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# Classes and Interfaces in #Fiji - 3580 results found.
NameDescriptionTypePackageFrameworkJavaDoc
A_Image5D_testClassFijijavadoc
AbortThrowing an instance of this class causes (silent) termination of the main compiler method.Classcom.sun.tools.javac.utilFijijavadoc
AboutDisplays a small information dialog about the Bio-Formats Plugins package.Classloci.pluginsFijijavadoc
About_RATSClassFijijavadoc
AboutDialogClassedfguiFijijavadoc
AboutDialogClassorg.imagearchive.lsm.toolbox.guiFijijavadoc
AbsClassimglib.ops.operator.unaryFijijavadoc
AbsClassscript.imglib.mathFijijavadoc
AbstractAffine3DClassscript.imglib.algorithm.fnFijijavadoc
AbstractAffineModelChunkClassedu.utexas.clm.archipelago.ijsupportFijijavadoc
AbstractAffineTile2DClassmpicbg.trakem2.alignFijijavadoc
AbstractAnimatorMother abstract class for animators that can animate the current view in a ViewerFrame instance.Classbdv.viewer.animateFijijavadoc
AbstractAnnotationAbstract class dedicated to draw overlayed annotations on a OverlayedImageCanvas.Classfiji.util.guiFijijavadoc
AbstractAnnotationValueVisitor6A skeletal visitor for annotation values with default behavior appropriate for the RELEASE_6Classjavax.lang.model.utilFijijavadoc
AbstractBlockMatchingClassmpicbg.ij.pluginFijijavadoc
AbstractDetectionClassmpicbg.spim.registration.detectionFijijavadoc
AbstractDialogClassedfguiFijijavadoc
AbstractEdfAlgorithmClassedfFijijavadoc
AbstractElementVisitor6A skeletal visitor of program elements with default behavior appropriate for the RELEASE_6Classjavax.lang.model.utilFijijavadoc
AbstractFeatureGrapherClassfiji.plugin.trackmate.featuresFijijavadoc
AbstractImgFactoryImgLoaderClassspim.fiji.spimdata.imgloadersFijijavadoc
AbstractImgLoaderClassspim.fiji.spimdata.imgloadersFijijavadoc
AbstractLayerAlignmentParamClassmpicbg.trakem2.alignFijijavadoc
AbstractLegacyViewerImgLoaderClassbdv.spimdata.legacyFijijavadoc

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AbstractNamedActionClassbdv.utilFijijavadoc
AbstractNormalizeClassscript.imglib.algorithm.fnFijijavadoc
AbstractOffscreenThreadTo be used in combination with the AbstractRepaintThread, as a thread to create graphics offscreen.Classini.trakem2.displayFijijavadoc
AbstractPanorama_ViewClassmpicbg.panoramaFijijavadoc
AbstractPointDescriptorClassmpicbg.pointdescriptorFijijavadoc
AbstractProcessorAn abstract annotation processor designed to be a convenient superclass for most concrete annotation processors.Classjavax.annotation.processingFijijavadoc
AbstractProviderClassfiji.plugin.trackmate.providersFijijavadoc
AbstractRegionalExtremaFinderClassmpicbg.imglib.algorithm.extremafinderFijijavadoc
AbstractRepaintThreadClassini.trakem2.displayFijijavadoc
AbstractSemiAutoTrackerA class made to perform semi-automated tracking of spots in TrackMate & The user has to select one spot, one a meaningful location.Classfiji.plugin.trackmate.detection.semiautoFijijavadoc
AbstractSequenceDescriptionA SPIM sequence consisting of a list of timepoints and a list of view setups.Classmpicbg.spim.data.generic.sequenceFijijavadoc
AbstractSequenceDescriptionUtilsClassmpicbg.spim.data.generic.sequenceFijijavadoc
AbstractSortedGrayLevelIteratorIterate over all pixels ordered by their gray levelAuthor:Steffen Jaensch, Steffen Jaensch Classmpicbg.imglib.cursor.specialFijijavadoc
AbstractSpecialCursorThis abstract cursor offer facilities for specialized cursor that are based on a LocalizableByDimCursor whose iteration domain is imposed.Classmpicbg.imglib.cursor.specialFijijavadoc
AbstractSpimDataClassmpicbg.spim.data.genericFijijavadoc
AbstractSpimSourceClassbdvFijijavadoc
AbstractTMActionClassfiji.plugin.trackmate.actionFijijavadoc
AbstractToolClassfiji.toolFijijavadoc
AbstractTrackingToolClassfiji.toolFijijavadoc
AbstractTrackMateModelViewAn abstract class for spot displayers, that can overlay detected spots and tracks on top of the image data.Classfiji.plugin.trackmate.visualizationFijijavadoc
AbstractTransformAnimatorMother abstract class for animators that animate the current view in a ViewerFrame instance by modifying the viewer transform.Classbdv.viewer.animateFijijavadoc
AbstractTreeTransferHandlerAdapted from freely available code by DeuDeu from http://forum.Classini.trakem2.treeFijijavadoc
AbstractTypeVisitor6A skeletal visitor of types with default behavior appropriate for the version 6 language level.Classjavax.lang.model.utilFijijavadoc
AbstractVectorClassmpicbg.imglib.cursor.vectorFijijavadoc
AbstractViewerSetupImgLoaderClassbdvFijijavadoc

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AbstractVolatileArrayA ShortArray with an isValid() flag.Classnet.imglib2.img.basictypeaccess.volatiles.arrayFijijavadoc
AbstractVolatileNativeNumericTypeAbstract base class for VolatileNumericTypes that wrap native NumericTypes.Classnet.imglib2.type.volatilesFijijavadoc
AbstractVolatileNativeRealTypeAbstract base class for VolatileRealTypes that wrapAuthor:Tobias Pietzsch Classnet.imglib2.type.volatilesFijijavadoc
Access Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandInterfaceimagewareFijijavadoc
AccumulateProjectorClassbdv.viewer.renderFijijavadoc
AccumulateProjectorARGBClassbdv.viewer.renderFijijavadoc
AccumulateProjectorFactoryInterfacebdv.viewer.renderFijijavadoc
AccumulatorA class allowing an easy accumulation of values visited by a TwinCursor.ClassalgorithmsFijijavadoc
ACosClassscript.imglib.mathFijijavadoc
ActionChooserDescriptorClassfiji.plugin.trackmate.gui.descriptorsFijijavadoc
ActionChooserPanelClassfiji.plugin.trackmate.gui.panelsFijijavadoc
ActionListenablePanelClassfiji.plugin.trackmate.gui.panelsFijijavadoc
ActionProviderClassfiji.plugin.trackmate.providersFijijavadoc
ActiveContours This class provides the getDeltaPhi function to the SparseFieldLevelSet: deltaPhi = - DELTA_T * image_term * (advection * ADVECTION_FORCE + curvature * CURVATURE_EPSILON)Classlevelsets.algorithmFijijavadoc
AdapterThis class just hands off to the ImageJ Updater The Fiji Updater moved to a new home: ImageJ2.Classfiji.updaterFijijavadoc
AdaptiveNonMaximalSuppressionClassmpicbg.imglib.algorithm.scalespaceFijijavadoc
AddClassimglib.ops.operator.binaryFijijavadoc
AddClassscript.imglib.mathFijijavadoc
Add_Empty_ChannelClassFijijavadoc
Add_Empty_FrameClassvideo2Fijijavadoc
Add_Empty_SliceClassFijijavadoc
AddARGBCompositeClassini.trakem2.display.graphicsFijijavadoc
AddConstantClassimglib.ops.operator.unaryFijijavadoc
AddNoiseClassimglib.ops.operator.unaryFijijavadoc
AdjustInputClassmpicbg.spim.postprocessing.deconvolution2Fijijavadoc

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AdjustInputClassspim.process.fusion.deconvolutionFijijavadoc
AdvancedDialogClassedfguiFijijavadoc
AffineAffine transforms an image using different interpolation schemes.Classimagescience.transformFijijavadoc
Affine2DClassscript.imglib.algorithmFijijavadoc
Affine3DPerforms a mathematically correct transformation of an image.Classscript.imglib.algorithmFijijavadoc
Affine3DHelpersHelpers to extract parts (rotation, scale, etc) from AffineTransform3D.Classbdv.utilFijijavadoc
Affine_From_LandmarksClasslandmarksFijijavadoc
AffineFromLandmarksClasslandmarksFijijavadoc
AffineModel2DClassmpicbg.trakem2.transformFijijavadoc
AffineModel3DClassmpicbg.trakem2.transformFijijavadoc
AffineTile2DClassmpicbg.trakem2.alignFijijavadoc
AffineTransform3DJsonSerializerClassbdv.img.remoteFijijavadoc
AffineTransformModeClassini.trakem2.displayFijijavadoc
Albert_TestClasstracingFijijavadoc
AlgorithmAn algorithm is an abstraction of techniques like the calculation of the Persons coefficient or Li'S ICQ.ClassalgorithmsFijijavadoc
AlgorithmInterfacempicbg.imglib.algorithmFijijavadoc
AlgorithmUtilClassscript.imglib.algorithm.fnFijijavadoc
AlignA collection of methods regarding SIFT-based alignment TODO Bring the methods and tasks into a class for each method and clean up this mess.Classmpicbg.trakem2.alignFijijavadoc
Align_ImageSelect two images with a Line ROI in each, and rotate/translate/scale one to Stacks are not explicitly supported, but a macro can easily use this pluginClassFijijavadoc
AlignLayersTaskRegister a range of layers using linear or non-linear transformations.Classmpicbg.trakem2.alignFijijavadoc
AlignmentUtilsClassmpicbg.trakem2.alignFijijavadoc
AlignTaskMethods collection to be called from the GUI for alignment tasks.Classmpicbg.trakem2.alignFijijavadoc
AllConnectedComponentsLabel all 8-connected components of a binary imageAuthor:Lee KamentskyClassmpicbg.imglib.algorithm.labelingFijijavadoc
AllKnownFilterClassorg.imagearchive.lsm.toolbox.guiFijijavadoc
AllToAllRegistrationClassspim.process.interestpointregistration.optimizationtypesFijijavadoc

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AllToAllRegistrationWithRangeClassspim.process.interestpointregistration.optimizationtypesFijijavadoc
AlphaClassscript.imglib.colorFijijavadoc
AlphanumComparatorThe Alphanum Algorithm is an improved sorting algorithm for strings containing numbers.Classfiji.plugin.trackmate.utilFijijavadoc
AlternateViewerClassview5dFijijavadoc
AmiraImporterParses an amira labelfield and imports the labels as AreaList instances into the project tree.Classini.trakem2.ioFijijavadoc
AmiraMeshDecoderClassamiraFijijavadoc
AmiraMeshEncoderClassamiraFijijavadoc
AmiraMeshReader_ClassFijijavadoc
AmiraMeshWriter_ClassFijijavadoc
AmiraParametersClassamiraFijijavadoc
AmiraSurfaceClassisosurfaceFijijavadoc
AmiraTableClassamiraFijijavadoc
AmiraTableEncoderClassamiraFijijavadoc
AmiraTableWriter_ClassFijijavadoc
Analyse_ParticlesThis plugin detectes sub-diffraction particles in a sequence of images, it is the main plugin for the QuickPALM package.ClassQuickPALMFijijavadoc
Analyze_ReaderThis plugin loads Analyze format files.ClassFijijavadoc
Analyze_WriterClassFijijavadoc
AnalyzeSkeleton_Main class of the ImageJ/Fiji plugin for skeleton analysis.Classsc.fiji.analyzeSkeletonFijijavadoc
AnalyzeTracings_ClasstracingFijijavadoc
AndClassimglib.ops.conditionFijijavadoc
AndClassimglib.ops.operator.binaryFijijavadoc
AndClassscript.imglib.mathFijijavadoc
AndConstantClassimglib.ops.operator.unaryFijijavadoc
AnElementClassview5dFijijavadoc
AngleDefines an angle which is part of the ViewSetup.Classmpicbg.spim.data.sequenceFijijavadoc

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Animated_Gif_ReaderClassioFijijavadoc
Anisotropic_Diffusion_2DClassanisotropic_diffusionFijijavadoc
AnisotropicDiffusionPerona & Malik Anisotropic diffusion This algorithm implements the so-called anisotropic diffusion scheme of Perona & Malik, 1990,Classmpicbg.imglib.algorithm.pdeFijijavadoc
AnnotateEnter annotations on symbols.Classcom.sun.tools.javac.compFijijavadoc
AnnotationMirrorRepresents an annotation.Interfacejavax.lang.model.elementFijijavadoc
AnnotationProcessingErrorError thrown for problems encountered during annotation processing.Classcom.sun.tools.javac.processingFijijavadoc
AnnotationProxyMakerA generator of dynamic proxy implementations of java.Classcom.sun.tools.javac.modelFijijavadoc
AnnotationTreeA tree node for an annotation.Interfacecom.sun.source.treeFijijavadoc
AnnotationValueRepresents a value of an annotation type element.Interfacejavax.lang.model.elementFijijavadoc
AnnotationValueVisitorA visitor of the values of annotation type elements, using a variant of the visitor design pattern.Interfacejavax.lang.model.elementFijijavadoc
APNGTranslatorContainer class for translators between OME and APNG formats.Classio.scif.ome.translatorsFijijavadoc
AppearanceCreatorClassoctreeFijijavadoc
AppearanceCreatorThis class is a helper class whose main task is to create Appearance objects for a specified axis and direction.ClassvoltexFijijavadoc
AppendSpimData2Classspim.process.fusion.exportFijijavadoc
AppendSpimData2HDF5Classspim.process.fusion.exportFijijavadoc
Apply_External_TransformationClassfiji.pluginFijijavadoc
Apply_TransformationClassspim.fiji.pluginFijijavadoc
ApplyParametersClassspim.fiji.plugin.applyFijijavadoc
ApplyTransformationPopupClassspim.fiji.spimdata.explorer.popupFijijavadoc
ArchipelagoClientClassedu.utexas.clm.archipelago.network.clientFijijavadoc
ArchipelagoFutureClassedu.utexas.clm.archipelago.computeFijijavadoc
ArchipelagoServerClassedu.utexas.clm.archipelago.network.serverFijijavadoc
ArchipelagoUIInterfaceedu.utexas.clm.archipelago.uiFijijavadoc
ArchipelagoUtilsClassedu.utexas.archipelagoFijijavadoc
ArchiveClientClassclientFijijavadoc

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AreaCalculationsClassfiji.geomFijijavadoc
AreaContainerInterfaceini.trakem2.displayFijijavadoc
AreaListA list of brush painted areas similar to a set of labelfields in Amira.Classini.trakem2.displayFijijavadoc
AreaList_CropClassedu.utexas.clm.cropFijijavadoc
AreaListCropClassedu.utexas.clm.cropFijijavadoc
AreaListVolumeWraps a list of Areas to be triangulated.Classij3dFijijavadoc
AreaTreeClassini.trakem2.displayFijijavadoc
AreaUtilsClassini.trakem2.utilsFijijavadoc
AreaWrapperClassini.trakem2.displayFijijavadoc
ArrayClassmpicbg.imglib.container.arrayFijijavadoc
Array3DClassmpicbg.imglib.container.arrayFijijavadoc
Array3DLocalizableByDimCursorClassmpicbg.imglib.cursor.arrayFijijavadoc
Array3DLocalizableByDimOutOfBoundsCursorClassmpicbg.imglib.cursor.arrayFijijavadoc
Array3DLocalizableCursorClassmpicbg.imglib.cursor.arrayFijijavadoc
ArrayAccessTreeA tree node for an array access expression.Interfacecom.sun.source.treeFijijavadoc
ArrayBaseClassfiji.utilFijijavadoc
ArrayContainerFactoryClassmpicbg.imglib.container.arrayFijijavadoc
ArrayConverter Copyright: Copyright (c) 2006Version:1.Classmpi.fruitfly.generalFijijavadoc
ArrayCursorClassmpicbg.imglib.cursor.arrayFijijavadoc
ArrayDataAccessInterfacempicbg.imglib.container.basictypecontainer.arrayFijijavadoc
ArrayLocalizableByDimCursorClassmpicbg.imglib.cursor.arrayFijijavadoc
ArrayLocalizableByDimOutOfBoundsCursorClassmpicbg.imglib.cursor.arrayFijijavadoc
ArrayLocalizableCursorClassmpicbg.imglib.cursor.arrayFijijavadoc
ArrayLocalizablePlaneCursorClassmpicbg.imglib.cursor.arrayFijijavadoc
ArrayTypeRepresents an array type.Interfacejavax.lang.model.typeFijijavadoc

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ArrayTypeTreeA tree node for an array type.Interfacecom.sun.source.treeFijijavadoc
ArrowClassutilFijijavadoc
ArrowDisplayerInterfaceutilFijijavadoc
ArrowOptionPanelClassfiji.utilFijijavadoc
ArrowShapeClassfiji.utilFijijavadoc
ArrowTool This plugin aims at being a convenient interactive tool for drawing arrow shape on ImageJ windows.Classfiji.utilFijijavadoc
ASinClassscript.imglib.mathFijijavadoc
AspectsContains aspect ratio or size information of up to 5D image elements.Classimagescience.imageFijijavadoc
AssertTreeA tree node for an 'assert' statement.Interfacecom.sun.source.treeFijijavadoc
AssignmentAlgorithmJust in case I want to try more than one implementation of the assignment algorithm.Interfacefiji.plugin.trackmate.tracking.oldlap.hungarianFijijavadoc
AssignmentProblemAn implementation of this: http://en.Classfiji.plugin.trackmate.tracking.oldlap.hungarianFijijavadoc
AssignmentTreeA tree node for an assignment expression.Interfacecom.sun.source.treeFijijavadoc
AssignOperationAn AssignOperation computes values in an output image.Classimglib.ops.operationFijijavadoc
ATanClassscript.imglib.mathFijijavadoc
ATan2Classscript.imglib.mathFijijavadoc
AttrThis is the main context-dependent analysis phase in GJC.Classcom.sun.tools.javac.compFijijavadoc
AttrContextContains information specific to the attribute and enter passes, to be used in place of the generic field in environments.Classcom.sun.tools.javac.compFijijavadoc
AttrContextEnvEnv specialized as Env This is NOT part of any supported API.Classcom.sun.tools.javac.compFijijavadoc
AttributeAn annotation value.Classcom.sun.tools.javac.codeFijijavadoc
AugmentedLandmarkWarp_ClassvibFijijavadoc
AuthenticationExceptionClassedu.utexas.clm.archipelago.exceptionFijijavadoc
Auto_Local_ThresholdClassfiji.thresholdFijijavadoc
Auto_ThresholdClassfiji.thresholdFijijavadoc
Auto_TracerClasstracingFijijavadoc
AutoLabellerClassoldsegmentersFijijavadoc

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AutoLabellerNaiveClassoldsegmentersFijijavadoc
AutomaticAngleSetupClassmpicbg.spim.preprocessingFijijavadoc
AutomaticBoundingBoxClassspim.process.fusion.boundingboxFijijavadoc
AutomaticReorientationClassspim.process.fusion.boundingboxFijijavadoc
AutoPointClasstracingFijijavadoc
AutoSearchThreadClasstracingFijijavadoc
AutoThresholdRegressionA class implementing the automatic finding of a threshold used for Person colocalisation calculation.ClassalgorithmsFijijavadoc
AutoTracerCanvasClasstracingFijijavadoc
AverageClassimglib.ops.operator.binaryFijijavadoc
AverageClassscript.imglib.mathFijijavadoc
Average_ColorClassFijijavadoc
Average_ImagesClassvibFijijavadoc
Average_Torsten_ResultsClassutilFijijavadoc
AverageBrainClassvib.app.moduleFijijavadoc
AverageBrain_ClassvibFijijavadoc
AverageContentClassmpicbg.spim.fusionFijijavadoc
AverageContentFactoryClassmpicbg.spim.fusionFijijavadoc
AveragePixelFusionClassmpicbg.stitching.fusionFijijavadoc
AveragePixelFusionIgnoreZeroClassmpicbg.stitching.fusionFijijavadoc
AvgFunctionClassimglib.ops.function.pnFijijavadoc
AxesContains information about the activity of the coordinate axes of up to 5D image data objects.Classimagescience.imageFijijavadoc
AxisConstantsThis interface stores some common constants.Interfaceij3dFijijavadoc
AxisLessThanClassimglib.ops.conditionFijijavadoc
BallClassini.trakem2.displayFijijavadoc
BalloonClassballoonstructureFijijavadoc

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BalloonPopulationClassballoonstructureFijijavadoc
BalloonSegmentation_ClassFijijavadoc
BalloonSequenceClassballoonstructureFijijavadoc
BandElementClasslevelsets.algorithmFijijavadoc
BandElementCacheA cache for BandElement objects - this avoids having to construct/destruct objects in algorithms that do frequent allocations/deallocations of thisClasslevelsets.algorithmFijijavadoc
BandpassClassmpicbg.imglib.algorithm.fftFijijavadoc
BandpassFilterClassscript.imglib.algorithmFijijavadoc
BarChartClassscript.imglib.analysisFijijavadoc
BaseFileManagerUtility methods for building a filemanager.Classcom.sun.tools.javac.utilFijijavadoc
BaseFileObjectThis is NOT part of any supported API.Classcom.sun.tools.javac.fileFijijavadoc
BasePairBitTypeClassmpicbg.imglib.type.labelFijijavadoc
BasePairCharTypeClassmpicbg.imglib.type.labelFijijavadoc
BasePairTypeInterfacempicbg.imglib.typeFijijavadoc
BasePairTypeDisplayClassmpicbg.imglib.image.displayFijijavadoc
BasicDetectorConfigurationPanelClassfiji.plugin.trackmate.gui.panels.detectorFijijavadoc
BasicDialogClassedfguiFijijavadoc
BasicImgLoaderProvides images for a sequence.Interfacempicbg.spim.data.generic.sequenceFijijavadoc
BasicMultiResolutionImgLoaderA BasicImgLoader providing multiple resolutions of each image.Interfacempicbg.spim.data.generic.sequenceFijijavadoc
BasicMultiResolutionSetupImgLoaderA BasicSetupImgLoader providing multiple resolutions of each image.Interfacempicbg.spim.data.generic.sequenceFijijavadoc
BasicSetupImgLoaderProvides images for one setup of aAuthor:Tobias Pietzsch Interfacempicbg.spim.data.generic.sequenceFijijavadoc
BasicViewDescriptionClassmpicbg.spim.data.generic.sequenceFijijavadoc
BasicViewSetupAn view setup is an Entity that may have a name, image size, and voxel size.Classmpicbg.spim.data.generic.sequenceFijijavadoc
Batch_Weka_SegmentationClassedu.utexas.archipelago.pluginFijijavadoc
BatchConverterBatch Converter Class - Adapted from Wayne Rasband's Batch Converter plug-in.Classorg.imagearchive.lsm.toolboxFijijavadoc
BatchDialogClassorg.imagearchive.lsm.toolbox.guiFijijavadoc

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BatchFilterClassorg.imagearchive.lsm.toolbox.guiFijijavadoc
BatchLog_ClassvibFijijavadoc
BatchOpenerThis class contains methods I would like to see incorporated into HandleExtraFileTypes, or elsewhere.ClassutilFijijavadoc
BatchWekaSegmentationClassedu.utexas.archipelago.segmentationFijijavadoc
BayesMVDeconvolutionClassmpicbg.spim.postprocessing.deconvolution2Fijijavadoc
BDVPopupClassspim.fiji.spimdata.explorer.popupFijijavadoc
BeadClassmpicbg.spim.registration.beadFijijavadoc
Bead_RegistrationClassfiji.pluginFijijavadoc
BeadIdentificationClassmpicbg.spim.registration.beadFijijavadoc
BeadRegistrationClassmpicbg.spim.registration.beadFijijavadoc
BeadSegmentationClassmpicbg.spim.registration.beadFijijavadoc
BeadStructureClassmpicbg.spim.registration.beadFijijavadoc
BeadTransformGroupClassmpicbg.spim.vis3dFijijavadoc
BeamSplitterClassorg.imagearchive.lsm.toolbox.info.scaninfoFijijavadoc
BeaudetxThis class implements Beaudet differentiation in x direction.ClassvolumeFijijavadoc
BehaviorCallbackInterfaceij3d.behaviorsFijijavadoc
BenchmarkInterfacempicbg.imglib.algorithmFijijavadoc
BenchmarkAlgorithmThis is a convenience implementation of an algorithm that implements Benchmark and Algorithm so that less code has to be re-implemented.Classmpicbg.imglib.algorithmFijijavadoc
BenesNamedPointClassvibFijijavadoc
BEPBBinBoundariesInferenceClassinferenceFijijavadoc
BEPBInferenceClassinferenceFijijavadoc
BEPBModelInferenceClassinferenceFijijavadoc
BFMiscellaneous plugins utility methods.Classloci.pluginsFijijavadoc
BFVirtualStackSubclass of VirtualStack that uses Bio-Formats to read planes on demand.Classloci.plugins.utilFijijavadoc
BigBrotherSupervise all threads, and report uncaught exceptions.Classini.trakem2.utilsFijijavadoc

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BigDataBrowserPlugInClassbdv.ijFijijavadoc
BigDataViewerClassbdvFijijavadoc
BigDataViewerActionsClassbdvFijijavadoc
BigDataViewerBoundingBoxClassspim.process.fusion.boundingboxFijijavadoc
BigDataViewerPlugInClassbdv.ijFijijavadoc
BigDataViewerTransformationWindowClassspim.fiji.plugin.applyFijijavadoc
BIJfftThis class implements a one-dimensional real->complex fast fourier transform Copyright (c) 1999-2004, Michael Abramoff.ClassbijnumFijijavadoc
BIJfhtThis class implements the fast Hartley transform on matrices and vectors (real float matrices).ClassbijnumFijijavadoc
BIJfitThis class implements useful linear and polynomial regression Press, Flannery, Teukolsky, Vetterling, Numerical Recipes in C 2nd ed, Cambridge University Press, 1986ClassbijnumFijijavadoc
BIJfunctionsThis class implements useful numerical functions from Press, Flannery, Teukolsky, Vetterling, Numerical Recipes in C 2nd ed, Cambridge University Press, 1986ClassbijnumFijijavadoc
BIJgifa Does a maximization of images with maximum signal power and signal to noise ratio.ClassbijnumFijijavadoc
BIJJacobiThis class implements the jacobi function as a Java class.ClassbijnumFijijavadoc
BIJknnk Nearest Neighborhood (brute-force) implementation.ClassbijnumFijijavadoc
BIJmatrix eigenvectors and others.ClassbijnumFijijavadoc
BIJmiMutual infromation processing routines.ClassbijnumFijijavadoc
BIJpcaPrincipal component analysis (PCA) on 2-D sequences (ie.ClassbijnumFijijavadoc
BIJpowellThis class implements Powell's multidimensional optimization.ClassbijnumFijijavadoc
BIJShortMatrix Simplified subset of BIJmatrix.ClassbijnumFijijavadoc
BIJstatsBIJ statistical methods inherited from MatLab.ClassbijnumFijijavadoc
BIJtransformThis class implements static transformation matrix operations for 2-D and 3-D transformation matrices.ClassbijnumFijijavadoc
BIJutilUtilities to link BIJ things to ImageJ.ClassbijnumFijijavadoc
Bilateral_FilterClassFijijavadoc
BilateralFilterClassvibFijijavadoc
Binary_to_Point_SelectionThis is a template for a plugin that requires one image to be opened, and takes it as parameter.Classfiji.selectionFijijavadoc
BinaryInterpolation2DGiven two binary images of the same dimensions, generate an interpolated image that sits somewhereClassini.trakem2.imagingFijijavadoc

