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# Classes and Interfaces in #Fiji - 3580 results found.
NameDescriptionTypePackageFramework
A_Image5D_testClassFiji
AbortThrowing an instance of this class causes (silent) termination of the main compiler method.Classcom.sun.tools.javac.utilFiji
AboutDisplays a small information dialog about the Bio-Formats Plugins package.Classloci.pluginsFiji
About_RATSClassFiji
AboutDialogClassedfguiFiji
AboutDialogClassorg.imagearchive.lsm.toolbox.guiFiji
AbsClassimglib.ops.operator.unaryFiji
AbsClassscript.imglib.mathFiji
AbstractAffine3DClassscript.imglib.algorithm.fnFiji
AbstractAffineModelChunkClassedu.utexas.clm.archipelago.ijsupportFiji
AbstractAffineTile2DClassmpicbg.trakem2.alignFiji
AbstractAnimatorMother abstract class for animators that can animate the current view in a ViewerFrame instance.Classbdv.viewer.animateFiji
AbstractAnnotationAbstract class dedicated to draw overlayed annotations on a OverlayedImageCanvas.Classfiji.util.guiFiji
AbstractAnnotationValueVisitor6A skeletal visitor for annotation values with default behavior appropriate for the RELEASE_6Classjavax.lang.model.utilFiji
AbstractBlockMatchingClassmpicbg.ij.pluginFiji
AbstractDetectionClassmpicbg.spim.registration.detectionFiji
AbstractDialogClassedfguiFiji
AbstractEdfAlgorithmClassedfFiji
AbstractElementVisitor6A skeletal visitor of program elements with default behavior appropriate for the RELEASE_6Classjavax.lang.model.utilFiji
AbstractFeatureGrapherClassfiji.plugin.trackmate.featuresFiji
AbstractImgFactoryImgLoaderClassspim.fiji.spimdata.imgloadersFiji
AbstractImgLoaderClassspim.fiji.spimdata.imgloadersFiji
AbstractLayerAlignmentParamClassmpicbg.trakem2.alignFiji
AbstractLegacyViewerImgLoaderClassbdv.spimdata.legacyFiji
AbstractNamedActionClassbdv.utilFiji
AbstractNormalizeClassscript.imglib.algorithm.fnFiji
AbstractOffscreenThreadTo be used in combination with the AbstractRepaintThread, as a thread to create graphics offscreen.Classini.trakem2.displayFiji
AbstractPanorama_ViewClassmpicbg.panoramaFiji
AbstractPointDescriptorClassmpicbg.pointdescriptorFiji
AbstractProcessorAn abstract annotation processor designed to be a convenient superclass for most concrete annotation processors.Classjavax.annotation.processingFiji
AbstractProviderClassfiji.plugin.trackmate.providersFiji
AbstractRegionalExtremaFinderClassmpicbg.imglib.algorithm.extremafinderFiji
AbstractRepaintThreadClassini.trakem2.displayFiji
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.semiautoFiji
AbstractSequenceDescriptionA SPIM sequence consisting of a list of timepoints and a list of view setups.Classmpicbg.spim.data.generic.sequenceFiji
AbstractSequenceDescriptionUtilsClassmpicbg.spim.data.generic.sequenceFiji
AbstractSortedGrayLevelIteratorIterate over all pixels ordered by their gray levelAuthor:Steffen Jaensch, Steffen Jaensch Classmpicbg.imglib.cursor.specialFiji
AbstractSpecialCursorThis abstract cursor offer facilities for specialized cursor that are based on a LocalizableByDimCursor whose iteration domain is imposed.Classmpicbg.imglib.cursor.specialFiji
AbstractSpimDataClassmpicbg.spim.data.genericFiji
AbstractSpimSourceClassbdvFiji
AbstractTMActionClassfiji.plugin.trackmate.actionFiji
AbstractToolClassfiji.toolFiji
AbstractTrackingToolClassfiji.toolFiji
AbstractTrackMateModelViewAn abstract class for spot displayers, that can overlay detected spots and tracks on top of the image data.Classfiji.plugin.trackmate.visualizationFiji
AbstractTransformAnimatorMother abstract class for animators that animate the current view in a ViewerFrame instance by modifying the viewer transform.Classbdv.viewer.animateFiji
AbstractTreeTransferHandlerAdapted from freely available code by DeuDeu from http://forum.Classini.trakem2.treeFiji
AbstractTypeVisitor6A skeletal visitor of types with default behavior appropriate for the version 6 language level.Classjavax.lang.model.utilFiji
AbstractVectorClassmpicbg.imglib.cursor.vectorFiji
AbstractViewerSetupImgLoaderClassbdvFiji
AbstractVolatileArrayA ShortArray with an isValid() flag.Classnet.imglib2.img.basictypeaccess.volatiles.arrayFiji
AbstractVolatileNativeNumericTypeAbstract base class for VolatileNumericTypes that wrap native NumericTypes.Classnet.imglib2.type.volatilesFiji
AbstractVolatileNativeRealTypeAbstract base class for VolatileRealTypes that wrapAuthor:Tobias Pietzsch Classnet.imglib2.type.volatilesFiji
Access Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandInterfaceimagewareFiji
AccumulateProjectorClassbdv.viewer.renderFiji
AccumulateProjectorARGBClassbdv.viewer.renderFiji
AccumulateProjectorFactoryInterfacebdv.viewer.renderFiji
AccumulatorA class allowing an easy accumulation of values visited by a TwinCursor.ClassalgorithmsFiji
ACosClassscript.imglib.mathFiji
ActionChooserDescriptorClassfiji.plugin.trackmate.gui.descriptorsFiji
ActionChooserPanelClassfiji.plugin.trackmate.gui.panelsFiji
ActionListenablePanelClassfiji.plugin.trackmate.gui.panelsFiji
ActionProviderClassfiji.plugin.trackmate.providersFiji
ActiveContours This class provides the getDeltaPhi function to the SparseFieldLevelSet: deltaPhi = - DELTA_T * image_term * (advection * ADVECTION_FORCE + curvature * CURVATURE_EPSILON)Classlevelsets.algorithmFiji
AdapterThis class just hands off to the ImageJ Updater The Fiji Updater moved to a new home: ImageJ2.Classfiji.updaterFiji
AdaptiveNonMaximalSuppressionClassmpicbg.imglib.algorithm.scalespaceFiji
AddClassimglib.ops.operator.binaryFiji
AddClassscript.imglib.mathFiji
Add_Empty_ChannelClassFiji
Add_Empty_FrameClassvideo2Fiji
Add_Empty_SliceClassFiji
AddARGBCompositeClassini.trakem2.display.graphicsFiji
AddConstantClassimglib.ops.operator.unaryFiji
AddNoiseClassimglib.ops.operator.unaryFiji
AdjustInputClassmpicbg.spim.postprocessing.deconvolution2Fiji
AdjustInputClassspim.process.fusion.deconvolutionFiji
AdvancedDialogClassedfguiFiji
AffineAffine transforms an image using different interpolation schemes.Classimagescience.transformFiji
Affine2DClassscript.imglib.algorithmFiji
Affine3DPerforms a mathematically correct transformation of an image.Classscript.imglib.algorithmFiji
Affine3DHelpersHelpers to extract parts (rotation, scale, etc) from AffineTransform3D.Classbdv.utilFiji
Affine_From_LandmarksClasslandmarksFiji
AffineFromLandmarksClasslandmarksFiji
AffineModel2DClassmpicbg.trakem2.transformFiji
AffineModel3DClassmpicbg.trakem2.transformFiji
AffineTile2DClassmpicbg.trakem2.alignFiji
AffineTransform3DJsonSerializerClassbdv.img.remoteFiji
AffineTransformModeClassini.trakem2.displayFiji
Albert_TestClasstracingFiji
AlgorithmAn algorithm is an abstraction of techniques like the calculation of the Persons coefficient or Li'S ICQ.ClassalgorithmsFiji
AlgorithmInterfacempicbg.imglib.algorithmFiji
AlgorithmUtilClassscript.imglib.algorithm.fnFiji
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.alignFiji
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 pluginClassFiji
AlignLayersTaskRegister a range of layers using linear or non-linear transformations.Classmpicbg.trakem2.alignFiji
AlignmentUtilsClassmpicbg.trakem2.alignFiji
AlignTaskMethods collection to be called from the GUI for alignment tasks.Classmpicbg.trakem2.alignFiji
AllConnectedComponentsLabel all 8-connected components of a binary imageAuthor:Lee KamentskyClassmpicbg.imglib.algorithm.labelingFiji
AllKnownFilterClassorg.imagearchive.lsm.toolbox.guiFiji
AllToAllRegistrationClassspim.process.interestpointregistration.optimizationtypesFiji
AllToAllRegistrationWithRangeClassspim.process.interestpointregistration.optimizationtypesFiji
AlphaClassscript.imglib.colorFiji
AlphanumComparatorThe Alphanum Algorithm is an improved sorting algorithm for strings containing numbers.Classfiji.plugin.trackmate.utilFiji
AlternateViewerClassview5dFiji
AmiraImporterParses an amira labelfield and imports the labels as AreaList instances into the project tree.Classini.trakem2.ioFiji
AmiraMeshDecoderClassamiraFiji
AmiraMeshEncoderClassamiraFiji
AmiraMeshReader_ClassFiji
AmiraMeshWriter_ClassFiji
AmiraParametersClassamiraFiji
AmiraSurfaceClassisosurfaceFiji
AmiraTableClassamiraFiji
AmiraTableEncoderClassamiraFiji
AmiraTableWriter_ClassFiji
Analyse_ParticlesThis plugin detectes sub-diffraction particles in a sequence of images, it is the main plugin for the QuickPALM package.ClassQuickPALMFiji
Analyze_ReaderThis plugin loads Analyze format files.ClassFiji
Analyze_WriterClassFiji
AnalyzeSkeleton_Main class of the ImageJ/Fiji plugin for skeleton analysis.Classsc.fiji.analyzeSkeletonFiji
AnalyzeTracings_ClasstracingFiji
AndClassimglib.ops.conditionFiji
AndClassimglib.ops.operator.binaryFiji
AndClassscript.imglib.mathFiji
AndConstantClassimglib.ops.operator.unaryFiji
AnElementClassview5dFiji
AngleDefines an angle which is part of the ViewSetup.Classmpicbg.spim.data.sequenceFiji
Animated_Gif_ReaderClassioFiji
Anisotropic_Diffusion_2DClassanisotropic_diffusionFiji
AnisotropicDiffusionPerona & Malik Anisotropic diffusion This algorithm implements the so-called anisotropic diffusion scheme of Perona & Malik, 1990,Classmpicbg.imglib.algorithm.pdeFiji
AnnotateEnter annotations on symbols.Classcom.sun.tools.javac.compFiji
AnnotationMirrorRepresents an annotation.Interfacejavax.lang.model.elementFiji
AnnotationProcessingErrorError thrown for problems encountered during annotation processing.Classcom.sun.tools.javac.processingFiji
AnnotationProxyMakerA generator of dynamic proxy implementations of java.Classcom.sun.tools.javac.modelFiji
AnnotationTreeA tree node for an annotation.Interfacecom.sun.source.treeFiji
AnnotationValueRepresents a value of an annotation type element.Interfacejavax.lang.model.elementFiji
AnnotationValueVisitorA visitor of the values of annotation type elements, using a variant of the visitor design pattern.Interfacejavax.lang.model.elementFiji
APNGTranslatorContainer class for translators between OME and APNG formats.Classio.scif.ome.translatorsFiji
AppearanceCreatorClassoctreeFiji
AppearanceCreatorThis class is a helper class whose main task is to create Appearance objects for a specified axis and direction.ClassvoltexFiji
AppendSpimData2Classspim.process.fusion.exportFiji
AppendSpimData2HDF5Classspim.process.fusion.exportFiji
Apply_External_TransformationClassfiji.pluginFiji
Apply_TransformationClassspim.fiji.pluginFiji
ApplyParametersClassspim.fiji.plugin.applyFiji
ApplyTransformationPopupClassspim.fiji.spimdata.explorer.popupFiji
ArchipelagoClientClassedu.utexas.clm.archipelago.network.clientFiji
ArchipelagoFutureClassedu.utexas.clm.archipelago.computeFiji
ArchipelagoServerClassedu.utexas.clm.archipelago.network.serverFiji
ArchipelagoUIInterfaceedu.utexas.clm.archipelago.uiFiji
ArchipelagoUtilsClassedu.utexas.archipelagoFiji
ArchiveClientClassclientFiji
AreaCalculationsClassfiji.geomFiji
AreaContainerInterfaceini.trakem2.displayFiji
AreaListA list of brush painted areas similar to a set of labelfields in Amira.Classini.trakem2.displayFiji
AreaList_CropClassedu.utexas.clm.cropFiji
AreaListCropClassedu.utexas.clm.cropFiji
AreaListVolumeWraps a list of Areas to be triangulated.Classij3dFiji
AreaTreeClassini.trakem2.displayFiji
AreaUtilsClassini.trakem2.utilsFiji
AreaWrapperClassini.trakem2.displayFiji
ArrayClassmpicbg.imglib.container.arrayFiji
Array3DClassmpicbg.imglib.container.arrayFiji
Array3DLocalizableByDimCursorClassmpicbg.imglib.cursor.arrayFiji
Array3DLocalizableByDimOutOfBoundsCursorClassmpicbg.imglib.cursor.arrayFiji
Array3DLocalizableCursorClassmpicbg.imglib.cursor.arrayFiji
ArrayAccessTreeA tree node for an array access expression.Interfacecom.sun.source.treeFiji
ArrayBaseClassfiji.utilFiji
ArrayContainerFactoryClassmpicbg.imglib.container.arrayFiji
ArrayConverter Copyright: Copyright (c) 2006Version:1.Classmpi.fruitfly.generalFiji
ArrayCursorClassmpicbg.imglib.cursor.arrayFiji
ArrayDataAccessInterfacempicbg.imglib.container.basictypecontainer.arrayFiji
ArrayLocalizableByDimCursorClassmpicbg.imglib.cursor.arrayFiji
ArrayLocalizableByDimOutOfBoundsCursorClassmpicbg.imglib.cursor.arrayFiji
ArrayLocalizableCursorClassmpicbg.imglib.cursor.arrayFiji
ArrayLocalizablePlaneCursorClassmpicbg.imglib.cursor.arrayFiji
ArrayTypeRepresents an array type.Interfacejavax.lang.model.typeFiji
ArrayTypeTreeA tree node for an array type.Interfacecom.sun.source.treeFiji
ArrowClassutilFiji
ArrowDisplayerInterfaceutilFiji
ArrowOptionPanelClassfiji.utilFiji
ArrowShapeClassfiji.utilFiji
ArrowTool This plugin aims at being a convenient interactive tool for drawing arrow shape on ImageJ windows.Classfiji.utilFiji
ASinClassscript.imglib.mathFiji
AspectsContains aspect ratio or size information of up to 5D image elements.Classimagescience.imageFiji
AssertTreeA tree node for an 'assert' statement.Interfacecom.sun.source.treeFiji
AssignmentAlgorithmJust in case I want to try more than one implementation of the assignment algorithm.Interfacefiji.plugin.trackmate.tracking.oldlap.hungarianFiji
AssignmentProblemAn implementation of this: http://en.Classfiji.plugin.trackmate.tracking.oldlap.hungarianFiji
AssignmentTreeA tree node for an assignment expression.Interfacecom.sun.source.treeFiji
AssignOperationAn AssignOperation computes values in an output image.Classimglib.ops.operationFiji
ATanClassscript.imglib.mathFiji
ATan2Classscript.imglib.mathFiji
AttrThis is the main context-dependent analysis phase in GJC.Classcom.sun.tools.javac.compFiji
AttrContextContains information specific to the attribute and enter passes, to be used in place of the generic field in environments.Classcom.sun.tools.javac.compFiji
AttrContextEnvEnv specialized as Env This is NOT part of any supported API.Classcom.sun.tools.javac.compFiji
AttributeAn annotation value.Classcom.sun.tools.javac.codeFiji
AugmentedLandmarkWarp_ClassvibFiji
AuthenticationExceptionClassedu.utexas.clm.archipelago.exceptionFiji
Auto_Local_ThresholdClassfiji.thresholdFiji
Auto_ThresholdClassfiji.thresholdFiji
Auto_TracerClasstracingFiji
AutoLabellerClassoldsegmentersFiji
AutoLabellerNaiveClassoldsegmentersFiji
AutomaticAngleSetupClassmpicbg.spim.preprocessingFiji
AutomaticBoundingBoxClassspim.process.fusion.boundingboxFiji
AutomaticReorientationClassspim.process.fusion.boundingboxFiji
AutoPointClasstracingFiji
AutoSearchThreadClasstracingFiji
AutoThresholdRegressionA class implementing the automatic finding of a threshold used for Person colocalisation calculation.ClassalgorithmsFiji
AutoTracerCanvasClasstracingFiji
AverageClassimglib.ops.operator.binaryFiji
AverageClassscript.imglib.mathFiji
Average_ColorClassFiji
Average_ImagesClassvibFiji
Average_Torsten_ResultsClassutilFiji
AverageBrainClassvib.app.moduleFiji
AverageBrain_ClassvibFiji
AverageContentClassmpicbg.spim.fusionFiji
AverageContentFactoryClassmpicbg.spim.fusionFiji
AveragePixelFusionClassmpicbg.stitching.fusionFiji
AveragePixelFusionIgnoreZeroClassmpicbg.stitching.fusionFiji
AvgFunctionClassimglib.ops.function.pnFiji
AxesContains information about the activity of the coordinate axes of up to 5D image data objects.Classimagescience.imageFiji
AxisConstantsThis interface stores some common constants.Interfaceij3dFiji
AxisLessThanClassimglib.ops.conditionFiji
BallClassini.trakem2.displayFiji
BalloonClassballoonstructureFiji
BalloonPopulationClassballoonstructureFiji
BalloonSegmentation_ClassFiji
BalloonSequenceClassballoonstructureFiji
BandElementClasslevelsets.algorithmFiji
BandElementCacheA cache for BandElement objects - this avoids having to construct/destruct objects in algorithms that do frequent allocations/deallocations of thisClasslevelsets.algorithmFiji
BandpassClassmpicbg.imglib.algorithm.fftFiji
BandpassFilterClassscript.imglib.algorithmFiji
BarChartClassscript.imglib.analysisFiji
BaseFileManagerUtility methods for building a filemanager.Classcom.sun.tools.javac.utilFiji
BaseFileObjectThis is NOT part of any supported API.Classcom.sun.tools.javac.fileFiji
BasePairBitTypeClassmpicbg.imglib.type.labelFiji
BasePairCharTypeClassmpicbg.imglib.type.labelFiji
BasePairTypeInterfacempicbg.imglib.typeFiji
BasePairTypeDisplayClassmpicbg.imglib.image.displayFiji
BasicDetectorConfigurationPanelClassfiji.plugin.trackmate.gui.panels.detectorFiji
BasicDialogClassedfguiFiji
BasicImgLoaderProvides images for a sequence.Interfacempicbg.spim.data.generic.sequenceFiji
BasicMultiResolutionImgLoaderA BasicImgLoader providing multiple resolutions of each image.Interfacempicbg.spim.data.generic.sequenceFiji
BasicMultiResolutionSetupImgLoaderA BasicSetupImgLoader providing multiple resolutions of each image.Interfacempicbg.spim.data.generic.sequenceFiji
BasicSetupImgLoaderProvides images for one setup of aAuthor:Tobias Pietzsch Interfacempicbg.spim.data.generic.sequenceFiji
BasicViewDescriptionClassmpicbg.spim.data.generic.sequenceFiji
BasicViewSetupAn view setup is an Entity that may have a name, image size, and voxel size.Classmpicbg.spim.data.generic.sequenceFiji
Batch_Weka_SegmentationClassedu.utexas.archipelago.pluginFiji
BatchConverterBatch Converter Class - Adapted from Wayne Rasband's Batch Converter plug-in.Classorg.imagearchive.lsm.toolboxFiji
BatchDialogClassorg.imagearchive.lsm.toolbox.guiFiji
BatchFilterClassorg.imagearchive.lsm.toolbox.guiFiji
BatchLog_ClassvibFiji
BatchOpenerThis class contains methods I would like to see incorporated into HandleExtraFileTypes, or elsewhere.ClassutilFiji
BatchWekaSegmentationClassedu.utexas.archipelago.segmentationFiji
BayesMVDeconvolutionClassmpicbg.spim.postprocessing.deconvolution2Fiji
BDVPopupClassspim.fiji.spimdata.explorer.popupFiji
BeadClassmpicbg.spim.registration.beadFiji
Bead_RegistrationClassfiji.pluginFiji
BeadIdentificationClassmpicbg.spim.registration.beadFiji
BeadRegistrationClassmpicbg.spim.registration.beadFiji
BeadSegmentationClassmpicbg.spim.registration.beadFiji
BeadStructureClassmpicbg.spim.registration.beadFiji
BeadTransformGroupClassmpicbg.spim.vis3dFiji
BeamSplitterClassorg.imagearchive.lsm.toolbox.info.scaninfoFiji
BeaudetxThis class implements Beaudet differentiation in x direction.ClassvolumeFiji
BehaviorCallbackInterfaceij3d.behaviorsFiji
BenchmarkInterfacempicbg.imglib.algorithmFiji
BenchmarkAlgorithmThis is a convenience implementation of an algorithm that implements Benchmark and Algorithm so that less code has to be re-implemented.Classmpicbg.imglib.algorithmFiji
BenesNamedPointClassvibFiji
BEPBBinBoundariesInferenceClassinferenceFiji
BEPBInferenceClassinferenceFiji
BEPBModelInferenceClassinferenceFiji
BFMiscellaneous plugins utility methods.Classloci.pluginsFiji
BFVirtualStackSubclass of VirtualStack that uses Bio-Formats to read planes on demand.Classloci.plugins.utilFiji
BigBrotherSupervise all threads, and report uncaught exceptions.Classini.trakem2.utilsFiji
BigDataBrowserPlugInClassbdv.ijFiji
BigDataViewerClassbdvFiji
BigDataViewerActionsClassbdvFiji
BigDataViewerBoundingBoxClassspim.process.fusion.boundingboxFiji
BigDataViewerPlugInClassbdv.ijFiji
BigDataViewerTransformationWindowClassspim.fiji.plugin.applyFiji
BIJfftThis class implements a one-dimensional real->complex fast fourier transform Copyright (c) 1999-2004, Michael Abramoff.ClassbijnumFiji
BIJfhtThis class implements the fast Hartley transform on matrices and vectors (real float matrices).ClassbijnumFiji
BIJfitThis class implements useful linear and polynomial regression Press, Flannery, Teukolsky, Vetterling, Numerical Recipes in C 2nd ed, Cambridge University Press, 1986ClassbijnumFiji
BIJfunctionsThis class implements useful numerical functions from Press, Flannery, Teukolsky, Vetterling, Numerical Recipes in C 2nd ed, Cambridge University Press, 1986ClassbijnumFiji
BIJgifa Does a maximization of images with maximum signal power and signal to noise ratio.ClassbijnumFiji
BIJJacobiThis class implements the jacobi function as a Java class.ClassbijnumFiji
BIJknnk Nearest Neighborhood (brute-force) implementation.ClassbijnumFiji
BIJmatrix eigenvectors and others.ClassbijnumFiji
BIJmiMutual infromation processing routines.ClassbijnumFiji
BIJpcaPrincipal component analysis (PCA) on 2-D sequences (ie.ClassbijnumFiji
BIJpowellThis class implements Powell's multidimensional optimization.ClassbijnumFiji
BIJShortMatrix Simplified subset of BIJmatrix.ClassbijnumFiji
BIJstatsBIJ statistical methods inherited from MatLab.ClassbijnumFiji
BIJtransformThis class implements static transformation matrix operations for 2-D and 3-D transformation matrices.ClassbijnumFiji
BIJutilUtilities to link BIJ things to ImageJ.ClassbijnumFiji
Bilateral_FilterClassFiji
BilateralFilterClassvibFiji
Binary_to_Point_SelectionThis is a template for a plugin that requires one image to be opened, and takes it as parameter.Classfiji.selectionFiji
BinaryInterpolation2DGiven two binary images of the same dimensions, generate an interpolated image that sits somewhereClassini.trakem2.imagingFiji
BinaryInterpolation2DGiven two binary images of the same dimensions, generate an interpolated image that sits somewhereClassmpicbg.imglib.algorithm.labelingFiji
BinaryInterpolatorClassvibFiji
BinaryOperationClassscript.imglib.math.fnFiji
BinaryOperatorInterfaceimglib.ops.operatorFiji
BinaryOperatorFunctionClassimglib.ops.function.p2Fiji
BinaryTreeA tree node for a binary expression.Interfacecom.sun.source.treeFiji
BinBoundariesComputationClassinferenceFiji
BinBoundariesInferenceClassinferenceFiji
BinClassificationInferenceClassinferenceFiji
BinomialBinomial coefficientsVersion:$Id: Binomial.Classpal.mathFiji
BinomialGeneratorBinomial random number generator.Classimagescience.randomFiji
BioFormatsFormatWraps an ImageReader in a SCIFIO Format, allowing proprietary Bio-Formats readers to be used in SCIFIO-based applications.Classio.scif.bfFiji
BioFormatsTranslatorContainer class for translators between BioFormats and OME formats.Classio.scif.bf.omeFiji
Biorad_ReaderImports a Z series(image stack) from a Biorad MRC 600 confocal microscope.ClassFiji
Biorad_WriterClassFiji
BisectionStepperTry to converge a threshold based on an update value condition.ClassalgorithmsFiji
BitAccessInterfacempicbg.imglib.container.basictypecontainerFiji
BitArrayClassmpicbg.imglib.container.basictypecontainer.arrayFiji
BitDynamicContainerClassmpicbg.imglib.container.dynamicFiji
BitDynamicContainerAccessorClassmpicbg.imglib.container.dynamicFiji
BitsA class for extensible, mutable bit sets.Classcom.sun.tools.javac.utilFiji
BitStreamReadClasscustomnode.u3dFiji
BitStreamWriteClasscustomnode.u3dFiji
BitTypeClassmpicbg.imglib.type.logicFiji
BitTypeDisplayClassmpicbg.imglib.image.displayFiji
BlasClassbijnumFiji
BleachCorrectionClassemblcmciFiji
BleachCorrection_ExpoFitClassemblcmciFiji
BleachCorrection_MHClassemblcmciFiji
BleachCorrection_SimpleRatioClassemblcmciFiji
BlendingUtility functions for blending images together, to remove contrast seams.Classini.trakem2.imagingFiji
BlendingClassmpicbg.spim.fusionFiji
BlendingRealRandomAccess that computed cosine-blending for a certain intervalAuthor:Stephan Preibisch (stephan.Classspim.process.fusion.weightsFiji
BlendingFactoryClassmpicbg.spim.fusionFiji
BlendingPixelFusionClassmpicbg.stitching.fusionFiji
BlendingPixelFusionIgnoreZeroClassmpicbg.stitching.fusionFiji
BlendingRealRandomAccessClassspim.process.fusion.weightsFiji
BlendingSimpleClassmpicbg.spim.fusionFiji
BlendingSimpleFactoryClassmpicbg.spim.fusionFiji
Blob_Segmentation_in_3DA mouse listener for point-and-click segmentation and measurement of pixel clouds in an Image3DUniverse.Classij3d.segmentationFiji
BlockClassmpicbg.spim.postprocessing.deconvolution2Fiji
BlockClassspim.process.cudaFiji
BlockGeneratorInterfacespim.process.cudaFiji
BlockGeneratorFixedSizePreciseClassspim.process.cudaFiji
BlockGeneratorVariableSizePreciseThis BlockGenerator cares that the overlap within the image is accounted for and that an outofbounds strategy is taken into account.Classspim.process.cudaFiji
BlockGeneratorVariableSizeSimpleThis BlockGenerator only cares that the overlap within the image is accounted for, not about an outofbounds strategy.Classspim.process.cudaFiji
BlockingFetchQueuesQueueing structure (intended for cells to be fetched).Classbdv.img.cacheFiji
BlockLogDetectorClassfiji.plugin.trackmate.detectionFiji
BlockLogDetectorConfigurationPanelClassfiji.plugin.trackmate.gui.panels.detectorFiji
BlockLogDetectorFactoryClassfiji.plugin.trackmate.detectionFiji
BlockMatching_ExtractPoinRoiClassmpicbg.ij.pluginFiji
BlockMatching_TestParametersClassmpicbg.ij.pluginFiji
BlockMatchPairCallableClassmpicbg.trakem2.align.concurrentFiji
BlockTreeA tree node for a statement block.Interfacecom.sun.source.treeFiji
BlueClassscript.imglib.colorFiji
BMPConstantsProvides constants used with BMP format.Classnet.sf.image4j.codec.bmpFiji
BMPDecoderDecodes images in BMP format.Classnet.sf.image4j.codec.bmpFiji
BMPEncoderEncodes images in BMP format.Classnet.sf.image4j.codec.bmpFiji
BMPImageContains a decoded BMP image, as well as information about the source encoded image.Classnet.sf.image4j.codec.bmpFiji
BMPTranslatorContainer class for translators between OME and BMP formats.Classio.scif.ome.translatorsFiji
BookmarksClassbdv.tools.bookmarksFiji
BookmarksEditorClassbdv.tools.bookmarksFiji
BookmarkTextOverlayAnimatorDraw one line of text in the center or bottom right of the display.Classbdv.tools.bookmarksFiji
BooksteinClassmath3dFiji
Bookstein_From_LandmarksClasslandmarksFiji
BooksteinFromLandmarksClasslandmarksFiji
BooksteinTransformClassvib.transformsFiji
BooleanOptionA boolean option for one of the plugins.Classloci.plugins.prefsFiji
BooleanTypeInterfacempicbg.imglib.typeFiji
BootstrapBootstrap the ImageJ UpdaterAuthor:Johannes SchindelinClassfiji.updaterFiji
BorderBorder - draws a configurable borderAuthor:DTAI, IncorporatedClassvib.segmentFiji
BorderPanelA panel with a border and an optional title.ClassFiji
BordersContains the dimensions of the borders of up to 5D image data objects.Classimagescience.imageFiji
BottleInterfaceedu.utexas.clm.archipelago.network.translationFiji
BottlerInterfaceedu.utexas.clm.archipelago.network.translationFiji
BoundedIntervalA interval consisting of BoundedValue minimum and maximum that can span any interval in a given range.Classbdv.utilFiji
BoundedTypeBasicImgLoaderInterfacempicbg.spim.data.generic.sequenceFiji
BoundedValueA int variable that can take any value in a given range.Classbdv.utilFiji
BoundingBoxClassij3d.shapesFiji
BoundingBoxThe bounding box that contains a region from the minimum inclusive to the maximum non-inclusive.Classmpicbg.imglib.labelingFiji
BoundingBoxClassspim.fiji.spimdata.boundingboxFiji
BoundingBoxDialogClassbdv.tools.boundingboxFiji
BoundingBoxesClassspim.fiji.spimdata.boundingboxFiji
BoundingBoxGUIClassspim.process.fusion.boundingboxFiji
