(VectorDataTransform) - Method in class ini.trakem2.display.Dissector
 
apply(Layer, Area, CoordinateTransform) - Method in class ini.trakem2.display.DLabel
 
apply(VectorDataTransform) - Method in class ini.trakem2.display.DLabel
 
apply(int) - Method in interface ini.trakem2.display.DoStep
Returns true on success.
apply() - Method in class ini.trakem2.display.inspect.InspectPatchTrianglesMode
 
apply(Class<?>, AffineTransform) - Method in class ini.trakem2.display.Layer
Preconcatenate the given AffineTransform to all Displayable objects of class c, without respecting their links.
apply(int) - Method in class ini.trakem2.display.Layer.DoMoveDisplayable
 
apply(int) - Method in class ini.trakem2.display.LayerSet.DoChangeTrees
 
apply(int) - Method in class ini.trakem2.display.LayerSet.DoMoveZDisplayable
 
apply() - Method in class ini.trakem2.display.ManualAlignMode
 
apply() - Method in interface ini.trakem2.display.Mode
 
apply(CoordinateTransform, Area) - Method in class ini.trakem2.display.Node
 
apply(VectorDataTransform) - Method in class ini.trakem2.display.Node
 
apply(Node.Operation<T>, Iterator<Node<T>>) - Method in class ini.trakem2.display.Node
 
apply(Node<I>) - Method in interface ini.trakem2.display.Node.Operation
 
apply() - Method in class ini.trakem2.display.NonLinearTransformMode
 
apply(Set<Layer>) - Method in class ini.trakem2.display.NonLinearTransformMode
 
apply(Layer, Area, CoordinateTransform) - Method in class ini.trakem2.display.Pipe
 
apply(VectorDataTransform) - Method in class ini.trakem2.display.Pipe
 
apply(Layer, Area, CoordinateTransform) - Method in class ini.trakem2.display.Polyline
 
apply(VectorDataTransform) - Method in class ini.trakem2.display.Polyline
 
apply(Layer, Area, CoordinateTransform) - Method in class ini.trakem2.display.Profile
 
apply(VectorDataTransform) - Method in class ini.trakem2.display.Profile
 
apply(int, double[]) - Method in class ini.trakem2.display.Selection
 
apply(Layer, Area, CoordinateTransform) - Method in class ini.trakem2.display.Tree
 
apply(VectorDataTransform) - Method in class ini.trakem2.display.Tree
 
apply(CoordinateTransform, Area) - Method in class ini.trakem2.display.Treeline.RadiusNode
 
apply(VectorDataTransform) - Method in class ini.trakem2.display.Treeline.RadiusNode
 
apply(Layer, Area, CoordinateTransform) - Method in interface ini.trakem2.display.VectorData
Applies the 2D transform @ict (which is expected to operate on the world coordinates version of the data contained here) only to the data that falls within the @param roi (in world coords), and then recomputes the bounding box and affine transform (to a translation or identity).
apply(VectorDataTransform) - Method in interface ini.trakem2.display.VectorData
 
apply(Collection<Displayable>) - Method in class ini.trakem2.imaging.ContrastEnhancerWrapper
 
apply(int) - Method in class ini.trakem2.tree.RenameThingStep
 
apply(CoordinateTransform, Area, Area) - Static method in class ini.trakem2.utils.M
Apply in place the @param ict to the Area @param a, but only for the part that intersects the roi.
apply(VectorDataTransform, Area) - Static method in class ini.trakem2.utils.M
 
apply(VectorDataTransform, Area, boolean) - Static method in class ini.trakem2.utils.M
Parts of @param a not intersected by any of @param vdt rois will be left untouched if @param remove_outside is false.
apply(CoordinateTransform, double[][], int, double[]) - Static method in class ini.trakem2.utils.M
Reuses the @param fp to apply in place.
apply(O) - Method in interface ini.trakem2.utils.Operation
 
apply(double[], double[]) - Method in class jitk.spline.ThinPlateR2LogRSplineKernelTransform
 
apply(double[], double[], boolean) - Method in class jitk.spline.ThinPlateR2LogRSplineKernelTransform
Transform a source vector pt into a target vector result.
apply(double[]) - Method in class jitk.spline.ThinPlateR2LogRSplineKernelTransform
Transforms the input point according to the thin plate spline stored by this object.
apply(double[]) - Method in class lenscorrection.PolynomialModel2D
 
apply(Point3d) - Method in class math3d.Bookstein
 
apply(double[][], double[]) - Static method in class math3d.FastMatrixN
Calculates b in Ax = b
apply(float[][], float[]) - Static method in class math3d.FloatMatrixN
Calculates b in Ax = b
apply(double[]) - Method in class mpicbg.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) - 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
 
ApplyButtonListener() - Constructor for class mpicbg.spim.segmentation.InteractiveDoG.ApplyButtonListener
 
ApplyButtonListener(Frame, BigDataViewer) - Constructor for class spim.fiji.plugin.apply.BigDataViewerTransformationWindow.ApplyButtonListener
 
applyByStrength(Model, float) - Method in class stitching.model.PointMatch
Apply a Model to PointMatch.p1 with a given amount, update distance.
applyCal(Specify_Calibration.Cal, SpimData, List<ViewId>) - Static method in class spim.fiji.plugin.Specify_Calibration
 
applyCalibration(ImagePlus) - Method in class loci.plugins.in.Calibrator
Applies spatial calibrations to an image stack.
applyChannels(LoadParseQueryXML) - Method in class spim.fiji.plugin.Duplicate_Transformation
 
applyChecked(double) - Method in class org.janelia.thickness.lut.AbstractLUTGrid
 
applyChecked(double) - Method in class org.janelia.thickness.lut.AbstractLUTRealTransform
 
applyChecked(double, int, int) - Method in class org.janelia.thickness.lut.AbstractLUTRealTransformField
 
applyChecked(int) - Method in class org.janelia.thickness.lut.AbstractPerumtationTransform
 
applyClassifier(Instances, int, int, int) - Method in class trainableSegmentation.Trainable_Segmentation
Deprecated.
Apply current classifier to set of instances
applyClassifier(String, String, String, String, String, String) - Static method in class trainableSegmentation.Weka_Segmentation
Apply current classifier to specific image (2D or stack)
applyClassifier(ImagePlus) - Method in class trainableSegmentation.WekaSegmentation
Apply current classifier to a given image.
applyClassifier(ImagePlus, int, boolean) - Method in class trainableSegmentation.WekaSegmentation
Apply current classifier to a given image.
applyClassifier(ImagePlus, ImagePlus, int, boolean) - Method in class trainableSegmentation.WekaSegmentation
Apply current classifier to a given image with precomputed features.
applyClassifier(ImagePlus, FeatureStackArray, int, boolean) - Method in class trainableSegmentation.WekaSegmentation
Apply current classifier to a given image with precomputed features.
applyClassifier(boolean) - Method in class trainableSegmentation.WekaSegmentation
Apply current classifier to current image.
applyClassifier(int, boolean) - Method in class trainableSegmentation.WekaSegmentation
Apply current classifier to current image.
applyClassifier(Instances, int, int, int, boolean) - Method in class trainableSegmentation.WekaSegmentation
Apply current classifier to set of instances
applyClassifier(FeatureStackArray, int, boolean) - Method in class trainableSegmentation.WekaSegmentation
Apply current classifier to a set of feature vectors (given in a feature stack array).
applyClassifierMT(ImagePlus, int, boolean) - Method in class trainableSegmentation.WekaSegmentation
Apply current classifier to a given image in a complete concurrent way.
applyClassifierToTestData() - Method in class trainableSegmentation.Trainable_Segmentation
Deprecated.
Apply classifier to test data
applyClassifierToTestData() - Method in class trainableSegmentation.Weka_Segmentation
Apply classifier to test data.
applyClassifierToTestImage(ImagePlus, int) - Method in class trainableSegmentation.Trainable_Segmentation
Deprecated.
Apply current classifier to image
applyColors(List<ImagePlus>) - Method in class loci.plugins.in.Colorizer
 
applyColors(ImagePlus, int, Color[], int) - Static method in class org.imagearchive.lsm.toolbox.ReaderToolkit
 
applyCoordinateTransform(ImagePlus, CoordinateTransform, int, boolean, int[]) - Static method in class register_virtual_stack.Transform_Virtual_Stack_MT
Apply a coordinate transform to a given image
applyCorrection - Variable in class lenscorrection.Distortion_Correction.PluginParam
 
applyEntropy(ImageProcessor, int, int) - Method in class trainableSegmentation.filters.Entropy_Filter
Apply entropy filter to an image
applyFilter(Filter) - Method in class levelsets.ij.ImageContainer
Applies the passed Filter on every image in the container.
applyFilter(Filter, int, int) - Method in class levelsets.ij.ImageContainer
Applies the passed filter on the selected range of images
applyFilter(ImageProcessor, int, int, int) - Method in class trainableSegmentation.filters.Kuwahara
Apply filter to input image (in place)
applyFilters(Image) - Method in class ini.trakem2.display.Display
 
applyFilters(ImageProcessor) - Method in class ini.trakem2.display.Display
 
applyFilters(ImagePlus) - Method in class ini.trakem2.display.Display
 
ApplyHistSelection() - Method in class view5d.My3DData
 
applyIllums(LoadParseQueryXML) - Method in class spim.fiji.plugin.Duplicate_Transformation
 
applyInPlace(double[]) - Method in class bdv.viewer.animate.SimilarityModel3D
 
applyInPlace(double[]) - Method in class bunwarpj.trakem2.transform.CubicBSplineTransform
 
applyInPlace(double[]) - Method in class jitk.spline.ThinPlateR2LogRSplineKernelTransform
Transform pt in place.
applyInPlace(double[]) - Method in class lenscorrection.PolynomialModel2D
 
applyInPlace(double[]) - Method in class mpicbg.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[], double[]) - Method in class bdv.img.TpsTransformWrapper
 
applyInverse(float[], float[]) - Method in class bdv.img.TpsTransformWrapper
 
applyInverse(RealPositionable, RealLocalizable) - Method in class bdv.img.TpsTransformWrapper
 
applyInverse(double[]) - Method in class bdv.viewer.animate.SimilarityModel3D
 
applyInverse(double[]) - Method in class mpicbg.panorama.EquirectangularProjection
 
applyInverse(double[]) - Method in class mpicbg.panorama.RectlinearCamera
 
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.panorama.EquirectangularProjection
 
applyInverseInPlace(double[]) - Method in class mpicbg.panorama.RectlinearCamera
 
applyInverseInPlace(AbstractAffineModel3D<?>, Point3d) - Static method in class mpicbg.spim.mpicbg.Java3d
 