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BinaryInterpolation2DGiven two binary images of the same dimensions, generate an interpolated image that sits somewhereClassmpicbg.imglib.algorithm.labelingFijijavadoc
BinaryInterpolatorClassvibFijijavadoc
BinaryOperationClassscript.imglib.math.fnFijijavadoc
BinaryOperatorInterfaceimglib.ops.operatorFijijavadoc
BinaryOperatorFunctionClassimglib.ops.function.p2Fijijavadoc
BinaryTreeA tree node for a binary expression.Interfacecom.sun.source.treeFijijavadoc
BinBoundariesComputationClassinferenceFijijavadoc
BinBoundariesInferenceClassinferenceFijijavadoc
BinClassificationInferenceClassinferenceFijijavadoc
BinomialBinomial coefficientsVersion:$Id: Binomial.Classpal.mathFijijavadoc
BinomialGeneratorBinomial random number generator.Classimagescience.randomFijijavadoc
BioFormatsFormatWraps an ImageReader in a SCIFIO Format, allowing proprietary Bio-Formats readers to be used in SCIFIO-based applications.Classio.scif.bfFijijavadoc
BioFormatsTranslatorContainer class for translators between BioFormats and OME formats.Classio.scif.bf.omeFijijavadoc
Biorad_ReaderImports a Z series(image stack) from a Biorad MRC 600 confocal microscope.ClassFijijavadoc
Biorad_WriterClassFijijavadoc
BisectionStepperTry to converge a threshold based on an update value condition.ClassalgorithmsFijijavadoc
BitAccessInterfacempicbg.imglib.container.basictypecontainerFijijavadoc
BitArrayClassmpicbg.imglib.container.basictypecontainer.arrayFijijavadoc
BitDynamicContainerClassmpicbg.imglib.container.dynamicFijijavadoc
BitDynamicContainerAccessorClassmpicbg.imglib.container.dynamicFijijavadoc
BitsA class for extensible, mutable bit sets.Classcom.sun.tools.javac.utilFijijavadoc
BitStreamReadClasscustomnode.u3dFijijavadoc
BitStreamWriteClasscustomnode.u3dFijijavadoc
BitTypeClassmpicbg.imglib.type.logicFijijavadoc
BitTypeDisplayClassmpicbg.imglib.image.displayFijijavadoc

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BlasClassbijnumFijijavadoc
BleachCorrectionClassemblcmciFijijavadoc
BleachCorrection_ExpoFitClassemblcmciFijijavadoc
BleachCorrection_MHClassemblcmciFijijavadoc
BleachCorrection_SimpleRatioClassemblcmciFijijavadoc
BlendingUtility functions for blending images together, to remove contrast seams.Classini.trakem2.imagingFijijavadoc
BlendingClassmpicbg.spim.fusionFijijavadoc
BlendingRealRandomAccess that computed cosine-blending for a certain intervalAuthor:Stephan Preibisch (stephan.Classspim.process.fusion.weightsFijijavadoc
BlendingFactoryClassmpicbg.spim.fusionFijijavadoc
BlendingPixelFusionClassmpicbg.stitching.fusionFijijavadoc
BlendingPixelFusionIgnoreZeroClassmpicbg.stitching.fusionFijijavadoc
BlendingRealRandomAccessClassspim.process.fusion.weightsFijijavadoc
BlendingSimpleClassmpicbg.spim.fusionFijijavadoc
BlendingSimpleFactoryClassmpicbg.spim.fusionFijijavadoc
Blob_Segmentation_in_3DA mouse listener for point-and-click segmentation and measurement of pixel clouds in an Image3DUniverse.Classij3d.segmentationFijijavadoc
BlockClassmpicbg.spim.postprocessing.deconvolution2Fijijavadoc
BlockClassspim.process.cudaFijijavadoc
BlockGeneratorInterfacespim.process.cudaFijijavadoc
BlockGeneratorFixedSizePreciseClassspim.process.cudaFijijavadoc
BlockGeneratorVariableSizePreciseThis BlockGenerator cares that the overlap within the image is accounted for and that an outofbounds strategy is taken into account.Classspim.process.cudaFijijavadoc
BlockGeneratorVariableSizeSimpleThis BlockGenerator only cares that the overlap within the image is accounted for, not about an outofbounds strategy.Classspim.process.cudaFijijavadoc
BlockingFetchQueuesQueueing structure (intended for cells to be fetched).Classbdv.img.cacheFijijavadoc
BlockLogDetectorClassfiji.plugin.trackmate.detectionFijijavadoc
BlockLogDetectorConfigurationPanelClassfiji.plugin.trackmate.gui.panels.detectorFijijavadoc
BlockLogDetectorFactoryClassfiji.plugin.trackmate.detectionFijijavadoc

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BlockMatching_ExtractPoinRoiClassmpicbg.ij.pluginFijijavadoc
BlockMatching_TestParametersClassmpicbg.ij.pluginFijijavadoc
BlockMatchPairCallableClassmpicbg.trakem2.align.concurrentFijijavadoc
BlockTreeA tree node for a statement block.Interfacecom.sun.source.treeFijijavadoc
BlueClassscript.imglib.colorFijijavadoc
BMPConstantsProvides constants used with BMP format.Classnet.sf.image4j.codec.bmpFijijavadoc
BMPDecoderDecodes images in BMP format.Classnet.sf.image4j.codec.bmpFijijavadoc
BMPEncoderEncodes images in BMP format.Classnet.sf.image4j.codec.bmpFijijavadoc
BMPImageContains a decoded BMP image, as well as information about the source encoded image.Classnet.sf.image4j.codec.bmpFijijavadoc
BMPTranslatorContainer class for translators between OME and BMP formats.Classio.scif.ome.translatorsFijijavadoc
BookmarksClassbdv.tools.bookmarksFijijavadoc
BookmarksEditorClassbdv.tools.bookmarksFijijavadoc
BookmarkTextOverlayAnimatorDraw one line of text in the center or bottom right of the display.Classbdv.tools.bookmarksFijijavadoc
BooksteinClassmath3dFijijavadoc
Bookstein_From_LandmarksClasslandmarksFijijavadoc
BooksteinFromLandmarksClasslandmarksFijijavadoc
BooksteinTransformClassvib.transformsFijijavadoc
BooleanOptionA boolean option for one of the plugins.Classloci.plugins.prefsFijijavadoc
BooleanTypeInterfacempicbg.imglib.typeFijijavadoc
BootstrapBootstrap the ImageJ UpdaterAuthor:Johannes SchindelinClassfiji.updaterFijijavadoc
BorderBorder - draws a configurable borderAuthor:DTAI, IncorporatedClassvib.segmentFijijavadoc
BorderPanelA panel with a border and an optional title.ClassFijijavadoc
BordersContains the dimensions of the borders of up to 5D image data objects.Classimagescience.imageFijijavadoc
BottleInterfaceedu.utexas.clm.archipelago.network.translationFijijavadoc
BottlerInterfaceedu.utexas.clm.archipelago.network.translationFijijavadoc

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BoundedIntervalA interval consisting of BoundedValue minimum and maximum that can span any interval in a given range.Classbdv.utilFijijavadoc
BoundedTypeBasicImgLoaderInterfacempicbg.spim.data.generic.sequenceFijijavadoc
BoundedValueA int variable that can take any value in a given range.Classbdv.utilFijijavadoc
BoundingBoxClassij3d.shapesFijijavadoc
BoundingBoxThe bounding box that contains a region from the minimum inclusive to the maximum non-inclusive.Classmpicbg.imglib.labelingFijijavadoc
BoundingBoxClassspim.fiji.spimdata.boundingboxFijijavadoc
BoundingBoxDialogClassbdv.tools.boundingboxFijijavadoc
BoundingBoxesClassspim.fiji.spimdata.boundingboxFijijavadoc
BoundingBoxGUIClassspim.process.fusion.boundingboxFijijavadoc
BoundingBoxOverlayClassbdv.tools.boundingboxFijijavadoc
BoundingBoxPopupClassspim.fiji.spimdata.explorer.popupFijijavadoc
BoundingBoxUtilClassbdv.tools.boundingboxFijijavadoc
BoundingSphereClassij3d.shapesFijijavadoc
BoundKindClasscom.sun.tools.javac.codeFijijavadoc
BoundsContains bounding box information of up to 5D shapes.Classimagescience.shapeFijijavadoc
BoundsCheckedFunctionreturns a very large number instead of the function value if arguments are out of bound (useful for minimization withClasspal.mathFijijavadoc
BoundsInclusiveClassvib.transformsFijijavadoc
BoxClasscustomnodeFijijavadoc
BoxRealRandomAccessibleClassbdv.tools.boundingboxFijijavadoc
BoxSelectionPanelClassbdv.tools.boundingboxFijijavadoc
BreakTreeA tree node for a 'break' statement.Interfacecom.sun.source.treeFijijavadoc
Bresenham3DClassutilFijijavadoc
BrightnessClassscript.imglib.colorFijijavadoc
BrightnessDialogAdjust brightness and colors for individual (or groups of) setups.Classbdv.tools.brightnessFijijavadoc
BrowserOptionsWindowExtension of JFrame that allows the user to adjust caching settings.Classloci.plugins.utilFijijavadoc

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BSplineThis class implements basic operations to work with cubic B-splines.ClassmathFijijavadoc
BSplineModelClass for representing the images and the deformations by cubic B-splines: Both, images and deformations, are stored in multi-resolution pyramids.ClassbunwarpjFijijavadoc
BucketA Bucket is a subarea of the Layer area, which contains either other Buckets or a map of stack_index vs.Classini.trakem2.displayFijijavadoc
BucketableInterfaceini.trakem2.displayFijijavadoc
Buffer Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandInterfaceimagewareFijijavadoc
BufferedImageBuilderClasslevelsets.filterFijijavadoc
Bug_SubmitterA plugin for reporting bugs to Fiji's BugZilla bug tracker.ClassBug_SubmitterFijijavadoc
Builder Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandClassimagewareFijijavadoc
BundleClassview5dFijijavadoc
bUnwarpJ_Main class for the image registration plugin for ImageJ/Fiji.ClassbunwarpjFijijavadoc
BureaucratSets a Worker thread to work, and waits until it finishes, blocking all user interface input until then, except for zoom and pan, for all given projects.Classini.trakem2.utilsFijijavadoc
Byte3DArrayInterfaceadtFijijavadoc
ByteAccess Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandClassimagewareFijijavadoc
ByteAccessInterfacempicbg.imglib.container.basictypecontainerFijijavadoc
ByteArrayA dynamic array of byte values.Classimagescience.arrayFijijavadoc
ByteArrayClassmpicbg.imglib.container.basictypecontainer.arrayFijijavadoc
ByteBufferA byte buffer is a flexible array which grows when elements are appended.Classcom.sun.tools.javac.utilFijijavadoc
ByteBuffer Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandClassimagewareFijijavadoc
ByteCodesBytecode instruction codes, as well as typecodes used as instruction modifiers.Interfacecom.sun.tools.javac.jvmFijijavadoc
ByteDynamicContainerClassmpicbg.imglib.container.dynamicFijijavadoc
ByteDynamicContainerAccessorClassmpicbg.imglib.container.dynamicFijijavadoc
ByteElementClassview5dFijijavadoc
ByteImageAn image containing up to 5D elements of type byte.Classimagescience.imageFijijavadoc
ByteImagePlusImagePlusContainer for byte-stored data.Classmpicbg.imglib.container.imageplusFijijavadoc
BytePointwise Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandClassimagewareFijijavadoc

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ByteProbabilityUser: Tom Larkworthy class that encodeds probilities as UNSIGNED bytes and makes things go seriously fast!ClassadtFijijavadoc
ByteProcess Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandClassimagewareFijijavadoc
ByteSet Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandClassimagewareFijijavadoc
ByteTypeClassmpicbg.imglib.type.numeric.integerFijijavadoc
CacheThis is the part of the VolatileGlobalCellCache interface that is exposed to the renderer directly (that is, not via images).Interfacebdv.img.cacheFijijavadoc
CacheAccess is not synchronized, that is your duty.Classini.trakem2.persistenceFijijavadoc
CacheArrayLoaderInterfacebdv.img.cacheFijijavadoc
CachedCellImgClassbdv.img.cacheFijijavadoc
CacheFSInfoCaching implementation of FSInfo.Classcom.sun.tools.javac.fileFijijavadoc
CacheHintsHints to the cache on how to handle cell requests.Classbdv.img.cacheFijijavadoc
CacheIoTimingUtilities for per ThreadGroup measuring and budgeting of time spentAuthor:Tobias Pietzsch Classbdv.img.cacheFijijavadoc
CachingThreadClassini.trakem2.utilsFijijavadoc
Calculator_PlusThis plugin does various calculations on two images or stacks.ClassFijijavadoc
CalibratedImgClassspim.fiji.spimdata.imgloadersFijijavadoc
CalibrationClassspim.fiji.spimdata.imgloadersFijijavadoc
Calibration5DExtension of the Calibration class to 5 Dimensions.Classi5d.calFijijavadoc
CalibratorLogic for calibrating images.Classloci.plugins.inFijijavadoc
CannyAdapted from the Sun Java Forums.Classlevelsets.filterFijijavadoc
CanvasImageClassmpicbg.imglib.algorithmFijijavadoc
CaptureOverlayActionClassfiji.plugin.trackmate.actionFijijavadoc
CaseTreeA tree node for a 'case' in a 'switch' statement.Interfacecom.sun.source.treeFijijavadoc
CatchTreeA tree node for a 'catch' block in a 'try' statement.Interfacecom.sun.source.treeFijijavadoc
CategoryJComboBoxA JcomboBox that displays categories, and return the category the selectedAuthor:Jean-Yves Tinevez, adapted fromClassfiji.plugin.trackmate.gui.panels.componentsFijijavadoc
CatmaidImageLoaderClassbdv.img.catmaidFijijavadoc
CatmaidVolatileIntArrayLoaderClassbdv.img.catmaidFijijavadoc

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CbrtClassscript.imglib.mathFijijavadoc
CeilClassscript.imglib.mathFijijavadoc
CellClassmpicbg.imglib.container.cellFijijavadoc
Cell_CounterClassFijijavadoc
CellCntrImageCanvasClassFijijavadoc
CellCntrMarkerClassFijijavadoc
CellCntrMarkerVectorClassFijijavadoc
CellContainerClassmpicbg.imglib.container.cellFijijavadoc
CellContainerFactoryClassmpicbg.imglib.container.cellFijijavadoc
CellCounterClassFijijavadoc
CellCounterOptionsOptions for the Cell Counter plugin.ClassFijijavadoc
CellCursorClassmpicbg.imglib.cursor.cellFijijavadoc
CellLocalizableByDimCursorClassmpicbg.imglib.cursor.cellFijijavadoc
CellLocalizableByDimOutOfBoundsCursorClassmpicbg.imglib.cursor.cellFijijavadoc
CellLocalizableCursorClassmpicbg.imglib.cursor.cellFijijavadoc
CellLocalizablePlaneCursorClassmpicbg.imglib.cursor.cellFijijavadoc
CellVoyagerDataExporterClassbdv.ij.export.tilesFijijavadoc
Center_TransformationClassvibFijijavadoc
CenterlineSlice Lionel.ClassutilsFijijavadoc
CenterTransformationClassvib.app.moduleFijijavadoc
CentralDiffThis class implements a four point central difference gradient kernel.ClassvolumeFijijavadoc
CentralityFollowing pseudo-code from: Ulrik Brandes.Classini.trakem2.analysisFijijavadoc
ChangeAttributeIdClassbdv.spimdata.toolsFijijavadoc
ChangeViewSetupIdClassbdv.spimdata.toolsFijijavadoc
ChannelClassini.trakem2.displayFijijavadoc

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ChannelDefines a channel which is part of the ViewSetup.Classmpicbg.spim.data.sequenceFijijavadoc
ChannelClassscript.imglib.colorFijijavadoc
ContourSetInterfaceedu.utexas.clm.reconstructreader.reconstructFijijavadoc
ContrastAdjustmentModeClassini.trakem2.displayFijijavadoc
ContrastEnhancerWrapperClassini.trakem2.imagingFijijavadoc
ContrastPlotCopied and modified from Wayne Rasband's ImageJ ContrastPlot inner class in ij.Classini.trakem2.imagingFijijavadoc
ControlClassfiji.plugin.volumeviewerFijijavadoc
ControlClickBehaviorA class to provide the behavior on control-clicking oncontent in the 3D viewer.Classini.trakem2.display.d3dFijijavadoc
ControlJPanelGUI panel to interactively segmentate an image with SIOX.Classorg.siox.exampleFijijavadoc
ControlJPanelThis class implements the interactive buttons for the Siox segmentation GUI.ClasssioxFijijavadoc
ControlPanelFrameClassorg.imagearchive.lsm.toolbox.guiFijijavadoc
ControlWindowStatic class that shows one project per tab in a JFrame.Classini.trakem2Fijijavadoc
ConvertUtility class for static conversion methods between numbers and strings in various formats.Classcom.sun.tools.javac.utilFijijavadoc
Convert_Red_To_MagentaClassfiji.colorFijijavadoc
Convert_Red_To_Magenta_ClipboardClassfiji.colorFijijavadoc
ConverterInterfacempicbg.imglib.functionFijijavadoc
ConverterSetupModify the range and color of the converter for a source.Interfacebdv.tools.brightnessFijijavadoc
ConvertUtilProvides useful methods for converting images from one colour depth to another.Classnet.sf.image4j.utilFijijavadoc
ConvexBranchesDecompositionA class that can decompose the tracks of a Model in convex branches.Classfiji.plugin.trackmate.graphFijijavadoc
ConvolutionFilterPerforms a convolution operation on the input image.Classlevelsets.filterFijijavadoc
Convolve3dClassprocess3dFijijavadoc
Convolve_3dClassprocess3dFijijavadoc
Convolver Routines to convolve a 1D signal applying mirror boundary conditions.ClassimagewareFijijavadoc
ConvolverThis class implements convolution operations on image planes and volumes.ClassvolumeFijijavadoc
CoordinateClassini.trakem2.displayFijijavadoc

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CoordinateEncapsulates a three-dimensional Coordinate.Classlevelsets.algorithmFijijavadoc
CoordinatesContains 5D integer coordinates.Classimagescience.imageFijijavadoc
CoordinateSystemClassij3d.shapesFijijavadoc
CoordinateTransformInvertibleCoordinateTransform with String import and export as used inInterfacempicbg.trakem2.transformFijijavadoc
CoordinateTransformInterfacestitching.modelFijijavadoc
CoordinateTransformListClassmpicbg.trakem2.transformFijijavadoc
CoordinateTransformXMLClassini.trakem2.ioFijijavadoc
CoordsCursorAbstract cursor that offers facilities to move the cursor origin (whatever this means for the concrete implementation) by giving physical coordinates, convertedClassmpicbg.imglib.cursor.specialFijijavadoc
CoordSystem3dClassmpicbg.spim.registration.detection.descriptorFijijavadoc
CoordSystemSecure3dClassmpicbg.spim.registration.detection.descriptorFijijavadoc
CopyClassimglib.ops.operator.binaryFijijavadoc
CopyClassimglib.ops.operator.unaryFijijavadoc
CopyOverlayActionClassfiji.plugin.trackmate.actionFijijavadoc
CopyTransparentZeroClassimglib.ops.operator.binaryFijijavadoc
Correct_DriftClassQuickPALMFijijavadoc
Correct_Drift2ClassQuickPALMFijijavadoc
CorrectBackgroundClassini.trakem2.imaging.filtersFijijavadoc
CorrelationClassdistanceFijijavadoc
CorrespondenceExtractionInterfacempicbg.spim.registration.detection.descriptorFijijavadoc
CorrespondingInterestPointsDefines a pair of corresponding interest pointsAuthor:Stephan Preibisch (stephan.Classspim.fiji.spimdata.interestpointsFijijavadoc
CosClassscript.imglib.mathFijijavadoc
CoshClassscript.imglib.mathFijijavadoc
CostesSignificanceTestClassalgorithmsFijijavadoc
CostFunctionInterface representing a function that can calculate the cost to link a source object to a target object.Interfacefiji.plugin.trackmate.tracking.sparselap.costfunctionFijijavadoc
CostFunctionsInterface for cost function classes, which take a Matrix and fill in values according to the cost function.Interfacefiji.plugin.trackmate.tracking.oldlap.costfunctionFijijavadoc

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CostMatrixCreatorInterface for function that can generate a SparseCostMatrix from assignment candidates.Interfacefiji.plugin.trackmate.tracking.sparselap.costmatrixFijijavadoc
Count_FilesClassspimopenerFijijavadoc
Count_LabelsClassutilFijijavadoc
Counter3DClassUtilitiesFijijavadoc
CountingTaskFactoryClassini.trakem2.parallelFijijavadoc
CoverMakerUtilsUtility methods for Fiji's Cover Maker script.Classfiji.utilFijijavadoc
CPDragAndDropClassorg.imagearchive.lsm.toolbox.guiFijijavadoc
CPU_MeterClassFijijavadoc
Create_3D_calibrationThis plugin creates a 3D calibration table by observing the width and height change of beads over depth (caused by astigmatism).ClassQuickPALMFijijavadoc
CreateSymbolsUsed to generate a "symbol file" representing rt.Classcom.sun.tools.javac.symFijijavadoc
CreateTracingVolume_ClasstracingFijijavadoc
CreditsClassbunwarpjFijijavadoc
CropClassimagescience.transformFijijavadoc
CropDialogClassbdv.tools.cropFijijavadoc
CropDialogBio-Formats Importer crop options dialog box.Classloci.plugins.inFijijavadoc
CropEditor_ClassFijijavadoc
CropImgLoaderThis ImgLoader provides views and transformations into a cropped region of a data-set (provided by list of Sources).Classbdv.tools.cropFijijavadoc
CrossCorrelationClassmpicbg.imglib.algorithm.correlationFijijavadoc
CrossCorrelation2DClassmpi.fruitfly.registrationFijijavadoc
CrossCorrelationResult2DClassstitchingFijijavadoc
CrossCorrelationResult3DClassstitchingFijijavadoc
CRTableThis class contains the CharacterRangeTable for some method and the hashtable for mapping trees or lists of trees to theirClasscom.sun.tools.javac.jvmFijijavadoc
CRTFlagsThe CharacterRangeTable flags indicating type of an entry.Interfacecom.sun.tools.javac.jvmFijijavadoc
CSVReaderA very simple CSV reader released under a commercial-friendly license.Classutil.opencsvFijijavadoc
CSVWriterA very simple CSV writer released under a commercial-friendly license.Classutil.opencsvFijijavadoc

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CubeTriangular mesh of a cube in 3D.Classimagescience.meshFijijavadoc
CubeClassoctreeFijijavadoc
CubeDataClassoctreeFijijavadoc
CubicBSplineTransformClass to implement elastic transforms based on cubic B-splines.Classbunwarpj.trakem2.transformFijijavadoc
CUDADeviceClassspim.process.cudaFijijavadoc
CUDAFourierConvolutionInterfacespim.process.cudaFijijavadoc
CUDASeparableConvolutionInterface to load the native library for separable convolution using CUDA/CPU (https://github.Interfacespim.process.cudaFijijavadoc
CUDASeparableConvolutionFunctionsExecutes gaussian convolution using the native CUDA implementation (https://github.Classspim.process.cudaFijijavadoc
CUDAStandardFunctionsInterfacespim.process.cudaFijijavadoc
CUDAToolsClassmpicbg.spim.postprocessing.deconvolution2Fijijavadoc
CUDAToolsClassspim.process.cudaFijijavadoc
CumulativeQueueClass to create a cumulative queue in bUnwarpJ.ClassbunwarpjFijijavadoc
CurrentSliceClassfiji.utilFijijavadoc
CursorThe Cursor interface The Cursor is responsible for iterating over the image.Interfacempicbg.imglib.cursorFijijavadoc
CursorFactorySome static cursor creation utilities.Classorg.siox.exampleFijijavadoc
CursorImplWe use the class CursorImpl instead of implementing methods here so that other classes can only implement Cursor and extend other classes instead.Classmpicbg.imglib.cursorFijijavadoc
CursorLinkInterfacempicbg.imglib.cursor.linkFijijavadoc
Curvatures_Classfiji.featuresFijijavadoc
CustomCanvasClassvib.segmentFijijavadoc
CustomIndexedTriangleMeshClasscustomnodeFijijavadoc
CustomLineMeshClasscustomnodeFijijavadoc
CustomMeshClasscustomnodeFijijavadoc
Check Code Snippets / Samples for customnode.CustomMesh
CustomMeshNodeClasscustomnodeFijijavadoc
CustomMultiMeshClasscustomnodeFijijavadoc
CustomPointMeshClasscustomnodeFijijavadoc

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CustomQuadMeshClasscustomnodeFijijavadoc
CustomStackWindowClassvib.segmentFijijavadoc
CustomTransparentTriangleMeshClasscustomnodeFijijavadoc
CustomTriangleMeshClasscustomnodeFijijavadoc
CustomVolumeBehavior2 CustomVolumeBehavior2 implements the special Java 3d Picking behavior needed by the Volume_Calculator.ClassvolumeCalculatorFijijavadoc
CVMKalmanFilterA Kalman filter that deals with a single particle motion in 3D with a constant velocity vector.Classfiji.plugin.trackmate.tracking.kalmanFijijavadoc
CylinderTriangular mesh of a cylinder in 3D.Classimagescience.meshFijijavadoc
CZLSMInfoClassorg.imagearchive.lsm.reader.infoFijijavadoc
CZLSMInfoExtendedClassorg.imagearchive.lsm.toolbox.infoFijijavadoc
Daltonize_This plugin can simulate color blindness.ClassFijijavadoc
Data_ExplorerClassspim.fiji.pluginFijijavadoc
DataAccessInterfacempicbg.imglib.container.basictypecontainerFijijavadoc
DataBlockClasscustomnode.u3dFijijavadoc
DataBrowserExtension of StackWindow with additional UI trimmings for animation, virtual stack caching options, metadata, and general beautification.Classloci.plugins.utilFijijavadoc
DataChannelClassorg.imagearchive.lsm.toolbox.info.scaninfoFijijavadoc
DataChunkAn abstract class to help support objects that might not otherwise be Serializable This class should be considered volatile and subject to change.Classedu.utexas.clm.archipelago.dataFijijavadoc
DataContainerThe DataContainer keeps all the source data, jobName, pre-processing results and algorithm results that have been computed.ClassgadgetsFijijavadoc
DataTypeClassorg.imagearchive.lsm.toolbox.info.scaninfoFijijavadoc
DateUtilsClassFijijavadoc
DBLoaderClassini.trakem2.persistenceFijijavadoc
DBObjectBase class of all objects that can be saved in a database or XML file.Classini.trakem2.persistenceFijijavadoc
DCTInterpolatorClassmpicbg.imglib.interpolation.dctFijijavadoc
DCTInterpolatorFactoryClassmpicbg.imglib.interpolation.dctFijijavadoc
DebugClassfijiFijijavadoc
DebugClassfiji.plugin.trackmateFijijavadoc

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DeclaredTypeRepresents a declared type, either a class type or an interface type.Interfacejavax.lang.model.typeFijijavadoc
DeconvolverInterfacempicbg.spim.postprocessing.deconvolution2Fijijavadoc
DefaultAnimatableUniverseClassij3dFijijavadoc
DefaultCostMatrixCreatorA CostMatrixCreator that build a cost matrix from 3 lists containing the sources, the targets and the associated costs.Classfiji.plugin.trackmate.tracking.sparselap.costmatrixFijijavadoc
DefaultExecutorProviderDefault Executor Provider, which creates ExecutorServices from java.Classini.trakem2.parallelFijijavadoc
DefaultFijiServiceThe default initializer for the Fiji legacy application.ClassfijiFijijavadoc
DefaultFileFilterFilter for use in a JFileChooser.Classfiji.plugin.trackmate.utilFijijavadoc
DefaultGraphicsSourceHandles default mode, i.Classini.trakem2.display.graphicsFijijavadoc
DefaultImgTitlerClassspim.process.fusion.exportFijijavadoc
DefaultLabelingCursorStrategyA relatively conservative strategy suitable for blobby objects - retain the bounding boxes and raster starts and reconstruct the Classmpicbg.imglib.labelingFijijavadoc
DefaultLabelingCursorStrategyFactoryClassmpicbg.imglib.labelingFijijavadoc
DefaultLegacyPostRefreshMenusLegacyPostRefreshMenus plugin that ensures the MenuRefresher runs after the Refresh Menus command isClassfijiFijijavadoc
DefaultMinAndMaxSets the minimum to zero and the maximum to the maximum supported, or 255 for FloatProcessor and any other unknown ImageProcessor.Classini.trakem2.imaging.filtersFijijavadoc
DefaultMipmapOrderingThe standard mipmap ordering strategy for local hdf5 data.Classbdv.viewer.renderFijijavadoc
DefaultModeClassini.trakem2.displayFijijavadoc
DefaultOMEMetadataServiceDefault implementation of OMEMetadataService.Classio.scif.ome.servicesFijijavadoc
DefaultOMETranslatorBasic translator for OME Metadata.Classio.scif.ome.translatorsFijijavadoc
DefaultOMEXMLServiceDefault implementation of OMEXMLService.Classio.scif.ome.servicesFijijavadoc
DefaultTemplateClassedu.utexas.clm.reconstructreader.trakem2Fijijavadoc
DefaultTreeTransferHandlerAdapted from freely available code by DeuDeu from http://forum.Classini.trakem2.treeFijijavadoc
DefaultUniverseClassij3dFijijavadoc
DeferredArray3DClasslevelsets.algorithmFijijavadoc
DeferredByteArray3DClasslevelsets.algorithmFijijavadoc
DeferredDoubleArray3DClasslevelsets.algorithmFijijavadoc
DeferredIntArray3DClasslevelsets.algorithmFijijavadoc