BoundingBoxOverlayClassbdv.tools.boundingboxFiji
BoundingBoxPopupClassspim.fiji.spimdata.explorer.popupFiji
BoundingBoxUtilClassbdv.tools.boundingboxFiji
BoundingSphereClassij3d.shapesFiji
BoundKindClasscom.sun.tools.javac.codeFiji
BoundsContains bounding box information of up to 5D shapes.Classimagescience.shapeFiji
BoundsCheckedFunctionreturns a very large number instead of the function value if arguments are out of bound (useful for minimization withClasspal.mathFiji
BoundsInclusiveClassvib.transformsFiji
BoxClasscustomnodeFiji
BoxRealRandomAccessibleClassbdv.tools.boundingboxFiji
BoxSelectionPanelClassbdv.tools.boundingboxFiji
BreakTreeA tree node for a 'break' statement.Interfacecom.sun.source.treeFiji
Bresenham3DClassutilFiji
BrightnessClassscript.imglib.colorFiji
BrightnessDialogAdjust brightness and colors for individual (or groups of) setups.Classbdv.tools.brightnessFiji
BrowserOptionsWindowExtension of JFrame that allows the user to adjust caching settings.Classloci.plugins.utilFiji
BSplineThis class implements basic operations to work with cubic B-splines.ClassmathFiji
BSplineModelClass for representing the images and the deformations by cubic B-splines: Both, images and deformations, are stored in multi-resolution pyramids.ClassbunwarpjFiji
BucketA Bucket is a subarea of the Layer area, which contains either other Buckets or a map of stack_index vs.Classini.trakem2.displayFiji
BucketableInterfaceini.trakem2.displayFiji
Buffer Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandInterfaceimagewareFiji
BufferedImageBuilderClasslevelsets.filterFiji
Bug_SubmitterA plugin for reporting bugs to Fiji's BugZilla bug tracker.ClassBug_SubmitterFiji
Builder Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandClassimagewareFiji
BundleClassview5dFiji
bUnwarpJ_Main class for the image registration plugin for ImageJ/Fiji.ClassbunwarpjFiji
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.utilsFiji
Byte3DArrayInterfaceadtFiji
ByteAccess Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandClassimagewareFiji
ByteAccessInterfacempicbg.imglib.container.basictypecontainerFiji
ByteArrayA dynamic array of byte values.Classimagescience.arrayFiji
ByteArrayClassmpicbg.imglib.container.basictypecontainer.arrayFiji
ByteBufferA byte buffer is a flexible array which grows when elements are appended.Classcom.sun.tools.javac.utilFiji
ByteBuffer Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandClassimagewareFiji
ByteCodesBytecode instruction codes, as well as typecodes used as instruction modifiers.Interfacecom.sun.tools.javac.jvmFiji
ByteDynamicContainerClassmpicbg.imglib.container.dynamicFiji
ByteDynamicContainerAccessorClassmpicbg.imglib.container.dynamicFiji
ByteElementClassview5dFiji
ByteImageAn image containing up to 5D elements of type byte.Classimagescience.imageFiji
ByteImagePlusImagePlusContainer for byte-stored data.Classmpicbg.imglib.container.imageplusFiji
BytePointwise Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandClassimagewareFiji
ByteProbabilityUser: Tom Larkworthy class that encodeds probilities as UNSIGNED bytes and makes things go seriously fast!ClassadtFiji
ByteProcess Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandClassimagewareFiji
ByteSet Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandClassimagewareFiji
ByteTypeClassmpicbg.imglib.type.numeric.integerFiji
CacheThis is the part of the VolatileGlobalCellCache interface that is exposed to the renderer directly (that is, not via images).Interfacebdv.img.cacheFiji
CacheAccess is not synchronized, that is your duty.Classini.trakem2.persistenceFiji
CacheArrayLoaderInterfacebdv.img.cacheFiji
CachedCellImgClassbdv.img.cacheFiji
CacheFSInfoCaching implementation of FSInfo.Classcom.sun.tools.javac.fileFiji
CacheHintsHints to the cache on how to handle cell requests.Classbdv.img.cacheFiji
CacheIoTimingUtilities for per ThreadGroup measuring and budgeting of time spentAuthor:Tobias Pietzsch Classbdv.img.cacheFiji
CachingThreadClassini.trakem2.utilsFiji
Calculator_PlusThis plugin does various calculations on two images or stacks.ClassFiji
CalibratedImgClassspim.fiji.spimdata.imgloadersFiji
CalibrationClassspim.fiji.spimdata.imgloadersFiji
Calibration5DExtension of the Calibration class to 5 Dimensions.Classi5d.calFiji
CalibratorLogic for calibrating images.Classloci.plugins.inFiji
CannyAdapted from the Sun Java Forums.Classlevelsets.filterFiji
CanvasImageClassmpicbg.imglib.algorithmFiji
CaptureOverlayActionClassfiji.plugin.trackmate.actionFiji
CaseTreeA tree node for a 'case' in a 'switch' statement.Interfacecom.sun.source.treeFiji
CatchTreeA tree node for a 'catch' block in a 'try' statement.Interfacecom.sun.source.treeFiji
CategoryJComboBoxA JcomboBox that displays categories, and return the category the selectedAuthor:Jean-Yves Tinevez, adapted fromClassfiji.plugin.trackmate.gui.panels.componentsFiji
CatmaidImageLoaderClassbdv.img.catmaidFiji
CatmaidVolatileIntArrayLoaderClassbdv.img.catmaidFiji
CbrtClassscript.imglib.mathFiji
CeilClassscript.imglib.mathFiji
CellClassmpicbg.imglib.container.cellFiji
Cell_CounterClassFiji
CellCntrImageCanvasClassFiji
CellCntrMarkerClassFiji
CellCntrMarkerVectorClassFiji
CellContainerClassmpicbg.imglib.container.cellFiji
CellContainerFactoryClassmpicbg.imglib.container.cellFiji
CellCounterClassFiji
CellCounterOptionsOptions for the Cell Counter plugin.ClassFiji
CellCursorClassmpicbg.imglib.cursor.cellFiji
CellLocalizableByDimCursorClassmpicbg.imglib.cursor.cellFiji
CellLocalizableByDimOutOfBoundsCursorClassmpicbg.imglib.cursor.cellFiji
CellLocalizableCursorClassmpicbg.imglib.cursor.cellFiji
CellLocalizablePlaneCursorClassmpicbg.imglib.cursor.cellFiji
CellVoyagerDataExporterClassbdv.ij.export.tilesFiji
Center_TransformationClassvibFiji
CenterlineSlice Lionel.ClassutilsFiji
CenterTransformationClassvib.app.moduleFiji
CentralDiffThis class implements a four point central difference gradient kernel.ClassvolumeFiji
CentralityFollowing pseudo-code from: Ulrik Brandes.Classini.trakem2.analysisFiji
ChangeAttributeIdClassbdv.spimdata.toolsFiji
ChangeViewSetupIdClassbdv.spimdata.toolsFiji
ChannelClassini.trakem2.displayFiji
ChannelDefines a channel which is part of the ViewSetup.Classmpicbg.spim.data.sequenceFiji
ChannelClassscript.imglib.colorFiji
ContourSetInterfaceedu.utexas.clm.reconstructreader.reconstructFiji
ContrastAdjustmentModeClassini.trakem2.displayFiji
ContrastEnhancerWrapperClassini.trakem2.imagingFiji
ContrastPlotCopied and modified from Wayne Rasband's ImageJ ContrastPlot inner class in ij.Classini.trakem2.imagingFiji
ControlClassfiji.plugin.volumeviewerFiji
ControlClickBehaviorA class to provide the behavior on control-clicking oncontent in the 3D viewer.Classini.trakem2.display.d3dFiji
ControlJPanelGUI panel to interactively segmentate an image with SIOX.Classorg.siox.exampleFiji
ControlJPanelThis class implements the interactive buttons for the Siox segmentation GUI.ClasssioxFiji
ControlPanelFrameClassorg.imagearchive.lsm.toolbox.guiFiji
ControlWindowStatic class that shows one project per tab in a JFrame.Classini.trakem2Fiji
ConvertUtility class for static conversion methods between numbers and strings in various formats.Classcom.sun.tools.javac.utilFiji
Convert_Red_To_MagentaClassfiji.colorFiji
Convert_Red_To_Magenta_ClipboardClassfiji.colorFiji
ConverterInterfacempicbg.imglib.functionFiji
ConverterSetupModify the range and color of the converter for a source.Interfacebdv.tools.brightnessFiji
ConvertUtilProvides useful methods for converting images from one colour depth to another.Classnet.sf.image4j.utilFiji
ConvexBranchesDecompositionA class that can decompose the tracks of a Model in convex branches.Classfiji.plugin.trackmate.graphFiji
ConvolutionFilterPerforms a convolution operation on the input image.Classlevelsets.filterFiji
Convolve3dClassprocess3dFiji
Convolve_3dClassprocess3dFiji
Convolver Routines to convolve a 1D signal applying mirror boundary conditions.ClassimagewareFiji
ConvolverThis class implements convolution operations on image planes and volumes.ClassvolumeFiji
CoordinateClassini.trakem2.displayFiji
CoordinateEncapsulates a three-dimensional Coordinate.Classlevelsets.algorithmFiji
CoordinatesContains 5D integer coordinates.Classimagescience.imageFiji
CoordinateSystemClassij3d.shapesFiji
CoordinateTransformInvertibleCoordinateTransform with String import and export as used inInterfacempicbg.trakem2.transformFiji
CoordinateTransformInterfacestitching.modelFiji
CoordinateTransformListClassmpicbg.trakem2.transformFiji
CoordinateTransformXMLClassini.trakem2.ioFiji
CoordsCursorAbstract cursor that offers facilities to move the cursor origin (whatever this means for the concrete implementation) by giving physical coordinates, convertedClassmpicbg.imglib.cursor.specialFiji
CoordSystem3dClassmpicbg.spim.registration.detection.descriptorFiji
CoordSystemSecure3dClassmpicbg.spim.registration.detection.descriptorFiji
CopyClassimglib.ops.operator.binaryFiji
CopyClassimglib.ops.operator.unaryFiji
CopyOverlayActionClassfiji.plugin.trackmate.actionFiji
CopyTransparentZeroClassimglib.ops.operator.binaryFiji
Correct_DriftClassQuickPALMFiji
Correct_Drift2ClassQuickPALMFiji
CorrectBackgroundClassini.trakem2.imaging.filtersFiji
CorrelationClassdistanceFiji
CorrespondenceExtractionInterfacempicbg.spim.registration.detection.descriptorFiji
CorrespondingInterestPointsDefines a pair of corresponding interest pointsAuthor:Stephan Preibisch (stephan.Classspim.fiji.spimdata.interestpointsFiji
CosClassscript.imglib.mathFiji
CoshClassscript.imglib.mathFiji
CostesSignificanceTestClassalgorithmsFiji
CostFunctionInterface representing a function that can calculate the cost to link a source object to a target object.Interfacefiji.plugin.trackmate.tracking.sparselap.costfunctionFiji
CostFunctionsInterface for cost function classes, which take a Matrix and fill in values according to the cost function.Interfacefiji.plugin.trackmate.tracking.oldlap.costfunctionFiji
CostMatrixCreatorInterface for function that can generate a SparseCostMatrix from assignment candidates.Interfacefiji.plugin.trackmate.tracking.sparselap.costmatrixFiji
Count_FilesClassspimopenerFiji
Count_LabelsClassutilFiji
Counter3DClassUtilitiesFiji
CountingTaskFactoryClassini.trakem2.parallelFiji
CoverMakerUtilsUtility methods for Fiji's Cover Maker script.Classfiji.utilFiji
CPDragAndDropClassorg.imagearchive.lsm.toolbox.guiFiji
CPU_MeterClassFiji
Create_3D_calibrationThis plugin creates a 3D calibration table by observing the width and height change of beads over depth (caused by astigmatism).ClassQuickPALMFiji
CreateSymbolsUsed to generate a "symbol file" representing rt.Classcom.sun.tools.javac.symFiji
CreateTracingVolume_ClasstracingFiji
CreditsClassbunwarpjFiji
CropClassimagescience.transformFiji
CropDialogClassbdv.tools.cropFiji
CropDialogBio-Formats Importer crop options dialog box.Classloci.plugins.inFiji
CropEditor_ClassFiji
CropImgLoaderThis ImgLoader provides views and transformations into a cropped region of a data-set (provided by list of Sources).Classbdv.tools.cropFiji
CrossCorrelationClassmpicbg.imglib.algorithm.correlationFiji
CrossCorrelation2DClassmpi.fruitfly.registrationFiji
CrossCorrelationResult2DClassstitchingFiji
CrossCorrelationResult3DClassstitchingFiji
CRTableThis class contains the CharacterRangeTable for some method and the hashtable for mapping trees or lists of trees to theirClasscom.sun.tools.javac.jvmFiji
CRTFlagsThe CharacterRangeTable flags indicating type of an entry.Interfacecom.sun.tools.javac.jvmFiji
CSVReaderA very simple CSV reader released under a commercial-friendly license.Classutil.opencsvFiji
CSVWriterA very simple CSV writer released under a commercial-friendly license.Classutil.opencsvFiji
CubeTriangular mesh of a cube in 3D.Classimagescience.meshFiji
CubeClassoctreeFiji
CubeDataClassoctreeFiji
CubicBSplineTransformClass to implement elastic transforms based on cubic B-splines.Classbunwarpj.trakem2.transformFiji
CUDADeviceClassspim.process.cudaFiji
CUDAFourierConvolutionInterfacespim.process.cudaFiji
CUDASeparableConvolutionInterface to load the native library for separable convolution using CUDA/CPU (https://github.Interfacespim.process.cudaFiji
CUDASeparableConvolutionFunctionsExecutes gaussian convolution using the native CUDA implementation (https://github.Classspim.process.cudaFiji
CUDAStandardFunctionsInterfacespim.process.cudaFiji
CUDAToolsClassmpicbg.spim.postprocessing.deconvolution2Fiji
CUDAToolsClassspim.process.cudaFiji
CumulativeQueueClass to create a cumulative queue in bUnwarpJ.ClassbunwarpjFiji
CurrentSliceClassfiji.utilFiji
CursorThe Cursor interface The Cursor is responsible for iterating over the image.Interfacempicbg.imglib.cursorFiji
CursorFactorySome static cursor creation utilities.Classorg.siox.exampleFiji
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.cursorFiji
CursorLinkInterfacempicbg.imglib.cursor.linkFiji
Curvatures_Classfiji.featuresFiji
CustomCanvasClassvib.segmentFiji
CustomIndexedTriangleMeshClasscustomnodeFiji
CustomLineMeshClasscustomnodeFiji
CustomMeshClasscustomnodeFiji
CustomMeshNodeClasscustomnodeFiji
CustomMultiMeshClasscustomnodeFiji
CustomPointMeshClasscustomnodeFiji
CustomQuadMeshClasscustomnodeFiji
CustomStackWindowClassvib.segmentFiji
CustomTransparentTriangleMeshClasscustomnodeFiji
CustomTriangleMeshClasscustomnodeFiji
CustomVolumeBehavior2 CustomVolumeBehavior2 implements the special Java 3d Picking behavior needed by the Volume_Calculator.ClassvolumeCalculatorFiji
CVMKalmanFilterA Kalman filter that deals with a single particle motion in 3D with a constant velocity vector.Classfiji.plugin.trackmate.tracking.kalmanFiji
CylinderTriangular mesh of a cylinder in 3D.Classimagescience.meshFiji
CZLSMInfoClassorg.imagearchive.lsm.reader.infoFiji
CZLSMInfoExtendedClassorg.imagearchive.lsm.toolbox.infoFiji
Daltonize_This plugin can simulate color blindness.ClassFiji
Data_ExplorerClassspim.fiji.pluginFiji
DataAccessInterfacempicbg.imglib.container.basictypecontainerFiji
DataBlockClasscustomnode.u3dFiji
DataBrowserExtension of StackWindow with additional UI trimmings for animation, virtual stack caching options, metadata, and general beautification.Classloci.plugins.utilFiji
DataChannelClassorg.imagearchive.lsm.toolbox.info.scaninfoFiji
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.dataFiji
DataContainerThe DataContainer keeps all the source data, jobName, pre-processing results and algorithm results that have been computed.ClassgadgetsFiji
DataTypeClassorg.imagearchive.lsm.toolbox.info.scaninfoFiji
DateUtilsClassFiji
DBLoaderClassini.trakem2.persistenceFiji
DBObjectBase class of all objects that can be saved in a database or XML file.Classini.trakem2.persistenceFiji
DCTInterpolatorClassmpicbg.imglib.interpolation.dctFiji
DCTInterpolatorFactoryClassmpicbg.imglib.interpolation.dctFiji
DebugClassfijiFiji
DebugClassfiji.plugin.trackmateFiji
DeclaredTypeRepresents a declared type, either a class type or an interface type.Interfacejavax.lang.model.typeFiji
DeconvolverInterfacempicbg.spim.postprocessing.deconvolution2Fiji
DefaultAnimatableUniverseClassij3dFiji
DefaultCostMatrixCreatorA CostMatrixCreator that build a cost matrix from 3 lists containing the sources, the targets and the associated costs.Classfiji.plugin.trackmate.tracking.sparselap.costmatrixFiji
DefaultExecutorProviderDefault Executor Provider, which creates ExecutorServices from java.Classini.trakem2.parallelFiji
DefaultFijiServiceThe default initializer for the Fiji legacy application.ClassfijiFiji
DefaultFileFilterFilter for use in a JFileChooser.Classfiji.plugin.trackmate.utilFiji
DefaultGraphicsSourceHandles default mode, i.Classini.trakem2.display.graphicsFiji
DefaultImgTitlerClassspim.process.fusion.exportFiji
DefaultLabelingCursorStrategyA relatively conservative strategy suitable for blobby objects - retain the bounding boxes and raster starts and reconstruct the Classmpicbg.imglib.labelingFiji
DefaultLabelingCursorStrategyFactoryClassmpicbg.imglib.labelingFiji
DefaultLegacyPostRefreshMenusLegacyPostRefreshMenus plugin that ensures the MenuRefresher runs after the Refresh Menus command isClassfijiFiji
DefaultMinAndMaxSets the minimum to zero and the maximum to the maximum supported, or 255 for FloatProcessor and any other unknown ImageProcessor.Classini.trakem2.imaging.filtersFiji
DefaultMipmapOrderingThe standard mipmap ordering strategy for local hdf5 data.Classbdv.viewer.renderFiji
DefaultModeClassini.trakem2.displayFiji
DefaultOMEMetadataServiceDefault implementation of OMEMetadataService.Classio.scif.ome.servicesFiji
DefaultOMETranslatorBasic translator for OME Metadata.Classio.scif.ome.translatorsFiji
DefaultOMEXMLServiceDefault implementation of OMEXMLService.Classio.scif.ome.servicesFiji
DefaultTemplateClassedu.utexas.clm.reconstructreader.trakem2Fiji
DefaultTreeTransferHandlerAdapted from freely available code by DeuDeu from http://forum.Classini.trakem2.treeFiji
DefaultUniverseClassij3dFiji
DeferredArray3DClasslevelsets.algorithmFiji
DeferredByteArray3DClasslevelsets.algorithmFiji
DeferredDoubleArray3DClasslevelsets.algorithmFiji
DeferredIntArray3DClasslevelsets.algorithmFiji
DeferredObjectArray3DClasslevelsets.algorithmFiji
Define_Bounding_BoxClassspim.fiji.pluginFiji
Define_Multi_View_DatasetClassspim.fiji.pluginFiji
Deformable_RegistrationClassvibFiji
DeInterleave_ClassFiji
Delaunay_VoronoiDraw Delaunay triangulation or Voronoi Diagram as an overlay.ClassFiji
DelaunayTriangulationA 2D Delaunay Triangulation (DT) with incremental site insertion.ClassdelaunayFiji
Delete_FrameClassvideo2Fiji
DeltaVision_ConverterClassFiji
DemoThis class is an applet demonstration of the EDF.ClassFiji
DemodulationClassFlowJFiji
DenseFieldLevelSetClasslevelsets.algorithmFiji
Descriptor_based_registrationClasspluginFiji
Descriptor_based_series_registrationClasspluginFiji
DescriptorParametersClasspluginFiji
Despeckle_ClassFiji
DetailsFrameClassorg.imagearchive.lsm.toolbox.guiFiji
DetectInterestPointsPopupClassspim.fiji.spimdata.explorer.popupFiji
DetectionClassmpicbg.spim.registration.detectionFiji
DetectionClassspim.process.interestpointregistrationFiji
DetectionChannelClassorg.imagearchive.lsm.toolbox.info.scaninfoFiji
DetectionDescriptorClassfiji.plugin.trackmate.gui.descriptorsFiji
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.detectionFiji
DetectionRegistrationClassmpicbg.spim.registration.detectionFiji
DetectionSegmentationClassmpicbg.spim.registration.detectionFiji
DetectionSegmentationClassprocessFiji
DetectionStructureClassmpicbg.spim.registration.detectionFiji
DetectionUtilsClassfiji.plugin.trackmate.detectionFiji
DetectionViewClassmpicbg.spim.registration.detectionFiji
DetectorChoiceDescriptorClassfiji.plugin.trackmate.gui.descriptorsFiji
DetectorConfigurationDescriptorClassfiji.plugin.trackmate.gui.descriptorsFiji
DetectorKeysClassfiji.plugin.trackmate.detectionFiji
DetectorProviderClassfiji.plugin.trackmate.providersFiji
DevUtilClassmpicbg.imglib.utilFiji
DHMClassspim.fiji.datasetmanagerFiji
DHMImgLoaderClassspim.fiji.spimdata.imgloadersFiji
DHMMetaDataClassspim.fiji.datasetmanagerFiji
DiagnosticInterface for diagnostics from tools.Interfacejavax.toolsFiji
DiagnosticCollectorProvides an easy way to collect diagnostics in a list.Classjavax.toolsFiji
DiagnosticFormatterA formatter for diagnostic messages.Classcom.sun.tools.javac.utilFiji
DiagnosticListenerInterface for receiving diagnostics from tools.Interfacejavax.toolsFiji
Dichromacy_ClassFiji
DICOMTranslatorContainer class for translators between OME and DICOM formats.Classio.scif.ome.translatorsFiji
DifferenceClassimglib.ops.operator.binaryFiji
DifferenceClassscript.imglib.mathFiji
DifferenceARGBCompositeClassini.trakem2.display.graphicsFiji
DifferenceOfClassspim.fiji.plugin.interestpointdetectionFiji
DifferenceOfGaussianClassmpicbg.imglib.algorithm.scalespaceFiji
DifferenceOfGaussianClassspim.fiji.plugin.interestpointdetectionFiji
DifferenceOfGaussianCUDAClassspim.process.interestpointdetectionFiji
DifferenceOfGaussianNewPeakFinderClassspim.process.interestpointdetectionFiji
DifferenceOfGaussianPeakClassmpicbg.imglib.algorithm.scalespaceFiji
DifferenceOfGaussianRealClassmpicbg.imglib.algorithm.scalespaceFiji
DifferenceOfGaussianReal1Classmpicbg.imglib.algorithm.scalespaceFiji
DifferenceOfMeanClassspim.fiji.plugin.interestpointdetectionFiji
DifferentialEvolutionglobal minimization of a real-valued function of several variables without using derivatives using a genetic algorithmClasspal.mathFiji
Differentials_ClassFiji
DifferentiatorComputes Gaussian derivatives of images.Classimagescience.featureFiji
DiffusionThis is a class that implements nonlinear diffusion in 2D.ClassvolumeFiji
Diffusion3DThis is a class that implements nonlinear diffusion in 2D, 3D and 4D.ClassvolumeFiji
DiffusionInterpol2ClassvibFiji
DiffusionInterpol2_ClassvibFiji
DilatationClasslevelsets.filterFiji
DilateClassscript.imglib.algorithmFiji
Dilate_This class implements the dilation filter.Classprocess3dFiji
DimensionClassfiji.plugin.trackmateFiji
DimensionalityInterfacempicbg.imglib.cursor.vectorFiji
DimensionsContains the dimensions of up to 5D image data objects.Classimagescience.imageFiji
DimsAndExistenceThe dimensions of an image and a flag indicating whether that image exists (can be loaded)Classbdv.img.hdf5Fiji
DirectAccessContainerInterfacempicbg.imglib.containerFiji
DirectAccessContainerFactoryClassmpicbg.imglib.containerFiji
DirectAccessContainerImplClassmpicbg.imglib.containerFiji
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.roiFiji
DirectCrossCorrDirectCrossCorr performs direct cross-correlation of a kernel against an image.Classmpicbg.imglib.algorithm.roiFiji
Directionality_Usage This plugin is used to infer the preferred orientation of structures present in the input image.Classfiji.analyze.directionalityFiji
Dirichlet_EdgeClassvib.edgeFiji
DiscCursorClassmpicbg.imglib.cursor.specialFiji
DiscreteIntHistogramBinFactoryA HistogramBinFactory to be used to create a discrete Histogram over integer-valued Type's.Classmpicbg.imglib.algorithm.histogram.discreteFiji
DispatcherClassini.trakem2.utilsFiji
Display Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandClassimagewareFiji
DisplayA Display is a class to show a Layer and enable mouse and keyboard manipulation of all its components.Classini.trakem2.displayFiji
DisplayClassmpicbg.imglib.image.displayFiji
Display3DOne Display3D instance for each LayerSet (maximum).Classini.trakem2.displayFiji
Display3DGUIClassini.trakem2.display.d3dFiji
Display_ViewClassspim.fiji.pluginFiji
DisplayableThe class that any element to be drawn on a Display must extend.Classini.trakem2.displayFiji
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.displayFiji
DisplayablePanelClassini.trakem2.displayFiji
DisplayCanvasClassini.trakem2.displayFiji
DisplayChangeEventTo be raised when a property of the image display has been changedSee Also:Serialized FormClassFiji
DisplayChangeListenerThe Listener interface for receiving DisplayChange events.InterfaceFiji
DisplayHandlerLogic for displaying images and metadata onscreen using ImageJ.Classloci.plugins.inFiji
DisplayImageClassspim.process.fusion.exportFiji
DisplayModeClassbdv.viewerFiji
DisplayNavigatorClassini.trakem2.displayFiji
DisplaySettingsEventAn event object fired when the user changes one of the display settings through this GUI panel.Classfiji.plugin.trackmate.guiFiji
DisplaySettingsListenerInterface for classes that listen to display settings changes on a GUI.Interfacefiji.plugin.trackmate.guiFiji
DisplayViewPopupClassspim.fiji.spimdata.explorer.popupFiji
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.displayFiji
Distance_RidgeClasssc.fiji.localThicknessFiji
Distance_Transform_3DClassprocess3dFiji
DistanceComparatorCompares which Leaf is closer to another LeafAuthor:Johannes Schindelin and Stephan PreibischClassfiji.utilFiji
DistanceComparatorCompares which Leaf is closer to another LeafAuthor:Johannes Schindelin, Stephan PreibischClassmpicbg.imglib.algorithm.kdtreeFiji
DistanceTransform3DClassprocess3dFiji
Distortion_CorrectionClasslenscorrectionFiji
DistortionCorrectionTaskMethods collection to be called from the GUI for alignment tasks.ClasslenscorrectionFiji
DistributionInferenceClassinferenceFiji
DitherClassscript.imglib.algorithmFiji
DivideClassimglib.ops.operator.binaryFiji
DivideClassscript.imglib.mathFiji
DivideByConstantClassimglib.ops.operator.unaryFiji
DLabelThis class is named funny to avoid confusion with java.Classini.trakem2.displayFiji
DM3_ReaderClassioFiji
DNDInsertImageClassini.trakem2.utilsFiji
DNDTreeA JTree which has a built-in drag and drop feature.Classini.trakem2.treeFiji
DocCommentScannerAn extension to the base lexical analyzer that captures and processes the contents of doc comments.Classcom.sun.tools.javac.parserFiji
DoGThis is a 1D Difference of Gaussian convolution kernel.ClassvolumeFiji
DoG2DThis is a 2D Difference of Gaussian convolution kernel.ClassvolumeFiji
DoG3DThis is a 3D Difference of Gaussian convolution kernel.ClassvolumeFiji
DogDetectorClassfiji.plugin.trackmate.detectionFiji
DogDetectorConfigurationPanelClassfiji.plugin.trackmate.gui.panels.detectorFiji
DogDetectorFactoryClassfiji.plugin.trackmate.detectionFiji
DoGMaximumClassmpicbg.spim.registration.bead.laplaceFiji
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.analysisFiji
DOMClassmpicbg.spim.segmentationFiji
DomainCursorAbstract class for CoordsCursors that iterate over a domain which size can be determined by a single parameter.Classmpicbg.imglib.cursor.specialFiji
DomXmlExporterClassorg.imagearchive.lsm.toolboxFiji
DoneButtonListenerClassselectionFiji
DoStepInterfaceini.trakem2.displayFiji
DoubleAccess Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandClassimagewareFiji
DoubleAccessInterfacempicbg.imglib.container.basictypecontainerFiji
DoubleArrayClassfiji.utilFiji
DoubleArrayA dynamic array of double values.Classimagescience.arrayFiji
DoubleArrayClassmpicbg.imglib.container.basictypecontainer.arrayFiji
DoubleBuffer Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandClassimagewareFiji
DoubleDynamicContainerClassmpicbg.imglib.container.dynamicFiji
DoubleDynamicContainerAccessorClassmpicbg.imglib.container.dynamicFiji
DoubleElementClassview5dFiji
DoubleOptionA double option for one of the plugins.Classloci.plugins.prefsFiji
DoublePointwise Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandClassimagewareFiji
DoubleProcess Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandClassimagewareFiji
DoubleSet Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandClassimagewareFiji
DoubleSliderClassspimopenerFiji
DoubleTypeClassmpicbg.imglib.type.numeric.realFiji