applyInverseInPlace(AbstractAffineModel3D<?>, Point3d, double[]) - Static method in class mpicbg.spim.mpicbg.Java3d
 
applyInverseInPlace(double[]) - Method in class mpicbg.trakem2.transform.TransformMesh
Catch non-invertible locations outside of the meshes boundaries and transfer them with the affine defined by the `closest' affine (the affine whose summed up control points distances to location are smallest).
applyInverseInPlace(float[]) - Method in interface stitching.model.InvertibleCoordinateTransform
apply the inverse of the model to a point location
applyInverseInPlace(float[]) - Method in class stitching.model.TranslationModel2D
 
applyInverseInPlace(float[]) - Method in class stitching.model.TranslationModel3D
 
applyLayerTransformToPatch(Patch, CoordinateTransform) - Static method in class mpicbg.trakem2.align.Util
 
applyLayerWise(Collection<Layer>) - Method in class ini.trakem2.imaging.ContrastEnhancerWrapper
 
applyLocalizedPattern(String) - Method in class HybridDateFormat
This method sets the formatting pattern that should be used by this object.
ApplyLog(double) - Method in class view5d.PixelDisplay
 
applyLSTAMP(ImagePlus, LSMFileInfo) - Method in class org.imagearchive.lsm.toolbox.gui.ControlPanelFrame
 
applyMedianFilter(RandomAccessibleInterval<R>) - Static method in class fiji.plugin.trackmate.detection.DetectionUtils
Apply a simple 3x3 median filter to the target image.
applyMetaData(Image<?>, IFormatReader) - Static method in class mpicbg.imglib.io.LOCI
 
applyMethodStack(List<RecordedImageProcessor.MethodEntry>) - Method in class loci.plugins.util.RecordedImageProcessor
 
applyModels(SpimData, double, int, Map<ViewDescription, ImgLib2Temp.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.
applyShifts(double[], double[], double[], PermutationTransform, Options) - Method in class org.janelia.thickness.inference.InferFromMatrix
 
applySurfaceColors(ImagePlus) - Method in class ij3d.Content
 
applySurfaceColors(ImagePlus) - Method in class ij3d.ContentInstant
 
applySurfaceColors(Content) - Method in class ij3d.Executer
 
applyTable(int[]) - Method in class loci.plugins.util.RecordedImageProcessor
 
applyThreshold(ImageProcessor, Roi, int, int) - Static method in class vib.Local_Threshold
 
applyTimepoints(LoadParseQueryXML) - Method in class spim.fiji.plugin.Duplicate_Transformation
 
applyTo - Variable in class spim.fiji.plugin.apply.ApplyParameters
 
applyToChoice - Static variable in class spim.fiji.plugin.Apply_Transformation
 
applyToSlab(Node.Operation<T>) - Method in class ini.trakem2.display.Node
Apply @param op to this Node and all its subtree nodes until reaching a branch node or end node, inclusive.
applyToSubtree(Node.Operation<T>) - Method in class ini.trakem2.display.Node
Apply @param op to this Node and all its subtree nodes.
applyTransform(double[]) - Method in class ij3d.Content
 
applyTransform(Transform3D) - Method in class ij3d.Content
 
applyTransform(double[]) - Method in class ij3d.ContentInstant
 
applyTransform(Transform3D) - Method in class ij3d.ContentInstant
 
applyTransform(Content) - Method in class ij3d.Executer
 
applyTransform(String) - Static method in class ij3d.ImageJ3DViewer
 
applyTransform() - Method in class ini.trakem2.display.DisplayCanvas
 
applyTransform(ArrayList<Point>) - Method in class mpicbg.pointdescriptor.test.TestPointDescriptor
 
applyTransformationMT(ImagePlus, ImagePlus, BSplineModel, int, double[][], double[][]) - Static method in class bunwarpj.MiscTools
Apply a given B-spline transformation to the source (gray-scale) image.
ApplyTransformationPopup - Class in spim.fiji.spimdata.explorer.popup
 
ApplyTransformationPopup() - Constructor for class spim.fiji.spimdata.explorer.popup.ApplyTransformationPopup
 
ApplyTransformationPopup.MyActionListener - Class in spim.fiji.spimdata.explorer.popup
 
applyTransformationToSource(int, double[][], double[][]) - Method in class bunwarpj.MainDialog
Apply the transformation defined by the spline coefficients to the source image.
applyTransformationToSource(ImagePlus, ImagePlus, BSplineModel, int, double[][], double[][]) - Static method in class bunwarpj.MiscTools
Deprecated. 
applyTransformationToSource(ImagePlus, ImagePlus, BSplineModel, BSplineModel, BSplineModel, int, double[][], double[][]) - Static method in class bunwarpj.MiscTools
Deprecated. 
applyTransformationToSourceMT(ImagePlus, ImagePlus, int, double[][], double[][]) - Static method in class bunwarpj.MiscTools
Apply a given B-spline transformation to the source (gray-scale) image.
applyTransformationToSourceMT(ImagePlus, ImagePlus, BSplineModel, int, double[][], double[][]) - Static method in class bunwarpj.MiscTools
Apply a given B-spline transformation to the source (gray-scale) image.
applyTransformReverse(List<PointMatch>, CoordinateTransform) - Static method in class register_virtual_stack.Register_Virtual_Stack_MT
Apply a transformation to the second point (P2) of a list of Point matches
applyTransformRotationXYZ(double, double, double) - Method in class jRenderer3D.JRenderer3D
Changes the rotation of x-, y-, and z-axis by the values of changeX and changeY.
applyTransforms(Map<Displayable, AffineTransform>) - Static method in class ini.trakem2.display.LayerSet
 
applyTransformToLayer(Layer, CoordinateTransform, Filter<Patch>) - Static method in class mpicbg.trakem2.align.ElasticLayerAlignment
 
applyTransformToLayer(Layer, AffineTransform, Filter<Patch>) - Static method in class mpicbg.trakem2.align.RegularizedAffineLayerAlignment
 
applyTransformToSource(String, ImagePlus, ImagePlus) - Static method in class bunwarpj.bUnwarpJ_
Apply transform loaded from file to source image (in place).
applyTransformToStack(String, ImagePlus, ImagePlus) - Static method in class bunwarpj.MiscTools
Apply transform saved on a file to all slices of moving image
applyTranslation(float, float, float) - Method in class ij3d.Content
 
applyTSTAMP(ImagePlus, LSMFileInfo) - Method in class org.imagearchive.lsm.toolbox.gui.ControlPanelFrame
 
applyWithoutTranslation(double, double, double) - Method in class vib.FastMatrix
 
applyWithoutTranslation(Point3d) - Method in class vib.FastMatrix
 
applyWithoutTranslation(float, float, float) - Method in class vib.FloatMatrix
 
applyWithoutTranslation(Point3d) - Method in class vib.FloatMatrix
 
applyZSTAMP(ImagePlus, LSMFileInfo) - Method in class org.imagearchive.lsm.toolbox.gui.ControlPanelFrame
 
approximateEntropy(RandomAccessibleInterval<FloatType>, ImgFactory<ComplexFloatType>, double[], double[]) - Method in class spim.process.fusion.weights.ContentBased
 
approximateInverseCoords(double[], ImagePlus, double[][], double[][]) - Static method in class bunwarpj.MiscTools
Approximate the transformed coordinates of a point from the moving image into the fixed image.
approximateTransferPixel(int[]) - Method in class ini.trakem2.display.Patch
Transfer an 8-bit or RGB pixel to this image color space, interpolating; the pvalue is modified in place.
ArchipelagoClient - Class in edu.utexas.clm.archipelago.network.client
 
ArchipelagoClient(long, InputStream, OutputStream) - Constructor for class edu.utexas.clm.archipelago.network.client.ArchipelagoClient
 
ArchipelagoClient(long, InputStream, OutputStream, TransceiverExceptionListener) - Constructor for class edu.utexas.clm.archipelago.network.client.ArchipelagoClient
 
ArchipelagoFuture<T> - Class in edu.utexas.clm.archipelago.compute
 
ArchipelagoFuture(Scheduler) - Constructor for class edu.utexas.clm.archipelago.compute.ArchipelagoFuture
 
ArchipelagoFuture(Scheduler, T) - Constructor for class edu.utexas.clm.archipelago.compute.ArchipelagoFuture
 
ArchipelagoServer - Class in edu.utexas.clm.archipelago.network.server
 
ArchipelagoUI - Interface in edu.utexas.clm.archipelago.ui
 
ArchipelagoUtils - Class in edu.utexas.archipelago
 
ArchiveClient - Class in client
 
ArchiveClient(Applet) - Constructor for class client.ArchiveClient
 
ArchiveClient(Applet, String) - Constructor for class client.ArchiveClient
 
archiveClient - Variable in class tracing.SimpleNeuriteTracer
 
area(PathIterator) - Static method in class fiji.geom.AreaCalculations
Computes the surface area of the path or multiple specified paths.
Area() - Constructor for class fiji.geom.AreaCalculations.Area
 
area - Variable in class ini.trakem2.display.Patch.TransformProperties
 
area - Variable in class sc.fiji.balloonSegmentation.structure.Balloon
 
area - Variable in class sc.fiji.balloonSegmentation.structure.BalloonPopulation
 
area_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.
arg - Variable in class loci.plugins.LociExporter
Argument passed to setup method.
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
 
ARGBFloatConverter() - Constructor for class bigwarp.BigWarpRealExporter.ARGBFloatConverter
 
ARGBtoRandomARGBColorConverter<R> - Class in net.imglib2.display
 
ARGBtoRandomARGBColorConverter(double, double) - Constructor for class net.imglib2.display.ARGBtoRandomARGBColorConverter
 
ARGBtoRandomARGBColorConverter.ToGray - Class in net.imglib2.display
A converter from a ARGB to ARGB that initially converts the input color to grayscale, then scales the resulting grayscale value with the set color.
ARGBtoRandomARGBColorConverter.VolatileToGray - Class in net.imglib2.display
 
args - Static variable in class loci.plugins.shortcut.ShortcutPanel
Details for installed plugins.
ARMED - Static variable in class vib.segment.ImageButton
 
armijoCondition(double, double) - Method in class jitk.spline.TransformInverseGradientDescent
Returns true if the armijo condition is satisfied.
arrangement - Variable in class stitching.GridLayout
 
arrangeWindowsMenuItem - Variable in class tracing.NeuriteTracerResultsDialog
 
Array<T extends Type<T>,A extends DataAccess> - Class in mpicbg.imglib.container.array
TODO
Array(ArrayContainerFactory, A, int[], int) - Constructor for class mpicbg.imglib.container.array.Array
 