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DeferredObjectArray3DClasslevelsets.algorithmFijijavadoc
Define_Bounding_BoxClassspim.fiji.pluginFijijavadoc
Define_Multi_View_DatasetClassspim.fiji.pluginFijijavadoc
Deformable_RegistrationClassvibFijijavadoc
DeInterleave_ClassFijijavadoc
Delaunay_VoronoiDraw Delaunay triangulation or Voronoi Diagram as an overlay.ClassFijijavadoc
DelaunayTriangulationA 2D Delaunay Triangulation (DT) with incremental site insertion.ClassdelaunayFijijavadoc
Delete_FrameClassvideo2Fijijavadoc
DeltaVision_ConverterClassFijijavadoc
DemoThis class is an applet demonstration of the EDF.ClassFijijavadoc
Check Code Snippets / Samples for .Demo
DemodulationClassFlowJFijijavadoc
DenseFieldLevelSetClasslevelsets.algorithmFijijavadoc
Descriptor_based_registrationClasspluginFijijavadoc
Descriptor_based_series_registrationClasspluginFijijavadoc
DescriptorParametersClasspluginFijijavadoc
Despeckle_ClassFijijavadoc
DetailsFrameClassorg.imagearchive.lsm.toolbox.guiFijijavadoc
DetectInterestPointsPopupClassspim.fiji.spimdata.explorer.popupFijijavadoc
DetectionClassmpicbg.spim.registration.detectionFijijavadoc
DetectionClassspim.process.interestpointregistrationFijijavadoc
DetectionChannelClassorg.imagearchive.lsm.toolbox.info.scaninfoFijijavadoc
DetectionDescriptorClassfiji.plugin.trackmate.gui.descriptorsFijijavadoc
DetectionIdentificationThe DetectionIdentification object stores the link (via ID) to an Detection-object and not an actual instance, but a link to the ViewDataBeads object where it belongs to.Classmpicbg.spim.registration.detectionFijijavadoc
DetectionRegistrationClassmpicbg.spim.registration.detectionFijijavadoc
DetectionSegmentationClassmpicbg.spim.registration.detectionFijijavadoc

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DetectionSegmentationClassprocessFijijavadoc
DetectionStructureClassmpicbg.spim.registration.detectionFijijavadoc
DetectionUtilsClassfiji.plugin.trackmate.detectionFijijavadoc
DetectionViewClassmpicbg.spim.registration.detectionFijijavadoc
DetectorChoiceDescriptorClassfiji.plugin.trackmate.gui.descriptorsFijijavadoc
DetectorConfigurationDescriptorClassfiji.plugin.trackmate.gui.descriptorsFijijavadoc
DetectorKeysClassfiji.plugin.trackmate.detectionFijijavadoc
Check Code Snippets / Samples for fiji.plugin.trackmate.detection.DetectorKeys
DetectorProviderClassfiji.plugin.trackmate.providersFijijavadoc
DevUtilClassmpicbg.imglib.utilFijijavadoc
DHMClassspim.fiji.datasetmanagerFijijavadoc
DHMImgLoaderClassspim.fiji.spimdata.imgloadersFijijavadoc
DHMMetaDataClassspim.fiji.datasetmanagerFijijavadoc
DiagnosticInterface for diagnostics from tools.Interfacejavax.toolsFijijavadoc
DiagnosticCollectorProvides an easy way to collect diagnostics in a list.Classjavax.toolsFijijavadoc
DiagnosticFormatterA formatter for diagnostic messages.Classcom.sun.tools.javac.utilFijijavadoc
DiagnosticListenerInterface for receiving diagnostics from tools.Interfacejavax.toolsFijijavadoc
Dichromacy_ClassFijijavadoc
DICOMTranslatorContainer class for translators between OME and DICOM formats.Classio.scif.ome.translatorsFijijavadoc
DifferenceClassimglib.ops.operator.binaryFijijavadoc
DifferenceClassscript.imglib.mathFijijavadoc
DifferenceARGBCompositeClassini.trakem2.display.graphicsFijijavadoc
DifferenceOfClassspim.fiji.plugin.interestpointdetectionFijijavadoc
DifferenceOfGaussianClassmpicbg.imglib.algorithm.scalespaceFijijavadoc
DifferenceOfGaussianClassspim.fiji.plugin.interestpointdetectionFijijavadoc
DifferenceOfGaussianCUDAClassspim.process.interestpointdetectionFijijavadoc

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DifferenceOfGaussianNewPeakFinderClassspim.process.interestpointdetectionFijijavadoc
DifferenceOfGaussianPeakClassmpicbg.imglib.algorithm.scalespaceFijijavadoc
DifferenceOfGaussianRealClassmpicbg.imglib.algorithm.scalespaceFijijavadoc
DifferenceOfGaussianReal1Classmpicbg.imglib.algorithm.scalespaceFijijavadoc
DifferenceOfMeanClassspim.fiji.plugin.interestpointdetectionFijijavadoc
DifferentialEvolutionglobal minimization of a real-valued function of several variables without using derivatives using a genetic algorithmClasspal.mathFijijavadoc
Differentials_ClassFijijavadoc
DifferentiatorComputes Gaussian derivatives of images.Classimagescience.featureFijijavadoc
DiffusionThis is a class that implements nonlinear diffusion in 2D.ClassvolumeFijijavadoc
Diffusion3DThis is a class that implements nonlinear diffusion in 2D, 3D and 4D.ClassvolumeFijijavadoc
DiffusionInterpol2ClassvibFijijavadoc
DiffusionInterpol2_ClassvibFijijavadoc
DilatationClasslevelsets.filterFijijavadoc
DilateClassscript.imglib.algorithmFijijavadoc
Dilate_This class implements the dilation filter.Classprocess3dFijijavadoc
DimensionClassfiji.plugin.trackmateFijijavadoc
DimensionalityInterfacempicbg.imglib.cursor.vectorFijijavadoc
DimensionsContains the dimensions of up to 5D image data objects.Classimagescience.imageFijijavadoc
DimsAndExistenceThe dimensions of an image and a flag indicating whether that image exists (can be loaded)Classbdv.img.hdf5Fijijavadoc
DirectAccessContainerInterfacempicbg.imglib.containerFijijavadoc
DirectAccessContainerFactoryClassmpicbg.imglib.containerFijijavadoc
DirectAccessContainerImplClassmpicbg.imglib.containerFijijavadoc
DirectConvolutionDirectConvolution is an ROIAlgorithm designed to do both convolution and cross-correlation by operating on the image and kernel directly, rather than by using such time-saving tricks asClassmpicbg.imglib.algorithm.roiFijijavadoc
DirectCrossCorrDirectCrossCorr performs direct cross-correlation of a kernel against an image.Classmpicbg.imglib.algorithm.roiFijijavadoc
Directionality_Usage This plugin is used to infer the preferred orientation of structures present in the input image.Classfiji.analyze.directionalityFijijavadoc

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Dirichlet_EdgeClassvib.edgeFijijavadoc
DiscCursorClassmpicbg.imglib.cursor.specialFijijavadoc
DiscreteIntHistogramBinFactoryA HistogramBinFactory to be used to create a discrete Histogram over integer-valued Type's.Classmpicbg.imglib.algorithm.histogram.discreteFijijavadoc
DispatcherClassini.trakem2.utilsFijijavadoc
Display Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandClassimagewareFijijavadoc
DisplayA Display is a class to show a Layer and enable mouse and keyboard manipulation of all its components.Classini.trakem2.displayFijijavadoc
DisplayClassmpicbg.imglib.image.displayFijijavadoc
Display3DOne Display3D instance for each LayerSet (maximum).Classini.trakem2.displayFijijavadoc
Display3DGUIClassini.trakem2.display.d3dFijijavadoc
Display_ViewClassspim.fiji.pluginFijijavadoc
DisplayableThe class that any element to be drawn on a Display must extend.Classini.trakem2.displayFijijavadoc
DisplayableChooserA class to be used when a click to select Displayable objects on the Display detects that there are more than one under the mouse cursor.Classini.trakem2.displayFijijavadoc
DisplayablePanelClassini.trakem2.displayFijijavadoc
DisplayCanvasClassini.trakem2.displayFijijavadoc
DisplayChangeEventTo be raised when a property of the image display has been changedSee Also:Serialized FormClassFijijavadoc
DisplayChangeListenerThe Listener interface for receiving DisplayChange events.InterfaceFijijavadoc
DisplayHandlerLogic for displaying images and metadata onscreen using ImageJ.Classloci.plugins.inFijijavadoc
DisplayImageClassspim.process.fusion.exportFijijavadoc
DisplayModeClassbdv.viewerFijijavadoc
DisplayNavigatorClassini.trakem2.displayFijijavadoc
DisplaySettingsEventAn event object fired when the user changes one of the display settings through this GUI panel.Classfiji.plugin.trackmate.guiFijijavadoc
DisplaySettingsListenerInterface for classes that listen to display settings changes on a GUI.Interfacefiji.plugin.trackmate.guiFijijavadoc
DisplayViewPopupClassspim.fiji.spimdata.explorer.popupFijijavadoc
Dissector Each label is simply a cross marker with a number attached; labels are grouped; each member label of the group has the same number.Classini.trakem2.displayFijijavadoc
Distance_RidgeClasssc.fiji.localThicknessFijijavadoc

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Distance_Transform_3DClassprocess3dFijijavadoc
DistanceComparatorCompares which Leaf is closer to another LeafAuthor:Johannes Schindelin and Stephan PreibischClassfiji.utilFijijavadoc
DistanceComparatorCompares which Leaf is closer to another LeafAuthor:Johannes Schindelin, Stephan PreibischClassmpicbg.imglib.algorithm.kdtreeFijijavadoc
DistanceTransform3DClassprocess3dFijijavadoc
Distortion_CorrectionClasslenscorrectionFijijavadoc
DistortionCorrectionTaskMethods collection to be called from the GUI for alignment tasks.ClasslenscorrectionFijijavadoc
DistributionInferenceClassinferenceFijijavadoc
DitherClassscript.imglib.algorithmFijijavadoc
DivideClassimglib.ops.operator.binaryFijijavadoc
DivideClassscript.imglib.mathFijijavadoc
DivideByConstantClassimglib.ops.operator.unaryFijijavadoc
DLabelThis class is named funny to avoid confusion with java.Classini.trakem2.displayFijijavadoc
DM3_ReaderClassioFijijavadoc
DNDInsertImageClassini.trakem2.utilsFijijavadoc
DNDTreeA JTree which has a built-in drag and drop feature.Classini.trakem2.treeFijijavadoc
DocCommentScannerAn extension to the base lexical analyzer that captures and processes the contents of doc comments.Classcom.sun.tools.javac.parserFijijavadoc
DoGThis is a 1D Difference of Gaussian convolution kernel.ClassvolumeFijijavadoc
DoG2DThis is a 2D Difference of Gaussian convolution kernel.ClassvolumeFijijavadoc
DoG3DThis is a 3D Difference of Gaussian convolution kernel.ClassvolumeFijijavadoc
DogDetectorClassfiji.plugin.trackmate.detectionFijijavadoc
DogDetectorConfigurationPanelClassfiji.plugin.trackmate.gui.panels.detectorFijijavadoc
DogDetectorFactoryClassfiji.plugin.trackmate.detectionFijijavadoc
DoGMaximumClassmpicbg.spim.registration.bead.laplaceFijijavadoc
DoGPeaksPerform a difference of Gaussian on the given Image, and this class itself becomes the List of found peaks, each as a float[] array that specifies its position.Classscript.imglib.analysisFijijavadoc
DOMClassmpicbg.spim.segmentationFijijavadoc

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DomainCursorAbstract class for CoordsCursors that iterate over a domain which size can be determined by a single parameter.Classmpicbg.imglib.cursor.specialFijijavadoc
DomXmlExporterClassorg.imagearchive.lsm.toolboxFijijavadoc
DoneButtonListenerClassselectionFijijavadoc
DoStepInterfaceini.trakem2.displayFijijavadoc
DoubleAccess Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandClassimagewareFijijavadoc
DoubleAccessInterfacempicbg.imglib.container.basictypecontainerFijijavadoc
DoubleArrayClassfiji.utilFijijavadoc
DoubleArrayA dynamic array of double values.Classimagescience.arrayFijijavadoc
DoubleArrayClassmpicbg.imglib.container.basictypecontainer.arrayFijijavadoc
DoubleBuffer Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandClassimagewareFijijavadoc
DoubleDynamicContainerClassmpicbg.imglib.container.dynamicFijijavadoc
DoubleDynamicContainerAccessorClassmpicbg.imglib.container.dynamicFijijavadoc
DoubleElementClassview5dFijijavadoc
DoubleOptionA double option for one of the plugins.Classloci.plugins.prefsFijijavadoc
DoublePointwise Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandClassimagewareFijijavadoc
DoubleProcess Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandClassimagewareFijijavadoc
DoubleSet Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandClassimagewareFijijavadoc
DoubleSliderClassspimopenerFijijavadoc
DoubleTypeClassmpicbg.imglib.type.numeric.realFijijavadoc
DoWhileLoopTreeA tree node for a 'do' statement.Interfacecom.sun.source.treeFijijavadoc
DownsampleClassbdv.exportFijijavadoc
DownSampleClassmpicbg.imglib.algorithm.gaussFijijavadoc
DownsampleClassscript.imglib.algorithmFijijavadoc
DownsampleClassspim.process.interestpointdetectionFijijavadoc
DownsampleLogDetectorClassfiji.plugin.trackmate.detectionFijijavadoc

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DownSampleLogDetectorConfigurationPanelClassfiji.plugin.trackmate.gui.panels.detectorFijijavadoc
DownsampleLogDetectorFactoryClassfiji.plugin.trackmate.detectionFijijavadoc
DownsamplerHelper class for running the " Image > Scale.Classmpicbg.stitchingFijijavadoc
DownsamplerClassmpicbg.trakem2.utilFijijavadoc
DownsamplerMipMapsClassini.trakem2.persistenceFijijavadoc
Draw_RoiClassvideo2Fijijavadoc
DTDClassmpicbg.trakem2.transformFijijavadoc
DTDParserReads either a DOCTYPE chunk from an xml file or a .Classini.trakem2.treeFijijavadoc
DummyCanvasClasssc.fiji.timelapseFijijavadoc
DummyNodeShellA dummy implementation of NodeShell, for use with volunteer nodes.Classedu.utexas.clm.archipelago.network.shellFijijavadoc
DummySpotColorGeneratorA dummy spot color generator that always return the default color.Classfiji.plugin.trackmate.visualizationFijijavadoc
DummyTrackColorGeneratorA dummy track color generator that always return the default color.Classfiji.plugin.trackmate.visualizationFijijavadoc
DuplexClassedu.utexas.clm.archipelago.dataFijijavadoc
Duplicate_FrameClassvideo2Fijijavadoc
Duplicate_Image5DClassFijijavadoc
Duplicate_TransformationClassspim.fiji.pluginFijijavadoc
Dynamic_ResliceDynamic reslice of a stack.Classfiji.stacksFijijavadoc
DynamicContainerClassmpicbg.imglib.container.dynamicFijijavadoc
DynamicContainerAccessorClassmpicbg.imglib.container.dynamicFijijavadoc
DynamicContainerFactoryClassmpicbg.imglib.container.dynamicFijijavadoc
DynamicCursorClassmpicbg.imglib.cursor.dynamicFijijavadoc
DynamicLocalizableByDimCursorClassmpicbg.imglib.cursor.dynamicFijijavadoc
DynamicLocalizableByDimOutOfBoundsCursorClassmpicbg.imglib.cursor.dynamicFijijavadoc
DynamicLocalizableCursorClassmpicbg.imglib.cursor.dynamicFijijavadoc
DynamicLocalizablePlaneCursorClassmpicbg.imglib.cursor.dynamicFijijavadoc

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EasyDisplayClassresultsFijijavadoc
EasyLoggerInterfaceedu.utexas.clm.archipelago.utilFijijavadoc
EDF_Easy_This class is a plugin of ImageJ.ClassFijijavadoc
EDF_Expert_ClassFijijavadoc
EDF_Viewer3D_ClassFijijavadoc
EdfComplexWaveletsClassedfFijijavadoc
EdfRealWaveletsClassedfFijijavadoc
EdfSobelClassedfFijijavadoc
EdfVarianceClassedfFijijavadoc
EdfWaveletMaximumModulusClassedfFijijavadoc
EdgeThis class represents the edge between two vertices in an undirected graph.Classsc.fiji.analyzeSkeletonFijijavadoc
EdgeAnalyzerInterface for analyzers that can compute scalar numerical features for an edge of a TrackMate model.Interfacefiji.plugin.trackmate.features.edgesFijijavadoc
EdgeAnalyzerProviderA provider for the edge analyzers provided in the GUI.Classfiji.plugin.trackmate.providersFijijavadoc
EdgeContractionClasscustomnodeFijijavadoc
EdgeDetectors_ClassvibFijijavadoc
EdgeFeatureCalculatorA class dedicated to centralizing the calculation of the numerical features of spots, through EdgeAnalyzers.Classfiji.plugin.trackmate.featuresFijijavadoc
EdgeFeatureGrapherClassfiji.plugin.trackmate.featuresFijijavadoc
EdgesDetects edges in images.Classimagescience.featureFijijavadoc
EdgeTargetAnalyzerClassfiji.plugin.trackmate.features.edgesFijijavadoc
EdgeTimeLocationAnalyzerClassfiji.plugin.trackmate.features.edgesFijijavadoc
EdgeVelocityAnalyzerClassfiji.plugin.trackmate.features.edgesFijijavadoc
Edit_VideoClassvideoFijijavadoc
EditAmiraParameters_ClassvibFijijavadoc
EditionsTo extract and represent the sequence of editions that convert any N-dimensional vector string to any other of the same number of dimensions.Classini.trakem2.vectorFijijavadoc
EDTClassfiji.process3dFijijavadoc

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EDT_S1DClasssc.fiji.localThicknessFijijavadoc
EfficientBayesianBasedClassspim.process.fusion.deconvolutionFijijavadoc
EigenResultsDoubleClasstracingFijijavadoc
EigenResultsFloatClasstracingFijijavadoc
Eigensystem2x2DoubleClassmath3dFijijavadoc
Eigensystem2x2FloatClassmath3dFijijavadoc
Eigensystem3x3DoubleClassmath3dFijijavadoc
Eigensystem3x3FloatClassmath3dFijijavadoc
ElasticLayerAlignmentClassmpicbg.trakem2.alignFijijavadoc
ElasticMontageClassmpicbg.trakem2.alignFijijavadoc
ElasticTransform_ClassvibFijijavadoc
ElasticTransformedImageClassvibFijijavadoc
ElementRepresents a program element such as a package, class, or method.Interfacejavax.lang.model.elementFijijavadoc
ElementFilterFilters for selecting just the elements of interest from a collection of elements.Classjavax.lang.model.utilFijijavadoc
ElementKindThe kind of an element.Classjavax.lang.model.elementFijijavadoc
ElementKindVisitor6A visitor of program elements based on their kind with default behavior appropriate for the RELEASE_6 source version.Classjavax.lang.model.utilFijijavadoc
ElementsUtility methods for operating on program elements.Interfacejavax.lang.model.utilFijijavadoc
ElementScanner6A scanning visitor of program elements with default behavior appropriate for the RELEASE_6Classjavax.lang.model.utilFijijavadoc
ElementVisitorA visitor of program elements, in the style of the visitor design pattern.Interfacejavax.lang.model.elementFijijavadoc
EllipseAn ellipse in the x-y plane.Classimagescience.shapeFijijavadoc
EmbedEmbeds an image into a larger image.Classimagescience.transformFijijavadoc
EmptyProjectorClassbdv.viewer.renderFijijavadoc
EmptyStatementTreeA tree node for an empty (skip) statement.Interfacecom.sun.source.treeFijijavadoc
EndianUtilsProvides utility methods for endian conversions [big-endian to little-endian; little-endian to big-endian].Classnet.sf.image4j.ioFijijavadoc
EndModuleClassvib.app.moduleFijijavadoc

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EndPosParserThis class is similar to Parser except that it stores ending positions for the tree nodes.Classcom.sun.tools.javac.parserFijijavadoc
EnhanceContrastUses the @{link ContrastEnhancer.Classini.trakem2.imaging.filtersFijijavadoc
EnhancedForLoopTreeA tree node for an "enhanced" 'for' loop statement.Interfacecom.sun.source.treeFijijavadoc
EnterThis class enters symbols for all encountered definitions into the symbol table.Classcom.sun.tools.javac.compFijijavadoc
EntitySomething that has a unique id.Classmpicbg.spim.data.generic.baseFijijavadoc
EntityUtilsClassmpicbg.spim.data.generic.baseFijijavadoc
EntropyClassmpicbg.spim.fusion.entropyFijijavadoc
EntropyFastClassmpicbg.spim.fusionFijijavadoc
EntropyFastFactoryClassmpicbg.spim.fusionFijijavadoc
EntropyFloatArray3DClassmpicbg.spim.fusion.entropyFijijavadoc
EnvA class for environments, instances of which are passed as arguments to tree visitors.Classcom.sun.tools.javac.compFijijavadoc
EPSTranslatorContainer class for translators between OME and EPS formats.Classio.scif.ome.translatorsFijijavadoc
Equality_ExampleAn example that demonstrates one potential peril of the Cluster ExecutorService.Classedu.utexas.clm.archipelago.exampleFijijavadoc
EqualizePlugin containing methods to equalize imageas and volumes.ClassvolumeFijijavadoc
EqualizeHistogramClassini.trakem2.imaging.filtersFijijavadoc
EquirectangularPanorama_ViewClassmpicbg.panoramaFijijavadoc
EquirectangularProjectionA rectlinear projection from equirectangular coordinates (longitude, latitude).Classmpicbg.panoramaFijijavadoc
ErodeClassscript.imglib.algorithmFijijavadoc
Erode_This class implements the erosion filter.Classprocess3dFijijavadoc
ErosionClasslevelsets.filterFijijavadoc
ErroneousTreeA tree node to stand in for a malformed expression.Interfacecom.sun.source.treeFijijavadoc
ErrorFunctionerror function and related stuffVersion:$Id: ErrorFunction.Classpal.mathFijijavadoc
ErrorStatisticClassstitching.modelFijijavadoc
ErrorTypeRepresents a class or interface type that cannot be properly modeled.Interfacejavax.lang.model.typeFijijavadoc
EuclideanClassdistanceFijijavadoc

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EventClassorg.imagearchive.lsm.toolbox.infoFijijavadoc
EventListClassorg.imagearchive.lsm.toolbox.infoFijijavadoc
ExecutableElementRepresents a method, constructor, or initializer (static or instance) of a class or interface, including annotation typeInterfacejavax.lang.model.elementFijijavadoc
ExecutableTypeRepresents the type of an executable.Interfacejavax.lang.model.typeFijijavadoc
ExecuterClassij3dFijijavadoc
ExecutorProviderAllow the source ExecutorServices in TrakEM2 to be configured.Classini.trakem2.parallelFijijavadoc
ExistingByteArraysInstead of creating new cell arrays, it return the corresponding array from a predefined listAuthor:Stephan Preibisch (stephan.Classmpicbg.imglib.wrapperFijijavadoc
ExistingCharArraysInstead of creating new cell arrays, it return the corresponding array from a predefined listAuthor:Stephan Preibisch (stephan.Classmpicbg.imglib.wrapperFijijavadoc
ExistingDoubleArraysInstead of creating new cell arrays, it return the corresponding array from a predefined listAuthor:Stephan Preibisch (stephan.Classmpicbg.imglib.wrapperFijijavadoc
ExistingFloatArraysInstead of creating new cell arrays, it return the corresponding array from a predefined listAuthor:Stephan Preibisch (stephan.Classmpicbg.imglib.wrapperFijijavadoc
ExistingIntArraysInstead of creating new cell arrays, it return the corresponding array from a predefined listAuthor:Stephan Preibisch (stephan.Classmpicbg.imglib.wrapperFijijavadoc
ExistingLongArraysInstead of creating new cell arrays, it return the corresponding array from a predefined listAuthor:Stephan Preibisch (stephan.Classmpicbg.imglib.wrapperFijijavadoc
ExistingShortArraysInstead of creating new cell arrays, it return the corresponding array from a predefined listAuthor:Stephan Preibisch (stephan.Classmpicbg.imglib.wrapperFijijavadoc
ExpClassimglib.ops.operator.unaryFijijavadoc
ExpClassscript.imglib.mathFijijavadoc
Expm1Classscript.imglib.mathFijijavadoc
ExponentialGeneratorExponential random number generator.Classimagescience.randomFijijavadoc
ExponentialMathTypeInterfacempicbg.imglib.type.numericFijijavadoc
Export_EPSClassioFijijavadoc
ExportableChartPanelClassfiji.plugin.trackmate.utilFijijavadoc
ExportCellVoyagerPlugInClassbdv.ijFijijavadoc
ExportedTileClassmpicbg.trakem2.transformFijijavadoc
ExporterCore logic for the Bio-Formats Exporter ImageJ plugin.Classloci.plugins.outFijijavadoc
ExportImagePlusPlugInImageJ plugin to export the current image to xml/hdf5.Classbdv.ijFijijavadoc
ExportMesh_ClassmarchingcubesFijijavadoc

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ExportMipmapInfoClassbdv.exportFijijavadoc
ExportSpimData2HDF5Classspim.process.fusion.exportFijijavadoc
ExportSpimData2TIFFClassspim.process.fusion.exportFijijavadoc
ExportSpimFusionPlugInClassbdv.ijFijijavadoc
ExportSpimSequencePlugInClassbdv.ijFijijavadoc
ExportStatsToIJActionClassfiji.plugin.trackmate.actionFijijavadoc
ExportTracksToXMLClassfiji.plugin.trackmate.actionFijijavadoc
ExportUnsignedShortClassmpicbg.trakem2.transformFijijavadoc
Exposure_Blend_Two_StacksClassutilFijijavadoc
ExpressionStatementTreeA tree node for an expression statement.Interfacecom.sun.source.treeFijijavadoc
ExpressionTreeA tree node used as the base class for the different types ofSince:1.Interfacecom.sun.source.treeFijijavadoc
ExtendedDepthOfFieldClassedfguiFijijavadoc
ExtendedPointMatchClassselectionFijijavadoc
ExtensionFileFilterFile filter for JFileChooser, filtering regular files according to their extensions.Classorg.siox.exampleFijijavadoc
Extract_Images_From_PDFExtract all images from a PDF file (or from an URL given as argument), and open them all within ImageJ in their original resolution.ClassioFijijavadoc
Extract_SurfaceClassvibFijijavadoc
ExtractPSFClassmpicbg.spim.postprocessing.deconvolutionFijijavadoc
ExtractPSFClassspim.process.fusion.deconvolutionFijijavadoc
ExtractTrackStackActionClassfiji.plugin.trackmate.actionFijijavadoc
ExtremaClasssc.fiji.timelapseFijijavadoc
ExtremizerFinds local extrema in images.Classimagescience.segmentFijijavadoc
FactoryInterfacempicbg.imglibFijijavadoc
FakeAccessInterfacempicbg.imglib.container.basictypecontainerFijijavadoc
FakeArrayClassmpicbg.imglib.container.basictypecontainer.arrayFijijavadoc
FakeImagePlusNeed a non-null ImagePlus for the ImageCanvas, even if fake.Classini.trakem2.displayFijijavadoc