DoWhileLoopTreeA tree node for a 'do' statement.Interfacecom.sun.source.treeFiji
DownsampleClassbdv.exportFiji
DownSampleClassmpicbg.imglib.algorithm.gaussFiji
DownsampleClassscript.imglib.algorithmFiji
DownsampleClassspim.process.interestpointdetectionFiji
DownsampleLogDetectorClassfiji.plugin.trackmate.detectionFiji
DownSampleLogDetectorConfigurationPanelClassfiji.plugin.trackmate.gui.panels.detectorFiji
DownsampleLogDetectorFactoryClassfiji.plugin.trackmate.detectionFiji
DownsamplerHelper class for running the " Image > Scale.Classmpicbg.stitchingFiji
DownsamplerClassmpicbg.trakem2.utilFiji
DownsamplerMipMapsClassini.trakem2.persistenceFiji
Draw_RoiClassvideo2Fiji
DTDClassmpicbg.trakem2.transformFiji
DTDParserReads either a DOCTYPE chunk from an xml file or a .Classini.trakem2.treeFiji
DummyCanvasClasssc.fiji.timelapseFiji
DummyNodeShellA dummy implementation of NodeShell, for use with volunteer nodes.Classedu.utexas.clm.archipelago.network.shellFiji
DummySpotColorGeneratorA dummy spot color generator that always return the default color.Classfiji.plugin.trackmate.visualizationFiji
DummyTrackColorGeneratorA dummy track color generator that always return the default color.Classfiji.plugin.trackmate.visualizationFiji
DuplexClassedu.utexas.clm.archipelago.dataFiji
Duplicate_FrameClassvideo2Fiji
Duplicate_Image5DClassFiji
Duplicate_TransformationClassspim.fiji.pluginFiji
Dynamic_ResliceDynamic reslice of a stack.Classfiji.stacksFiji
DynamicContainerClassmpicbg.imglib.container.dynamicFiji
DynamicContainerAccessorClassmpicbg.imglib.container.dynamicFiji
DynamicContainerFactoryClassmpicbg.imglib.container.dynamicFiji
DynamicCursorClassmpicbg.imglib.cursor.dynamicFiji
DynamicLocalizableByDimCursorClassmpicbg.imglib.cursor.dynamicFiji
DynamicLocalizableByDimOutOfBoundsCursorClassmpicbg.imglib.cursor.dynamicFiji
DynamicLocalizableCursorClassmpicbg.imglib.cursor.dynamicFiji
DynamicLocalizablePlaneCursorClassmpicbg.imglib.cursor.dynamicFiji
EasyDisplayClassresultsFiji
EasyLoggerInterfaceedu.utexas.clm.archipelago.utilFiji
EDF_Easy_This class is a plugin of ImageJ.ClassFiji
EDF_Expert_ClassFiji
EDF_Viewer3D_ClassFiji
EdfComplexWaveletsClassedfFiji
EdfRealWaveletsClassedfFiji
EdfSobelClassedfFiji
EdfVarianceClassedfFiji
EdfWaveletMaximumModulusClassedfFiji
EdgeThis class represents the edge between two vertices in an undirected graph.Classsc.fiji.analyzeSkeletonFiji
EdgeAnalyzerInterface for analyzers that can compute scalar numerical features for an edge of a TrackMate model.Interfacefiji.plugin.trackmate.features.edgesFiji
EdgeAnalyzerProviderA provider for the edge analyzers provided in the GUI.Classfiji.plugin.trackmate.providersFiji
EdgeContractionClasscustomnodeFiji
EdgeDetectors_ClassvibFiji
EdgeFeatureCalculatorA class dedicated to centralizing the calculation of the numerical features of spots, through EdgeAnalyzers.Classfiji.plugin.trackmate.featuresFiji
EdgeFeatureGrapherClassfiji.plugin.trackmate.featuresFiji
EdgesDetects edges in images.Classimagescience.featureFiji
EdgeTargetAnalyzerClassfiji.plugin.trackmate.features.edgesFiji
EdgeTimeLocationAnalyzerClassfiji.plugin.trackmate.features.edgesFiji
EdgeVelocityAnalyzerClassfiji.plugin.trackmate.features.edgesFiji
Edit_VideoClassvideoFiji
EditAmiraParameters_ClassvibFiji
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.vectorFiji
EDTClassfiji.process3dFiji
EDT_S1DClasssc.fiji.localThicknessFiji
EfficientBayesianBasedClassspim.process.fusion.deconvolutionFiji
EigenResultsDoubleClasstracingFiji
EigenResultsFloatClasstracingFiji
Eigensystem2x2DoubleClassmath3dFiji
Eigensystem2x2FloatClassmath3dFiji
Eigensystem3x3DoubleClassmath3dFiji
Eigensystem3x3FloatClassmath3dFiji
ElasticLayerAlignmentClassmpicbg.trakem2.alignFiji
ElasticMontageClassmpicbg.trakem2.alignFiji
ElasticTransform_ClassvibFiji
ElasticTransformedImageClassvibFiji
ElementRepresents a program element such as a package, class, or method.Interfacejavax.lang.model.elementFiji
ElementFilterFilters for selecting just the elements of interest from a collection of elements.Classjavax.lang.model.utilFiji
ElementKindThe kind of an element.Classjavax.lang.model.elementFiji
ElementKindVisitor6A visitor of program elements based on their kind with default behavior appropriate for the RELEASE_6 source version.Classjavax.lang.model.utilFiji
ElementsUtility methods for operating on program elements.Interfacejavax.lang.model.utilFiji
ElementScanner6A scanning visitor of program elements with default behavior appropriate for the RELEASE_6Classjavax.lang.model.utilFiji
ElementVisitorA visitor of program elements, in the style of the visitor design pattern.Interfacejavax.lang.model.elementFiji
EllipseAn ellipse in the x-y plane.Classimagescience.shapeFiji
EmbedEmbeds an image into a larger image.Classimagescience.transformFiji
EmptyProjectorClassbdv.viewer.renderFiji
EmptyStatementTreeA tree node for an empty (skip) statement.Interfacecom.sun.source.treeFiji
EndianUtilsProvides utility methods for endian conversions [big-endian to little-endian; little-endian to big-endian].Classnet.sf.image4j.ioFiji
EndModuleClassvib.app.moduleFiji
EndPosParserThis class is similar to Parser except that it stores ending positions for the tree nodes.Classcom.sun.tools.javac.parserFiji
EnhanceContrastUses the @{link ContrastEnhancer.Classini.trakem2.imaging.filtersFiji
EnhancedForLoopTreeA tree node for an "enhanced" 'for' loop statement.Interfacecom.sun.source.treeFiji
EnterThis class enters symbols for all encountered definitions into the symbol table.Classcom.sun.tools.javac.compFiji
EntitySomething that has a unique id.Classmpicbg.spim.data.generic.baseFiji
EntityUtilsClassmpicbg.spim.data.generic.baseFiji
EntropyClassmpicbg.spim.fusion.entropyFiji
EntropyFastClassmpicbg.spim.fusionFiji
EntropyFastFactoryClassmpicbg.spim.fusionFiji
EntropyFloatArray3DClassmpicbg.spim.fusion.entropyFiji
EnvA class for environments, instances of which are passed as arguments to tree visitors.Classcom.sun.tools.javac.compFiji
EPSTranslatorContainer class for translators between OME and EPS formats.Classio.scif.ome.translatorsFiji
Equality_ExampleAn example that demonstrates one potential peril of the Cluster ExecutorService.Classedu.utexas.clm.archipelago.exampleFiji
EqualizePlugin containing methods to equalize imageas and volumes.ClassvolumeFiji
EqualizeHistogramClassini.trakem2.imaging.filtersFiji
EquirectangularPanorama_ViewClassmpicbg.panoramaFiji
EquirectangularProjectionA rectlinear projection from equirectangular coordinates (longitude, latitude).Classmpicbg.panoramaFiji
ErodeClassscript.imglib.algorithmFiji
Erode_This class implements the erosion filter.Classprocess3dFiji
ErosionClasslevelsets.filterFiji
ErroneousTreeA tree node to stand in for a malformed expression.Interfacecom.sun.source.treeFiji
ErrorFunctionerror function and related stuffVersion:$Id: ErrorFunction.Classpal.mathFiji
ErrorStatisticClassstitching.modelFiji
ErrorTypeRepresents a class or interface type that cannot be properly modeled.Interfacejavax.lang.model.typeFiji
EuclideanClassdistanceFiji
EventClassorg.imagearchive.lsm.toolbox.infoFiji
EventListClassorg.imagearchive.lsm.toolbox.infoFiji
ExecutableElementRepresents a method, constructor, or initializer (static or instance) of a class or interface, including annotation typeInterfacejavax.lang.model.elementFiji
ExecutableTypeRepresents the type of an executable.Interfacejavax.lang.model.typeFiji
ExecuterClassij3dFiji
ExecutorProviderAllow the source ExecutorServices in TrakEM2 to be configured.Classini.trakem2.parallelFiji
ExistingByteArraysInstead of creating new cell arrays, it return the corresponding array from a predefined listAuthor:Stephan Preibisch (stephan.Classmpicbg.imglib.wrapperFiji
ExistingCharArraysInstead of creating new cell arrays, it return the corresponding array from a predefined listAuthor:Stephan Preibisch (stephan.Classmpicbg.imglib.wrapperFiji
ExistingDoubleArraysInstead of creating new cell arrays, it return the corresponding array from a predefined listAuthor:Stephan Preibisch (stephan.Classmpicbg.imglib.wrapperFiji
ExistingFloatArraysInstead of creating new cell arrays, it return the corresponding array from a predefined listAuthor:Stephan Preibisch (stephan.Classmpicbg.imglib.wrapperFiji
ExistingIntArraysInstead of creating new cell arrays, it return the corresponding array from a predefined listAuthor:Stephan Preibisch (stephan.Classmpicbg.imglib.wrapperFiji
ExistingLongArraysInstead of creating new cell arrays, it return the corresponding array from a predefined listAuthor:Stephan Preibisch (stephan.Classmpicbg.imglib.wrapperFiji
ExistingShortArraysInstead of creating new cell arrays, it return the corresponding array from a predefined listAuthor:Stephan Preibisch (stephan.Classmpicbg.imglib.wrapperFiji
ExpClassimglib.ops.operator.unaryFiji
ExpClassscript.imglib.mathFiji
Expm1Classscript.imglib.mathFiji
ExponentialGeneratorExponential random number generator.Classimagescience.randomFiji
ExponentialMathTypeInterfacempicbg.imglib.type.numericFiji
Export_EPSClassioFiji
ExportableChartPanelClassfiji.plugin.trackmate.utilFiji
ExportCellVoyagerPlugInClassbdv.ijFiji
ExportedTileClassmpicbg.trakem2.transformFiji
ExporterCore logic for the Bio-Formats Exporter ImageJ plugin.Classloci.plugins.outFiji
ExportImagePlusPlugInImageJ plugin to export the current image to xml/hdf5.Classbdv.ijFiji
ExportMesh_ClassmarchingcubesFiji
ExportMipmapInfoClassbdv.exportFiji
ExportSpimData2HDF5Classspim.process.fusion.exportFiji
ExportSpimData2TIFFClassspim.process.fusion.exportFiji
ExportSpimFusionPlugInClassbdv.ijFiji
ExportSpimSequencePlugInClassbdv.ijFiji
ExportStatsToIJActionClassfiji.plugin.trackmate.actionFiji
ExportTracksToXMLClassfiji.plugin.trackmate.actionFiji
ExportUnsignedShortClassmpicbg.trakem2.transformFiji
Exposure_Blend_Two_StacksClassutilFiji
ExpressionStatementTreeA tree node for an expression statement.Interfacecom.sun.source.treeFiji
ExpressionTreeA tree node used as the base class for the different types ofSince:1.Interfacecom.sun.source.treeFiji
ExtendedDepthOfFieldClassedfguiFiji
ExtendedPointMatchClassselectionFiji
ExtensionFileFilterFile filter for JFileChooser, filtering regular files according to their extensions.Classorg.siox.exampleFiji
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.ClassioFiji
Extract_SurfaceClassvibFiji
ExtractPSFClassmpicbg.spim.postprocessing.deconvolutionFiji
ExtractPSFClassspim.process.fusion.deconvolutionFiji
ExtractTrackStackActionClassfiji.plugin.trackmate.actionFiji
ExtremaClasssc.fiji.timelapseFiji
ExtremizerFinds local extrema in images.Classimagescience.segmentFiji
FactoryInterfacempicbg.imglibFiji
FakeAccessInterfacempicbg.imglib.container.basictypecontainerFiji
FakeArrayClassmpicbg.imglib.container.basictypecontainer.arrayFiji
FakeImagePlusNeed a non-null ImagePlus for the ImageCanvas, even if fake.Classini.trakem2.displayFiji
FakeImageWindowA class to prevent ROIs from failing.Classini.trakem2.displayFiji
FakeTypeClassmpicbg.imglib.type.labelFiji
Fast_FourierTransformClassregistration3dFiji
FastIntegralImageWritten following the code in ImgLib1's IntegralImage2 and ScaleAreaAveraging2d, authored by Stephan Preibisch and Albert Cardona.Classini.trakem2.imagingFiji
FastLAPTrackerClassfiji.plugin.trackmate.tracking.oldlapFiji
FastLAPTrackerFactoryClassfiji.plugin.trackmate.tracking.oldlapFiji
FastMarchingClasslevelsets.algorithmFiji
FastMarchingBandElementVoxel element for the Fast Marching trial set.Classlevelsets.algorithmFiji
FastMatrixClassvibFiji
FastMatrixNClassmath3dFiji
FastMatrixTransformClassvib.transformsFiji
FatalErrorThrowing an instance of this class causes immediate termination of the main compiler method.Classcom.sun.tools.javac.utilFiji
FeatureAnalyzerInterfacefiji.plugin.trackmate.featuresFiji
FeatureColorGeneratorInterface for color generator that can color objects based on a feature identified by a String.Interfacefiji.plugin.trackmate.visualizationFiji
FeatureFilterA helper class to store a feature filter.Classfiji.plugin.trackmate.featuresFiji
FeatureModelThis class represents the part of the Model that is in charge of dealing with spot features and track features.Classfiji.plugin.trackmateFiji
FeaturePenaltyCostFunctionA cost function that tempers a square distance cost by difference in feature This cost is calculated as follow:Classfiji.plugin.trackmate.tracking.sparselap.costfunctionFiji
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.componentsFiji
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.trackschemeFiji
FFTComputes forward and inverse Fourier transforms of images.Classimagescience.fourierFiji
FFTClasssc.fiji.timelapseFiji
FFTClassscript.imglib.algorithmFiji
FFT_Classprocess3dFiji
FFTFunctionsClassmpicbg.imglib.algorithm.fftFiji
FibonacciHeapClassutilFiji
FibonacciHeapDoubleClassutilFiji
FibonacciHeapIntClassutilFiji
FIBSEM_ReaderOpens the proprietary FIB-SEM format used at Janelia FarmAuthor:Stephan Preibisch (stephan.ClassioFiji
FieldMapViewClasses extending this class acquire a read-only Map interface to access its declared fields via the reflection API provided by Class.Classini.trakem2.utilsFiji
Fiji_ArchipelagoClassedu.utexas.clm.archipelagoFiji
FijiAppConfigurationClassfiji.patchesFiji
FijiArchipelagoClassedu.utexas.clm.archipelagoFiji
FijiClassLoaderSpecial class loader for ImageJ 1.ClassfijiFiji
FijiServiceCommon Fiji initialization.InterfacefijiFiji
FijiToolsClassfijiFiji
FileAndChannelClassutilFiji
FileBottleClassedu.utexas.clm.archipelago.network.translationFiji
FileBottlerClassedu.utexas.clm.archipelago.network.translationFiji
FileChunkClassedu.utexas.clm.archipelago.dataFiji
FileCreationClassutilFiji
FileDialogDecoratorClassfiji.guiFiji
FileGroupClassvib.appFiji
FileGroupDialogClassvib.app.guiFiji
FileListenerInterfacefsalignFiji
FileObjectFile abstraction for tools.Interfacejavax.toolsFiji
FileOpenMenuEntryClassfiji.plugin.timelapsedisplayFiji
FilePathRepairA class to manage "file not found" problems.Classini.trakem2.persistenceFiji
FilePatternDialogBio-Formats Importer file pattern dialog box.Classloci.plugins.inFiji
FilePreparerClassoctreeFiji
FilerThis interface supports the creation of new files by an annotation processor.Interfacejavax.annotation.processingFiji
FilerExceptionIndicates a Filer detected an attempt to open a file that would violate the guarantees provided by the Filer.Classjavax.annotation.processingFiji
FileTemplateClassedu.utexas.clm.reconstructreader.trakem2Fiji
FileTranslatorInterfaceedu.utexas.clm.archipelago.network.translationFiji
FillClasstracingFiji
Fill_holesClassFiji
FillerProgressCallbackInterfacetracingFiji
FillerThreadClasstracingFiji
FillWindowClasstracingFiji
FilterInterfaceini.trakem2.utilsFiji
FilterThis interface is implemented by all classes performing operations on input images and returning output imagesInterfacelevelsets.filterFiji
FilterEditorClassini.trakem2.imaging.filtersFiji
FilteredMemberListUtility to construct a view of a symbol's members, filtering out unwanted elements such as synthetic ones.Classcom.sun.tools.javac.modelFiji
FilterGuiPanelClassfiji.plugin.trackmate.gui.panels.componentsFiji
FilterPanelClassfiji.plugin.trackmate.gui.panelsFiji
FinalActionClass to launch the registration in bUnwarpJ.ClassbunwarpjFiji
FinalVoxelDimensionsAn implementation of VoxelDimensions.Classmpicbg.spim.data.sequenceFiji
Find_Connected_RegionsClassutilFiji
Find_MinimaClassprocess3dFiji
FindConnectedRegionsClassutilFiji
FindIt_ClassFiji
FindMinimaClassprocess3dFiji
FineTuneProgressListenerInterfacelandmarksFiji
FineTuneThreadClasslandmarksFiji
FirstIterationFuse one portion of a paralell fusion, supports no weightsAuthor:Stephan Preibisch (stephan.Classspim.process.fusion.deconvolutionFiji
Fit_SphereClassvibFiji
FitFunctionInterface for fitting-target functions.Interfacempicbg.imglib.algorithm.peakFiji
FittingProgressAn implementation of the MultiTaskProgress interface that updates the ImageJ progress barClasstracingFiji
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.exportFiji
FixedModelThis model just applies some other TranslationInvariantModel without computing anything.Classmpicbg.pointdescriptor.modelFiji
FixedNameImgTitlerClassspim.process.fusion.exportFiji
FJClassfeaturejFiji
FJ_AboutClassfeaturejFiji
FJ_DerivativesClassfeaturejFiji
FJ_EdgesClassfeaturejFiji
FJ_HelpClassfeaturejFiji
FJ_HessianClassfeaturejFiji
FJ_LaplacianClassfeaturejFiji
FJ_OptionsClassfeaturejFiji
FJ_PanelClassfeaturejFiji
FJ_StatisticsClassfeaturejFiji
FJ_StructureClassfeaturejFiji
FlagNodeClassfiji.plugin.trackmate.tracking.kdtreeFiji
FlagsAccess flags and other modifiers for Java classes and members.Classcom.sun.tools.javac.codeFiji
FlexWidgetsCustom widgets for configuring Bio-Formats Flex support.Classloci.plugins.configFiji
FloatAccess Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandClassimagewareFiji
FloatAccessInterfacempicbg.imglib.container.basictypecontainerFiji
FloatArrayClassfiji.utilFiji
FloatArrayA dynamic array of float values.Classimagescience.arrayFiji
FloatArray Copyright: Copyright (c) 2006Version:1.Classmpi.fruitfly.math.datastructuresFiji
FloatArrayClassmpicbg.imglib.container.basictypecontainer.arrayFiji
FloatArrayClassstitchingFiji
FloatArray2DTitle: PhaseCorrelation2D Copyright: Copyright (c) 2007Classmpi.fruitfly.math.datastructuresFiji
FloatArray2DClassstitchingFiji
FloatArray3D Copyright: Copyright (c) 2007 This program is free software; you can redistribute it and/orClassmpi.fruitfly.math.datastructuresFiji
FloatArray3DClassstitchingFiji
FloatArray4D Copyright: Copyright (c) 2006Version:1.Classmpi.fruitfly.math.datastructuresFiji
FloatBuffer Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandClassimagewareFiji
FloatDynamicContainerClassmpicbg.imglib.container.dynamicFiji
FloatDynamicContainerAccessorClassmpicbg.imglib.container.dynamicFiji
FloatElementClassview5dFiji
FloatImageAn image containing up to 5D elements of type float.Classimagescience.imageFiji
FloatImageOperationClassscript.imglib.math.fnFiji
FloatImagePlusImagePlusContainer for float-stored data.Classmpicbg.imglib.container.imageplusFiji
FloatMatrixClassvibFiji
FloatMatrixNClassmath3dFiji
FloatPointwise Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandClassimagewareFiji
FloatProcess Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandClassimagewareFiji
FloatProcessorChunkClassedu.utexas.clm.archipelago.ijsupportFiji
FloatProcessorT2Classini.trakem2.imagingFiji
FloatSet Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandClassimagewareFiji
FloatTypeClassmpicbg.imglib.type.numeric.realFiji
Flood_FillClassprocess3dFiji
FloorClassscript.imglib.mathFiji
FlowThis pass implements dataflow analysis for Java programs.Classcom.sun.tools.javac.compFiji
Flow3JColorNoiseMapperThis class maps a flow field in color spotnoise field.ClassFlowJFiji
Flow3JDynamicColorMapperThis class maps dynamic color of a flow field.ClassFlowJFiji
FlowJ_ClassFiji
FlowJColorNoiseMapperThis class maps a flow field in colored spotnoise format.ClassFlowJFiji
FlowJDisplayOFDisplay class implements the 2D display of 2D flow fields in different formats.ClassFlowJFiji
FlowJDynamicColorThis is a class that implements 2D and 3D Dynamic Color Mapping.ClassFlowJFiji
FlowJDynamicColorMapperClassFlowJFiji
FlowJErrorClassFlowJFiji
FlowJExceptionClassFlowJFiji
FlowJFleetClassFlowJFiji
FlowJFlowThis class implements 2D flow fields and methods (including reading and writing and utility methods).ClassFlowJFiji
FlowJLucasThis is a class that implements the Lucas and Kanade optical flow algorithm.ClassFlowJFiji
FlowJMapperThis class is the superclass for the OF display mappers.ClassFlowJFiji
FlowJQuiverMapperThis class maps a quiver map of a flow field.ClassFlowJFiji
FlowJSinghClassFlowJFiji
FlowJSpotNoiseThis class implements spot noise displaying of flow fields.ClassFlowJFiji
FlowJSpotNoiseMapperThis class maps spotnoise of a flow field.ClassFlowJFiji
FlowJUrasClassFlowJFiji
FlowJUserInterfaceThis class links the FlowJ classes to the ImageJ interface.ClassFlowJFiji
FloydSteinbergDitheringClassmpicbg.imglib.algorithm.floydsteinbergFiji
FMathPerforms elementary mathematical operations and function evaluations.Classimagescience.utilityFiji
FMath The FMath class provides methods for carrying out a number of elementary mathematical operations.ClassimagewareFiji
FolderWatcherClassfsalignFiji
ForLoopTreeA tree node for a basic 'for' loop statement.Interfacecom.sun.source.treeFiji
FormatEntryA list entry for the configuration window's Formats tab.Classloci.plugins.configFiji
FormatterConverts floating-point numbers to formatted strings.Classimagescience.utilityFiji
ForwardingFileObjectForwards calls to a given file object.Classjavax.toolsFiji
ForwardingJavaFileManagerForwards calls to a given file manager.Classjavax.toolsFiji
ForwardingJavaFileObjectForwards calls to a given file object.Classjavax.toolsFiji
FourierConvolutionClassmpicbg.imglib.algorithm.fftFiji
FourierTransformClassmpicbg.imglib.algorithm.fftFiji
Frangi_Classfiji.featuresFiji
FreeHandProfileClassini.trakem2.displayFiji
FromContinuousBranchesClassfiji.plugin.trackmate.graphFiji
FromOMETranslatorAbstract base class for all io.Classio.scif.ome.translatorsFiji
FS_Align_TrakEM2ClassfsalignFiji
FSAlignListenerClassfsalignFiji
FSInfoGet meta-info about files.Classcom.sun.tools.javac.fileFiji
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.persistenceFiji
FullInfoMeshClasscustomnodeFiji
FunctionInterfacempicbg.imglib.functionFiji
Function1Interface for function that compute values from a single input and store it in Author:Jean-Yves InevezInterfacefiji.plugin.trackmate.graphFiji
Function2Interface for function that compute values from a two inputs and store it in Author:Jean-Yves InevezInterfacefiji.plugin.trackmate.graphFiji
FusionManages the fusion for all types except the overlayfusionAuthor:Stephan Preibisch (stephan.Classmpicbg.stitching.fusionFiji
FusionClassspim.fiji.plugin.fusionFiji
FusionControlClassmpicbg.spim.fusionFiji
FusionHelperClassspim.process.fusionFiji
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.imgloaderFiji
FusionPopupClassspim.fiji.spimdata.explorer.popupFiji
FusionResultClassbdv.ij.exportFiji
GaborCosThis class implements a Gabor (even) cosine wave 1d convolution kernel for separated convolutions.ClassvolumeFiji
GaborSinThis class implements a Gabor (odd) sine wave 1d convolution kernel for separated convolutions.ClassvolumeFiji
GammaClassimglib.ops.operator.unaryFiji
GammaFunctionClasspal.mathFiji
GammaGeneratorGamma random number generator of positive integer order.Classimagescience.randomFiji
GapClosingCostFunctionGap closing cost function used with LAPTracker.Classfiji.plugin.trackmate.tracking.oldlap.costfunctionFiji
GaussClassscript.imglib.algorithmFiji
GaussContentClassmpicbg.spim.fusionFiji
GaussContentFactoryClassmpicbg.spim.fusionFiji
GaussianThis is a 1D separated 0-th order Gaussian convolution kernel.ClassvolumeFiji
Gaussian2DThis is a 2D separated 0 order Gaussian convolution kernel.ClassvolumeFiji
Gaussian3DThis is a 3D separated 0 order Gaussian convolution kernel.ClassvolumeFiji
Gaussian_Stack_FocuserClasssc.fiji.timelapseFiji
GaussianBlurSmooth with a Gaussian.Classini.trakem2.imaging.filtersFiji
GaussianConvolutionClassmpicbg.imglib.algorithm.gaussFiji
GaussianConvolution2Classmpicbg.imglib.algorithm.gaussFiji
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.gaussFiji
GaussianConvolution4Classmpicbg.imglib.algorithm.gaussFiji
GaussianConvolutionRealClassmpicbg.imglib.algorithm.gaussFiji
GaussianDerivativeThis class implement a scale space Gaussian n-th order derivative 1d convolution kernel for separated convolutions.ClassvolumeFiji
GaussianGenerationCallbackInterfacefeaturesFiji
GaussianGeneratorGaussian random number generator.Classimagescience.randomFiji
GaussianMaskFitClassprocessFiji
GaussianMultiDLMA n-dimensional Gaussian peak function, representing an elliptical Gaussian, with axis constrained to be aligned with the main axis.Classmpicbg.imglib.algorithm.peakFiji
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.peakFiji
GaussianStackFocuserClassspimopenerFiji
GenThis pass maps flat Java (i.Classcom.sun.tools.javac.jvmFiji
GeneralClassmpi.fruitfly.mathFiji
GeneralizedDEOptimizerProvides an general interface to the DifferentialEvolution class that is not tied to a certain number of parameters (as DifferentialEvolution is).Classpal.mathFiji
Generic_Resave_HDF5Classspim.fiji.plugin.resaveFiji
GenericAffineTile2DClassmpicbg.trakem2.alignFiji
GenericByteTypeClassmpicbg.imglib.type.numeric.integerFiji
GenericCursorLinkClassmpicbg.imglib.cursor.linkFiji
GenericDialogAppenderInterfacespim.fiji.plugin.utilFiji
GenericDialogPlusThe GenericDialogPlus class enhances the GenericDialog by a few additional methods.Classfiji.util.guiFiji
GenericIntTypeClassmpicbg.imglib.type.numeric.integerFiji
GenericLoadParseQueryXMLInterface for interactive parsing of spimdata XMLsAuthor:Stephan Preibisch (stephan.Classspim.fiji.plugin.queryXMLFiji
GenericShortTypeClassmpicbg.imglib.type.numeric.integerFiji
GeodesicActiveContour Caselles et.Classlevelsets.algorithmFiji
GeometricHasherClass that actually computes the geometric hashingAuthor:Stephan Preibisch (stephan.Classspim.process.interestpointregistration.geometrichashingFiji
GeometricHashingClassspim.process.interestpointregistration.geometrichashingFiji
GeometricHashingPairwiseClassspim.process.interestpointregistration.geometrichashingFiji
GeometricHashingParametersClassspim.process.interestpointregistration.geometrichashingFiji
GeometryCreatorClassoctreeFiji
GeometryCreatorThis class is a helper class whose main task is to create Geometry objects for a specified axis and direction.ClassvoltexFiji
Gif_Stack_WriterClassioFiji
GlobalErrorStatisticsInterfacempicbg.spim.registration.bead.errorFiji
GlobalErrorStatisticsImplClassmpicbg.spim.registration.bead.errorFiji
GlobalOptClassspim.process.interestpointregistrationFiji
GlobalOptimizationClassmpicbg.stitchingFiji
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.optimizationtypesFiji
GlobalOptimizationTypeA certain type of global optimization, must be able to define all view pairs that need to be matched and optimized inidivduallyClassspim.process.interestpointregistration.optimizationtypesFiji
GradientClassfiji.plugin.volumeviewerFiji
GradientClassprocess3dFiji
Gradient_Classprocess3dFiji
GradientWatershedThis class labels an image where the objects in question have edges that are defined by sharp intensity gradients and haveClassmpicbg.imglib.algorithm.labelingFiji