Array3D<T extends Type<T>,A extends DataAccess> - Class in mpicbg.imglib.container.array
TODO
Array3D(ArrayContainerFactory, A, int, int, int, int) - Constructor for class mpicbg.imglib.container.array.Array3D
 
Array3DLocalizableByDimCursor<T extends Type<T>> - Class in mpicbg.imglib.cursor.array
TODO
Array3DLocalizableByDimCursor(Array3D<T, ?>, Image<T>, T) - Constructor for class mpicbg.imglib.cursor.array.Array3DLocalizableByDimCursor
 
Array3DLocalizableByDimOutOfBoundsCursor<T extends Type<T>> - Class in mpicbg.imglib.cursor.array
TODO
Array3DLocalizableByDimOutOfBoundsCursor(Array3D<T, ?>, Image<T>, T, OutOfBoundsStrategyFactory<T>) - Constructor for class mpicbg.imglib.cursor.array.Array3DLocalizableByDimOutOfBoundsCursor
 
Array3DLocalizableCursor<T extends Type<T>> - Class in mpicbg.imglib.cursor.array
TODO
Array3DLocalizableCursor(Array3D<T, ?>, Image<T>, T) - Constructor for class mpicbg.imglib.cursor.array.Array3DLocalizableCursor
 
ArrayBase<ArrayType,BaseType> - Class in fiji.util
 
ArrayBase(int, int, Class) - Constructor for class fiji.util.ArrayBase
 
ArrayBase(int, Class) - Constructor for class fiji.util.ArrayBase
 
ArrayContainerFactory - Class in mpicbg.imglib.container.array
TODO
ArrayContainerFactory() - Constructor for class mpicbg.imglib.container.array.ArrayContainerFactory
 
ArrayConverter - Class in mpi.fruitfly.general
Title:
ArrayConverter() - Constructor for class mpi.fruitfly.general.ArrayConverter
 
ArrayCursor<T extends Type<T>> - Class in mpicbg.imglib.cursor.array
TODO
ArrayCursor(Array<T, ?>, Image<T>, T) - Constructor for class mpicbg.imglib.cursor.array.ArrayCursor
 
ArrayDataAccess<A> - Interface in mpicbg.imglib.container.basictypecontainer.array
TODO
ArrayImgLoader(T) - Constructor for class bdv.ij.export.imgloader.FusionImageLoader.ArrayImgLoader
 
arrayIndex - Variable in class mpicbg.imglib.labeling.LocalizableLabelingCursor
 
ArrayIterable(Iterable<double[]>) - Constructor for class org.janelia.thickness.inference.visitor.CorrelationFitVisitor.ArrayIterable
 
ArrayLocalizableByDimCursor<T extends Type<T>> - Class in mpicbg.imglib.cursor.array
TODO
ArrayLocalizableByDimCursor(Array<T, ?>, Image<T>, T) - Constructor for class mpicbg.imglib.cursor.array.ArrayLocalizableByDimCursor
 
ArrayLocalizableByDimOutOfBoundsCursor<T extends Type<T>> - Class in mpicbg.imglib.cursor.array
TODO
ArrayLocalizableByDimOutOfBoundsCursor(Array<T, ?>, Image<T>, T, OutOfBoundsStrategyFactory<T>) - Constructor for class mpicbg.imglib.cursor.array.ArrayLocalizableByDimOutOfBoundsCursor
 
ArrayLocalizableCursor<T extends Type<T>> - Class in mpicbg.imglib.cursor.array
TODO
ArrayLocalizableCursor(Array<T, ?>, Image<T>, T) - Constructor for class mpicbg.imglib.cursor.array.ArrayLocalizableCursor
 
ArrayLocalizablePlaneCursor<T extends Type<T>> - Class in mpicbg.imglib.cursor.array
TODO
ArrayLocalizablePlaneCursor(Array<T, ?>, Image<T>, T) - Constructor for class mpicbg.imglib.cursor.array.ArrayLocalizablePlaneCursor
 
ArraySortedIndices - Class in org.janelia.utility.arrays
 
ArraySortedIndices() - Constructor for class org.janelia.utility.arrays.ArraySortedIndices
 
ArrayToByteProcessor(ImageProcessor, int[][]) - Static method in class mpi.fruitfly.general.ImageArrayConverter
 
ArrayToByteProcessor(ImageProcessor, float[][]) - Static method in class mpi.fruitfly.general.ImageArrayConverter
 
ArrayToFloatProcessor(ImageProcessor, double[], int, int) - Static method in class mpi.fruitfly.general.ImageArrayConverter
 
ArrayToFloatProcessor(ImageProcessor, float[], int, int) - Static method in class mpi.fruitfly.general.ImageArrayConverter
 
arrayType - Variable in class mpicbg.imglib.cursor.special.SortedGrayLevelIteratorArrayContainerOnly
 
ARROW - Static variable in class ini.trakem2.display.DLabel
 
Arrow - Class in util
 
Arrow(Color, double, double, double, double, double, double, int) - Constructor for class util.Arrow
 
ArrowDisplayer - Interface in util
 
ArrowOptionPanel - Class in fiji.util
 
ArrowOptionPanel(ArrowShape, BasicStroke) - Constructor for class fiji.util.ArrowOptionPanel
Instantiates the config panel with using settings from arguments.
ArrowOptionPanel() - Constructor for class fiji.util.ArrowOptionPanel
 
ArrowShape - Class in fiji.util
 
ArrowShape() - Constructor for class fiji.util.ArrowShape
 
ArrowShape(ArrowShape.ArrowStyle) - Constructor for class fiji.util.ArrowShape
 
ArrowShape(ArrowShape.ArrowStyle, double) - Constructor for class fiji.util.ArrowShape
 
ArrowShape.ArrowStyle - Enum in fiji.util
 
ArrowTool - Class in fiji.util
ArrowTool plugin
ArrowTool() - Constructor for class fiji.util.ArrowTool
 
asAffine3D() - Method in interface mpicbg.spim.data.registration.ViewTransform
A representation of this ViewTransform as a 3D AffineGet.
asAffine3D() - Method in class mpicbg.spim.data.registration.ViewTransformAffine
 
asArray(int, double) - Static method in class script.imglib.algorithm.fn.AlgorithmUtil
Copy the given double value into each index of a double[] array of length .
asBufferedImage(Image) - Static method in class ini.trakem2.io.ImageSaver
 
asChart() - Method in class script.imglib.analysis.Histogram
 
asChart(boolean) - Method in class script.imglib.analysis.Histogram
Return the JFreeChart with this histogram, and as a side effect, show it in a JFrame that provides the means to edit the dimensions and also the plot properties via a popup menu.
ASCII - Variable in class amira.AmiraMeshDecoder
 
ASCII - Static variable in class isosurface.MeshExporter
 
asContent(Display3D) - Method in class ini.trakem2.display.Display3D.VectorStringContent
 
asDoubleArray(Collection<Number>) - Static method in class script.imglib.algorithm.fn.AlgorithmUtil
 
asDoubleArray(float[]) - Static method in class script.imglib.algorithm.fn.AlgorithmUtil
 
asGrey(BufferedImage) - Static method in class ini.trakem2.io.ImageSaver
If the given BufferedImage is of type TYPE_BYTE_GRAY, it will simply return it.
asHexRGBColor(Color) - Static method in class ini.trakem2.utils.Utils
 
asHexRGBColor(StringBuilder, Color) - Static method in class ini.trakem2.utils.Utils
 
asImage() - Method in class script.imglib.analysis.BarChart
 
asImage(JFreeChart) - Static method in class script.imglib.analysis.ChartUtils
 
asImage(JFreeChart, int, int) - Static method in class script.imglib.analysis.ChartUtils
 
asImage() - Method in class script.imglib.analysis.Histogram
 
asImage() - Method in class script.imglib.color.fn.ColorFunction
 
asImage(int) - Method in class script.imglib.color.fn.ColorFunction
 
asImage() - Method in class script.imglib.math.fn.FloatImageOperation
Evaluate this operation as an Image<FloatType>.
asImage(int) - Method in class script.imglib.math.fn.FloatImageOperation
Evaluate this operation as an Image<FloatType> using the defined number of parallel threads.
asImage() - Method in interface script.imglib.math.fn.ImageComputation
 
asImage(int) - Method in interface script.imglib.math.fn.ImageComputation
 
ASin - Class in script.imglib.math
TODO
ASin(Image<? extends RealType<?>>) - Constructor for class script.imglib.math.ASin
 
ASin(IFunction) - Constructor for class script.imglib.math.ASin
 
ASin(Number) - Constructor for class script.imglib.math.ASin
 
ask_params - Variable in class levelsets.ij.LevelSet
 
askAdjustRadius(Node<Float>) - Method in class ini.trakem2.display.Treeline
 
askForFileForLoading(File, String, Frame, Logger) - Static method in class fiji.plugin.trackmate.io.IOUtils
Prompts the user for a xml file to load from.
askForFileForSaving(File, Frame, Logger) - Static method in class fiji.plugin.trackmate.io.IOUtils
Prompts the user for a xml file to save to.
askForFixedTiles(GlobalOptimizationSubset, GlobalOptimizationType, Set<ViewId>, String) - Method in class spim.fiji.plugin.Interest_Point_Registration
 
askForFolder(File, String, Frame, Logger) - Static method in class fiji.plugin.trackmate.io.IOUtils
Prompts the user for a target folder.
askForNewTag(int) - Method in class ini.trakem2.display.LayerSet
 
askForReferenceTile(GlobalOptimizationSubset, GlobalOptimizationType, String) - Method in class spim.fiji.plugin.Interest_Point_Registration
 
askForRegistrations(GenericDialog) - Method in class spim.fiji.plugin.Duplicate_Transformation
 
askForXMLTemplate(Project) - Method in class ini.trakem2.persistence.Loader
Ask for the user to provide a template XML file to extract a root TemplateThing.
askToFinish() - Method in class landmarks.FineTuneThread
 
askToRemoveTag(int) - Method in class ini.trakem2.display.LayerSet
Returns false if the dialog was canceled or there wasn't any tag to remove.
askWhenMoreThan - Static variable in class spim.fiji.spimdata.explorer.popup.DisplayViewPopup
 
askWhenMoreThan - Static variable in class spim.fiji.spimdata.explorer.popup.RemoveTransformationPopup
 
askWhenMoreThan - Static variable in class spim.fiji.spimdata.explorer.popup.ResavePopup
 
asList(long[]) - Static method in class ini.trakem2.utils.Utils
 
asList(long[], int, int) - Static method in class ini.trakem2.utils.Utils
 
asOptionPanel() - Method in class ini.trakem2.display.AreaWrapper.PaintParameters
 