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FakeImageWindowA class to prevent ROIs from failing.Classini.trakem2.displayFijijavadoc
FakeTypeClassmpicbg.imglib.type.labelFijijavadoc
Fast_FourierTransformClassregistration3dFijijavadoc
FastIntegralImageWritten following the code in ImgLib1's IntegralImage2 and ScaleAreaAveraging2d, authored by Stephan Preibisch and Albert Cardona.Classini.trakem2.imagingFijijavadoc
FastLAPTrackerClassfiji.plugin.trackmate.tracking.oldlapFijijavadoc
FastLAPTrackerFactoryClassfiji.plugin.trackmate.tracking.oldlapFijijavadoc
FastMarchingClasslevelsets.algorithmFijijavadoc
FastMarchingBandElementVoxel element for the Fast Marching trial set.Classlevelsets.algorithmFijijavadoc
FastMatrixClassvibFijijavadoc
FastMatrixNClassmath3dFijijavadoc
FastMatrixTransformClassvib.transformsFijijavadoc
FatalErrorThrowing an instance of this class causes immediate termination of the main compiler method.Classcom.sun.tools.javac.utilFijijavadoc
FeatureAnalyzerInterfacefiji.plugin.trackmate.featuresFijijavadoc
FeatureColorGeneratorInterface for color generator that can color objects based on a feature identified by a String.Interfacefiji.plugin.trackmate.visualizationFijijavadoc
FeatureFilterA helper class to store a feature filter.Classfiji.plugin.trackmate.featuresFijijavadoc
FeatureModelThis class represents the part of the Model that is in charge of dealing with spot features and track features.Classfiji.plugin.trackmateFijijavadoc
FeaturePenaltyCostFunctionA cost function that tempers a square distance cost by difference in feature This cost is calculated as follow:Classfiji.plugin.trackmate.tracking.sparselap.costfunctionFijijavadoc
FeaturePlotSelectionPanelA simple Panel to allow the selection of a X key amongst an enum, and of multiple Y keys from the same enum.Classfiji.plugin.trackmate.gui.panels.componentsFijijavadoc
FeaturePlotSelectionPanelA simple Panel to allow the selection of a X key amongst an enum, and of multiple Y keys from the same enum.Classfiji.plugin.trackmate.visualization.trackschemeFijijavadoc
FFTComputes forward and inverse Fourier transforms of images.Classimagescience.fourierFijijavadoc
FFTClasssc.fiji.timelapseFijijavadoc
FFTClassscript.imglib.algorithmFijijavadoc
FFT_Classprocess3dFijijavadoc
FFTFunctionsClassmpicbg.imglib.algorithm.fftFijijavadoc
FibonacciHeapClassutilFijijavadoc

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FibonacciHeapDoubleClassutilFijijavadoc
FibonacciHeapIntClassutilFijijavadoc
FIBSEM_ReaderOpens the proprietary FIB-SEM format used at Janelia FarmAuthor:Stephan Preibisch (stephan.ClassioFijijavadoc
FieldMapViewClasses extending this class acquire a read-only Map interface to access its declared fields via the reflection API provided by Class.Classini.trakem2.utilsFijijavadoc
Fiji_ArchipelagoClassedu.utexas.clm.archipelagoFijijavadoc
FijiAppConfigurationClassfiji.patchesFijijavadoc
FijiArchipelagoClassedu.utexas.clm.archipelagoFijijavadoc
FijiClassLoaderSpecial class loader for ImageJ 1.ClassfijiFijijavadoc
FijiServiceCommon Fiji initialization.InterfacefijiFijijavadoc
FijiToolsClassfijiFijijavadoc
FileAndChannelClassutilFijijavadoc
FileBottleClassedu.utexas.clm.archipelago.network.translationFijijavadoc
FileBottlerClassedu.utexas.clm.archipelago.network.translationFijijavadoc
FileChunkClassedu.utexas.clm.archipelago.dataFijijavadoc
FileCreationClassutilFijijavadoc
FileDialogDecoratorClassfiji.guiFijijavadoc
FileGroupClassvib.appFijijavadoc
FileGroupDialogClassvib.app.guiFijijavadoc
FileListenerInterfacefsalignFijijavadoc
FileObjectFile abstraction for tools.Interfacejavax.toolsFijijavadoc
FileOpenMenuEntryClassfiji.plugin.timelapsedisplayFijijavadoc
FilePathRepairA class to manage "file not found" problems.Classini.trakem2.persistenceFijijavadoc
FilePatternDialogBio-Formats Importer file pattern dialog box.Classloci.plugins.inFijijavadoc
FilePreparerClassoctreeFijijavadoc
FilerThis interface supports the creation of new files by an annotation processor.Interfacejavax.annotation.processingFijijavadoc

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FilerExceptionIndicates a Filer detected an attempt to open a file that would violate the guarantees provided by the Filer.Classjavax.annotation.processingFijijavadoc
FileTemplateClassedu.utexas.clm.reconstructreader.trakem2Fijijavadoc
FileTranslatorInterfaceedu.utexas.clm.archipelago.network.translationFijijavadoc
FillClasstracingFijijavadoc
Fill_holesClassFijijavadoc
FillerProgressCallbackInterfacetracingFijijavadoc
FillerThreadClasstracingFijijavadoc
FillWindowClasstracingFijijavadoc
FilterInterfaceini.trakem2.utilsFijijavadoc
FilterThis interface is implemented by all classes performing operations on input images and returning output imagesInterfacelevelsets.filterFijijavadoc
FilterEditorClassini.trakem2.imaging.filtersFijijavadoc
FilteredMemberListUtility to construct a view of a symbol's members, filtering out unwanted elements such as synthetic ones.Classcom.sun.tools.javac.modelFijijavadoc
FilterGuiPanelClassfiji.plugin.trackmate.gui.panels.componentsFijijavadoc
FilterPanelClassfiji.plugin.trackmate.gui.panelsFijijavadoc
FinalActionClass to launch the registration in bUnwarpJ.ClassbunwarpjFijijavadoc
FinalVoxelDimensionsAn implementation of VoxelDimensions.Classmpicbg.spim.data.sequenceFijijavadoc
Find_Connected_RegionsClassutilFijijavadoc
Find_MinimaClassprocess3dFijijavadoc
FindConnectedRegionsClassutilFijijavadoc
FindIt_ClassFijijavadoc
FindMinimaClassprocess3dFijijavadoc
FineTuneProgressListenerInterfacelandmarksFijijavadoc
FineTuneThreadClasslandmarksFijijavadoc
FirstIterationFuse one portion of a paralell fusion, supports no weightsAuthor:Stephan Preibisch (stephan.Classspim.process.fusion.deconvolutionFijijavadoc
Fit_SphereClassvibFijijavadoc

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FitFunctionInterface for fitting-target functions.Interfacempicbg.imglib.algorithm.peakFijijavadoc
FittingProgressAn implementation of the MultiTaskProgress interface that updates the ImageJ progress barClasstracingFijijavadoc
FixAbsolutePathsInHdf5PartitionsOlder versions of multi-partition hdf5 export had a bug that caused absolute paths to be used in the master hdf5 to link into the partitions.Classbdv.ij.exportFijijavadoc
FixedModelThis model just applies some other TranslationInvariantModel without computing anything.Classmpicbg.pointdescriptor.modelFijijavadoc
FixedNameImgTitlerClassspim.process.fusion.exportFijijavadoc
FJClassfeaturejFijijavadoc
FJ_AboutClassfeaturejFijijavadoc
FJ_DerivativesClassfeaturejFijijavadoc
FJ_EdgesClassfeaturejFijijavadoc
FJ_HelpClassfeaturejFijijavadoc
FJ_HessianClassfeaturejFijijavadoc
FJ_LaplacianClassfeaturejFijijavadoc
FJ_OptionsClassfeaturejFijijavadoc
FJ_PanelClassfeaturejFijijavadoc
FJ_StatisticsClassfeaturejFijijavadoc
FJ_StructureClassfeaturejFijijavadoc
FlagNodeClassfiji.plugin.trackmate.tracking.kdtreeFijijavadoc
FlagsAccess flags and other modifiers for Java classes and members.Classcom.sun.tools.javac.codeFijijavadoc
FlexWidgetsCustom widgets for configuring Bio-Formats Flex support.Classloci.plugins.configFijijavadoc
FloatAccess Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandClassimagewareFijijavadoc
FloatAccessInterfacempicbg.imglib.container.basictypecontainerFijijavadoc
FloatArrayClassfiji.utilFijijavadoc
FloatArrayA dynamic array of float values.Classimagescience.arrayFijijavadoc
FloatArray Copyright: Copyright (c) 2006Version:1.Classmpi.fruitfly.math.datastructuresFijijavadoc
FloatArrayClassmpicbg.imglib.container.basictypecontainer.arrayFijijavadoc

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FloatArrayClassstitchingFijijavadoc
FloatArray2DTitle: PhaseCorrelation2D Copyright: Copyright (c) 2007Classmpi.fruitfly.math.datastructuresFijijavadoc
FloatArray2DClassstitchingFijijavadoc
FloatArray3D Copyright: Copyright (c) 2007 This program is free software; you can redistribute it and/orClassmpi.fruitfly.math.datastructuresFijijavadoc
FloatArray3DClassstitchingFijijavadoc
FloatArray4D Copyright: Copyright (c) 2006Version:1.Classmpi.fruitfly.math.datastructuresFijijavadoc
FloatBuffer Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandClassimagewareFijijavadoc
FloatDynamicContainerClassmpicbg.imglib.container.dynamicFijijavadoc
FloatDynamicContainerAccessorClassmpicbg.imglib.container.dynamicFijijavadoc
FloatElementClassview5dFijijavadoc
FloatImageAn image containing up to 5D elements of type float.Classimagescience.imageFijijavadoc
FloatImageOperationClassscript.imglib.math.fnFijijavadoc
FloatImagePlusImagePlusContainer for float-stored data.Classmpicbg.imglib.container.imageplusFijijavadoc
FloatMatrixClassvibFijijavadoc
FloatMatrixNClassmath3dFijijavadoc
FloatPointwise Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandClassimagewareFijijavadoc
FloatProcess Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandClassimagewareFijijavadoc
FloatProcessorChunkClassedu.utexas.clm.archipelago.ijsupportFijijavadoc
FloatProcessorT2Classini.trakem2.imagingFijijavadoc
FloatSet Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandClassimagewareFijijavadoc
FloatTypeClassmpicbg.imglib.type.numeric.realFijijavadoc
Flood_FillClassprocess3dFijijavadoc
FloorClassscript.imglib.mathFijijavadoc
FlowThis pass implements dataflow analysis for Java programs.Classcom.sun.tools.javac.compFijijavadoc
Flow3JColorNoiseMapperThis class maps a flow field in color spotnoise field.ClassFlowJFijijavadoc

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Flow3JDynamicColorMapperThis class maps dynamic color of a flow field.ClassFlowJFijijavadoc
FlowJ_ClassFijijavadoc
FlowJColorNoiseMapperThis class maps a flow field in colored spotnoise format.ClassFlowJFijijavadoc
FlowJDisplayOFDisplay class implements the 2D display of 2D flow fields in different formats.ClassFlowJFijijavadoc
FlowJDynamicColorThis is a class that implements 2D and 3D Dynamic Color Mapping.ClassFlowJFijijavadoc
FlowJDynamicColorMapperClassFlowJFijijavadoc
FlowJErrorClassFlowJFijijavadoc
FlowJExceptionClassFlowJFijijavadoc
FlowJFleetClassFlowJFijijavadoc
FlowJFlowThis class implements 2D flow fields and methods (including reading and writing and utility methods).ClassFlowJFijijavadoc
FlowJLucasThis is a class that implements the Lucas and Kanade optical flow algorithm.ClassFlowJFijijavadoc
FlowJMapperThis class is the superclass for the OF display mappers.ClassFlowJFijijavadoc
FlowJQuiverMapperThis class maps a quiver map of a flow field.ClassFlowJFijijavadoc
FlowJSinghClassFlowJFijijavadoc
FlowJSpotNoiseThis class implements spot noise displaying of flow fields.ClassFlowJFijijavadoc
FlowJSpotNoiseMapperThis class maps spotnoise of a flow field.ClassFlowJFijijavadoc
FlowJUrasClassFlowJFijijavadoc
FlowJUserInterfaceThis class links the FlowJ classes to the ImageJ interface.ClassFlowJFijijavadoc
FloydSteinbergDitheringClassmpicbg.imglib.algorithm.floydsteinbergFijijavadoc
FMathPerforms elementary mathematical operations and function evaluations.Classimagescience.utilityFijijavadoc
FMath The FMath class provides methods for carrying out a number of elementary mathematical operations.ClassimagewareFijijavadoc
FolderWatcherClassfsalignFijijavadoc
ForLoopTreeA tree node for a basic 'for' loop statement.Interfacecom.sun.source.treeFijijavadoc
FormatEntryA list entry for the configuration window's Formats tab.Classloci.plugins.configFijijavadoc
FormatterConverts floating-point numbers to formatted strings.Classimagescience.utilityFijijavadoc

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ForwardingFileObjectForwards calls to a given file object.Classjavax.toolsFijijavadoc
ForwardingJavaFileManagerForwards calls to a given file manager.Classjavax.toolsFijijavadoc
ForwardingJavaFileObjectForwards calls to a given file object.Classjavax.toolsFijijavadoc
FourierConvolutionClassmpicbg.imglib.algorithm.fftFijijavadoc
FourierTransformClassmpicbg.imglib.algorithm.fftFijijavadoc
Frangi_Classfiji.featuresFijijavadoc
FreeHandProfileClassini.trakem2.displayFijijavadoc
FromContinuousBranchesClassfiji.plugin.trackmate.graphFijijavadoc
FromOMETranslatorAbstract base class for all io.Classio.scif.ome.translatorsFijijavadoc
FS_Align_TrakEM2ClassfsalignFijijavadoc
FSAlignListenerClassfsalignFijijavadoc
FSInfoGet meta-info about files.Classcom.sun.tools.javac.fileFijijavadoc
FSLoaderA class to rely on memory only; except images which are rolled from a folder or their original location and flushed when memory is needed for more.Classini.trakem2.persistenceFijijavadoc
FullInfoMeshClasscustomnodeFijijavadoc
FunctionInterfacempicbg.imglib.functionFijijavadoc
Function1Interface for function that compute values from a single input and store it in Author:Jean-Yves InevezInterfacefiji.plugin.trackmate.graphFijijavadoc
Function2Interface for function that compute values from a two inputs and store it in Author:Jean-Yves InevezInterfacefiji.plugin.trackmate.graphFijijavadoc
FusionManages the fusion for all types except the overlayfusionAuthor:Stephan Preibisch (stephan.Classmpicbg.stitching.fusionFijijavadoc
FusionClassspim.fiji.plugin.fusionFijijavadoc
FusionControlClassmpicbg.spim.fusionFijijavadoc
FusionHelperClassspim.process.fusionFijijavadoc
FusionImageLoaderThis ImgLoader loads images that represent a 3D stack as a sequence of slice with one image file per slice, such as created by StephanClassbdv.ij.export.imgloaderFijijavadoc
FusionPopupClassspim.fiji.spimdata.explorer.popupFijijavadoc
FusionResultClassbdv.ij.exportFijijavadoc
GaborCosThis class implements a Gabor (even) cosine wave 1d convolution kernel for separated convolutions.ClassvolumeFijijavadoc

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GaborSinThis class implements a Gabor (odd) sine wave 1d convolution kernel for separated convolutions.ClassvolumeFijijavadoc
GammaClassimglib.ops.operator.unaryFijijavadoc
GammaFunctionClasspal.mathFijijavadoc
GammaGeneratorGamma random number generator of positive integer order.Classimagescience.randomFijijavadoc
GapClosingCostFunctionGap closing cost function used with LAPTracker.Classfiji.plugin.trackmate.tracking.oldlap.costfunctionFijijavadoc
GaussClassscript.imglib.algorithmFijijavadoc
GaussContentClassmpicbg.spim.fusionFijijavadoc
GaussContentFactoryClassmpicbg.spim.fusionFijijavadoc
GaussianThis is a 1D separated 0-th order Gaussian convolution kernel.ClassvolumeFijijavadoc
Gaussian2DThis is a 2D separated 0 order Gaussian convolution kernel.ClassvolumeFijijavadoc
Gaussian3DThis is a 3D separated 0 order Gaussian convolution kernel.ClassvolumeFijijavadoc
Gaussian_Stack_FocuserClasssc.fiji.timelapseFijijavadoc
GaussianBlurSmooth with a Gaussian.Classini.trakem2.imaging.filtersFijijavadoc
GaussianConvolutionClassmpicbg.imglib.algorithm.gaussFijijavadoc
GaussianConvolution2Classmpicbg.imglib.algorithm.gaussFijijavadoc
GaussianConvolution3Computes a Gaussian Convolution on any Type(A) for which is defined how to convert it into a NumericType(B) on which the convolution is performed and back to the desired output Type(C).Classmpicbg.imglib.algorithm.gaussFijijavadoc
GaussianConvolution4Classmpicbg.imglib.algorithm.gaussFijijavadoc
GaussianConvolutionRealClassmpicbg.imglib.algorithm.gaussFijijavadoc
GaussianDerivativeThis class implement a scale space Gaussian n-th order derivative 1d convolution kernel for separated convolutions.ClassvolumeFijijavadoc
GaussianGenerationCallbackInterfacefeaturesFijijavadoc
GaussianGeneratorGaussian random number generator.Classimagescience.randomFijijavadoc
GaussianMaskFitClassprocessFijijavadoc
GaussianMultiDLMA n-dimensional Gaussian peak function, representing an elliptical Gaussian, with axis constrained to be aligned with the main axis.Classmpicbg.imglib.algorithm.peakFijijavadoc
GaussianPeakFitterNDA simple class fit a gaussian to the peaks in a n-dim, 0-background The gaussian can have a different sigma in any direction, but the ellipse main axes still needClassmpicbg.imglib.algorithm.peakFijijavadoc
GaussianStackFocuserClassspimopenerFijijavadoc

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GenThis pass maps flat Java (i.Classcom.sun.tools.javac.jvmFijijavadoc
GeneralClassmpi.fruitfly.mathFijijavadoc
GeneralizedDEOptimizerProvides an general interface to the DifferentialEvolution class that is not tied to a certain number of parameters (as DifferentialEvolution is).Classpal.mathFijijavadoc
Generic_Resave_HDF5Classspim.fiji.plugin.resaveFijijavadoc
GenericAffineTile2DClassmpicbg.trakem2.alignFijijavadoc
GenericByteTypeClassmpicbg.imglib.type.numeric.integerFijijavadoc
GenericCursorLinkClassmpicbg.imglib.cursor.linkFijijavadoc
GenericDialogAppenderInterfacespim.fiji.plugin.utilFijijavadoc
GenericDialogPlusThe GenericDialogPlus class enhances the GenericDialog by a few additional methods.Classfiji.util.guiFijijavadoc
GenericIntTypeClassmpicbg.imglib.type.numeric.integerFijijavadoc
GenericLoadParseQueryXMLInterface for interactive parsing of spimdata XMLsAuthor:Stephan Preibisch (stephan.Classspim.fiji.plugin.queryXMLFijijavadoc
GenericShortTypeClassmpicbg.imglib.type.numeric.integerFijijavadoc
GeodesicActiveContour Caselles et.Classlevelsets.algorithmFijijavadoc
GeometricHasherClass that actually computes the geometric hashingAuthor:Stephan Preibisch (stephan.Classspim.process.interestpointregistration.geometrichashingFijijavadoc
GeometricHashingClassspim.process.interestpointregistration.geometrichashingFijijavadoc
GeometricHashingPairwiseClassspim.process.interestpointregistration.geometrichashingFijijavadoc
GeometricHashingParametersClassspim.process.interestpointregistration.geometrichashingFijijavadoc
GeometryCreatorClassoctreeFijijavadoc
GeometryCreatorThis class is a helper class whose main task is to create Geometry objects for a specified axis and direction.ClassvoltexFijijavadoc
Gif_Stack_WriterClassioFijijavadoc
GlobalErrorStatisticsInterfacempicbg.spim.registration.bead.errorFijijavadoc
GlobalErrorStatisticsImplClassmpicbg.spim.registration.bead.errorFijijavadoc
GlobalOptClassspim.process.interestpointregistrationFijijavadoc
GlobalOptimizationClassmpicbg.stitchingFijijavadoc
GlobalOptimizationSubsetDefines a subset of views that need to be matched and then a global optimization In case of a registration of individual timepoints, each timepoint would be oneClassspim.process.interestpointregistration.optimizationtypesFijijavadoc

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GlobalOptimizationTypeA certain type of global optimization, must be able to define all view pairs that need to be matched and optimized inidivduallyClassspim.process.interestpointregistration.optimizationtypesFijijavadoc
GradientClassfiji.plugin.volumeviewerFijijavadoc
GradientClassprocess3dFijijavadoc
Gradient_Classprocess3dFijijavadoc
GradientWatershedThis class labels an image where the objects in question have edges that are defined by sharp intensity gradients and haveClassmpicbg.imglib.algorithm.labelingFijijavadoc
GraphClass wrapping some basic structures that are used to represent a graph.ClassgraphcutFijijavadoc
GraphClassini.trakem2.analysisFijijavadoc
GraphThis class represents an undirected graph to allow visiting the skeleton in an efficient wayClasssc.fiji.analyzeSkeletonFijijavadoc
Graph_CutPlugin interface to the graph cut algorithm.ClassgraphcutFijijavadoc
GraphContentNodeGraphContentNode is a 3D Viewer ContentNode designed to be the structure returned by the AnalyzedGraph class as a Java 3D representation of the vascular treeClassvolumeCalculatorFijijavadoc
GraphCutClass implementing the grach cut algorithm.ClassgraphcutFijijavadoc
GrapherDescriptorClassfiji.plugin.trackmate.gui.descriptorsFijijavadoc
GrapherPanelClassfiji.plugin.trackmate.guiFijijavadoc
GraphFrameClassfiji.plugin.timelapsedisplayFijijavadoc
GraphFrameClassspim.process.interestpointregistration.registrationstatisticsFijijavadoc
GraphicalMediaWikiClientClassfijiFijijavadoc
GraphicsSourceInterfaceini.trakem2.display.graphicsFijijavadoc
GraphSegmentSplitterClassfiji.plugin.trackmate.tracking.sparselap.costmatrixFijijavadoc
GraphUtilsClassfiji.plugin.trackmate.graphFijijavadoc
GrayMorphology_ClassFijijavadoc
GreenClassscript.imglib.colorFijijavadoc
GreyScaleFilterClasslevelsets.filterFijijavadoc
GreyTransformationClassvib.app.moduleFijijavadoc
GreyValueErosionPerforms a grey value erosion operation on the input using a defineable mask.Classlevelsets.filterFijijavadoc
GridLayoutClassstitchingFijijavadoc

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GridTypeClasspluginFijijavadoc
GroupingModeClassini.trakem2.displayFijijavadoc
GuiClassfiji.plugin.volumeviewerFijijavadoc
GuiBuilderClassguiFijijavadoc
GUIButtonClassorg.imagearchive.lsm.toolbox.guiFijijavadoc
GUIHelperClassspim.fiji.plugin.utilFijijavadoc
GUIMakerClassorg.imagearchive.lsm.toolbox.guiFijijavadoc
GUIMenuItemClassorg.imagearchive.lsm.toolbox.guiFijijavadoc
GuiUtilsClassfiji.plugin.trackmate.guiFijijavadoc
HandleExtraFileTypesClassFijijavadoc
Harris_Corner_DetectorClassprocess3dFijijavadoc
HDF5AccessHackClassbdv.img.imarisFijijavadoc
Hdf5ImageLoaderClassbdv.img.hdf5Fijijavadoc
Hdf5VolatileShortArrayLoaderClassbdv.img.hdf5Fijijavadoc
HDFPreprocessorClassio.scif.formats.imarisFijijavadoc
HDFUtilsClassio.scif.formats.imarisFijijavadoc
HDFWriterClassio.scif.formats.imarisFijijavadoc
HeartBeatClassedu.utexas.clm.archipelago.dataFijijavadoc
Helmholtz_AnalysisThis plugin uses the Helmholtz equation to estimage the wavelength of a harmonic image.ClassFijijavadoc
HelpDialogClassbdv.toolsFijijavadoc
HessianComputes Hessian eigenimages.Classimagescience.featureFijijavadoc
HessianThis class implements computing the Hessian tensor matrix of an image, and computing the determinant (to detect blobs) and largest eigenvalues (to detect edges).ClassvolumeFijijavadoc
Hessian_CP_MeasuresClassfeaturesFijijavadoc
HessianEvalueProcessorClassfeaturesFijijavadoc
HistogramClassmpicbg.imglib.algorithm.histogramFijijavadoc

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HistogramAn histogram of the image (or an image computed from an IFunction) between its minimum and maximum values,Classscript.imglib.analysisFijijavadoc
HistogramClassspim.fiji.plugin.thinoutFijijavadoc
Histogram2DRepresents the creation of a 2D histogram between two images.ClassalgorithmsFijijavadoc
Histogram_2DClassutilFijijavadoc
HistogramBinHistogramBin is used by to represent the bins of a histogram.Classmpicbg.imglib.algorithm.histogramFijijavadoc
HistogramBinFactoryThe HistogramBinFactory interface is used by Histogram to generate HistogramBins and HistogramKeys.Interfacempicbg.imglib.algorithm.histogramFijijavadoc
HistogramKeyHistogramKeys are used by Histogram to key HistogramBins Author:Larry LindseyClassmpicbg.imglib.algorithm.histogramFijijavadoc
HistogramMatcherClasshistogram2Fijijavadoc
HistogramPlotClasshistogram2Fijijavadoc
HistoryA class to represent a generic undo/redo history.Classini.trakem2.utilsFijijavadoc
HomogeneousMappingClassmpicbg.panoramaFijijavadoc
HomographyModel2DClassmpicbg.trakem2.transformFijijavadoc
HoughLineTransformA class that extends HoughTransform to handle Hough Line voting over an edge map.Classmpicbg.imglib.algorithm.transformationFijijavadoc
HoughLineTransformClassscript.imglib.algorithmFijijavadoc
HoughTransformClassmpicbg.imglib.algorithm.transformationFijijavadoc
HSBClassscript.imglib.colorFijijavadoc
HSBOpClassscript.imglib.color.fnFijijavadoc
HtmlPageLoaderClassorg.imagearchive.lsm.toolbox.guiFijijavadoc
HueClassscript.imglib.colorFijijavadoc
HuiskenImageLoaderThis ImgLoader implementation uses Benjamin Schmid's to load images in Jan Husiken's format.Classbdv.ij.export.imgloaderFijijavadoc
HungarianAlgorithmAn implementation of the classic Hungarian algorithm for the assignment problem.Classfiji.plugin.trackmate.tracking.oldlap.hungarianFijijavadoc
HybridDateFormatSimpleDateFormat provides convenient methods for parsing and formatting dates using Gregorian calendars (see java.ClassFijijavadoc
HyperSphereIteratorIterate over all pixels in an n-dimensional sphere.Classmpicbg.imglib.cursor.specialFijijavadoc
Hyperstack_rearrangerClassfiji.stacksFijijavadoc
HyperStackDisplayerClassfiji.plugin.trackmate.visualization.hyperstackFijijavadoc

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HyperStackDisplayerFactoryClassfiji.plugin.trackmate.visualization.hyperstackFijijavadoc
HyperVolumeThis is a class that implements a float hyper (4D) volumes and operations including convolutions on it.ClassvolumeFijijavadoc
Hypervolume_OpenerOpens a folder of image stacks as one big stack ("Hypervolume").ClassFijijavadoc
HypotClassscript.imglib.mathFijijavadoc
I5D_aboutClassFijijavadoc
I5DResourceProvides Image5D utility methods.Classimagescience.utilityFijijavadoc
I5DVirtualStackThis class represents an array of disk-resident images.Classi5dFijijavadoc
Icns_ReaderClassioFijijavadoc
Icns_WriterClassioFijijavadoc
IcnsCodecClassiconsupport.icnsFijijavadoc
ICO_ReaderClassioFijijavadoc
ICO_WriterClassioFijijavadoc
ICOConstantsProvides constants used with ICO format.Classnet.sf.image4j.codec.icoFijijavadoc
ICODecoderDecodes images in ICO format.Classnet.sf.image4j.codec.icoFijijavadoc
ICOEncoderEncodes images in ICO format.Classnet.sf.image4j.codec.icoFijijavadoc
ICOImageContains a decoded ICO image, as well as information about the source encoded ICO image.Classnet.sf.image4j.codec.icoFijijavadoc
IconEntryRepresents an IconEntry structure, which contains information about an ICO image.Classnet.sf.image4j.codec.icoFijijavadoc
IconSuiteClassiconsupport.icnsFijijavadoc
ICPClassmpicbg.icpFijijavadoc
ICSTranslatorContainer class for to and from ICS/OME formatsAuthor:Mark Hiner hinerm at gmail.Classio.scif.ome.translatorsFijijavadoc
IcyTrackExporterClassfiji.plugin.trackmate.actionFijijavadoc
IcyTrackFormatWriterClassfiji.plugin.trackmate.ioFijijavadoc
IcyXmlReaderA reader for the XML files generated in the TrackManager of the Icy software The reader requires a calibration s to operate, so as to generate a properClassfiji.plugin.trackmate.ioFijijavadoc
IdDialogBio-Formats Importer id chooser dialog box.Classloci.plugins.inFijijavadoc
IdentifierTreeA tree node for an identifier expression.Interfacecom.sun.source.treeFijijavadoc

