├── .gitignore ├── .gitlab-ci.yml ├── .kernel ├── CHANGELOG.md ├── CODE-OF-CONDUCT.md ├── CONTRIBUTING.md ├── LICENSE.md ├── README.md ├── ext ├── Contents │ ├── Info.plist │ ├── MacOS │ │ └── JavaApplicationStub │ ├── PkgInfo │ └── Resources │ │ └── icy.icns ├── colormap │ ├── ametrine.xml │ ├── isolum.xml │ ├── morgenstemning.xml │ └── parula.xml ├── icy ├── icy.exe └── version.xml ├── pom-updater.xml ├── pom.xml └── src └── main ├── java └── org │ └── bioimageanalysis │ ├── extension │ └── kernel │ │ ├── filtering │ │ ├── GaussianFiltering.java │ │ ├── LocalMaxFiltering.java │ │ ├── convolution │ │ │ ├── Axis.java │ │ │ ├── Convolution1D.java │ │ │ ├── ConvolutionException.java │ │ │ ├── GaussianKernel1D.java │ │ │ ├── IKernel.java │ │ │ └── IKernel1D.java │ │ └── selection │ │ │ ├── LocalMaxMethod.java │ │ │ ├── SelectionFilter.java │ │ │ └── ThreadedSelectionFilter.java │ │ └── roi │ │ ├── descriptor │ │ ├── intensity │ │ │ ├── ROIMaxIntensityDescriptor.java │ │ │ ├── ROIMeanIntensityDescriptor.java │ │ │ ├── ROIMinIntensityDescriptor.java │ │ │ ├── ROIStandardDeviationDescriptor.java │ │ │ └── ROISumIntensityDescriptor.java │ │ ├── logical │ │ │ ├── ROIContainedDescriptor.java │ │ │ └── ROIIntersectedDescriptor.java │ │ ├── measure │ │ │ ├── ROIAreaDescriptor.java │ │ │ ├── ROIContourDescriptor.java │ │ │ ├── ROIInteriorDescriptor.java │ │ │ ├── ROIMassCenterCDescriptor.java │ │ │ ├── ROIMassCenterTDescriptor.java │ │ │ ├── ROIMassCenterXDescriptor.java │ │ │ ├── ROIMassCenterYDescriptor.java │ │ │ ├── ROIMassCenterZDescriptor.java │ │ │ ├── ROIPerimeterDescriptor.java │ │ │ ├── ROISurfaceAreaDescriptor.java │ │ │ └── ROIVolumeDescriptor.java │ │ └── property │ │ │ ├── ROIColorDescriptor.java │ │ │ ├── ROIIconDescriptor.java │ │ │ ├── ROIIdDescriptor.java │ │ │ ├── ROINameDescriptor.java │ │ │ ├── ROIOpacityDescriptor.java │ │ │ ├── ROIPositionCDescriptor.java │ │ │ ├── ROIPositionTDescriptor.java │ │ │ ├── ROIPositionXDescriptor.java │ │ │ ├── ROIPositionYDescriptor.java │ │ │ ├── ROIPositionZDescriptor.java │ │ │ ├── ROIReadOnlyDescriptor.java │ │ │ ├── ROISizeCDescriptor.java │ │ │ ├── ROISizeTDescriptor.java │ │ │ ├── ROISizeXDescriptor.java │ │ │ ├── ROISizeYDescriptor.java │ │ │ └── ROISizeZDescriptor.java │ │ ├── morphology │ │ ├── ROIDilationCalculator.java │ │ ├── ROIDistanceTransformCalculator.java │ │ ├── ROIErosionCalculator.java │ │ └── skeletonization │ │ │ ├── MinimumSpanningTreeCalculator.java │ │ │ ├── ROISkeletonCalculator.java │ │ │ └── TopologicalDescriptor.java │ │ ├── roi2d │ │ ├── ROI2DArea.java │ │ ├── ROI2DEllipse.java │ │ ├── ROI2DLine.java │ │ ├── ROI2DPath.java │ │ ├── ROI2DPoint.java │ │ ├── ROI2DPolyLine.java │ │ ├── ROI2DPolygon.java │ │ ├── ROI2DRectShape.java │ │ ├── ROI2DRectangle.java │ │ └── ROI2DShape.java │ │ └── roi3d │ │ ├── ROI3DArea.java │ │ ├── ROI3DBox.java │ │ ├── ROI3DBoxShape.java │ │ ├── ROI3DCylinder.java │ │ ├── ROI3DFlatPolygon.java │ │ ├── ROI3DLine.java │ │ ├── ROI3DPoint.java │ │ ├── ROI3DPolyLine.java │ │ ├── ROI3DShape.java │ │ ├── ROI3DStack.java │ │ └── ROI3DZShape.java │ ├── icy │ ├── Icy.java │ ├── common │ │ ├── CPUMonitor.java │ │ ├── Version.java │ │ ├── collection │ │ │ ├── CollectionUtil.java │ │ │ ├── array │ │ │ │ ├── Array1DUtil.java │ │ │ │ ├── Array2DUtil.java │ │ │ │ ├── Array3DUtil.java │ │ │ │ ├── ArrayType.java │ │ │ │ ├── ArrayUtil.java │ │ │ │ ├── ByteArrayConvert.java │ │ │ │ └── DynamicArray.java │ │ │ └── list │ │ │ │ ├── RecentFileList.java │ │ │ │ ├── RecentList.java │ │ │ │ ├── RecentListEvent.java │ │ │ │ └── RecentListListener.java │ │ ├── color │ │ │ └── ColorUtil.java │ │ ├── datetime │ │ │ ├── Chronometer.java │ │ │ └── DateUtil.java │ │ ├── event │ │ │ ├── CollapsibleEvent.java │ │ │ └── UpdateEventHandler.java │ │ ├── exception │ │ │ ├── TooLargeArrayException.java │ │ │ └── UnsupportedFormatException.java │ │ ├── geom │ │ │ ├── GeomUtil.java │ │ │ ├── areax │ │ │ │ ├── AreaOpX.java │ │ │ │ ├── AreaX.java │ │ │ │ ├── AreaXBody.java │ │ │ │ ├── AreaXOperation.java │ │ │ │ ├── AreaXRules.java │ │ │ │ ├── BoundsRules.java │ │ │ │ ├── ChainEndX.java │ │ │ │ ├── CrossingsX.java │ │ │ │ ├── CurveLinkX.java │ │ │ │ ├── CurveList.java │ │ │ │ ├── CurveX.java │ │ │ │ ├── EdgeX.java │ │ │ │ ├── EmptyPathException.java │ │ │ │ ├── Intersections.java │ │ │ │ ├── Order0X.java │ │ │ │ ├── Order1X.java │ │ │ │ ├── Order2X.java │ │ │ │ ├── Order3X.java │ │ │ │ ├── RawChainArrayList.java │ │ │ │ ├── RawCurveArrayList.java │ │ │ │ ├── RawEdgeArrayList.java │ │ │ │ ├── RawLinkArrayList.java │ │ │ │ ├── RawSortedEdgeArrayList.java │ │ │ │ └── ShapeBounds.java │ │ │ ├── cylinder │ │ │ │ └── Cylinder3D.java │ │ │ ├── dimension │ │ │ │ ├── Dimension2D.java │ │ │ │ ├── Dimension3D.java │ │ │ │ ├── Dimension4D.java │ │ │ │ └── Dimension5D.java │ │ │ ├── line │ │ │ │ ├── Line2DIterator.java │ │ │ │ ├── Line3D.java │ │ │ │ └── Line3DIterator.java │ │ │ ├── point │ │ │ │ ├── Point2DUtil.java │ │ │ │ ├── Point3D.java │ │ │ │ ├── Point4D.java │ │ │ │ └── Point5D.java │ │ │ ├── poly │ │ │ │ ├── FlatPolygon3D.java │ │ │ │ ├── Polygon2D.java │ │ │ │ ├── Polyline2D.java │ │ │ │ └── Polyline3D.java │ │ │ ├── position │ │ │ │ ├── Position2DIterator.java │ │ │ │ └── Position5DIterator.java │ │ │ ├── rectangle │ │ │ │ ├── Rectangle2DUtil.java │ │ │ │ ├── Rectangle3D.java │ │ │ │ ├── Rectangle4D.java │ │ │ │ └── Rectangle5D.java │ │ │ └── shape │ │ │ │ ├── BoxShape3D.java │ │ │ │ ├── Shape3D.java │ │ │ │ ├── ShapeUtil.java │ │ │ │ └── ZShape3D.java │ │ ├── listener │ │ │ ├── AcceptListener.java │ │ │ ├── ChangeListener.java │ │ │ ├── NotifyListener.java │ │ │ ├── ProgressListener.java │ │ │ └── weak │ │ │ │ └── WeakListener.java │ │ ├── math │ │ │ ├── ArrayMath.java │ │ │ ├── DataIteratorMath.java │ │ │ ├── FPSMeter.java │ │ │ ├── Histogram.java │ │ │ ├── HungarianAlgorithm.java │ │ │ ├── Interpolator.java │ │ │ ├── MathUtil.java │ │ │ ├── MultiSmoothMover.java │ │ │ ├── Random.java │ │ │ ├── RateMeter.java │ │ │ ├── Scaler.java │ │ │ ├── ScalerEvent.java │ │ │ ├── ScalerListener.java │ │ │ ├── SmoothMover.java │ │ │ └── UnitUtil.java │ │ ├── reflect │ │ │ ├── ClassUtil.java │ │ │ └── ReflectionUtil.java │ │ ├── string │ │ │ └── StringUtil.java │ │ └── type │ │ │ ├── DataIterator.java │ │ │ ├── DataIteratorUtil.java │ │ │ ├── DataType.java │ │ │ ├── TypeUtil.java │ │ │ └── value │ │ │ ├── AbstractValue.java │ │ │ ├── BooleanValue.java │ │ │ ├── ByteValue.java │ │ │ ├── DoubleValue.java │ │ │ ├── FloatValue.java │ │ │ ├── IntegerValue.java │ │ │ ├── LongValue.java │ │ │ └── ShortValue.java │ ├── extension │ │ ├── ExtensionConfig.java │ │ ├── ExtensionDescriptor.java │ │ ├── ExtensionInstaller.java │ │ ├── ExtensionLoader.java │ │ ├── abstract_ │ │ │ └── Extension.java │ │ └── plugin │ │ │ ├── PluginDescriptor.java │ │ │ ├── PluginInstaller.java │ │ │ ├── PluginLauncher.java │ │ │ ├── PluginLoader.java │ │ │ ├── PluginRepositoryLoader.java │ │ │ ├── PluginUpdater.java │ │ │ ├── abstract_ │ │ │ ├── Plugin.java │ │ │ ├── PluginActionable.java │ │ │ ├── PluginConfiguration.java │ │ │ ├── PluginFileImporter.java │ │ │ ├── PluginImporter.java │ │ │ ├── PluginSequenceExporter.java │ │ │ ├── PluginSequenceFileExporter.java │ │ │ ├── PluginSequenceFileImporter.java │ │ │ ├── PluginSequenceIdImporter.java │ │ │ └── PluginSequenceImporter.java │ │ │ ├── annotation_ │ │ │ ├── IcyPluginDescription.java │ │ │ ├── IcyPluginIcon.java │ │ │ ├── IcyPluginName.java │ │ │ ├── IcyROIPlugin.java │ │ │ ├── ROIPoints.java │ │ │ └── ROIType.java │ │ │ ├── classloader │ │ │ ├── AbstractClassLoader.java │ │ │ ├── ClasspathResources.java │ │ │ ├── Configuration.java │ │ │ ├── JarClassLoader.java │ │ │ ├── JarResources.java │ │ │ ├── ProxyClassLoader.java │ │ │ ├── ResourceType.java │ │ │ └── exception │ │ │ │ ├── JclException.java │ │ │ │ └── ResourceNotFoundException.java │ │ │ ├── interface_ │ │ │ ├── PluginBundled.java │ │ │ ├── PluginCanvas.java │ │ │ ├── PluginDaemon.java │ │ │ ├── PluginLibrary.java │ │ │ ├── PluginNoEDTConstructor.java │ │ │ ├── PluginROI.java │ │ │ ├── PluginROIDescriptor.java │ │ │ ├── PluginScriptFactory.java │ │ │ ├── PluginSearchProvider.java │ │ │ ├── PluginThreaded.java │ │ │ └── PluginUndoable.java │ │ │ └── property │ │ │ ├── BooleanProperty.java │ │ │ ├── ColorProperty.java │ │ │ ├── ColorSelectionProperty.java │ │ │ ├── DoubleProperty.java │ │ │ ├── FileProperty.java │ │ │ ├── FloatProperty.java │ │ │ ├── IntegerProperty.java │ │ │ ├── LongProperty.java │ │ │ ├── MultipleNumberSelectionProperty.java │ │ │ ├── MultipleSelectionProperty.java │ │ │ ├── MultipleStringSelectionProperty.java │ │ │ ├── NumberProperty.java │ │ │ ├── NumberSelectionProperty.java │ │ │ ├── Property.java │ │ │ ├── SelectionProperty.java │ │ │ ├── StringProperty.java │ │ │ ├── StringSelectionProperty.java │ │ │ └── gui │ │ │ ├── PropertyCheckBox.java │ │ │ ├── PropertyColorChooser.java │ │ │ ├── PropertyComboBox.java │ │ │ ├── PropertyComponent.java │ │ │ ├── PropertyNumberSpinner.java │ │ │ ├── PropertyPanel.java │ │ │ └── PropertyTextField.java │ ├── gui │ │ ├── CustomPopupFactory.java │ │ ├── EventUtil.java │ │ ├── FontUtil.java │ │ ├── GraphicsUtil.java │ │ ├── GuiUtil.java │ │ ├── LookAndFeelUtil.java │ │ ├── SwingUtil.java │ │ ├── WindowPositionSaver.java │ │ ├── action │ │ │ ├── ActionManager.java │ │ │ ├── CanvasActions.java │ │ │ ├── FileActions.java │ │ │ ├── GeneralActions.java │ │ │ ├── IcyAbstractAction.java │ │ │ ├── PreferencesActions.java │ │ │ ├── RoiActions.java │ │ │ ├── SequenceOperationActions.java │ │ │ ├── ViewerActions.java │ │ │ └── WindowActions.java │ │ ├── canvas │ │ │ ├── Canvas2D.java │ │ │ ├── Canvas2DSettingPanel.java │ │ │ ├── CanvasLayerEvent.java │ │ │ ├── CanvasLayerListener.java │ │ │ ├── IcyCanvas.java │ │ │ ├── IcyCanvas2D.java │ │ │ ├── IcyCanvas3D.java │ │ │ ├── IcyCanvasEvent.java │ │ │ ├── IcyCanvasListener.java │ │ │ ├── Layer.java │ │ │ └── VtkCanvas.java │ │ ├── clipboard │ │ │ ├── Clipboard.java │ │ │ ├── TransferableImage.java │ │ │ └── TransferableNull.java │ │ ├── component │ │ │ ├── ComponentUtil.java │ │ │ ├── WeakComponentListener.java │ │ │ ├── button │ │ │ │ ├── ColorChooserButton.java │ │ │ │ ├── IcyButton.java │ │ │ │ ├── IcyRadioButton.java │ │ │ │ ├── IcyToggleButton.java │ │ │ │ └── ThumbnailComponent.java │ │ │ ├── combo │ │ │ │ └── SwimmingObjectChooser.java │ │ │ ├── editor │ │ │ │ ├── SliderCellEditor.java │ │ │ │ ├── SpecialValueSpinnerEditor.java │ │ │ │ └── VisibleCellEditor.java │ │ │ ├── field │ │ │ │ ├── IcyTextField.java │ │ │ │ ├── IcyTextFieldHint.java │ │ │ │ └── NumberTextField.java │ │ │ ├── icon │ │ │ │ ├── ColorIcon.java │ │ │ │ ├── IcyIconPack.java │ │ │ │ ├── IcySVG.java │ │ │ │ ├── IcySVGIcon.java │ │ │ │ ├── IcySVGImage.java │ │ │ │ └── SVGResource.java │ │ │ ├── menu │ │ │ │ ├── IcyCheckBoxMenuItem.java │ │ │ │ ├── IcyMenu.java │ │ │ │ ├── IcyMenuItem.java │ │ │ │ ├── IcyPluginMenuItem.java │ │ │ │ ├── IcyROIMenuItem.java │ │ │ │ └── IcyRadioButtonMenuItem.java │ │ │ ├── model │ │ │ │ ├── SpecialValueSpinnerModel.java │ │ │ │ └── XMLTreeModel.java │ │ │ ├── panel │ │ │ │ ├── AbstractRoisPanel.java │ │ │ │ ├── BorderedPanel.java │ │ │ │ ├── ColorComponent.java │ │ │ │ ├── ExtTabbedPanel.java │ │ │ │ ├── ExternalizablePanel.java │ │ │ │ ├── HistogramPanel.java │ │ │ │ ├── ImageComponent.java │ │ │ │ ├── PopupPanel.java │ │ │ │ ├── RangeComponent.java │ │ │ │ └── Region2DComponent.java │ │ │ ├── renderer │ │ │ │ ├── ColormapComboBoxRenderer.java │ │ │ │ ├── CustomComboBoxRenderer.java │ │ │ │ ├── ImageTableCellRenderer.java │ │ │ │ ├── LabelComboBoxRenderer.java │ │ │ │ ├── NativeArrayTableCellRenderer.java │ │ │ │ ├── SliderCellRenderer.java │ │ │ │ └── VisibleCellRenderer.java │ │ │ ├── scrollpane │ │ │ │ └── ExcelTable.java │ │ │ ├── slider │ │ │ │ ├── IcySlider.java │ │ │ │ ├── RangeSlider.java │ │ │ │ └── RangeSliderUI.java │ │ │ ├── spinner │ │ │ │ └── SpecialValueSpinner.java │ │ │ ├── tabbedpane │ │ │ │ ├── CheckTabbedPane.java │ │ │ │ └── CloseableTabbedPane.java │ │ │ └── table │ │ │ │ └── IcyTable.java │ │ ├── dialog │ │ │ ├── ActionDialog.java │ │ │ ├── ConfirmDialog.java │ │ │ ├── ExtensionInstallerDialog.java │ │ │ ├── IdConfirmDialog.java │ │ │ ├── ImporterSelectionDialog.java │ │ │ ├── LoaderDialog.java │ │ │ ├── LoaderOptionPanel.java │ │ │ ├── MessageDialog.java │ │ │ ├── OpenDialog.java │ │ │ ├── SaveDialog.java │ │ │ ├── SaverDialog.java │ │ │ ├── SaverOptionPanel.java │ │ │ └── SeriesSelectionDialog.java │ │ ├── frame │ │ │ ├── AboutFrame.java │ │ │ ├── ActionFrame.java │ │ │ ├── CatalogFrame.java │ │ │ ├── ConfirmFrame.java │ │ │ ├── ExitFrame.java │ │ │ ├── GenericFrame.java │ │ │ ├── IcyExternalFrame.java │ │ │ ├── IcyFrame.java │ │ │ ├── IcyFrameAdapter.java │ │ │ ├── IcyFrameEvent.java │ │ │ ├── IcyFrameListener.java │ │ │ ├── IcyInternalFrame.java │ │ │ ├── NewVersionFrame.java │ │ │ ├── SplashScreenFrame.java │ │ │ ├── TitledFrame.java │ │ │ ├── error │ │ │ │ ├── ErrorReportFrame.java │ │ │ │ └── ErrorReportPanel.java │ │ │ ├── progress │ │ │ │ ├── AnnounceFrame.java │ │ │ │ ├── CancelableProgressFrame.java │ │ │ │ ├── DownloadFrame.java │ │ │ │ ├── FailedAnnounceFrame.java │ │ │ │ ├── FileFrame.java │ │ │ │ ├── ProgressFrame.java │ │ │ │ ├── SuccessfullAnnounceFrame.java │ │ │ │ ├── TaskFrame.java │ │ │ │ ├── ToolTipFrame.java │ │ │ │ └── WarningAnnounceFrame.java │ │ │ └── sequence │ │ │ │ ├── ActiveSequenceActionFrame.java │ │ │ │ └── SequenceActionFrame.java │ │ ├── listener │ │ │ ├── ActiveSequenceListener.java │ │ │ ├── ActiveViewerListener.java │ │ │ ├── GlobalOverlayListener.java │ │ │ ├── GlobalPluginListener.java │ │ │ ├── GlobalROIListener.java │ │ │ ├── GlobalSequenceListener.java │ │ │ ├── GlobalViewerListener.java │ │ │ ├── ROIToolChangeListener.java │ │ │ ├── SkinChangeListener.java │ │ │ ├── WeakActiveSequenceListener.java │ │ │ ├── WeakActiveViewerListener.java │ │ │ ├── WeakIcyFrameListener.java │ │ │ ├── WeakSkinChangeListener.java │ │ │ ├── WeakWindowFocusListener.java │ │ │ └── WeakWindowListener.java │ │ ├── lut │ │ │ ├── ColormapIcon.java │ │ │ ├── ColormapPanel.java │ │ │ ├── ColormapViewer.java │ │ │ ├── LUTChannelViewer.java │ │ │ ├── LUTViewer.java │ │ │ ├── ScalerBoundsSettingDialog.java │ │ │ ├── ScalerPanel.java │ │ │ └── ScalerViewer.java │ │ ├── main │ │ │ ├── IcyDesktopPane.java │ │ │ ├── MainFrame.java │ │ │ ├── MainInterface.java │ │ │ ├── MainInterfaceBatch.java │ │ │ ├── MainInterfaceGui.java │ │ │ └── TaskFrameManager.java │ │ ├── menu │ │ │ ├── AbstractApplicationMenu.java │ │ │ ├── ApplicationMenuBar.java │ │ │ ├── ApplicationMenuFile.java │ │ │ ├── ApplicationMenuHelp.java │ │ │ ├── ApplicationMenuPlugins.java │ │ │ ├── ApplicationMenuROI.java │ │ │ ├── ApplicationMenuSequence.java │ │ │ ├── ApplicationMenuView.java │ │ │ ├── MenuCallback.java │ │ │ └── search │ │ │ │ ├── SearchBar.java │ │ │ │ ├── SearchProducerTableCellRenderer.java │ │ │ │ ├── SearchResultPanel.java │ │ │ │ ├── SearchResultTableCellRenderer.java │ │ │ │ └── SearchResultTableModel.java │ │ ├── plugin │ │ │ ├── PluginComboBoxRenderer.java │ │ │ ├── PluginDetailPanel.java │ │ │ ├── PluginErrorReport.java │ │ │ └── PluginUpdateFrame.java │ │ ├── preferences │ │ │ ├── EditRepositoryDialog.java │ │ │ ├── ExtensionListPreferencePanel.java │ │ │ ├── ExtensionLocalPreferencePanel.java │ │ │ ├── GUICanvasPreferencePanel.java │ │ │ ├── GeneralPreferencePanel.java │ │ │ ├── MagicWandPreferencePanel.java │ │ │ ├── NetworkPreferencePanel.java │ │ │ ├── PluginListPreferencePanel.java │ │ │ ├── PluginLocalPreferencePanel.java │ │ │ ├── PluginOnlinePreferencePanel.java │ │ │ ├── PluginPreferencePanel.java │ │ │ ├── PluginStartupPreferencePanel.java │ │ │ ├── PreferenceFrame.java │ │ │ ├── PreferencePanel.java │ │ │ └── RepositoryPreferencePanel.java │ │ ├── render │ │ │ ├── IcyVtkPanel.java │ │ │ ├── VtkJoglPanel.java │ │ │ └── VtkSettingPanel.java │ │ ├── roi │ │ │ ├── RoiControlPanel.java │ │ │ ├── RoiSettingFrame.java │ │ │ └── RoiSettingPanel.java │ │ ├── sequence │ │ │ ├── SequenceChooser.java │ │ │ ├── SequenceChooserPanel.java │ │ │ ├── SequenceChooserPreviewPanel.java │ │ │ ├── SequenceInfosPanel.java │ │ │ ├── SequenceMetadataPanel.java │ │ │ ├── SequencePreviewPanel.java │ │ │ ├── SequencePropertiesDialog.java │ │ │ ├── SequencePropertiesPanel.java │ │ │ └── tools │ │ │ │ ├── PositionAlignmentPanel.java │ │ │ │ ├── SequenceBaseResizePanel.java │ │ │ │ ├── SequenceCanvasResizeFrame.java │ │ │ │ ├── SequenceCanvasResizePanel.java │ │ │ │ ├── SequenceDimensionAdjustFrame.java │ │ │ │ ├── SequenceDimensionAdjustPanel.java │ │ │ │ ├── SequenceDimensionConvertFrame.java │ │ │ │ ├── SequenceDimensionConvertPanel.java │ │ │ │ ├── SequenceDimensionExtendFrame.java │ │ │ │ ├── SequenceDimensionExtendPanel.java │ │ │ │ ├── SequenceDimensionMergeFrame.java │ │ │ │ ├── SequenceDimensionMergePanel.java │ │ │ │ ├── SequenceResizeFrame.java │ │ │ │ └── SequenceResizePanel.java │ │ ├── swimmingpool │ │ │ ├── SwimmingPoolViewer.java │ │ │ └── SwimmingPoolViewerPanel.java │ │ ├── toolbar │ │ │ ├── IcyToolbar.java │ │ │ ├── InspectorBar.java │ │ │ ├── ROIBar.java │ │ │ ├── StatusBar.java │ │ │ ├── TaskProgress.java │ │ │ ├── button │ │ │ │ ├── ConsoleButton.java │ │ │ │ ├── EHCacheButton.java │ │ │ │ ├── HistoryButton.java │ │ │ │ ├── LayersButton.java │ │ │ │ ├── MemoryMonitorButton.java │ │ │ │ ├── NotificationButton.java │ │ │ │ ├── ROIDrawButton.java │ │ │ │ ├── ROIPanelButton.java │ │ │ │ └── SequenceButton.java │ │ │ ├── container │ │ │ │ ├── InspectorPanel.java │ │ │ │ ├── StatusPanel.java │ │ │ │ └── ToolbarContainer.java │ │ │ └── panel │ │ │ │ ├── LayerControlPanel.java │ │ │ │ ├── LayersPanel.java │ │ │ │ ├── OutputConsolePanel.java │ │ │ │ ├── RoisPanel.java │ │ │ │ ├── SequencePanel.java │ │ │ │ ├── ToolbarPanel.java │ │ │ │ └── UndoManagerPanel.java │ │ ├── undo │ │ │ ├── AbstractIcyUndoableEdit.java │ │ │ ├── IcyUndoManager.java │ │ │ ├── IcyUndoManagerListener.java │ │ │ ├── IcyUndoableEdit.java │ │ │ ├── IcyUndoableEditEvent.java │ │ │ └── IcyUndoableEditListener.java │ │ └── viewer │ │ │ ├── MouseImageInfosPanel.java │ │ │ ├── TNavigationPanel.java │ │ │ ├── Viewer.java │ │ │ ├── ViewerAdapter.java │ │ │ ├── ViewerEvent.java │ │ │ ├── ViewerListener.java │ │ │ ├── WeakViewerListener.java │ │ │ └── ZNavigationPanel.java │ ├── io │ │ ├── FileImporter.java │ │ ├── FileUtil.java │ │ ├── ImageFileFormat.java │ │ ├── Importer.java │ │ ├── Loader.java │ │ ├── ResourceUtil.java │ │ ├── Saver.java │ │ ├── SequenceFileExporter.java │ │ ├── SequenceFileGroupImporter.java │ │ ├── SequenceFileImporter.java │ │ ├── SequenceFileSticher.java │ │ ├── jar │ │ │ └── JarUtil.java │ │ ├── xls │ │ │ └── XLSXUtil.java │ │ ├── xml │ │ │ ├── XMLPersistent.java │ │ │ ├── XMLPersistentHelper.java │ │ │ └── XMLUtil.java │ │ ├── yaml │ │ │ ├── YAMLFile.java │ │ │ ├── YAMLPersistent.java │ │ │ └── YAMLUtil.java │ │ └── zip │ │ │ └── ZipUtil.java │ ├── model │ │ ├── OMEUtil.java │ │ ├── cache │ │ │ ├── AbstractCache.java │ │ │ ├── CacheException.java │ │ │ ├── EHCache3.java │ │ │ └── ImageCache.java │ │ ├── colormap │ │ │ ├── FireColorMap.java │ │ │ ├── FromRGBColorMap.java │ │ │ ├── GlowColorMap.java │ │ │ ├── HSVColorMap.java │ │ │ ├── IceColorMap.java │ │ │ ├── IcyColorMap.java │ │ │ ├── IcyColorMapComponent.java │ │ │ ├── IcyColorMapEvent.java │ │ │ ├── IcyColorMapListener.java │ │ │ ├── JETColorMap.java │ │ │ └── LinearColorMap.java │ │ ├── colormodel │ │ │ ├── ByteColorModel.java │ │ │ ├── DoubleColorModel.java │ │ │ ├── FloatColorModel.java │ │ │ ├── IcyColorModel.java │ │ │ ├── IcyColorModelEvent.java │ │ │ ├── IcyColorModelListener.java │ │ │ ├── IntColorModel.java │ │ │ ├── LongColorModel.java │ │ │ ├── ShortColorModel.java │ │ │ ├── UByteColorModel.java │ │ │ ├── UIntColorModel.java │ │ │ ├── ULongColorModel.java │ │ │ └── UShortColorModel.java │ │ ├── colorspace │ │ │ ├── IcyColorSpace.java │ │ │ ├── IcyColorSpaceEvent.java │ │ │ └── IcyColorSpaceListener.java │ │ ├── image │ │ │ ├── ARGBImageBuilder.java │ │ │ ├── AbstractImageProvider.java │ │ │ ├── ChannelPosition.java │ │ │ ├── IcyBufferedImage.java │ │ │ ├── IcyBufferedImageCursor.java │ │ │ ├── IcyBufferedImageEvent.java │ │ │ ├── IcyBufferedImageListener.java │ │ │ ├── IcyBufferedImageUtil.java │ │ │ ├── ImageDataIterator.java │ │ │ ├── ImagePosition.java │ │ │ ├── ImageProvider.java │ │ │ ├── ImageUtil.java │ │ │ ├── IntensityInfo.java │ │ │ └── PixelPosition.java │ │ ├── lut │ │ │ ├── LUT.java │ │ │ ├── LUTEvent.java │ │ │ └── LUTListener.java │ │ ├── overlay │ │ │ ├── ImageOverlay.java │ │ │ ├── Overlay.java │ │ │ ├── OverlayEvent.java │ │ │ ├── OverlayListener.java │ │ │ ├── VtkPainter.java │ │ │ ├── WeakOverlayListener.java │ │ │ └── anchor │ │ │ │ ├── Anchor2D.java │ │ │ │ ├── Anchor3D.java │ │ │ │ ├── LineAnchor2D.java │ │ │ │ ├── LineAnchor3D.java │ │ │ │ ├── PathAnchor2D.java │ │ │ │ ├── RectAnchor2D.java │ │ │ │ ├── RectAnchor3D.java │ │ │ │ └── ZBoxAnchor3D.java │ │ ├── render │ │ │ ├── opengl │ │ │ │ └── OpenGLUtil.java │ │ │ └── vtk │ │ │ │ ├── VtkArrowObject.java │ │ │ │ ├── VtkBinaryVolume.java │ │ │ │ ├── VtkCPUVolumeMapper.java │ │ │ │ ├── VtkCylinderObject.java │ │ │ │ ├── VtkImageVolume.java │ │ │ │ ├── VtkPlaneObject.java │ │ │ │ └── VtkUtil.java │ │ ├── roi │ │ │ ├── ROI.java │ │ │ ├── ROI2D.java │ │ │ ├── ROI3D.java │ │ │ ├── ROIDescriptor.java │ │ │ ├── ROIEvent.java │ │ │ ├── ROIIterator.java │ │ │ ├── ROIListener.java │ │ │ ├── ROIUtil.java │ │ │ ├── descriptor │ │ │ │ └── IntensityDescriptorInfos.java │ │ │ ├── edit │ │ │ │ ├── AbstractPoint2DROIEdit.java │ │ │ │ ├── AbstractPoint3DROIEdit.java │ │ │ │ ├── AbstractROIEdit.java │ │ │ │ ├── AbstractROIsEdit.java │ │ │ │ ├── Area2DChangeROIEdit.java │ │ │ │ ├── BoundsROIEdit.java │ │ │ │ ├── BoundsROIsEdit.java │ │ │ │ ├── DefaultROIEdit.java │ │ │ │ ├── Point2DAddedROIEdit.java │ │ │ │ ├── Point2DMovedROIEdit.java │ │ │ │ ├── Point2DRemovedROIEdit.java │ │ │ │ ├── Point3DAddedROIEdit.java │ │ │ │ ├── Point3DMovedROIEdit.java │ │ │ │ ├── Point3DRemovedROIEdit.java │ │ │ │ ├── PositionROIEdit.java │ │ │ │ ├── PositionROIsEdit.java │ │ │ │ ├── PropertyROIEdit.java │ │ │ │ └── PropertyROIsEdit.java │ │ │ ├── mask │ │ │ │ ├── BooleanMask2D.java │ │ │ │ ├── BooleanMask2DIterator.java │ │ │ │ ├── BooleanMask3D.java │ │ │ │ ├── BooleanMask4D.java │ │ │ │ └── BooleanMask5D.java │ │ │ ├── tool │ │ │ │ ├── MagicWand.java │ │ │ │ ├── ROILineCutter.java │ │ │ │ └── ROIMagicWand.java │ │ │ └── watershed │ │ │ │ ├── FloodingStructure.java │ │ │ │ ├── LabeledPixel.java │ │ │ │ ├── Point3D.java │ │ │ │ └── ROIWatershedCalculator.java │ │ ├── sequence │ │ │ ├── AbstractSequenceModel.java │ │ │ ├── DimensionId.java │ │ │ ├── MetaDataUtil.java │ │ │ ├── Sequence.java │ │ │ ├── SequenceAdapter.java │ │ │ ├── SequenceBuilder.java │ │ │ ├── SequenceCacheManager.java │ │ │ ├── SequenceCursor.java │ │ │ ├── SequenceDataIterator.java │ │ │ ├── SequenceEvent.java │ │ │ ├── SequenceExporter.java │ │ │ ├── SequenceIdImporter.java │ │ │ ├── SequenceImporter.java │ │ │ ├── SequenceListener.java │ │ │ ├── SequenceModel.java │ │ │ ├── SequencePersistent.java │ │ │ ├── SequencePrefetcher.java │ │ │ ├── SequenceUtil.java │ │ │ ├── VolumetricImage.java │ │ │ ├── VolumetricImageCursor.java │ │ │ ├── WeakSequenceListener.java │ │ │ └── edit │ │ │ │ ├── AbstractROISequenceEdit.java │ │ │ │ ├── AbstractROIsSequenceEdit.java │ │ │ │ ├── AbstractSequenceEdit.java │ │ │ │ ├── DataSequenceEdit.java │ │ │ │ ├── DefaultSequenceEdit.java │ │ │ │ ├── MetadataSequenceEdit.java │ │ │ │ ├── ROIAddSequenceEdit.java │ │ │ │ ├── ROIAddsSequenceEdit.java │ │ │ │ ├── ROIRemoveSequenceEdit.java │ │ │ │ ├── ROIRemovesSequenceEdit.java │ │ │ │ ├── ROIReplaceSequenceEdit.java │ │ │ │ └── ROIReplacesSequenceEdit.java │ │ └── swimmingPool │ │ │ ├── SwimmingObject.java │ │ │ ├── SwimmingPool.java │ │ │ ├── SwimmingPoolEvent.java │ │ │ ├── SwimmingPoolEventType.java │ │ │ ├── SwimmingPoolListener.java │ │ │ ├── SwimmingPoolObjectPanel.java │ │ │ └── WeakSwimmingPoolListener.java │ ├── network │ │ ├── NetworkUtil.java │ │ ├── URLUtil.java │ │ ├── WebInterface.java │ │ ├── auth │ │ │ └── AuthenticationInfo.java │ │ ├── search │ │ │ ├── OnlineSearchResultProducer.java │ │ │ ├── SearchEngine.java │ │ │ ├── SearchResult.java │ │ │ ├── SearchResultConsumer.java │ │ │ └── SearchResultProducer.java │ │ └── update │ │ │ ├── ElementDescriptor.java │ │ │ ├── IcyUpdater.java │ │ │ └── Updater.java │ └── system │ │ ├── FileDrop.java │ │ ├── IcyExceptionHandler.java │ │ ├── IcyHandledException.java │ │ ├── MMJUtil.java │ │ ├── SingleInstanceCheck.java │ │ ├── SystemUtil.java │ │ ├── UserUtil.java │ │ ├── audit │ │ ├── Audit.java │ │ └── AuditStorage.java │ │ ├── logging │ │ └── IcyLogger.java │ │ ├── os │ │ └── AppleUtil.java │ │ ├── preferences │ │ ├── ApplicationPreferences.java │ │ ├── CanvasPreferences.java │ │ ├── GeneralPreferences.java │ │ ├── IcyPreferences.java │ │ ├── MagicWandPreferences.java │ │ ├── NetworkPreferences.java │ │ ├── PluginLocalPreferences.java │ │ ├── PluginOnlinePreferences.java │ │ ├── PluginPreferences.java │ │ ├── PluginsPreferences.java │ │ ├── RepositoryPreferences.java │ │ └── XMLPreferences.java │ │ └── thread │ │ ├── InstanceProcessor.java │ │ ├── Processor.java │ │ ├── SingleProcessor.java │ │ └── ThreadUtil.java │ └── updater │ ├── Main.java │ └── UpdateFrame.java ├── java21 └── org │ └── bioimageanalysis │ └── icy │ ├── extension │ └── plugin │ │ ├── classloader │ │ └── JarClassLoader.java │ │ └── property │ │ ├── MultipleSelectionProperty.java │ │ ├── SelectionProperty.java │ │ └── gui │ │ └── PropertyPanel.java │ ├── gui │ ├── component │ │ └── renderer │ │ │ └── ImageTableCellRenderer.java │ └── viewer │ │ └── Viewer.java │ ├── io │ └── SequenceFileSticher.java │ ├── model │ ├── image │ │ ├── AbstractImageProvider.java │ │ └── IcyBufferedImage.java │ └── roi │ │ ├── ROIUtil.java │ │ └── tool │ │ └── ROIMagicWand.java │ └── system │ └── MMJUtil.java ├── java25 └── org │ └── bioimageanalysis │ └── icy │ └── system │ └── MMJUtil.java └── resources ├── fonts ├── JetBrainsMono-Bold.ttf └── JetBrainsMono-Medium.ttf ├── icon ├── alpha │ ├── roi.png │ ├── roi_area.png │ ├── roi_box.png │ ├── roi_cylinder.png │ ├── roi_flat_polygon3D.png │ ├── roi_line.png │ ├── roi_oval.png │ ├── roi_point.png │ ├── roi_polygon.png │ ├── roi_polyline.png │ └── roi_rectangle.png ├── png │ └── icy_macos.png └── svg │ ├── color │ ├── argb_image.svg │ ├── extension_default.svg │ ├── grayscale_image.svg │ ├── icy_macos.svg │ ├── icy_transparent.svg │ ├── icy_white_bg.svg │ ├── rgb_image.svg │ └── transparency.svg │ └── mono │ ├── 3d_axis.svg │ ├── 3d_box_bounds.svg │ ├── add.svg │ ├── arrow_down.svg │ ├── arrow_left.svg │ ├── arrow_right.svg │ ├── arrow_up.svg │ ├── bolt.svg │ ├── bracket_left.svg │ ├── bracket_right.svg │ ├── bug_report.svg │ ├── camera.svg │ ├── camera_roll.svg │ ├── center_focus_strong.svg │ ├── check.svg │ ├── check_circle.svg │ ├── circle.svg │ ├── circle_fill.svg │ ├── clear_all.svg │ ├── close.svg │ ├── content_copy.svg │ ├── convert_shape.svg │ ├── crop.svg │ ├── cube_slice.svg │ ├── cut.svg │ ├── dashboard.svg │ ├── database.svg │ ├── delete.svg │ ├── delete_sweep.svg │ ├── deployed_code.svg │ ├── description.svg │ ├── device_reset.svg │ ├── drag_pan.svg │ ├── draw_abstract.svg │ ├── east.svg │ ├── edit.svg │ ├── error.svg │ ├── export_notes.svg │ ├── extension.svg │ ├── file_open.svg │ ├── file_save.svg │ ├── filter_1.svg │ ├── filter_2.svg │ ├── filter_3.svg │ ├── filter_4.svg │ ├── filter_5.svg │ ├── filter_6.svg │ ├── filter_7.svg │ ├── filter_8.svg │ ├── filter_9.svg │ ├── filter_9_plus.svg │ ├── filter_none.svg │ ├── first_page.svg │ ├── flag.svg │ ├── flash_off.svg │ ├── flash_on.svg │ ├── folder.svg │ ├── folder_open.svg │ ├── format_align_center.svg │ ├── format_align_justify.svg │ ├── format_align_left.svg │ ├── format_align_right.svg │ ├── gesture_select.svg │ ├── grain.svg │ ├── grid_off.svg │ ├── grid_on.svg │ ├── group_work.svg │ ├── handyman.svg │ ├── help.svg │ ├── history.svg │ ├── hourglass.svg │ ├── image.svg │ ├── image_aspect_ratio.svg │ ├── image_broken.svg │ ├── image_resize.svg │ ├── indeterminate_question.svg │ ├── info.svg │ ├── invert_colors.svg │ ├── keyboard.svg │ ├── keyboard_arrow_down.svg │ ├── keyboard_arrow_left.svg │ ├── keyboard_arrow_right.svg │ ├── keyboard_arrow_up.svg │ ├── laps.svg │ ├── last_page.svg │ ├── layers.svg │ ├── layers_clear.svg │ ├── line.svg │ ├── lock.svg │ ├── lock_open.svg │ ├── magic_wand.svg │ ├── measure_centimeter.svg │ ├── my_location.svg │ ├── north.svg │ ├── north_east.svg │ ├── north_west.svg │ ├── note_add.svg │ ├── notifications.svg │ ├── notifications_important.svg │ ├── notifications_unread.svg │ ├── null.svg │ ├── open_in_new.svg │ ├── pause_circle.svg │ ├── pentagon.svg │ ├── photo_camera.svg │ ├── photo_library.svg │ ├── picture_add.svg │ ├── picture_in_picture.svg │ ├── picture_metadata.svg │ ├── play_circle.svg │ ├── point.svg │ ├── point_scan.svg │ ├── power_settings_new.svg │ ├── radio_button_checked.svg │ ├── radio_button_partial.svg │ ├── radio_button_unchecked.svg │ ├── recenter.svg │ ├── rectangle.svg │ ├── redo.svg │ ├── remove.svg │ ├── repeat.svg │ ├── repeat_on.svg │ ├── replay.svg │ ├── roi_area.svg │ ├── roi_boolean.svg │ ├── roi_boolean_and.svg │ ├── roi_boolean_not.svg │ ├── roi_boolean_or.svg │ ├── roi_boolean_substract.svg │ ├── roi_boolean_xor.svg │ ├── roi_dilate.svg │ ├── roi_distance_map.svg │ ├── roi_ellipse.svg │ ├── roi_erode.svg │ ├── roi_exterior.svg │ ├── roi_interior.svg │ ├── roi_line.svg │ ├── roi_point.svg │ ├── roi_polygon.svg │ ├── roi_polyline.svg │ ├── roi_rectangle.svg │ ├── roi_split.svg │ ├── rotate_left.svg │ ├── rotate_right.svg │ ├── ruler.svg │ ├── save.svg │ ├── save_as.svg │ ├── search.svg │ ├── settings.svg │ ├── settings_photo_camera.svg │ ├── settings_video_camera.svg │ ├── shading.svg │ ├── skip_next.svg │ ├── skip_previous.svg │ ├── south.svg │ ├── south_east.svg │ ├── south_west.svg │ ├── star.svg │ ├── stop_circle.svg │ ├── stroke_full.svg │ ├── switch_access_2.svg │ ├── terminal.svg │ ├── theme.svg │ ├── theme_dark.svg │ ├── theme_light.svg │ ├── timeline.svg │ ├── tv_options_input_settings.svg │ ├── undo.svg │ ├── unfold_less.svg │ ├── unfold_more.svg │ ├── union.svg │ ├── update.svg │ ├── update_disabled.svg │ ├── vertical_align_top.svg │ ├── videocam.svg │ ├── view_column.svg │ ├── view_module.svg │ ├── view_quilt.svg │ ├── view_stream.svg │ ├── visibility.svg │ ├── visibility_off.svg │ ├── warning.svg │ ├── west.svg │ ├── widgets.svg │ ├── zoom_in.svg │ ├── zoom_out.svg │ └── zoom_out_map.svg ├── image ├── help │ ├── icy_prefs.png │ ├── ij_detached.jpg │ ├── magic_wand.png │ ├── main_menu.png │ ├── menubar_macOS.png │ ├── viewer_virtual.jpg │ └── virtual_mode.jpg └── splash │ 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