asOptionPanel() - Method in class ini.trakem2.imaging.Segmentation.FastMarchingParam
 
asPaintable(List<? extends Paintable>) - Method in class ini.trakem2.display.graphics.DefaultGraphicsSource
Returns the list given as argument without any modification.
asPaintable(List<? extends Paintable>) - Method in interface ini.trakem2.display.graphics.GraphicsSource
Takes as list of Paintable and returns the same or another list with perhaps a different number of Paintable objects, or some replaced by new Paintable instances.
asPaintable(List<? extends Paintable>) - Method in class ini.trakem2.display.graphics.TestGraphicsSource
Replaces all Patch instances by a smiley face.
asPaintable(List<? extends Paintable>) - Method in class ini.trakem2.display.GroupingMode.GroupedGraphicsSource
Returns the list given as argument without any modification.
asPath(double, double, double, String) - Method in class tracing.SearchNode
 
asPathReversed(double, double, double, String) - Method in class tracing.SearchNode
 
aspectField - Variable in class VolumeJ.VJUserInterface
 
aspectx - Variable in class volume.Volume
Anisotropy measure of the volume.
aspectx - Static variable in class VolumeJ.VJUserInterface
 
aspecty - Variable in class volume.Volume
Anisotropy measure of the volume.
aspecty - Static variable in class VolumeJ.VJUserInterface
 
aspectz - Variable in class volume.Volume
Anisotropy measure of the volume.
aspectz - Static variable in class VolumeJ.VJUserInterface
 
asPoint() - Method in class ini.trakem2.display.Node
 
asPoint(Node<T>, boolean) - Method in class ini.trakem2.display.Tree
Return the Node as a point in space.
asPoints(float[]) - Method in class script.imglib.analysis.DoGPeaks
Returns a list of peaks as Java3D points if possible: Point2f for 2D images Point3f for 3D images Point4f for 4D images
asPoints() - Method in class script.imglib.analysis.DoGPeaks
Returns a list of peaks as Java3D points: Point2f for 2D images, Point3f for 3D images, and Point4f for 4D images.
asPoints(Number) - Method in class script.imglib.analysis.DoGPeaks
Returns a list of peaks as Java3D points: Point2f for 2D images, Point3f for 3D images, and Point4f for 4D images.
asRGBABytes(int[], byte[], byte[]) - Static method in class ini.trakem2.imaging.P
 
asRGBBytes(int[]) - Static method in class ini.trakem2.imaging.P
 
asSafePath(String) - Static method in class ini.trakem2.persistence.FSLoader
Takes a String and returns a copy with the following conversions: / to -, space to _, and \ to -.
assembleAllMetaData(SequenceDescription, Collection<? extends ViewId>) - Static method in class spim.fiji.plugin.Apply_Transformation
Should be called before registration to make sure all metadata is right
assembleAllViewPairs() - Method in class spim.process.interestpointregistration.optimizationtypes.AllToAllRegistration
 
assembleAllViewPairs() - Method in class spim.process.interestpointregistration.optimizationtypes.AllToAllRegistrationWithRange
 
assembleAllViewPairs() - Method in class spim.process.interestpointregistration.optimizationtypes.GlobalOptimizationType
 
assembleAllViewPairs() - Method in class spim.process.interestpointregistration.optimizationtypes.IndividualTimepointRegistration
 
assembleAllViewPairs() - Method in class spim.process.interestpointregistration.optimizationtypes.ReferenceTimepointRegistration
 
assembleAngles(List<Angle>) - Method in class spim.fiji.plugin.Duplicate_Transformation
 
assembleAvailableCorrespondences(HashMap<Channel, ArrayList<EfficientBayesianBased.Correspondence>>, HashMap<Channel, Integer>, boolean) - Method in class spim.process.fusion.deconvolution.EfficientBayesianBased
 
assembleChannels(List<Channel>) - Method in class spim.fiji.plugin.Duplicate_Transformation
 
assembleChannels(List<Channel>) - Method in class spim.process.fusion.boundingbox.AutomaticBoundingBox
 
assembleDefaultPattern() - Method in class spim.fiji.datasetmanager.StackList
 
assembleFixedTiles(SpimData2, List<ViewId>, List<ChannelProcess>, TimePoint) - Static method in class spim.process.interestpointregistration.optimizationtypes.ReferenceTimepointRegistration
All tiles of the reference timepoint are fixed, nothing else
assembleIllums(List<Illumination>) - Method in class spim.fiji.plugin.Duplicate_Transformation
 
assembleInputData(SpimData2, TimePoint, Channel, List<ViewId>) - Static method in class spim.process.fusion.FusionHelper
 
assembleNewViewSetupsFusion(SpimData2, List<ViewId>, BoundingBoxGUI, String, String) - Static method in class spim.process.fusion.weightedavg.WeightedAverageFusion
Creates one new Angle and one new Illumination for the fused dataset.
assembleNewViewSetupsSequential(SpimData2, List<ViewId>, BoundingBoxGUI) - Static method in class spim.process.fusion.weightedavg.WeightedAverageFusion
Duplicates all Angles and Illuminations that are processed.
assemblePartialSpimData2(SpimData2, List<ViewId>, File, List<String>) - Static method in class spim.fiji.plugin.resave.Resave_TIFF
Assembles a new SpimData2 based on the subset of timepoints and viewsetups as selected by the user.
assembleRegistrationNames(SpimData, List<ViewId>) - Static method in class spim.fiji.plugin.util.GUIHelper
 
assembleResults() - Method in class sc.fiji.analyzeSkeleton.AnalyzeSkeleton_
Returns the analysis results in a SkeletonResult object.
assembleSpimData2(List<TimePoint>, List<ViewSetup>, File) - Static method in class spim.process.fusion.export.ExportSpimData2TIFF
Assembles a new SpimData2 based on the timepoints and viewsetups.
assembleTimepoints(List<TimePoint>) - Method in class spim.fiji.plugin.Duplicate_Transformation
 
assembleTimepoints(TimePoints) - Static method in class spim.fiji.plugin.Interest_Point_Registration
 
assembleTimepoints(List<TimePoint>) - Method in class spim.process.fusion.boundingbox.AutomaticBoundingBox
 
assertEquals(String, Object, String, Object) - Static method in class sc.fiji.timelapse.PolygonRoiPublic
 
assertEquals(String, Object, String, Object, int) - Static method in class sc.fiji.timelapse.PolygonRoiPublic
 
assertEquals(String, boolean, String, boolean) - Static method in class sc.fiji.timelapse.PolygonRoiPublic
 
assertEquals(String, byte, String, byte) - Static method in class sc.fiji.timelapse.PolygonRoiPublic
 
assertEquals(String, short, String, short) - Static method in class sc.fiji.timelapse.PolygonRoiPublic
 
assertEquals(String, int, String, int) - Static method in class sc.fiji.timelapse.PolygonRoiPublic
 
assertEquals(String, long, String, long) - Static method in class sc.fiji.timelapse.PolygonRoiPublic
 
assertEquals(String, float, String, float) - Static method in class sc.fiji.timelapse.PolygonRoiPublic
 
assertEquals(String, double, String, double) - Static method in class sc.fiji.timelapse.PolygonRoiPublic
 
assertEquals(String, String, String, String) - Static method in class sc.fiji.timelapse.PolygonRoiPublic
 
Assign3DData(Container, ImgPanel, My3DData) - Method in class view5d.AlternateViewer
 
assignListenerToHelpButton(String, ActionListener) - Method in class sholl.gui.EnhancedGenericDialog
Adds a "Help" button and attaches the specified listener to it.
Assignment(int, int, double) - Constructor for class fiji.plugin.trackmate.tracking.sparselap.costmatrix.DefaultCostMatrixCreator.Assignment
 
AssignmentAlgorithm - Interface in fiji.plugin.trackmate.tracking.oldlap.hungarian
Just in case I want to try more than one implementation of the assignment algorithm.
AssignmentProblem - Class in fiji.plugin.trackmate.tracking.oldlap.hungarian
An implementation of this: http://en.wikipedia.org/wiki/Hungarian_algorithm
AssignmentProblem(double[][]) - Constructor for class fiji.plugin.trackmate.tracking.oldlap.hungarian.AssignmentProblem
 
assignNewAttributeIds(AbstractSpimData<?>, Map<String, Set<Integer>>) - Static method in class bdv.spimdata.tools.ChangeAttributeId
For the specified spimData data set, re-assign attribute id's that are already in use.
assignNewViewSetupIds(AbstractSpimData<?>, Set<Integer>) - Static method in class bdv.spimdata.tools.ChangeViewSetupId
For the specified spimData data set, re-assign setup id's that are already in use.
AssignOperation<T extends RealType<T>> - Class in imglib.ops.operation
An AssignOperation computes values in an output image.
AssignOperation(Image<T>[], Image<T>, RealFunction<T>) - Constructor for class imglib.ops.operation.AssignOperation
 
assignOtherChannel(Channel, HashMap<Channel, ChannelPSF>) - Method in class spim.process.fusion.deconvolution.ProcessForDeconvolution
 
AssignPixelDisplay(PixelDisplay) - Method in class view5d.AlternateViewer
 
assignPointMatches(List<P>, List<P>) - Method in interface mpicbg.icp.PointMatchIdentification
 
assignPointMatches(List<P>, List<P>) - Method in class mpicbg.icp.SimplePointMatchIdentification
 
assignPopupToHelpButton(JPopupMenu) - Method in class sholl.gui.EnhancedGenericDialog
Attaches the specified JPopupMenu to the GenericDialog "Help" button renamed "More »".
assignPopupToHelpButton(String, JPopupMenu) - Method in class sholl.gui.EnhancedGenericDialog
Adds a "Help" button and attaches the specified JPopupMenu to it.
assignSliceTo(int, Roi, int) - Method in class vib.segment.CustomStackWindow
 
assignViewsToTiles(M, List<ViewId>, boolean) - Static method in class spim.process.interestpointregistration.GlobalOpt
 
assoc(BufferedImage) - Method in class ini.trakem2.display.DisplayCanvas.Screenshot
Associate @param img to this, with a new sid.
asVectorString2D(Polygon, double) - Static method in class ini.trakem2.utils.M
 
asVectorString3D() - Method in interface ini.trakem2.display.Line3D
 
asVectorString3D() - Method in class ini.trakem2.display.Pipe
Returns a non-calibrated VectorString3D.
asVectorString3D() - Method in class ini.trakem2.display.Polyline
Returns a non-calibrated VectorString3D.
asVertices() - Method in class ini.trakem2.display.Tree
Return a representation of this Tree with Vertex instead of Node.
asVolatile() - Method in class bdv.viewer.SourceAndConverter
 
asVolatile() - Method in class bdv.viewer.state.SourceState
 
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
 
at(int, int, int) - Method in class VolumeJ.VJShape
 
ATan - Class in script.imglib.math
TODO
ATan(Image<? extends RealType<?>>) - Constructor for class script.imglib.math.ATan
 