GraphClass wrapping some basic structures that are used to represent a graph.ClassgraphcutFiji
GraphClassini.trakem2.analysisFiji
GraphThis class represents an undirected graph to allow visiting the skeleton in an efficient wayClasssc.fiji.analyzeSkeletonFiji
Graph_CutPlugin interface to the graph cut algorithm.ClassgraphcutFiji
GraphContentNodeGraphContentNode is a 3D Viewer ContentNode designed to be the structure returned by the AnalyzedGraph class as a Java 3D representation of the vascular treeClassvolumeCalculatorFiji
GraphCutClass implementing the grach cut algorithm.ClassgraphcutFiji
GrapherDescriptorClassfiji.plugin.trackmate.gui.descriptorsFiji
GrapherPanelClassfiji.plugin.trackmate.guiFiji
GraphFrameClassfiji.plugin.timelapsedisplayFiji
GraphFrameClassspim.process.interestpointregistration.registrationstatisticsFiji
GraphicalMediaWikiClientClassfijiFiji
GraphicsSourceInterfaceini.trakem2.display.graphicsFiji
GraphSegmentSplitterClassfiji.plugin.trackmate.tracking.sparselap.costmatrixFiji
GraphUtilsClassfiji.plugin.trackmate.graphFiji
GrayMorphology_ClassFiji
GreenClassscript.imglib.colorFiji
GreyScaleFilterClasslevelsets.filterFiji
GreyTransformationClassvib.app.moduleFiji
GreyValueErosionPerforms a grey value erosion operation on the input using a defineable mask.Classlevelsets.filterFiji
GridLayoutClassstitchingFiji
GridTypeClasspluginFiji
GroupingModeClassini.trakem2.displayFiji
GuiClassfiji.plugin.volumeviewerFiji
GuiBuilderClassguiFiji
GUIButtonClassorg.imagearchive.lsm.toolbox.guiFiji
GUIHelperClassspim.fiji.plugin.utilFiji
GUIMakerClassorg.imagearchive.lsm.toolbox.guiFiji
GUIMenuItemClassorg.imagearchive.lsm.toolbox.guiFiji
GuiUtilsClassfiji.plugin.trackmate.guiFiji
HandleExtraFileTypesClassFiji
Harris_Corner_DetectorClassprocess3dFiji
HDF5AccessHackClassbdv.img.imarisFiji
Hdf5ImageLoaderClassbdv.img.hdf5Fiji
Hdf5VolatileShortArrayLoaderClassbdv.img.hdf5Fiji
HDFPreprocessorClassio.scif.formats.imarisFiji
HDFUtilsClassio.scif.formats.imarisFiji
HDFWriterClassio.scif.formats.imarisFiji
HeartBeatClassedu.utexas.clm.archipelago.dataFiji
Helmholtz_AnalysisThis plugin uses the Helmholtz equation to estimage the wavelength of a harmonic image.ClassFiji
HelpDialogClassbdv.toolsFiji
HessianComputes Hessian eigenimages.Classimagescience.featureFiji
HessianThis class implements computing the Hessian tensor matrix of an image, and computing the determinant (to detect blobs) and largest eigenvalues (to detect edges).ClassvolumeFiji
Hessian_CP_MeasuresClassfeaturesFiji
HessianEvalueProcessorClassfeaturesFiji
HistogramClassmpicbg.imglib.algorithm.histogramFiji
HistogramAn histogram of the image (or an image computed from an IFunction) between its minimum and maximum values,Classscript.imglib.analysisFiji
HistogramClassspim.fiji.plugin.thinoutFiji
Histogram2DRepresents the creation of a 2D histogram between two images.ClassalgorithmsFiji
Histogram_2DClassutilFiji
HistogramBinHistogramBin is used by to represent the bins of a histogram.Classmpicbg.imglib.algorithm.histogramFiji
HistogramBinFactoryThe HistogramBinFactory interface is used by Histogram to generate HistogramBins and HistogramKeys.Interfacempicbg.imglib.algorithm.histogramFiji
HistogramKeyHistogramKeys are used by Histogram to key HistogramBins Author:Larry LindseyClassmpicbg.imglib.algorithm.histogramFiji
HistogramMatcherClasshistogram2Fiji
HistogramPlotClasshistogram2Fiji
HistoryA class to represent a generic undo/redo history.Classini.trakem2.utilsFiji
HomogeneousMappingClassmpicbg.panoramaFiji
HomographyModel2DClassmpicbg.trakem2.transformFiji
HoughLineTransformA class that extends HoughTransform to handle Hough Line voting over an edge map.Classmpicbg.imglib.algorithm.transformationFiji
HoughLineTransformClassscript.imglib.algorithmFiji
HoughTransformClassmpicbg.imglib.algorithm.transformationFiji
HSBClassscript.imglib.colorFiji
HSBOpClassscript.imglib.color.fnFiji
HtmlPageLoaderClassorg.imagearchive.lsm.toolbox.guiFiji
HueClassscript.imglib.colorFiji
HuiskenImageLoaderThis ImgLoader implementation uses Benjamin Schmid's to load images in Jan Husiken's format.Classbdv.ij.export.imgloaderFiji
HungarianAlgorithmAn implementation of the classic Hungarian algorithm for the assignment problem.Classfiji.plugin.trackmate.tracking.oldlap.hungarianFiji
HybridDateFormatSimpleDateFormat provides convenient methods for parsing and formatting dates using Gregorian calendars (see java.ClassFiji
HyperSphereIteratorIterate over all pixels in an n-dimensional sphere.Classmpicbg.imglib.cursor.specialFiji
Hyperstack_rearrangerClassfiji.stacksFiji
HyperStackDisplayerClassfiji.plugin.trackmate.visualization.hyperstackFiji
HyperStackDisplayerFactoryClassfiji.plugin.trackmate.visualization.hyperstackFiji
HyperVolumeThis is a class that implements a float hyper (4D) volumes and operations including convolutions on it.ClassvolumeFiji
Hypervolume_OpenerOpens a folder of image stacks as one big stack ("Hypervolume").ClassFiji
HypotClassscript.imglib.mathFiji
I5D_aboutClassFiji
I5DResourceProvides Image5D utility methods.Classimagescience.utilityFiji
I5DVirtualStackThis class represents an array of disk-resident images.Classi5dFiji
Icns_ReaderClassioFiji
Icns_WriterClassioFiji
IcnsCodecClassiconsupport.icnsFiji
ICO_ReaderClassioFiji
ICO_WriterClassioFiji
ICOConstantsProvides constants used with ICO format.Classnet.sf.image4j.codec.icoFiji
ICODecoderDecodes images in ICO format.Classnet.sf.image4j.codec.icoFiji
ICOEncoderEncodes images in ICO format.Classnet.sf.image4j.codec.icoFiji
ICOImageContains a decoded ICO image, as well as information about the source encoded ICO image.Classnet.sf.image4j.codec.icoFiji
IconEntryRepresents an IconEntry structure, which contains information about an ICO image.Classnet.sf.image4j.codec.icoFiji
IconSuiteClassiconsupport.icnsFiji
ICPClassmpicbg.icpFiji
ICSTranslatorContainer class for to and from ICS/OME formatsAuthor:Mark Hiner hinerm at gmail.Classio.scif.ome.translatorsFiji
IcyTrackExporterClassfiji.plugin.trackmate.actionFiji
IcyTrackFormatWriterClassfiji.plugin.trackmate.ioFiji
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.ioFiji
IdDialogBio-Formats Importer id chooser dialog box.Classloci.plugins.inFiji
IdentifierTreeA tree node for an identifier expression.Interfacecom.sun.source.treeFiji
IdentifyClasslineageFiji
IDT_Interpolate_BinaryClassvibFiji
IEEEremainderClassscript.imglib.mathFiji
IepGuiGUI for the plugin Image_Expression_Parser When launched it displays a window allowing the user to enter a mathematical expression,Classfiji.processFiji
IFilterInterfaceini.trakem2.imaging.filtersFiji
IFormatWidgetsInterface for defining custom widgets for a specific file format reader.Interfaceloci.plugins.configFiji
IFT_Classprocess3dFiji
IfTreeA tree node for an 'if' statement.Interfacecom.sun.source.treeFiji
IFunctionInterfacescript.imglib.math.fnFiji
IHDF5AccessInterfacebdv.img.imarisFiji
IJ1LogServiceA log service adapter for ImageJ 1.ClassfijiFiji
IJ1PatcherPatch ij.ClassfijiFiji
IJ1StatusServiceA status service adapter for ImageJ 1.ClassfijiFiji
IJ_Alt_Key_ListenerClassfijiFiji
IJ_RobotClassFiji
IJAdapterClassij3dFiji
IJErrorA class to easily show the stack trace of an error in different operating systems.Classini.trakem2.utilsFiji
IJEventMulticasterMulticaster for events special to ImageJ Example how to implement an object, which fires DisplayChangeEvents using theClassFiji
IJLoggerClassedu.utexas.clm.archipelago.utilFiji
IJPopupLoggerClassedu.utexas.clm.archipelago.utilFiji
IJStatusEchoerEchoes status messages to the ImageJ status bar.Classloci.plugins.utilFiji
IlluminationDefines an illumination direction which is part of the ViewSetup.Classmpicbg.spim.data.sequenceFiji
IlluminationChannelClassorg.imagearchive.lsm.toolbox.info.scaninfoFiji
ImageAbstract base class for images containing up to 5D elements.Classimagescience.imageFiji
ImageClassmpicbg.imglib.imageFiji
Image3DMenubarClassij3dFiji
Image3DUniverseClassij3dFiji
Image5D (t).Classi5dFiji
Image5D_ExtensionsMacro extensions for Image5D.ClassFiji
Image5D_Stack_to_RGBConverts the current timeframe of an Image5D to an RGB stack using the current view settings.ClassFiji
Image5D_to_StackClassFiji
Image5DAdapterClassadapterFiji
Image5DCanvasClassi5d.guiFiji
Image5DLayout image and a channelControl panel to the right of the image.Classi5d.guiFiji
Image5DWindowImageWindow for Image5Ds.Classi5d.guiFiji
Image_Expression_ParserImage expression parser This plugins parses mathematical expressions and compute results using images as variables.Classfiji.processFiji
Image_FusionClassspim.fiji.pluginFiji
ImageAccessImageAccess is an interface layer to facilitate the access to the pixels of ImageJ images.ClassimagewareFiji
ImageAccessImageAccess is an interface layer to facilitate the access to the pixels of ImageJ images.ClasswaveletsFiji
ImageAdapterClassadapterFiji
ImageArrayConverterClassmpi.fruitfly.generalFiji
ImageBlockDeblockA FijiArchipelago-compatible class for splitting an image into smaller blocks, then recombining into the original image shape, potentially after processing.Classedu.utexas.archipelago.imageFiji
ImageButtonImageButton - A button component with an image in itAuthor:DTAI, IncorporatedSee Also:Serialized FormClassvib.segmentFiji
ImageBytesRepresent an image with byte arrays: 2 channels: grey + alphaClassini.trakem2.persistenceFiji
ImageCalculatorClassmpicbg.imglib.algorithm.mathFiji
ImageCalculatorInPlaceClassmpicbg.imglib.algorithm.mathFiji
ImageCalculatorRevisedThis plugin implements the Process/Image Calculator command.ClassutilFiji
ImageCanvasClassview5dFiji
ImageCanvas3DClassij3dFiji
ImageCollectionElementClassmpicbg.stitchingFiji
ImageComputationInterfacescript.imglib.math.fnFiji
ImageContainerClasslevelsets.ijFiji
ImageConverterClassmpicbg.imglib.algorithm.mathFiji
ImageDataInterfaceini.trakem2.displayFiji
ImageDirectoryClassorg.imagearchive.lsm.reader.infoFiji
ImageErrClassview5dFiji
ImageFactoryClassmpicbg.imglib.imageFiji
ImageFileFilterFilters out non-accepted image formats.Classini.trakem2.ioFiji
ImageFileHeaderClassini.trakem2.ioFiji
ImageFilterClassmpi.fruitfly.registrationFiji
ImageFilterClassorg.imagearchive.lsm.toolbox.guiFiji
ImageFocusListenerClassorg.imagearchive.lsm.toolbox.guiFiji
ImageFunctionClassscript.imglib.math.fnFiji
ImageInformationClassstitchingFiji
ImageInterpolationClassmpicbg.stitching.fusionFiji
ImageJMain entry point into ImageJ.Classnet.imagejFiji
ImageJ1UISimple ImageJ 1.Classfiji.updaterFiji
ImageJ3DViewerClassij3dFiji
ImageJ_3D_ViewerClassij3dFiji
ImageJCommandListenerIntercept ImageJ menu commands if the current active image is a FakeImagePlus (from a ini.Classini.trakem2.displayFiji
ImageJFunctionsClassmpicbg.imglib.image.display.imagejFiji
ImageJVirtualDisplayClassmpicbg.imglib.image.display.imagejFiji
ImageJVirtualStackClassmpicbg.imglib.image.display.imagejFiji
ImageListenerClassfsalignFiji
ImageMetaDataClassvib.appFiji
ImageOpenerReads in an imglib Image using Bio-Formats.Classmpicbg.imglib.ioFiji
ImageOverlayThis class implements an overlay based on an image.ClassgraphcutFiji
ImageOverlayThis class implements an overlay based on an image.ClasssioxFiji
ImagePaneGUI Component to display a BufferedImage with a zoom factor and an optional selection.Classorg.siox.exampleFiji
ImagePlusAdapterClassmpicbg.imglib.imageFiji
ImagePlusChooserClassfiji.plugin.trackmate.gui.panels.componentsFiji
ImagePlusContainerA Container that stores data in an aray of 2d-slices each as a linear array of basic types.Classmpicbg.imglib.container.imageplusFiji
ImagePlusContainerFactoryFactory that creates an appropriate ImagePlusContainer.Classmpicbg.imglib.container.imageplusFiji
ImagePlusCursorBasic Iterator for a ImagePlusContainersAuthor:Stephan Preibisch, Stephan SaalfeldClassmpicbg.imglib.cursor.imageplusFiji
ImagePlusCursor2DBasic Iterator for 2d ImagePlusContainersAuthor:Stephan Saalfeld, Stephan Saalfeld Classmpicbg.imglib.cursor.imageplusFiji
ImagePlusImgLoaderThis BasicImgLoader implementation returns a wrapped, converted ImagePlus.Classbdv.ij.export.imgloaderFiji
ImagePlusLocalizableByDimCursorPositionable for a ImagePlusContainersAuthor:Stephan Preibisch, Stephan SaalfeldClassmpicbg.imglib.cursor.imageplusFiji
ImagePlusLocalizableByDimOutOfBoundsCursorPositionable with OutOfBoundsStrategy for a ImagePlusContainersClassmpicbg.imglib.cursor.imageplusFiji
ImagePlusLocalizableCursorLocalizing Iterator for a ImagePlusContainersAuthor:Stephan Preibisch, Stephan SaalfeldClassmpicbg.imglib.cursor.imageplusFiji
ImagePlusLocalizablePlaneCursorClassmpicbg.imglib.cursor.imageplusFiji
ImagePlusReaderA high-level reader for ImagePlus objects.Classloci.plugins.inFiji
ImagePlusTimePointClassmpicbg.stitchingFiji
ImagePortionClassspim.process.fusionFiji
ImagePreprocessorAny class implementing this interface is suitable as an image preprocessor for a TrakEM2 project.Interfaceini.trakem2.imagingFiji
ImagePreviewClassorg.imagearchive.lsm.toolbox.guiFiji
ImageProcessorReaderA low-level reader for ImageProcessor objects.Classloci.plugins.utilFiji
ImageProcessorSourceRetrieves ImageJ image processors from an image reader.Classloci.plugins.utilFiji
ImageProgressContainerClasslevelsets.ijFiji
ImagePropertiesInterfacempicbg.imglib.containerFiji
ImageSaverProvides the necessary thread-safe image file saver utilities.Classini.trakem2.ioFiji
ImageScienceContains the name and version number of the ImageScience library.ClassimagescienceFiji
ImageStackImageLoaderClassbdv.img.imagestackFiji
ImageStatisticsClassnet.imglib2.algorithm.mathFiji
ImageTransformClassmpicbg.imglib.algorithm.transformationFiji
ImageUtilProvides utility methods for handling images (java.Classnet.sf.image4j.utilFiji
ImageWare Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandInterfaceimagewareFiji
ImageWindow3DClassij3dFiji
ImarisClassbdv.img.imarisFiji
ImarisFormatSCIFIO Format supporting the writer for Imaris 5.Classio.scif.formatsFiji
ImarisImageLoaderClassbdv.img.imarisFiji
ImarisVolatileByteArrayLoaderClassbdv.img.imarisFiji
ImarisVolatileFloatArrayLoaderClassbdv.img.imarisFiji
ImarisVolatileShortArrayLoaderClassbdv.img.imarisFiji
ImarisWriterClassio.scif.formats.imarisFiji
ImgExportInterfacespim.process.fusion.exportFiji
ImgExportTitleInterfacespim.process.fusion.exportFiji
ImgLibA simple wrapper class that is supposed to contain only functions for scripting.Classscript.imglibFiji
ImgLib1Provides non-copying wrapping from Imglib1 to Imglib2 (cell, array)Author:Stephan Preibisch (stephan.Classmpicbg.imglib.wrapperFiji
ImgLib2Provides non-copying wrapping from Imglib2 to Imglib1 (cell, array)Author:Stephan Preibisch (stephan.Classmpicbg.imglib.wrapperFiji
ImgLib2TempClassspim.fijiFiji
ImgLibAbsClassfiji.expressionparser.functionFiji
ImgLibAddClassfiji.expressionparser.functionFiji
ImgLibArcCosineClassfiji.expressionparser.functionFiji
ImgLibArcSineClassfiji.expressionparser.functionFiji
ImgLibArcTangentClassfiji.expressionparser.functionFiji
ImgLibArcTangent2Classfiji.expressionparser.functionFiji
ImgLibBandPassFilterClassfiji.expressionparser.functionFiji
ImgLibCeilClassfiji.expressionparser.functionFiji
ImgLibComparisonClassfiji.expressionparser.functionFiji
ImgLibCosineClassfiji.expressionparser.functionFiji
ImgLibDitheringClassfiji.expressionparser.functionFiji
ImgLibDivideClassfiji.expressionparser.functionFiji
ImgLibExceptionClassmpicbg.imglib.exceptionFiji
ImgLibExpClassfiji.expressionparser.functionFiji
ImgLibFloorClassfiji.expressionparser.functionFiji
ImgLibFunctionInterfacefiji.expressionparser.functionFiji
ImgLibGaussConvClassfiji.expressionparser.functionFiji
ImgLibLogClassfiji.expressionparser.functionFiji
ImgLibLogicalClassfiji.expressionparser.functionFiji
ImgLibModulusClassfiji.expressionparser.functionFiji
ImgLibMultiplyClassfiji.expressionparser.functionFiji
ImgLibNormalizeClassfiji.expressionparser.functionFiji
ImgLibNumberFactoryThis is a number factory that will be used to generate internal representation of number within the expression parser logic.Classfiji.expressionparserFiji
ImgLibOperatorSetClassfiji.expressionparserFiji
ImgLibParserClassfiji.expressionparserFiji
ImgLibPowerClassfiji.expressionparser.functionFiji
ImgLibRoundClassfiji.expressionparser.functionFiji
ImgLibSaverClassmpicbg.spim.ioFiji
ImgLibSineClassfiji.expressionparser.functionFiji
ImgLibSquareRootClassfiji.expressionparser.functionFiji
ImgLibSubtractClassfiji.expressionparser.functionFiji
ImgLibTangentClassfiji.expressionparser.functionFiji
ImgLibUMinusClassfiji.expressionparser.functionFiji
ImgLibUtilsClassfiji.expressionparserFiji
ImgLibVolumeThis class encapsulates an mpicbg.Classini.trakem2.utilsFiji
ImgLoaderA BasicImgLoader that is able to also provide each image converted to FloatType.Interfacempicbg.spim.data.sequenceFiji
ImgLoaderHintInterfacempicbg.spim.data.generic.sequenceFiji
ImgLoaderHintsDefault set of ImgLoaderHint.Classmpicbg.spim.data.generic.sequenceFiji
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.sequenceFiji
ImgLoadersClassmpicbg.spim.data.generic.sequenceFiji
ImgPanelClassview5dFiji
ImgTitlerInterfacespim.process.fusion.exportFiji
Implicit_Interpolate_BinaryClassFiji
ImporterCore logic for the Bio-Formats Importer ImageJ plugin.Classloci.plugins.inFiji
ImporterDialogAbstract superclass of importer dialogs.Classloci.plugins.inFiji
ImporterMetadataHelper class for storing original metadata key/value pairs.Classloci.plugins.inFiji
ImporterOptionsHelper class for managing Bio-Formats Importer options.Classloci.plugins.inFiji
ImporterPrompterHelper class for presenting the user with dialog boxes for configuring importer options.Classloci.plugins.inFiji
ImportPlugInImageJ plugin to import a raw image from xml/hdf5.Classbdv.ijFiji
ImportProcessManages the import preparation process.Classloci.plugins.inFiji
ImportStepAn enumeration of the steps in the import preparation process.Classloci.plugins.inFiji
ImportTreeA tree node for an import statement.Interfacecom.sun.source.treeFiji
IndependentSpotFeatureAnalyzerClassfiji.plugin.trackmate.features.spotFiji
IndividualTimepointRegistrationA registration type where each timepoint is registered individuallyAuthor:Stephan Preibisch (stephan.Classspim.process.interestpointregistration.optimizationtypesFiji
InferHelper class for type parameter inference, used by the attribution phase.Classcom.sun.tools.javac.compFiji
InferenceClassinferenceFiji
InferenceCallerInterfaceinferenceFiji
InfoFrameClassorg.imagearchive.lsm.toolbox.guiFiji
InfoHeaderRepresents a bitmap InfoHeader structure, which provides header information.Classnet.sf.image4j.codec.bmpFiji
InfoNodeClassorg.imagearchive.lsm.toolbox.guiFiji
InfoPaneClassfiji.plugin.trackmate.visualization.trackschemeFiji
InfoPanelClassvib.segmentFiji
InitFilterDescriptorClassfiji.plugin.trackmate.gui.descriptorsFiji
InitFilterPanelClassfiji.plugin.trackmate.gui.panelsFiji
InitializeViewerStateClassbdv.toolsFiji
InputActionBindingsMaintains lists of ActionMaps and InputMaps, which are chained to a concatenated InputMap and aClassbdv.viewerFiji
InputCheckThis class implements some basic checks for the input image data.ClassalgorithmsFiji
InputStreamLoggerClassedu.utexas.clm.archipelago.utilFiji
Insert_StackClassvideo2Fiji
InspectJarClassfijiFiji
InspectPatchTrianglesModeA view-only mode that shows, using LayerSet.Classini.trakem2.display.inspectFiji
InstallWizardA wizard for walking users through installation of third party libraries and plugins used by the Bio-Formats plugins.Classloci.plugins.configFiji
InstanceOfTreeA tree node for an 'instanceof' expression.Interfacecom.sun.source.treeFiji
IntAccessInterfacempicbg.imglib.container.basictypecontainerFiji
IntArrayClassfiji.utilFiji
IntArrayA dynamic array of int values.Classimagescience.arrayFiji
IntArrayClassmpicbg.imglib.container.basictypecontainer.arrayFiji
IntArrayListAn ArrayList that uses primitive ints for the key rather than objects to avoid costly usage of Integer wrappers.Classorg.siox.utilFiji
IntArraySorterSorts and int[] according to a custom comparator.ClassalgorithmsFiji
IntComparatorInterfacealgorithmsFiji
IntDynamicContainerClassmpicbg.imglib.container.dynamicFiji
IntDynamicContainerAccessorClassmpicbg.imglib.container.dynamicFiji
IntegerElementClassview5dFiji
IntegerFieldClassini.trakem2.utilsFiji
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.sequenceFiji
IntegerTypeInterfacempicbg.imglib.type.numericFiji
IntegerTypeConverterConverts an IntegerType into another one without doing any range checkingAuthor:Stephan PreibischClassmpicbg.imglib.functionFiji
IntegerTypeDisplayClassmpicbg.imglib.image.displayFiji
IntegerTypeImplClassmpicbg.imglib.type.numeric.integerFiji
IntegralHistogram2dAn integral histogram for 2d images.Classini.trakem2.imagingFiji
IntegralImagen-dimensional integral image that stores sums using type .Classmpicbg.imglib.algorithm.integralFiji
IntegralImage3dClassmpicbg.spim.segmentationFiji
IntegralImageDoubleSpecial implementation for double using the basic type to sum up the individual lines.Classmpicbg.imglib.algorithm.integralFiji
IntegralImageLongSpecial implementation for long using the basic type to sum up the individual lines.Classmpicbg.imglib.algorithm.integralFiji
IntegralImageMipMapsClassini.trakem2.persistenceFiji
Interactive_3D_Surface_PlotClassFiji
Interactive_Remove_DetectionsClassspim.fiji.pluginFiji
InteractiveBehaviorThis class interprets mouse and keyboard events and invokes the desired actions.Classij3d.behaviorsFiji
InteractiveDoGAn interactive tool for determining the required sigma and peak thresholdAuthor:Stephan PreibischClassmpicbg.spim.segmentationFiji
InteractiveIntegralAn interactive tool for determining the required radius and peak thresholdAuthor:Stephan PreibischClassmpicbg.spim.segmentationFiji
InteractiveMeshDecimationClassij3d.guiFiji
InteractiveProjectionsClassspim.fiji.plugin.removedetectionsFiji
InteractiveTracerCanvasClasstracingFiji
InteractiveTransformDialogClassij3d.guiFiji
InteractiveViewPlatformTransformerThis class extends ViewPlatformTransformer, to transform mouse events into real world transformations.Classij3d.behaviorsFiji
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.pluginFiji
Interest_Point_RegistrationClassspim.fiji.pluginFiji
InterestPointSingle interest point, extends mpicbg Point by an idAuthor:Stephan Preibisch (stephan.Classspim.fiji.spimdata.interestpointsFiji
InterestPointDetectionClassspim.fiji.plugin.interestpointdetectionFiji
InterestPointExplorerClassspim.fiji.spimdata.explorer.interestpointFiji
InterestPointExplorerPanelClassspim.fiji.spimdata.explorer.interestpointFiji
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.interestpointsFiji
InterestPointOverlayClassspim.fiji.spimdata.explorer.interestpointFiji
InterestPointRegistrationClassspim.fiji.plugin.interestpointregistrationFiji
InterestPointsExplorerPopupClassspim.fiji.spimdata.explorer.popupFiji
InterestPointTableModelClassspim.fiji.spimdata.explorer.interestpointFiji
InterpolatedImageClassvibFiji
InterpolatePaintScaleThis class implements a PaintScale that generate colors interpolated within a list of given color, using a linear scale.Classorg.jfree.chart.rendererFiji
InterpolationInterpolation methods.Classbdv.viewerFiji
InterpolationClassfiji.plugin.volumeviewerFiji
InterpolatorInterfacempicbg.imglib.interpolationFiji
Interpolator1DInterfacempicbg.imglib.interpolationFiji
Interpolator2DInterfacempicbg.imglib.interpolationFiji
Interpolator3DInterfacempicbg.imglib.interpolationFiji
InterpolatorFactoryClassmpicbg.imglib.interpolationFiji
InterpolatorImplClassmpicbg.imglib.interpolationFiji
IntervalA range on the number line with a min() and max() point.Classmpicbg.stitching.fusionFiji
IntervalAndTransformClassbdv.viewer.overlayFiji
IntervalBoundingBoxClassbdv.utilFiji
IntFieldTextField that takes only integers, and sends an ActionEvent when the integer Value has changed either by hitting return or byClassFiji
IntHashMapA hashmap that uses primitive ints for the key rather than objects to avoid costly usage of Integer wrappers.Classorg.siox.utilFiji
IntImagePlusImagePlusContainer for integer-stored data.Classmpicbg.imglib.container.imageplusFiji
IntSliderClassFiji
IntTypeClassmpicbg.imglib.type.numeric.integerFiji
InverseFFTClassscript.imglib.algorithmFiji
InverseFourierConvolutionConvolve an image with the inverse of a kernel which is division in the Fourier domain.Classmpicbg.imglib.algorithm.fftFiji
InverseFourierTransformClassmpicbg.imglib.algorithm.fftFiji
InverseTransformDescriptionClassmpicbg.imglib.image.display.imagejFiji
InvertClassimglib.ops.operator.unaryFiji
InvertClassini.trakem2.imaging.filtersFiji
InvertibleCoordinateTransformInvertibleCoordinateTransform with String import and export as used inInterfacempicbg.trakem2.transformFiji
InvertibleCoordinateTransformInterfacestitching.modelFiji
InvertibleCoordinateTransformListClassmpicbg.trakem2.transformFiji
InvertibleModelClassstitching.modelFiji
InvokeLaterThis class helps with invoking tasks much, much later.Classfiji.guiFiji
IODialogClass to create the Input/Output dialog to deal with the files to keep the information of bUnwarpJ.ClassbunwarpjFiji
IOFunctionsClassmpicbg.spim.ioFiji
IOUtilsA collection of static utilities for the input/output of xml files.Classfiji.plugin.trackmate.ioFiji
IPLab_ReaderThis plugin opens images in the IPLab/Windows (.ClassioFiji
ISBIChallengeExporterClassfiji.plugin.trackmate.actionFiji
IsoData_ClassifierClassFiji
IsolatedPixelWeightenerClassmpicbg.spim.fusionFiji
IsolatedPixelWeightenerFactoryInterfacempicbg.spim.fusionFiji
ItemsA helper class for code generation.Classcom.sun.tools.javac.jvmFiji
IterableThe Iterable interface provides basic functionality for iterating over an Image.Interfacempicbg.imglib.cursorFiji
IterationStatusInterfaceimglib.ops.observerFiji
IterativeClosestPointIterative closest point implementationAuthor:Stephan Preibisch (stephan.Classspim.process.interestpointregistration.icpFiji
IterativeClosestPointPairwiseClassspim.process.interestpointregistration.icpFiji
IterativeClosestPointParametersClassspim.process.interestpointregistration.icpFiji
JacobiThis class implements the jacobi function as a Java class.ClassbijnumFiji
JacobiDoubleClassmath3dFiji
JacobiFloatClassmath3dFiji
JaqamanLinkerLinks two lists of objects based on the LAP framework described in Jaqaman et al.Classfiji.plugin.trackmate.tracking.sparselap.linkerFiji
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.costmatrixFiji
JaqamanSegmentCostMatrixCreatorThis class generates the top-left quadrant of the LAP segment linking cost matrix, following Jaqaman et al.Classfiji.plugin.trackmate.tracking.sparselap.costmatrixFiji