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IdentifyClasslineageFijijavadoc
IDT_Interpolate_BinaryClassvibFijijavadoc
IEEEremainderClassscript.imglib.mathFijijavadoc
IepGuiGUI for the plugin Image_Expression_Parser When launched it displays a window allowing the user to enter a mathematical expression,Classfiji.processFijijavadoc
IFilterInterfaceini.trakem2.imaging.filtersFijijavadoc
IFormatWidgetsInterface for defining custom widgets for a specific file format reader.Interfaceloci.plugins.configFijijavadoc
IFT_Classprocess3dFijijavadoc
IfTreeA tree node for an 'if' statement.Interfacecom.sun.source.treeFijijavadoc
IFunctionInterfacescript.imglib.math.fnFijijavadoc
IHDF5AccessInterfacebdv.img.imarisFijijavadoc
IJ1LogServiceA log service adapter for ImageJ 1.ClassfijiFijijavadoc
IJ1PatcherPatch ij.ClassfijiFijijavadoc
IJ1StatusServiceA status service adapter for ImageJ 1.ClassfijiFijijavadoc
IJ_Alt_Key_ListenerClassfijiFijijavadoc
IJ_RobotClassFijijavadoc
IJAdapterClassij3dFijijavadoc
IJErrorA class to easily show the stack trace of an error in different operating systems.Classini.trakem2.utilsFijijavadoc
IJEventMulticasterMulticaster for events special to ImageJ Example how to implement an object, which fires DisplayChangeEvents using theClassFijijavadoc
IJLoggerClassedu.utexas.clm.archipelago.utilFijijavadoc
IJPopupLoggerClassedu.utexas.clm.archipelago.utilFijijavadoc
IJStatusEchoerEchoes status messages to the ImageJ status bar.Classloci.plugins.utilFijijavadoc
IlluminationDefines an illumination direction which is part of the ViewSetup.Classmpicbg.spim.data.sequenceFijijavadoc
IlluminationChannelClassorg.imagearchive.lsm.toolbox.info.scaninfoFijijavadoc
ImageAbstract base class for images containing up to 5D elements.Classimagescience.imageFijijavadoc
ImageClassmpicbg.imglib.imageFijijavadoc

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Image3DMenubarClassij3dFijijavadoc
Image3DUniverseClassij3dFijijavadoc
Image5D (t).Classi5dFijijavadoc
Image5D_ExtensionsMacro extensions for Image5D.ClassFijijavadoc
Image5D_Stack_to_RGBConverts the current timeframe of an Image5D to an RGB stack using the current view settings.ClassFijijavadoc
Image5D_to_StackClassFijijavadoc
Image5DAdapterClassadapterFijijavadoc
Image5DCanvasClassi5d.guiFijijavadoc
Image5DLayout image and a channelControl panel to the right of the image.Classi5d.guiFijijavadoc
Image5DWindowImageWindow for Image5Ds.Classi5d.guiFijijavadoc
Image_Expression_ParserImage expression parser This plugins parses mathematical expressions and compute results using images as variables.Classfiji.processFijijavadoc
Image_FusionClassspim.fiji.pluginFijijavadoc
ImageAccessImageAccess is an interface layer to facilitate the access to the pixels of ImageJ images.ClassimagewareFijijavadoc
ImageAccessImageAccess is an interface layer to facilitate the access to the pixels of ImageJ images.ClasswaveletsFijijavadoc
ImageAdapterClassadapterFijijavadoc
ImageArrayConverterClassmpi.fruitfly.generalFijijavadoc
ImageBlockDeblockA FijiArchipelago-compatible class for splitting an image into smaller blocks, then recombining into the original image shape, potentially after processing.Classedu.utexas.archipelago.imageFijijavadoc
ImageButtonImageButton - A button component with an image in itAuthor:DTAI, IncorporatedSee Also:Serialized FormClassvib.segmentFijijavadoc
ImageBytesRepresent an image with byte arrays: 2 channels: grey + alphaClassini.trakem2.persistenceFijijavadoc
ImageCalculatorClassmpicbg.imglib.algorithm.mathFijijavadoc
ImageCalculatorInPlaceClassmpicbg.imglib.algorithm.mathFijijavadoc
ImageCalculatorRevisedThis plugin implements the Process/Image Calculator command.ClassutilFijijavadoc
ImageCanvasClassview5dFijijavadoc
ImageCanvas3DClassij3dFijijavadoc
ImageCollectionElementClassmpicbg.stitchingFijijavadoc

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ImageComputationInterfacescript.imglib.math.fnFijijavadoc
ImageContainerClasslevelsets.ijFijijavadoc
ImageConverterClassmpicbg.imglib.algorithm.mathFijijavadoc
ImageDataInterfaceini.trakem2.displayFijijavadoc
ImageDirectoryClassorg.imagearchive.lsm.reader.infoFijijavadoc
ImageErrClassview5dFijijavadoc
ImageFactoryClassmpicbg.imglib.imageFijijavadoc
ImageFileFilterFilters out non-accepted image formats.Classini.trakem2.ioFijijavadoc
ImageFileHeaderClassini.trakem2.ioFijijavadoc
ImageFilterClassmpi.fruitfly.registrationFijijavadoc
ImageFilterClassorg.imagearchive.lsm.toolbox.guiFijijavadoc
ImageFocusListenerClassorg.imagearchive.lsm.toolbox.guiFijijavadoc
ImageFunctionClassscript.imglib.math.fnFijijavadoc
ImageInformationClassstitchingFijijavadoc
ImageInterpolationClassmpicbg.stitching.fusionFijijavadoc
ImageJMain entry point into ImageJ.Classnet.imagejFijijavadoc
ImageJ1UISimple ImageJ 1.Classfiji.updaterFijijavadoc
ImageJ3DViewerClassij3dFijijavadoc
ImageJ_3D_ViewerClassij3dFijijavadoc
ImageJCommandListenerIntercept ImageJ menu commands if the current active image is a FakeImagePlus (from a ini.Classini.trakem2.displayFijijavadoc
ImageJFunctionsClassmpicbg.imglib.image.display.imagejFijijavadoc
ImageJVirtualDisplayClassmpicbg.imglib.image.display.imagejFijijavadoc
ImageJVirtualStackClassmpicbg.imglib.image.display.imagejFijijavadoc
ImageListenerClassfsalignFijijavadoc
ImageMetaDataClassvib.appFijijavadoc

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ImageOpenerReads in an imglib Image using Bio-Formats.Classmpicbg.imglib.ioFijijavadoc
ImageOverlayThis class implements an overlay based on an image.ClassgraphcutFijijavadoc
ImageOverlayThis class implements an overlay based on an image.ClasssioxFijijavadoc
ImagePaneGUI Component to display a BufferedImage with a zoom factor and an optional selection.Classorg.siox.exampleFijijavadoc
ImagePlusAdapterClassmpicbg.imglib.imageFijijavadoc
ImagePlusChooserClassfiji.plugin.trackmate.gui.panels.componentsFijijavadoc
ImagePlusContainerA Container that stores data in an aray of 2d-slices each as a linear array of basic types.Classmpicbg.imglib.container.imageplusFijijavadoc
ImagePlusContainerFactoryFactory that creates an appropriate ImagePlusContainer.Classmpicbg.imglib.container.imageplusFijijavadoc
ImagePlusCursorBasic Iterator for a ImagePlusContainersAuthor:Stephan Preibisch, Stephan SaalfeldClassmpicbg.imglib.cursor.imageplusFijijavadoc
ImagePlusCursor2DBasic Iterator for 2d ImagePlusContainersAuthor:Stephan Saalfeld, Stephan Saalfeld Classmpicbg.imglib.cursor.imageplusFijijavadoc
ImagePlusImgLoaderThis BasicImgLoader implementation returns a wrapped, converted ImagePlus.Classbdv.ij.export.imgloaderFijijavadoc
ImagePlusLocalizableByDimCursorPositionable for a ImagePlusContainersAuthor:Stephan Preibisch, Stephan SaalfeldClassmpicbg.imglib.cursor.imageplusFijijavadoc
ImagePlusLocalizableByDimOutOfBoundsCursorPositionable with OutOfBoundsStrategy for a ImagePlusContainersClassmpicbg.imglib.cursor.imageplusFijijavadoc
ImagePlusLocalizableCursorLocalizing Iterator for a ImagePlusContainersAuthor:Stephan Preibisch, Stephan SaalfeldClassmpicbg.imglib.cursor.imageplusFijijavadoc
ImagePlusLocalizablePlaneCursorClassmpicbg.imglib.cursor.imageplusFijijavadoc
ImagePlusReaderA high-level reader for ImagePlus objects.Classloci.plugins.inFijijavadoc
ImagePlusTimePointClassmpicbg.stitchingFijijavadoc
ImagePortionClassspim.process.fusionFijijavadoc
ImagePreprocessorAny class implementing this interface is suitable as an image preprocessor for a TrakEM2 project.Interfaceini.trakem2.imagingFijijavadoc
ImagePreviewClassorg.imagearchive.lsm.toolbox.guiFijijavadoc
ImageProcessorReaderA low-level reader for ImageProcessor objects.Classloci.plugins.utilFijijavadoc
ImageProcessorSourceRetrieves ImageJ image processors from an image reader.Classloci.plugins.utilFijijavadoc
ImageProgressContainerClasslevelsets.ijFijijavadoc
ImagePropertiesInterfacempicbg.imglib.containerFijijavadoc
ImageSaverProvides the necessary thread-safe image file saver utilities.Classini.trakem2.ioFijijavadoc

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ImageScienceContains the name and version number of the ImageScience library.ClassimagescienceFijijavadoc
ImageStackImageLoaderClassbdv.img.imagestackFijijavadoc
ImageStatisticsClassnet.imglib2.algorithm.mathFijijavadoc
ImageTransformClassmpicbg.imglib.algorithm.transformationFijijavadoc
ImageUtilProvides utility methods for handling images (java.Classnet.sf.image4j.utilFijijavadoc
ImageWare Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandInterfaceimagewareFijijavadoc
ImageWindow3DClassij3dFijijavadoc
ImarisClassbdv.img.imarisFijijavadoc
ImarisFormatSCIFIO Format supporting the writer for Imaris 5.Classio.scif.formatsFijijavadoc
ImarisImageLoaderClassbdv.img.imarisFijijavadoc
ImarisVolatileByteArrayLoaderClassbdv.img.imarisFijijavadoc
ImarisVolatileFloatArrayLoaderClassbdv.img.imarisFijijavadoc
ImarisVolatileShortArrayLoaderClassbdv.img.imarisFijijavadoc
ImarisWriterClassio.scif.formats.imarisFijijavadoc
ImgExportInterfacespim.process.fusion.exportFijijavadoc
ImgExportTitleInterfacespim.process.fusion.exportFijijavadoc
ImgLibA simple wrapper class that is supposed to contain only functions for scripting.Classscript.imglibFijijavadoc
ImgLib1Provides non-copying wrapping from Imglib1 to Imglib2 (cell, array)Author:Stephan Preibisch (stephan.Classmpicbg.imglib.wrapperFijijavadoc
ImgLib2Provides non-copying wrapping from Imglib2 to Imglib1 (cell, array)Author:Stephan Preibisch (stephan.Classmpicbg.imglib.wrapperFijijavadoc
ImgLib2TempClassspim.fijiFijijavadoc
ImgLibAbsClassfiji.expressionparser.functionFijijavadoc
ImgLibAddClassfiji.expressionparser.functionFijijavadoc
ImgLibArcCosineClassfiji.expressionparser.functionFijijavadoc
ImgLibArcSineClassfiji.expressionparser.functionFijijavadoc
ImgLibArcTangentClassfiji.expressionparser.functionFijijavadoc

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ImgLibArcTangent2Classfiji.expressionparser.functionFijijavadoc
ImgLibBandPassFilterClassfiji.expressionparser.functionFijijavadoc
ImgLibCeilClassfiji.expressionparser.functionFijijavadoc
ImgLibComparisonClassfiji.expressionparser.functionFijijavadoc
ImgLibCosineClassfiji.expressionparser.functionFijijavadoc
ImgLibDitheringClassfiji.expressionparser.functionFijijavadoc
ImgLibDivideClassfiji.expressionparser.functionFijijavadoc
ImgLibExceptionClassmpicbg.imglib.exceptionFijijavadoc
ImgLibExpClassfiji.expressionparser.functionFijijavadoc
ImgLibFloorClassfiji.expressionparser.functionFijijavadoc
ImgLibFunctionInterfacefiji.expressionparser.functionFijijavadoc
ImgLibGaussConvClassfiji.expressionparser.functionFijijavadoc
ImgLibLogClassfiji.expressionparser.functionFijijavadoc
ImgLibLogicalClassfiji.expressionparser.functionFijijavadoc
ImgLibModulusClassfiji.expressionparser.functionFijijavadoc
ImgLibMultiplyClassfiji.expressionparser.functionFijijavadoc
ImgLibNormalizeClassfiji.expressionparser.functionFijijavadoc
ImgLibNumberFactoryThis is a number factory that will be used to generate internal representation of number within the expression parser logic.Classfiji.expressionparserFijijavadoc
ImgLibOperatorSetClassfiji.expressionparserFijijavadoc
ImgLibParserClassfiji.expressionparserFijijavadoc
ImgLibPowerClassfiji.expressionparser.functionFijijavadoc
ImgLibRoundClassfiji.expressionparser.functionFijijavadoc
ImgLibSaverClassmpicbg.spim.ioFijijavadoc
ImgLibSineClassfiji.expressionparser.functionFijijavadoc
ImgLibSquareRootClassfiji.expressionparser.functionFijijavadoc

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ImgLibSubtractClassfiji.expressionparser.functionFijijavadoc
ImgLibTangentClassfiji.expressionparser.functionFijijavadoc
ImgLibUMinusClassfiji.expressionparser.functionFijijavadoc
ImgLibUtilsClassfiji.expressionparserFijijavadoc
ImgLibVolumeThis class encapsulates an mpicbg.Classini.trakem2.utilsFijijavadoc
ImgLoaderA BasicImgLoader that is able to also provide each image converted to FloatType.Interfacempicbg.spim.data.sequenceFijijavadoc
ImgLoaderHintInterfacempicbg.spim.data.generic.sequenceFijijavadoc
ImgLoaderHintsDefault set of ImgLoaderHint.Classmpicbg.spim.data.generic.sequenceFijijavadoc
ImgLoaderIoAnnotation for a class that creates a BasicImgLoader for a specific format (the format is specified in the XML "ImageLoader" element).Classmpicbg.spim.data.generic.sequenceFijijavadoc
ImgLoadersClassmpicbg.spim.data.generic.sequenceFijijavadoc
ImgPanelClassview5dFijijavadoc
ImgTitlerInterfacespim.process.fusion.exportFijijavadoc
Implicit_Interpolate_BinaryClassFijijavadoc
ImporterCore logic for the Bio-Formats Importer ImageJ plugin.Classloci.plugins.inFijijavadoc
ImporterDialogAbstract superclass of importer dialogs.Classloci.plugins.inFijijavadoc
ImporterMetadataHelper class for storing original metadata key/value pairs.Classloci.plugins.inFijijavadoc
ImporterOptionsHelper class for managing Bio-Formats Importer options.Classloci.plugins.inFijijavadoc
ImporterPrompterHelper class for presenting the user with dialog boxes for configuring importer options.Classloci.plugins.inFijijavadoc
ImportPlugInImageJ plugin to import a raw image from xml/hdf5.Classbdv.ijFijijavadoc
ImportProcessManages the import preparation process.Classloci.plugins.inFijijavadoc
ImportStepAn enumeration of the steps in the import preparation process.Classloci.plugins.inFijijavadoc
ImportTreeA tree node for an import statement.Interfacecom.sun.source.treeFijijavadoc
IndependentSpotFeatureAnalyzerClassfiji.plugin.trackmate.features.spotFijijavadoc
IndividualTimepointRegistrationA registration type where each timepoint is registered individuallyAuthor:Stephan Preibisch (stephan.Classspim.process.interestpointregistration.optimizationtypesFijijavadoc
InferHelper class for type parameter inference, used by the attribution phase.Classcom.sun.tools.javac.compFijijavadoc

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InferenceClassinferenceFijijavadoc
InferenceCallerInterfaceinferenceFijijavadoc
InfoFrameClassorg.imagearchive.lsm.toolbox.guiFijijavadoc
InfoHeaderRepresents a bitmap InfoHeader structure, which provides header information.Classnet.sf.image4j.codec.bmpFijijavadoc
InfoNodeClassorg.imagearchive.lsm.toolbox.guiFijijavadoc
InfoPaneClassfiji.plugin.trackmate.visualization.trackschemeFijijavadoc
InfoPanelClassvib.segmentFijijavadoc
InitFilterDescriptorClassfiji.plugin.trackmate.gui.descriptorsFijijavadoc
InitFilterPanelClassfiji.plugin.trackmate.gui.panelsFijijavadoc
InitializeViewerStateClassbdv.toolsFijijavadoc
InputActionBindingsMaintains lists of ActionMaps and InputMaps, which are chained to a concatenated InputMap and aClassbdv.viewerFijijavadoc
InputCheckThis class implements some basic checks for the input image data.ClassalgorithmsFijijavadoc
InputStreamLoggerClassedu.utexas.clm.archipelago.utilFijijavadoc
Insert_StackClassvideo2Fijijavadoc
InspectJarClassfijiFijijavadoc
Check Code Snippets / Samples for fiji.InspectJar
InspectPatchTrianglesModeA view-only mode that shows, using LayerSet.Classini.trakem2.display.inspectFijijavadoc
InstallWizardA wizard for walking users through installation of third party libraries and plugins used by the Bio-Formats plugins.Classloci.plugins.configFijijavadoc
InstanceOfTreeA tree node for an 'instanceof' expression.Interfacecom.sun.source.treeFijijavadoc
IntAccessInterfacempicbg.imglib.container.basictypecontainerFijijavadoc
IntArrayClassfiji.utilFijijavadoc
IntArrayA dynamic array of int values.Classimagescience.arrayFijijavadoc
IntArrayClassmpicbg.imglib.container.basictypecontainer.arrayFijijavadoc
IntArrayListAn ArrayList that uses primitive ints for the key rather than objects to avoid costly usage of Integer wrappers.Classorg.siox.utilFijijavadoc
IntArraySorterSorts and int[] according to a custom comparator.ClassalgorithmsFijijavadoc
IntComparatorInterfacealgorithmsFijijavadoc

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IntDynamicContainerClassmpicbg.imglib.container.dynamicFijijavadoc
IntDynamicContainerAccessorClassmpicbg.imglib.container.dynamicFijijavadoc
IntegerElementClassview5dFijijavadoc
IntegerFieldClassini.trakem2.utilsFijijavadoc
IntegerPatternClass with static methods to deal with integer patterns defining ranges of numbers and create String instances based on simple expressions like {aaa} or {t}.Classmpicbg.spim.data.sequenceFijijavadoc
IntegerTypeInterfacempicbg.imglib.type.numericFijijavadoc
IntegerTypeConverterConverts an IntegerType into another one without doing any range checkingAuthor:Stephan PreibischClassmpicbg.imglib.functionFijijavadoc
IntegerTypeDisplayClassmpicbg.imglib.image.displayFijijavadoc
IntegerTypeImplClassmpicbg.imglib.type.numeric.integerFijijavadoc
IntegralHistogram2dAn integral histogram for 2d images.Classini.trakem2.imagingFijijavadoc
IntegralImagen-dimensional integral image that stores sums using type .Classmpicbg.imglib.algorithm.integralFijijavadoc
IntegralImage3dClassmpicbg.spim.segmentationFijijavadoc
IntegralImageDoubleSpecial implementation for double using the basic type to sum up the individual lines.Classmpicbg.imglib.algorithm.integralFijijavadoc
IntegralImageLongSpecial implementation for long using the basic type to sum up the individual lines.Classmpicbg.imglib.algorithm.integralFijijavadoc
IntegralImageMipMapsClassini.trakem2.persistenceFijijavadoc
Interactive_3D_Surface_PlotClassFijijavadoc
Interactive_Remove_DetectionsClassspim.fiji.pluginFijijavadoc
InteractiveBehaviorThis class interprets mouse and keyboard events and invokes the desired actions.Classij3d.behaviorsFijijavadoc
InteractiveDoGAn interactive tool for determining the required sigma and peak thresholdAuthor:Stephan PreibischClassmpicbg.spim.segmentationFijijavadoc
InteractiveIntegralAn interactive tool for determining the required radius and peak thresholdAuthor:Stephan PreibischClassmpicbg.spim.segmentationFijijavadoc
InteractiveMeshDecimationClassij3d.guiFijijavadoc
InteractiveProjectionsClassspim.fiji.plugin.removedetectionsFijijavadoc
InteractiveTracerCanvasClasstracingFijijavadoc
InteractiveTransformDialogClassij3d.guiFijijavadoc
InteractiveViewPlatformTransformerThis class extends ViewPlatformTransformer, to transform mouse events into real world transformations.Classij3d.behaviorsFijijavadoc

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Interest_Point_DetectionPlugin to detect interest points, store them on disk, and link them into the XML Different plugins to detect interest points are supported, needs to implement theClassspim.fiji.pluginFijijavadoc
Interest_Point_RegistrationClassspim.fiji.pluginFijijavadoc
InterestPointSingle interest point, extends mpicbg Point by an idAuthor:Stephan Preibisch (stephan.Classspim.fiji.spimdata.interestpointsFijijavadoc
InterestPointDetectionClassspim.fiji.plugin.interestpointdetectionFijijavadoc
InterestPointExplorerClassspim.fiji.spimdata.explorer.interestpointFijijavadoc
InterestPointExplorerPanelClassspim.fiji.spimdata.explorer.interestpointFijijavadoc
InterestPointListA list of interest points for a certain label, can save and load from textfile as specified in the XMLAuthor:Stephan Preibisch (stephan.Classspim.fiji.spimdata.interestpointsFijijavadoc
InterestPointOverlayClassspim.fiji.spimdata.explorer.interestpointFijijavadoc
InterestPointRegistrationClassspim.fiji.plugin.interestpointregistrationFijijavadoc
InterestPointsExplorerPopupClassspim.fiji.spimdata.explorer.popupFijijavadoc
InterestPointTableModelClassspim.fiji.spimdata.explorer.interestpointFijijavadoc
InterpolatedImageClassvibFijijavadoc
InterpolatePaintScaleThis class implements a PaintScale that generate colors interpolated within a list of given color, using a linear scale.Classorg.jfree.chart.rendererFijijavadoc
InterpolationInterpolation methods.Classbdv.viewerFijijavadoc
InterpolationClassfiji.plugin.volumeviewerFijijavadoc
InterpolatorInterfacempicbg.imglib.interpolationFijijavadoc
Interpolator1DInterfacempicbg.imglib.interpolationFijijavadoc
Interpolator2DInterfacempicbg.imglib.interpolationFijijavadoc
Interpolator3DInterfacempicbg.imglib.interpolationFijijavadoc
InterpolatorFactoryClassmpicbg.imglib.interpolationFijijavadoc
InterpolatorImplClassmpicbg.imglib.interpolationFijijavadoc
IntervalA range on the number line with a min() and max() point.Classmpicbg.stitching.fusionFijijavadoc
IntervalAndTransformClassbdv.viewer.overlayFijijavadoc
IntervalBoundingBoxClassbdv.utilFijijavadoc
IntFieldTextField that takes only integers, and sends an ActionEvent when the integer Value has changed either by hitting return or byClassFijijavadoc

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IntHashMapA hashmap that uses primitive ints for the key rather than objects to avoid costly usage of Integer wrappers.Classorg.siox.utilFijijavadoc
IntImagePlusImagePlusContainer for integer-stored data.Classmpicbg.imglib.container.imageplusFijijavadoc
IntSliderClassFijijavadoc
IntTypeClassmpicbg.imglib.type.numeric.integerFijijavadoc
InverseFFTClassscript.imglib.algorithmFijijavadoc
InverseFourierConvolutionConvolve an image with the inverse of a kernel which is division in the Fourier domain.Classmpicbg.imglib.algorithm.fftFijijavadoc
InverseFourierTransformClassmpicbg.imglib.algorithm.fftFijijavadoc
InverseTransformDescriptionClassmpicbg.imglib.image.display.imagejFijijavadoc
InvertClassimglib.ops.operator.unaryFijijavadoc
InvertClassini.trakem2.imaging.filtersFijijavadoc
InvertibleCoordinateTransformInvertibleCoordinateTransform with String import and export as used inInterfacempicbg.trakem2.transformFijijavadoc
InvertibleCoordinateTransformInterfacestitching.modelFijijavadoc
InvertibleCoordinateTransformListClassmpicbg.trakem2.transformFijijavadoc
InvertibleModelClassstitching.modelFijijavadoc
InvokeLaterThis class helps with invoking tasks much, much later.Classfiji.guiFijijavadoc
IODialogClass to create the Input/Output dialog to deal with the files to keep the information of bUnwarpJ.ClassbunwarpjFijijavadoc
IOFunctionsClassmpicbg.spim.ioFijijavadoc
IOUtilsA collection of static utilities for the input/output of xml files.Classfiji.plugin.trackmate.ioFijijavadoc
IPLab_ReaderThis plugin opens images in the IPLab/Windows (.ClassioFijijavadoc
ISBIChallengeExporterClassfiji.plugin.trackmate.actionFijijavadoc
IsoData_ClassifierClassFijijavadoc
IsolatedPixelWeightenerClassmpicbg.spim.fusionFijijavadoc
IsolatedPixelWeightenerFactoryInterfacempicbg.spim.fusionFijijavadoc
ItemsA helper class for code generation.Classcom.sun.tools.javac.jvmFijijavadoc
IterableThe Iterable interface provides basic functionality for iterating over an Image.Interfacempicbg.imglib.cursorFijijavadoc

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IterationStatusInterfaceimglib.ops.observerFijijavadoc
IterativeClosestPointIterative closest point implementationAuthor:Stephan Preibisch (stephan.Classspim.process.interestpointregistration.icpFijijavadoc
IterativeClosestPointPairwiseClassspim.process.interestpointregistration.icpFijijavadoc
IterativeClosestPointParametersClassspim.process.interestpointregistration.icpFijijavadoc
JacobiThis class implements the jacobi function as a Java class.ClassbijnumFijijavadoc
JacobiDoubleClassmath3dFijijavadoc
JacobiFloatClassmath3dFijijavadoc
JaqamanLinkerLinks two lists of objects based on the LAP framework described in Jaqaman et al.Classfiji.plugin.trackmate.tracking.sparselap.linkerFijijavadoc
JaqamanLinkingCostMatrixCreatorA CostMatrixCreator that can generate a cost matrix from a list of sources, a list of targets and a CostFunction that can generate aClassfiji.plugin.trackmate.tracking.sparselap.costmatrixFijijavadoc
JaqamanSegmentCostMatrixCreatorThis class generates the top-left quadrant of the LAP segment linking cost matrix, following Jaqaman et al.Classfiji.plugin.trackmate.tracking.sparselap.costmatrixFijijavadoc
Java3dClassmpicbg.spim.mpicbgFijijavadoc
JavacElementsUtility methods for operating on program elements.Classcom.sun.tools.javac.modelFijijavadoc
JavacFileManagerThis class provides access to the source, class and other files used by the compiler and related tools.Classcom.sun.tools.javac.fileFijijavadoc
JavacFilerThe FilerImplementation class must maintain a number of constraints.Classcom.sun.tools.javac.processingFijijavadoc
JavacMessagerAn implementation of the Messager built on top of log.Classcom.sun.tools.javac.processingFijijavadoc
JavaCompilerThis class could be the main entry point for GJC when GJC is used as a component in a larger software system.Classcom.sun.tools.javac.mainFijijavadoc
JavaCompilerInterfacejavax.toolsFijijavadoc
JavacOptionTODO: describe com.Interfacecom.sun.tools.javac.mainFijijavadoc
JavacProcessingEnvironmentObjects of this class hold and manage the state needed to support annotation processing.Classcom.sun.tools.javac.processingFijijavadoc
JavacRoundEnvironmentObject providing state about a prior round of annotation processing.Classcom.sun.tools.javac.processingFijijavadoc
JavacScopeProvides an implementation of Scope.Classcom.sun.tools.javac.apiFijijavadoc
JavacTaskProvides access to functionality specific to the JDK Java Compiler, javac.Classcom.sun.source.utilFijijavadoc
JavacTaskImplProvides access to functionality specific to the JDK Java Compiler, javac.Classcom.sun.tools.javac.apiFijijavadoc
JavacToolTODO: describe com.Classcom.sun.tools.javac.apiFijijavadoc
JavacTreesProvides an implementation of Trees.Classcom.sun.tools.javac.apiFijijavadoc