ATan(IFunction) - Constructor for class script.imglib.math.ATan
 
ATan(Number) - Constructor for class script.imglib.math.ATan
 
ATan2 - Class in script.imglib.math
TODO
ATan2(Image<? extends RealType<?>>, Image<? extends RealType<?>>) - Constructor for class script.imglib.math.ATan2
 
ATan2(IFunction, Image<? extends RealType<?>>) - Constructor for class script.imglib.math.ATan2
 
ATan2(Image<? extends RealType<?>>, IFunction) - Constructor for class script.imglib.math.ATan2
 
ATan2(IFunction, IFunction) - Constructor for class script.imglib.math.ATan2
 
ATan2(Image<? extends RealType<?>>, Number) - Constructor for class script.imglib.math.ATan2
 
ATan2(Number, Image<? extends RealType<?>>) - Constructor for class script.imglib.math.ATan2
 
ATan2(IFunction, Number) - Constructor for class script.imglib.math.ATan2
 
ATan2(Number, IFunction) - Constructor for class script.imglib.math.ATan2
 
ATan2(Number, Number) - Constructor for class script.imglib.math.ATan2
 
atGoal(int, int, int, boolean) - Method in class tracing.SearchThread
 
atGoal(int, int, int, boolean) - Method in class tracing.TracerThread
 
attenuate(VJShade) - Method in class VolumeJ.VJAlphaColor
 
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_Local_Threshold - Class in fiji.threshold
 
Auto_Local_Threshold() - Constructor for class fiji.threshold.Auto_Local_Threshold
 
Auto_Threshold - Class in fiji.threshold
 
Auto_Threshold() - Constructor for class fiji.threshold.Auto_Threshold
 
Auto_Tracer - Class in tracing
 
Auto_Tracer() - Constructor for class tracing.Auto_Tracer
 
Auto_Tracer.TubenessComparator - Class in tracing
 
autoActivationMenuItem - Variable in class tracing.NeuriteTracerResultsDialog
 
autoCanvasActivation - Variable in class tracing.SimpleNeuriteTracer
 
autocorr(double[], int) - Static method in class bijnum.BIJstats
Computes autocorrelation up to maxk for the time series data.
autocov(double[], int) - Static method in class bijnum.BIJstats
Computes autocovariance up to maxk for the time series data.
AutoLabeller - Class in oldsegmenters
User: Tom Larkworthy Date: 12-Jul-2006 Time: 19:10:47
AutoLabeller(String) - Constructor for class oldsegmenters.AutoLabeller
 
AutoLabeller.LabelStats - Class in oldsegmenters
 
AutoLabellerNaive - Class in oldsegmenters
User: Tom Larkworthy Date: 12-Jul-2006 Time: 19:12:08
AutoLabellerNaive(String) - Constructor for class oldsegmenters.AutoLabellerNaive
 
AutomaticAngleSetup - Class in mpicbg.spim.preprocessing
 
AutomaticAngleSetup(ViewStructure) - Constructor for class mpicbg.spim.preprocessing.AutomaticAngleSetup
 
AutomaticBoundingBox - Class in spim.process.fusion.boundingbox
 
AutomaticBoundingBox(SpimData2, List<ViewId>) - Constructor for class spim.process.fusion.boundingbox.AutomaticBoundingBox
 
AutomaticReorientation - Class in spim.process.fusion.boundingbox
 
AutomaticReorientation(SpimData2, List<ViewId>) - Constructor for class spim.process.fusion.boundingbox.AutomaticReorientation
 
AutomaticReorientation.Reorientation - Enum in spim.process.fusion.boundingbox
 
autoMinMax() - Method in class fiji.plugin.trackmate.gui.panels.components.ColorByFeatureGUIPanel
 
autoMinMax() - Method in class fiji.plugin.trackmate.gui.panels.components.SetColorScaleDialog
 
autoMinMax() - Method in class fiji.plugin.trackmate.visualization.DummySpotColorGenerator
 
autoMinMax() - Method in class fiji.plugin.trackmate.visualization.DummyTrackColorGenerator
 
autoMinMax() - Method in class fiji.plugin.trackmate.visualization.ManualEdgeColorGenerator
 
autoMinMax() - Method in class fiji.plugin.trackmate.visualization.ManualSpotColorGenerator
 
autoMinMax() - Method in interface fiji.plugin.trackmate.visualization.MinMaxAdjustable
Automatically computes the min & max values from this object current content.
autoMinMax() - Method in class fiji.plugin.trackmate.visualization.PerEdgeFeatureColorGenerator
 
autoMinMax() - Method in class fiji.plugin.trackmate.visualization.PerTrackFeatureColorGenerator
 
autoMinMax() - Method in class fiji.plugin.trackmate.visualization.SpotColorGenerator
 
autoMinMax() - Method in class fiji.plugin.trackmate.visualization.SpotColorGeneratorPerTrackFeature
 
AutoPoint - Class in tracing
 
AutoPoint(int, int, int) - Constructor for class tracing.AutoPoint
 
autoSavePdf - Variable in class sc.fiji.coloc.Coloc_2
 
autosaver - Static variable in class ini.trakem2.persistence.FSLoader
 
autoscale_after_filtering - Variable in class ini.trakem2.imaging.Segmentation.FastMarchingParam
 
autoscaleBox - Variable in class loci.plugins.in.MainDialog
 
autoscroll(Point) - Method in class ini.trakem2.tree.DNDTree
 
AutoSearchThread - Class in tracing
 
AutoSearchThread(ImagePlus, float[][], AutoPoint, float, SinglePathsGraph) - Constructor for class tracing.AutoSearchThread
 
autoThreshold() - Method in class loci.plugins.util.RecordedImageProcessor
 
AutoThresholdRegression<T extends RealType<T>> - Class in sc.fiji.coloc.algorithms
A class implementing the automatic finding of a threshold used for Pearson colocalisation calculation.
AutoThresholdRegression(PearsonsCorrelation<T>) - Constructor for class sc.fiji.coloc.algorithms.AutoThresholdRegression
 
AutoThresholdRegression(PearsonsCorrelation<T>, AutoThresholdRegression.Implementation) - Constructor for class sc.fiji.coloc.algorithms.AutoThresholdRegression
 
AutoThresholdRegression.Implementation - Enum in sc.fiji.coloc.algorithms
 
autoTrace(ImagePlus) - Method in class tracing.Auto_Tracer
 
AutoTracerCanvas - Class in tracing
 
AutoTracerCanvas(ImagePlus, PaneOwner, int, PathAndFillManager) - Constructor for class tracing.AutoTracerCanvas
 
available - Static variable in class ini.trakem2.imaging.filters.FilterEditor
 
availableFeatures - Static variable in class trainableSegmentation.FeatureStack
names of available filters
availableFeatures - Static variable in class trainableSegmentation.FeatureStack3D
names of available filters
avef() - Method in class parObject
 
average(Roi) - Method in class FlowJ.FlowJError
 
average(Roi) - Method in class FlowJ.FlowJFlow
 
average - Variable in class ij3d.Volume
Flag indicating that the channels should be averaged
Average - Class in imglib.ops.operator.binary
TODO
Average() - Constructor for class imglib.ops.operator.binary.Average
 
average(Point3d[]) - Static method in class math3d.Point3d
 
average(int, int) - Static method in class org.siox.util.Utils
Averages two ARGB colors.
Average - Class in script.imglib.math
TODO
Average(Image<? extends RealType<?>>, Image<? extends RealType<?>>) - Constructor for class script.imglib.math.Average
 
Average(IFunction, Image<? extends RealType<?>>) - Constructor for class script.imglib.math.Average
 
Average(Image<? extends RealType<?>>, IFunction) - Constructor for class script.imglib.math.Average
 
Average(IFunction, IFunction) - Constructor for class script.imglib.math.Average
 
Average(Image<? extends RealType<?>>, Number) - Constructor for class script.imglib.math.Average
 
Average(Number, Image<? extends RealType<?>>) - Constructor for class script.imglib.math.Average
 
Average(IFunction, Number) - Constructor for class script.imglib.math.Average
 
Average(Number, IFunction) - Constructor for class script.imglib.math.Average
 
Average(Number, Number) - Constructor for class script.imglib.math.Average
 
Average(Object...) - Constructor for class script.imglib.math.Average
 
average(FastMatrix[]) - Static method in class vib.FastMatrix
 
average(FloatMatrix[]) - Static method in class vib.FloatMatrix
 
Average_Color - Class in <Unnamed>
 
Average_Color() - Constructor for class Average_Color
 
Average_Images - Class in vib
 
Average_Images() - Constructor for class vib.Average_Images
 
Average_Torsten_Results - Class in util
 
Average_Torsten_Results() - Constructor for class util.Average_Torsten_Results
 
averageAllChannels(Image<T>, int[], ImagePlus, int) - Static method in class mpicbg.stitching.PairWiseStitchingImgLib
Averages all channels into the target image.
averageAllChannels(Image<T>, ArrayList<Image<S>>, int[]) - Static method in class mpicbg.stitching.PairWiseStitchingImgLib
Averages all channels into the target image.
averageAlpha() - Method in class FlowJ.FlowJFlow
Return the angle of the previously computed average flow.
AverageBrain - Class in vib.app.module
 
AverageBrain() - Constructor for class vib.app.module.AverageBrain
 
AverageBrain_ - Class in vib
 
AverageBrain_() - Constructor for class vib.AverageBrain_
 
AverageByteLoader(Volume.InputImage) - Constructor for class ij3d.Volume.AverageByteLoader
 
AverageContent - Class in mpicbg.spim.fusion
 
AverageContent(ViewDataBeads, ContainerFactory) - Constructor for class mpicbg.spim.fusion.AverageContent
 
AverageContentFactory - Class in mpicbg.spim.fusion
 
AverageContentFactory(ContainerFactory) - Constructor for class mpicbg.spim.fusion.AverageContentFactory
 
averageFromDirectoryList(ArrayList<File>) - Static method in class util.Average_Torsten_Results
 
averageMagnitude() - Method in class FlowJ.FlowJFlow
Return the length of the previously computed average flow.
averageOverVelocity() - Method in class FlowJ.FlowJError
 
AveragePixelFusion - Class in mpicbg.stitching.fusion
 
AveragePixelFusion() - Constructor for class mpicbg.stitching.fusion.AveragePixelFusion
 