Java3dClassmpicbg.spim.mpicbgFiji
JavacElementsUtility methods for operating on program elements.Classcom.sun.tools.javac.modelFiji
JavacFileManagerThis class provides access to the source, class and other files used by the compiler and related tools.Classcom.sun.tools.javac.fileFiji
JavacFilerThe FilerImplementation class must maintain a number of constraints.Classcom.sun.tools.javac.processingFiji
JavacMessagerAn implementation of the Messager built on top of log.Classcom.sun.tools.javac.processingFiji
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.mainFiji
JavaCompilerInterfacejavax.toolsFiji
JavacOptionTODO: describe com.Interfacecom.sun.tools.javac.mainFiji
JavacProcessingEnvironmentObjects of this class hold and manage the state needed to support annotation processing.Classcom.sun.tools.javac.processingFiji
JavacRoundEnvironmentObject providing state about a prior round of annotation processing.Classcom.sun.tools.javac.processingFiji
JavacScopeProvides an implementation of Scope.Classcom.sun.tools.javac.apiFiji
JavacTaskProvides access to functionality specific to the JDK Java Compiler, javac.Classcom.sun.source.utilFiji
JavacTaskImplProvides access to functionality specific to the JDK Java Compiler, javac.Classcom.sun.tools.javac.apiFiji
JavacToolTODO: describe com.Classcom.sun.tools.javac.apiFiji
JavacTreesProvides an implementation of Trees.Classcom.sun.tools.javac.apiFiji
JavacTypesUtility methods for operating on types.Classcom.sun.tools.javac.modelFiji
JavaFileManagerInterfacejavax.toolsFiji
JavaFileObjectInterfacejavax.toolsFiji
JavassistHelperClassfijiFiji
JCDiagnosticAn abstraction of a diagnostic message generated by the compiler.Classcom.sun.tools.javac.utilFiji
JCTreeRoot class for abstract syntax tree nodes.Classcom.sun.tools.javac.treeFiji
JFileChooserDecoratorClassfiji.guiFiji
JFrameCommandFinderClassfiji.util.guiFiji
JGraphXAdapterClassfiji.plugin.trackmate.visualization.trackschemeFiji
JImagePanelThis is a Canvas used to display images in a Window.Classfiji.util.guiFiji
JLabelLoggerClassfiji.plugin.trackmate.utilFiji
JNIClassfijiFiji
JNumericTextFieldClassfiji.plugin.trackmate.gui.panels.componentsFiji
JonkerVolgenantAlgorithm Based on: Jonker, R.Classfiji.plugin.trackmate.tracking.oldlap.hungarianFiji
JPanelColorByFeatureGUIClassfiji.plugin.trackmate.gui.panels.componentsFiji
JPanelFeaturePenaltyClassfiji.plugin.trackmate.gui.panels.componentsFiji
JPanelFeatureSelectionGuiClassfiji.plugin.trackmate.gui.panels.componentsFiji
JPanelTrackerSettingsMainClassfiji.plugin.trackmate.gui.panels.trackerFiji
JRenderer3DThe framework JRenderer3D provides the possibility to implement easily a 3D display for ImageJ plugins.ClassjRenderer3DFiji
JRulerRuler component for ScrollDisplay.Classorg.siox.exampleFiji
JSchUtilityClassedu.utexas.clm.archipelago.network.shell.sshFiji
Just_Certain_LabelsClassutilFiji
Kalman_FilterClassFiji
KalmanTrackerClassfiji.plugin.trackmate.tracking.kalmanFiji
KalmanTrackerConfigPanelClassfiji.plugin.trackmate.gui.panels.trackerFiji
KalmanTrackerFactoryClassfiji.plugin.trackmate.tracking.kalmanFiji
KD_CartoonClassFiji
KDTreeClassfiji.utilFiji
KDTreeClassmpicbg.imglib.algorithm.kdtreeFiji
KendallTauRankCorrelationThis algorithm calculates Kendall's Tau-b rank correlation coefficient http://en.ClassalgorithmsFiji
KernelThis class is the generic type for all 1D, 2D and 3D kernels.ClassvolumeFiji
Kernel1DThis class is the generic type for all 1D kernels.ClassvolumeFiji
Kernel2DThis class is the generic type for all 2D kernels.ClassvolumeFiji
Kernel3DThis class is the generic type for all 3D kernels.ClassvolumeFiji
Kernel4DThis class is the generic type for all 4D kernels.ClassvolumeFiji
KeyPropertiesClassbdv.utilFiji
KeywordsMap from Name to Token and Token to String.Classcom.sun.tools.javac.parserFiji
KindsInternal symbol kinds, which distinguish between elements of different subclasses of Symbol.Classcom.sun.tools.javac.codeFiji
KinematicsClassutilsFiji
KLTClassFiji
Koala_Bin_ReaderClassioFiji
Kuwahara_FilterClassFiji
Kuwahara_LinearStructure_Filter_v3A version of the Kuwahara filter that uses linear kernels rather than square ones.ClassFiji
KymographMouseListenerClasssc.fiji.timelapseFiji
LabelClassvib.app.moduleFiji
LabelBinaryOpsIf an underscore is added to this class name this will run as a plugin that operates the close operation.ClassoldsegmentersFiji
LabelBrush_ClassoldsegmentersFiji
LabelCenterTransformationClassvib.app.moduleFiji
LabelDiffusionTransformationClassvib.app.moduleFiji
LabeledStatementTreeA tree node for a labeled statement.Interfacecom.sun.source.treeFiji
LabelingA labeling represents the assignment of zero or more labels to theAuthor:Lee KamentskyClassmpicbg.imglib.labelingFiji
LabelingCursorStrategyInterfacempicbg.imglib.labelingFiji
LabelingCursorStrategyFactoryInterfacempicbg.imglib.labelingFiji
LabelingTypeThe LabelingType represents a labeling of a pixel with zero or more labelings of type T.Classmpicbg.imglib.labelingFiji
LabelInterpolator_Generates label data for unlabelled slices based on the data in the nearest slices First unlabelled slices are differentiated from labelled ones viaClassoldsegmentersFiji
LabelPopUpClassspim.fiji.spimdata.explorer.popupFiji
LabelThresholder_ClassoldsegmentersFiji
LanczosInterpolatorClassmpicbg.imglib.interpolation.lanczosFiji
LanczosInterpolatorFactoryClassmpicbg.imglib.interpolation.lanczosFiji
LAPJV tailored for sparse cost matrices.Classfiji.plugin.trackmate.tracking.sparselap.linkerFiji
Laplace_Classprocess3dFiji
LaPlaceFunctionsClassmpicbg.spim.registration.bead.laplaceFiji
LaplacianComputes the Laplacian of images.Classimagescience.featureFiji
LAPTracker This class tracks objects by formulating the problem as a Linear Assignment For reference, see: Jaqaman, K.Classfiji.plugin.trackmate.tracking.oldlapFiji
LAPTrackerCostMatrixCreatorContains the mutually shared fields and private functions used by the two cost matrix classes LinkingCostMatrixCreator and TrackSegmentCostMatrixCreatorClassfiji.plugin.trackmate.tracking.oldlap.costmatrixFiji
LAPTrackerFactoryClassfiji.plugin.trackmate.tracking.oldlapFiji
LAPTrackerSettingsPanelClassfiji.plugin.trackmate.gui.panels.trackerFiji
LAPUtilsClassfiji.plugin.trackmate.trackingFiji
LaserClassorg.imagearchive.lsm.toolbox.info.scaninfoFiji
LassoClasspluginFiji
Lasso_ClasspluginFiji
LayerClassini.trakem2.displayFiji
LayerBottleClassedu.utexas.clm.archipelago.ijsupport.bottleFiji
LayerBottlerClassedu.utexas.clm.archipelago.ijsupport.bottleFiji
LayerPanelClassini.trakem2.displayFiji
LayerSetA LayerSet is a container for a list of Layer.Classini.trakem2.displayFiji
LayerStackThis class represents an entire LayerSet of Patch objects only, as it is presented read-only to ImageJ.Classini.trakem2.imagingFiji
LayerThingClassini.trakem2.treeFiji
LayerTreeClassini.trakem2.treeFiji
LayoutCharactersAn interface containing layout character constants used in Java This is NOT part of any supported API.Interfacecom.sun.tools.javac.utilFiji
LazyVirtualStackClassini.trakem2.imagingFiji
LeafInterfacefiji.util.nodeFiji
LeafInterfacempicbg.imglib.algorithm.kdtree.nodeFiji
LegacyAppConfigurationOld interface for configuring the legacy application appearance.Interfaceimagej.legacy.pluginFiji
LegacyBasicImgLoaderInterfacempicbg.spim.data.legacyFiji
LegacyBasicImgLoaderWrapperClassmpicbg.spim.data.legacyFiji
LegacyDHMImgLoaderClassspim.fiji.spimdata.imgloadersFiji
LegacyEditorOld interface for the editor to use instead of ImageJ 1.Interfaceimagej.legacy.pluginFiji
LegacyImgLoaderInterfacempicbg.spim.data.legacyFiji
LegacyImgLoaderWrapperClassmpicbg.spim.data.legacyFiji
LegacyLightSheetZ1ImgLoaderClassspim.fiji.spimdata.imgloadersFiji
LegacyMicroManagerImgLoaderClassspim.fiji.spimdata.imgloadersFiji
LegacyStackImageLoaderThis ImgLoader loads images that represent a 3D stack in a single file, for example in tif, lsm, or czi format.Classbdv.ij.export.imgloaderFiji
LegacyStackImgLoaderClassspim.fiji.spimdata.imgloadersFiji
LegacyStackImgLoaderIJClassspim.fiji.spimdata.imgloadersFiji
LegacyStackImgLoaderLOCIClassspim.fiji.spimdata.imgloadersFiji
LegacyTileImgLoaderClassbdv.ij.export.tilesFiji
LegacyViewerImgLoaderInterfacebdv.spimdata.legacyFiji
LegacyViewerImgLoaderExtWrapperClassbdv.spimdata.legacyFiji
LegacyViewerImgLoaderWrapperClassbdv.spimdata.legacyFiji
Leica_SP_ReaderOpens multi-image 8-bits tiff files created by Leica confocal microscope systems using each channels own LUT.ClassleicaFiji
Leica_SP_WriterClassleicaFiji
LeicaSPReaderOpens multi-image 8-bits tiff files created by Leica confocal microscope systems using each channels own LUT.ClassleicaFiji
LevelSetClasslevelsets.ijFiji
LevelSetFactory This class encapsulates all known implementations for Level Sets and their parameters.Classlevelsets.algorithmFiji
LevelSetImplementation Stub class for all Level set variants.Classlevelsets.algorithmFiji
LevenbergMarquardtSolverA collection of static utils implementing a plain Levenberg-Marquardt least-square curve fitting algorithm.Classmpicbg.imglib.algorithm.peakFiji
LevenshteinClassfiji.utilFiji
LexerThe lexical analyzer maps an input stream consisting of ASCII characters and Unicode escapes into a token sequence.Interfacecom.sun.tools.javac.parserFiji
LibraryCheckerUtility methods for verifying that classes are present and versions are correct.Classloci.plugins.utilFiji
LibraryEntryA list entry for the configuration window's Libraries tab.Classloci.plugins.configFiji
LightSheetZ1Classspim.fiji.datasetmanagerFiji
LightSheetZ1ImgLoaderClassspim.fiji.spimdata.imgloadersFiji
LightSheetZ1MetaDataClassspim.fiji.datasetmanagerFiji
LiHistogram2DRepresents the creation of a 2D histogram between two images.ClassalgorithmsFiji
LiICQThis algorithm calculates Li et al.ClassalgorithmsFiji
LimitsClassutilFiji
LineClassmath3dFiji
Line3DBy definition, only ZDisplayable objects may implement Line3D.Interfaceini.trakem2.displayFiji
Line3DThis class represents a line in 3D coordinate system.ClassjRenderer3DFiji
LineageClassifierLineage classifier class 2009 Ignacio Arganda-Carreras and Sergio Jimenez-CelorrioClasslineageFiji
Linear_GradientClassfiji.drawingFiji
LinearDistanceClassmpicbg.pointdescriptor.similarityFiji
LinearIntensityMapTransfer intensities by a linear function y=ax+b with the coefficients a and b being stored as aClassorg.janelia.intensityFiji
LinearInterpolatorClassmpicbg.imglib.interpolation.linearFiji
LinearInterpolator1DClassmpicbg.imglib.interpolation.linearFiji
LinearInterpolator2DClassmpicbg.imglib.interpolation.linearFiji
LinearInterpolator2DRealTypeClassmpicbg.imglib.interpolation.linearFiji
LinearInterpolator3DClassmpicbg.imglib.interpolation.linearFiji
LinearInterpolator3DRealTypeClassmpicbg.imglib.interpolation.linearFiji
LinearInterpolatorFactoryClassmpicbg.imglib.interpolation.linearFiji
LinearRegressionClasssc.fiji.timelapseFiji
LineFunctionconverts a multivariate function into a univariate functionAuthor:Korbinian StrimmerClasspal.mathFiji
LineMapProvides methods to convert between character positions and line numbers for a compilation unit.Interfacecom.sun.source.treeFiji
LineReaderReads text line-by-line from a character stream using buffering for efficiency.Classimagescience.utilityFiji
LinkedPointClassmpicbg.pointdescriptorFiji
LinkingCostFunctionLinking cost function used with LAPTracker.Classfiji.plugin.trackmate.tracking.oldlap.costfunctionFiji
LinkingCostMatrixCreatorCreates the cost matrix described in Figure 1b in the paper.Classfiji.plugin.trackmate.tracking.oldlap.costmatrixFiji
LinkNew3DViewerActionClassfiji.plugin.trackmate.actionFiji
LintA class for handling -Xlint suboptions and @SuppresssWarnings.Classcom.sun.tools.javac.codeFiji
ListA class for generic linked lists.Classcom.sun.tools.javac.utilFiji
ListBoxImageClassorg.imagearchive.lsm.toolbox.guiFiji
ListBufferA class for constructing lists by appending elements.Classcom.sun.tools.javac.utilFiji
ListChooserPanelA panel to let the user choose what displayer he wants to use.Classfiji.plugin.trackmate.gui.panelsFiji
ListImgCellsLoadClassmpicbg.imglib.wrapperFiji
ListListenerClassselectionFiji
LiteralTreeA tree node for a literal expression.Interfacecom.sun.source.treeFiji
LittleEndianInputStreamReads little-endian data from a source InputStream by reversing byte ordering.Classnet.sf.image4j.ioFiji
LittleEndianOutputStreamWrites little-endian data to a target OutputStream by reversing byte ordering.Classnet.sf.image4j.ioFiji
LittleEndianRandomAccessFileProvides endian conversions for input and output with a RandomAccessFile.Classnet.sf.image4j.ioFiji
Load_Auto_TracesClasstracingFiji
Load_particles_tableFromImgClassQuickPALMFiji
Load_SegmentationClasssioxFiji
LoadCellClassmpicbg.imglib.wrapperFiji
LoadDescriptorClassfiji.plugin.trackmate.gui.descriptorsFiji
LoaderHandle all data-related issues with a virtualization engine, including load/unload and saving, saving as and overwriting.Classini.trakem2.persistenceFiji
LoadICYTrackPlugIn_Classfiji.plugin.trackmateFiji
LoadingStrategyenum LoadingStrategyDescribes how the cache processes requests for cells with missing data.Classbdv.img.cacheFiji
LoadListenerClassselectionFiji
LoadParseQueryXMLClassspim.fiji.plugin.queryXMLFiji
LoadTrackMatePlugIn_Classfiji.plugin.trackmateFiji
Local_Thickness_DriverClasssc.fiji.localThicknessFiji
Local_Thickness_ParallelClasssc.fiji.localThicknessFiji
Local_ThresholdClassvibFiji
LocalCoordinateSystemPointDescriptorClassmpicbg.pointdescriptorFiji
LocalHistogramClassmmorphoFiji
LocalizableThe Localizable interface add functionality to return the current position.Interfacempicbg.imglib.cursorFiji
Localizable3DInterfacempicbg.imglib.cursorFiji
LocalizableByDimInterfacempicbg.imglib.cursorFiji
LocalizableByDim3DInterfacempicbg.imglib.cursorFiji
LocalizableByDimCursorInterfacempicbg.imglib.cursorFiji
LocalizableByDimCursor3DInterfacempicbg.imglib.cursorFiji
LocalizableCursorInterfacempicbg.imglib.cursorFiji
LocalizableCursor3DInterfacempicbg.imglib.cursorFiji
LocalizableLabelingCursorA cursor that only visits labeled pixels.Classmpicbg.imglib.labelingFiji
LocalizableLabelingPerimeterCursorClassmpicbg.imglib.labelingFiji
LocalizablePlaneInterfacempicbg.imglib.cursorFiji
LocalizablePlaneCursorInterfacempicbg.imglib.cursorFiji
LocalizablePointClassmpicbg.imglib.algorithm.mathFiji
LocalizationClassspim.process.interestpointdetectionFiji
LocalNeighborhoodCursorClassmpicbg.imglib.cursor.specialFiji
LocalNeighborhoodCursor3DClassmpicbg.imglib.cursor.specialFiji
LocalNeighborhoodCursor3DOptimizedClassmpicbg.imglib.cursor.specialFiji
LocalNeighborhoodCursorFactoryClassmpicbg.imglib.cursor.specialFiji
LocalRigidRegistration_ClassvibFiji
LocalThicknessWrapperA class which can be used to programmatically run and control the various steps in local thickness map calculations.Classsc.fiji.localThicknessFiji
LocationDialogBio-Formats Importer location chooser dialog box.Classloci.plugins.inFiji
LOCIClassmpicbg.imglib.ioFiji
LociConfigAn ImageJ plugin for displaying the Bio-Formats plugins configuration dialog.Classloci.plugins.configFiji
LociExporterImageJ plugin for writing files using the OME Bio-Formats package.Classloci.pluginsFiji
LociFunctionsThis class provides macro extensions in ImageJ for Bio-Formats.Classloci.plugins.macroFiji
LociImporterImageJ plugin for reading files using the OME Bio-Formats package.Classloci.pluginsFiji
LociInstallerAn ImageJ plugin for installing and upgrading libraries related to the Bio-Formats plugins.Classloci.plugins.configFiji
LociPrefsUtility methods for ImageJ preferences for Bio-Formats plugins.Classloci.plugins.utilFiji
LockFor thread synchronization.Classini.trakem2.utilsFiji
LogA class for error logs.Classcom.sun.tools.javac.utilFiji
LogClassimglib.ops.operator.unaryFiji
LogClassscript.imglib.mathFiji
LogUtility class to deal with logging.Classstitching.utilsFiji
LoGThis is a 2D Laplacian of Gaussian convolution kernel.ClassvolumeFiji
Log10Classscript.imglib.mathFiji
Log1pClassscript.imglib.mathFiji
LogDetectorClassfiji.plugin.trackmate.detectionFiji
LogDetectorConfigurationPanelConfiguration panel for spot detectors based on LoG detector.Classfiji.plugin.trackmate.gui.panels.detectorFiji
LogDetectorFactoryClassfiji.plugin.trackmate.detectionFiji
LogFuncsClassinferenceFiji
LoggerThis class is used to log messages occurring during TrackMate execution.Classfiji.plugin.trackmateFiji
LoggingInputStreamA class to monitor an input stream for speed and total byte download.Classini.trakem2.ioFiji
LogHistogramDatasetA HistogramDataset that returns the log of the count in each bin (plus one), so as to have a logarithmic plot.Classorg.jfree.data.statisticsFiji
LogPaneClassedfguiFiji
LogPanelA panel using s JTextPane to log events.Classfiji.plugin.trackmate.guiFiji
LogPanelDescriptorClassfiji.plugin.trackmate.gui.descriptorsFiji
LogSingletonClassedfFiji
LOI_InterpolatorClasssc.fiji.timelapseFiji
LOI_Interpolator_ToolClasssc.fiji.timelapseFiji
LongAccessInterfacempicbg.imglib.container.basictypecontainerFiji
LongArrayA dynamic array of long values.Classimagescience.arrayFiji
LongArrayClassmpicbg.imglib.container.basictypecontainer.arrayFiji
LongDynamicContainerClassmpicbg.imglib.container.dynamicFiji
LongDynamicContainerAccessorClassmpicbg.imglib.container.dynamicFiji
LongTypeClassmpicbg.imglib.type.numeric.integerFiji
LookupTableClassfiji.plugin.volumeviewerFiji
LowerThis pass translates away some syntactic sugar: inner classes, class literals, assertions, foreach loops, etc.Classcom.sun.tools.javac.compFiji
LRFFTClassmpicbg.spim.postprocessing.deconvolution2Fiji
LRFFTThreadsClassmpicbg.spim.postprocessing.deconvolution2Fiji
LRInputClassmpicbg.spim.postprocessing.deconvolution2Fiji
LSM_ReaderClassFiji
LSM_ToolboxClassFiji
LSMFileInfoClassorg.imagearchive.lsm.reader.infoFiji
LsmImageTableModelClassorg.imagearchive.lsm.toolbox.guiFiji
LSS16_ReaderClassioFiji
LSS16_WriterClassioFiji
LucyRichardsonFFTClassmpicbg.spim.postprocessing.deconvolutionFiji
LucyRichardsonMultiViewDeconvolutionClassmpicbg.spim.postprocessing.deconvolutionFiji
LuminanceClassscript.imglib.colorFiji
LuraWaveUtility methods for dealing with proprietary LuraWave licensing.Classloci.plugins.utilFiji
LUTBlueClassini.trakem2.imaging.filtersFiji
LUTCustomClassini.trakem2.imaging.filtersFiji
LUTCyanClassini.trakem2.imaging.filtersFiji
LUTDialogClassij3d.guiFiji
LUTGreenClassini.trakem2.imaging.filtersFiji
LUTInfoClassorg.imagearchive.lsm.toolbox.infoFiji
LUTMagentaClassini.trakem2.imaging.filtersFiji
LUTOrangeClassini.trakem2.imaging.filtersFiji
LUTRedClassini.trakem2.imaging.filtersFiji
LUTYellowClassini.trakem2.imaging.filtersFiji
MTrakEM2's mathematician.Classini.trakem2.utilsFiji
MachineAccuracydetermines machine accuracyAuthor:Korbinian Strimmer, Alexei DrummondClasspal.mathFiji
MacroFunctionsConvenience class that simplifies implemention of ImageJ macro extensions.Classloci.plugins.macroFiji
MainThe programmatic interface for the Java Programming Language Except for the two methodsClasscom.sun.tools.javacFiji
MainThis class provides a commandline interface to the GJC compiler.Classcom.sun.tools.javac.mainFiji
MainMain entry point into Fiji.ClassfijiFiji
MainAccess the command-line interface of the ImageJ UpdaterAuthor:Johannes SchindelinClassfiji.updaterFiji
MainSimple class with main method for testing Image5D behavior.ClassFiji
MainClassnet.imagejFiji
MainClass to start the SIOX demo as GUI application or as Applet.Classorg.siox.exampleFiji
MainClassForDebuggingClassfijiFiji
MainDialogClass to create the dialog for bUnwarpJ.ClassbunwarpjFiji
MainDialogBio-Formats Importer general options dialog box.Classloci.plugins.inFiji
Make_MontageDoes Montages of Image5Ds with help of ij.ClassFiji
Make_TransitionClassvideo2Fiji
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.utilFiji
MandersColocalizationThis algorithm calculates Manders et al.ClassalgorithmsFiji
ManhattanDistanceClassmpicbg.pointdescriptor.similarityFiji
Manual_Landmark_SelectionClasspluginFiji
Manual_TrackingClassFiji
ManualAlignModeClassini.trakem2.displayFiji
ManualDetectorFactoryClassfiji.plugin.trackmate.detectionFiji
ManualEdgeColorAnalyzerClassfiji.plugin.trackmate.features.manualFiji
ManualEdgeColorGeneratorClassfiji.plugin.trackmate.visualizationFiji
ManualSourceTransformsClassbdv.tools.transformationFiji
ManualSpotColorAnalyzerFactoryClassfiji.plugin.trackmate.features.manualFiji
ManualSpotColorGeneratorClassfiji.plugin.trackmate.visualizationFiji
ManualTrackerFactoryClassfiji.plugin.trackmate.trackingFiji
ManualTrackingGUIControllerClassfiji.plugin.trackmate.guiFiji
ManualTrackingPlugIn_Classfiji.plugin.trackmateFiji
ManualTransformationClassbdv.tools.transformationFiji
ManualTransformationEditorClassbdv.tools.transformationFiji
MAPInferenceClassinferenceFiji
MappingFusionParalellClassmpicbg.spim.fusionFiji
MappingFusionParalellMaxWeightClassmpicbg.spim.fusionFiji
MappingFusionSequentialClassmpicbg.spim.fusionFiji
MappingFusionSequentialDifferentOutputClassmpicbg.spim.fusionFiji
MarkerClassorg.imagearchive.lsm.toolbox.info.scaninfoFiji
MarkerListsClassview5dFiji
MaskThis class is responsible for the mask preprocessing that takes place concurrently with user-interface events.ClassbunwarpjFiji
MaskClassvoltexFiji
Mask_Of_Nearby_PointsClassutilFiji
MaskFactoryClassgadgetsFiji
MaskPredicateClassnet.imglib2.predicateFiji
MaskThicknessMapWithOriginalAn additional image processing step to LocalThickness, which removes pixels from the thickness map, which are background in the original image.Classsc.fiji.localThicknessFiji
MasterModelClassorg.imagearchive.lsm.toolboxFiji
MatchClassselectionFiji
MatcherInterfacempicbg.pointdescriptor.matcherFiji
MatchingClassprocessFiji
MatchIntensitiesClassorg.janelia.intensityFiji
MatchPointListThe interestpoint list from a certain channel;Author:Stephan Preibisch (stephan.Classspim.process.interestpointregistrationFiji
MaterialListClassvib.segmentFiji
MathLibClassmpicbg.imglib.algorithm.mathFiji
MathToolsThis class has the math methods to deal with b-splines and images.ClassbunwarpjFiji
MathUtilsHandy utility functions which have some Mathematical relavance.Classpal.mathFiji
MaxClassimglib.ops.operator.binaryFiji
MaxClassimglib.ops.operator.unaryFiji
MaxClassscript.imglib.mathFiji
Max_ProjectClassspim.fiji.pluginFiji
MaxEntHistogramClassvibFiji
MaxEntQuantization_ClassvibFiji
Maximum_Classprocess3dFiji
MaximumProjectorClassspimopenerFiji
MaxPixelFusionClassmpicbg.stitching.fusionFiji
MaxPixelFusionIgnoreZeroClassmpicbg.stitching.fusionFiji
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.projectionFiji
MaxProjectPopupClassspim.fiji.spimdata.explorer.popupFiji
MC_TestClassFiji
MCCubeClassini.trakem2.utilsFiji
MCCubeClassmarchingcubesFiji
MCTriangulatorClassini.trakem2.utilsFiji
MCTriangulatorClassmarchingcubesFiji
Median_Classprocess3dFiji
MedianFilterPerforms a median filtering on the input image.Classlevelsets.filterFiji
MedianFilterMedian filter / morphological operation.Classmpicbg.imglib.algorithm.roiFiji
MedianFilterClassscript.imglib.algorithmFiji
MedianFilter2DA simple median filter that operates on 1D, 2D or 3D images.Classfiji.plugin.trackmate.detection.utilFiji
MedianPixelFusionClassmpicbg.stitching.fusionFiji
MedianPixelFusionIgnoreZeroClassmpicbg.stitching.fusionFiji
MediaWikiClientClassfijiFiji
MemberEnterThis is the second phase of Enter, in which classes are completed by entering their members into the class scope usingClasscom.sun.tools.javac.compFiji
MemberSelectTreeA tree node for a member access expression.Interfacecom.sun.source.treeFiji
MemoryThis plugin implements the Edit/Options/Memory & Threads.ClassfijiFiji
MemoryDialogBio-Formats Importer memory usage confirmation dialog box.Classloci.plugins.inFiji
MemoryProfilerClassfijiFiji
Menu_FontClassFiji
MenuItemDiverterA temporary diverter for all the menu items Use this class to intercept the next click on a menu item.Classfiji.utilFiji
MenuItemHelperClassfiji.utilFiji
MenuRefresherClassfijiFiji
Merge_Cluster_JobsClassspim.fiji.pluginFiji
MergeClusterJobsClassspim.fiji.plugin.clusterFiji
MergeExampleClassbdv.spimdata.toolsFiji
MergeFileActionClassfiji.plugin.trackmate.actionFiji
MergePartitionListClassbdv.spimdata.toolsFiji
MergerClassini.trakem2.utilsFiji
MergeToolsClassbdv.spimdata.toolsFiji
MergingCostFunctionMerging cost function used with LAPTracker.Classfiji.plugin.trackmate.tracking.oldlap.costfunctionFiji
MersenneTwisterFastMersenneTwisterFast: A simulation quality fast random number generator (MT19937)Classpal.mathFiji
Mesh_MakerClasscustomnodeFiji
Mesh_MakerClassij3dFiji
MeshEditorClassisosurfaceFiji
Meshes_From_Label_FileClassutilFiji
MeshExporterClassisosurfaceFiji
MeshGroupClassisosurfaceFiji
MeshLoaderClasscustomnodeFiji
MeshMakerClasscustomnodeFiji
MeshMakerClassij3dFiji
MeshPropertiesReferences.ClassisosurfaceFiji
MessageListenerInterfaceedu.utexas.clm.archipelago.listenFiji
MessageOverlayAnimatorDraw lines of text in the lower right corner of the display.Classbdv.viewer.animateFiji
MessagerA Messager provides the way for an annotation processor to report error messages, warnings, and other notices.Interfacejavax.annotation.processingFiji
MessagesSupport for localized messages.Classcom.sun.tools.javac.utilFiji
MessageTypeMessageType enumeration used for ClusterMessages.Classedu.utexas.clm.archipelago.listenFiji
MessageXCClassedu.utexas.clm.archipelago.networkFiji
MessengerDisplays various types of messages.Classimagescience.utilityFiji
MetaImage_CWriterClassioFiji
MetaImage_ReaderClassioFiji
MetaImage_WriterClassioFiji
MethodInvocationTreeA tree node for a method invocation expression.Interfacecom.sun.source.treeFiji
MethodTreeA tree node for a method or annotation type element declaration.Interfacecom.sun.source.treeFiji
MFWithGradientinterface for a function of several variables with a gradientAuthor:Korbinian StrimmerInterfacepal.mathFiji
MicroManagerClassspim.fiji.datasetmanagerFiji
MicroManagerImgLoaderClassspim.fiji.spimdata.imgloadersFiji
MicromanagerTranslatorContainer class for translators between OME and Micromanager formats.Classio.scif.ome.translatorsFiji
MIJMatlab to ImageJ interface.ClassFiji
MinClassimglib.ops.operator.binaryFiji
MinClassimglib.ops.operator.unaryFiji
MinClassscript.imglib.mathFiji
MinFilterThresholdClassspim.process.fusion.boundingbox.automaticFiji
Minimum_Classprocess3dFiji
MinimumProjectorClassspimopenerFiji
MinMaxAdjustableSimple interface for objects whose effects depend on a minimal and maximal double value that can be adjusted manually or automatically.Interfacefiji.plugin.trackmate.visualizationFiji
MinMaxGroupAn int interval.Classbdv.tools.brightnessFiji