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JavacTypesUtility methods for operating on types.Classcom.sun.tools.javac.modelFijijavadoc
JavaFileManagerInterfacejavax.toolsFijijavadoc
JavaFileObjectInterfacejavax.toolsFijijavadoc
JavassistHelperClassfijiFijijavadoc
JCDiagnosticAn abstraction of a diagnostic message generated by the compiler.Classcom.sun.tools.javac.utilFijijavadoc
JCTreeRoot class for abstract syntax tree nodes.Classcom.sun.tools.javac.treeFijijavadoc
JFileChooserDecoratorClassfiji.guiFijijavadoc
JFrameCommandFinderClassfiji.util.guiFijijavadoc
JGraphXAdapterClassfiji.plugin.trackmate.visualization.trackschemeFijijavadoc
JImagePanelThis is a Canvas used to display images in a Window.Classfiji.util.guiFijijavadoc
JLabelLoggerClassfiji.plugin.trackmate.utilFijijavadoc
JNIClassfijiFijijavadoc
JNumericTextFieldClassfiji.plugin.trackmate.gui.panels.componentsFijijavadoc
JonkerVolgenantAlgorithm Based on: Jonker, R.Classfiji.plugin.trackmate.tracking.oldlap.hungarianFijijavadoc
JPanelColorByFeatureGUIClassfiji.plugin.trackmate.gui.panels.componentsFijijavadoc
JPanelFeaturePenaltyClassfiji.plugin.trackmate.gui.panels.componentsFijijavadoc
JPanelFeatureSelectionGuiClassfiji.plugin.trackmate.gui.panels.componentsFijijavadoc
JPanelTrackerSettingsMainClassfiji.plugin.trackmate.gui.panels.trackerFijijavadoc
JRenderer3DThe framework JRenderer3D provides the possibility to implement easily a 3D display for ImageJ plugins.ClassjRenderer3DFijijavadoc
JRulerRuler component for ScrollDisplay.Classorg.siox.exampleFijijavadoc
JSchUtilityClassedu.utexas.clm.archipelago.network.shell.sshFijijavadoc
Just_Certain_LabelsClassutilFijijavadoc
Kalman_FilterClassFijijavadoc
KalmanTrackerClassfiji.plugin.trackmate.tracking.kalmanFijijavadoc
KalmanTrackerConfigPanelClassfiji.plugin.trackmate.gui.panels.trackerFijijavadoc

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KalmanTrackerFactoryClassfiji.plugin.trackmate.tracking.kalmanFijijavadoc
KD_CartoonClassFijijavadoc
KDTreeClassfiji.utilFijijavadoc
KDTreeClassmpicbg.imglib.algorithm.kdtreeFijijavadoc
KendallTauRankCorrelationThis algorithm calculates Kendall's Tau-b rank correlation coefficient http://en.ClassalgorithmsFijijavadoc
KernelThis class is the generic type for all 1D, 2D and 3D kernels.ClassvolumeFijijavadoc
Kernel1DThis class is the generic type for all 1D kernels.ClassvolumeFijijavadoc
Kernel2DThis class is the generic type for all 2D kernels.ClassvolumeFijijavadoc
Kernel3DThis class is the generic type for all 3D kernels.ClassvolumeFijijavadoc
Kernel4DThis class is the generic type for all 4D kernels.ClassvolumeFijijavadoc
KeyPropertiesClassbdv.utilFijijavadoc
KeywordsMap from Name to Token and Token to String.Classcom.sun.tools.javac.parserFijijavadoc
KindsInternal symbol kinds, which distinguish between elements of different subclasses of Symbol.Classcom.sun.tools.javac.codeFijijavadoc
KinematicsClassutilsFijijavadoc
KLTClassFijijavadoc
Koala_Bin_ReaderClassioFijijavadoc
Kuwahara_FilterClassFijijavadoc
Kuwahara_LinearStructure_Filter_v3A version of the Kuwahara filter that uses linear kernels rather than square ones.ClassFijijavadoc
KymographMouseListenerClasssc.fiji.timelapseFijijavadoc
LabelClassvib.app.moduleFijijavadoc
LabelBinaryOpsIf an underscore is added to this class name this will run as a plugin that operates the close operation.ClassoldsegmentersFijijavadoc
LabelBrush_ClassoldsegmentersFijijavadoc
LabelCenterTransformationClassvib.app.moduleFijijavadoc
LabelDiffusionTransformationClassvib.app.moduleFijijavadoc
LabeledStatementTreeA tree node for a labeled statement.Interfacecom.sun.source.treeFijijavadoc

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LabelingA labeling represents the assignment of zero or more labels to theAuthor:Lee KamentskyClassmpicbg.imglib.labelingFijijavadoc
LabelingCursorStrategyInterfacempicbg.imglib.labelingFijijavadoc
LabelingCursorStrategyFactoryInterfacempicbg.imglib.labelingFijijavadoc
LabelingTypeThe LabelingType represents a labeling of a pixel with zero or more labelings of type T.Classmpicbg.imglib.labelingFijijavadoc
LabelInterpolator_Generates label data for unlabelled slices based on the data in the nearest slices First unlabelled slices are differentiated from labelled ones viaClassoldsegmentersFijijavadoc
LabelPopUpClassspim.fiji.spimdata.explorer.popupFijijavadoc
LabelThresholder_ClassoldsegmentersFijijavadoc
LanczosInterpolatorClassmpicbg.imglib.interpolation.lanczosFijijavadoc
LanczosInterpolatorFactoryClassmpicbg.imglib.interpolation.lanczosFijijavadoc
LAPJV tailored for sparse cost matrices.Classfiji.plugin.trackmate.tracking.sparselap.linkerFijijavadoc
Laplace_Classprocess3dFijijavadoc
LaPlaceFunctionsClassmpicbg.spim.registration.bead.laplaceFijijavadoc
LaplacianComputes the Laplacian of images.Classimagescience.featureFijijavadoc
LAPTracker This class tracks objects by formulating the problem as a Linear Assignment For reference, see: Jaqaman, K.Classfiji.plugin.trackmate.tracking.oldlapFijijavadoc
LAPTrackerCostMatrixCreatorContains the mutually shared fields and private functions used by the two cost matrix classes LinkingCostMatrixCreator and TrackSegmentCostMatrixCreatorClassfiji.plugin.trackmate.tracking.oldlap.costmatrixFijijavadoc
LAPTrackerFactoryClassfiji.plugin.trackmate.tracking.oldlapFijijavadoc
LAPTrackerSettingsPanelClassfiji.plugin.trackmate.gui.panels.trackerFijijavadoc
LAPUtilsClassfiji.plugin.trackmate.trackingFijijavadoc
LaserClassorg.imagearchive.lsm.toolbox.info.scaninfoFijijavadoc
LassoClasspluginFijijavadoc
Lasso_ClasspluginFijijavadoc
LayerClassini.trakem2.displayFijijavadoc
LayerBottleClassedu.utexas.clm.archipelago.ijsupport.bottleFijijavadoc
LayerBottlerClassedu.utexas.clm.archipelago.ijsupport.bottleFijijavadoc
LayerPanelClassini.trakem2.displayFijijavadoc

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LayerSetA LayerSet is a container for a list of Layer.Classini.trakem2.displayFijijavadoc
LayerStackThis class represents an entire LayerSet of Patch objects only, as it is presented read-only to ImageJ.Classini.trakem2.imagingFijijavadoc
LayerThingClassini.trakem2.treeFijijavadoc
LayerTreeClassini.trakem2.treeFijijavadoc
LayoutCharactersAn interface containing layout character constants used in Java This is NOT part of any supported API.Interfacecom.sun.tools.javac.utilFijijavadoc
LazyVirtualStackClassini.trakem2.imagingFijijavadoc
LeafInterfacefiji.util.nodeFijijavadoc
LeafInterfacempicbg.imglib.algorithm.kdtree.nodeFijijavadoc
LegacyAppConfigurationOld interface for configuring the legacy application appearance.Interfaceimagej.legacy.pluginFijijavadoc
LegacyBasicImgLoaderInterfacempicbg.spim.data.legacyFijijavadoc
LegacyBasicImgLoaderWrapperClassmpicbg.spim.data.legacyFijijavadoc
LegacyDHMImgLoaderClassspim.fiji.spimdata.imgloadersFijijavadoc
LegacyEditorOld interface for the editor to use instead of ImageJ 1.Interfaceimagej.legacy.pluginFijijavadoc
LegacyImgLoaderInterfacempicbg.spim.data.legacyFijijavadoc
LegacyImgLoaderWrapperClassmpicbg.spim.data.legacyFijijavadoc
LegacyLightSheetZ1ImgLoaderClassspim.fiji.spimdata.imgloadersFijijavadoc
LegacyMicroManagerImgLoaderClassspim.fiji.spimdata.imgloadersFijijavadoc
LegacyStackImageLoaderThis ImgLoader loads images that represent a 3D stack in a single file, for example in tif, lsm, or czi format.Classbdv.ij.export.imgloaderFijijavadoc
LegacyStackImgLoaderClassspim.fiji.spimdata.imgloadersFijijavadoc
LegacyStackImgLoaderIJClassspim.fiji.spimdata.imgloadersFijijavadoc
LegacyStackImgLoaderLOCIClassspim.fiji.spimdata.imgloadersFijijavadoc
LegacyTileImgLoaderClassbdv.ij.export.tilesFijijavadoc
LegacyViewerImgLoaderInterfacebdv.spimdata.legacyFijijavadoc
LegacyViewerImgLoaderExtWrapperClassbdv.spimdata.legacyFijijavadoc
LegacyViewerImgLoaderWrapperClassbdv.spimdata.legacyFijijavadoc

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Leica_SP_ReaderOpens multi-image 8-bits tiff files created by Leica confocal microscope systems using each channels own LUT.ClassleicaFijijavadoc
Leica_SP_WriterClassleicaFijijavadoc
LeicaSPReaderOpens multi-image 8-bits tiff files created by Leica confocal microscope systems using each channels own LUT.ClassleicaFijijavadoc
LevelSetClasslevelsets.ijFijijavadoc
LevelSetFactory This class encapsulates all known implementations for Level Sets and their parameters.Classlevelsets.algorithmFijijavadoc
LevelSetImplementation Stub class for all Level set variants.Classlevelsets.algorithmFijijavadoc
LevenbergMarquardtSolverA collection of static utils implementing a plain Levenberg-Marquardt least-square curve fitting algorithm.Classmpicbg.imglib.algorithm.peakFijijavadoc
LevenshteinClassfiji.utilFijijavadoc
LexerThe lexical analyzer maps an input stream consisting of ASCII characters and Unicode escapes into a token sequence.Interfacecom.sun.tools.javac.parserFijijavadoc
LibraryCheckerUtility methods for verifying that classes are present and versions are correct.Classloci.plugins.utilFijijavadoc
LibraryEntryA list entry for the configuration window's Libraries tab.Classloci.plugins.configFijijavadoc
LightSheetZ1Classspim.fiji.datasetmanagerFijijavadoc
LightSheetZ1ImgLoaderClassspim.fiji.spimdata.imgloadersFijijavadoc
LightSheetZ1MetaDataClassspim.fiji.datasetmanagerFijijavadoc
LiHistogram2DRepresents the creation of a 2D histogram between two images.ClassalgorithmsFijijavadoc
LiICQThis algorithm calculates Li et al.ClassalgorithmsFijijavadoc
LimitsClassutilFijijavadoc
LineClassmath3dFijijavadoc
Line3DBy definition, only ZDisplayable objects may implement Line3D.Interfaceini.trakem2.displayFijijavadoc
Line3DThis class represents a line in 3D coordinate system.ClassjRenderer3DFijijavadoc
LineageClassifierLineage classifier class 2009 Ignacio Arganda-Carreras and Sergio Jimenez-CelorrioClasslineageFijijavadoc
Linear_GradientClassfiji.drawingFijijavadoc
LinearDistanceClassmpicbg.pointdescriptor.similarityFijijavadoc
LinearIntensityMapTransfer intensities by a linear function y=ax+b with the coefficients a and b being stored as aClassorg.janelia.intensityFijijavadoc
LinearInterpolatorClassmpicbg.imglib.interpolation.linearFijijavadoc

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LinearInterpolator1DClassmpicbg.imglib.interpolation.linearFijijavadoc
LinearInterpolator2DClassmpicbg.imglib.interpolation.linearFijijavadoc
LinearInterpolator2DRealTypeClassmpicbg.imglib.interpolation.linearFijijavadoc
LinearInterpolator3DClassmpicbg.imglib.interpolation.linearFijijavadoc
LinearInterpolator3DRealTypeClassmpicbg.imglib.interpolation.linearFijijavadoc
LinearInterpolatorFactoryClassmpicbg.imglib.interpolation.linearFijijavadoc
LinearRegressionClasssc.fiji.timelapseFijijavadoc
LineFunctionconverts a multivariate function into a univariate functionAuthor:Korbinian StrimmerClasspal.mathFijijavadoc
LineMapProvides methods to convert between character positions and line numbers for a compilation unit.Interfacecom.sun.source.treeFijijavadoc
LineReaderReads text line-by-line from a character stream using buffering for efficiency.Classimagescience.utilityFijijavadoc
LinkedPointClassmpicbg.pointdescriptorFijijavadoc
LinkingCostFunctionLinking cost function used with LAPTracker.Classfiji.plugin.trackmate.tracking.oldlap.costfunctionFijijavadoc
LinkingCostMatrixCreatorCreates the cost matrix described in Figure 1b in the paper.Classfiji.plugin.trackmate.tracking.oldlap.costmatrixFijijavadoc
LinkNew3DViewerActionClassfiji.plugin.trackmate.actionFijijavadoc
LintA class for handling -Xlint suboptions and @SuppresssWarnings.Classcom.sun.tools.javac.codeFijijavadoc
ListA class for generic linked lists.Classcom.sun.tools.javac.utilFijijavadoc
ListBoxImageClassorg.imagearchive.lsm.toolbox.guiFijijavadoc
ListBufferA class for constructing lists by appending elements.Classcom.sun.tools.javac.utilFijijavadoc
ListChooserPanelA panel to let the user choose what displayer he wants to use.Classfiji.plugin.trackmate.gui.panelsFijijavadoc
ListImgCellsLoadClassmpicbg.imglib.wrapperFijijavadoc
ListListenerClassselectionFijijavadoc
LiteralTreeA tree node for a literal expression.Interfacecom.sun.source.treeFijijavadoc
LittleEndianInputStreamReads little-endian data from a source InputStream by reversing byte ordering.Classnet.sf.image4j.ioFijijavadoc
LittleEndianOutputStreamWrites little-endian data to a target OutputStream by reversing byte ordering.Classnet.sf.image4j.ioFijijavadoc
LittleEndianRandomAccessFileProvides endian conversions for input and output with a RandomAccessFile.Classnet.sf.image4j.ioFijijavadoc

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Load_Auto_TracesClasstracingFijijavadoc
Load_particles_tableFromImgClassQuickPALMFijijavadoc
Load_SegmentationClasssioxFijijavadoc
LoadCellClassmpicbg.imglib.wrapperFijijavadoc
LoadDescriptorClassfiji.plugin.trackmate.gui.descriptorsFijijavadoc
LoaderHandle all data-related issues with a virtualization engine, including load/unload and saving, saving as and overwriting.Classini.trakem2.persistenceFijijavadoc
LoadICYTrackPlugIn_Classfiji.plugin.trackmateFijijavadoc
LoadingStrategyenum LoadingStrategyDescribes how the cache processes requests for cells with missing data.Classbdv.img.cacheFijijavadoc
LoadListenerClassselectionFijijavadoc
LoadParseQueryXMLClassspim.fiji.plugin.queryXMLFijijavadoc
LoadTrackMatePlugIn_Classfiji.plugin.trackmateFijijavadoc
Local_Thickness_DriverClasssc.fiji.localThicknessFijijavadoc
Local_Thickness_ParallelClasssc.fiji.localThicknessFijijavadoc
Local_ThresholdClassvibFijijavadoc
LocalCoordinateSystemPointDescriptorClassmpicbg.pointdescriptorFijijavadoc
LocalHistogramClassmmorphoFijijavadoc
LocalizableThe Localizable interface add functionality to return the current position.Interfacempicbg.imglib.cursorFijijavadoc
Localizable3DInterfacempicbg.imglib.cursorFijijavadoc
LocalizableByDimInterfacempicbg.imglib.cursorFijijavadoc
LocalizableByDim3DInterfacempicbg.imglib.cursorFijijavadoc
LocalizableByDimCursorInterfacempicbg.imglib.cursorFijijavadoc
LocalizableByDimCursor3DInterfacempicbg.imglib.cursorFijijavadoc
LocalizableCursorInterfacempicbg.imglib.cursorFijijavadoc
LocalizableCursor3DInterfacempicbg.imglib.cursorFijijavadoc
LocalizableLabelingCursorA cursor that only visits labeled pixels.Classmpicbg.imglib.labelingFijijavadoc

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LocalizableLabelingPerimeterCursorClassmpicbg.imglib.labelingFijijavadoc
LocalizablePlaneInterfacempicbg.imglib.cursorFijijavadoc
LocalizablePlaneCursorInterfacempicbg.imglib.cursorFijijavadoc
LocalizablePointClassmpicbg.imglib.algorithm.mathFijijavadoc
LocalizationClassspim.process.interestpointdetectionFijijavadoc
LocalNeighborhoodCursorClassmpicbg.imglib.cursor.specialFijijavadoc
LocalNeighborhoodCursor3DClassmpicbg.imglib.cursor.specialFijijavadoc
LocalNeighborhoodCursor3DOptimizedClassmpicbg.imglib.cursor.specialFijijavadoc
LocalNeighborhoodCursorFactoryClassmpicbg.imglib.cursor.specialFijijavadoc
LocalRigidRegistration_ClassvibFijijavadoc
LocalThicknessWrapperA class which can be used to programmatically run and control the various steps in local thickness map calculations.Classsc.fiji.localThicknessFijijavadoc
LocationDialogBio-Formats Importer location chooser dialog box.Classloci.plugins.inFijijavadoc
LOCIClassmpicbg.imglib.ioFijijavadoc
LociConfigAn ImageJ plugin for displaying the Bio-Formats plugins configuration dialog.Classloci.plugins.configFijijavadoc
LociExporterImageJ plugin for writing files using the OME Bio-Formats package.Classloci.pluginsFijijavadoc
LociFunctionsThis class provides macro extensions in ImageJ for Bio-Formats.Classloci.plugins.macroFijijavadoc
LociImporterImageJ plugin for reading files using the OME Bio-Formats package.Classloci.pluginsFijijavadoc
LociInstallerAn ImageJ plugin for installing and upgrading libraries related to the Bio-Formats plugins.Classloci.plugins.configFijijavadoc
LociPrefsUtility methods for ImageJ preferences for Bio-Formats plugins.Classloci.plugins.utilFijijavadoc
LockFor thread synchronization.Classini.trakem2.utilsFijijavadoc
LogA class for error logs.Classcom.sun.tools.javac.utilFijijavadoc
LogClassimglib.ops.operator.unaryFijijavadoc
LogClassscript.imglib.mathFijijavadoc
LogUtility class to deal with logging.Classstitching.utilsFijijavadoc
LoGThis is a 2D Laplacian of Gaussian convolution kernel.ClassvolumeFijijavadoc

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Log10Classscript.imglib.mathFijijavadoc
Log1pClassscript.imglib.mathFijijavadoc
LogDetectorClassfiji.plugin.trackmate.detectionFijijavadoc
LogDetectorConfigurationPanelConfiguration panel for spot detectors based on LoG detector.Classfiji.plugin.trackmate.gui.panels.detectorFijijavadoc
LogDetectorFactoryClassfiji.plugin.trackmate.detectionFijijavadoc
LogFuncsClassinferenceFijijavadoc
LoggerThis class is used to log messages occurring during TrackMate execution.Classfiji.plugin.trackmateFijijavadoc
LoggingInputStreamA class to monitor an input stream for speed and total byte download.Classini.trakem2.ioFijijavadoc
LogHistogramDatasetA HistogramDataset that returns the log of the count in each bin (plus one), so as to have a logarithmic plot.Classorg.jfree.data.statisticsFijijavadoc
LogPaneClassedfguiFijijavadoc
LogPanelA panel using s JTextPane to log events.Classfiji.plugin.trackmate.guiFijijavadoc
LogPanelDescriptorClassfiji.plugin.trackmate.gui.descriptorsFijijavadoc
LogSingletonClassedfFijijavadoc
LOI_InterpolatorClasssc.fiji.timelapseFijijavadoc
LOI_Interpolator_ToolClasssc.fiji.timelapseFijijavadoc
LongAccessInterfacempicbg.imglib.container.basictypecontainerFijijavadoc
LongArrayA dynamic array of long values.Classimagescience.arrayFijijavadoc
LongArrayClassmpicbg.imglib.container.basictypecontainer.arrayFijijavadoc
LongDynamicContainerClassmpicbg.imglib.container.dynamicFijijavadoc
LongDynamicContainerAccessorClassmpicbg.imglib.container.dynamicFijijavadoc
LongTypeClassmpicbg.imglib.type.numeric.integerFijijavadoc
LookupTableClassfiji.plugin.volumeviewerFijijavadoc
LowerThis pass translates away some syntactic sugar: inner classes, class literals, assertions, foreach loops, etc.Classcom.sun.tools.javac.compFijijavadoc
LRFFTClassmpicbg.spim.postprocessing.deconvolution2Fijijavadoc
LRFFTThreadsClassmpicbg.spim.postprocessing.deconvolution2Fijijavadoc

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LRInputClassmpicbg.spim.postprocessing.deconvolution2Fijijavadoc
LSM_ReaderClassFijijavadoc
LSM_ToolboxClassFijijavadoc
LSMFileInfoClassorg.imagearchive.lsm.reader.infoFijijavadoc
LsmImageTableModelClassorg.imagearchive.lsm.toolbox.guiFijijavadoc
LSS16_ReaderClassioFijijavadoc
LSS16_WriterClassioFijijavadoc
LucyRichardsonFFTClassmpicbg.spim.postprocessing.deconvolutionFijijavadoc
LucyRichardsonMultiViewDeconvolutionClassmpicbg.spim.postprocessing.deconvolutionFijijavadoc
LuminanceClassscript.imglib.colorFijijavadoc
LuraWaveUtility methods for dealing with proprietary LuraWave licensing.Classloci.plugins.utilFijijavadoc
LUTBlueClassini.trakem2.imaging.filtersFijijavadoc
LUTCustomClassini.trakem2.imaging.filtersFijijavadoc
LUTCyanClassini.trakem2.imaging.filtersFijijavadoc
LUTDialogClassij3d.guiFijijavadoc
LUTGreenClassini.trakem2.imaging.filtersFijijavadoc
LUTInfoClassorg.imagearchive.lsm.toolbox.infoFijijavadoc
LUTMagentaClassini.trakem2.imaging.filtersFijijavadoc
LUTOrangeClassini.trakem2.imaging.filtersFijijavadoc
LUTRedClassini.trakem2.imaging.filtersFijijavadoc
LUTYellowClassini.trakem2.imaging.filtersFijijavadoc
MTrakEM2's mathematician.Classini.trakem2.utilsFijijavadoc
MachineAccuracydetermines machine accuracyAuthor:Korbinian Strimmer, Alexei DrummondClasspal.mathFijijavadoc
MacroFunctionsConvenience class that simplifies implemention of ImageJ macro extensions.Classloci.plugins.macroFijijavadoc
MainThe programmatic interface for the Java Programming Language Except for the two methodsClasscom.sun.tools.javacFijijavadoc

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MainThis class provides a commandline interface to the GJC compiler.Classcom.sun.tools.javac.mainFijijavadoc
MainMain entry point into Fiji.ClassfijiFijijavadoc
MainAccess the command-line interface of the ImageJ UpdaterAuthor:Johannes SchindelinClassfiji.updaterFijijavadoc
MainSimple class with main method for testing Image5D behavior.ClassFijijavadoc
MainClassnet.imagejFijijavadoc
MainClass to start the SIOX demo as GUI application or as Applet.Classorg.siox.exampleFijijavadoc
MainClassForDebuggingClassfijiFijijavadoc
MainDialogClass to create the dialog for bUnwarpJ.ClassbunwarpjFijijavadoc
MainDialogBio-Formats Importer general options dialog box.Classloci.plugins.inFijijavadoc
Make_MontageDoes Montages of Image5Ds with help of ij.ClassFijijavadoc
Make_TransitionClassvideo2Fijijavadoc
MandatoryWarningHandlerA handler to process mandatory warnings, setting up a deferred diagnostic to be printed at the end of the compilation if some warnings get suppressedClasscom.sun.tools.javac.utilFijijavadoc
MandersColocalizationThis algorithm calculates Manders et al.ClassalgorithmsFijijavadoc
ManhattanDistanceClassmpicbg.pointdescriptor.similarityFijijavadoc
Manual_Landmark_SelectionClasspluginFijijavadoc
Manual_TrackingClassFijijavadoc
ManualAlignModeClassini.trakem2.displayFijijavadoc
ManualDetectorFactoryClassfiji.plugin.trackmate.detectionFijijavadoc
ManualEdgeColorAnalyzerClassfiji.plugin.trackmate.features.manualFijijavadoc
ManualEdgeColorGeneratorClassfiji.plugin.trackmate.visualizationFijijavadoc
ManualSourceTransformsClassbdv.tools.transformationFijijavadoc
ManualSpotColorAnalyzerFactoryClassfiji.plugin.trackmate.features.manualFijijavadoc
ManualSpotColorGeneratorClassfiji.plugin.trackmate.visualizationFijijavadoc
ManualTrackerFactoryClassfiji.plugin.trackmate.trackingFijijavadoc
ManualTrackingGUIControllerClassfiji.plugin.trackmate.guiFijijavadoc

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ManualTrackingPlugIn_Classfiji.plugin.trackmateFijijavadoc
ManualTransformationClassbdv.tools.transformationFijijavadoc
ManualTransformationEditorClassbdv.tools.transformationFijijavadoc
MAPInferenceClassinferenceFijijavadoc
MappingFusionParalellClassmpicbg.spim.fusionFijijavadoc
MappingFusionParalellMaxWeightClassmpicbg.spim.fusionFijijavadoc
MappingFusionSequentialClassmpicbg.spim.fusionFijijavadoc
MappingFusionSequentialDifferentOutputClassmpicbg.spim.fusionFijijavadoc
MarkerClassorg.imagearchive.lsm.toolbox.info.scaninfoFijijavadoc
MarkerListsClassview5dFijijavadoc
MaskThis class is responsible for the mask preprocessing that takes place concurrently with user-interface events.ClassbunwarpjFijijavadoc
MaskClassvoltexFijijavadoc
Mask_Of_Nearby_PointsClassutilFijijavadoc
MaskFactoryClassgadgetsFijijavadoc
MaskPredicateClassnet.imglib2.predicateFijijavadoc
MaskThicknessMapWithOriginalAn additional image processing step to LocalThickness, which removes pixels from the thickness map, which are background in the original image.Classsc.fiji.localThicknessFijijavadoc
MasterModelClassorg.imagearchive.lsm.toolboxFijijavadoc
MatchClassselectionFijijavadoc
MatcherInterfacempicbg.pointdescriptor.matcherFijijavadoc
MatchingClassprocessFijijavadoc
MatchIntensitiesClassorg.janelia.intensityFijijavadoc
MatchPointListThe interestpoint list from a certain channel;Author:Stephan Preibisch (stephan.Classspim.process.interestpointregistrationFijijavadoc
MaterialListClassvib.segmentFijijavadoc
MathLibClassmpicbg.imglib.algorithm.mathFijijavadoc
MathToolsThis class has the math methods to deal with b-splines and images.ClassbunwarpjFijijavadoc