AveragePixelFusionIgnoreZero - Class in mpicbg.stitching.fusion
 
AveragePixelFusionIgnoreZero() - Constructor for class mpicbg.stitching.fusion.AveragePixelFusionIgnoreZero
 
Averager() - Constructor for class vib.NaiveResampler.Averager
 
avex() - Method in class parObject
 
avey() - Method in class parObject
 
avg(float[], float[]) - Static method in class bijnum.BIJstats
 
avg(float[]) - Static method in class bijnum.BIJstats
Compute average of all values in vector v.
avg(float[][]) - Static method in class bijnum.BIJstats
Compute average of all values in vector v.
avg(double[]) - Static method in class bijnum.BIJstats
Compute average of all values in vector v.
avg - Variable in class CPU_Meter.CPUMeter
 
avg(int) - Method in class mpicbg.imglib.image.display.imagej.RGBALegacyTypeDisplay
 
AVG - Static variable in class stitching.CommonFunctions
 
avg_grey - Variable in class levelsets.ij.StateContainer
 
AVG_PHYS_DIST - Static variable in class ini.trakem2.analysis.Compare
 
avgError - Variable in class mpicbg.spim.registration.bead.error.GlobalErrorStatisticsImpl
 
avgError - Variable in class mpicbg.spim.registration.bead.error.ViewErrorPairWise
 
AvgFunction<T extends RealType<T>> - Class in imglib.ops.function.pn
TODO
AvgFunction() - Constructor for class imglib.ops.function.pn.AvgFunction
 
avgLocalError - Variable in class mpicbg.spim.registration.bead.error.GlobalErrorStatisticsImpl
 
avgNoExtremes(float[], float) - Static method in class bijnum.BIJstats
 
avgPixels - Variable in class spim.fiji.plugin.fusion.Fusion
 
awtEventMaskList - Static variable in class org.janelia.utility.ui.RepeatingReleasedEventsFixer
 
ax - Variable in class mpicbg.pointdescriptor.LocalCoordinateSystemPointDescriptor
 
axes - Variable in class FlowJ.FlowJMapper
 
axes - Variable in class plugin.Descriptor_based_registration
 
axes - Variable in class tracing.ShollAnalysisDialog.ShollResults
 
AXES_LOG_LOG - Static variable in class tracing.ShollAnalysisDialog
 
AXES_NORMAL - Static variable in class tracing.ShollAnalysisDialog
 
AXES_SEMI_LOG - Static variable in class tracing.ShollAnalysisDialog
 
axesChoice - Variable in class spim.fiji.plugin.Apply_Transformation
 
axesGroup - Variable in class tracing.ShollAnalysisDialog
 
axesParameters - Static variable in class tracing.ShollAnalysisDialog
 
axis - Static variable in class VolumeJ.VJUserInterface
 
AxisAngle4d - Class in spim.vecmath
A four-element axis angle represented by double-precision floating point x,y,z,angle components.
AxisAngle4d(double, double, double, double) - Constructor for class spim.vecmath.AxisAngle4d
Constructs and initializes an AxisAngle4d from the specified x, y, z, and angle.
AxisAngle4d(double[]) - Constructor for class spim.vecmath.AxisAngle4d
Constructs and initializes an AxisAngle4d from the components contained in the array.
AxisAngle4d(AxisAngle4d) - Constructor for class spim.vecmath.AxisAngle4d
Constructs and initializes an AxisAngle4d from the specified AxisAngle4d.
AxisAngle4d(AxisAngle4f) - Constructor for class spim.vecmath.AxisAngle4d
Constructs and initializes an AxisAngle4d from the specified AxisAngle4f.
AxisAngle4d(Vector3d, double) - Constructor for class spim.vecmath.AxisAngle4d
Constructs and initializes an AxisAngle4d from the specified axis and angle.
AxisAngle4d() - Constructor for class spim.vecmath.AxisAngle4d
Constructs and initializes an AxisAngle4d to (0,0,1,0).
AxisAngle4f - Class in spim.vecmath
A four-element axis angle represented by single-precision floating point x,y,z,angle components.
AxisAngle4f(float, float, float, float) - Constructor for class spim.vecmath.AxisAngle4f
Constructs and initializes a AxisAngle4f from the specified xyzw coordinates.
AxisAngle4f(float[]) - Constructor for class spim.vecmath.AxisAngle4f
Constructs and initializes an AxisAngle4f from the array of length 4.
AxisAngle4f(AxisAngle4f) - Constructor for class spim.vecmath.AxisAngle4f
Constructs and initializes an AxisAngle4f from the specified AxisAngle4f.
AxisAngle4f(AxisAngle4d) - Constructor for class spim.vecmath.AxisAngle4f
Constructs and initializes an AxisAngle4f from the specified AxisAngle4d.
AxisAngle4f(Vector3f, float) - Constructor for class spim.vecmath.AxisAngle4f
Constructs and initializes an AxisAngle4f from the specified axis and angle.
AxisAngle4f() - Constructor for class spim.vecmath.AxisAngle4f
Constructs and initializes an AxisAngle4f to (0,0,1,0).
axisChoice - Variable in class VolumeJ.VJUserInterface
 
AxisConstants - Interface in ij3d
This interface stores some common constants.
axisIndex - Variable in class voltex.VolumeRenderer
The index in the switch, given the direction
AxisLessThan<T extends RealType<T>> - Class in imglib.ops.condition
TODO
AxisLessThan(int, int) - Constructor for class imglib.ops.condition.AxisLessThan
 
AxisOrder - Enum in bdv.util
 
axisOrder(AxisOrder) - Method in class bdv.util.BdvOptions
Specified when adding a stack.
axisOrder() - Method in class bdv.util.BdvOptions.Values
 
axisSwitch - Variable in class voltex.VolumeRenderer
A Switch, which holds 6 OrderedGroups, one for each direction

B

b - Variable in class edu.utexas.clm.archipelago.data.Duplex
 
B(int[], int) - Static method in class fiji.threshold.Auto_Threshold
 
b - Variable in class fiji.util.Levenshtein
 
b - Variable in class ini.trakem2.display.Tree.Pair
Two nodes of a tree; there is a unique path that goes from a to b.
b - Variable in class ini.trakem2.imaging.filters.LUTCustom
 
b - Variable in class math3d.Triangle
 
B - Variable in class mpicbg.spim.registration.bead.laplace.DoGMaximum
 
b - Variable in class mpicbg.trakem2.util.Downsampler.Pair
 
b - Variable in class mpicbg.trakem2.util.Pair
 
b - Variable in class mpicbg.trakem2.util.Triple
 
b - Variable in class sc.fiji.timelapse.LinearRegression
 
b() - Method in class script.imglib.math.fn.BinaryOperation
 
b - Variable in class spim.fiji.ImgLib2Temp.ValuePair
 
b - Variable in class volume.VolumeRGB
The brightness of each voxel as a byte (0-225).
b - Variable in class VolumeJ.VJAlphaColor
 
b - Variable in class VolumeJ.VJrgbValue
 
B_CHANNEL - Variable in class org.imagearchive.lsm.toolbox.info.LUTInfo
 
B_SIZE - Variable in class org.imagearchive.lsm.toolbox.info.LUTInfo
 
B_TYPE - Variable in class org.imagearchive.lsm.toolbox.info.LUTInfo
 
BACK - Static variable in interface ij3d.AxisConstants
 
BACK - Static variable in class sc.fiji.analyzeSkeleton.Edge
"back" edge classification constant for Depth-first search (DFS)
backBufferComposite - Variable in class fiji.util.gui.OverlayedImageCanvas
 
backCheckbox - Variable in class VolumeJ.VJUserInterface
 
background - Variable in class ini.trakem2.tree.DNDTree
 
background - Variable in class mpicbg.imglib.container.shapelist.ShapeList
 
background - Variable in class mpicbg.spim.io.SPIMConfiguration
 
BACKGROUND_COLOR_1 - Static variable in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeGraphComponent
 
BACKGROUND_COLOR_2 - Static variable in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeGraphComponent
 
BACKGROUND_CONFIDENCE - Static variable in class org.siox.SioxSegmentator
Confidence for a region likely being background.
backgroundAndSpectrum() - Static method in class util.FindConnectedRegions
 
backgroundAndSpectrum(int) - Static method in class util.FindConnectedRegions
 
backgroundColor - Static variable in class mpicbg.spim.vis3d.VisualizeBeads
 
backgroundEnabled - Static variable in class Series_Labeler
 
backgroundRoi - Variable in class siox.SegmentationGUI
 
backingCache - Variable in class bdv.img.cache.VolatileGlobalCellCache
 
backproject(Volume) - Method in class VolumeJ.VJProjection
Backprojection around a single axis y.
backtrackingLineSearch(double, double, int, double) - Method in class jitk.spline.TransformInverseGradientDescent
Uses Backtracking Line search to determine a step size.
backwardPass() - Method in class process3d.DistanceTransform3D
 
BakeManualTransformationPopup - Class in spim.fiji.spimdata.explorer.popup
 
BakeManualTransformationPopup() - Constructor for class spim.fiji.spimdata.explorer.popup.BakeManualTransformationPopup
 
BalancedRandomForest - Class in ai
This class implements a Balanced Random Forest classifier, it is an ensemble classifier of random trees where all classes have the same representation in the training process.
BalancedRandomForest() - Constructor for class ai.BalancedRandomForest
 
BalancedRandomTree - Class in ai
This class implements a random tree based on the split function specified by the template in Splitter
BalancedRandomTree(Instances, ArrayList<Integer>, Splitter) - Constructor for class ai.BalancedRandomTree
Build random tree for a balanced random forest
balanceTrainingData(Instances) - Static method in class trainableSegmentation.WekaSegmentation
Balance number of instances per class
balanceTrainingData() - Method in class trainableSegmentation.WekaSegmentation
Balance number of instances per class (in the loaded training data)
Ball - Class in ini.trakem2.display
 
Ball(Project, String, double, double) - Constructor for class ini.trakem2.display.Ball
 
Ball(Project, long, String, float, float, float, boolean, Color, boolean, AffineTransform) - Constructor for class ini.trakem2.display.Ball
Construct an unloaded Ball from the database.
Ball(Project, long, HashMap<String, String>, HashMap<Displayable, String>) - Constructor for class ini.trakem2.display.Ball
Construct a Ball from an XML entry.
BALL - Static variable in class script.imglib.algorithm.fn.Morph
 
BallList - Variable in class sc.fiji.balloonSegmentation.structure.BalloonPopulation
 