MinMaxMedianThis class implements the minimum, maximum and median filter.Classprocess3dFiji
MinPixelFusionClassmpicbg.stitching.fusionFiji
MinPixelFusionIgnoreZeroClassmpicbg.stitching.fusionFiji
MipMapImageA MipMap is a container for an Image and its corresponding inverse x/y scale relative to an original ImageClassini.trakem2.displayFiji
MipmapInfoDescription of available mipmap levels for a BasicViewSetup.Classbdv.img.hdf5Fiji
MipmapOrderingInterfacebdv.viewer.renderFiji
MipmapTransformsClassbdv.utilFiji
MirrorClassimagescience.transformFiji
MirrorMirrors an n-dimensional image along an axis (one of the dimensions).Classspim.process.fusion.deconvolutionFiji
MirroredTypeExceptionThrown when an application attempts to access the Class object corresponding to a TypeMirror.Classjavax.lang.model.typeFiji
MirroredTypesExceptionThrown when an application attempts to access a sequence of Class objects each corresponding to a TypeMirror.Classjavax.lang.model.typeFiji
MirrorImageMirrors an n-dimensional image along an axis (one of the dimensions).Classmpicbg.imglib.algorithm.mirrorFiji
MiscToolsDifferent tools for the bUnwarpJ interface.ClassbunwarpjFiji
MissingPreconditionExceptionAn exception class for missing preconditions for algorithm execution.ClassalgorithmsFiji
MissingViewsClassmpicbg.spim.data.sequenceFiji
ModeInterfaceini.trakem2.displayFiji
ModelThe model for the data managed by TrackMate trackmate.Classfiji.plugin.trackmateFiji
ModelAbstract class for arbitrary transformation models to be applied to Points in n-dimensional space.Classstitching.modelFiji
ModelBased3dClassmpicbg.spim.registration.detection.descriptorFiji
ModelChangeEventClassfiji.plugin.trackmateFiji
ModelChangeListenerAn interface for listeners that will be notified when a ModelAuthor:Jean-Yves Tinevez Interfacefiji.plugin.trackmateFiji
ModelessQuestionsClassutilFiji
ModelFeatureUpdaterA utility class that listens to the change occurring in a model, and updates its spot, edge and track features accordingly.Classfiji.plugin.trackmate.featuresFiji
ModelInferenceClassinferenceFiji
ModelLinkClassspim.fiji.plugin.applyFiji
ModelPointDescriptorClassmpicbg.pointdescriptorFiji
ModelPriorMatcherThis class does a simple matching but computes a normalizationFactor based a given model prior.Classmpicbg.pointdescriptor.matcherFiji
ModelPriorSubsetMatcherClassmpicbg.pointdescriptor.matcherFiji
ModelToolsA collection of static utilities made to ease the manipulation of a TrackMate Model and SelectionModel.Classfiji.plugin.trackmate.utilFiji
ModifiableIntervalClassbdv.utilFiji
ModifierRepresents a modifier on a program element such as a class, method, or field.Classjavax.lang.model.elementFiji
ModifiersTreeA tree node for the modifiers, including annotations, for a declaration.Interfacecom.sun.source.treeFiji
ModuleClassvib.app.moduleFiji
ModuleListenerInterfacevib.app.moduleFiji
MontageClassini.trakem2.utilsFiji
MorphMorphological operations such as Open, Close, Erode and Dilate.Classscript.imglib.algorithm.fnFiji
MorphCloseClose morphological operation.Classmpicbg.imglib.algorithm.roiFiji
MorphDilateDilation morphological operation.Classmpicbg.imglib.algorithm.roiFiji
MorphErodeErosion morphological operation.Classmpicbg.imglib.algorithm.roiFiji
MorphologicalOperatorBase class for all morphological operations.Classlevelsets.filterFiji
MorphologicalOperatorsClassedfFiji
MorphOpenOpen morphological operation.Classmpicbg.imglib.algorithm.roiFiji
MorphoProcessorClassmmorphoFiji
MosaicJ_ClassFiji
Motion3DClassmpicbg.spim.vis3dFiji
MouseCursorProvides custom-made mouse cursors.Classimagescience.utilityFiji
MouseListenerTimelapseClassfiji.plugin.timelapsedisplayFiji
MouseListenerTimelapseClassspim.process.interestpointregistration.registrationstatisticsFiji
MouseListenerValueClassspim.fiji.plugin.thinoutFiji
Move_RoiClassvideo2Fiji
Moving_Least_SquaresThis plugin implements the algorithms from the paper Image Deformation Using Moving Least Squares, Schaefer S.ClassFiji
MovingLeastSquaresTransformClassmpicbg.trakem2.transformFiji
MovingLeastSquaresTransform2Classmpicbg.trakem2.transformFiji
MTJGenialClassFiji
MTJMessageClassFiji
MTJQuestionClassFiji
MTrack2_Uses ImageJ's particle analyzer to track the movement of multiple objects through a stack.ClassFiji
MTrackJ_ClassFiji
MTrackJ_WebsiteClassFiji
Multi_View_DeconvolutionClassfiji.pluginFiji
Multi_View_FusionClassfiji.pluginFiji
MultiBoxOverlayPaint an overlay showing multiple transformed boxes (interval + transform).Classbdv.viewer.overlayFiji
MultiBoxOverlayRendererRender multibox overlay corresponding to a ViewerState into aAuthor:Tobias Pietzsch Classbdv.viewer.overlayFiji
MultiImageIteratorClassimglib.ops.operationFiji
MultiOrthoGroupThis class extends VoltexGroup.ClassorthosliceFiji
MultiOrthosliceClassorthosliceFiji
MultipageTiffReaderAdapted version from the MicroManager codebase that supports the new diSPIM related tags and multiple-file reading.Classspim.fiji.spimdata.imgloadersFiji
MultipleImageProcessorClassFiji
MultipleKymograph_Time space plot is created.ClassFiji
MultipleOverlay_Plugin for multiple line selction.ClassFiji
MultiplyClassimglib.ops.operator.binaryFiji
MultiplyClassscript.imglib.mathFiji
MultiplyARGBCompositeClassini.trakem2.display.graphicsFiji
MultiplyByConstantClassimglib.ops.operator.unaryFiji
MultiResolutionImgLoaderAn ImgLoader providing multiple resolutions of each image.Interfacempicbg.spim.data.sequenceFiji
MultiResolutionRendererA Renderer that uses a coarse-to-fine rendering scheme.Classbdv.viewer.renderFiji
MultiResolutionSetupImgLoaderA SetupImgLoader providing multiple resolutions of each image.Interfacempicbg.spim.data.sequenceFiji
MultiTaskProgressInterfacefiji.featuresFiji
MultiTaskProgressInterfacetracingFiji
MultiThreadedInterfacempicbg.imglib.algorithmFiji
MultiThreadedAlgorithmThis is a convenience implementation of an algorithm that implements MultiThreaded and Algorithm so that less code has to be re-implemented.Classmpicbg.imglib.algorithmFiji
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.algorithmFiji
MultiThreadingTitle: MultiThreading Copyright: Copyright (c) 2007Classmpi.fruitfly.generalFiji
MultivariateFunctioninterface for a function of several variablesAuthor:Korbinian StrimmerInterfacepal.mathFiji
MultivariateMinimumabstract base class for minimisation of a multivariate functionAuthor:Korbinian StrimmerClasspal.mathFiji
MultiViewDatasetDefinitionInterfacespim.fiji.datasetmanagerFiji
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.hungarianFiji
MutualInformationClassdistanceFiji
MVDeconFFTClassspim.process.fusion.deconvolutionFiji
MVDeconFFTThreadsClassspim.process.fusion.deconvolutionFiji
MVDeconInputClassspim.process.fusion.deconvolutionFiji
MVDeconvolutionClassspim.process.fusion.deconvolutionFiji
mxScaledLabelShapeThis is a shape that is made to display a cell in a way that suits for our spots objects.Classfiji.plugin.trackmate.visualization.trackschemeFiji
mxSideTextShapeA text shape that draws edge label along the edge line and parallel to it.Classfiji.plugin.trackmate.visualization.trackschemeFiji
My3DDataClassview5dFiji
MyMultiLineLabelClassspim.fiji.plugin.utilFiji
MySliderClassedfguiFiji
MyTableRendererClassedfguiFiji
NaiveResamplerClassvibFiji
NameAn abstraction for internal compiler strings.Classcom.sun.tools.javac.utilFiji
NameAn immutable sequence of characters.Interfacejavax.lang.model.elementFiji
Name_PointsClasslandmarksFiji
NamedContainerA small container to name objects by overriding the toString method.ClassresultsFiji
NamedEntityAn Entity that has a name.Classmpicbg.spim.data.generic.baseFiji
NamedPointSetClasslandmarksFiji
NamedPointWorldClasslandmarksFiji
NamePatternClassspim.fiji.spimdataFiji
NamePointsClasslandmarksFiji
NativeLibraryToolsClassspim.process.cudaFiji
NavigationActionsClassbdv.viewerFiji
ND2WidgetsCustom widgets for configuring Bio-Formats ND2 support.Classloci.plugins.configFiji
NearestNeighborFlagSearchOnKDTreeClassfiji.plugin.trackmate.tracking.kdtreeFiji
NearestNeighborInterpolatorClassmpicbg.imglib.interpolation.nearestneighborFiji
NearestNeighborInterpolator1DClassmpicbg.imglib.interpolation.nearestneighborFiji
NearestNeighborInterpolator2DClassmpicbg.imglib.interpolation.nearestneighborFiji
NearestNeighborInterpolator3DClassmpicbg.imglib.interpolation.nearestneighborFiji
NearestNeighborInterpolatorFactoryClassmpicbg.imglib.interpolation.nearestneighborFiji
NearestNeighborSearchClassfiji.utilFiji
NearestNeighborSearchClassmpicbg.imglib.algorithm.kdtreeFiji
NearestNeighborTrackerClassfiji.plugin.trackmate.tracking.kdtreeFiji
NearestNeighborTrackerFactoryClassfiji.plugin.trackmate.tracking.kdtreeFiji
NearestNeighborTrackerSettingsPanelClassfiji.plugin.trackmate.gui.panels.trackerFiji
NearPointClasstracingFiji
NestingKindThe nesting kind of a type element.Classjavax.lang.model.elementFiji
NeuriteTracerResultsDialogClasstracingFiji
NeuroMLClassini.trakem2.ioFiji
New_DB_ProjectClassini.trakem2Fiji
New_Image5DCreates and displays a new Image5D.ClassFiji
New_ProjectClassini.trakem2Fiji
New_VideoClassvideo2Fiji
NewAnalyzeTracings_ClasstracingFiji
NewArrayTreeA tree node for an expression to create a new instance of an array.Interfacecom.sun.source.treeFiji
NewClassTreeA tree node to declare a new instance of a class.Interfacecom.sun.source.treeFiji
NIOByteArrayClassmpicbg.imglib.container.basictypecontainer.arrayFiji
NIOCharArrayClassmpicbg.imglib.container.basictypecontainer.arrayFiji
NIODoubleArrayClassmpicbg.imglib.container.basictypecontainer.arrayFiji
NIOFloatArrayCore array type used for float[] dataAuthor:Stephan Preibisch, Stephan Saalfeld, Rick LentzClassmpicbg.imglib.container.basictypecontainer.arrayFiji
NIOIntArrayClassmpicbg.imglib.container.basictypecontainer.arrayFiji
NIOLongArrayClassmpicbg.imglib.container.basictypecontainer.arrayFiji
NIOShortArrayClassmpicbg.imglib.container.basictypecontainer.arrayFiji
NNearestNeighborSearchClassfiji.utilFiji
NNearestNeighborSearchClassmpicbg.imglib.algorithm.kdtreeFiji
NodeInterfacefiji.util.nodeFiji
NodeCan only have one parent, so there aren't cyclic graphs.Classini.trakem2.displayFiji
NodeInterfacempicbg.imglib.algorithm.kdtree.nodeFiji
NodeConfigurationUIClassedu.utexas.clm.archipelago.uiFiji
NodeCoordinatorClassedu.utexas.clm.archipelago.network.nodeFiji
NodeParametersClassedu.utexas.clm.archipelago.network.nodeFiji
NodeParametersFactoryClassedu.utexas.clm.archipelago.network.nodeFiji
NodeShellInterface used to start remote nodes and potentially execute shell commands.Interfaceedu.utexas.clm.archipelago.network.shellFiji
NodeShellListenerInterfaceedu.utexas.clm.archipelago.listenFiji
NodeShellParametersA class to support parameters for various kinds of node shells.Classedu.utexas.clm.archipelago.network.shellFiji
NodeShellUserInfoClassedu.utexas.clm.archipelago.network.shell.sshFiji
NodeStateListenerInterfaceedu.utexas.clm.archipelago.listenFiji
NoninvertibleModelExceptionSignalizes that the Model is not invertible.Classstitching.modelFiji
NonLeafClassfiji.util.nodeFiji
NonLeafClassmpicbg.imglib.algorithm.kdtree.nodeFiji
NonLinearCoordinateTransformClassmpicbg.trakem2.transformFiji
NonLinearTransformClasslenscorrectionFiji
NonLinearTransformModeClassini.trakem2.displayFiji
NoopAdapterClassij3dFiji
NormalEstimatorClassmath3dFiji
NormalizeClassini.trakem2.imaging.filtersFiji
NormalizeBecomes a normalized version of the given image, within min and max bounds, where all pixels take values between 0 and 1.Classscript.imglib.algorithmFiji
NormalizeImageFloatNormalizes a given Image so that the sum of all of its pixels is equal to one (or approximately so).Classmpicbg.imglib.algorithm.mathFiji
NormalizeImageMinMaxClassmpicbg.imglib.algorithm.mathFiji
NormalizeLocalContrastClassini.trakem2.imaging.filtersFiji
NormalizeSumClassscript.imglib.algorithmFiji
NormalizingRandomAccessClassspim.process.fusion.weightsFiji
NormalizingRandomAccessibleIntervalClassspim.process.fusion.weightsFiji
NormMinMaxClassmpicbg.imglib.algorithm.functionFiji
NoSuitablePointsExceptionClassmpicbg.pointdescriptor.exceptionFiji
NotClassimglib.ops.conditionFiji
NotEnoughDataPointsExceptionSignalizes that there were not enough data points available to estimate theSee Also:Serialized FormClassstitching.modelFiji
NotesDialogClassorg.imagearchive.lsm.toolbox.guiFiji
NoTypeA pseudo-type used where no actual type is appropriate.Interfacejavax.lang.model.typeFiji
Nrrd_ReaderImageJ plugin to read a file in Gordon Kindlmann's NRRD or 'nearly raw raster data' format, a simple format which handlesClassioFiji
Nrrd_WriterClassioFiji
NrrdHeaderClass to read and represent the header of a NRRD file.ClassnrrdFiji
NrrdInfoThis class contains the key information that describes a nrrd file The expectation is that it will be generated by parsing an existing fileClassnrrdFiji
NRRDTranslatorContainer class for translators between OME and NRRD formats.Classio.scif.ome.translatorsFiji
NucleiConfigurationClassmpicbg.spim.registration.segmentationFiji
NucleusClassmpicbg.spim.registration.segmentationFiji
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.segmentationFiji
NucleusStructureClassmpicbg.spim.registration.segmentationFiji
NullFunctionNullFunction is a function that does not change the output.Classimglib.ops.function.pnFiji
NullLinkClassmpicbg.imglib.cursor.linkFiji
NullLoggerClassedu.utexas.clm.archipelago.utilFiji
NullTypeRepresents the null type.Interfacejavax.lang.model.typeFiji
NumberedStringSorterSorts an array of Strings treating any sequences of digits as numbers, not single digits.Classi5d.utilFiji
NumberFunctionClassscript.imglib.math.fnFiji
NumberParserA static utility class for parsing numbers from strings.Classfiji.utilFiji
NumberUtilsClassspim.fiji.spimdata.imgloadersFiji
NumericalDerivativeapproximates numerically the first and second derivatives of a function of a single variable and approximates gradient andClasspal.mathFiji
NumericTypeInterfacempicbg.imglib.type.numericFiji
OBFTranslatorContainer class for translators between OME and OBF formats.Classio.scif.ome.translatorsFiji
Object3DClassUtilitiesFiji
Object_InspectorClassfiji.debuggingFiji
OctreeDialogClassoctreeFiji
OldAppConfigurationFall-back plugin for ij-legacy.Classfiji.patchesFiji
OldLegacyEditorFall-back plugin for ij-legacy.Classfiji.patchesFiji
OMEMetadataio.Classio.scif.omeFiji
OMEMetadataServiceA utility class for working with OME metadata objects, including MetadataStore and MetadataRetrieve.Interfaceio.scif.ome.servicesFiji
OMETIFFFormatOMETiffReader is the file format reader for OME-TIFF files.Classio.scif.ome.formatsFiji
OMETIFFTranslatorContainer class for translators between OME and OMETIFF formats.Classio.scif.ome.translatorsFiji
OMETranslatorAbstract base class for all Translator implementations that operate on OMEMetadata.Classio.scif.ome.translatorsFiji
OMEXMLFormatFormat for OME-XML files.Classio.scif.ome.formatsFiji
OMEXMLServiceSCIFIO service wrapper for OMEXMLService.Interfaceio.scif.ome.servicesFiji
OMEXMLToolCommandSCIFIOToolCommand plugin for printing OME-XML.Classio.scif.ome.commandsFiji
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.utilFiji
OpenClassscript.imglib.algorithmFiji
Open_DAT_EMMENUClassioFiji
Open_DB_ProjectClassini.trakem2Fiji
Open_DF3ClassioFiji
Open_Image5DClassFiji
Open_MRC_LeginonClassioFiji
Open_ProjectClassini.trakem2Fiji
Open_Series_As_Image5DOpens a series of images or image stacks and converts it to an Image5D.ClassFiji
Open_VideoClassvideo2Fiji
OpenConnectomeDatasetAn openconnecto.Classbdv.img.openconnectomeFiji
OpenConnectomeImageLoaderClassbdv.img.openconnectomeFiji
OpenConnectomeProjectoenconnecto.Classbdv.img.openconnectomeFiji
OpenConnectomeTokenInfoClassbdv.img.openconnectomeFiji
OpenConnectomeVolatileArrayLoaderClassbdv.img.openconnectomeFiji
OpenerGenericDialogClassspimopenerFiji
OpenImage5DAdapterThis class contains static methods, which handle the "open"-specific features of OpenImage5DWindow and OpenStackWindow: ClassFiji
OpenImage5DWindowImage5DWindow, which issues DispChanged Events to registered Listeners, when the displayed slice has been changed.ClassFiji
OpenImagePlusPlugInImageJ plugin to show the current image in BigDataViewer.Classbdv.ijFiji
OpenImarisPlugInClassbdv.ijFiji
OpenImgClassspim.fiji.plugin.utilFiji
OpenStackAdapterThis class contains static methods, which handle the "open"-specific features of - converting a StackWindow to the appropriate classClassFiji
OpenStackWindowStackWindow, which issues DispChanged Events to registered Listeners, when the displayed slice has been changed.ClassFiji
OperationInterfaceini.trakem2.utilsFiji
OptionBase class for an option for one of the plugins.Classloci.plugins.prefsFiji
OptionCheckerInterface for recognizing options.Interfacejavax.toolsFiji
OptionNameTODO: describe com.Classcom.sun.tools.javac.mainFiji
OptionPanelClassini.trakem2.utilsFiji
OptionsA table of all command-line options.Classcom.sun.tools.javac.utilFiji
OptionsClassvib.appFiji
OptionsDialogBase class for options dialogs.Classloci.plugins.prefsFiji
OptionsListBase class for ImageJ preferences for plugins.Classloci.plugins.prefsFiji
OrClassimglib.ops.conditionFiji
OrClassimglib.ops.operator.binaryFiji
OrClassscript.imglib.mathFiji
OrConstantClassimglib.ops.operator.unaryFiji
OrderedTransformationsClassvib.transformsFiji
OrthogonalLineFunctionconverts a multivariate function into a univariate function by keeping all but one argument constantClasspal.mathFiji
OrthogonalSearchminimization of a real-valued function of several variables without using derivatives, using the simpleClasspal.mathFiji
OrthoGroupThis class extends VoltexGroup.ClassorthosliceFiji
OrthosliceOrthoslice extends VolumeRenderer and modifies it in a way so that not the whole volume is displayed, but only three orthogonal slices through theClassorthosliceFiji
OtherInstanceClassfijiFiji
OutOfBoundsStrategyClassmpicbg.imglib.outofboundsFiji
OutOfBoundsStrategyFactoryClassmpicbg.imglib.outofboundsFiji
OutOfBoundsStrategyMirrorClassmpicbg.imglib.outofboundsFiji
OutOfBoundsStrategyMirrorExpWindowingClassmpicbg.imglib.outofboundsFiji
OutOfBoundsStrategyMirrorExpWindowingFactoryClassmpicbg.imglib.outofboundsFiji
OutOfBoundsStrategyMirrorFactoryClassmpicbg.imglib.outofboundsFiji
OutOfBoundsStrategyPeriodicClassmpicbg.imglib.outofboundsFiji
OutOfBoundsStrategyPeriodicFactoryClassmpicbg.imglib.outofboundsFiji
OutOfBoundsStrategyValueClassmpicbg.imglib.outofboundsFiji
OutOfBoundsStrategyValueFactoryClassmpicbg.imglib.outofboundsFiji
OutputAlgorithmInterfacempicbg.imglib.algorithmFiji
OutputFunctionInterface for functions that return a new object, computed from two input arguments.Interfacefiji.plugin.trackmate.graphFiji
OverlapFusionThis class implements a fusion where only the pixel value of one of the images is used.Classmpicbg.stitching.fusionFiji
OverlapPropertiesClassstitchingFiji
OverlayClassini.trakem2.displayFiji
Overlay_RegisteredClassutilFiji
OverlayAnimatorInterfacebdv.viewer.animateFiji
OverlayedImageCanvasExtension of ImageCanvas to allow multiple overlaysAuthor:Ignacio Arganda-Carreras and Johannes SchindelinSee Also:Serialized FormClassfiji.util.guiFiji
OverlayFusionClassmpicbg.stitching.fusionFiji
OverlayFusionClassprocessFiji
OverlayRegisteredClassutilFiji
PClassini.trakem2.imagingFiji
Package_MakerClassfiji.packagingFiji
PackageElementRepresents a package program element.Interfacejavax.lang.model.elementFiji
PackagerClassfiji.packagingFiji
PaintableInterfaceini.trakem2.displayFiji
PaintInvertibleCoordinateTransformThreadClassstitching.modelFiji
PairA generic class for pairs.Classcom.sun.tools.javac.utilFiji
PairClassmpicbg.trakem2.utilFiji
PairIteratorAn iterator over pairs of types.Interfacenet.imglib2Fiji
PairwiseMatchClassspim.process.interestpointregistrationFiji
PairWiseStitchingImgLibPairwise Stitching of two ImagePlus using ImgLib1 and PhaseCorrelation.Classmpicbg.stitchingFiji
PairWiseStitchingResultClassmpicbg.stitchingFiji
PaletteA palette of 100 different colors.Classimagescience.colorFiji
PaneOwnerInterfacestacksFiji
Panorama_ViewClassmpicbg.panoramaFiji
PanoramaCameraClassmpicbg.panoramaFiji
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.parallelFiji
ParamThis class stores the parameters to apply the consistent elastic registration and it is independent of the primary GUI.ClassbunwarpjFiji
ParameterizedTypeTreeA tree node for a type expression involving type parameters.Interfacecom.sun.source.treeFiji
ParametersClassedfguiFiji
ParenthesizedTreeA tree node for a parenthesized expression.Interfacecom.sun.source.treeFiji
parObjectClassFiji
ParsePatternClassmpicbg.spim.ioFiji
ParserThe parser maps a token sequence into an abstract syntax tree.Classcom.sun.tools.javac.parserFiji
ParticleClassprocessFiji
Particle_Analyzer_3DClassprocess3dFiji
ParticleSaverClassQuickPALMFiji
PartitionPartition describes one partition file of a dataset that is split across multiple hdf5 files.Classbdv.img.hdf5Fiji
PatchClassini.trakem2.displayFiji
PatchBottleClassedu.utexas.clm.archipelago.ijsupport.bottleFiji
PatchBottlerClassedu.utexas.clm.archipelago.ijsupport.bottleFiji
PatchScriptClassini.trakem2.scriptingFiji
PatchStackAssumed is all Patch instances in the array are of the same size, live in consecutive layers of the same thickness.Classini.trakem2.imagingFiji
PathClasstracingFiji
PathAndFillListenerInterfacetracingFiji
PathAndFillManagerClasstracingFiji
PathColorsCanvasClasstracingFiji
PathDownsamplerClasstracingFiji
PathFitterClasstracingFiji
PathResultClasstracingFiji
PathsThis class converts command line arguments, environment variables and system properties (in File.Classcom.sun.tools.javac.fileFiji
PathSubstitutingFileTranslatorClassedu.utexas.clm.archipelago.network.translationFiji
PathTransformerThe int values are indexes into the image's samples, with z being 0-based.InterfacetracingFiji
PathWindowClasstracingFiji
Pbd16InputStreamDecompresses a binary InputStream using Sean Murphy's fast PBD pack-bits plus difference encoding.Classorg.janelia.vaa3d.readerFiji
Pbd8InputStreamDecompresses a binary InputStream using Sean Murphy's fast PBD pack-bits plus difference encoding.Classorg.janelia.vaa3d.readerFiji
PbdInputStreamBase class for Pbd8InputStream and Pbd16InputStream.Classorg.janelia.vaa3d.readerFiji
PCA_RegistrationClassvib.oldregistrationFiji
PDF_ViewerClassioFiji
PDF_WriterClassioFiji
PDFWriterClassresultsFiji
PeakClassmpicbg.stitchingFiji
Peak_Counter_ToolClasssc.fiji.timelapseFiji
PearsonsCorrelationA class that represents the mean calculation of the two source images in the data container.ClassalgorithmsFiji
PenaltyClassutilFiji
PerEdgeFeatureColorGeneratorClassfiji.plugin.trackmate.visualizationFiji
PerformanceProfilerA Javassist-backed performance profiler.ClassfijiFiji
PerTrackFeatureColorGeneratorA TrackColorGenerator that generate colors based on the whole trackAuthor:Jean-Yves TinevezClassfiji.plugin.trackmate.visualizationFiji
PhaseCorrelationClassmpicbg.imglib.algorithm.fftFiji
PhaseCorrelationCalculatorClassini.trakem2.imagingFiji
PhaseCorrelationPeakClassmpicbg.imglib.algorithm.fftFiji
PicClassfiji.plugin.volumeviewerFiji
PickerThis class is a helper class which implements functions for picking.Classij3d.behaviorsFiji
PickImagePeaksThis class implements a very simple peak-picker, with optional ellipsoidal peak suppression.Classmpicbg.imglib.algorithm.mathFiji
PickPeaksClassscript.imglib.analysisFiji
PictWidgetsCustom widgets for configuring Bio-Formats PICT support.Classloci.plugins.configFiji
PiecewiseLinearCdfClasshistogram2Fiji
PipeClassij3dFiji
PipeClassini.trakem2.displayFiji
PipelineImageClassio.scif.formats.imarisFiji
PIV_analyser This plugin calculates the optic flow for each pair of images made with the given stack.ClassFiji
PIVAnalyserTestDriveClassFiji
PixelDisplayClassview5dFiji
PixelFusionInterfacempicbg.stitching.fusionFiji
PixelGridContainerInterfacempicbg.imglib.containerFiji
PixelGridContainerFactoryClassmpicbg.imglib.containerFiji
PixelGridContainerImplClassmpicbg.imglib.containerFiji
PixelOnBorderClassimglib.ops.conditionFiji
PixelPairsInterfacedistanceFiji
PixelStatsClass used to track statistics with low memory footprint where large number data sets are expected User: Tom LarkworthyClassadtFiji
PlanarAccessInterface allowing access to data on a plane-by-plane basis.Interfacempicbg.imglib.container.basictypecontainerFiji
PlanarContainerA Container that stores data in an array of 2d-slices each as a linear array of basic types.Classmpicbg.imglib.container.planarFiji
PlanarContainerFactoryFactory that creates an appropriate PlanarContainer.Classmpicbg.imglib.container.planarFiji
PlanarCursorBasic Iterator for PlanarContainersAuthor:Stephan Preibisch, Stephan SaalfeldClassmpicbg.imglib.cursor.planarFiji
PlanarCursor2DBasic Iterator for 2d PlanarContainersAuthor:Stephan Saalfeld, Stephan Saalfeld Classmpicbg.imglib.cursor.planarFiji
PlanarLocalizableByDimCursorPositionable for a PlanarContainersAuthor:Stephan Preibisch, Stephan SaalfeldClassmpicbg.imglib.cursor.planarFiji
PlanarLocalizableByDimOutOfBoundsCursorPositionable with OutOfBoundsStrategy for aAuthor:Stephan Preibisch, Stephan SaalfeldClassmpicbg.imglib.cursor.planarFiji
PlanarLocalizableCursorLocalizing Iterator for a PlanarContainersAuthor:Stephan Preibisch, Stephan SaalfeldClassmpicbg.imglib.cursor.planarFiji
PlanarLocalizablePlaneCursorClassmpicbg.imglib.cursor.planarFiji
PlaneClassmath3dFiji
Plot_DotsClassprocess3dFiji
PlotNSpotsVsTimeActionClassfiji.plugin.trackmate.actionFiji
PlotUtilsClasssc.fiji.timelapseFiji
PluginHelperClassbdv.ij.utilFiji
PluginHelperClassspim.fiji.plugin.resaveFiji
PlugInInstallerClassfijiFiji
PntClassdelaunayFiji
PointA point in 5D space.Classimagescience.shapeFiji
PointThis class represents a 3D point or position on a 3D image.Classsc.fiji.analyzeSkeletonFiji
PointAn n-dimensional point.Classstitching.modelFiji
Point2DClassstitchingFiji
Point3DThis class represents a point in a 3D coordinate system.ClassjRenderer3DFiji
Point3dClassmath3dFiji
Point3DClassstitchingFiji
PointActionClass for all actions related with points in the bUnwarpJ interface: moving, adding and deleting landmarks, and painting the masks.ClassbunwarpjFiji
PointBottleA PointBottle to support synchronized point objects across cluster nodesSee Also:Serialized FormClassedu.utexas.clm.archipelago.ijsupport.bottleFiji
PointBottlerClassedu.utexas.clm.archipelago.ijsupport.bottleFiji
PointHandlerClass to deal with handle points in bUnwarpJ: here we have the methods to paint the landmarks and the masks.ClassbunwarpjFiji
PointInImageClasstracingFiji
PointListClassvibFiji