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MathUtilsHandy utility functions which have some Mathematical relavance.Classpal.mathFijijavadoc
MaxClassimglib.ops.operator.binaryFijijavadoc
MaxClassimglib.ops.operator.unaryFijijavadoc
MaxClassscript.imglib.mathFijijavadoc
Max_ProjectClassspim.fiji.pluginFijijavadoc
MaxEntHistogramClassvibFijijavadoc
MaxEntQuantization_ClassvibFijijavadoc
Maximum_Classprocess3dFijijavadoc
MaximumProjectorClassspimopenerFijijavadoc
MaxPixelFusionClassmpicbg.stitching.fusionFijijavadoc
MaxPixelFusionIgnoreZeroClassmpicbg.stitching.fusionFijijavadoc
MaxProjectionComputes a maximum projection along an arbitrary dimension, if the image in 1-dimensional it will return an Image of size 1 with the max valueAuthor:Stephan Preibisch (stephan.Classmpicbg.imglib.algorithm.projectionFijijavadoc
MaxProjectPopupClassspim.fiji.spimdata.explorer.popupFijijavadoc
MC_TestClassFijijavadoc
MCCubeClassini.trakem2.utilsFijijavadoc
MCCubeClassmarchingcubesFijijavadoc
MCTriangulatorClassini.trakem2.utilsFijijavadoc
MCTriangulatorClassmarchingcubesFijijavadoc
Median_Classprocess3dFijijavadoc
MedianFilterPerforms a median filtering on the input image.Classlevelsets.filterFijijavadoc
MedianFilterMedian filter / morphological operation.Classmpicbg.imglib.algorithm.roiFijijavadoc
MedianFilterClassscript.imglib.algorithmFijijavadoc
MedianFilter2DA simple median filter that operates on 1D, 2D or 3D images.Classfiji.plugin.trackmate.detection.utilFijijavadoc
MedianPixelFusionClassmpicbg.stitching.fusionFijijavadoc
MedianPixelFusionIgnoreZeroClassmpicbg.stitching.fusionFijijavadoc

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MediaWikiClientClassfijiFijijavadoc
MemberEnterThis is the second phase of Enter, in which classes are completed by entering their members into the class scope usingClasscom.sun.tools.javac.compFijijavadoc
MemberSelectTreeA tree node for a member access expression.Interfacecom.sun.source.treeFijijavadoc
MemoryThis plugin implements the Edit/Options/Memory & Threads.ClassfijiFijijavadoc
MemoryDialogBio-Formats Importer memory usage confirmation dialog box.Classloci.plugins.inFijijavadoc
MemoryProfilerClassfijiFijijavadoc
Menu_FontClassFijijavadoc
MenuItemDiverterA temporary diverter for all the menu items Use this class to intercept the next click on a menu item.Classfiji.utilFijijavadoc
MenuItemHelperClassfiji.utilFijijavadoc
MenuRefresherClassfijiFijijavadoc
Merge_Cluster_JobsClassspim.fiji.pluginFijijavadoc
MergeClusterJobsClassspim.fiji.plugin.clusterFijijavadoc
MergeExampleClassbdv.spimdata.toolsFijijavadoc
MergeFileActionClassfiji.plugin.trackmate.actionFijijavadoc
MergePartitionListClassbdv.spimdata.toolsFijijavadoc
MergerClassini.trakem2.utilsFijijavadoc
MergeToolsClassbdv.spimdata.toolsFijijavadoc
MergingCostFunctionMerging cost function used with LAPTracker.Classfiji.plugin.trackmate.tracking.oldlap.costfunctionFijijavadoc
MersenneTwisterFastMersenneTwisterFast: A simulation quality fast random number generator (MT19937)Classpal.mathFijijavadoc
Mesh_MakerClasscustomnodeFijijavadoc
Mesh_MakerClassij3dFijijavadoc
MeshEditorClassisosurfaceFijijavadoc
Meshes_From_Label_FileClassutilFijijavadoc
MeshExporterClassisosurfaceFijijavadoc
MeshGroupClassisosurfaceFijijavadoc

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MeshLoaderClasscustomnodeFijijavadoc
MeshMakerClasscustomnodeFijijavadoc
MeshMakerClassij3dFijijavadoc
MeshPropertiesReferences.ClassisosurfaceFijijavadoc
MessageListenerInterfaceedu.utexas.clm.archipelago.listenFijijavadoc
MessageOverlayAnimatorDraw lines of text in the lower right corner of the display.Classbdv.viewer.animateFijijavadoc
MessagerA Messager provides the way for an annotation processor to report error messages, warnings, and other notices.Interfacejavax.annotation.processingFijijavadoc
MessagesSupport for localized messages.Classcom.sun.tools.javac.utilFijijavadoc
MessageTypeMessageType enumeration used for ClusterMessages.Classedu.utexas.clm.archipelago.listenFijijavadoc
MessageXCClassedu.utexas.clm.archipelago.networkFijijavadoc
MessengerDisplays various types of messages.Classimagescience.utilityFijijavadoc
MetaImage_CWriterClassioFijijavadoc
MetaImage_ReaderClassioFijijavadoc
MetaImage_WriterClassioFijijavadoc
MethodInvocationTreeA tree node for a method invocation expression.Interfacecom.sun.source.treeFijijavadoc
MethodTreeA tree node for a method or annotation type element declaration.Interfacecom.sun.source.treeFijijavadoc
MFWithGradientinterface for a function of several variables with a gradientAuthor:Korbinian StrimmerInterfacepal.mathFijijavadoc
MicroManagerClassspim.fiji.datasetmanagerFijijavadoc
MicroManagerImgLoaderClassspim.fiji.spimdata.imgloadersFijijavadoc
MicromanagerTranslatorContainer class for translators between OME and Micromanager formats.Classio.scif.ome.translatorsFijijavadoc
MIJMatlab to ImageJ interface.ClassFijijavadoc
MinClassimglib.ops.operator.binaryFijijavadoc
MinClassimglib.ops.operator.unaryFijijavadoc
MinClassscript.imglib.mathFijijavadoc
MinFilterThresholdClassspim.process.fusion.boundingbox.automaticFijijavadoc

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Minimum_Classprocess3dFijijavadoc
MinimumProjectorClassspimopenerFijijavadoc
MinMaxAdjustableSimple interface for objects whose effects depend on a minimal and maximal double value that can be adjusted manually or automatically.Interfacefiji.plugin.trackmate.visualizationFijijavadoc
MinMaxGroupAn int interval.Classbdv.tools.brightnessFijijavadoc
MinMaxMedianThis class implements the minimum, maximum and median filter.Classprocess3dFijijavadoc
MinPixelFusionClassmpicbg.stitching.fusionFijijavadoc
MinPixelFusionIgnoreZeroClassmpicbg.stitching.fusionFijijavadoc
MipMapImageA MipMap is a container for an Image and its corresponding inverse x/y scale relative to an original ImageClassini.trakem2.displayFijijavadoc
MipmapInfoDescription of available mipmap levels for a BasicViewSetup.Classbdv.img.hdf5Fijijavadoc
MipmapOrderingInterfacebdv.viewer.renderFijijavadoc
MipmapTransformsClassbdv.utilFijijavadoc
MirrorClassimagescience.transformFijijavadoc
MirrorMirrors an n-dimensional image along an axis (one of the dimensions).Classspim.process.fusion.deconvolutionFijijavadoc
MirroredTypeExceptionThrown when an application attempts to access the Class object corresponding to a TypeMirror.Classjavax.lang.model.typeFijijavadoc
MirroredTypesExceptionThrown when an application attempts to access a sequence of Class objects each corresponding to a TypeMirror.Classjavax.lang.model.typeFijijavadoc
MirrorImageMirrors an n-dimensional image along an axis (one of the dimensions).Classmpicbg.imglib.algorithm.mirrorFijijavadoc
MiscToolsDifferent tools for the bUnwarpJ interface.ClassbunwarpjFijijavadoc
MissingPreconditionExceptionAn exception class for missing preconditions for algorithm execution.ClassalgorithmsFijijavadoc
MissingViewsClassmpicbg.spim.data.sequenceFijijavadoc
ModeInterfaceini.trakem2.displayFijijavadoc
ModelThe model for the data managed by TrackMate trackmate.Classfiji.plugin.trackmateFijijavadoc
ModelAbstract class for arbitrary transformation models to be applied to Points in n-dimensional space.Classstitching.modelFijijavadoc
ModelBased3dClassmpicbg.spim.registration.detection.descriptorFijijavadoc
ModelChangeEventClassfiji.plugin.trackmateFijijavadoc
ModelChangeListenerAn interface for listeners that will be notified when a ModelAuthor:Jean-Yves Tinevez Interfacefiji.plugin.trackmateFijijavadoc

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ModelessQuestionsClassutilFijijavadoc
ModelFeatureUpdaterA utility class that listens to the change occurring in a model, and updates its spot, edge and track features accordingly.Classfiji.plugin.trackmate.featuresFijijavadoc
ModelInferenceClassinferenceFijijavadoc
ModelLinkClassspim.fiji.plugin.applyFijijavadoc
ModelPointDescriptorClassmpicbg.pointdescriptorFijijavadoc
ModelPriorMatcherThis class does a simple matching but computes a normalizationFactor based a given model prior.Classmpicbg.pointdescriptor.matcherFijijavadoc
ModelPriorSubsetMatcherClassmpicbg.pointdescriptor.matcherFijijavadoc
ModelToolsA collection of static utilities made to ease the manipulation of a TrackMate Model and SelectionModel.Classfiji.plugin.trackmate.utilFijijavadoc
ModifiableIntervalClassbdv.utilFijijavadoc
ModifierRepresents a modifier on a program element such as a class, method, or field.Classjavax.lang.model.elementFijijavadoc
ModifiersTreeA tree node for the modifiers, including annotations, for a declaration.Interfacecom.sun.source.treeFijijavadoc
ModuleClassvib.app.moduleFijijavadoc
ModuleListenerInterfacevib.app.moduleFijijavadoc
MontageClassini.trakem2.utilsFijijavadoc
MorphMorphological operations such as Open, Close, Erode and Dilate.Classscript.imglib.algorithm.fnFijijavadoc
MorphCloseClose morphological operation.Classmpicbg.imglib.algorithm.roiFijijavadoc
MorphDilateDilation morphological operation.Classmpicbg.imglib.algorithm.roiFijijavadoc
MorphErodeErosion morphological operation.Classmpicbg.imglib.algorithm.roiFijijavadoc
MorphologicalOperatorBase class for all morphological operations.Classlevelsets.filterFijijavadoc
MorphologicalOperatorsClassedfFijijavadoc
MorphOpenOpen morphological operation.Classmpicbg.imglib.algorithm.roiFijijavadoc
MorphoProcessorClassmmorphoFijijavadoc
MosaicJ_ClassFijijavadoc
Motion3DClassmpicbg.spim.vis3dFijijavadoc
MouseCursorProvides custom-made mouse cursors.Classimagescience.utilityFijijavadoc

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MouseListenerTimelapseClassfiji.plugin.timelapsedisplayFijijavadoc
MouseListenerTimelapseClassspim.process.interestpointregistration.registrationstatisticsFijijavadoc
MouseListenerValueClassspim.fiji.plugin.thinoutFijijavadoc
Move_RoiClassvideo2Fijijavadoc
Moving_Least_SquaresThis plugin implements the algorithms from the paper Image Deformation Using Moving Least Squares, Schaefer S.ClassFijijavadoc
MovingLeastSquaresTransformClassmpicbg.trakem2.transformFijijavadoc
MovingLeastSquaresTransform2Classmpicbg.trakem2.transformFijijavadoc
MTJGenialClassFijijavadoc
MTJMessageClassFijijavadoc
MTJQuestionClassFijijavadoc
MTrack2_Uses ImageJ's particle analyzer to track the movement of multiple objects through a stack.ClassFijijavadoc
MTrackJ_ClassFijijavadoc
MTrackJ_WebsiteClassFijijavadoc
Multi_View_DeconvolutionClassfiji.pluginFijijavadoc
Multi_View_FusionClassfiji.pluginFijijavadoc
MultiBoxOverlayPaint an overlay showing multiple transformed boxes (interval + transform).Classbdv.viewer.overlayFijijavadoc
MultiBoxOverlayRendererRender multibox overlay corresponding to a ViewerState into aAuthor:Tobias Pietzsch Classbdv.viewer.overlayFijijavadoc
MultiImageIteratorClassimglib.ops.operationFijijavadoc
MultiOrthoGroupThis class extends VoltexGroup.ClassorthosliceFijijavadoc
MultiOrthosliceClassorthosliceFijijavadoc
MultipageTiffReaderAdapted version from the MicroManager codebase that supports the new diSPIM related tags and multiple-file reading.Classspim.fiji.spimdata.imgloadersFijijavadoc
MultipleImageProcessorClassFijijavadoc
MultipleKymograph_Time space plot is created.ClassFijijavadoc
MultipleOverlay_Plugin for multiple line selction.ClassFijijavadoc
MultiplyClassimglib.ops.operator.binaryFijijavadoc

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MultiplyClassscript.imglib.mathFijijavadoc
MultiplyARGBCompositeClassini.trakem2.display.graphicsFijijavadoc
MultiplyByConstantClassimglib.ops.operator.unaryFijijavadoc
MultiResolutionImgLoaderAn ImgLoader providing multiple resolutions of each image.Interfacempicbg.spim.data.sequenceFijijavadoc
MultiResolutionRendererA Renderer that uses a coarse-to-fine rendering scheme.Classbdv.viewer.renderFijijavadoc
MultiResolutionSetupImgLoaderA SetupImgLoader providing multiple resolutions of each image.Interfacempicbg.spim.data.sequenceFijijavadoc
MultiTaskProgressInterfacefiji.featuresFijijavadoc
MultiTaskProgressInterfacetracingFijijavadoc
MultiThreadedInterfacempicbg.imglib.algorithmFijijavadoc
MultiThreadedAlgorithmThis is a convenience implementation of an algorithm that implements MultiThreaded and Algorithm so that less code has to be re-implemented.Classmpicbg.imglib.algorithmFijijavadoc
MultiThreadedBenchmarkAlgorithmThis is a convenience implementation of an algorithm that implements MultiThreaded, Benchmark and Algorithm so that less code has to be re-implemented.Classmpicbg.imglib.algorithmFijijavadoc
MultiThreadingTitle: MultiThreading Copyright: Copyright (c) 2007Classmpi.fruitfly.generalFijijavadoc
MultivariateFunctioninterface for a function of several variablesAuthor:Korbinian StrimmerInterfacepal.mathFijijavadoc
MultivariateMinimumabstract base class for minimisation of a multivariate functionAuthor:Korbinian StrimmerClasspal.mathFijijavadoc
MultiViewDatasetDefinitionInterfacespim.fiji.datasetmanagerFijijavadoc
MunkresKuhnAlgorithmThis implements optimal matching between two sets given a weight matrix (where the goal is to minimize the cumulative weight of the matches).Classfiji.plugin.trackmate.tracking.oldlap.hungarianFijijavadoc
MutualInformationClassdistanceFijijavadoc
MVDeconFFTClassspim.process.fusion.deconvolutionFijijavadoc
MVDeconFFTThreadsClassspim.process.fusion.deconvolutionFijijavadoc
MVDeconInputClassspim.process.fusion.deconvolutionFijijavadoc
MVDeconvolutionClassspim.process.fusion.deconvolutionFijijavadoc
mxScaledLabelShapeThis is a shape that is made to display a cell in a way that suits for our spots objects.Classfiji.plugin.trackmate.visualization.trackschemeFijijavadoc
mxSideTextShapeA text shape that draws edge label along the edge line and parallel to it.Classfiji.plugin.trackmate.visualization.trackschemeFijijavadoc
My3DDataClassview5dFijijavadoc
MyMultiLineLabelClassspim.fiji.plugin.utilFijijavadoc

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MySliderClassedfguiFijijavadoc
MyTableRendererClassedfguiFijijavadoc
NaiveResamplerClassvibFijijavadoc
NameAn abstraction for internal compiler strings.Classcom.sun.tools.javac.utilFijijavadoc
NameAn immutable sequence of characters.Interfacejavax.lang.model.elementFijijavadoc
Name_PointsClasslandmarksFijijavadoc
NamedContainerA small container to name objects by overriding the toString method.ClassresultsFijijavadoc
NamedEntityAn Entity that has a name.Classmpicbg.spim.data.generic.baseFijijavadoc
NamedPointSetClasslandmarksFijijavadoc
NamedPointWorldClasslandmarksFijijavadoc
NamePatternClassspim.fiji.spimdataFijijavadoc
NamePointsClasslandmarksFijijavadoc
NativeLibraryToolsClassspim.process.cudaFijijavadoc
NavigationActionsClassbdv.viewerFijijavadoc
ND2WidgetsCustom widgets for configuring Bio-Formats ND2 support.Classloci.plugins.configFijijavadoc
NearestNeighborFlagSearchOnKDTreeClassfiji.plugin.trackmate.tracking.kdtreeFijijavadoc
NearestNeighborInterpolatorClassmpicbg.imglib.interpolation.nearestneighborFijijavadoc
NearestNeighborInterpolator1DClassmpicbg.imglib.interpolation.nearestneighborFijijavadoc
NearestNeighborInterpolator2DClassmpicbg.imglib.interpolation.nearestneighborFijijavadoc
NearestNeighborInterpolator3DClassmpicbg.imglib.interpolation.nearestneighborFijijavadoc
NearestNeighborInterpolatorFactoryClassmpicbg.imglib.interpolation.nearestneighborFijijavadoc
NearestNeighborSearchClassfiji.utilFijijavadoc
NearestNeighborSearchClassmpicbg.imglib.algorithm.kdtreeFijijavadoc
NearestNeighborTrackerClassfiji.plugin.trackmate.tracking.kdtreeFijijavadoc
NearestNeighborTrackerFactoryClassfiji.plugin.trackmate.tracking.kdtreeFijijavadoc

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NearestNeighborTrackerSettingsPanelClassfiji.plugin.trackmate.gui.panels.trackerFijijavadoc
NearPointClasstracingFijijavadoc
NestingKindThe nesting kind of a type element.Classjavax.lang.model.elementFijijavadoc
NeuriteTracerResultsDialogClasstracingFijijavadoc
NeuroMLClassini.trakem2.ioFijijavadoc
New_DB_ProjectClassini.trakem2Fijijavadoc
New_Image5DCreates and displays a new Image5D.ClassFijijavadoc
New_ProjectClassini.trakem2Fijijavadoc
New_VideoClassvideo2Fijijavadoc
NewAnalyzeTracings_ClasstracingFijijavadoc
NewArrayTreeA tree node for an expression to create a new instance of an array.Interfacecom.sun.source.treeFijijavadoc
NewClassTreeA tree node to declare a new instance of a class.Interfacecom.sun.source.treeFijijavadoc
NIOByteArrayClassmpicbg.imglib.container.basictypecontainer.arrayFijijavadoc
NIOCharArrayClassmpicbg.imglib.container.basictypecontainer.arrayFijijavadoc
NIODoubleArrayClassmpicbg.imglib.container.basictypecontainer.arrayFijijavadoc
NIOFloatArrayCore array type used for float[] dataAuthor:Stephan Preibisch, Stephan Saalfeld, Rick LentzClassmpicbg.imglib.container.basictypecontainer.arrayFijijavadoc
NIOIntArrayClassmpicbg.imglib.container.basictypecontainer.arrayFijijavadoc
NIOLongArrayClassmpicbg.imglib.container.basictypecontainer.arrayFijijavadoc
NIOShortArrayClassmpicbg.imglib.container.basictypecontainer.arrayFijijavadoc
NNearestNeighborSearchClassfiji.utilFijijavadoc
NNearestNeighborSearchClassmpicbg.imglib.algorithm.kdtreeFijijavadoc
NodeInterfacefiji.util.nodeFijijavadoc
NodeCan only have one parent, so there aren't cyclic graphs.Classini.trakem2.displayFijijavadoc
NodeInterfacempicbg.imglib.algorithm.kdtree.nodeFijijavadoc
NodeConfigurationUIClassedu.utexas.clm.archipelago.uiFijijavadoc

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NodeCoordinatorClassedu.utexas.clm.archipelago.network.nodeFijijavadoc
NodeParametersClassedu.utexas.clm.archipelago.network.nodeFijijavadoc
NodeParametersFactoryClassedu.utexas.clm.archipelago.network.nodeFijijavadoc
NodeShellInterface used to start remote nodes and potentially execute shell commands.Interfaceedu.utexas.clm.archipelago.network.shellFijijavadoc
NodeShellListenerInterfaceedu.utexas.clm.archipelago.listenFijijavadoc
NodeShellParametersA class to support parameters for various kinds of node shells.Classedu.utexas.clm.archipelago.network.shellFijijavadoc
NodeShellUserInfoClassedu.utexas.clm.archipelago.network.shell.sshFijijavadoc
NodeStateListenerInterfaceedu.utexas.clm.archipelago.listenFijijavadoc
NoninvertibleModelExceptionSignalizes that the Model is not invertible.Classstitching.modelFijijavadoc
NonLeafClassfiji.util.nodeFijijavadoc
NonLeafClassmpicbg.imglib.algorithm.kdtree.nodeFijijavadoc
NonLinearCoordinateTransformClassmpicbg.trakem2.transformFijijavadoc
NonLinearTransformClasslenscorrectionFijijavadoc
NonLinearTransformModeClassini.trakem2.displayFijijavadoc
NoopAdapterClassij3dFijijavadoc
NormalEstimatorClassmath3dFijijavadoc
NormalizeClassini.trakem2.imaging.filtersFijijavadoc
NormalizeBecomes a normalized version of the given image, within min and max bounds, where all pixels take values between 0 and 1.Classscript.imglib.algorithmFijijavadoc
NormalizeImageFloatNormalizes a given Image so that the sum of all of its pixels is equal to one (or approximately so).Classmpicbg.imglib.algorithm.mathFijijavadoc
NormalizeImageMinMaxClassmpicbg.imglib.algorithm.mathFijijavadoc
NormalizeLocalContrastClassini.trakem2.imaging.filtersFijijavadoc
NormalizeSumClassscript.imglib.algorithmFijijavadoc
NormalizingRandomAccessClassspim.process.fusion.weightsFijijavadoc
NormalizingRandomAccessibleIntervalClassspim.process.fusion.weightsFijijavadoc
NormMinMaxClassmpicbg.imglib.algorithm.functionFijijavadoc

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NoSuitablePointsExceptionClassmpicbg.pointdescriptor.exceptionFijijavadoc
NotClassimglib.ops.conditionFijijavadoc
NotEnoughDataPointsExceptionSignalizes that there were not enough data points available to estimate theSee Also:Serialized FormClassstitching.modelFijijavadoc
NotesDialogClassorg.imagearchive.lsm.toolbox.guiFijijavadoc
NoTypeA pseudo-type used where no actual type is appropriate.Interfacejavax.lang.model.typeFijijavadoc
Nrrd_ReaderImageJ plugin to read a file in Gordon Kindlmann's NRRD or 'nearly raw raster data' format, a simple format which handlesClassioFijijavadoc
Nrrd_WriterClassioFijijavadoc
NrrdHeaderClass to read and represent the header of a NRRD file.ClassnrrdFijijavadoc
NrrdInfoThis class contains the key information that describes a nrrd file The expectation is that it will be generated by parsing an existing fileClassnrrdFijijavadoc
NRRDTranslatorContainer class for translators between OME and NRRD formats.Classio.scif.ome.translatorsFijijavadoc
NucleiConfigurationClassmpicbg.spim.registration.segmentationFijijavadoc
NucleusClassmpicbg.spim.registration.segmentationFijijavadoc
NucleusIdentificationThe BeadIdentification object stores the link (via ID) to an Bead-object and not an actual instance, but a link to the ViewDataBeads object where it belongs to.Classmpicbg.spim.registration.segmentationFijijavadoc
NucleusStructureClassmpicbg.spim.registration.segmentationFijijavadoc
NullFunctionNullFunction is a function that does not change the output.Classimglib.ops.function.pnFijijavadoc
NullLinkClassmpicbg.imglib.cursor.linkFijijavadoc
NullLoggerClassedu.utexas.clm.archipelago.utilFijijavadoc
NullTypeRepresents the null type.Interfacejavax.lang.model.typeFijijavadoc
NumberedStringSorterSorts an array of Strings treating any sequences of digits as numbers, not single digits.Classi5d.utilFijijavadoc
NumberFunctionClassscript.imglib.math.fnFijijavadoc
NumberParserA static utility class for parsing numbers from strings.Classfiji.utilFijijavadoc
NumberUtilsClassspim.fiji.spimdata.imgloadersFijijavadoc
NumericalDerivativeapproximates numerically the first and second derivatives of a function of a single variable and approximates gradient andClasspal.mathFijijavadoc
NumericTypeInterfacempicbg.imglib.type.numericFijijavadoc
OBFTranslatorContainer class for translators between OME and OBF formats.Classio.scif.ome.translatorsFijijavadoc

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Object3DClassUtilitiesFijijavadoc
Object_InspectorClassfiji.debuggingFijijavadoc
OctreeDialogClassoctreeFijijavadoc
OldAppConfigurationFall-back plugin for ij-legacy.Classfiji.patchesFijijavadoc
OldLegacyEditorFall-back plugin for ij-legacy.Classfiji.patchesFijijavadoc
OMEMetadataio.Classio.scif.omeFijijavadoc
OMEMetadataServiceA utility class for working with OME metadata objects, including MetadataStore and MetadataRetrieve.Interfaceio.scif.ome.servicesFijijavadoc
OMETIFFFormatOMETiffReader is the file format reader for OME-TIFF files.Classio.scif.ome.formatsFijijavadoc
OMETIFFTranslatorContainer class for translators between OME and OMETIFF formats.Classio.scif.ome.translatorsFijijavadoc
OMETranslatorAbstract base class for all Translator implementations that operate on OMEMetadata.Classio.scif.ome.translatorsFijijavadoc
OMEXMLFormatFormat for OME-XML files.Classio.scif.ome.formatsFijijavadoc
OMEXMLServiceSCIFIO service wrapper for OMEXMLService.Interfaceio.scif.ome.servicesFijijavadoc
OMEXMLToolCommandSCIFIOToolCommand plugin for printing OME-XML.Classio.scif.ome.commandsFijijavadoc
OnRequestUpdaterThis class extends Thread and is suited to call methods that are typically called often, but takes time to complete, such as display refreshing.Classfiji.plugin.trackmate.utilFijijavadoc
OpenClassscript.imglib.algorithmFijijavadoc
Open_DAT_EMMENUClassioFijijavadoc
Open_DB_ProjectClassini.trakem2Fijijavadoc
Open_DF3ClassioFijijavadoc
Open_Image5DClassFijijavadoc
Open_MRC_LeginonClassioFijijavadoc
Open_ProjectClassini.trakem2Fijijavadoc
Open_Series_As_Image5DOpens a series of images or image stacks and converts it to an Image5D.ClassFijijavadoc
Open_VideoClassvideo2Fijijavadoc
OpenConnectomeDatasetAn openconnecto.Classbdv.img.openconnectomeFijijavadoc
OpenConnectomeImageLoaderClassbdv.img.openconnectomeFijijavadoc