Balloon - Class in sc.fiji.balloonSegmentation.structure
 
Balloon(int, int, int, ImageProcessor, BalloonPopulation, int) - Constructor for class sc.fiji.balloonSegmentation.structure.Balloon
Balloon Constructor used before inflation: need initial spatial coordinates (x,y) and ID of the balloon to be given
Balloon(int[], int[], int, ImageProcessor, BalloonPopulation, int) - Constructor for class sc.fiji.balloonSegmentation.structure.Balloon
Balloon Constructor with of previously shaped structure: need list spatial coordinates (x,y) of the vertices of the envelop and ID of the balloon to be given
BalloonPopulation - Class in sc.fiji.balloonSegmentation.structure
 
BalloonPopulation(ImageProcessor, int, int) - Constructor for class sc.fiji.balloonSegmentation.structure.BalloonPopulation
BalloonPopulation constructor: need to specify the image processor it is associated with and the id of the population
BalloonSegmentation_ - Class in sc.fiji.balloonSegmentation
TODO
BalloonSegmentation_() - Constructor for class sc.fiji.balloonSegmentation.BalloonSegmentation_
 
BalloonSequence - Class in sc.fiji.balloonSegmentation.structure
 
BalloonSequence(ImagePlus) - Constructor for class sc.fiji.balloonSegmentation.structure.BalloonSequence
BalloonSequence constructor: initiate a sequence of Balloon population from a stack of images
ballRadiusMultiplier - Static variable in class tracing.SimpleNeuriteTracer
 
BAND - Static variable in class levelsets.algorithm.FastMarching
Constant for Band elements
BandElement - Class in levelsets.algorithm
Encapsulates voxel data in an object - this is important for managing voxels in collections.
BandElement(int, int, int, double) - Constructor for class levelsets.algorithm.BandElement
Constructs a new BandElement
BandElementCache - Class in levelsets.algorithm
A cache for BandElement objects - this avoids having to construct/destruct objects in algorithms that do frequent allocations/deallocations of this type (which is straining for the Java virtual machine).
BandElementCache(int) - Constructor for class levelsets.algorithm.BandElementCache
Creates a new instance of BandElementCache
Bandpass<T extends NumericType<T>> - Class in mpicbg.imglib.algorithm.fft
TODO
Bandpass(Image<T>, int, int) - Constructor for class mpicbg.imglib.algorithm.fft.Bandpass
 
BandpassFilter<T extends RealType<T>> - Class in script.imglib.algorithm
TODO
BandpassFilter(Image<T>, int, int) - Constructor for class script.imglib.algorithm.BandpassFilter
 
BandpassFilter(IFunction, int, int) - Constructor for class script.imglib.algorithm.BandpassFilter
 
BAR - Static variable in class script.imglib.algorithm.fn.Morph
 
BarChart - Class in script.imglib.analysis
TODO
BarChart(Collection<? extends Number>) - Constructor for class script.imglib.analysis.BarChart
 
BarChart(Collection<? extends Number>, String, String, String) - Constructor for class script.imglib.analysis.BarChart
 
BarChart(Map<? extends Number, ? extends Number>) - Constructor for class script.imglib.analysis.BarChart
 
BarChart(Map<? extends Number, ? extends Number>, String, String, String) - Constructor for class script.imglib.analysis.BarChart
 
baryCenter(double[], double[]) - Static method in class sholl.Sholl_Utils
Calculates the centroid of a non-self-intersecting closed polygon.
BASE_ERROR_MESSAGE - Static variable in class fiji.plugin.trackmate.detection.BlockLogDetector
 
BASE_ERROR_MESSAGE - Static variable in class fiji.plugin.trackmate.detection.DogDetector
 
BASE_ERROR_MESSAGE - Static variable in class fiji.plugin.trackmate.detection.semiauto.AbstractSemiAutoTracker
 
BASE_JAVADOC_URL - Static variable in class net.imagej.ui.swing.ops.OpFinder
 
baseArray - Variable in class fiji.util.DoubleArray
Deprecated.
 
baseArray - Variable in class fiji.util.FloatArray
Deprecated.
 
baseArray - Variable in class fiji.util.IntArray
Deprecated.
 
baseErrorMessage - Variable in class fiji.plugin.trackmate.detection.DownsampleLogDetector
 
baseErrorMessage - Variable in class fiji.plugin.trackmate.detection.LogDetector
 
baseFolder - Variable in class mpicbg.spim.io.ProgramConfiguration
 
BasePairBitType - Class in mpicbg.imglib.type.label
TODO
BasePairBitType(DirectAccessContainer<BasePairBitType, ? extends BitAccess>) - Constructor for class mpicbg.imglib.type.label.BasePairBitType
 
BasePairBitType(BasePairBitType.Base) - Constructor for class mpicbg.imglib.type.label.BasePairBitType
 
BasePairBitType() - Constructor for class mpicbg.imglib.type.label.BasePairBitType
 
BasePairBitType.Base - Enum in mpicbg.imglib.type.label
 
BasePairCharType - Class in mpicbg.imglib.type.label
TODO
BasePairCharType(DirectAccessContainer<BasePairCharType, ? extends CharAccess>) - Constructor for class mpicbg.imglib.type.label.BasePairCharType
 
BasePairCharType(BasePairBitType.Base) - Constructor for class mpicbg.imglib.type.label.BasePairCharType
 
BasePairCharType(char) - Constructor for class mpicbg.imglib.type.label.BasePairCharType
 
BasePairCharType() - Constructor for class mpicbg.imglib.type.label.BasePairCharType
 
BasePairType<T extends BasePairType<T>> - Interface in mpicbg.imglib.type
TODO
BasePairTypeDisplay<T extends BasePairType<T>> - Class in mpicbg.imglib.image.display
TODO
BasePairTypeDisplay(Image<T>) - Constructor for class mpicbg.imglib.image.display.BasePairTypeDisplay
 
basePath - Variable in class org.janelia.thickness.inference.visitor.FileSaverVisitor
 
BASEPATH_TAG - Static variable in class mpicbg.spim.data.XmlKeys
 
baseToValue() - Method in interface mpicbg.imglib.type.BasePairType
 
baseToValue() - Method in class mpicbg.imglib.type.label.BasePairBitType
 
baseToValue() - Method in class mpicbg.imglib.type.label.BasePairCharType
 
baseUrl - Variable in class bdv.img.remote.RemoteImageLoader
 
baseXfmList - Variable in class bigwarp.BigWarp
 
BasicDetectorConfigurationPanel - Class in fiji.plugin.trackmate.gui.panels.detector
 
BasicDetectorConfigurationPanel(Settings, Model, String, String) - Constructor for class fiji.plugin.trackmate.gui.panels.detector.BasicDetectorConfigurationPanel
 
BasicImgLoader - Interface in mpicbg.spim.data.generic.sequence
Provides images for a sequence.
BasicMultiResolutionImgLoader - Interface in mpicbg.spim.data.generic.sequence
A BasicImgLoader providing multiple resolutions of each image.
BasicMultiResolutionSetupImgLoader<T> - Interface in mpicbg.spim.data.generic.sequence
A BasicSetupImgLoader providing multiple resolutions of each image.
BasicParam() - Constructor for class lenscorrection.Distortion_Correction.BasicParam
 
BasicSetupImgLoader<T> - Interface in mpicbg.spim.data.generic.sequence
Provides images for one setup of a sequence.
BasicViewDescription<V extends BasicViewSetup> - Class in mpicbg.spim.data.generic.sequence
TODO
BasicViewDescription(int, int, boolean, AbstractSequenceDescription<? extends V, ?, ?>) - Constructor for class mpicbg.spim.data.generic.sequence.BasicViewDescription
TODO
BasicViewSetup - Class in mpicbg.spim.data.generic.sequence
An view setup is an Entity that may have a name, image size, and voxel size.
BasicViewSetup(int, String, Dimensions, VoxelDimensions) - Constructor for class mpicbg.spim.data.generic.sequence.BasicViewSetup
 
BasicViewSetup() - Constructor for class mpicbg.spim.data.generic.sequence.BasicViewSetup
 
Batch_Weka_Segmentation - Class in edu.utexas.archipelago.plugin
 
Batch_Weka_Segmentation() - Constructor for class edu.utexas.archipelago.plugin.Batch_Weka_Segmentation
 
BatchConverter - Class in org.imagearchive.lsm.toolbox
Batch Converter Class - Adapted from Wayne Rasband's Batch Converter plug-in.
BatchConverter(MasterModel) - Constructor for class org.imagearchive.lsm.toolbox.BatchConverter
 
BatchDialog - Class in org.imagearchive.lsm.toolbox.gui
 
BatchDialog(Object, MasterModel) - Constructor for class org.imagearchive.lsm.toolbox.gui.BatchDialog
 
BatchFilter - Class in org.imagearchive.lsm.toolbox.gui
 
BatchFilter() - Constructor for class org.imagearchive.lsm.toolbox.gui.BatchFilter
 
batchFineTune(String, String, String) - Method in class landmarks.NamePoints
 
BatchLog_ - Class in vib
 
BatchLog_() - Constructor for class vib.BatchLog_
 
BatchOpener - Class in util
This class contains methods I would like to see incorporated into HandleExtraFileTypes, or elsewhere.
BatchOpener() - Constructor for class util.BatchOpener
 
BatchOpener.ChannelsAndLoader - Class in util
A helper class to return the array of ImagePlus as well as an indication of the file loader that was used.
BatchOpener.ImageLoaderException - Exception in util
 
BatchOpener.NoSuchChannelException - Exception in util
 
batchProcessImages() - Method in class graphcut.Graph_Cut
Apply graph cut to several images
BatchWekaSegmentation - Class in edu.utexas.archipelago.segmentation
 
BatchWekaSegmentation(File, int[], int[]) - Constructor for class edu.utexas.archipelago.segmentation.BatchWekaSegmentation
 
BatchWekaSegmentation(File, int[], int[], Cluster) - Constructor for class edu.utexas.archipelago.segmentation.BatchWekaSegmentation
 
BatchWekaSegmentation.WekaSegmentationCallable - Class in edu.utexas.archipelago.segmentation
 
BayesMVDeconvolution - Class in mpicbg.spim.postprocessing.deconvolution2
 
BayesMVDeconvolution(LRInput, LRFFT.PSFTYPE, int, double, double, int, String) - Constructor for class mpicbg.spim.postprocessing.deconvolution2.BayesMVDeconvolution
 