PointListDialogThis class represents a window which can hold a set of PointListPanels.Classij3d.pointlistFiji
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.pointlistFiji
PointListShapeThis class extends BranchGroup to represent a PointList as a number of spheres in the universe.Classij3d.pointlistFiji
PointMatchA link between two Points that are expected to be ideally at the same location in the world coordinate space.Classstitching.modelFiji
PointMatchFilterInterfaceorg.janelia.intensityFiji
PointMatchGenericClassmpicbg.spim.mpicbgFiji
PointMatchIdentificationInterfacempicbg.icpFiji
PointMatchStitchingClassmpicbg.stitchingFiji
PointNodeClassmpicbg.pointdescriptor.testFiji
PointPicker_This class is the only one that is accessed directly by imageJ; it attaches listeners and dies.ClassFiji
Pointsclass that represents a collection of Points Optimized for infrequent addAll operations, by simply adding a reference to the child Points objectClassadtFiji
Points_DialogClassvibFiji
PointSelectionBehaviorClasstracingFiji
PointToolbarClass to deal with the point toolbar option in the bUnwarpJ interface: draw the toolbar and change between tools.ClassbunwarpjFiji
Pointwise Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandInterfaceimagewareFiji
PoissonGeneratorPoisson random number generator.Classimagescience.randomFiji
PolygonA polygon in the x-y plane.Classimagescience.shapeFiji
PolygonRoiPublicClasssc.fiji.timelapseFiji
PolylineA sequence of points that make multiple chained line segments.Classini.trakem2.displayFiji
PolynomialModel2DA wrpper for NonLinearTransform and the AbstractAffineModel2D to which it is regularized.ClasslenscorrectionFiji
PolynomialTransform2Dn-th order 2d polynomial transform.Classmpicbg.trakem2.transformFiji
PoolAn internal structure that corresponds to the constant pool of a classfile.Classcom.sun.tools.javac.jvmFiji
PositionA class that defines source code positions as simple character offsets from the beginning of the file.Classcom.sun.tools.javac.utilFiji
PositionLabelClassview5dFiji
PostProcessingClassedfFiji
PowClassscript.imglib.mathFiji
PrecisionClassmpicbg.imglib.algorithmFiji
PreDeconvolutionFusionClassmpicbg.spim.fusionFiji
PreDeconvolutionFusionInterfaceInterfacempicbg.spim.fusionFiji
PreDeconvolutionFusionSequentialClassmpicbg.spim.fusionFiji
PreDefinedBoundingBoxClassspim.process.fusion.boundingboxFiji
PredefinedCellContainerFactoryClassmpicbg.imglib.wrapperFiji
PredicateInterfacenet.imglib2.predicateFiji
PredicateCursorThe PredicateCursor traverses a whole image but only returns those pixels for which the Predicate returns true.Classnet.imglib2Fiji
PrefetcherClassbdv.viewer.renderFiji
PrefilterPrefilters an array or image for different interpolation schemes.Classimagescience.transformFiji
PrefsClassbdv.utilFiji
Prettify_Wiki_ScreenshotClassfijiFiji
PrettyPrints out a tree as an indented Java source program.Classcom.sun.tools.javac.treeFiji
PreviewRegistrationClassmpicbg.spim.vis3dFiji
PrimitiveClasscustomnodeFiji
PrimitiveDialogsClassij3d.guiFiji
PrimitiveTypeRepresents a primitive type.Interfacejavax.lang.model.typeFiji
PrimitiveTypeTreeA tree node for a primitive type.Interfacecom.sun.source.treeFiji
PrintingProcessorA processor which prints out elements.Classcom.sun.tools.javac.processingFiji
PrintSequenceMipmapInfoClassbdv.utilFiji
PrintStreamLoggerClassedu.utexas.clm.archipelago.utilFiji
Process Biomedical Imaging Group Ecole Polytechnique Federale de Lausanne, Lausanne, SwitzerlandInterfaceimagewareFiji
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.parallelFiji
ProcessClassscript.imglib.algorithmFiji
ProcessDOGClassspim.process.interestpointdetectionFiji
ProcessDOMClassspim.process.interestpointdetectionFiji
ProcessForDeconvolutionFused individual images for each input stack, uses the exporter directlyAuthor:Stephan Preibisch (stephan.Classspim.process.fusion.deconvolutionFiji
ProcessFusionClassspim.process.fusion.weightedavgFiji
ProcessIndependentFused individual images for each input stack, uses the exporter directlyAuthor:Stephan Preibisch (stephan.Classspim.process.fusion.weightedavgFiji
ProcessIndependentPortionFuse one portion of a paralell fusion, supports no weightsAuthor:Stephan Preibisch (stephan.Classspim.process.fusion.weightedavgFiji
ProcessingEnvironmentAn annotation processing tool framework will provide an annotation processor with an object implementing this interface so the processor can use facilitiesInterfacejavax.annotation.processingFiji
ProcessListenerProcessListener interface, used to notify when a ProcessManager has been returned fromAuthor:Larry LindseyInterfaceedu.utexas.clm.archipelago.listenFiji
ProcessManagerClassedu.utexas.clm.archipelago.computeFiji
ProcessManagerCoreComparatorClassedu.utexas.clm.archipelago.utilFiji
ProcessorThe interface for an annotation processor.Interfacejavax.annotation.processingFiji
ProcessParalellClassspim.process.fusion.weightedavgFiji
ProcessParalellPortionFuse one portion of a paralell fusion, supports no weightsAuthor:Stephan Preibisch (stephan.Classspim.process.fusion.weightedavgFiji
ProcessParalellPortionWeightFuse one portion of a paralell fusion, supports one weight functionAuthor:Stephan Preibisch (stephan.Classspim.process.fusion.weightedavgFiji
ProcessParalellPortionWeightsFuse one portion of a paralell fusion, supports many weight functionsAuthor:Stephan Preibisch (stephan.Classspim.process.fusion.weightedavgFiji
ProcessSequentialClassspim.process.fusion.weightedavgFiji
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.weightedavgFiji
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.weightedavgFiji
ProcessSequentialPortionWeightsFuse one portion of a paralell fusion, supports many weight functionsAuthor:Stephan Preibisch (stephan.Classspim.process.fusion.weightedavgFiji
ProcessTopologyClassedfFiji
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.displayFiji
ProfileStackClasssc.fiji.timelapseFiji
ProgramConfiguration Copyright: Copyright (c) 2006 Company: Diplomarbeit - IZBI Leipzig/TU DresdenClassmpicbg.spim.ioFiji
ProgressBarClassbunwarpjFiji
ProgressCanvasClasslandmarksFiji
ProgressIndicatorClassvib.app.guiFiji
ProgressorWrapper around ImageJ's progress bar.Classimagescience.utilityFiji
ProgressTrackerClassimglib.ops.observerFiji
ProgressWindowClasslandmarksFiji
ProgressWriterInterfacebdv.exportFiji
ProgressWriterConsoleClassbdv.exportFiji
ProgressWriterIJClassbdv.ij.utilFiji
ProgressWriterIJClassspim.fiji.plugin.resaveFiji
ProjectThe top-level class in control.Classini.trakem2Fiji
ProjectorInterfacespimopenerFiji
ProjectThingClassini.trakem2.treeFiji
ProjectTilerClassini.trakem2.persistenceFiji
ProjectToolbarClassini.trakem2.utilsFiji
ProjectTreeA class to hold a tree of Thing nodesSee Also:Serialized FormClassini.trakem2.treeFiji
PropagatedExceptionUsed to propagate exceptions through to the user.Classcom.sun.tools.javac.utilFiji
ProposeMipmapsPropose number of mipmap levels, as well subsampling factors and chunk size Choice of proposed chunksize is not based on any hard benchmark dataClassbdv.exportFiji
Psychomorph_TEM_ReaderClassFiji
QTWidgetsCustom widgets for configuring Bio-Formats QuickTime support.Classloci.plugins.configFiji
Quantile_Based_NormalizationClassutilFiji
QuaternionClassmpicbg.pointdescriptor.matcherFiji
QueueJumpingKeyListenerClasstracingFiji
QueueListenerInterfaceedu.utexas.clm.archipelago.listenFiji
QuickCallableClassedu.utexas.clm.archipelago.computeFiji
QuickRunnableClassedu.utexas.clm.archipelago.computeFiji
Quicksortable Copyright: Copyright (c) 2007 This program is free software; you can redistribute it and/orInterfacempi.fruitfly.mathFiji
QuicksortableInterfacestitchingFiji
Radial_GradientClassfiji.drawingFiji
Radial_ResliceClassfiji.stacksFiji
RadiusNeighborSearchClassfiji.utilFiji
RadiusNeighborSearchClassmpicbg.imglib.algorithm.kdtreeFiji
RadiusToEstimatedActionClassfiji.plugin.trackmate.actionFiji
RagMipMapsLike RawMipMaps, but the alpha channel is compressed with GZIP.Classini.trakem2.ioFiji
RandomClassscript.imglib.mathFiji
RandomAccessInputStreamWrapperWrapper class to convert RandomAccessInputStream to RandomAccessInputStream.Classio.scif.bf.wrapperFiji
RandomAccessInputStreamWrapperWrapper class to convert RandomAccessInputStream to RandomAccessInputStream.Classio.scif.commonFiji
RandomGeneratorInterface for random number generators.Interfaceimagescience.randomFiji
RandomizerClassimagescience.randomFiji
RandPermutation Lionel.ClassutilsFiji
RangeDialogBio-Formats Importer range chooser dialog box.Classloci.plugins.inFiji
RankFilterClassini.trakem2.imaging.filtersFiji
RANSACClassspim.process.interestpointregistrationFiji
RANSACParametersClassspim.process.interestpointregistrationFiji
RansacRegressionFilterClassorg.janelia.intensityFiji
RansacRegressionReduceFilterClassorg.janelia.intensityFiji
Raster_RigidClassvibFiji
RATS_RATS_ (Robust Automatic Threshold Selection) ImageJ plugin.ClassFiji
RATSQuadtreeClassFiji
RawMipMapsClassini.trakem2.ioFiji
ReaderClassorg.imagearchive.lsm.readerFiji
ReaderClassorg.imagearchive.lsm.toolboxFiji
ReaderToolkitClassorg.imagearchive.lsm.toolboxFiji
ReadXMLClassFiji
RealARGBColorConverterClassnet.imglib2.displayFiji
RealARGBColorConverterSetupClassbdv.tools.brightnessFiji
RealFunctionInterfaceimglib.ops.functionFiji
RealHistogramBinFactoryClassmpicbg.imglib.algorithm.histogram.arbitraryFiji
RealRandomAccessibleSourceA Source wrapping some RealRandomAccessible.Classbdv.utilFiji
RealTypeInterfacempicbg.imglib.type.numericFiji
RealTypeConverterClassmpicbg.imglib.functionFiji
RealTypeDisplayClassmpicbg.imglib.image.displayFiji
RealTypeImplClassmpicbg.imglib.type.numeric.realFiji
RebinPlugin which takes an ImagePlus and rebins the pixel values to the specified range.Classprocess3dFiji
Rebin_Plugin which takes an ImagePlus and rebins the pixel values to the specified range.Classprocess3dFiji
RecalculateFeatureActionClassfiji.plugin.trackmate.actionFiji
Recent_CommandsClassfiji.utilFiji
ReciprocalClassimglib.ops.operator.unaryFiji
RecognizedOptionsTODO: describe com.Classcom.sun.tools.javac.mainFiji
Reconstruct_DatasetClassQuickPALMFiji
Reconstruct_ReaderClassedu.utexas.clm.reconstructreader.reconstructFiji
Reconstruct_WriterClassedu.utexas.clm.reconstructreader.trakem2Fiji
ReconstructAreaReconstruct an Area from a list of XML ClassFiji
SynchronizedTreeA tree node for a 'synchronized' statement.Interfacecom.sun.source.treeFiji
TagClassini.trakem2.displayFiji
TaggableInterfaceini.trakem2.displayFiji
TanClassscript.imglib.mathFiji
TanhClassscript.imglib.mathFiji
TarBz2PackagerClassfiji.packagingFiji
TargetThe classfile version target.Classcom.sun.tools.javac.jvmFiji
TarGzPackagerClassfiji.packagingFiji
TarPackagerClassfiji.packagingFiji
TaskEventProvides details about work that has been done by the JDK Java Compiler, javac.Classcom.sun.source.utilFiji
TaskFactoryClassini.trakem2.parallelFiji
TaskListenerProvides a listener to monitor the activity of the JDK Java Compiler, javac.Interfacecom.sun.source.utilFiji
TaskOnEDTClassini.trakem2.utilsFiji
TemplateThingClassini.trakem2.treeFiji
TemplateTreeClassini.trakem2.treeFiji
TerminalThe two possible segments, represented as special terminal nodes in the graph.ClassgraphcutFiji
Test_ClusterClassedu.utexas.clm.archipelago.exampleFiji
Test_Java3DClassFiji
Test_JEPClassfiji.processFiji
Test_SaveFor testing ImageJ extensions for saving extra MetadataAuthor:Joachim WalterClassFiji
Test_Single_VoxelClassij3dFiji
Test_Single_VoxelClasstracingFiji
TestClassifierClasslineageFiji
TestComputeCurvatures_ClassfeaturesFiji
TestGraphicsSourceClassini.trakem2.display.graphicsFiji
TestKDTreeClassfiji.utilFiji
TestKDTreeClassmpicbg.imglib.algorithm.kdtreeFiji
TestPointDescriptorClassmpicbg.pointdescriptor.testFiji
TetrahedronClassmath3dFiji
Text3DThis class represents a text element in a 3D coordinate system.ClassjRenderer3DFiji
TextAreaWriterWriter implementation that writes to a JTextArea document.Classloci.plugins.configFiji
TextFieldFocusTextField that sends an ActionEvent when the integer Value has changed either by hitting return (as the normal AWT TextField) or byClassFiji
TextFileAccessClassmpicbg.spim.ioFiji
TextFileAccessClassmpicbg.stitchingFiji
TextOverlayAnimatorDraw one line of text in the center or bottom right of the display.Classbdv.viewer.animateFiji
Texture_By_RefClasstextureByRefFiji
Texture_By_Ref_colClasstextureByRefFiji
TFalpha1Classfiji.plugin.volumeviewerFiji
TFalpha2Classfiji.plugin.volumeviewerFiji
TFalpha3Classfiji.plugin.volumeviewerFiji
TFalpha4Classfiji.plugin.volumeviewerFiji
TFrgbClassfiji.plugin.volumeviewerFiji
TGMMImporterClassfiji.plugin.trackmate.ioFiji
ThingInterfaceini.trakem2.treeFiji
ThinOut_DetectionsClassspim.fiji.pluginFiji
ThinPlateR2LogRSplineKernelTransform Began as a port of itk's itkKernelTransform.Classjitk.splineFiji
ThinPlateSplineMappingClassmpicbg.ijFiji
ThinPlateSplineTransformClassmpicbg.trakem2.transformFiji
Thread_KillerClassFiji
ThreadEdfClassedfguiFiji
ThreadsClassspimFiji
ThreadTopoProcClassedfguiFiji
Three_Pane_CropClassstacksFiji
ThreePaneContainerClassstacksFiji
ThreePaneContainer_ClassstacksFiji
ThreePaneCropClassstacksFiji
ThreePaneCropCanvasClassstacksFiji
ThreePanesClassstacksFiji
ThreePanes_ClassstacksFiji
ThreePanesCanvasClassstacksFiji
ThresholdClassvib.transformsFiji
ThresholdedClassdistanceFiji
ThresholderClassimagescience.segmentFiji
ThresholderClassvib.segmentFiji
ThresholdModeAn enumerator for different modes of threshold handling.ClassgadgetsFiji
ThrowTreeA tree node for a 'throw' statement.Interfacecom.sun.source.treeFiji
ThumbLoaderLoads thumbnails for Bio-Formats Importer series chooser in a separate thread.Classloci.plugins.inFiji
TicTocClassfiji.utilFiji
TiffDelegateWidgetsCustom widgets for configuring Bio-Formats TIFF support.Classloci.plugins.configFiji
TIFFTranslatorContainer class for translators between OME and TIFF formats.Classio.scif.ome.translatorsFiji
TileClassstitching.modelFiji
TileCanvasClassi5d.guiFiji
TileConfigurationClassmpicbg.trakem2.alignFiji
TileConfigurationA configuration of rigidly transformed tiles.Classstitching.modelFiji
TileConfigurationPhaseCorrelationClassmpicbg.spim.mpicbgFiji
TileConfigurationSPIMClassmpicbg.spim.mpicbgFiji
TileConfigurationStitchingClassmpicbg.stitchingFiji
TileImgLoaderClassbdv.ij.export.tilesFiji
TileSPIMClassmpicbg.spim.mpicbgFiji
Time_StamperClassFiji
TimeDirectedDepthFirstIteratorClassfiji.plugin.trackmate.graphFiji
TimeDirectedNeighborIndexClassfiji.plugin.trackmate.graphFiji
TimeDirectedSortedDepthFirstIteratorClassfiji.plugin.trackmate.graphFiji
TimeLapseDisplayClassfiji.plugin.timelapsedisplayFiji
TimeLapseDisplayClassspim.process.interestpointregistration.registrationstatisticsFiji
TimelapseListenerInterfaceij3dFiji
TimelineClassview4dFiji
TimelineGUIThis class implements the window with the controls for the 4D viewer.Classview4dFiji
TimePointClassio.scif.formats.imarisFiji
TimePointClassmpicbg.spim.data.sequenceFiji
TimePointListenerInterfacebdv.viewerFiji
TimePointsClassmpicbg.spim.data.sequenceFiji
TimePointsPatternClassmpicbg.spim.data.sequenceFiji
TimerFacilitates measuring of the computation time consumed by a process.Classimagescience.utilityFiji
TimerClassorg.imagearchive.lsm.toolbox.info.scaninfoFiji
TimeStampsClassorg.imagearchive.lsm.toolbox.infoFiji
TissueStatisticsClassvib.app.moduleFiji
TissueStatistics_ClassvibFiji
TitledThingInterfaceini.trakem2.treeFiji
TJClasstransformjFiji
TJ_AboutClasstransformjFiji
TJ_AffineClasstransformjFiji
TJ_CropClasstransformjFiji
TJ_EmbedClasstransformjFiji
TJ_HelpClasstransformjFiji
TJ_MatrixClasstransformjFiji
TJ_MirrorClasstransformjFiji
TJ_OptionsClasstransformjFiji
TJ_PanelClasstransformjFiji
TJ_RotateClasstransformjFiji
TJ_ScaleClasstransformjFiji
TJ_TranslateClasstransformjFiji
TJ_TurnClasstransformjFiji
TMLHandlerCreates the project objects from an XML file (TrakEM2 Markup Language Handler).Classini.trakem2.persistenceFiji
TMUtilsClassfiji.plugin.trackmate.utilFiji
TmXmlKeysContains the key string used for xml marshaling.Classfiji.plugin.trackmate.ioFiji
TmXmlReaderClassfiji.plugin.trackmate.ioFiji
TmXmlReader_v12A compatibility xml loader than can load TrackMate xml file saved for version prior to 2.Classfiji.plugin.trackmate.ioFiji
TmXmlReader_v20Classfiji.plugin.trackmate.ioFiji
TmXmlWriterClassfiji.plugin.trackmate.ioFiji
ToAST25_ClassFiji
ToDegreesClassscript.imglib.mathFiji
TodoA queue of all as yet unattributed classes.Classcom.sun.tools.javac.compFiji
Toggle_Cluster_OptionsClassspim.fiji.pluginFiji
ToggleDialogActionClassbdv.toolsFiji
TokenAn interface that defines codes for Java source tokens returned from lexical analysis.Classcom.sun.tools.javac.parserFiji
ToolCommon interface for tools that can be invoked from a program.Interfacejavax.toolsFiji
ToolProviderProvides methods for locating tool providers, for example, providers of compilers.Classjavax.toolsFiji
ToolsClassedfFiji
ToolToggleListenerInterfacefiji.toolFiji
ToolWithOptionsInterfacefiji.toolFiji
ToOMETranslatorAbstract base class for all io.Classio.scif.ome.translatorsFiji
ToplevelImageJAppAn extension of ImageJApp that provides the legacy ImageJ 1.Classnet.imagej.appFiji
ToRadiansClassscript.imglib.mathFiji
TorstenRaw_GZ_ReaderThis plugin loads the raw binary files returnedby Torsten Rohlfing's softwareClassioFiji
TPlugInInterfaceini.trakem2.pluginFiji
TraceLoaderListenerInterfacetracingFiji
TracerCanvasClasstracingFiji
TracerThreadClasstracingFiji
TrackClassorg.imagearchive.lsm.toolbox.info.scaninfoFiji
TrackAnalyzerMother interface for the classes that can compute the feature of tracks.Interfacefiji.plugin.trackmate.features.trackFiji
TrackAnalyzerProviderA provider for the track analyzers provided in the GUI.Classfiji.plugin.trackmate.providersFiji
TrackBranchAnalysisClassfiji.plugin.trackmate.actionFiji
TrackBranchingAnalyzerClassfiji.plugin.trackmate.features.trackFiji
TrackColorGeneratorInterface for functions that can generate track colors, with a different color for each vertex and edge.Interfacefiji.plugin.trackmate.visualizationFiji
TrackDisplayNodeClassfiji.plugin.trackmate.visualization.threedviewerFiji
TrackDurationAnalyzerClassfiji.plugin.trackmate.features.trackFiji
TrackerChoiceDescriptorClassfiji.plugin.trackmate.gui.descriptorsFiji
TrackerConfigurationDescriptorClassfiji.plugin.trackmate.gui.descriptorsFiji
TrackerKeysClassfiji.plugin.trackmate.trackingFiji
TrackerProviderClassfiji.plugin.trackmate.providersFiji
TrackFeatureCalculatorA class dedicated to centralizing the calculation of the numerical features of tracks, through TrackAnalyzers.Classfiji.plugin.trackmate.featuresFiji
TrackFeatureGrapherClassfiji.plugin.trackmate.featuresFiji
TrackFilterDescriptorClassfiji.plugin.trackmate.gui.descriptorsFiji
TrackIndexAnalyzerClassfiji.plugin.trackmate.features.trackFiji
TrackingDescriptorClassfiji.plugin.trackmate.gui.descriptorsFiji
TrackLocationAnalyzerClassfiji.plugin.trackmate.features.trackFiji
TrackMate The TrackMate_ class runs on the currently active time-lapse image (2D or 3D) and both identifies and tracks bright spots over time.Classfiji.plugin.trackmateFiji
TrackMateActionThis interface describe a track mate action, that can be run on a TrackMate object to change its content or properties.Interfacefiji.plugin.trackmate.actionFiji
TrackMateActionFactoryInterfacefiji.plugin.trackmate.actionFiji
TrackMateBatchClassfiji.plugin.trackmateFiji
TrackMateGUIControllerClassfiji.plugin.trackmate.guiFiji
TrackMateGUIModelClassfiji.plugin.trackmate.guiFiji
TrackMateModelViewInterfacefiji.plugin.trackmate.visualizationFiji
TrackMateModuleInterface for TrackMate modules.Interfacefiji.plugin.trackmateFiji
TrackMatePlugIn_Classfiji.plugin.trackmateFiji
TrackMateWizardClassfiji.plugin.trackmate.guiFiji
TrackModelA component of Model specialized for tracksAuthor:Jean-Yves TinevezClassfiji.plugin.trackmateFiji
TrackNavigatorClassfiji.plugin.trackmate.utilFiji
TrackOverlayThe overlay class in charge of drawing the tracks on the hyperstack window.Classfiji.plugin.trackmate.visualization.hyperstackFiji
TrackSchemeClassfiji.plugin.trackmate.visualization.trackschemeFiji
TrackSchemeActionsClassfiji.plugin.trackmate.visualization.trackschemeFiji
TrackSchemeFactoryClassfiji.plugin.trackmate.visualization.trackschemeFiji
TrackSchemeFrameClassfiji.plugin.trackmate.visualization.trackschemeFiji
TrackSchemeGraphComponentClassfiji.plugin.trackmate.visualization.trackschemeFiji
TrackSchemeGraphLayoutThis mxGraphLayout arranges cells on a graph in lanes corresponding to tracks.Classfiji.plugin.trackmate.visualization.trackschemeFiji
TrackSchemeKeyboardHandlerClassfiji.plugin.trackmate.visualization.trackschemeFiji
TrackSchemePopupMenuClassfiji.plugin.trackmate.visualization.trackschemeFiji
TrackSchemeStylistClassfiji.plugin.trackmate.visualization.trackschemeFiji
TrackSchemeSvgCanvasClassfiji.plugin.trackmate.visualization.trackschemeFiji
TrackSchemeToolbarClassfiji.plugin.trackmate.visualization.trackschemeFiji
TrackSegmentCostMatrixCreatorCreates the cost matrix roughly described in Figure 1c in the paper: Jaqaman, K.Classfiji.plugin.trackmate.tracking.oldlap.costmatrixFiji
TrackSpeedStatisticsAnalyzerClassfiji.plugin.trackmate.features.trackFiji
TrackSpotQualityFeatureAnalyzerClassfiji.plugin.trackmate.features.trackFiji
TrakEM2ArchipelagoClassedu.utexas.clm.archipelago.ijsupportFiji
TrakEM2MLParserA class to parse a file in TrakEM2 XML format.Classini.trakem2.treeFiji
Trakem2TranslatorClassedu.utexas.clm.reconstructreader.trakem2Fiji
TransceiverExceptionListenerInterfaceedu.utexas.clm.archipelago.listenFiji
TransceiverListenerInterfaceedu.utexas.clm.archipelago.listenFiji
Transfer_Channel_SettingsClassFiji
TransferableNodeAdapted from freely available code by DeuDeu from http://forum.Classini.trakem2.treeFiji
TransformRepresents a 3D affine transformation matrix.Classimagescience.transformFiji
TransformInterfacevib.transformsFiji
Transform_IOClassmath3dFiji
Transform_ThinPlateSplineSmooth image deformation using landmark based deformation by means of Thin Plate Spline inspired by the implementation of Kitware (ITK).ClassFiji
Transform_Virtual_Stack_MTFiji plugin to transform sequences of images in a concurrent (multi-thread) way.Classregister_virtual_stackFiji
TransformationClass to perform the transformation for bUnwarpJ: It stores the information about the bidirectional or unidirectional registration.ClassbunwarpjFiji
TransformationAttemptClasslandmarksFiji
TransformationModelClassspim.process.interestpointregistrationFiji
TransformationStepClassini.trakem2.displayFiji
TransformAwareBufferedImageOverlayRendererClassbdv.viewer.renderFiji
TransformAwareRenderTargetInterfacebdv.viewer.renderFiji
TransformedImageClassvibFiji
TransformedInterpolatedRealRandomAccessClassspim.process.fusion.weightsFiji
TransformedRealRandomAccessibleIntervalClassspim.process.fusion.weightsFiji
TransformedSourceA Source that wraps another Source and allows to decorate it with an extra AffineTransform3D.Classbdv.tools.transformationFiji
TransformerThis class implements static methods for transforming images and volumes.ClassvolumeFiji
TransformImagesClassvib.app.moduleFiji
TransformInputFuse one portion of a paralell fusion, supports no weightsAuthor:Stephan Preibisch (stephan.Classspim.process.fusion.deconvolutionFiji
TransformInputAndWeightsFuse one portion of a paralell fusion, supports no weightsAuthor:Stephan Preibisch (stephan.Classspim.process.fusion.deconvolutionFiji
TransformInverseGradientDescentClassjitk.splineFiji
TransformIOThis class provides simple IO for affine transforms.Classmath3dFiji
TransformMeshClassmpicbg.trakem2.transformFiji
TransformMeshMappingCreates automatically cropped mappings and inverse mappings of images using a TransformMesh.Classmpicbg.trakem2.transformFiji
TransformMeshMappingWithMasksSpecialized TransformMapping for Patches, that is, rendering the image, outside mask and mask in one go instead three.Classmpicbg.trakem2.transformFiji
TransformUtilsClassmpicbg.utilFiji
TransformWeightsFuse one portion of a paralell fusion, supports no weightsAuthor:Stephan Preibisch (stephan.Classspim.process.fusion.deconvolutionFiji
TranslateTranslates an image using different interpolation schemes.Classimagescience.transformFiji
TranslationAnimatorAn animator that just executes a constant speed translation of the current viewpoint to a target location, keeping all other view parameters constant.Classbdv.viewer.animateFiji
TranslationInvariantAffineModel3D3d-affine transformation models to be applied to points in 3d-space.Classmpicbg.pointdescriptor.modelFiji
TranslationInvariantFixedModelThis model just applies some other TranslationInvariantModel without computing anything.Classmpicbg.pointdescriptor.modelFiji
TranslationInvariantModelThis class is a subtle hint that Models which are used to fit AbstractPointDescriptors should be translation invariant.Classmpicbg.pointdescriptor.modelFiji
TranslationInvariantRigidModel2D2d-rigid transformation models to be applied to points in 2d-space.Classmpicbg.pointdescriptor.modelFiji
TranslationInvariantRigidModel3D3d-rigid transformation models to be applied to points in 3d-space.Classmpicbg.pointdescriptor.modelFiji
TranslationInvariantSimilarityModel3D3d-rigid transformation models to be applied to points in 3d-space.Classmpicbg.pointdescriptor.modelFiji
TranslationModel2DClassmpicbg.trakem2.transformFiji
TranslationModel2DClassstitching.modelFiji
TranslationModel3DClassmpicbg.trakem2.transformFiji
TranslationModel3DClassstitching.modelFiji
TranslationTile2DClassmpicbg.trakem2.alignFiji
TransTypesThis pass translates Generic Java to conventional Java.Classcom.sun.tools.javac.compFiji
TreeCommon interface for all nodes in an abstract syntax tree.Classcom.sun.source.treeFiji
TreeA sequence of points ordered in a set of connected branches.Classini.trakem2.displayFiji
TreeConnectorsViewList all connectors whose origins intersect with the given tree.Classini.trakem2.displayFiji
TreeCopierCreates a copy of a tree, using a given TreeMaker.Classcom.sun.tools.javac.treeFiji
TreeInfoUtility class containing inspector methods for trees.Classcom.sun.tools.javac.treeFiji
TreelineClassini.trakem2.displayFiji
TreelineGraphEditorClasstreelineFiji
TreeMakerFactory class for trees.Classcom.sun.tools.javac.treeFiji
TreePathA path of tree nodes, typically used to represent the sequence of ancestor nodes of a tree node up to the top level CompilationUnitTree node.Classcom.sun.source.utilFiji
TreePathScannerA TreeVisitor that visits all the child tree nodes, and provides support for maintaining a path for the parent nodes.Classcom.sun.source.utilFiji