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OpenConnectomeProjectoenconnecto.Classbdv.img.openconnectomeFijijavadoc
OpenConnectomeTokenInfoClassbdv.img.openconnectomeFijijavadoc
OpenConnectomeVolatileArrayLoaderClassbdv.img.openconnectomeFijijavadoc
OpenerGenericDialogClassspimopenerFijijavadoc
OpenImage5DAdapterThis class contains static methods, which handle the "open"-specific features of OpenImage5DWindow and OpenStackWindow: ClassFijijavadoc
OpenImage5DWindowImage5DWindow, which issues DispChanged Events to registered Listeners, when the displayed slice has been changed.ClassFijijavadoc
OpenImagePlusPlugInImageJ plugin to show the current image in BigDataViewer.Classbdv.ijFijijavadoc
OpenImarisPlugInClassbdv.ijFijijavadoc
OpenImgClassspim.fiji.plugin.utilFijijavadoc
OpenStackAdapterThis class contains static methods, which handle the "open"-specific features of - converting a StackWindow to the appropriate classClassFijijavadoc
OpenStackWindowStackWindow, which issues DispChanged Events to registered Listeners, when the displayed slice has been changed.ClassFijijavadoc
OperationInterfaceini.trakem2.utilsFijijavadoc
OptionBase class for an option for one of the plugins.Classloci.plugins.prefsFijijavadoc
OptionCheckerInterface for recognizing options.Interfacejavax.toolsFijijavadoc
OptionNameTODO: describe com.Classcom.sun.tools.javac.mainFijijavadoc
OptionPanelClassini.trakem2.utilsFijijavadoc
OptionsA table of all command-line options.Classcom.sun.tools.javac.utilFijijavadoc
OptionsClassvib.appFijijavadoc
OptionsDialogBase class for options dialogs.Classloci.plugins.prefsFijijavadoc
OptionsListBase class for ImageJ preferences for plugins.Classloci.plugins.prefsFijijavadoc
OrClassimglib.ops.conditionFijijavadoc
OrClassimglib.ops.operator.binaryFijijavadoc
OrClassscript.imglib.mathFijijavadoc
OrConstantClassimglib.ops.operator.unaryFijijavadoc
OrderedTransformationsClassvib.transformsFijijavadoc

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OrthogonalLineFunctionconverts a multivariate function into a univariate function by keeping all but one argument constantClasspal.mathFijijavadoc
OrthogonalSearchminimization of a real-valued function of several variables without using derivatives, using the simpleClasspal.mathFijijavadoc
OrthoGroupThis class extends VoltexGroup.ClassorthosliceFijijavadoc
OrthosliceOrthoslice extends VolumeRenderer and modifies it in a way so that not the whole volume is displayed, but only three orthogonal slices through theClassorthosliceFijijavadoc
OtherInstanceClassfijiFijijavadoc
OutOfBoundsStrategyClassmpicbg.imglib.outofboundsFijijavadoc
OutOfBoundsStrategyFactoryClassmpicbg.imglib.outofboundsFijijavadoc
OutOfBoundsStrategyMirrorClassmpicbg.imglib.outofboundsFijijavadoc
OutOfBoundsStrategyMirrorExpWindowingClassmpicbg.imglib.outofboundsFijijavadoc
OutOfBoundsStrategyMirrorExpWindowingFactoryClassmpicbg.imglib.outofboundsFijijavadoc
OutOfBoundsStrategyMirrorFactoryClassmpicbg.imglib.outofboundsFijijavadoc
OutOfBoundsStrategyPeriodicClassmpicbg.imglib.outofboundsFijijavadoc
OutOfBoundsStrategyPeriodicFactoryClassmpicbg.imglib.outofboundsFijijavadoc
OutOfBoundsStrategyValueClassmpicbg.imglib.outofboundsFijijavadoc
OutOfBoundsStrategyValueFactoryClassmpicbg.imglib.outofboundsFijijavadoc
OutputAlgorithmInterfacempicbg.imglib.algorithmFijijavadoc
OutputFunctionInterface for functions that return a new object, computed from two input arguments.Interfacefiji.plugin.trackmate.graphFijijavadoc
OverlapFusionThis class implements a fusion where only the pixel value of one of the images is used.Classmpicbg.stitching.fusionFijijavadoc
OverlapPropertiesClassstitchingFijijavadoc
OverlayClassini.trakem2.displayFijijavadoc
Overlay_RegisteredClassutilFijijavadoc
OverlayAnimatorInterfacebdv.viewer.animateFijijavadoc
OverlayedImageCanvasExtension of ImageCanvas to allow multiple overlaysAuthor:Ignacio Arganda-Carreras and Johannes SchindelinSee Also:Serialized FormClassfiji.util.guiFijijavadoc
OverlayFusionClassmpicbg.stitching.fusionFijijavadoc
OverlayFusionClassprocessFijijavadoc

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OverlayRegisteredClassutilFijijavadoc
PClassini.trakem2.imagingFijijavadoc
Package_MakerClassfiji.packagingFijijavadoc
PackageElementRepresents a package program element.Interfacejavax.lang.model.elementFijijavadoc
PackagerClassfiji.packagingFijijavadoc
PaintableInterfaceini.trakem2.displayFijijavadoc
PaintInvertibleCoordinateTransformThreadClassstitching.modelFijijavadoc
PairA generic class for pairs.Classcom.sun.tools.javac.utilFijijavadoc
PairClassmpicbg.trakem2.utilFijijavadoc
PairIteratorAn iterator over pairs of types.Interfacenet.imglib2Fijijavadoc
PairwiseMatchClassspim.process.interestpointregistrationFijijavadoc
PairWiseStitchingImgLibPairwise Stitching of two ImagePlus using ImgLib1 and PhaseCorrelation.Classmpicbg.stitchingFijijavadoc
PairWiseStitchingResultClassmpicbg.stitchingFijijavadoc
PaletteA palette of 100 different colors.Classimagescience.colorFijijavadoc
PaneOwnerInterfacestacksFijijavadoc
Panorama_ViewClassmpicbg.panoramaFijijavadoc
PanoramaCameraClassmpicbg.panoramaFijijavadoc
ParallelMappingLike clojure's pmap, given a sequence of inputs obtained from an Iterable, this Iterable will apply a function to each input ahead of consumptionClassini.trakem2.parallelFijijavadoc
ParamThis class stores the parameters to apply the consistent elastic registration and it is independent of the primary GUI.ClassbunwarpjFijijavadoc
ParameterizedTypeTreeA tree node for a type expression involving type parameters.Interfacecom.sun.source.treeFijijavadoc
ParametersClassedfguiFijijavadoc
ParenthesizedTreeA tree node for a parenthesized expression.Interfacecom.sun.source.treeFijijavadoc
parObjectClassFijijavadoc
ParsePatternClassmpicbg.spim.ioFijijavadoc
ParserThe parser maps a token sequence into an abstract syntax tree.Classcom.sun.tools.javac.parserFijijavadoc

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ParticleClassprocessFijijavadoc
Particle_Analyzer_3DClassprocess3dFijijavadoc
ParticleSaverClassQuickPALMFijijavadoc
PartitionPartition describes one partition file of a dataset that is split across multiple hdf5 files.Classbdv.img.hdf5Fijijavadoc
PatchClassini.trakem2.displayFijijavadoc
PatchBottleClassedu.utexas.clm.archipelago.ijsupport.bottleFijijavadoc
PatchBottlerClassedu.utexas.clm.archipelago.ijsupport.bottleFijijavadoc
PatchScriptClassini.trakem2.scriptingFijijavadoc
PatchStackAssumed is all Patch instances in the array are of the same size, live in consecutive layers of the same thickness.Classini.trakem2.imagingFijijavadoc
PathClasstracingFijijavadoc
PathAndFillListenerInterfacetracingFijijavadoc
PathAndFillManagerClasstracingFijijavadoc
PathColorsCanvasClasstracingFijijavadoc
PathDownsamplerClasstracingFijijavadoc
PathFitterClasstracingFijijavadoc
PathResultClasstracingFijijavadoc
PathsThis class converts command line arguments, environment variables and system properties (in File.Classcom.sun.tools.javac.fileFijijavadoc
PathSubstitutingFileTranslatorClassedu.utexas.clm.archipelago.network.translationFijijavadoc
PathTransformerThe int values are indexes into the image's samples, with z being 0-based.InterfacetracingFijijavadoc
PathWindowClasstracingFijijavadoc
Pbd16InputStreamDecompresses a binary InputStream using Sean Murphy's fast PBD pack-bits plus difference encoding.Classorg.janelia.vaa3d.readerFijijavadoc
Pbd8InputStreamDecompresses a binary InputStream using Sean Murphy's fast PBD pack-bits plus difference encoding.Classorg.janelia.vaa3d.readerFijijavadoc
PbdInputStreamBase class for Pbd8InputStream and Pbd16InputStream.Classorg.janelia.vaa3d.readerFijijavadoc
PCA_RegistrationClassvib.oldregistrationFijijavadoc
PDF_ViewerClassioFijijavadoc

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PDF_WriterClassioFijijavadoc
PDFWriterClassresultsFijijavadoc
PeakClassmpicbg.stitchingFijijavadoc
Peak_Counter_ToolClasssc.fiji.timelapseFijijavadoc
PearsonsCorrelationA class that represents the mean calculation of the two source images in the data container.ClassalgorithmsFijijavadoc
PenaltyClassutilFijijavadoc
PerEdgeFeatureColorGeneratorClassfiji.plugin.trackmate.visualizationFijijavadoc
PerformanceProfilerA Javassist-backed performance profiler.ClassfijiFijijavadoc
PerTrackFeatureColorGeneratorA TrackColorGenerator that generate colors based on the whole trackAuthor:Jean-Yves TinevezClassfiji.plugin.trackmate.visualizationFijijavadoc
PhaseCorrelationClassmpicbg.imglib.algorithm.fftFijijavadoc
PhaseCorrelationCalculatorClassini.trakem2.imagingFijijavadoc
PhaseCorrelationPeakClassmpicbg.imglib.algorithm.fftFijijavadoc
PicClassfiji.plugin.volumeviewerFijijavadoc
PickerThis class is a helper class which implements functions for picking.Classij3d.behaviorsFijijavadoc
PickImagePeaksThis class implements a very simple peak-picker, with optional ellipsoidal peak suppression.Classmpicbg.imglib.algorithm.mathFijijavadoc
PickPeaksClassscript.imglib.analysisFijijavadoc
PictWidgetsCustom widgets for configuring Bio-Formats PICT support.Classloci.plugins.configFijijavadoc
PiecewiseLinearCdfClasshistogram2Fijijavadoc
PipeClassij3dFijijavadoc
PipeClassini.trakem2.displayFijijavadoc
PipelineImageClassio.scif.formats.imarisFijijavadoc
PIV_analyser This plugin calculates the optic flow for each pair of images made with the given stack.ClassFijijavadoc
PIVAnalyserTestDriveClassFijijavadoc
PixelDisplayClassview5dFijijavadoc
PixelFusionInterfacempicbg.stitching.fusionFijijavadoc

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PixelGridContainerInterfacempicbg.imglib.containerFijijavadoc
PixelGridContainerFactoryClassmpicbg.imglib.containerFijijavadoc
PixelGridContainerImplClassmpicbg.imglib.containerFijijavadoc
PixelOnBorderClassimglib.ops.conditionFijijavadoc
PixelPairsInterfacedistanceFijijavadoc
PixelStatsClass used to track statistics with low memory footprint where large number data sets are expected User: Tom LarkworthyClassadtFijijavadoc
PlanarAccessInterface allowing access to data on a plane-by-plane basis.Interfacempicbg.imglib.container.basictypecontainerFijijavadoc
PlanarContainerA Container that stores data in an array of 2d-slices each as a linear array of basic types.Classmpicbg.imglib.container.planarFijijavadoc
PlanarContainerFactoryFactory that creates an appropriate PlanarContainer.Classmpicbg.imglib.container.planarFijijavadoc
PlanarCursorBasic Iterator for PlanarContainersAuthor:Stephan Preibisch, Stephan SaalfeldClassmpicbg.imglib.cursor.planarFijijavadoc
PlanarCursor2DBasic Iterator for 2d PlanarContainersAuthor:Stephan Saalfeld, Stephan Saalfeld Classmpicbg.imglib.cursor.planarFijijavadoc
PlanarLocalizableByDimCursorPositionable for a PlanarContainersAuthor:Stephan Preibisch, Stephan SaalfeldClassmpicbg.imglib.cursor.planarFijijavadoc
PlanarLocalizableByDimOutOfBoundsCursorPositionable with OutOfBoundsStrategy for aAuthor:Stephan Preibisch, Stephan SaalfeldClassmpicbg.imglib.cursor.planarFijijavadoc
PlanarLocalizableCursorLocalizing Iterator for a PlanarContainersAuthor:Stephan Preibisch, Stephan SaalfeldClassmpicbg.imglib.cursor.planarFijijavadoc
PlanarLocalizablePlaneCursorClassmpicbg.imglib.cursor.planarFijijavadoc
PlaneClassmath3dFijijavadoc
Plot_DotsClassprocess3dFijijavadoc
PlotNSpotsVsTimeActionClassfiji.plugin.trackmate.actionFijijavadoc
PlotUtilsClasssc.fiji.timelapseFijijavadoc
PluginHelperClassbdv.ij.utilFijijavadoc
PluginHelperClassspim.fiji.plugin.resaveFijijavadoc
PlugInInstallerClassfijiFijijavadoc
PntClassdelaunayFijijavadoc
PointA point in 5D space.Classimagescience.shapeFijijavadoc
PointThis class represents a 3D point or position on a 3D image.Classsc.fiji.analyzeSkeletonFijijavadoc

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PointAn n-dimensional point.Classstitching.modelFijijavadoc
Point2DClassstitchingFijijavadoc
Point3DThis class represents a point in a 3D coordinate system.ClassjRenderer3DFijijavadoc
Point3dClassmath3dFijijavadoc
Point3DClassstitchingFijijavadoc
PointActionClass for all actions related with points in the bUnwarpJ interface: moving, adding and deleting landmarks, and painting the masks.ClassbunwarpjFijijavadoc
PointBottleA PointBottle to support synchronized point objects across cluster nodesSee Also:Serialized FormClassedu.utexas.clm.archipelago.ijsupport.bottleFijijavadoc
PointBottlerClassedu.utexas.clm.archipelago.ijsupport.bottleFijijavadoc
PointHandlerClass to deal with handle points in bUnwarpJ: here we have the methods to paint the landmarks and the masks.ClassbunwarpjFijijavadoc
PointInImageClasstracingFijijavadoc
PointListClassvibFijijavadoc
PointListDialogThis class represents a window which can hold a set of PointListPanels.Classij3d.pointlistFijijavadoc
PointListPanelThis class is a Panel showing a PointList as a list, which allows to modify the point list: Adding, deleting points, moving them up and down, etc.Classij3d.pointlistFijijavadoc
PointListShapeThis class extends BranchGroup to represent a PointList as a number of spheres in the universe.Classij3d.pointlistFijijavadoc
PointMatchA link between two Points that are expected to be ideally at the same location in the world coordinate space.Classstitching.modelFijijavadoc
PointMatchFilterInterfaceorg.janelia.intensityFijijavadoc
PointMatchGenericClassmpicbg.spim.mpicbgFijijavadoc
PointMatchIdentificationInterfacempicbg.icpFijijavadoc
PointMatchStitchingClassmpicbg.stitchingFijijavadoc
PointNodeClassmpicbg.pointdescriptor.testFijijavadoc
PointPicker_This class is the only one that is accessed directly by imageJ; it attaches listeners and dies.ClassFijijavadoc
Pointsclass that represents a collection of Points Optimized for infrequent addAll operations, by simply adding a reference to the child Points objectClassadtFijijavadoc
Points_DialogClassvibFijijavadoc
PointSelectionBehaviorClasstracingFijijavadoc
PointToolbarClass to deal with the point toolbar option in the bUnwarpJ interface: draw the toolbar and change between tools.ClassbunwarpjFijijavadoc

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Pointwise Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandInterfaceimagewareFijijavadoc
PoissonGeneratorPoisson random number generator.Classimagescience.randomFijijavadoc
PolygonA polygon in the x-y plane.Classimagescience.shapeFijijavadoc
PolygonRoiPublicClasssc.fiji.timelapseFijijavadoc
PolylineA sequence of points that make multiple chained line segments.Classini.trakem2.displayFijijavadoc
PolynomialModel2DA wrpper for NonLinearTransform and the AbstractAffineModel2D to which it is regularized.ClasslenscorrectionFijijavadoc
PolynomialTransform2Dn-th order 2d polynomial transform.Classmpicbg.trakem2.transformFijijavadoc
PoolAn internal structure that corresponds to the constant pool of a classfile.Classcom.sun.tools.javac.jvmFijijavadoc
PositionA class that defines source code positions as simple character offsets from the beginning of the file.Classcom.sun.tools.javac.utilFijijavadoc
PositionLabelClassview5dFijijavadoc
PostProcessingClassedfFijijavadoc
PowClassscript.imglib.mathFijijavadoc
PrecisionClassmpicbg.imglib.algorithmFijijavadoc
PreDeconvolutionFusionClassmpicbg.spim.fusionFijijavadoc
PreDeconvolutionFusionInterfaceInterfacempicbg.spim.fusionFijijavadoc
PreDeconvolutionFusionSequentialClassmpicbg.spim.fusionFijijavadoc
PreDefinedBoundingBoxClassspim.process.fusion.boundingboxFijijavadoc
PredefinedCellContainerFactoryClassmpicbg.imglib.wrapperFijijavadoc
PredicateInterfacenet.imglib2.predicateFijijavadoc
PredicateCursorThe PredicateCursor traverses a whole image but only returns those pixels for which the Predicate returns true.Classnet.imglib2Fijijavadoc
PrefetcherClassbdv.viewer.renderFijijavadoc
PrefilterPrefilters an array or image for different interpolation schemes.Classimagescience.transformFijijavadoc
PrefsClassbdv.utilFijijavadoc
Prettify_Wiki_ScreenshotClassfijiFijijavadoc
PrettyPrints out a tree as an indented Java source program.Classcom.sun.tools.javac.treeFijijavadoc

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PreviewRegistrationClassmpicbg.spim.vis3dFijijavadoc
PrimitiveClasscustomnodeFijijavadoc
PrimitiveDialogsClassij3d.guiFijijavadoc
PrimitiveTypeRepresents a primitive type.Interfacejavax.lang.model.typeFijijavadoc
PrimitiveTypeTreeA tree node for a primitive type.Interfacecom.sun.source.treeFijijavadoc
PrintingProcessorA processor which prints out elements.Classcom.sun.tools.javac.processingFijijavadoc
PrintSequenceMipmapInfoClassbdv.utilFijijavadoc
PrintStreamLoggerClassedu.utexas.clm.archipelago.utilFijijavadoc
Process Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandInterfaceimagewareFijijavadoc
ProcessFor all methods, if the number of processors given as argument is zero or larger than the maximum available plus 2, the number of processors will be adjusted to fall within the range [1, max+2].Classini.trakem2.parallelFijijavadoc
ProcessClassscript.imglib.algorithmFijijavadoc
ProcessDOGClassspim.process.interestpointdetectionFijijavadoc
ProcessDOMClassspim.process.interestpointdetectionFijijavadoc
ProcessForDeconvolutionFused individual images for each input stack, uses the exporter directlyAuthor:Stephan Preibisch (stephan.Classspim.process.fusion.deconvolutionFijijavadoc
ProcessFusionClassspim.process.fusion.weightedavgFijijavadoc
ProcessIndependentFused individual images for each input stack, uses the exporter directlyAuthor:Stephan Preibisch (stephan.Classspim.process.fusion.weightedavgFijijavadoc
ProcessIndependentPortionFuse one portion of a paralell fusion, supports no weightsAuthor:Stephan Preibisch (stephan.Classspim.process.fusion.weightedavgFijijavadoc
ProcessingEnvironmentAn annotation processing tool framework will provide an annotation processor with an object implementing this interface so the processor can use facilitiesInterfacejavax.annotation.processingFijijavadoc
ProcessListenerProcessListener interface, used to notify when a ProcessManager has been returned fromAuthor:Larry LindseyInterfaceedu.utexas.clm.archipelago.listenFijijavadoc
ProcessManagerClassedu.utexas.clm.archipelago.computeFijijavadoc
ProcessManagerCoreComparatorClassedu.utexas.clm.archipelago.utilFijijavadoc
ProcessorThe interface for an annotation processor.Interfacejavax.annotation.processingFijijavadoc
ProcessParalellClassspim.process.fusion.weightedavgFijijavadoc
ProcessParalellPortionFuse one portion of a paralell fusion, supports no weightsAuthor:Stephan Preibisch (stephan.Classspim.process.fusion.weightedavgFijijavadoc
ProcessParalellPortionWeightFuse one portion of a paralell fusion, supports one weight functionAuthor:Stephan Preibisch (stephan.Classspim.process.fusion.weightedavgFijijavadoc

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ProcessParalellPortionWeightsFuse one portion of a paralell fusion, supports many weight functionsAuthor:Stephan Preibisch (stephan.Classspim.process.fusion.weightedavgFijijavadoc
ProcessSequentialClassspim.process.fusion.weightedavgFijijavadoc
ProcessSequentialPortionFuse one portion of a sequential fusion, supports no weights This is basically identical to the parallel fusion except it does store the weightsClassspim.process.fusion.weightedavgFijijavadoc
ProcessSequentialPortionWeightFuse one portion of a sequential fusion, supports one weight function This is basically identical to the parallel fusion except it does store the weightsClassspim.process.fusion.weightedavgFijijavadoc
ProcessSequentialPortionWeightsFuse one portion of a paralell fusion, supports many weight functionsAuthor:Stephan Preibisch (stephan.Classspim.process.fusion.weightedavgFijijavadoc
ProcessTopologyClassedfFijijavadoc
ProfileA class to be a user-outlined profile over an image, which is painted with a particular color and also holds an associated text label.Classini.trakem2.displayFijijavadoc
ProfileStackClasssc.fiji.timelapseFijijavadoc
ProgramConfiguration Copyright: Copyright (c) 2006 Company: Diplomarbeit - IZBI Leipzig/TU DresdenClassmpicbg.spim.ioFijijavadoc
ProgressBarClassbunwarpjFijijavadoc
ProgressCanvasClasslandmarksFijijavadoc
ProgressIndicatorClassvib.app.guiFijijavadoc
ProgressorWrapper around ImageJ's progress bar.Classimagescience.utilityFijijavadoc
ProgressTrackerClassimglib.ops.observerFijijavadoc
ProgressWindowClasslandmarksFijijavadoc
ProgressWriterInterfacebdv.exportFijijavadoc
ProgressWriterConsoleClassbdv.exportFijijavadoc
ProgressWriterIJClassbdv.ij.utilFijijavadoc
ProgressWriterIJClassspim.fiji.plugin.resaveFijijavadoc
ProjectThe top-level class in control.Classini.trakem2Fijijavadoc
ProjectorInterfacespimopenerFijijavadoc
ProjectThingClassini.trakem2.treeFijijavadoc
ProjectTilerClassini.trakem2.persistenceFijijavadoc
ProjectToolbarClassini.trakem2.utilsFijijavadoc
ProjectTreeA class to hold a tree of Thing nodesSee Also:Serialized FormClassini.trakem2.treeFijijavadoc

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PropagatedExceptionUsed to propagate exceptions through to the user.Classcom.sun.tools.javac.utilFijijavadoc
ProposeMipmapsPropose number of mipmap levels, as well subsampling factors and chunk size Choice of proposed chunksize is not based on any hard benchmark dataClassbdv.exportFijijavadoc
Psychomorph_TEM_ReaderClassFijijavadoc
QTWidgetsCustom widgets for configuring Bio-Formats QuickTime support.Classloci.plugins.configFijijavadoc
Quantile_Based_NormalizationClassutilFijijavadoc
QuaternionClassmpicbg.pointdescriptor.matcherFijijavadoc
QueueJumpingKeyListenerClasstracingFijijavadoc
QueueListenerInterfaceedu.utexas.clm.archipelago.listenFijijavadoc
QuickCallableClassedu.utexas.clm.archipelago.computeFijijavadoc
QuickRunnableClassedu.utexas.clm.archipelago.computeFijijavadoc
Quicksortable Copyright: Copyright (c) 2007 This program is free software; you can redistribute it and/orInterfacempi.fruitfly.mathFijijavadoc
QuicksortableInterfacestitchingFijijavadoc
Radial_GradientClassfiji.drawingFijijavadoc
Radial_ResliceClassfiji.stacksFijijavadoc
RadiusNeighborSearchClassfiji.utilFijijavadoc
RadiusNeighborSearchClassmpicbg.imglib.algorithm.kdtreeFijijavadoc
RadiusToEstimatedActionClassfiji.plugin.trackmate.actionFijijavadoc
RagMipMapsLike RawMipMaps, but the alpha channel is compressed with GZIP.Classini.trakem2.ioFijijavadoc
RandomClassscript.imglib.mathFijijavadoc
RandomAccessInputStreamWrapperWrapper class to convert RandomAccessInputStream to RandomAccessInputStream.Classio.scif.bf.wrapperFijijavadoc
RandomAccessInputStreamWrapperWrapper class to convert RandomAccessInputStream to RandomAccessInputStream.Classio.scif.commonFijijavadoc
RandomGeneratorInterface for random number generators.Interfaceimagescience.randomFijijavadoc
RandomizerClassimagescience.randomFijijavadoc
RandPermutation Lionel.ClassutilsFijijavadoc
RangeDialogBio-Formats Importer range chooser dialog box.Classloci.plugins.inFijijavadoc

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RankFilterClassini.trakem2.imaging.filtersFijijavadoc
RANSACClassspim.process.interestpointregistrationFijijavadoc
RANSACParametersClassspim.process.interestpointregistrationFijijavadoc
RansacRegressionFilterClassorg.janelia.intensityFijijavadoc
RansacRegressionReduceFilterClassorg.janelia.intensityFijijavadoc
Raster_RigidClassvibFijijavadoc
RATS_RATS_ (Robust Automatic Threshold Selection) ImageJ plugin.ClassFijijavadoc
RATSQuadtreeClassFijijavadoc
RawMipMapsClassini.trakem2.ioFijijavadoc
ReaderClassorg.imagearchive.lsm.readerFijijavadoc
ReaderClassorg.imagearchive.lsm.toolboxFijijavadoc
ReaderToolkitClassorg.imagearchive.lsm.toolboxFijijavadoc
ReadXMLClassFijijavadoc
RealARGBColorConverterClassnet.imglib2.displayFijijavadoc
RealARGBColorConverterSetupClassbdv.tools.brightnessFijijavadoc
RealFunctionInterfaceimglib.ops.functionFijijavadoc
RealHistogramBinFactoryClassmpicbg.imglib.algorithm.histogram.arbitraryFijijavadoc
RealRandomAccessibleSourceA Source wrapping some RealRandomAccessible.Classbdv.utilFijijavadoc
RealTypeInterfacempicbg.imglib.type.numericFijijavadoc
RealTypeConverterClassmpicbg.imglib.functionFijijavadoc
RealTypeDisplayClassmpicbg.imglib.image.displayFijijavadoc
RealTypeImplClassmpicbg.imglib.type.numeric.realFijijavadoc
RebinPlugin which takes an ImagePlus and rebins the pixel values to the specified range.Classprocess3dFijijavadoc
Rebin_Plugin which takes an ImagePlus and rebins the pixel values to the specified range.Classprocess3dFijijavadoc
RecalculateFeatureActionClassfiji.plugin.trackmate.actionFijijavadoc

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Recent_CommandsClassfiji.utilFijijavadoc
ReciprocalClassimglib.ops.operator.unaryFijijavadoc
RecognizedOptionsTODO: describe com.Classcom.sun.tools.javac.mainFijijavadoc
Reconstruct_DatasetClassQuickPALMFijijavadoc
Reconstruct_ReaderClassedu.utexas.clm.reconstructreader.reconstructFijijavadoc
Reconstruct_WriterClassedu.utexas.clm.reconstructreader.trakem2Fijijavadoc
ReconstructAreaReconstruct an Area from a list of XML Subscribe to Java News and Posts. Get latest updates and posts on Java from Buggybread.com
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RegionAn arbitrarily but discretely shaped region in the x-y plane.Classimagescience.shapeFijijavadocRegionClassini.trakem2.displayFijijavadocRegionalExtremaFactoryProvides a way for the user to automatically create the appropriate RegionalMaximaFinder class without having to deal with the dimensionality.Classmpicbg.imglib.algorithm.extremafinderFijijavadocRegionalExtremaFinderProvides a quick algorithm for finding regional maxima in 2- or 3-dimensional images.Interfacempicbg.imglib.algorithm.extremafinderFijijavadocRegionalExtremaFinder2D* This class finds the regional extrema of a 3 dimensional image.Classmpicbg.imglib.algorithm.extremafinderFijijavadocRegionalExtremaFinder3DThis class finds the regional extrema of a 3 dimensional image.Classmpicbg.imglib.algorithm.extremafinderFijijavadocRegionOfInterestCursorClassmpicbg.imglib.cursor.specialFiji