BB - Static variable in interface ij3d.ContentConstants
 
Bbuf - Static variable in class ini.trakem2.io.ImageSaver
 
bck(int) - Method in class bigwarp.source.GridRandomAccess
 
bck(int) - Method in class bigwarp.source.GridRealRandomAccess
 
bck(int) - Method in class bigwarp.source.WarpMagnitudeRandomAccess
 
bck(int) - Method in class fiji.plugin.trackmate.detection.util.SquareNeighborhood3x3
 
bck(int) - Method in class mpicbg.imglib.cursor.array.Array3DLocalizableByDimCursor
 
bck(int) - Method in class mpicbg.imglib.cursor.array.Array3DLocalizableByDimOutOfBoundsCursor
 
bck(int) - Method in class mpicbg.imglib.cursor.array.ArrayLocalizableByDimCursor
 
bck(int) - Method in class mpicbg.imglib.cursor.array.ArrayLocalizableByDimOutOfBoundsCursor
 
bck(int) - Method in class mpicbg.imglib.cursor.cell.CellLocalizableByDimCursor
 
bck(int) - Method in class mpicbg.imglib.cursor.cell.CellLocalizableByDimOutOfBoundsCursor
 
bck(int) - Method in class mpicbg.imglib.cursor.constant.ConstantLocalizableByDimCursor
 
bck(int) - Method in class mpicbg.imglib.cursor.constant.ConstantLocalizableByDimOutOfBoundsCursor
 
bck(int) - Method in class mpicbg.imglib.cursor.dynamic.DynamicLocalizableByDimCursor
 
bck(int) - Method in class mpicbg.imglib.cursor.dynamic.DynamicLocalizableByDimOutOfBoundsCursor
 
bck(int) - Method in class mpicbg.imglib.cursor.link.GenericCursorLink
 
bck(int) - Method in class mpicbg.imglib.cursor.link.NullLink
 
bck(int) - Method in interface mpicbg.imglib.cursor.LocalizableByDim
 
bck(int) - Method in class mpicbg.imglib.cursor.planar.PlanarLocalizableByDimCursor
 
bck(int) - Method in class mpicbg.imglib.cursor.planar.PlanarLocalizableByDimOutOfBoundsCursor
 
bck(int) - Method in class mpicbg.imglib.cursor.shapelist.ShapeListLocalizableByDimCursor
 
bck(int) - Method in class mpicbg.imglib.cursor.shapelist.ShapeListLocalizableByDimOutOfBoundsCursor
 
bck(int) - Method in class spim.process.fusion.weights.BlendingRealRandomAccess
 
bck(int) - Method in class spim.process.fusion.weights.NormalizingRandomAccess
 
bck(int) - Method in class spim.process.fusion.weights.TransformedInterpolatedRealRandomAccess
 
bckX() - Method in class mpicbg.imglib.cursor.array.Array3DLocalizableByDimCursor
 
bckX() - Method in class mpicbg.imglib.cursor.array.Array3DLocalizableByDimOutOfBoundsCursor
 
bckX() - Method in interface mpicbg.imglib.cursor.LocalizableByDim3D
 
bckY() - Method in class mpicbg.imglib.cursor.array.Array3DLocalizableByDimCursor
 
bckY() - Method in class mpicbg.imglib.cursor.array.Array3DLocalizableByDimOutOfBoundsCursor
 
bckY() - Method in interface mpicbg.imglib.cursor.LocalizableByDim3D
 
bckZ() - Method in class mpicbg.imglib.cursor.array.Array3DLocalizableByDimCursor
 
bckZ() - Method in class mpicbg.imglib.cursor.array.Array3DLocalizableByDimOutOfBoundsCursor
 
bckZ() - Method in interface mpicbg.imglib.cursor.LocalizableByDim3D
 
bcomposite - Static variable in class FlowJ.FlowJSpotNoise
 
bdv - package bdv
 
Bdv - Interface in bdv.util
Something that has a BdvHandle.
bdv - Variable in class spim.fiji.spimdata.explorer.popup.BDVPopup
 
bdv.cache - package bdv.cache
 
bdv.export - package bdv.export
 
bdv.gui - package bdv.gui
 
bdv.ij - package bdv.ij
 
bdv.ij.export - package bdv.ij.export
 
bdv.ij.export.imgloader - package bdv.ij.export.imgloader
 
bdv.ij.export.tiles - package bdv.ij.export.tiles
 
bdv.ij.util - package bdv.ij.util
 
bdv.img - package bdv.img
 
bdv.img.cache - package bdv.img.cache
 
bdv.img.catmaid - package bdv.img.catmaid
 
bdv.img.hdf5 - package bdv.img.hdf5
 
bdv.img.imagestack - package bdv.img.imagestack
 
bdv.img.imaris - package bdv.img.imaris
 
bdv.img.openconnectome - package bdv.img.openconnectome
 
bdv.img.remote - package bdv.img.remote
 
bdv.img.virtualstack - package bdv.img.virtualstack
 
bdv.spimdata - package bdv.spimdata
 
bdv.spimdata.legacy - package bdv.spimdata.legacy
 
bdv.spimdata.tools - package bdv.spimdata.tools
 
bdv.tools - package bdv.tools
 
bdv.tools.bookmarks - package bdv.tools.bookmarks
 
bdv.tools.boundingbox - package bdv.tools.boundingbox
 
bdv.tools.brightness - package bdv.tools.brightness
 
bdv.tools.crop - package bdv.tools.crop
 
bdv.tools.transformation - package bdv.tools.transformation
 
bdv.util - package bdv.util
 
bdv.util.volatiles - package bdv.util.volatiles
 
bdv.viewer - package bdv.viewer
 
bdv.viewer.animate - package bdv.viewer.animate
 
bdv.viewer.overlay - package bdv.viewer.overlay
 
bdv.viewer.render - package bdv.viewer.render
 
bdv.viewer.state - package bdv.viewer.state
 
BDVChecker(BigDataViewer, Label, Label, Label) - Constructor for class spim.fiji.plugin.apply.BigDataViewerTransformationWindow.BDVChecker
 
BdvFunctions - Class in bdv.util
all show methods return a Bdv which can be used to add more stuff to the same window
BdvFunctions() - Constructor for class bdv.util.BdvFunctions
 
BdvHandle - Class in bdv.util
Represents a BigDataViewer frame or panel and can be used to get to the bdv internals.
BdvHandle(BdvOptions) - Constructor for class bdv.util.BdvHandle
 
BdvHandleFrame - Class in bdv.util
 
BdvHandlePanel - Class in bdv.util
 
BdvHandlePanel(Frame, BdvOptions) - Constructor for class bdv.util.BdvHandlePanel
 
bdvOptions - Variable in class bdv.util.BdvHandle
 
BdvOptions - Class in bdv.util
Optional parameters for BdvFunctions.
BdvOptions() - Constructor for class bdv.util.BdvOptions
 
BdvOptions.Values - Class in bdv.util
Read-only BdvOptions values.
BdvOverlay - Class in bdv.util
An overlay that can be shown with BdvFunctions.showOverlay(BdvOverlay, String, BdvOptions): This method will add a dummy Source and ConverterSetup to the BigDataViewer such that the visibility, display range, and color for the overlay can be adjusted by the user, like for a normal Source.
BdvOverlay() - Constructor for class bdv.util.BdvOverlay
 
BdvOverlaySource<O extends OverlayRenderer> - Class in bdv.util
 
BdvOverlaySource(BdvHandle, int, PlaceHolderConverterSetup, SourceAndConverter<UnsignedShortType>, PlaceHolderOverlayInfo, O) - Constructor for class bdv.util.BdvOverlaySource
 
BdvPointsSource - Class in bdv.util
 
BdvPointsSource(BdvHandle, int, PlaceHolderConverterSetup, SourceAndConverter<UnsignedShortType>, PlaceHolderOverlayInfo, PointsOverlay) - Constructor for class bdv.util.BdvPointsSource
 
BDVPopup - Class in spim.fiji.spimdata.explorer.popup
 
BDVPopup() - Constructor for class spim.fiji.spimdata.explorer.popup.BDVPopup
 
bdvPopup() - Static method in class spim.fiji.spimdata.explorer.ViewSetupExplorerPanel
 
BDVPopup.MyActionListener - Class in spim.fiji.spimdata.explorer.popup
 
bdvRunning() - Static method in class spim.fiji.spimdata.explorer.popup.BDVPopup
 
BdvSource - Class in bdv.util
 
BdvSource(BdvHandle, int) - Constructor for class bdv.util.BdvSource
 
bdvSources - Variable in class bdv.util.BdvHandle
 
BdvStackSource<T> - Class in bdv.util
 
BdvStackSource(BdvHandle, int, T, List<ConverterSetup>, List<SourceAndConverter<T>>) - Constructor for class bdv.util.BdvStackSource
 
BdvVirtualChannelSource - Class in bdv.util
 
BdvVirtualChannelSource(BdvHandle, int, PlaceHolderConverterSetup, SourceAndConverter<ARGBType>, PlaceHolderOverlayInfo, VirtualChannels.ChannelSourceCoordinator) - Constructor for class bdv.util.BdvVirtualChannelSource
 
Bead - Class in mpicbg.spim.registration.bead
 
Bead(int, Point3d, ViewDataBeads) - Constructor for class mpicbg.spim.registration.bead.Bead
 
Bead(int, double[], ViewDataBeads) - Constructor for class mpicbg.spim.registration.bead.Bead
 
Bead_Registration - Class in fiji.plugin
 
Bead_Registration() - Constructor for class fiji.plugin.Bead_Registration
 
beadBrightness - Static variable in class fiji.plugin.Bead_Registration
 
beadColor - Static variable in class mpicbg.spim.vis3d.VisualizeBeads
 
BeadIdentification - Class in mpicbg.spim.registration.bead
 
BeadIdentification(Bead) - Constructor for class mpicbg.spim.registration.bead.BeadIdentification
 
BeadIdentification(int, ViewDataBeads) - Constructor for class mpicbg.spim.registration.bead.BeadIdentification
 
beadRegister - Variable in class mpicbg.spim.registration.ViewStructure
The object that handles registration
BeadRegistration - Class in mpicbg.spim.registration.bead
 
BeadRegistration(ViewStructure) - Constructor for class mpicbg.spim.registration.bead.BeadRegistration
Instantiates the object with a certain ViewStructure it is working on when using non-static method calls
beads - Variable in class mpicbg.spim.registration.ViewDataBeads
The Object for storing the potential beads
beadSegment - Variable in class mpicbg.spim.registration.ViewStructure
The object that handles segmentation
BeadSegmentation - Class in mpicbg.spim.registration.bead
 
BeadSegmentation(ViewStructure) - Constructor for class mpicbg.spim.registration.bead.BeadSegmentation
 
beadSize - Static variable in class mpicbg.spim.vis3d.VisualizeBeads
 
BeadStructure - Class in mpicbg.spim.registration.bead
 
BeadStructure() - Constructor for class mpicbg.spim.registration.bead.