TreesBridges JSR 199, JSR 269, and the Tree API.Classcom.sun.source.utilFiji
TreeScannerA TreeVisitor that visits all the child tree nodes.Classcom.sun.source.utilFiji
TreeScannerA subclass of Tree.Classcom.sun.tools.javac.treeFiji
TreeTranslatorA subclass of Tree.Classcom.sun.tools.javac.treeFiji
TreeVisitorA visitor of trees, in the style of the visitor design pattern.Interfacecom.sun.source.treeFiji
TriangleClassmath3dFiji
Triangle_AlgorithmClassFiji
TriangulationA Triangulation on vertices (generic type V).ClassdelaunayFiji
TriangulatorInterfaceisosurfaceFiji
TrimNotVisibleActionClassfiji.plugin.trackmate.actionFiji
TripleClassmpicbg.trakem2.utilFiji
TryTreeA tree node for a 'try' statement.Interfacecom.sun.source.treeFiji
TubeClasscustomnodeFiji
Tubeness_ClassfeaturesFiji
TubenessProcessorClassfeaturesFiji
TubularGeodesicsTracerClasstracingFiji
TurboReg_This class is the only one that is accessed directly by imageJ; it launches a modeless dialog and dies.ClassFiji
TurnRotates an image multiples of 90 degrees around its principal axes.Classimagescience.transformFiji
TwinCursorThe TwinCursor moves over two images with respect to a mask.Classnet.imglib2Fiji
Two_Point_CorrelationClassFiji
TwoOperandsAbstractFunctionClassfiji.expressionparser.functionFiji
TwoOperandsPixelBasedAbstractFunctionClassfiji.expressionparser.functionFiji
TwoValuesClassdistanceFiji
TypeThis class represents Java types.Classcom.sun.tools.javac.codeFiji
TypeThe Type class is responsible for computing.Interfacempicbg.imglib.typeFiji
TypeCastTreeA tree node for a type cast expression.Interfacecom.sun.source.treeFiji
TypeConverterClassmpicbg.imglib.typeFiji
TypedBasicImgLoaderInterfacempicbg.spim.data.generic.sequenceFiji
TypedHashMapAn extended HashMap that throws UnsupportedOperationException for calls to HashMap.Classini.trakem2.utilsFiji
TypeElementRepresents a class or interface program element.Interfacejavax.lang.model.elementFiji
TypeImplClassmpicbg.imglib.typeFiji
TypeKindThe kind of a type mirror.Classjavax.lang.model.typeFiji
TypeKindVisitor6A visitor of types based on their kind with default behavior appropriate for the RELEASE_6 source version.Classjavax.lang.model.utilFiji
TypeMirrorRepresents a type in the Java programming language.Interfacejavax.lang.model.typeFiji
TypeParameterElementRepresents a formal type parameter of a generic class, interface, method, or constructor element.Interfacejavax.lang.model.elementFiji
TypeParameterTreeA tree node for a type parameter.Interfacecom.sun.source.treeFiji
TypesUtility class containing various operations on types.Classcom.sun.tools.javac.codeFiji
TypesUtility methods for operating on types.Interfacejavax.lang.model.utilFiji
TypeTagsAn interface for type tag values, which distinguish between different This is NOT part of any supported API.Classcom.sun.tools.javac.codeFiji
TypeVariableRepresents a type variable.Interfacejavax.lang.model.typeFiji
TypeVisitorA visitor of types, in the style of the visitor design pattern.Interfacejavax.lang.model.typeFiji
U3DExporter http://www.Classcustomnode.u3dFiji
UIUser interface abstraction of the ImageJ Updater adapter.Interfacefiji.updaterFiji
UIAdapterInterfaceij3dFiji
UnaryOperationClassscript.imglib.math.fnFiji
UnaryOperatorInterfaceimglib.ops.operatorFiji
UnaryOperatorFunctionClassimglib.ops.function.p1Fiji
UnaryTreeA tree node for postfix and unary expressions.Interfacecom.sun.source.treeFiji
UniformGeneratorUniform random number generator.Classimagescience.randomFiji
UnivariateFunctioninterface for a function of one variableAuthor:Korbinian StrimmerInterfacepal.mathFiji
UnivariateMinimumminimization of a real-valued function of one variable without using derivatives.Classpal.mathFiji
UniverseListenerInterfaceij3dFiji
UniverseSettingsClassij3dFiji
UniverseSynchronizerClassij3dFiji
UnknownAnnotationValueExceptionIndicates that an unknown kind of annotation value was encountered.Classjavax.lang.model.elementFiji
UnknownElementExceptionIndicates that an unknown kind of element was encountered.Classjavax.lang.model.elementFiji
UnknownTypeExceptionIndicates that an unknown kind of type was encountered.Classjavax.lang.model.typeFiji
Unpack_To_PNGClassstacksFiji
UnsetPixelClasslevelsets.filterFiji
Unsigned12BitTypeClassmpicbg.imglib.type.numeric.integerFiji
UnsignedByteTypeClassmpicbg.imglib.type.numeric.integerFiji
UnsignedIntTypeClassmpicbg.imglib.type.numeric.integerFiji
UnsignedShortTypeClassmpicbg.imglib.type.numeric.integerFiji
Unsparse3DByteArrayClassadtFiji
UnwarpJ_ClassFiji
UpdaterClassfiji.updaterFiji
UpdaterA plugin for updating the Bio-Formats plugins.Classloci.pluginsFiji
UpgradeDialogBio-Formats Importer upgrade checker dialog box.Classloci.plugins.inFiji
Upload_Image_To_WikiClassfijiFiji
UptodateCheckClassfiji.updaterFiji
UrnModelclass for drawing numbers from an urn with and without laying backClasspal.mathFiji
User_PluginsA class to find user plugins, i.ClassfijiFiji
USHORTPaintClassini.trakem2.display.paintFiji
UtilClassbdv.img.hdf5Fiji
UtilClasshistogram2Fiji
UtilClassini.trakem2.vectorFiji
UtilClassmpicbg.imglib.utilFiji
UtilClassmpicbg.panoramaFiji
UtilClassmpicbg.trakem2.alignFiji
UtilClassscript.imglib.math.fnFiji
UtilsClassedu.utexas.clm.reconstructreaderFiji
UtilsUtils class: stores generic widely used methods.Classini.trakem2.utilsFiji
UtilsUtil class made of static methods, meant to simplify the writing of special cursors.Classmpicbg.imglib.cursor.specialFiji
UtilsClassoldsegmentersFiji
UtilsCollection of auxiliary image processing methods used by the SioxSegmentator mainly for postprocessing.Classorg.siox.utilFiji
V3dRawImageStreamClassorg.janelia.vaa3d.readerFiji
Vaa3d_ReaderVaa3d_Reader class is a Fiji/ImageJ plugin for loading .Classorg.janelia.vaa3d.readerFiji
Vaa3d_WriterClassFiji
Vaa3dPbdToRawClassorg.janelia.vaa3d.readerFiji
ValueGreaterThanClassimglib.ops.conditionFiji
ValueLessThanClassimglib.ops.conditionFiji
ValueResultA small structure to keep decimal places information with numbers along with a name or a simple named text.ClassresultsFiji
ValueToNoiseClassini.trakem2.imaging.filtersFiji
VariableElementRepresents a field, enum constant, method or constructor parameter, local variable, or exception parameter.Interfacejavax.lang.model.elementFiji
VariableTreeA tree node for a variable declaration.Interfacecom.sun.source.treeFiji
VarianceClassedfFiji
VectorClassmpicbg.imglib.cursor.vectorFiji
Vector1dClassmpicbg.imglib.cursor.vectorFiji
Vector2dClassmpicbg.imglib.cursor.vectorFiji
Vector3Classini.trakem2.utilsFiji
Vector3dClassmpicbg.imglib.cursor.vectorFiji
Vector4dClassmpicbg.imglib.cursor.vectorFiji
VectorDataAn interface to represent Displayable objects that are not images.Interfaceini.trakem2.displayFiji
VectorDataTransformClassini.trakem2.displayFiji
VectorStringInterfaceini.trakem2.vectorFiji
VectorString2DClassini.trakem2.vectorFiji
VectorString3DClassini.trakem2.vectorFiji
VersionA utility class to deal with version numbers.Classfiji.plugin.trackmate.utilFiji
VersionClassmpicbg.spim.dataFiji
VersionClassspimFiji
VersionCheckerCompares version strings.Classimagescience.utilityFiji
VertexA class to express a Vertex in a graph.Classini.trakem2.analysisFiji
VertexThis class represents a vertex or node in a graph.Classsc.fiji.analyzeSkeletonFiji
VIBClassvibFiji
VIB_ProtocolClassFiji
VideoStackClassvideoFiji
View5DClassview5dFiji
View5D_Classview5dFiji
ViewAdjusterClassij3dFiji
ViewChoiceDescriptorClassfiji.plugin.trackmate.gui.descriptorsFiji
ViewDataBeadsClassmpicbg.spim.registrationFiji
ViewDescriptionClassmpicbg.spim.data.sequenceFiji
Viewer3dFunctionsClassmpicbg.spim.vis3dFiji
ViewerFrameA JFrame containing a ViewerPanel and associated InputActionBindings.Classbdv.viewerFiji
ViewerImgLoaderInterfacebdvFiji
ViewerOptionsOptional parameters for ViewerPanel.Classbdv.viewerFiji
ViewerPanelA JPanel for viewing multiple of Sources.Classbdv.viewerFiji
ViewErrorPairWiseClassmpicbg.spim.registration.bead.errorFiji
ViewErrorStatisticsThis class handles View-specific error analysis.Classmpicbg.spim.registration.bead.errorFiji
ViewerSetupImgLoaderInterfacebdvFiji
ViewerStateDescription of everything required to render the current image, such as the current timepoint, the visible and current sources and groups respectively,Classbdv.viewer.stateFiji
ViewExplorerSetableInterfacespim.fiji.spimdata.explorer.popupFiji
ViewFactoryInterfacefiji.plugin.trackmate.visualizationFiji
ViewIdIdentifies a particular view as a combination of a TimePoint id and aAuthor:Tobias Pietzsch Classmpicbg.spim.data.sequenceFiji
ViewIdUtilsClassmpicbg.spim.data.sequenceFiji
ViewInterestPointListsMaps from a String label to a list of interest points for a specific viewidAuthor:Stephan Preibisch (stephan.Classspim.fiji.spimdata.interestpointsFiji
ViewInterestPointsA class that organizes all interest point detections of all ViewDescriptions (which extend ViewId)Author:Stephan Preibisch (stephan.Classspim.fiji.spimdata.interestpointsFiji
ViewLevelIdClassbdv.img.hdf5Fiji
ViewPlatformTransformerThis class is a helper class which implements some functions for transforming the view part of the scene graph.Classij3d.behaviorsFiji
ViewProviderClassfiji.plugin.trackmate.providersFiji
ViewRegistrationClassmpicbg.spim.data.registrationFiji
ViewRegistrationsOnly contains a Map from ViewId to ViewRegistrationAuthor:Tobias Pietzsch Classmpicbg.spim.data.registrationFiji
ViewRegistrationsUtilsClassmpicbg.spim.data.registrationFiji
ViewSetupA collection of parameters describing the setup for a particular stack coming from a SPIM microscope (angle, illumination direction, etc).Classmpicbg.spim.data.sequenceFiji
ViewSetupAttributeIoClassmpicbg.spim.data.generic.baseFiji
ViewSetupAttributesClassmpicbg.spim.data.generic.baseFiji
ViewSetupExplorerClassspim.fiji.spimdata.explorerFiji
ViewSetupExplorerInfoBoxClassspim.fiji.spimdata.explorerFiji
ViewSetupExplorerPanelClassspim.fiji.spimdata.explorerFiji
ViewSetupsHelper methods for dealing with ViewSetup collections.Classmpicbg.spim.data.sequenceFiji
ViewSetupTableModelClassspim.fiji.spimdata.explorerFiji
ViewSetupUtilsClassspim.fiji.spimdataFiji
ViewSetupWrapperA copy of a ViewSetup with another id.Classbdv.ij.exportFiji
ViewStructureThis class stores the links to all Views and initializes the View-dependent error statisticsAuthor:Stephan PreibischClassmpicbg.spim.registrationFiji
ViewTransformInterfacempicbg.spim.data.registrationFiji
ViewTransformAffineClassmpicbg.spim.data.registrationFiji
ViewTransformGenericInterfacempicbg.spim.data.registrationFiji
ViewUtilsA collection of static utilities related to TrackMateModelViews.Classfiji.plugin.trackmate.visualizationFiji
Virtual_Image5D_OpenerClassFiji
VirtualImagePlusExtension of ImagePlus that supports Bio-Formats-driven virtual stacks.Classloci.plugins.utilFiji
VirtualPointNodeClassmpicbg.pointdescriptor.testFiji
VirtualReaderClassloci.plugins.utilFiji
VirtualStackImageLoaderImageLoader backed by a ImagePlus.Classbdv.img.virtualstackFiji
VirtualStackVolatileARGBArrayLoaderClassbdv.img.virtualstackFiji
VirtualStackVolatileByteArrayLoaderClassbdv.img.virtualstackFiji
VirtualStackVolatileFloatArrayLoaderClassbdv.img.virtualstackFiji
VirtualStackVolatileShortArrayLoaderClassbdv.img.virtualstackFiji
VisibilityAndGroupingManage visibility and currentness of sources and groups, as well as grouping of sources, and display mode.Classbdv.viewerFiji
VisibilityAndGroupingDialogClassbdv.toolsFiji
Visual_GrepClassFiji
VisualizationFunctionsClassmpicbg.spim.vis3dFiji
VisualizationSketchTikZClassmpicbg.spim.vis3dFiji
Visualize_DetectionsClassspim.fiji.pluginFiji
VisualizeBeadsClassmpicbg.spim.vis3dFiji
VisualizeDetectionsPopupClassspim.fiji.spimdata.explorer.popupFiji
VJAlphaColorThis class is the abstract type for an alphacolor, i.ClassVolumeJFiji
VJBackprojectionVJBackprojection.ClassVolumeJFiji
VJBinaryShell For patenting and copyrighting reasons all Javadoc comments have been removed.ClassVolumeJFiji
VJCell For patenting and copyrighting reasons all Javadoc comments have been removed.ClassVolumeJFiji
VJClassifierThis class is the superclass for all classifiers.ClassVolumeJFiji
VJClassifierGradientCTThis class implements the Gradient classification function with indexing for CT scans optimized.ClassVolumeJFiji
VJClassifierIntegerThis class is the superclass for all VJ classifier that work on Integer voxel values.ClassVolumeJFiji
VJClassifierIsosurfaceThis class implements the classifier for colored isosurface rendering.ClassVolumeJFiji
VJClassifierIsosurfaceGrayscaleThis class implements the classifier for a grayscale isosurface renderer.ClassVolumeJFiji
VJClassifierLevoyThis class implements the Levoy tent classification function with indexing.ClassVolumeJFiji
VJClassifierLevoyCueingThis class implements the Levoy tent classification function with depth cueing and indexing.ClassVolumeJFiji
VJClassifierLinearThis class implements a linear ramp classification function with indexing.ClassVolumeJFiji
VJClassifierLNoIndexThis class implements the Levoy tent classification function without indexing.ClassVolumeJFiji
VJClassifierLNotIndex0This class implements the Levoy tent classification function with indexing.ClassVolumeJFiji
VJClassifierRGBThis class implements a classifier for RGB vector volumes.ClassVolumeJFiji
VJClassifiersThis class is a class whose only purpose is to contain all VJClassifier class definitions.ClassVolumeJFiji
VJClassifierValueThis class implements a classification function on the voxel value only.ClassVolumeJFiji
VJCutoutVJCutout.ClassVolumeJFiji
VJGradientThis is a class that defines the gradient of a voxel.ClassVolumeJFiji
VJInterpolatorThis class is the abstract class for all volume interpolators and defines the methods for each of these classes.ClassVolumeJFiji
VJIsosurfaceRender For patenting and copyrighting reasons all informative Javadoc comments have been removed.ClassVolumeJFiji
VJLightThis class implements a volume rendering light, and adds to methods to manipulate the light.ClassVolumeJFiji
VJMatrixThis class implements a transformation matrix and 3D transformation methods on it.ClassVolumeJFiji
VJNearestNeighborThis class is the standard interpolator and implements nearest neighbor interpolation and interpolation of gradients.ClassVolumeJFiji
VJOutlineShaderVJOutlineShader implements outline shading.ClassVolumeJFiji
VJPhongShaderVJShader implements shading in a Phong illumination model, for ambient and diffuse shading only.ClassVolumeJFiji
VJPlaneVJPlane.ClassVolumeJFiji
VJProjectionThis class is a set of projections of an object.ClassVolumeJFiji
VJReconstructorVJReconstructor reconstructs volumes in an ImageJ stack of any anisotropy along any axis.ClassVolumeJFiji
VJRenderVJRender class.ClassVolumeJFiji
VJRendererVJRenderer class implements the context and support methods for Volume Rendering.ClassVolumeJFiji
VJRenderViewVJRenderView class implements a shell for rendering one or more views of a volume with a given renderer and volume.ClassVolumeJFiji
VJRenderViewCineThis subclass of VJRenderView implements cine mode rendering.ClassVolumeJFiji
VJRenderViewInteractiveVJRenderViewInteractive implements a shell for interactively modifying the view (by rotating etc).ClassVolumeJFiji
VJRenderViewSingleVJRenderView class implements a shell for viewing the one or more rendering of a volume with a given renderer.ClassVolumeJFiji
VJRenderViewStereoVJRenderViewStereo is a subclass of VJRenderView that implements the shell for rendering two stereo views for viewing with a stereo viewer.ClassVolumeJFiji
VJrgbValueVJrgbValue.ClassVolumeJFiji
VJShadeVJShade.ClassVolumeJFiji
VJShaderVJShader is the default null shader.ClassVolumeJFiji
VJShapeClassVolumeJFiji
VJSplineInterpolatorThis class implements cubic spline interpolation and interpolation of gradients.ClassVolumeJFiji
VJSurfaceJThis class offers SurfaceJ, a surface plotting plugin based on VJ.ClassVolumeJFiji
VJSurfacePlotShellThis class implements utility for surface plotting.ClassVolumeJFiji
VJThresholdedVolumeThis class creates thresholded (binary) volumes of any type of Volume.ClassVolumeJFiji
VJTrilinearThis class implements trilinear voxel interpolation and voxel gradient interpolation.ClassVolumeJFiji
VJUserInterfaceThis class links the VJ classes to the ImageJ interface.ClassVolumeJFiji
VJValue Contains a voxel value intended to be rendered, which may be int, float or vector etc.ClassVolumeJFiji
VJValueHSBContains an RGB volume voxel value in HSB format.ClassVolumeJFiji
VJViewerCanvasThis class is an interactive rendering viewer.ClassVolumeJFiji
VJViewspaceRenderVJViewspaceRender class.ClassVolumeJFiji
VJViewspaceUtilVJViewspaceUtil implements viewspace utility methods, that can be used to relate a volume in a transformation matrix to the coordinates of that volume in viewspace.ClassVolumeJFiji
VJVoxelLocThis class defines a voxel location for interpolation and rendering.ClassVolumeJFiji
VJZBuffer Copyright (c) 2001-2002, Michael Abramoff.ClassVolumeJFiji
VoidConverterClassmpicbg.imglib.functionFiji
VolatileAccessA basic type access that can contain valid or invalid data.Interfacenet.imglib2.img.basictypeaccess.volatilesFiji
VolatileARGBTypeA Volatile variant of UnsignedShortType.Classnet.imglib2.type.volatilesFiji
VolatileByteAccessInterfacenet.imglib2.img.basictypeaccess.volatilesFiji
VolatileByteArrayA ByteArray with an AbstractVolatileArray.Classnet.imglib2.img.basictypeaccess.volatiles.arrayFiji
VolatileCellClassbdv.img.cacheFiji
VolatileFloatAccessInterfacenet.imglib2.img.basictypeaccess.volatilesFiji
VolatileFloatArrayA FloatArray with an AbstractVolatileArray.Classnet.imglib2.img.basictypeaccess.volatiles.arrayFiji
VolatileFloatTypeClassnet.imglib2.type.volatilesFiji
VolatileGlobalCellCacheClassbdv.img.cacheFiji
VolatileHierarchyProjectorVolatileProjector for a hierarchy of Volatile inputs.Classbdv.viewer.renderFiji
VolatileImgCellsClassbdv.img.cacheFiji
VolatileIntAccessInterfacenet.imglib2.img.basictypeaccess.volatilesFiji
VolatileIntArrayA IntArray with an AbstractVolatileArray.Classnet.imglib2.img.basictypeaccess.volatiles.arrayFiji
VolatileProjectorInterfacebdv.viewer.renderFiji
VolatileShortAccessInterfacenet.imglib2.img.basictypeaccess.volatilesFiji
VolatileShortArrayA ShortArray with an AbstractVolatileArray.Classnet.imglib2.img.basictypeaccess.volatiles.arrayFiji
VolatileSpimSourceClassbdvFiji
VolatileUnsignedByteTypeA Volatile variant of UnsignedByteType.Classnet.imglib2.type.volatilesFiji
VolatileUnsignedShortTypeA Volatile variant of UnsignedShortType.Classnet.imglib2.type.volatilesFiji
VoltexGroupThis class extends ContentNode to display a Content as a Volume Rendering.ClassvoltexFiji
VoltexVolumeThis class encapsulates an image stack and provides various methods for retrieving data.ClassvoltexFiji
VolumeClassfiji.plugin.volumeviewerFiji
VolumeThis class encapsulates an image stack and provides various methods for retrieving data.Classij3dFiji
VolumeThis is an abstract super-class to implement volumes.ClassvolumeFiji
Volume_CalculatorThis is the Volume_Calculator ImageJ/Fiji plugin.ClassvolumeCalculatorFiji
Volume_EditorClasstextureByRefFiji
Volume_Reconstructor_Volume Reconstructor is a plugin for ImageJ that reconstructs volumes.ClassFiji
Volume_ViewerClassfiji.plugin.volumeviewerFiji
VolumeFloatThis class implements float volumes and operations including convolutions on it.ClassvolumeFiji
VolumeIntegerThis class implements int volumes and operations including convolutions on it.ClassvolumeFiji
VolumeIOThis is a class that implements reading and writing on float volumes.ClassvolumeFiji
VolumeJ_This class interfaces the VolumeJ package to a ImageJ plugin.ClassFiji
VolumeOctreeClassoctreeFiji
VolumeRendererThis class is the main class for creating a volume rendering.ClassvoltexFiji
VolumeRGBThis class implements RGB vector volumes.ClassvolumeFiji
VolumesAn instance of Volumes is used to keep track of the volume values accumulated by the Volume_Calculator plugin.ClassvolumeCalculatorFiji
VolumeShortThis class implements short volumes and operations including convolutions on it.ClassvolumeFiji
VolumesPanelClassvolumeCalculatorFiji
VoxelDimensionsInterfacempicbg.spim.data.sequenceFiji
VTKResourceResource class for working with the Visualization Toolkit (VTK) in the current environment.Classimagescience.utilityFiji
WaitForNextFrameBehaviorClassij3d.behaviorsFiji
WalkingAverage_Performs a walking average on a stack.ClassFiji
WarnerAn interface to support optional warnings, needed for support of unchecked conversions and unchecked casts.Classcom.sun.tools.javac.utilFiji
WarningA class representing a warning, combining a short and a long message.ClassresultsFiji
WatershedWatershed algorithms.Classmpicbg.imglib.algorithm.labelingFiji
WatershedClassutilsFiji
Wave2ColorConverts wavelengths of light to corresponding RGBA color values.Classimagescience.colorFiji
WavefrontExporterClasscustomnodeFiji
WavefrontLoaderClasscustomnodeFiji
WaveSplineThis class make a Spline wavelets transformation and its inverse.ClasswaveletsFiji
WaveSplineFilterThis class generates the Spline wavelets filters.ClasswaveletsFiji
WeightedAverageFusionClassspim.process.fusion.weightedavgFiji
WeightNormalizerClassspim.process.fusion.deconvolutionFiji
WhileLoopTreeA tree node for a 'while' loop statement.Interfacecom.sun.source.treeFiji
Wiki_EditorClassfijiFiji
WildcardTreeA tree node for a wildcard type argument.Interfacecom.sun.source.treeFiji
WildcardTypeRepresents a wildcard type argument.Interfacejavax.lang.model.typeFiji
WindowHelpersClassutilFiji
WindowToolsUtility methods for managing ImageJ dialogs and windows.Classloci.plugins.utilFiji
WizardPanelDescriptorA base descriptor class used to reference a Component panel for the Wizard, as well as provide general rules as to how the panel should behave.Interfacefiji.plugin.trackmate.gui.descriptorsFiji
WorkerClassini.trakem2.utilsFiji
WrapBasicImgLoaderClassbdv.spimdataFiji
WrapLayoutFlowLayout subclass that fully supports wrapping of components.Classfiji.plugin.trackmate.gui.panelsFiji
WrappingJavaFileManagerWraps all calls to a given file manager.Classcom.sun.tools.javac.apiFiji
WritableVirtualStackThis class represents an array of disk-resident images.Classvideo2Fiji
WriteSequenceToHdf5Create a hdf5 files containing image data from all views and all timepoints in a chunked, mipmaped representation.Classbdv.exportFiji
WriteXMLClassFiji
XCErrorAdapterClassedu.utexas.clm.archipelago.utilFiji
XfmUtilsClass with helper methods for debugging and testing the this thin plate spline implementation.Classjitk.splineFiji
XMLFileFilterAccepts .Classini.trakem2.ioFiji
XMLFunctionsClassmpicbg.spim.ioFiji
XMLFunctionsClassutilFiji
XmlHelpersClassmpicbg.spim.dataFiji
XmlIoAbstractSequenceDescriptionClassmpicbg.spim.data.generic.sequenceFiji
XmlIoAbstractSpimDataClassmpicbg.spim.data.genericFiji
XmlIoAngleClassmpicbg.spim.data.sequenceFiji
XmlIoBasicImgLoaderInterfacempicbg.spim.data.generic.sequenceFiji
XmlIoBasicViewSetupClassmpicbg.spim.data.generic.sequenceFiji
XmlIoBasicViewSetupsWrites and reads collections of a specific BasicViewSetup subclass as an XML section.Classmpicbg.spim.data.generic.sequenceFiji
XmlIoBoundingBoxesClassspim.fiji.spimdata.boundingboxFiji
XmlIoCatmaidImageLoaderClassbdv.img.catmaidFiji
XmlIoChannelClassmpicbg.spim.data.sequenceFiji
XmlIoDHMImgLoaderClassspim.fiji.spimdata.imgloadersFiji
XmlIoEntityWrites and reads objects of a specific subclass of Entity as XML When reading/writing an object, XmlIoEntity takes care of theClassmpicbg.spim.data.generic.baseFiji
XmlIoEntityMapWrites and reads collections of a specific Entity subclass as an XML section.Classmpicbg.spim.data.generic.baseFiji
XmlIoHdf5ImageLoaderClassbdv.img.hdf5Fiji
XmlIoIlluminationClassmpicbg.spim.data.sequenceFiji
XmlIoLightSheetZ1ImgLoaderClassspim.fiji.spimdata.imgloadersFiji
XmlIoMicroManagerImgLoaderClassspim.fiji.spimdata.imgloadersFiji
XmlIoMissingViewsClassmpicbg.spim.data.sequenceFiji
XmlIoNamedEntityXmlIoEntity for NamedEntity that also handles <>Author:Tobias Pietzsch Classmpicbg.spim.data.generic.baseFiji
XmlIoOpenConnectomeImageLoaderClassbdv.img.openconnectomeFiji
XmlIoRemoteImageLoaderClassbdv.img.remoteFiji
XmlIoSequenceDescriptionClassmpicbg.spim.data.sequenceFiji
XmlIoSingletonWrites and reads objects of a specific class as XML elements.Classmpicbg.spim.data.generic.baseFiji
XmlIoSpimDataClassmpicbg.spim.dataFiji
XmlIoSpimData2Classspim.fiji.spimdataFiji
XmlIoSpimDataMinimalClassbdv.spimdataFiji
XmlIoSpimDataMinimalLegacyClassbdv.spimdata.legacyFiji
XmlIoStackImgLoaderClassspim.fiji.spimdata.imgloadersFiji
XmlIoStackImgLoaderIJClassspim.fiji.spimdata.imgloadersFiji
XmlIoStackImgLoaderLOCIClassspim.fiji.spimdata.imgloadersFiji
XmlIoTimePointsClassmpicbg.spim.data.sequenceFiji
XmlIoTransformedSourcesClassbdv.tools.transformationFiji
XmlIoViewerStateClassbdv.viewer.stateFiji
XmlIoViewInterestPointsClassspim.fiji.spimdata.interestpointsFiji
XmlIoViewRegistrationClassmpicbg.spim.data.registrationFiji
XmlIoViewRegistrationsClassmpicbg.spim.data.registrationFiji
XmlIoViewSetupsClassmpicbg.spim.data.sequenceFiji
XmlIoViewTransformClassmpicbg.spim.data.registrationFiji
XmlKeysDefinition of tag and attribute names.Classmpicbg.spim.dataFiji
XmlKeysBoundingBoxClassspim.fiji.spimdata.boundingboxFiji
XmlKeysInterestPointsClassspim.fiji.spimdata.interestpointsFiji
XMLOptionsClassini.trakem2.persistenceFiji
XMLReaderClassspimopenerFiji
XMLTIFFImgTitlerClassspim.process.fusion.exportFiji
XorClassimglib.ops.operator.binaryFiji
XorClassscript.imglib.mathFiji
XorConstantClassimglib.ops.operator.unaryFiji
XPM_WriterClassioFiji
XYEdgeRendererClassfiji.plugin.trackmate.utilFiji
XYEdgeSeriesClassfiji.plugin.trackmate.utilFiji
XYEdgeSeriesCollectionClassfiji.plugin.trackmate.utilFiji
XYTextSimpleAnnotationClassorg.jfree.chart.annotationsFiji
YesNoDialogA modal dialog box with a one line message and "Yes" and "No" buttons.Classini.trakem2.displayFiji
z_Image5D_testClassFiji
Z_ProjectClassFiji
ZDisplayableFor Pipes and other objects that must be shown in all Layers of a LayerSet.Classini.trakem2.displayFiji
ZeroCrosserDetects zero-crossings in images.Classimagescience.segmentFiji
ZipArchiveThis is NOT part of any supported API.Classcom.sun.tools.javac.fileFiji
ZipFileIndexThis class implements building of index of a zip archive and access to it's context.Classcom.sun.tools.javac.fileFiji
ZipFileIndexArchiveThis is NOT part of any supported API.Classcom.sun.tools.javac.fileFiji
ZipPackagerClassfiji.packagingFiji
ZLibAnalyzerClassfijiFiji
_3D_objects_counterClassFiji
_3D_OC_OptionsClassFiji